[{"title":"Evolutionary proccesses in variable emvironments","ddc":["576"],"status":"public","_id":"1125","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"access_level":"closed","file_name":"Novak_thesis.pdf","file_size":3564901,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"6811","checksum":"81dcc838dfcf7aa0b1a27ecf4fe2da4e","date_updated":"2019-08-13T09:01:00Z","date_created":"2019-08-13T09:01:00Z"},{"success":1,"checksum":"30808d2f7ca920e09f63a95cdc49bffd","date_created":"2021-02-22T13:42:47Z","date_updated":"2021-02-22T13:42:47Z","file_id":"9186","relation":"main_file","creator":"dernst","file_size":2814384,"content_type":"application/pdf","access_level":"open_access","file_name":"2016_Novak_Thesis.pdf"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Natural environments are never constant but subject to spatial and temporal change on\r\nall scales, increasingly so due to human activity. Hence, it is crucial to understand the\r\nimpact of environmental variation on evolutionary processes. In this thesis, I present\r\nthree topics that share the common theme of environmental variation, yet illustrate its\r\neffect from different perspectives.\r\nFirst, I show how a temporally fluctuating environment gives rise to second-order\r\nselection on a modifier for stress-induced mutagenesis. Without fluctuations, when\r\npopulations are adapted to their environment, mutation rates are minimized. I argue\r\nthat a stress-induced mutator mechanism may only be maintained if the population is\r\nrepeatedly subjected to diverse environmental challenges, and I outline implications of\r\nthe presented results to antibiotic treatment strategies.\r\nSecond, I discuss my work on the evolution of dispersal. Besides reproducing\r\nknown results about the effect of heterogeneous habitats on dispersal, it identifies\r\nspatial changes in dispersal type frequencies as a source for selection for increased\r\npropensities to disperse. This concept contains effects of relatedness that are known\r\nto promote dispersal, and I explain how it identifies other forces selecting for dispersal\r\nand puts them on a common scale.\r\nThird, I analyse genetic variances of phenotypic traits under multivariate stabilizing\r\nselection. For the case of constant environments, I generalize known formulae of\r\nequilibrium variances to multiple traits and discuss how the genetic variance of a focal\r\ntrait is influenced by selection on background traits. I conclude by presenting ideas and\r\npreliminary work aiming at including environmental fluctuations in the form of moving\r\ntrait optima into the model.","lang":"eng"}],"page":"124","citation":{"short":"S. Novak, Evolutionary Proccesses in Variable Emvironments, Institute of Science and Technology Austria, 2016.","mla":"Novak, Sebastian. Evolutionary Proccesses in Variable Emvironments. Institute of Science and Technology Austria, 2016.","chicago":"Novak, Sebastian. “Evolutionary Proccesses in Variable Emvironments.” Institute of Science and Technology Austria, 2016.","ama":"Novak S. Evolutionary proccesses in variable emvironments. 2016.","apa":"Novak, S. (2016). Evolutionary proccesses in variable emvironments. Institute of Science and Technology Austria.","ieee":"S. Novak, “Evolutionary proccesses in variable emvironments,” Institute of Science and Technology Austria, 2016.","ista":"Novak S. 2016. Evolutionary proccesses in variable emvironments. Institute of Science and Technology Austria."},"date_published":"2016-07-01T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"01","department":[{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2016","date_updated":"2023-09-07T11:55:53Z","date_created":"2018-12-11T11:50:17Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"2023"}]},"author":[{"full_name":"Novak, Sebastian","orcid":"0000-0002-2519-824X","id":"461468AE-F248-11E8-B48F-1D18A9856A87","last_name":"Novak","first_name":"Sebastian"}],"publist_id":"6235","file_date_updated":"2021-02-22T13:42:47Z","oa":1,"language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"publication_identifier":{"issn":["2663-337X"]},"month":"07"},{"status":"public","title":"Intrinsic limits to gene regulation by global crosstalk","ddc":["576"],"intvolume":" 7","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1358","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"4919","checksum":"fe3f3a1526d180b29fe691ab11435b78","date_updated":"2020-07-14T12:44:46Z","date_created":"2018-12-12T10:12:01Z","access_level":"open_access","file_name":"IST-2016-627-v1+1_ncomms12307.pdf","content_type":"application/pdf","file_size":861805,"creator":"system"},{"content_type":"application/pdf","file_size":1084703,"creator":"system","file_name":"IST-2016-627-v1+2_ncomms12307-s1.pdf","access_level":"open_access","date_updated":"2020-07-14T12:44:46Z","date_created":"2018-12-12T10:12:02Z","checksum":"164864a1a675f3ad80e9917c27aba07f","relation":"main_file","file_id":"4920"}],"pubrep_id":"627","type":"journal_article","abstract":[{"lang":"eng","text":"Gene regulation relies on the specificity of transcription factor (TF)–DNA interactions. Limited specificity may lead to crosstalk: a regulatory state in which a gene is either incorrectly activated due to noncognate TF–DNA interactions or remains erroneously inactive. As each TF can have numerous interactions with noncognate cis-regulatory elements, crosstalk is inherently a global problem, yet has previously not been studied as such. We construct a theoretical framework to analyse the effects of global crosstalk on gene regulation. We find that crosstalk presents a significant challenge for organisms with low-specificity TFs, such as metazoans. Crosstalk is not easily mitigated by known regulatory schemes acting at equilibrium, including variants of cooperativity and combinatorial regulation. Our results suggest that crosstalk imposes a previously unexplored global constraint on the functioning and evolution of regulatory networks, which is qualitatively distinct from the known constraints that act at the level of individual gene regulatory elements."}],"publication":"Nature Communications","citation":{"ista":"Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. 2016. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 7, 12307.","apa":"Friedlander, T., Prizak, R., Guet, C. C., Barton, N. H., & Tkačik, G. (2016). Intrinsic limits to gene regulation by global crosstalk. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms12307","ieee":"T. Friedlander, R. Prizak, C. C. Guet, N. H. Barton, and G. Tkačik, “Intrinsic limits to gene regulation by global crosstalk,” Nature Communications, vol. 7. Nature Publishing Group, 2016.","ama":"Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 2016;7. doi:10.1038/ncomms12307","chicago":"Friedlander, Tamar, Roshan Prizak, Calin C Guet, Nicholas H Barton, and Gašper Tkačik. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms12307.","mla":"Friedlander, Tamar, et al. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” Nature Communications, vol. 7, 12307, Nature Publishing Group, 2016, doi:10.1038/ncomms12307.","short":"T. Friedlander, R. Prizak, C.C. Guet, N.H. Barton, G. Tkačik, Nature Communications 7 (2016)."},"date_published":"2016-08-04T00:00:00Z","scopus_import":1,"day":"04","has_accepted_license":"1","publication_status":"published","department":[{"_id":"GaTk"},{"_id":"NiBa"},{"_id":"CaGu"}],"publisher":"Nature Publishing Group","year":"2016","date_updated":"2023-09-07T12:53:49Z","date_created":"2018-12-11T11:51:34Z","volume":7,"author":[{"id":"36A5845C-F248-11E8-B48F-1D18A9856A87","last_name":"Friedlander","first_name":"Tamar","full_name":"Friedlander, Tamar"},{"id":"4456104E-F248-11E8-B48F-1D18A9856A87","first_name":"Roshan","last_name":"Prizak","full_name":"Prizak, Roshan"},{"orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C","full_name":"Guet, Calin C"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gasper","last_name":"Tkacik","full_name":"Tkacik, Gasper"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6071"}]},"article_number":"12307","license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2020-07-14T12:44:46Z","publist_id":"5887","ec_funded":1,"quality_controlled":"1","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"},{"call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/ncomms12307","month":"08"},{"article_processing_charge":"No","month":"09","day":"23","date_published":"2016-09-23T00:00:00Z","doi":"10.5061/dryad.s5s7r","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.s5s7r"}],"oa":1,"citation":{"short":"N.H. Barton, (2016).","mla":"Barton, Nicholas H. Data from: How Does Epistasis Influence the Response to Selection? Dryad, 2016, doi:10.5061/dryad.s5s7r.","chicago":"Barton, Nicholas H. “Data from: How Does Epistasis Influence the Response to Selection?” Dryad, 2016. https://doi.org/10.5061/dryad.s5s7r.","ama":"Barton NH. Data from: How does epistasis influence the response to selection? 2016. doi:10.5061/dryad.s5s7r","ieee":"N. H. Barton, “Data from: How does epistasis influence the response to selection?” Dryad, 2016.","apa":"Barton, N. H. (2016). Data from: How does epistasis influence the response to selection? Dryad. https://doi.org/10.5061/dryad.s5s7r","ista":"Barton NH. 2016. Data from: How does epistasis influence the response to selection?, Dryad, 10.5061/dryad.s5s7r."},"abstract":[{"text":"Much of quantitative genetics is based on the ‘infinitesimal model’, under which selection has a negligible effect on the genetic variance. This is typically justified by assuming a very large number of loci with additive effects. However, it applies even when genes interact, provided that the number of loci is large enough that selection on each of them is weak relative to random drift. In the long term, directional selection will change allele frequencies, but even then, the effects of epistasis on the ultimate change in trait mean due to selection may be modest. Stabilising selection can maintain many traits close to their optima, even when the underlying alleles are weakly selected. However, the number of traits that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this is hard to reconcile with the apparent complexity of many organisms. Just as for the mutation load, this limit can be evaded by a particular form of negative epistasis. A more robust limit is set by the variance in reproductive success. This suggests that selection accumulates information most efficiently in the infinitesimal regime, when selection on individual alleles is weak, and comparable with random drift. A review of evidence on selection strength suggests that although most variance in fitness may be because of alleles with large Nes, substantial amounts of adaptation may be because of alleles in the infinitesimal regime, in which epistasis has modest effects.","lang":"eng"}],"type":"research_data_reference","oa_version":"Published Version","date_created":"2021-07-23T11:45:47Z","date_updated":"2023-09-20T11:17:47Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1199"}]},"author":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"department":[{"_id":"NiBa"}],"publisher":"Dryad","title":"Data from: How does epistasis influence the response to selection?","status":"public","_id":"9710","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2016"},{"date_published":"2016-12-14T00:00:00Z","doi":"10.6084/m9.figshare.4315652.v1","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.4315652.v1","open_access":"1"}],"citation":{"chicago":"Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan P Bollback. “Data from Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” The Royal Society, 2016. https://doi.org/10.6084/m9.figshare.4315652.v1.","mla":"Fernandes Redondo, Rodrigo A., et al. Data from Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family. The Royal Society, 2016, doi:10.6084/m9.figshare.4315652.v1.","short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, (2016).","ista":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2016. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family, The Royal Society, 10.6084/m9.figshare.4315652.v1.","apa":"Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., & Bollback, J. P. (2016). Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. The Royal Society. https://doi.org/10.6084/m9.figshare.4315652.v1","ieee":"R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family.” The Royal Society, 2016.","ama":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. 2016. doi:10.6084/m9.figshare.4315652.v1"},"oa":1,"month":"12","day":"14","article_processing_charge":"No","author":[{"full_name":"Fernandes Redondo, Rodrigo A","last_name":"Fernandes Redondo","first_name":"Rodrigo A","orcid":"0000-0002-5837-2793","id":"409D5C96-F248-11E8-B48F-1D18A9856A87"},{"last_name":"de Vladar","first_name":"Harold","orcid":"0000-0002-5985-7653","id":"2A181218-F248-11E8-B48F-1D18A9856A87","full_name":"de Vladar, Harold"},{"full_name":"Włodarski, Tomasz","first_name":"Tomasz","last_name":"Włodarski"},{"full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","first_name":"Jonathan P"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1077"}]},"date_updated":"2023-09-20T11:56:33Z","date_created":"2021-08-10T08:29:47Z","oa_version":"Published Version","_id":"9864","year":"2016","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family","status":"public","publisher":"The Royal Society","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"abstract":[{"text":"Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the ϕX174 phage family by, first, reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima.","lang":"eng"}],"type":"research_data_reference"},{"date_updated":"2024-02-21T13:49:53Z","date_created":"2018-12-11T11:51:42Z","oa_version":"None","volume":117,"author":[{"full_name":"Ellis, Thomas","first_name":"Thomas","last_name":"Ellis","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254"},{"full_name":"Field, David","last_name":"Field","first_name":"David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"popular_science","status":"public","id":"5550"}]},"status":"public","publication_status":"published","title":"Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae","publisher":"Oxford University Press","department":[{"_id":"NiBa"}],"intvolume":" 117","_id":"1382","year":"2016","acknowledgement":"We thank Melinda Pickup, Spencer Barrett, Nick Barton and four anonymous reviewers for helpful discussions on previous versions of this manuscript. We also thank Jana Porsche for her efforts in tracking down the more obscure references.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Background and aims Angiosperms display remarkable diversity in flower colour, implying that transitions between pigmentation phenotypes must have been common. Despite progress in understanding transitions between anthocyanin (blue, purple, pink or red) and unpigmented (white) flowers, little is known about the evolutionary patterns of flower-colour transitions in lineages with both yellow and anthocyanin-pigmented flowers. This study investigates the relative rates of evolutionary transitions between different combinations of yellow- and anthocyanin-pigmentation phenotypes in the tribe Antirrhineae. Methods We surveyed taxonomic literature for data on anthocyanin and yellow floral pigmentation for 369 species across the tribe. We then reconstructed the phylogeny of 169 taxa and used phylogenetic comparative methods to estimate transition rates among pigmentation phenotypes across the phylogeny. Key Results In contrast to previous studies we found a bias towards transitions involving a gain in pigmentation, although transitions to phenotypes with both anthocyanin and yellow taxa are nevertheless extremely rare. Despite the dominance of yellow and anthocyanin-pigmented taxa, transitions between these phenotypes are constrained to move through a white intermediate stage, whereas transitions to double-pigmentation are very rare. The most abundant transitions are between anthocyanin-pigmented and unpigmented flowers, and similarly the most abundant polymorphic taxa were those with anthocyanin-pigmented and unpigmented flowers. Conclusions Our findings show that pigment evolution is limited by the presence of other floral pigments. This interaction between anthocyanin and yellow pigments constrains the breadth of potential floral diversity observed in nature. In particular, they suggest that selection has repeatedly acted to promote the spread of single-pigmented phenotypes across the Antirrhineae phylogeny. Furthermore, the correlation between transition rates and polymorphism suggests that the forces causing and maintaining variance in the short term reflect evolutionary processes on longer time scales.","lang":"eng"}],"issue":"7","publist_id":"5828","type":"journal_article","language":[{"iso":"eng"}],"date_published":"2016-06-01T00:00:00Z","doi":"10.1093/aob/mcw043","quality_controlled":"1","page":"1133 - 1140","publication":"Annals of Botany","citation":{"ista":"Ellis T, Field D. 2016. Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae. Annals of Botany. 117(7), 1133–1140.","apa":"Ellis, T., & Field, D. (2016). Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae. Annals of Botany. Oxford University Press. https://doi.org/10.1093/aob/mcw043","ieee":"T. Ellis and D. Field, “Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae,” Annals of Botany, vol. 117, no. 7. Oxford University Press, pp. 1133–1140, 2016.","ama":"Ellis T, Field D. Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae. Annals of Botany. 2016;117(7):1133-1140. doi:10.1093/aob/mcw043","chicago":"Ellis, Thomas, and David Field. “Repeated Gains in Yellow and Anthocyanin Pigmentation in Flower Colour Transitions in the Antirrhineae.” Annals of Botany. Oxford University Press, 2016. https://doi.org/10.1093/aob/mcw043.","mla":"Ellis, Thomas, and David Field. “Repeated Gains in Yellow and Anthocyanin Pigmentation in Flower Colour Transitions in the Antirrhineae.” Annals of Botany, vol. 117, no. 7, Oxford University Press, 2016, pp. 1133–40, doi:10.1093/aob/mcw043.","short":"T. Ellis, D. Field, Annals of Botany 117 (2016) 1133–1140."},"day":"1","month":"06","scopus_import":1},{"type":"research_data","datarep_id":"34","publist_id":"5828","file_date_updated":"2020-07-14T12:47:00Z","abstract":[{"lang":"eng","text":"We collected flower colour information on species in the tribe Antirrhineae from taxonomic literature. We also retreived molecular data from GenBank for as many of these species as possible to estimate phylogenetic relationships among these taxa. We then used the R package 'diversitree' to examine patterns of evolutionary transitions between anthocyanin and yellow pigmentation across the phylogeny.\r\n\r\nFor full details of the methods see:\r\nEllis TJ and Field DL \"Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae”, Annals of Botany (in press)"}],"license":"https://creativecommons.org/publicdomain/zero/1.0/","_id":"5550","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2016","publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"}],"title":"Flower colour data and phylogeny (NEXUS) files","ddc":["576"],"status":"public","related_material":{"record":[{"id":"1382","relation":"research_paper","status":"public"}]},"author":[{"full_name":"Ellis, Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254","first_name":"Thomas","last_name":"Ellis"},{"first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","full_name":"Field, David"}],"oa_version":"Published Version","file":[{"file_id":"5594","relation":"main_file","checksum":"950f85b80427d357bfeff09608ba02e9","date_updated":"2020-07-14T12:47:00Z","date_created":"2018-12-12T13:02:27Z","access_level":"open_access","file_name":"IST-2016-34-v1+1_tellis_flower_colour_data.zip","creator":"system","file_size":4468543,"content_type":"application/zip"}],"date_created":"2018-12-12T12:31:29Z","date_updated":"2024-02-21T13:49:54Z","article_processing_charge":"No","has_accepted_license":"1","month":"02","day":"19","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"ama":"Ellis T, Field D. Flower colour data and phylogeny (NEXUS) files. 2016. doi:10.15479/AT:ISTA:34","ista":"Ellis T, Field D. 2016. Flower colour data and phylogeny (NEXUS) files, Institute of Science and Technology Austria, 10.15479/AT:ISTA:34.","ieee":"T. Ellis and D. Field, “Flower colour data and phylogeny (NEXUS) files.” Institute of Science and Technology Austria, 2016.","apa":"Ellis, T., & Field, D. (2016). Flower colour data and phylogeny (NEXUS) files. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:34","mla":"Ellis, Thomas, and David Field. Flower Colour Data and Phylogeny (NEXUS) Files. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:34.","short":"T. Ellis, D. Field, (2016).","chicago":"Ellis, Thomas, and David Field. “Flower Colour Data and Phylogeny (NEXUS) Files.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:34."},"doi":"10.15479/AT:ISTA:34","date_published":"2016-02-19T00:00:00Z"},{"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Hybrid zones represent evolutionary laboratories, where recombination brings together alleles in combinations which have not previously been tested by selection. This provides an excellent opportunity to test the effect of molecular variation on fitness, and how this variation is able to spread through populations in a natural context. The snapdragon Antirrhinum majus is polymorphic in the wild for two loci controlling the distribution of yellow and magenta floral pigments. Where the yellow A. m. striatum and the magenta A. m. pseudomajus meet along a valley in the Spanish Pyrenees they form a stable hybrid zone Alleles at these loci recombine to give striking transgressive variation for flower colour. The sharp transition in phenotype over ~1km implies strong selection maintaining the hybrid zone. An indirect assay of pollinator visitation in the field found that pollinators forage in a positive-frequency dependent manner on Antirrhinum, matching previous data on fruit set. Experimental arrays and paternity analysis of wild-pollinated seeds demonstrated assortative mating for pigmentation alleles, and that pollinator behaviour alone is sufficient to explain this pattern. Selection by pollinators should be sufficiently strong to maintain the hybrid zone, although other mechanisms may be at work. At a broader scale I examined evolutionary transitions between yellow and anthocyanin pigmentation in the tribe Antirrhinae, and found that selection has acted strate that pollinators are a major determinant of reproductive success and mating patterns in wild Antirrhinum."}],"_id":"1398","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone","ddc":["576"],"pubrep_id":"526","file":[{"file_size":11928241,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2016-526-v1+1_Ellis_signed_thesis.pdf","checksum":"a89b17ff27cf92c9a15f6b3d46bd7e53","date_updated":"2020-07-14T12:44:48Z","date_created":"2018-12-12T10:14:51Z","relation":"main_file","file_id":"5106"}],"oa_version":"Published Version","day":"18","article_processing_charge":"No","has_accepted_license":"1","citation":{"ieee":"T. Ellis, “The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone,” Institute of Science and Technology Austria, 2016.","apa":"Ellis, T. (2016). The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_526 ","ista":"Ellis T. 2016. The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone. Institute of Science and Technology Austria.","ama":"Ellis T. The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone. 2016. doi:10.15479/AT:ISTA:TH_526 ","chicago":"Ellis, Thomas. “The Role of Pollinator-Mediated Selection in the Maintenance of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:TH_526 .","short":"T. Ellis, The Role of Pollinator-Mediated Selection in the Maintenance of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone, Institute of Science and Technology Austria, 2016.","mla":"Ellis, Thomas. The Role of Pollinator-Mediated Selection in the Maintenance of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:TH_526 ."},"page":"130","date_published":"2016-02-18T00:00:00Z","file_date_updated":"2020-07-14T12:44:48Z","publist_id":"5809","year":"2016","acknowledgement":"I am indebted to many people for their support during my PhD, but I particularly wish to thank Nick Barton for his guidance and intuition, and for encouraging me to take the time to look beyond the immediate topic of my PhD to understand the broader context. I am also especially grateful to David Field his bottomless patience, invaluable advice on experimental design, analysis and scientific writing, and for tireless work on the population surveys and genomic work without most of my thesis could not have happened. \r\n\r\nIt has been a pleasure to work with the combined strengths of the groups at The John Innes Centre, University of Toulouse and IST Austria. Thanks to Enrico Coen and his group for hosting me in Norwich in 2011 and especially for setting up the tag experiment. \r\n\r\nI thank David Field, Desmond Bradley and Maria Clara Melo-Hurtado for organising field collections, as well as Monique Burrus and Christophe Andalo and a large number of volunteers for their e ff orts helping with the field work. Furthermore I thank Coline Jaworski for providing seeds and for her input into the design of the experimental arrays, and Matthew Couchman for maintaining the database of. \r\n\r\nIn addition to those mentioned above, I am grateful to Melinda Pickup, Spencer Barrett, and four anonymous reviewers for their insightful comments on sections of this manuscript. I also thank Jana Porsche for her e ff orts in tracking down the more obscure references for chapter 5, and Jon Bollback for his advice about the analysis. \r\n\r\nI am indebted to Jon Ågren for his patience whilst I finished this thesis, and to Sylvia Cremer and Magnus Nordborg for taking the time to read and evaluate the thesis given a shorter deadline than was fair. \r\n\r\nA very positive aspect of my PhD has been the supportive atmosphere of IST. In particular, I have come to appreciate the enormous support from our group assistants Nicole Hotzy, Julia Asimakis, Christine Ostermann and Jerneja Beslagic. I also thank Christian Chaloupka and Stefan Hipfinger for their enthusiasm and readiness to help where possible in setting up our greenhouse and experiments. ","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"}],"author":[{"id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254","first_name":"Thomas","last_name":"Ellis","full_name":"Ellis, Thomas"}],"related_material":{"record":[{"relation":"popular_science","status":"public","id":"5553"},{"status":"public","relation":"popular_science","id":"5551"},{"id":"5552","status":"public","relation":"popular_science"}]},"date_created":"2018-12-11T11:51:47Z","date_updated":"2024-02-21T13:51:39Z","month":"02","publication_identifier":{"issn":["2663-337X"]},"oa":1,"doi":"10.15479/AT:ISTA:TH_526 ","degree_awarded":"PhD","supervisor":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"language":[{"iso":"eng"}]},{"oa":1,"language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"publication_identifier":{"issn":["2663-337X"]},"month":"07","department":[{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2016","acknowledgement":"This PhD thesis may not have been completed without the help and care I received from some peo- ple during my PhD life. I am especially grateful to Tiago Paixao, Gasper Tkacik, Nick Barton, not only for their scientific advices but also for their patience and support. I thank Calin Guet and Jonathan Bollback for allowing me to “play around” in their labs and get some experience on experimental evolution. I thank Magdalena Steinrueck and Fabienne Jesse for collaborating and sharing their experimental data with me. I thank Johannes Jaeger for reviewing my thesis. I thank all members of Barton group (aka bartonians) for their feedback, and all workers of IST Austria for making the best working conditions. Lastly, I thank two special women, Nejla Sag ̆lam and Setenay Dog ̆an, for their continuous support and encouragement. I truly had a great chance of having right people around me.","date_created":"2018-12-11T11:50:19Z","date_updated":"2024-02-21T13:50:34Z","related_material":{"record":[{"id":"1666","status":"public","relation":"part_of_dissertation"},{"id":"5554","status":"public","relation":"research_data"}]},"author":[{"full_name":"Tugrul, Murat","last_name":"Tugrul","first_name":"Murat","orcid":"0000-0002-8523-0758","id":"37C323C6-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"6229","file_date_updated":"2021-02-22T11:45:20Z","page":"89","citation":{"ama":"Tugrul M. Evolution of transcriptional regulatory sequences. 2016.","apa":"Tugrul, M. (2016). Evolution of transcriptional regulatory sequences. Institute of Science and Technology Austria.","ieee":"M. Tugrul, “Evolution of transcriptional regulatory sequences,” Institute of Science and Technology Austria, 2016.","ista":"Tugrul M. 2016. Evolution of transcriptional regulatory sequences. Institute of Science and Technology Austria.","short":"M. Tugrul, Evolution of Transcriptional Regulatory Sequences, Institute of Science and Technology Austria, 2016.","mla":"Tugrul, Murat. Evolution of Transcriptional Regulatory Sequences. Institute of Science and Technology Austria, 2016.","chicago":"Tugrul, Murat. “Evolution of Transcriptional Regulatory Sequences.” Institute of Science and Technology Austria, 2016."},"date_published":"2016-07-01T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"01","status":"public","title":"Evolution of transcriptional regulatory sequences","ddc":["576"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"1131","file":[{"access_level":"closed","file_name":"Tugrul_thesis_w_signature_page.pdf","content_type":"application/pdf","file_size":3695257,"creator":"dernst","relation":"main_file","file_id":"6810","checksum":"66cb61a59943e4fb7447c6a86be5ef51","date_created":"2019-08-13T08:53:52Z","date_updated":"2019-08-13T08:53:52Z"},{"creator":"dernst","content_type":"application/pdf","file_size":3880811,"file_name":"2016_Tugrul_Thesis.pdf","access_level":"open_access","date_updated":"2021-02-22T11:45:20Z","date_created":"2021-02-22T11:45:20Z","success":1,"checksum":"293e388d70563760f6b24c3e66283dda","file_id":"9182","relation":"main_file"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Evolution of gene regulation is important for phenotypic evolution and diversity. Sequence-specific binding of regulatory proteins is one of the key regulatory mechanisms determining gene expression. Although there has been intense interest in evolution of regulatory binding sites in the last decades, a theoretical understanding is far from being complete. In this thesis, I aim at a better understanding of the evolution of transcriptional regulatory binding sequences by using biophysical and population genetic models.\r\nIn the first part of the thesis, I discuss how to formulate the evolutionary dynamics of binding se- quences in a single isolated binding site and in promoter/enhancer regions. I develop a theoretical framework bridging between a thermodynamical model for transcription and a mutation-selection-drift model for monomorphic populations. I mainly address the typical evolutionary rates, and how they de- pend on biophysical parameters (e.g. binding length and specificity) and population genetic parameters (e.g. population size and selection strength).\r\nIn the second part of the thesis, I analyse empirical data for a better evolutionary and biophysical understanding of sequence-specific binding of bacterial RNA polymerase. First, I infer selection on regulatory and non-regulatory binding sites of RNA polymerase in the E. coli K12 genome. Second, I infer the chemical potential of RNA polymerase, an important but unknown physical parameter defining the threshold energy for strong binding. Furthermore, I try to understand the relation between the lac promoter sequence diversity and the LacZ activity variation among 20 bacterial isolates by constructing a simple but biophysically motivated gene expression model. Lastly, I lay out a statistical framework to predict adaptive point mutations in de novo promoter evolution in a selection experiment."}]},{"datarep_id":"37","type":"research_data","file_date_updated":"2020-07-14T12:47:01Z","abstract":[{"text":"Genotypic, phenotypic and demographic data for 2128 wild snapdragons and 1127 open-pollinated progeny from a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted) February 2016).\r\n\r\nTissue samples were sent to LGC Genomics in Berlin for DNA extraction, and genotyping at 70 SNP markers by KASPR genotyping. 29 of these SNPs failed to amplify reliably, and have been removed from this dataset.\r\n\r\nOther data were retreived from an online database of this population at www.antspec.org.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5553","year":"2016","status":"public","ddc":["576"],"title":"Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012","department":[{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","author":[{"orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David","full_name":"Field, David"},{"id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254","first_name":"Thomas","last_name":"Ellis","full_name":"Ellis, Thomas"}],"related_material":{"record":[{"relation":"research_paper","status":"public","id":"1398"}]},"contributor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","contributor_type":"project_manager"}],"date_updated":"2024-02-21T13:51:14Z","date_created":"2018-12-12T12:31:30Z","oa_version":"Published Version","file":[{"file_name":"IST-2016-37-v1+1_paternity_archive.zip","access_level":"open_access","creator":"system","content_type":"application/zip","file_size":132808,"file_id":"5620","relation":"main_file","date_created":"2018-12-12T13:03:02Z","date_updated":"2020-07-14T12:47:01Z","checksum":"4ae751b1fa4897fa216241f975a57313"}],"keyword":["paternity assignment","pedigree","matting patterns","assortative mating","Antirrhinum majus","frequency-dependent selection","plant-pollinator interaction"],"month":"02","day":"19","has_accepted_license":"1","article_processing_charge":"No","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"chicago":"Field, David, and Thomas Ellis. “Inference of Mating Patterns among Wild Snapdragons in a Natural Hybrid Zone in 2012.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:37.","mla":"Field, David, and Thomas Ellis. Inference of Mating Patterns among Wild Snapdragons in a Natural Hybrid Zone in 2012. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:37.","short":"D. Field, T. Ellis, (2016).","ista":"Field D, Ellis T. 2016. Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012, Institute of Science and Technology Austria, 10.15479/AT:ISTA:37.","apa":"Field, D., & Ellis, T. (2016). Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:37","ieee":"D. Field and T. Ellis, “Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012.” Institute of Science and Technology Austria, 2016.","ama":"Field D, Ellis T. Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012. 2016. doi:10.15479/AT:ISTA:37"},"doi":"10.15479/AT:ISTA:37","date_published":"2016-02-19T00:00:00Z"},{"publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"}],"title":"Data on pollinator observations and offpsring phenotypes","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5551","year":"2016","file":[{"checksum":"aa3eb85d52b110cd192aa23147c4d4f3","date_updated":"2020-07-14T12:47:01Z","date_created":"2018-12-12T13:05:12Z","file_id":"5640","relation":"main_file","creator":"system","content_type":"application/zip","file_size":32775,"access_level":"open_access","file_name":"IST-2016-35-v1+1_array_data.zip"}],"oa_version":"Published Version","date_created":"2018-12-12T12:31:29Z","date_updated":"2024-02-21T13:51:27Z","related_material":{"record":[{"relation":"research_paper","status":"public","id":"1398"}]},"contributor":[{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Field"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"author":[{"full_name":"Ellis, Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254","first_name":"Thomas","last_name":"Ellis"}],"type":"research_data","datarep_id":"35","abstract":[{"lang":"eng","text":"Data from array experiments investigating pollinator behaviour on snapdragons in controlled conditions, and their effect on plant mating. Data were collected as part of Tom Ellis' PhD thesis , submitted February 2016.\r\n\r\nWe placed a total of 36 plants in a grid inside a closed organza tent, with a single hive of commercially bred bumblebees (Bombus hortorum). We used only the yellow-flowered Antirrhinum majus striatum and the magenta-flowered Antirrhinum majus pseudomajus, at ratios of 6:36, 12:24, 18:18, 24:12 and 30:6.\r\n\r\nAfter 24 hours to learn how to deal with snapdragons, I observed pollinators foraging on plants, and recorded the transitions between plants. Thereafter seeds on plants were allowed to develops. A sample of these were grown to maturity when their flower colour could be determined, and they were scored as yellow, magenta, or hybrid."}],"file_date_updated":"2020-07-14T12:47:01Z","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"ama":"Ellis T. Data on pollinator observations and offpsring phenotypes. 2016. doi:10.15479/AT:ISTA:35","ista":"Ellis T. 2016. Data on pollinator observations and offpsring phenotypes, Institute of Science and Technology Austria, 10.15479/AT:ISTA:35.","ieee":"T. Ellis, “Data on pollinator observations and offpsring phenotypes.” Institute of Science and Technology Austria, 2016.","apa":"Ellis, T. (2016). Data on pollinator observations and offpsring phenotypes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:35","mla":"Ellis, Thomas. Data on Pollinator Observations and Offpsring Phenotypes. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:35.","short":"T. Ellis, (2016).","chicago":"Ellis, Thomas. “Data on Pollinator Observations and Offpsring Phenotypes.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:35."},"oa":1,"date_published":"2016-02-19T00:00:00Z","doi":"10.15479/AT:ISTA:35","article_processing_charge":"No","has_accepted_license":"1","month":"02","day":"19"},{"type":"research_data","datarep_id":"36","file_date_updated":"2020-07-14T12:47:01Z","abstract":[{"text":"Data on pollinator visitation to wild snapdragons in a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted February 2016).\r\n\r\nSnapdragon flowers have a mouth-like structure which pollinators must open to access nectar. We placed 5mm cellophane tags in these mouths, which are held in place by the pressure of the flower until a pollinator visits. When she opens the flower, the tag drops out, and one can infer a visit. We surveyed plants over multiple days in 2010, 2011 and 2012.\r\n\r\nAlso included are data on phenotypic and demographic variables which may be explanatory variables for pollinator visitation.","lang":"eng"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"}],"status":"public","title":"Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.","_id":"5552","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2016","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5625","date_updated":"2020-07-14T12:47:01Z","date_created":"2018-12-12T13:03:07Z","checksum":"cbc61b523d4d475a04a737d50dc470ef","file_name":"IST-2016-36-v1+1_tag_assay_archive.zip","access_level":"open_access","content_type":"application/zip","file_size":44905,"creator":"system"}],"date_created":"2018-12-12T12:31:30Z","date_updated":"2024-02-21T13:51:40Z","related_material":{"record":[{"relation":"research_paper","status":"public","id":"1398"}]},"contributor":[{"first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"author":[{"full_name":"Ellis, Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254","first_name":"Thomas","last_name":"Ellis"}],"article_processing_charge":"No","has_accepted_license":"1","day":"19","month":"02","citation":{"mla":"Ellis, Thomas. Pollinator Visitation Data for Wild Antirrhinum Majus Plants, with Phenotypic and Frequency Data. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:36.","short":"T. Ellis, (2016).","chicago":"Ellis, Thomas. “Pollinator Visitation Data for Wild Antirrhinum Majus Plants, with Phenotypic and Frequency Data.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:36.","ama":"Ellis T. Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data. 2016. doi:10.15479/AT:ISTA:36","ista":"Ellis T. 2016. Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data., Institute of Science and Technology Austria, 10.15479/AT:ISTA:36.","ieee":"T. Ellis, “Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.” Institute of Science and Technology Austria, 2016.","apa":"Ellis, T. (2016). Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:36"},"oa":1,"date_published":"2016-02-19T00:00:00Z","doi":"10.15479/AT:ISTA:36"},{"doi":"10.15479/AT:ISTA:43","date_published":"2016-05-12T00:00:00Z","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"mla":"Tugrul, Murat. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:43.","short":"M. Tugrul, (2016).","chicago":"Tugrul, Murat. “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:43.","ama":"Tugrul M. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. 2016. doi:10.15479/AT:ISTA:43","ista":"Tugrul M. 2016. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase, Institute of Science and Technology Austria, 10.15479/AT:ISTA:43.","apa":"Tugrul, M. (2016). Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:43","ieee":"M. Tugrul, “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016."},"has_accepted_license":"1","article_processing_charge":"No","month":"05","day":"12","keyword":["RNAP binding","de novo promoter evolution","lac promoter"],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1131"}]},"contributor":[{"id":"2C023F40-F248-11E8-B48F-1D18A9856A87","last_name":"Steinrück","contributor_type":"researcher","first_name":"Magdalena"},{"id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","last_name":"Jesse","first_name":"Fabienne"}],"author":[{"full_name":"Tugrul, Murat","last_name":"Tugrul","first_name":"Murat","orcid":"0000-0002-8523-0758","id":"37C323C6-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","file":[{"creator":"system","content_type":"application/zip","file_size":1123495,"access_level":"open_access","file_name":"IST-2016-43-v1+1_DATA_MTugrul_PhDThesis_Chapter3.zip","checksum":"1fc0a10bb7ce110fcb5e1fbe3cf0c4e2","date_updated":"2020-07-14T12:47:01Z","date_created":"2018-12-12T13:03:08Z","file_id":"5626","relation":"main_file"}],"date_updated":"2024-02-21T13:50:34Z","date_created":"2018-12-12T12:31:30Z","_id":"5554","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2016","publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"status":"public","title":"Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase","file_date_updated":"2020-07-14T12:47:01Z","abstract":[{"lang":"eng","text":"The data stored here is used in Murat Tugrul's PhD thesis (Chapter 3), which is related to the evolution of bacterial RNA polymerase binding.\r\nMagdalena Steinrueck (PhD Student in Calin Guet's group at IST Austria) performed the experiments and created the data on de novo promoter evolution. Fabienne Jesse (PhD Student in Jon Bollback's group at IST Austria) performed the experiments and created the data on lac promoter evolution."}],"type":"research_data","datarep_id":"43"},{"_id":"1430","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","status":"public","title":"First steps towards a runtime comparison of natural and artificial evolution","publication_status":"published","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publisher":"ACM","author":[{"last_name":"Paixao","first_name":"Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago"},{"last_name":"Sudholt","first_name":"Dirk","full_name":"Sudholt, Dirk"},{"first_name":"Jorge","last_name":"Heredia","full_name":"Heredia, Jorge"},{"orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87","last_name":"Trubenova","first_name":"Barbora","full_name":"Trubenova, Barbora"}],"date_created":"2018-12-11T11:51:58Z","date_updated":"2021-01-12T06:50:41Z","oa_version":"Preprint","type":"conference","abstract":[{"text":"Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired by natural evolution. In recent years the field of evolutionary computation has developed a rigorous analytical theory to analyse their runtime on many illustrative problems. Here we apply this theory to a simple model of natural evolution. In the Strong Selection Weak Mutation (SSWM) evolutionary regime the time between occurrence of new mutations is much longer than the time it takes for a new beneficial mutation to take over the population. In this situation, the population only contains copies of one genotype and evolution can be modelled as a (1+1)-type process where the probability of accepting a new genotype (improvements or worsenings) depends on the change in fitness. We present an initial runtime analysis of SSWM, quantifying its performance for various parameters and investigating differences to the (1+1) EA. We show that SSWM can have a moderate advantage over the (1+1) EA at crossing fitness valleys and study an example where SSWM outperforms the (1+1) EA by taking advantage of information on the fitness gradient.","lang":"eng"}],"ec_funded":1,"publist_id":"5768","publication":"Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation","main_file_link":[{"url":"http://arxiv.org/abs/1504.06260","open_access":"1"}],"oa":1,"citation":{"ama":"Paixao T, Sudholt D, Heredia J, Trubenova B. First steps towards a runtime comparison of natural and artificial evolution. In: Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation. ACM; 2015:1455-1462. doi:10.1145/2739480.2754758","ista":"Paixao T, Sudholt D, Heredia J, Trubenova B. 2015. First steps towards a runtime comparison of natural and artificial evolution. Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation. GECCO: Genetic and evolutionary computation conference, 1455–1462.","apa":"Paixao, T., Sudholt, D., Heredia, J., & Trubenova, B. (2015). First steps towards a runtime comparison of natural and artificial evolution. In Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation (pp. 1455–1462). Madrid, Spain: ACM. https://doi.org/10.1145/2739480.2754758","ieee":"T. Paixao, D. Sudholt, J. Heredia, and B. Trubenova, “First steps towards a runtime comparison of natural and artificial evolution,” in Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, Madrid, Spain, 2015, pp. 1455–1462.","mla":"Paixao, Tiago, et al. “First Steps towards a Runtime Comparison of Natural and Artificial Evolution.” Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, ACM, 2015, pp. 1455–62, doi:10.1145/2739480.2754758.","short":"T. Paixao, D. Sudholt, J. Heredia, B. Trubenova, in:, Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, ACM, 2015, pp. 1455–1462.","chicago":"Paixao, Tiago, Dirk Sudholt, Jorge Heredia, and Barbora Trubenova. “First Steps towards a Runtime Comparison of Natural and Artificial Evolution.” In Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, 1455–62. ACM, 2015. https://doi.org/10.1145/2739480.2754758."},"quality_controlled":"1","project":[{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7"}],"page":"1455 - 1462","conference":{"name":"GECCO: Genetic and evolutionary computation conference","start_date":"2015-07-11","location":"Madrid, Spain","end_date":"2015-07-15"},"date_published":"2015-07-11T00:00:00Z","doi":"10.1145/2739480.2754758","language":[{"iso":"eng"}],"scopus_import":1,"month":"07","day":"11"},{"scopus_import":1,"has_accepted_license":"1","day":"19","page":"1101 - 1112","citation":{"short":"N.H. Barton, M. Servedio, Evolution 69 (2015) 1101–1112.","mla":"Barton, Nicholas H., and Maria Servedio. “The Interpretation of Selection Coefficients.” Evolution, vol. 69, no. 5, Wiley, 2015, pp. 1101–12, doi:10.1111/evo.12641.","chicago":"Barton, Nicholas H, and Maria Servedio. “The Interpretation of Selection Coefficients.” Evolution. Wiley, 2015. https://doi.org/10.1111/evo.12641.","ama":"Barton NH, Servedio M. The interpretation of selection coefficients. Evolution. 2015;69(5):1101-1112. doi:10.1111/evo.12641","apa":"Barton, N. H., & Servedio, M. (2015). The interpretation of selection coefficients. Evolution. Wiley. https://doi.org/10.1111/evo.12641","ieee":"N. H. Barton and M. Servedio, “The interpretation of selection coefficients,” Evolution, vol. 69, no. 5. Wiley, pp. 1101–1112, 2015.","ista":"Barton NH, Servedio M. 2015. The interpretation of selection coefficients. Evolution. 69(5), 1101–1112."},"publication":"Evolution","date_published":"2015-03-19T00:00:00Z","type":"journal_article","issue":"5","abstract":[{"text":"Evolutionary biologists have an array of powerful theoretical techniques that can accurately predict changes in the genetic composition of populations. Changes in gene frequencies and genetic associations between loci can be tracked as they respond to a wide variety of evolutionary forces. However, it is often less clear how to decompose these various forces into components that accurately reflect the underlying biology. Here, we present several issues that arise in the definition and interpretation of selection and selection coefficients, focusing on insights gained through the examination of selection coefficients in multilocus notation. Using this notation, we discuss how its flexibility-which allows different biological units to be identified as targets of selection-is reflected in the interpretation of the coefficients that the notation generates. In many situations, it can be difficult to agree on whether loci can be considered to be under "direct" versus "indirect" selection, or to quantify this selection. We present arguments for what the terms direct and indirect selection might best encompass, considering a range of issues, from viability and sexual selection to kin selection. We show how multilocus notation can discriminate between direct and indirect selection, and describe when it can do so.","lang":"eng"}],"intvolume":" 69","status":"public","ddc":["570"],"title":"The interpretation of selection coefficients","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1519","file":[{"file_name":"IST-2016-560-v1+1_Interpreting_ML_coefficients_11.2.15_App.pdf","access_level":"open_access","file_size":188872,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"4822","date_created":"2018-12-12T10:10:34Z","date_updated":"2020-07-14T12:45:00Z","checksum":"fd8d23f476bc194419929b72ca265c02"},{"date_updated":"2020-07-14T12:45:00Z","date_created":"2018-12-12T10:10:35Z","checksum":"b774911e70044641d556e258efcb52ef","relation":"main_file","file_id":"4823","file_size":577415,"content_type":"application/pdf","creator":"system","file_name":"IST-2016-560-v1+2_Interpreting_ML_coefficients_11.2.15_mainText.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","pubrep_id":"560","month":"03","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/evo.12641","ec_funded":1,"publist_id":"5656","file_date_updated":"2020-07-14T12:45:00Z","department":[{"_id":"NiBa"}],"publisher":"Wiley","publication_status":"published","year":"2015","volume":69,"date_created":"2018-12-11T11:52:29Z","date_updated":"2021-01-12T06:51:20Z","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"},{"last_name":"Servedio","first_name":"Maria","full_name":"Servedio, Maria"}]},{"file":[{"file_id":"5244","relation":"main_file","checksum":"33b60ecfea60764756a9ee9df5eb65ca","date_updated":"2020-07-14T12:45:01Z","date_created":"2018-12-12T10:16:53Z","access_level":"open_access","file_name":"IST-2016-483-v1+1_1-s2.0-S0022519315003409-main.pdf","creator":"system","file_size":595307,"content_type":"application/pdf"}],"oa_version":"Published Version","pubrep_id":"483","status":"public","ddc":["570"],"title":"Toward a unifying framework for evolutionary processes","intvolume":" 383","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1542","abstract":[{"lang":"eng","text":"The theory of population genetics and evolutionary computation have been evolving separately for nearly 30 years. Many results have been independently obtained in both fields and many others are unique to its respective field. We aim to bridge this gap by developing a unifying framework for evolutionary processes that allows both evolutionary algorithms and population genetics models to be cast in the same formal framework. The framework we present here decomposes the evolutionary process into its several components in order to facilitate the identification of similarities between different models. In particular, we propose a classification of evolutionary operators based on the defining properties of the different components. We cast several commonly used operators from both fields into this common framework. Using this, we map different evolutionary and genetic algorithms to different evolutionary regimes and identify candidates with the most potential for the translation of results between the fields. This provides a unified description of evolutionary processes and represents a stepping stone towards new tools and results to both fields. "}],"type":"journal_article","date_published":"2015-10-21T00:00:00Z","page":"28 - 43","publication":" Journal of Theoretical Biology","citation":{"mla":"Paixao, Tiago, et al. “Toward a Unifying Framework for Evolutionary Processes.” Journal of Theoretical Biology, vol. 383, Elsevier, 2015, pp. 28–43, doi:10.1016/j.jtbi.2015.07.011.","short":"T. Paixao, G. Badkobeh, N.H. Barton, D. Çörüş, D. Dang, T. Friedrich, P. Lehre, D. Sudholt, A. Sutton, B. Trubenova, Journal of Theoretical Biology 383 (2015) 28–43.","chicago":"Paixao, Tiago, Golnaz Badkobeh, Nicholas H Barton, Doğan Çörüş, Duccuong Dang, Tobias Friedrich, Per Lehre, Dirk Sudholt, Andrew Sutton, and Barbora Trubenova. “Toward a Unifying Framework for Evolutionary Processes.” Journal of Theoretical Biology. Elsevier, 2015. https://doi.org/10.1016/j.jtbi.2015.07.011.","ama":"Paixao T, Badkobeh G, Barton NH, et al. Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology. 2015;383:28-43. doi:10.1016/j.jtbi.2015.07.011","ista":"Paixao T, Badkobeh G, Barton NH, Çörüş D, Dang D, Friedrich T, Lehre P, Sudholt D, Sutton A, Trubenova B. 2015. Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology. 383, 28–43.","ieee":"T. Paixao et al., “Toward a unifying framework for evolutionary processes,” Journal of Theoretical Biology, vol. 383. Elsevier, pp. 28–43, 2015.","apa":"Paixao, T., Badkobeh, G., Barton, N. H., Çörüş, D., Dang, D., Friedrich, T., … Trubenova, B. (2015). Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2015.07.011"},"day":"21","has_accepted_license":"1","scopus_import":1,"date_updated":"2021-01-12T06:51:29Z","date_created":"2018-12-11T11:52:37Z","volume":383,"author":[{"orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","first_name":"Tiago","full_name":"Paixao, Tiago"},{"full_name":"Badkobeh, Golnaz","last_name":"Badkobeh","first_name":"Golnaz"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Çörüş, Doğan","first_name":"Doğan","last_name":"Çörüş"},{"full_name":"Dang, Duccuong","first_name":"Duccuong","last_name":"Dang"},{"last_name":"Friedrich","first_name":"Tobias","full_name":"Friedrich, Tobias"},{"first_name":"Per","last_name":"Lehre","full_name":"Lehre, Per"},{"first_name":"Dirk","last_name":"Sudholt","full_name":"Sudholt, Dirk"},{"first_name":"Andrew","last_name":"Sutton","full_name":"Sutton, Andrew"},{"orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87","last_name":"Trubenova","first_name":"Barbora","full_name":"Trubenova, Barbora"}],"publication_status":"published","publisher":"Elsevier","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"year":"2015","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2020-07-14T12:45:01Z","publist_id":"5629","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.jtbi.2015.07.011","quality_controlled":"1","project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"month":"10"},{"language":[{"iso":"eng"}],"doi":"10.1007/s00285-014-0802-y","quality_controlled":"1","project":[{"_id":"25B67606-B435-11E9-9278-68D0E5697425","name":"L'OREAL Fellowship"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"06","date_created":"2018-12-11T11:53:32Z","date_updated":"2023-02-23T10:10:36Z","volume":70,"author":[{"full_name":"Uecker, Hildegard","orcid":"0000-0001-9435-2813","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","last_name":"Uecker","first_name":"Hildegard"},{"full_name":"Setter, Derek","first_name":"Derek","last_name":"Setter"},{"full_name":"Hermisson, Joachim","first_name":"Joachim","last_name":"Hermisson"}],"publication_status":"published","publisher":"Springer","department":[{"_id":"NiBa"}],"year":"2015","acknowledgement":"This work was made possible with financial support by the Vienna Science and Technology Fund (WWTF), by the Deutsche Forschungsgemeinschaft (DFG), Research Unit 1078 Natural selection in structured populations, by the Austrian Science Fund (FWF) via funding for the Vienna Graduate School for Population Genetics, and by a “For Women in Science” fellowship (L’Oréal Österreich in cooperation with the Austrian Commission for UNESCO and the Austrian Academy of Sciences with financial support from the Federal Ministry for Science and Research Austria).","file_date_updated":"2020-07-14T12:45:12Z","publist_id":"5442","date_published":"2015-06-01T00:00:00Z","page":"1523 - 1580","publication":"Journal of Mathematical Biology","citation":{"ama":"Uecker H, Setter D, Hermisson J. Adaptive gene introgression after secondary contact. Journal of Mathematical Biology. 2015;70(7):1523-1580. doi:10.1007/s00285-014-0802-y","ista":"Uecker H, Setter D, Hermisson J. 2015. Adaptive gene introgression after secondary contact. Journal of Mathematical Biology. 70(7), 1523–1580.","ieee":"H. Uecker, D. Setter, and J. Hermisson, “Adaptive gene introgression after secondary contact,” Journal of Mathematical Biology, vol. 70, no. 7. Springer, pp. 1523–1580, 2015.","apa":"Uecker, H., Setter, D., & Hermisson, J. (2015). Adaptive gene introgression after secondary contact. Journal of Mathematical Biology. Springer. https://doi.org/10.1007/s00285-014-0802-y","mla":"Uecker, Hildegard, et al. “Adaptive Gene Introgression after Secondary Contact.” Journal of Mathematical Biology, vol. 70, no. 7, Springer, 2015, pp. 1523–80, doi:10.1007/s00285-014-0802-y.","short":"H. Uecker, D. Setter, J. Hermisson, Journal of Mathematical Biology 70 (2015) 1523–1580.","chicago":"Uecker, Hildegard, Derek Setter, and Joachim Hermisson. “Adaptive Gene Introgression after Secondary Contact.” Journal of Mathematical Biology. Springer, 2015. https://doi.org/10.1007/s00285-014-0802-y."},"day":"01","has_accepted_license":"1","scopus_import":1,"oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":1321527,"creator":"system","file_name":"IST-2016-458-v1+1_s00285-014-0802-y.pdf","access_level":"open_access","date_created":"2018-12-12T10:14:27Z","date_updated":"2020-07-14T12:45:12Z","checksum":"00e3a67bda05d4cc165b3a48b41ef9ad","relation":"main_file","file_id":"5079"}],"pubrep_id":"458","title":"Adaptive gene introgression after secondary contact","status":"public","ddc":["576"],"intvolume":" 70","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1699","abstract":[{"lang":"eng","text":"By hybridization and backcrossing, alleles can surmount species boundaries and be incorporated into the genome of a related species. This introgression of genes is of particular evolutionary relevance if it involves the transfer of adaptations between populations. However, any beneficial allele will typically be associated with other alien alleles that are often deleterious and hamper the introgression process. In order to describe the introgression of an adaptive allele, we set up a stochastic model with an explicit genetic makeup of linked and unlinked deleterious alleles. Based on the theory of reducible multitype branching processes, we derive a recursive expression for the establishment probability of the beneficial allele after a single hybridization event. We furthermore study the probability that slightly deleterious alleles hitchhike to fixation. The key to the analysis is a split of the process into a stochastic phase in which the advantageous alleles establishes and a deterministic phase in which it sweeps to fixation. We thereafter apply the theory to a set of biologically relevant scenarios such as introgression in the presence of many unlinked or few closely linked deleterious alleles. A comparison to computer simulations shows that the approximations work well over a large parameter range."}],"issue":"7","type":"journal_article"},{"date_created":"2018-12-11T11:53:34Z","date_updated":"2021-01-12T06:52:38Z","volume":63,"oa_version":"None","author":[{"full_name":"Broadhurst, Linda","first_name":"Linda","last_name":"Broadhurst"},{"first_name":"Graham","last_name":"Fifield","full_name":"Fifield, Graham"},{"full_name":"Vanzella, Bindi","last_name":"Vanzella","first_name":"Bindi"},{"orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","first_name":"Melinda","full_name":"Pickup, Melinda"}],"title":"An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas","status":"public","publication_status":"published","department":[{"_id":"NiBa"}],"intvolume":" 63","publisher":"CSIRO","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1703","year":"2015","abstract":[{"text":"Vegetation clearing and land-use change have depleted many natural plant communities to the point where restoration is required. A major impediment to the success of rebuilding complex vegetation communities is having regular access to sufficient quantities of high-quality seed. Seed-production areas (SPAs) can help generate this seed, but these must be underpinned by a broad genetic base to maximise the evolutionary potential of restored populations. However, genetic bottlenecks can occur at the collection, establishment and production stages in SPAs, requiring genetic evaluation. This is especially relevant for species that may take many years before a return on SPA investment is realised. Two recently established yellow box (Eucalyptus melliodora A.Cunn. ex Schauer, Myrtaceae) SPAs were evaluated to determine whether genetic bottlenecks had occurred between seed collection and SPA establishment. No evidence was found to suggest that a significant loss of genetic diversity had occurred at this stage, although there was a significant difference in diversity between the two SPAs. Complex population genetic structure was also observed in the seed used to source the SPAs, with up to eight groups identified. Plant survival in the SPAs was influenced by seed collection location but not by SPA location and was not associated with genetic diversity. There were also no associations between genetic diversity and plant growth. These data highlighted the importance of chance events when establishing SPAs and indicated that the two yellow box SPAs are likely to provide genetically diverse seed sources for future restoration projects, especially by pooling seed from both SPAs.","lang":"eng"}],"publist_id":"5434","issue":"5","type":"journal_article","language":[{"iso":"eng"}],"date_published":"2015-05-26T00:00:00Z","doi":"10.1071/BT15023","quality_controlled":"1","page":"455 - 466","publication":"Australian Journal of Botany","citation":{"ama":"Broadhurst L, Fifield G, Vanzella B, Pickup M. An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas. Australian Journal of Botany. 2015;63(5):455-466. doi:10.1071/BT15023","ieee":"L. Broadhurst, G. Fifield, B. Vanzella, and M. Pickup, “An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas,” Australian Journal of Botany, vol. 63, no. 5. CSIRO, pp. 455–466, 2015.","apa":"Broadhurst, L., Fifield, G., Vanzella, B., & Pickup, M. (2015). An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas. Australian Journal of Botany. CSIRO. https://doi.org/10.1071/BT15023","ista":"Broadhurst L, Fifield G, Vanzella B, Pickup M. 2015. An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas. Australian Journal of Botany. 63(5), 455–466.","short":"L. Broadhurst, G. Fifield, B. Vanzella, M. Pickup, Australian Journal of Botany 63 (2015) 455–466.","mla":"Broadhurst, Linda, et al. “An Evaluation of the Genetic Structure of Seed Sources and the Maintenance of Genetic Diversity during Establishment of Two Yellow Box (Eucalyptus Melliodora) Seed-Production Areas.” Australian Journal of Botany, vol. 63, no. 5, CSIRO, 2015, pp. 455–66, doi:10.1071/BT15023.","chicago":"Broadhurst, Linda, Graham Fifield, Bindi Vanzella, and Melinda Pickup. “An Evaluation of the Genetic Structure of Seed Sources and the Maintenance of Genetic Diversity during Establishment of Two Yellow Box (Eucalyptus Melliodora) Seed-Production Areas.” Australian Journal of Botany. CSIRO, 2015. https://doi.org/10.1071/BT15023."},"day":"26","month":"05","scopus_import":1},{"author":[{"full_name":"Polechova, Jitka","orcid":"0000-0003-0951-3112","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","last_name":"Polechova","first_name":"Jitka"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"volume":112,"date_created":"2018-12-11T11:54:11Z","date_updated":"2021-01-12T06:53:24Z","pmid":1,"year":"2015","department":[{"_id":"NiBa"}],"publisher":"National Academy of Sciences","publication_status":"published","ec_funded":1,"publist_id":"5288","doi":"10.1073/pnas.1421515112","language":[{"iso":"eng"}],"external_id":{"pmid":["25941385"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443383/","open_access":"1"}],"oa":1,"project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"quality_controlled":"1","month":"05","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1818","intvolume":" 112","status":"public","title":"Limits to adaptation along environmental gradients","issue":"20","abstract":[{"lang":"eng","text":"Why do species not adapt to ever-wider ranges of conditions, gradually expanding their ecological niche and geographic range? Gene flow across environments has two conflicting effects: although it increases genetic variation, which is a prerequisite for adaptation, gene flow may swamp adaptation to local conditions. In 1956, Haldane proposed that, when the environment varies across space, "swamping" by gene flow creates a positive feedback between low population size and maladaptation, leading to a sharp range margin. However, current deterministic theory shows that, when variance can evolve, there is no such limit. Using simple analytical tools and simulations, we show that genetic drift can generate a sharp margin to a species' range, by reducing genetic variance below the level needed for adaptation to spatially variable conditions. Aided by separation of ecological and evolutionary timescales, the identified effective dimensionless parameters reveal a simple threshold that predicts when adaptation at the range margin fails. Two observable parameters determine the threshold: (i) the effective environmental gradient, which can be measured by the loss of fitness due to dispersal to a different environment; and (ii) the efficacy of selection relative to genetic drift. The theory predicts sharp range margins even in the absence of abrupt changes in the environment. Furthermore, it implies that gradual worsening of conditions across a species' habitat may lead to a sudden range fragmentation, when adaptation to a wide span of conditions within a single species becomes impossible."}],"type":"journal_article","date_published":"2015-05-19T00:00:00Z","citation":{"apa":"Polechova, J., & Barton, N. H. (2015). Limits to adaptation along environmental gradients. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1421515112","ieee":"J. Polechova and N. H. Barton, “Limits to adaptation along environmental gradients,” PNAS, vol. 112, no. 20. National Academy of Sciences, pp. 6401–6406, 2015.","ista":"Polechova J, Barton NH. 2015. Limits to adaptation along environmental gradients. PNAS. 112(20), 6401–6406.","ama":"Polechova J, Barton NH. Limits to adaptation along environmental gradients. PNAS. 2015;112(20):6401-6406. doi:10.1073/pnas.1421515112","chicago":"Polechova, Jitka, and Nicholas H Barton. “Limits to Adaptation along Environmental Gradients.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1421515112.","short":"J. Polechova, N.H. Barton, PNAS 112 (2015) 6401–6406.","mla":"Polechova, Jitka, and Nicholas H. Barton. “Limits to Adaptation along Environmental Gradients.” PNAS, vol. 112, no. 20, National Academy of Sciences, 2015, pp. 6401–06, doi:10.1073/pnas.1421515112."},"publication":"PNAS","page":"6401 - 6406","day":"19","scopus_import":1},{"month":"05","language":[{"iso":"eng"}],"doi":"10.1016/j.jtbi.2015.02.018","quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"grant_number":"243071","_id":"25DC711C-B435-11E9-9278-68D0E5697425","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","call_identifier":"FP7"}],"oa":1,"file_date_updated":"2020-07-14T12:45:19Z","ec_funded":1,"publist_id":"5251","date_updated":"2021-01-12T06:53:37Z","date_created":"2018-12-11T11:54:21Z","volume":372,"author":[{"first_name":"Sebastian","last_name":"Novak","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia"}],"publication_status":"published","publisher":"Elsevier","department":[{"_id":"NiBa"},{"_id":"SyCr"}],"year":"2015","day":"07","has_accepted_license":"1","scopus_import":1,"date_published":"2015-05-07T00:00:00Z","page":"54 - 64","publication":"Journal of Theoretical Biology","citation":{"apa":"Novak, S., & Cremer, S. (2015). Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2015.02.018","ieee":"S. Novak and S. Cremer, “Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates,” Journal of Theoretical Biology, vol. 372, no. 5. Elsevier, pp. 54–64, 2015.","ista":"Novak S, Cremer S. 2015. Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates. Journal of Theoretical Biology. 372(5), 54–64.","ama":"Novak S, Cremer S. Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates. Journal of Theoretical Biology. 2015;372(5):54-64. doi:10.1016/j.jtbi.2015.02.018","chicago":"Novak, Sebastian, and Sylvia Cremer. “Fungal Disease Dynamics in Insect Societies: Optimal Killing Rates and the Ambivalent Effect of High Social Interaction Rates.” Journal of Theoretical Biology. Elsevier, 2015. https://doi.org/10.1016/j.jtbi.2015.02.018.","short":"S. Novak, S. Cremer, Journal of Theoretical Biology 372 (2015) 54–64.","mla":"Novak, Sebastian, and Sylvia Cremer. “Fungal Disease Dynamics in Insect Societies: Optimal Killing Rates and the Ambivalent Effect of High Social Interaction Rates.” Journal of Theoretical Biology, vol. 372, no. 5, Elsevier, 2015, pp. 54–64, doi:10.1016/j.jtbi.2015.02.018."},"abstract":[{"text":"Entomopathogenic fungi are potent biocontrol agents that are widely used against insect pests, many of which are social insects. Nevertheless, theoretical investigations of their particular life history are scarce. We develop a model that takes into account the main distinguishing features between traditionally studied diseases and obligate killing pathogens, like the (biocontrol-relevant) insect-pathogenic fungi Metarhizium and Beauveria. First, obligate killing entomopathogenic fungi produce new infectious particles (conidiospores) only after host death and not yet on the living host. Second, the killing rates of entomopathogenic fungi depend strongly on the initial exposure dosage, thus we explicitly consider the pathogen load of individual hosts. Further, we make the model applicable not only to solitary host species, but also to group living species by incorporating social interactions between hosts, like the collective disease defences of insect societies. Our results identify the optimal killing rate for the pathogen that minimises its invasion threshold. Furthermore, we find that the rate of contact between hosts has an ambivalent effect: dense interaction networks between individuals are considered to facilitate disease outbreaks because of increased pathogen transmission. In social insects, this is compensated by their collective disease defences, i.e., social immunity. For the type of pathogens considered here, we show that even without social immunity, high contact rates between live individuals dilute the pathogen in the host colony and hence can reduce individual pathogen loads below disease-causing levels.","lang":"eng"}],"issue":"5","type":"journal_article","oa_version":"Submitted Version","file":[{"checksum":"3c0dcacc900bc45cc65a453dfda4ca43","date_created":"2018-12-12T10:18:07Z","date_updated":"2020-07-14T12:45:19Z","relation":"main_file","file_id":"5326","file_size":1546914,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2015-329-v1+1_manuscript.pdf"}],"pubrep_id":"329","title":"Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates","status":"public","ddc":["576"],"intvolume":" 372","_id":"1850","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"We consider mating strategies for females who search for males sequentially during a season of limited length. We show that the best strategy rejects a given male type if encountered before a time-threshold but accepts him after. For frequency-independent benefits, we obtain the optimal time-thresholds explicitly for both discrete and continuous distributions of males, and allow for mistakes being made in assessing the correct male type. When the benefits are indirect (genes for the offspring) and the population is under frequency-dependent ecological selection, the benefits depend on the mating strategy of other females as well. This case is particularly relevant to speciation models that seek to explore the stability of reproductive isolation by assortative mating under frequency-dependent ecological selection. We show that the indirect benefits are to be quantified by the reproductive values of couples, and describe how the evolutionarily stable time-thresholds can be found. We conclude with an example based on the Levene model, in which we analyze the evolutionarily stable assortative mating strategies and the strength of reproductive isolation provided by them."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1851","intvolume":" 69","title":"Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating","status":"public","ddc":["570"],"oa_version":"Submitted Version","file":[{"date_updated":"2020-07-14T12:45:19Z","date_created":"2020-05-15T09:05:34Z","checksum":"1e8be0b1d7598a78cd2623d8ee8e7798","file_id":"7855","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":967214,"file_name":"2015_Evolution_Priklopil.pdf","access_level":"open_access"}],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"09","citation":{"short":"T. Priklopil, E. Kisdi, M. Gyllenberg, Evolution 69 (2015) 1015–1026.","mla":"Priklopil, Tadeas, et al. “Evolutionarily Stable Mating Decisions for Sequentially Searching Females and the Stability of Reproductive Isolation by Assortative Mating.” Evolution, vol. 69, no. 4, Wiley, 2015, pp. 1015–26, doi:10.1111/evo.12618.","chicago":"Priklopil, Tadeas, Eva Kisdi, and Mats Gyllenberg. “Evolutionarily Stable Mating Decisions for Sequentially Searching Females and the Stability of Reproductive Isolation by Assortative Mating.” Evolution. Wiley, 2015. https://doi.org/10.1111/evo.12618.","ama":"Priklopil T, Kisdi E, Gyllenberg M. Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating. Evolution. 2015;69(4):1015-1026. doi:10.1111/evo.12618","ieee":"T. Priklopil, E. Kisdi, and M. Gyllenberg, “Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating,” Evolution, vol. 69, no. 4. Wiley, pp. 1015–1026, 2015.","apa":"Priklopil, T., Kisdi, E., & Gyllenberg, M. (2015). Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating. Evolution. Wiley. https://doi.org/10.1111/evo.12618","ista":"Priklopil T, Kisdi E, Gyllenberg M. 2015. Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating. Evolution. 69(4), 1015–1026."},"publication":"Evolution","page":"1015 - 1026","article_type":"original","date_published":"2015-02-09T00:00:00Z","publist_id":"5249","ec_funded":1,"file_date_updated":"2020-07-14T12:45:19Z","pmid":1,"year":"2015","publisher":"Wiley","department":[{"_id":"NiBa"},{"_id":"KrCh"}],"publication_status":"published","author":[{"id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","last_name":"Priklopil","first_name":"Tadeas","full_name":"Priklopil, Tadeas"},{"last_name":"Kisdi","first_name":"Eva","full_name":"Kisdi, Eva"},{"full_name":"Gyllenberg, Mats","last_name":"Gyllenberg","first_name":"Mats"}],"volume":69,"date_created":"2018-12-11T11:54:21Z","date_updated":"2022-06-07T10:52:37Z","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"month":"02","external_id":{"pmid":["25662095"]},"oa":1,"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"quality_controlled":"1","doi":"10.1111/evo.12618","language":[{"iso":"eng"}]},{"month":"02","quality_controlled":"1","oa":1,"external_id":{"arxiv":["1012.3298"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1012.3298"}],"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevE.91.022803","article_number":"022803","publist_id":"5213","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"American Institute of Physics","year":"2015","date_updated":"2021-01-12T06:53:49Z","date_created":"2018-12-11T11:54:31Z","volume":91,"author":[{"first_name":"Stephanie","last_name":"Keller-Schmidt","full_name":"Keller-Schmidt, Stephanie"},{"first_name":"Murat","last_name":"Tugrul","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8523-0758","full_name":"Tugrul, Murat"},{"first_name":"Víctor","last_name":"Eguíluz","full_name":"Eguíluz, Víctor"},{"full_name":"Hernandez Garcia, Emilio","last_name":"Hernandez Garcia","first_name":"Emilio"},{"full_name":"Klemm, Konstantin","first_name":"Konstantin","last_name":"Klemm"}],"scopus_import":1,"day":"02","article_processing_charge":"No","article_type":"original","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","citation":{"mla":"Keller-Schmidt, Stephanie, et al. “Anomalous Scaling in an Age-Dependent Branching Model.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 2, 022803, American Institute of Physics, 2015, doi:10.1103/PhysRevE.91.022803.","short":"S. Keller-Schmidt, M. Tugrul, V. Eguíluz, E. Hernandez Garcia, K. Klemm, Physical Review E Statistical Nonlinear and Soft Matter Physics 91 (2015).","chicago":"Keller-Schmidt, Stephanie, Murat Tugrul, Víctor Eguíluz, Emilio Hernandez Garcia, and Konstantin Klemm. “Anomalous Scaling in an Age-Dependent Branching Model.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2015. https://doi.org/10.1103/PhysRevE.91.022803.","ama":"Keller-Schmidt S, Tugrul M, Eguíluz V, Hernandez Garcia E, Klemm K. Anomalous scaling in an age-dependent branching model. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2015;91(2). doi:10.1103/PhysRevE.91.022803","ista":"Keller-Schmidt S, Tugrul M, Eguíluz V, Hernandez Garcia E, Klemm K. 2015. Anomalous scaling in an age-dependent branching model. Physical Review E Statistical Nonlinear and Soft Matter Physics. 91(2), 022803.","apa":"Keller-Schmidt, S., Tugrul, M., Eguíluz, V., Hernandez Garcia, E., & Klemm, K. (2015). Anomalous scaling in an age-dependent branching model. Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.91.022803","ieee":"S. Keller-Schmidt, M. Tugrul, V. Eguíluz, E. Hernandez Garcia, and K. Klemm, “Anomalous scaling in an age-dependent branching model,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 2. American Institute of Physics, 2015."},"date_published":"2015-02-02T00:00:00Z","type":"journal_article","abstract":[{"text":"We introduce a one-parametric family of tree growth models, in which branching probabilities decrease with branch age τ as τ-α. Depending on the exponent α, the scaling of tree depth with tree size n displays a transition between the logarithmic scaling of random trees and an algebraic growth. At the transition (α=1) tree depth grows as (logn)2. This anomalous scaling is in good agreement with the trend observed in evolution of biological species, thus providing a theoretical support for age-dependent speciation and associating it to the occurrence of a critical point.\r\n","lang":"eng"}],"issue":"2","status":"public","title":"Anomalous scaling in an age-dependent branching model","intvolume":" 91","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1883","oa_version":"Preprint"},{"language":[{"iso":"eng"}],"doi":"10.1371/journal.pone.0126907","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"month":"05","volume":10,"date_updated":"2023-02-23T14:07:48Z","date_created":"2018-12-11T11:54:07Z","related_material":{"record":[{"status":"public","relation":"research_data","id":"9715"},{"status":"public","relation":"research_data","id":"9772"}]},"author":[{"last_name":"Trubenova","first_name":"Barbora","orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87","full_name":"Trubenova, Barbora"},{"full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","last_name":"Novak","first_name":"Sebastian"},{"first_name":"Reinmar","last_name":"Hager","full_name":"Hager, Reinmar"}],"department":[{"_id":"NiBa"}],"publisher":"Public Library of Science","publication_status":"published","year":"2015","publist_id":"5299","file_date_updated":"2020-07-14T12:45:17Z","date_published":"2015-05-18T00:00:00Z","citation":{"ista":"Trubenova B, Novak S, Hager R. 2015. Indirect genetic effects and the dynamics of social interactions. PLoS One. 10(5).","apa":"Trubenova, B., Novak, S., & Hager, R. (2015). Indirect genetic effects and the dynamics of social interactions. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907","ieee":"B. Trubenova, S. Novak, and R. Hager, “Indirect genetic effects and the dynamics of social interactions,” PLoS One, vol. 10, no. 5. Public Library of Science, 2015.","ama":"Trubenova B, Novak S, Hager R. Indirect genetic effects and the dynamics of social interactions. PLoS One. 2015;10(5). doi:10.1371/journal.pone.0126907","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Indirect Genetic Effects and the Dynamics of Social Interactions.” PLoS One. Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.","mla":"Trubenova, Barbora, et al. “Indirect Genetic Effects and the Dynamics of Social Interactions.” PLoS One, vol. 10, no. 5, Public Library of Science, 2015, doi:10.1371/journal.pone.0126907.","short":"B. Trubenova, S. Novak, R. Hager, PLoS One 10 (2015)."},"publication":"PLoS One","has_accepted_license":"1","day":"18","scopus_import":1,"oa_version":"Published Version","file":[{"creator":"system","content_type":"application/pdf","file_size":2748982,"access_level":"open_access","file_name":"IST-2016-453-v1+1_journal.pone.0126907.pdf","checksum":"d3a4a58ef4bd3b3e2f32b7fd7af4a743","date_created":"2018-12-12T10:09:07Z","date_updated":"2020-07-14T12:45:17Z","file_id":"4730","relation":"main_file"}],"pubrep_id":"453","intvolume":" 10","status":"public","title":"Indirect genetic effects and the dynamics of social interactions","ddc":["570","576"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1809","issue":"5","abstract":[{"text":"Background: Indirect genetic effects (IGEs) occur when genes expressed in one individual alter the expression of traits in social partners. Previous studies focused on the evolutionary consequences and evolutionary dynamics of IGEs, using equilibrium solutions to predict phenotypes in subsequent generations. However, whether or not such steady states may be reached may depend on the dynamics of interactions themselves. Results: In our study, we focus on the dynamics of social interactions and indirect genetic effects and investigate how they modify phenotypes over time. Unlike previous IGE studies, we do not analyse evolutionary dynamics; rather we consider within-individual phenotypic changes, also referred to as phenotypic plasticity. We analyse iterative interactions, when individuals interact in a series of discontinuous events, and investigate the stability of steady state solutions and the dependence on model parameters, such as population size, strength, and the nature of interactions. We show that for interactions where a feedback loop occurs, the possible parameter space of interaction strength is fairly limited, affecting the evolutionary consequences of IGEs. We discuss the implications of our results for current IGE model predictions and their limitations.","lang":"eng"}],"type":"journal_article"},{"type":"research_data_reference","status":"public","title":"Description of the agent based simulations","publisher":"Public Library of Science","department":[{"_id":"NiBa"}],"year":"2015","_id":"9772","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_created":"2021-08-05T12:55:20Z","date_updated":"2023-02-23T10:15:25Z","oa_version":"Published Version","author":[{"first_name":"Barbora","last_name":"Trubenova","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora"},{"last_name":"Novak","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian"},{"full_name":"Hager, Reinmar","first_name":"Reinmar","last_name":"Hager"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1809"}]},"month":"05","day":"18","article_processing_charge":"No","citation":{"mla":"Trubenova, Barbora, et al. Description of the Agent Based Simulations. Public Library of Science, 2015, doi:10.1371/journal.pone.0126907.s003.","short":"B. Trubenova, S. Novak, R. Hager, (2015).","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Description of the Agent Based Simulations.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.s003.","ama":"Trubenova B, Novak S, Hager R. Description of the agent based simulations. 2015. doi:10.1371/journal.pone.0126907.s003","ista":"Trubenova B, Novak S, Hager R. 2015. Description of the agent based simulations, Public Library of Science, 10.1371/journal.pone.0126907.s003.","apa":"Trubenova, B., Novak, S., & Hager, R. (2015). Description of the agent based simulations. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907.s003","ieee":"B. Trubenova, S. Novak, and R. Hager, “Description of the agent based simulations.” Public Library of Science, 2015."},"doi":"10.1371/journal.pone.0126907.s003","date_published":"2015-05-18T00:00:00Z"},{"citation":{"ama":"Tugrul M, Paixao T, Barton NH, Tkačik G. Other fitness models for comparison & for interacting TFBSs. 2015. doi:10.1371/journal.pgen.1005639.s001","ieee":"M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Other fitness models for comparison & for interacting TFBSs.” Public Library of Science, 2015.","apa":"Tugrul, M., Paixao, T., Barton, N. H., & Tkačik, G. (2015). Other fitness models for comparison & for interacting TFBSs. Public Library of Science. https://doi.org/10.1371/journal.pgen.1005639.s001","ista":"Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Other fitness models for comparison & for interacting TFBSs, Public Library of Science, 10.1371/journal.pgen.1005639.s001.","short":"M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, (2015).","mla":"Tugrul, Murat, et al. Other Fitness Models for Comparison & for Interacting TFBSs. Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.s001.","chicago":"Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Other Fitness Models for Comparison & for Interacting TFBSs.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pgen.1005639.s001."},"doi":"10.1371/journal.pgen.1005639.s001","date_published":"2015-11-06T00:00:00Z","article_processing_charge":"No","day":"06","month":"11","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9712","year":"2015","department":[{"_id":"NiBa"},{"_id":"CaGu"},{"_id":"GaTk"}],"publisher":"Public Library of Science","status":"public","title":"Other fitness models for comparison & for interacting TFBSs","related_material":{"record":[{"id":"1666","relation":"used_in_publication","status":"public"}]},"author":[{"first_name":"Murat","last_name":"Tugrul","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8523-0758","full_name":"Tugrul, Murat"},{"full_name":"Paixao, Tiago","last_name":"Paixao","first_name":"Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"}],"oa_version":"Published Version","date_updated":"2023-02-23T10:09:08Z","date_created":"2021-07-23T12:00:37Z","type":"research_data_reference"},{"type":"research_data_reference","title":"Mathematical inference of the results","status":"public","department":[{"_id":"NiBa"}],"publisher":"Public Library of Science","_id":"9715","year":"2015","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_created":"2021-07-23T12:11:30Z","date_updated":"2023-02-23T10:15:25Z","oa_version":"Published Version","author":[{"last_name":"Trubenova","first_name":"Barbora","orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87","full_name":"Trubenova, Barbora"},{"full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","last_name":"Novak"},{"full_name":"Hager, Reinmar","last_name":"Hager","first_name":"Reinmar"}],"related_material":{"record":[{"id":"1809","relation":"used_in_publication","status":"public"}]},"day":"18","month":"05","article_processing_charge":"No","citation":{"ama":"Trubenova B, Novak S, Hager R. Mathematical inference of the results. 2015. doi:10.1371/journal.pone.0126907.s001","apa":"Trubenova, B., Novak, S., & Hager, R. (2015). Mathematical inference of the results. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907.s001","ieee":"B. Trubenova, S. Novak, and R. Hager, “Mathematical inference of the results.” Public Library of Science, 2015.","ista":"Trubenova B, Novak S, Hager R. 2015. Mathematical inference of the results, Public Library of Science, 10.1371/journal.pone.0126907.s001.","short":"B. Trubenova, S. Novak, R. Hager, (2015).","mla":"Trubenova, Barbora, et al. Mathematical Inference of the Results. Public Library of Science, 2015, doi:10.1371/journal.pone.0126907.s001.","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Mathematical Inference of the Results.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.s001."},"date_published":"2015-05-18T00:00:00Z","doi":"10.1371/journal.pone.0126907.s001"},{"type":"journal_article","issue":"11","abstract":[{"lang":"eng","text":"Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key regulatory mechanism that determines gene expression and hence heritable phenotypic variation. We use a biophysical model for directional selection on gene expression to estimate the rates of gain and loss of transcription factor binding sites (TFBS) in finite populations under both point and insertion/deletion mutations. Our results show that these rates are typically slow for a single TFBS in an isolated DNA region, unless the selection is extremely strong. These rates decrease drastically with increasing TFBS length or increasingly specific protein-DNA interactions, making the evolution of sites longer than ∼ 10 bp unlikely on typical eukaryotic speciation timescales. Similarly, evolution converges to the stationary distribution of binding sequences very slowly, making the equilibrium assumption questionable. The availability of longer regulatory sequences in which multiple binding sites can evolve simultaneously, the presence of “pre-sites” or partially decayed old sites in the initial sequence, and biophysical cooperativity between transcription factors, can all facilitate gain of TFBS and reconcile theoretical calculations with timescales inferred from comparative genomics."}],"intvolume":" 11","title":"Dynamics of transcription factor binding site evolution","status":"public","ddc":["576"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1666","file":[{"relation":"main_file","file_id":"4657","checksum":"a4e72fca5ccf40ddacf4d08c8e46b554","date_updated":"2020-07-14T12:45:10Z","date_created":"2018-12-12T10:07:58Z","access_level":"open_access","file_name":"IST-2016-463-v1+1_journal.pgen.1005639.pdf","content_type":"application/pdf","file_size":2580778,"creator":"system"}],"oa_version":"Published Version","pubrep_id":"463","scopus_import":1,"has_accepted_license":"1","day":"06","citation":{"ama":"Tugrul M, Paixao T, Barton NH, Tkačik G. Dynamics of transcription factor binding site evolution. PLoS Genetics. 2015;11(11). doi:10.1371/journal.pgen.1005639","apa":"Tugrul, M., Paixao, T., Barton, N. H., & Tkačik, G. (2015). Dynamics of transcription factor binding site evolution. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1005639","ieee":"M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Dynamics of transcription factor binding site evolution,” PLoS Genetics, vol. 11, no. 11. Public Library of Science, 2015.","ista":"Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Dynamics of transcription factor binding site evolution. PLoS Genetics. 11(11).","short":"M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, PLoS Genetics 11 (2015).","mla":"Tugrul, Murat, et al. “Dynamics of Transcription Factor Binding Site Evolution.” PLoS Genetics, vol. 11, no. 11, Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.","chicago":"Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Dynamics of Transcription Factor Binding Site Evolution.” PLoS Genetics. Public Library of Science, 2015. https://doi.org/10.1371/journal.pgen.1005639."},"publication":"PLoS Genetics","date_published":"2015-11-06T00:00:00Z","publist_id":"5483","ec_funded":1,"file_date_updated":"2020-07-14T12:45:10Z","publisher":"Public Library of Science","department":[{"_id":"NiBa"},{"_id":"CaGu"},{"_id":"GaTk"}],"publication_status":"published","year":"2015","volume":11,"date_updated":"2023-09-07T11:53:49Z","date_created":"2018-12-11T11:53:21Z","related_material":{"record":[{"status":"public","relation":"research_data","id":"9712"},{"id":"1131","status":"public","relation":"dissertation_contains"}]},"author":[{"last_name":"Tugrul","first_name":"Murat","orcid":"0000-0002-8523-0758","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","full_name":"Tugrul, Murat"},{"orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","first_name":"Tiago","full_name":"Paixao, Tiago"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"full_name":"Tkacik, Gasper","last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"month":"11","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1371/journal.pgen.1005639"},{"ec_funded":1,"publist_id":"5267","year":"2015","acknowledgement":"SNSF Early Postdoc.Mobility Fellowship, the grant number P2EZP2 148797.\r\n","publication_status":"published","publisher":"Springer","department":[{"_id":"ToHe"},{"_id":"CaGu"},{"_id":"NiBa"}],"author":[{"last_name":"Giacobbe","first_name":"Mirco","orcid":"0000-0001-8180-0904","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","full_name":"Giacobbe, Mirco"},{"full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"},{"first_name":"Ashutosh","last_name":"Gupta","id":"335E5684-F248-11E8-B48F-1D18A9856A87","full_name":"Gupta, Ashutosh"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","first_name":"Tiago"},{"full_name":"Petrov, Tatjana","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9041-0905","first_name":"Tatjana","last_name":"Petrov"}],"related_material":{"record":[{"id":"1351","status":"public","relation":"later_version"}]},"date_updated":"2023-09-20T11:06:03Z","date_created":"2018-12-11T11:54:16Z","volume":9035,"month":"04","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1410.7704"}],"quality_controlled":"1","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091"},{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"},{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"conference":{"end_date":"2015-04-18","start_date":"2015-04-11","location":"London, United Kingdom","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"doi":"10.1007/978-3-662-46681-0_47","language":[{"iso":"eng"}],"type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"The behaviour of gene regulatory networks (GRNs) is typically analysed using simulation-based statistical testing-like methods. In this paper, we demonstrate that we can replace this approach by a formal verification-like method that gives higher assurance and scalability. We focus on Wagner’s weighted GRN model with varying weights, which is used in evolutionary biology. In the model, weight parameters represent the gene interaction strength that may change due to genetic mutations. For a property of interest, we synthesise the constraints over the parameter space that represent the set of GRNs satisfying the property. We experimentally show that our parameter synthesis procedure computes the mutational robustness of GRNs –an important problem of interest in evolutionary biology– more efficiently than the classical simulation method. We specify the property in linear temporal logics. We employ symbolic bounded model checking and SMT solving to compute the space of GRNs that satisfy the property, which amounts to synthesizing a set of linear constraints on the weights.","lang":"eng"}],"_id":"1835","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Model checking gene regulatory networks","status":"public","intvolume":" 9035","oa_version":"Preprint","scopus_import":1,"series_title":"Lecture Notes in Computer Science","day":"01","citation":{"short":"M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, 9035 (2015) 469–483.","mla":"Giacobbe, Mirco, et al. Model Checking Gene Regulatory Networks. Vol. 9035, Springer, 2015, pp. 469–83, doi:10.1007/978-3-662-46681-0_47.","chicago":"Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago Paixao, and Tatjana Petrov. “Model Checking Gene Regulatory Networks.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-46681-0_47.","ama":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking gene regulatory networks. 2015;9035:469-483. doi:10.1007/978-3-662-46681-0_47","apa":"Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., & Petrov, T. (2015). Model checking gene regulatory networks. Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, London, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-46681-0_47","ieee":"M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov, “Model checking gene regulatory networks,” vol. 9035. Springer, pp. 469–483, 2015.","ista":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2015. Model checking gene regulatory networks. 9035, 469–483."},"page":"469 - 483","date_published":"2015-04-01T00:00:00Z"},{"date_published":"2015-09-29T00:00:00Z","publication":"Games","citation":{"ieee":"T. Priklopil and K. Chatterjee, “Evolution of decisions in population games with sequentially searching individuals,” Games, vol. 6, no. 4. MDPI, pp. 413–437, 2015.","apa":"Priklopil, T., & Chatterjee, K. (2015). Evolution of decisions in population games with sequentially searching individuals. Games. MDPI. https://doi.org/10.3390/g6040413","ista":"Priklopil T, Chatterjee K. 2015. Evolution of decisions in population games with sequentially searching individuals. Games. 6(4), 413–437.","ama":"Priklopil T, Chatterjee K. Evolution of decisions in population games with sequentially searching individuals. Games. 2015;6(4):413-437. doi:10.3390/g6040413","chicago":"Priklopil, Tadeas, and Krishnendu Chatterjee. “Evolution of Decisions in Population Games with Sequentially Searching Individuals.” Games. MDPI, 2015. https://doi.org/10.3390/g6040413.","short":"T. Priklopil, K. Chatterjee, Games 6 (2015) 413–437.","mla":"Priklopil, Tadeas, and Krishnendu Chatterjee. “Evolution of Decisions in Population Games with Sequentially Searching Individuals.” Games, vol. 6, no. 4, MDPI, 2015, pp. 413–37, doi:10.3390/g6040413."},"article_type":"original","page":"413 - 437","day":"29","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","pubrep_id":"448","file":[{"access_level":"open_access","file_name":"IST-2016-448-v1+1_games-06-00413.pdf","creator":"system","file_size":518832,"content_type":"application/pdf","file_id":"4959","relation":"main_file","checksum":"912e1acbaf201100f447a43e4d5958bd","date_created":"2018-12-12T10:12:41Z","date_updated":"2020-07-14T12:45:12Z"}],"oa_version":"Published Version","_id":"1681","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Evolution of decisions in population games with sequentially searching individuals","ddc":["000"],"intvolume":" 6","abstract":[{"lang":"eng","text":"In many social situations, individuals endeavor to find the single best possible partner, but are constrained to evaluate the candidates in sequence. Examples include the search for mates, economic partnerships, or any other long-term ties where the choice to interact involves two parties. Surprisingly, however, previous theoretical work on mutual choice problems focuses on finding equilibrium solutions, while ignoring the evolutionary dynamics of decisions. Empirically, this may be of high importance, as some equilibrium solutions can never be reached unless the population undergoes radical changes and a sufficient number of individuals change their decisions simultaneously. To address this question, we apply a mutual choice sequential search problem in an evolutionary game-theoretical model that allows one to find solutions that are favored by evolution. As an example, we study the influence of sequential search on the evolutionary dynamics of cooperation. For this, we focus on the classic snowdrift game and the prisoner’s dilemma game."}],"issue":"4","type":"journal_article","doi":"10.3390/g6040413","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"month":"09","publication_identifier":{"eissn":["2073-4336"]},"author":[{"full_name":"Priklopil, Tadeas","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","first_name":"Tadeas","last_name":"Priklopil"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"}],"date_updated":"2023-10-17T11:42:52Z","date_created":"2018-12-11T11:53:26Z","volume":6,"year":"2015","publication_status":"published","publisher":"MDPI","department":[{"_id":"NiBa"},{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:45:12Z","publist_id":"5467","ec_funded":1},{"date_published":"2014-03-04T00:00:00Z","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","citation":{"ama":"Kollár R, Bodova K, Nosek J, Tomáška Ľ. Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2014;89(3). doi:10.1103/PhysRevE.89.032701","ieee":"R. Kollár, K. Bodova, J. Nosek, and Ľ. Tomáška, “Mathematical model of alternative mechanism of telomere length maintenance,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 3. American Institute of Physics, 2014.","apa":"Kollár, R., Bodova, K., Nosek, J., & Tomáška, Ľ. (2014). Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.89.032701","ista":"Kollár R, Bodova K, Nosek J, Tomáška Ľ. 2014. Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. 89(3), 032701.","short":"R. Kollár, K. Bodova, J. Nosek, Ľ. Tomáška, Physical Review E Statistical Nonlinear and Soft Matter Physics 89 (2014).","mla":"Kollár, Richard, et al. “Mathematical Model of Alternative Mechanism of Telomere Length Maintenance.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 3, 032701, American Institute of Physics, 2014, doi:10.1103/PhysRevE.89.032701.","chicago":"Kollár, Richard, Katarina Bodova, Jozef Nosek, and Ľubomír Tomáška. “Mathematical Model of Alternative Mechanism of Telomere Length Maintenance.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2014. https://doi.org/10.1103/PhysRevE.89.032701."},"day":"04","article_processing_charge":"No","scopus_import":"1","oa_version":"Submitted Version","_id":"1896","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Mathematical model of alternative mechanism of telomere length maintenance","intvolume":" 89","abstract":[{"text":"Biopolymer length regulation is a complex process that involves a large number of biological, chemical, and physical subprocesses acting simultaneously across multiple spatial and temporal scales. An illustrative example important for genomic stability is the length regulation of telomeres - nucleoprotein structures at the ends of linear chromosomes consisting of tandemly repeated DNA sequences and a specialized set of proteins. Maintenance of telomeres is often facilitated by the enzyme telomerase but, particularly in telomerase-free systems, the maintenance of chromosomal termini depends on alternative lengthening of telomeres (ALT) mechanisms mediated by recombination. Various linear and circular DNA structures were identified to participate in ALT, however, dynamics of the whole process is still poorly understood. We propose a chemical kinetics model of ALT with kinetic rates systematically derived from the biophysics of DNA diffusion and looping. The reaction system is reduced to a coagulation-fragmentation system by quasi-steady-state approximation. The detailed treatment of kinetic rates yields explicit formulas for expected size distributions of telomeres that demonstrate the key role played by the J factor, a quantitative measure of bending of polymers. The results are in agreement with experimental data and point out interesting phenomena: an appearance of very long telomeric circles if the total telomere density exceeds a critical value (excess mass) and a nonlinear response of the telomere size distributions to the amount of telomeric DNA in the system. The results can be of general importance for understanding dynamics of telomeres in telomerase-independent systems as this mode of telomere maintenance is similar to the situation in tumor cells lacking telomerase activity. Furthermore, due to its universality, the model may also serve as a prototype of an interaction between linear and circular DNA structures in various settings.","lang":"eng"}],"issue":"3","type":"journal_article","doi":"10.1103/PhysRevE.89.032701","language":[{"iso":"eng"}],"main_file_link":[{"url":"http://arxiv.org/abs/1402.0430","open_access":"1"}],"oa":1,"month":"03","author":[{"last_name":"Kollár","first_name":"Richard","full_name":"Kollár, Richard"},{"full_name":"Bod'ová, Katarína","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7214-0171","first_name":"Katarína","last_name":"Bod'ová"},{"last_name":"Nosek","first_name":"Jozef","full_name":"Nosek, Jozef"},{"first_name":"Ľubomír","last_name":"Tomáška","full_name":"Tomáška, Ľubomír"}],"date_updated":"2022-08-01T10:50:10Z","date_created":"2018-12-11T11:54:35Z","volume":89,"year":"2014","acknowledgement":"The work was supported by the VEGA Grant No. 1/0459/13 (R.K. and K.B.).","publication_status":"published","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"publisher":"American Institute of Physics","publist_id":"5198","article_number":"032701"},{"doi":"10.1111/1365-2435.12207","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"month":"06","author":[{"first_name":"Thomas","last_name":"Ezard","full_name":"Ezard, Thomas"},{"full_name":"Prizak, Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","last_name":"Prizak","first_name":"Roshan"},{"last_name":"Hoyle","first_name":"Rebecca","full_name":"Hoyle, Rebecca"}],"date_created":"2018-12-11T11:54:40Z","date_updated":"2021-01-12T06:54:00Z","volume":28,"acknowledgement":"Engineering and Physical Sciences Research Council. Grant Number: EP/H031928/1","year":"2014","publication_status":"published","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"publisher":"Wiley-Blackwell","file_date_updated":"2020-07-14T12:45:20Z","publist_id":"5186","date_published":"2014-06-01T00:00:00Z","publication":"Functional Ecology","citation":{"ama":"Ezard T, Prizak R, Hoyle R. The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. 2014;28(3):693-701. doi:10.1111/1365-2435.12207","apa":"Ezard, T., Prizak, R., & Hoyle, R. (2014). The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. Wiley-Blackwell. https://doi.org/10.1111/1365-2435.12207","ieee":"T. Ezard, R. Prizak, and R. Hoyle, “The fitness costs of adaptation via phenotypic plasticity and maternal effects,” Functional Ecology, vol. 28, no. 3. Wiley-Blackwell, pp. 693–701, 2014.","ista":"Ezard T, Prizak R, Hoyle R. 2014. The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. 28(3), 693–701.","short":"T. Ezard, R. Prizak, R. Hoyle, Functional Ecology 28 (2014) 693–701.","mla":"Ezard, Thomas, et al. “The Fitness Costs of Adaptation via Phenotypic Plasticity and Maternal Effects.” Functional Ecology, vol. 28, no. 3, Wiley-Blackwell, 2014, pp. 693–701, doi:10.1111/1365-2435.12207.","chicago":"Ezard, Thomas, Roshan Prizak, and Rebecca Hoyle. “The Fitness Costs of Adaptation via Phenotypic Plasticity and Maternal Effects.” Functional Ecology. Wiley-Blackwell, 2014. https://doi.org/10.1111/1365-2435.12207."},"page":"693 - 701","day":"01","has_accepted_license":"1","scopus_import":1,"pubrep_id":"419","file":[{"relation":"main_file","file_id":"5167","checksum":"3cbe8623174709a8ceec2103246f8fe0","date_updated":"2020-07-14T12:45:20Z","date_created":"2018-12-12T10:15:45Z","access_level":"open_access","file_name":"IST-2016-419-v1+1_Ezard_et_al-2014-Functional_Ecology.pdf","content_type":"application/pdf","file_size":536154,"creator":"system"}],"oa_version":"Published Version","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"1909","title":"The fitness costs of adaptation via phenotypic plasticity and maternal effects","status":"public","ddc":["570"],"intvolume":" 28","abstract":[{"text":"Summary: Phenotypes are often environmentally dependent, which requires organisms to track environmental change. The challenge for organisms is to construct phenotypes using the most accurate environmental cue. Here, we use a quantitative genetic model of adaptation by additive genetic variance, within- and transgenerational plasticity via linear reaction norms and indirect genetic effects respectively. We show how the relative influence on the eventual phenotype of these components depends on the predictability of environmental change (fast or slow, sinusoidal or stochastic) and the developmental lag τ between when the environment is perceived and when selection acts. We then decompose expected mean fitness into three components (variance load, adaptation and fluctuation load) to study the fitness costs of within- and transgenerational plasticity. A strongly negative maternal effect coefficient m minimizes the variance load, but a strongly positive m minimises the fluctuation load. The adaptation term is maximized closer to zero, with positive or negative m preferred under different environmental scenarios. Phenotypic plasticity is higher when τ is shorter and when the environment changes frequently between seasonal extremes. Expected mean population fitness is highest away from highest observed levels of phenotypic plasticity. Within- and transgenerational plasticity act in concert to deliver well-adapted phenotypes, which emphasizes the need to study both simultaneously when investigating phenotypic evolution.","lang":"eng"}],"issue":"3","type":"journal_article"},{"scopus_import":1,"day":"01","publication":"Genetics","citation":{"ama":"Weissman D, Hallatschek O. The rate of adaptation in large sexual populations with linear chromosomes. Genetics. 2014;196(4):1167-1183. doi:10.1534/genetics.113.160705","ieee":"D. Weissman and O. Hallatschek, “The rate of adaptation in large sexual populations with linear chromosomes,” Genetics, vol. 196, no. 4. Genetics Society of America, pp. 1167–1183, 2014.","apa":"Weissman, D., & Hallatschek, O. (2014). The rate of adaptation in large sexual populations with linear chromosomes. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.113.160705","ista":"Weissman D, Hallatschek O. 2014. The rate of adaptation in large sexual populations with linear chromosomes. Genetics. 196(4), 1167–1183.","short":"D. Weissman, O. Hallatschek, Genetics 196 (2014) 1167–1183.","mla":"Weissman, Daniel, and Oskar Hallatschek. “The Rate of Adaptation in Large Sexual Populations with Linear Chromosomes.” Genetics, vol. 196, no. 4, Genetics Society of America, 2014, pp. 1167–83, doi:10.1534/genetics.113.160705.","chicago":"Weissman, Daniel, and Oskar Hallatschek. “The Rate of Adaptation in Large Sexual Populations with Linear Chromosomes.” Genetics. Genetics Society of America, 2014. https://doi.org/10.1534/genetics.113.160705."},"page":"1167 - 1183","date_published":"2014-04-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"In large populations, multiple beneficial mutations may be simultaneously spreading. In asexual populations, these mutations must either arise on the same background or compete against each other. In sexual populations, recombination can bring together beneficial alleles from different backgrounds, but tightly linked alleles may still greatly interfere with each other. We show for well-mixed populations that when this interference is strong, the genome can be seen as consisting of many effectively asexual stretches linked together. The rate at which beneficial alleles fix is thus roughly proportional to the rate of recombination and depends only logarithmically on the mutation supply and the strength of selection. Our scaling arguments also allow us to predict, with reasonable accuracy, the fitness distribution of fixed mutations when the mutational effect sizes are broad. We focus on the regime in which crossovers occur more frequently than beneficial mutations, as is likely to be the case for many natural populations."}],"issue":"4","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"1908","status":"public","title":"The rate of adaptation in large sexual populations with linear chromosomes","intvolume":" 196","oa_version":"Submitted Version","month":"04","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1307.0737","open_access":"1"}],"quality_controlled":"1","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}],"doi":"10.1534/genetics.113.160705","language":[{"iso":"eng"}],"ec_funded":1,"publist_id":"5187","year":"2014","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Genetics Society of America","author":[{"full_name":"Weissman, Daniel","id":"2D0CE020-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","last_name":"Weissman"},{"last_name":"Hallatschek","first_name":"Oskar","full_name":"Hallatschek, Oskar"}],"date_updated":"2021-01-12T06:53:59Z","date_created":"2018-12-11T11:54:39Z","volume":196},{"project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"quality_controlled":"1","oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4014306/","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1093/beheco/aru002","month":"02","publisher":"Oxford University Press","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2014","volume":25,"date_created":"2018-12-11T11:54:48Z","date_updated":"2021-01-12T06:54:11Z","author":[{"full_name":"Arbilly, Michal","last_name":"Arbilly","first_name":"Michal"},{"id":"2D0CE020-F248-11E8-B48F-1D18A9856A87","last_name":"Weissman","first_name":"Daniel","full_name":"Weissman, Daniel"},{"last_name":"Feldman","first_name":"Marcus","full_name":"Feldman, Marcus"},{"full_name":"Grodzinski, Uri","last_name":"Grodzinski","first_name":"Uri"}],"ec_funded":1,"publist_id":"5157","page":"487 - 495","citation":{"chicago":"Arbilly, Michal, Daniel Weissman, Marcus Feldman, and Uri Grodzinski. “An Arms Race between Producers and Scroungers Can Drive the Evolution of Social Cognition.” Behavioral Ecology. Oxford University Press, 2014. https://doi.org/10.1093/beheco/aru002.","mla":"Arbilly, Michal, et al. “An Arms Race between Producers and Scroungers Can Drive the Evolution of Social Cognition.” Behavioral Ecology, vol. 25, no. 3, Oxford University Press, 2014, pp. 487–95, doi:10.1093/beheco/aru002.","short":"M. Arbilly, D. Weissman, M. Feldman, U. Grodzinski, Behavioral Ecology 25 (2014) 487–495.","ista":"Arbilly M, Weissman D, Feldman M, Grodzinski U. 2014. An arms race between producers and scroungers can drive the evolution of social cognition. Behavioral Ecology. 25(3), 487–495.","apa":"Arbilly, M., Weissman, D., Feldman, M., & Grodzinski, U. (2014). An arms race between producers and scroungers can drive the evolution of social cognition. Behavioral Ecology. Oxford University Press. https://doi.org/10.1093/beheco/aru002","ieee":"M. Arbilly, D. Weissman, M. Feldman, and U. Grodzinski, “An arms race between producers and scroungers can drive the evolution of social cognition,” Behavioral Ecology, vol. 25, no. 3. Oxford University Press, pp. 487–495, 2014.","ama":"Arbilly M, Weissman D, Feldman M, Grodzinski U. An arms race between producers and scroungers can drive the evolution of social cognition. Behavioral Ecology. 2014;25(3):487-495. doi:10.1093/beheco/aru002"},"publication":"Behavioral Ecology","date_published":"2014-02-13T00:00:00Z","scopus_import":1,"day":"13","intvolume":" 25","status":"public","title":"An arms race between producers and scroungers can drive the evolution of social cognition","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"1936","oa_version":"Submitted Version","type":"journal_article","issue":"3","abstract":[{"text":"The social intelligence hypothesis states that the need to cope with complexities of social life has driven the evolution of advanced cognitive abilities. It is usually invoked in the context of challenges arising from complex intragroup structures, hierarchies, and alliances. However, a fundamental aspect of group living remains largely unexplored as a driving force in cognitive evolution: the competition between individuals searching for resources (producers) and conspecifics that parasitize their findings (scroungers). In populations of social foragers, abilities that enable scroungers to steal by outsmarting producers, and those allowing producers to prevent theft by outsmarting scroungers, are likely to be beneficial and may fuel a cognitive arms race. Using analytical theory and agent-based simulations, we present a general model for such a race that is driven by the producer-scrounger game and show that the race's plausibility is dramatically affected by the nature of the evolving abilities. If scrounging and scrounging avoidance rely on separate, strategy-specific cognitive abilities, arms races are short-lived and have a limited effect on cognition. However, general cognitive abilities that facilitate both scrounging and scrounging avoidance undergo stable, long-lasting arms races. Thus, ubiquitous foraging interactions may lead to the evolution of general cognitive abilities in social animals, without the requirement of complex intragroup structures.","lang":"eng"}]},{"doi":"10.1111/evo.12517","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1310.6077","open_access":"1"}],"project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"quality_controlled":"1","month":"12","author":[{"full_name":"Trotter, Meredith","last_name":"Trotter","first_name":"Meredith"},{"id":"2D0CE020-F248-11E8-B48F-1D18A9856A87","last_name":"Weissman","first_name":"Daniel","full_name":"Weissman, Daniel"},{"full_name":"Peterson, Grant","first_name":"Grant","last_name":"Peterson"},{"full_name":"Peck, Kayla","last_name":"Peck","first_name":"Kayla"},{"full_name":"Masel, Joanna","first_name":"Joanna","last_name":"Masel"}],"volume":68,"date_created":"2018-12-11T11:54:47Z","date_updated":"2021-01-12T06:54:10Z","acknowledgement":"Funded by National Institutes of Health. Grant Numbers: R01GM076041, R01GM104040 \r\n\r\nSimons Foundation\r\n\r\n","year":"2014","department":[{"_id":"NiBa"}],"publisher":"Wiley-Blackwell","publication_status":"published","ec_funded":1,"publist_id":"5162","date_published":"2014-12-01T00:00:00Z","citation":{"ama":"Trotter M, Weissman D, Peterson G, Peck K, Masel J. Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations. Evolution. 2014;68(12):3357-3367. doi:10.1111/evo.12517","ieee":"M. Trotter, D. Weissman, G. Peterson, K. Peck, and J. Masel, “Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations,” Evolution, vol. 68, no. 12. Wiley-Blackwell, pp. 3357–3367, 2014.","apa":"Trotter, M., Weissman, D., Peterson, G., Peck, K., & Masel, J. (2014). Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations. Evolution. Wiley-Blackwell. https://doi.org/10.1111/evo.12517","ista":"Trotter M, Weissman D, Peterson G, Peck K, Masel J. 2014. Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations. Evolution. 68(12), 3357–3367.","short":"M. Trotter, D. Weissman, G. Peterson, K. Peck, J. Masel, Evolution 68 (2014) 3357–3367.","mla":"Trotter, Meredith, et al. “Cryptic Genetic Variation Can Make "Irreducible Complexity" a Common Mode of Adaptation in Sexual Populations.” Evolution, vol. 68, no. 12, Wiley-Blackwell, 2014, pp. 3357–67, doi:10.1111/evo.12517.","chicago":"Trotter, Meredith, Daniel Weissman, Grant Peterson, Kayla Peck, and Joanna Masel. “Cryptic Genetic Variation Can Make "Irreducible Complexity" a Common Mode of Adaptation in Sexual Populations.” Evolution. Wiley-Blackwell, 2014. https://doi.org/10.1111/evo.12517."},"publication":"Evolution","page":"3357 - 3367","day":"01","scopus_import":1,"oa_version":"Submitted Version","_id":"1932","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","intvolume":" 68","status":"public","title":"Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations","issue":"12","abstract":[{"lang":"eng","text":"The existence of complex (multiple-step) genetic adaptations that are "irreducible" (i.e., all partial combinations are less fit than the original genotype) is one of the longest standing problems in evolutionary biology. In standard genetics parlance, these adaptations require the crossing of a wide adaptive valley of deleterious intermediate stages. Here, we demonstrate, using a simple model, that evolution can cross wide valleys to produce "irreducibly complex" adaptations by making use of previously cryptic mutations. When revealed by an evolutionary capacitor, previously cryptic mutants have higher initial frequencies than do new mutations, bringing them closer to a valley-crossing saddle in allele frequency space. Moreover, simple combinatorics implies an enormous number of candidate combinations exist within available cryptic genetic variation. We model the dynamics of crossing of a wide adaptive valley after a capacitance event using both numerical simulations and analytical approximations. Although individual valley crossing events become less likely as valleys widen, by taking the combinatorics of genotype space into account, we see that revealing cryptic variation can cause the frequent evolution of complex adaptations."}],"type":"journal_article"},{"month":"08","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}],"doi":"10.1016/j.tpb.2014.05.001","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:31Z","publist_id":"4816","ec_funded":1,"year":"2014","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Academic Press","author":[{"full_name":"Kelleher, Jerome","first_name":"Jerome","last_name":"Kelleher"},{"last_name":"Etheridge","first_name":"Alison","full_name":"Etheridge, Alison"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"date_created":"2018-12-11T11:56:06Z","date_updated":"2021-01-12T06:55:44Z","volume":95,"scopus_import":1,"day":"01","has_accepted_license":"1","publication":"Theoretical Population Biology","citation":{"apa":"Kelleher, J., Etheridge, A., & Barton, N. H. (2014). Coalescent simulation in continuous space: Algorithms for large neighbourhood size. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2014.05.001","ieee":"J. Kelleher, A. Etheridge, and N. H. Barton, “Coalescent simulation in continuous space: Algorithms for large neighbourhood size,” Theoretical Population Biology, vol. 95. Academic Press, pp. 13–23, 2014.","ista":"Kelleher J, Etheridge A, Barton NH. 2014. Coalescent simulation in continuous space: Algorithms for large neighbourhood size. Theoretical Population Biology. 95, 13–23.","ama":"Kelleher J, Etheridge A, Barton NH. Coalescent simulation in continuous space: Algorithms for large neighbourhood size. Theoretical Population Biology. 2014;95:13-23. doi:10.1016/j.tpb.2014.05.001","chicago":"Kelleher, Jerome, Alison Etheridge, and Nicholas H Barton. “Coalescent Simulation in Continuous Space: Algorithms for Large Neighbourhood Size.” Theoretical Population Biology. Academic Press, 2014. https://doi.org/10.1016/j.tpb.2014.05.001.","short":"J. Kelleher, A. Etheridge, N.H. Barton, Theoretical Population Biology 95 (2014) 13–23.","mla":"Kelleher, Jerome, et al. “Coalescent Simulation in Continuous Space: Algorithms for Large Neighbourhood Size.” Theoretical Population Biology, vol. 95, Academic Press, 2014, pp. 13–23, doi:10.1016/j.tpb.2014.05.001."},"page":"13 - 23","date_published":"2014-08-01T00:00:00Z","type":"journal_article","abstract":[{"text":"Many species have an essentially continuous distribution in space, in which there are no natural divisions between randomly mating subpopulations. Yet, the standard approach to modelling these populations is to impose an arbitrary grid of demes, adjusting deme sizes and migration rates in an attempt to capture the important features of the population. Such indirect methods are required because of the failure of the classical models of isolation by distance, which have been shown to have major technical flaws. A recently introduced model of extinction and recolonisation in two dimensions solves these technical problems, and provides a rigorous technical foundation for the study of populations evolving in a spatial continuum. The coalescent process for this model is simply stated, but direct simulation is very inefficient for large neighbourhood sizes. We present efficient and exact algorithms to simulate this coalescent process for arbitrary sample sizes and numbers of loci, and analyse these algorithms in detail.","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2168","ddc":["570"],"title":"Coalescent simulation in continuous space: Algorithms for large neighbourhood size","status":"public","intvolume":" 95","pubrep_id":"391","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2015-391-v1+1_1-s2.0-S0040580914000355-main.pdf","creator":"system","file_size":569005,"content_type":"application/pdf","file_id":"4839","relation":"main_file","checksum":"979d7a8034e9df198f068f0d251f31bd","date_created":"2018-12-12T10:10:49Z","date_updated":"2020-07-14T12:45:31Z"}]},{"type":"journal_article","publist_id":"4815","issue":"29","status":"public","title":"Diverse forms of selection in evolution and computer science","publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"NiBa"}],"intvolume":" 111","_id":"2169","year":"2014","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:56:07Z","date_updated":"2021-01-12T06:55:45Z","oa_version":"Submitted Version","volume":111,"author":[{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sebastian","last_name":"Novak","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian"},{"last_name":"Paixao","first_name":"Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago"}],"scopus_import":1,"month":"07","day":"22","quality_controlled":"1","page":"10398 - 10399","publication":"PNAS","oa":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4115508/"}],"citation":{"chicago":"Barton, Nicholas H, Sebastian Novak, and Tiago Paixao. “Diverse Forms of Selection in Evolution and Computer Science.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1410107111.","mla":"Barton, Nicholas H., et al. “Diverse Forms of Selection in Evolution and Computer Science.” PNAS, vol. 111, no. 29, National Academy of Sciences, 2014, pp. 10398–99, doi:10.1073/pnas.1410107111.","short":"N.H. Barton, S. Novak, T. Paixao, PNAS 111 (2014) 10398–10399.","ista":"Barton NH, Novak S, Paixao T. 2014. Diverse forms of selection in evolution and computer science. PNAS. 111(29), 10398–10399.","ieee":"N. H. Barton, S. Novak, and T. Paixao, “Diverse forms of selection in evolution and computer science,” PNAS, vol. 111, no. 29. National Academy of Sciences, pp. 10398–10399, 2014.","apa":"Barton, N. H., Novak, S., & Paixao, T. (2014). Diverse forms of selection in evolution and computer science. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1410107111","ama":"Barton NH, Novak S, Paixao T. Diverse forms of selection in evolution and computer science. PNAS. 2014;111(29):10398-10399. doi:10.1073/pnas.1410107111"},"language":[{"iso":"eng"}],"date_published":"2014-07-22T00:00:00Z","doi":"10.1073/pnas.1410107111"},{"type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"When polygenic traits are under stabilizing selection, many different combinations of alleles allow close adaptation to the optimum. If alleles have equal effects, all combinations that result in the same deviation from the optimum are equivalent. Furthermore, the genetic variance that is maintained by mutation-selection balance is 2μ/S per locus, where μ is the mutation rate and S the strength of stabilizing selection. In reality, alleles vary in their effects, making the fitness landscape asymmetric and complicating analysis of the equilibria. We show that that the resulting genetic variance depends on the fraction of alleles near fixation, which contribute by 2μ/S, and on the total mutational effects of alleles that are at intermediate frequency. The inpplayfi between stabilizing selection and mutation leads to a sharp transition: alleles with effects smaller than a threshold value of 2 remain polymorphic, whereas those with larger effects are fixed. The genetic load in equilibrium is less than for traits of equal effects, and the fitness equilibria are more similar. We find p the optimum is displaced, alleles with effects close to the threshold value sweep first, and their rate of increase is bounded by Long-term response leads in general to well-adapted traits, unlike the case of equal effects that often end up at a suboptimal fitness peak. However, the particular peaks to which the populations converge are extremely sensitive to the initial states and to the speed of the shift of the optimum trait value."}],"_id":"2174","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","intvolume":" 197","title":"Stability and response of polygenic traits to stabilizing selection and mutation","status":"public","oa_version":"Submitted Version","scopus_import":1,"day":"01","citation":{"ama":"De Vladar H, Barton NH. Stability and response of polygenic traits to stabilizing selection and mutation. Genetics. 2014;197(2):749-767. doi:10.1534/genetics.113.159111","ista":"De Vladar H, Barton NH. 2014. Stability and response of polygenic traits to stabilizing selection and mutation. Genetics. 197(2), 749–767.","ieee":"H. De Vladar and N. H. Barton, “Stability and response of polygenic traits to stabilizing selection and mutation,” Genetics, vol. 197, no. 2. Genetics Society of America, pp. 749–767, 2014.","apa":"De Vladar, H., & Barton, N. H. (2014). Stability and response of polygenic traits to stabilizing selection and mutation. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.113.159111","mla":"De Vladar, Harold, and Nicholas H. Barton. “Stability and Response of Polygenic Traits to Stabilizing Selection and Mutation.” Genetics, vol. 197, no. 2, Genetics Society of America, 2014, pp. 749–67, doi:10.1534/genetics.113.159111.","short":"H. De Vladar, N.H. Barton, Genetics 197 (2014) 749–767.","chicago":"De Vladar, Harold, and Nicholas H Barton. “Stability and Response of Polygenic Traits to Stabilizing Selection and Mutation.” Genetics. Genetics Society of America, 2014. https://doi.org/10.1534/genetics.113.159111."},"publication":"Genetics","page":"749 - 767","date_published":"2014-06-01T00:00:00Z","ec_funded":1,"publist_id":"4809","year":"2014","publisher":"Genetics Society of America","department":[{"_id":"NiBa"}],"publication_status":"published","author":[{"full_name":"De Vladar, Harold","first_name":"Harold","last_name":"De Vladar"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"volume":197,"date_updated":"2021-01-12T06:55:47Z","date_created":"2018-12-11T11:56:08Z","month":"06","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1404.1017"}],"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"quality_controlled":"1","doi":"10.1534/genetics.113.159111","language":[{"iso":"eng"}]},{"issue":"1","publist_id":"4695","abstract":[{"text":"The pattern of inheritance and mechanism of sex determination can have important evolutionary consequences. We studied probabilistic sex determination in the ciliate Tetrahymena thermophila, which was previously shown to cause evolution of skewed sex ratios. We find that the genetic background alters the sex determination patterns of mat alleles in heterozygotes and that allelic interaction can differentially influence the expression probability of the 7 sexes. We quantify the dominance relationships between several mat alleles and find that A-type alleles, which specify sex I, are indeed recessive to B-type alleles, which are unable to specify that sex. Our results provide additional support for the presence of modifier loci and raise implications for the dynamics of sex ratios in populations of T. thermophila.","lang":"eng"}],"type":"journal_article","oa_version":"None","volume":105,"date_created":"2018-12-11T11:56:35Z","date_updated":"2022-08-25T14:45:42Z","author":[{"full_name":"Phadke, Sujal","last_name":"Phadke","first_name":"Sujal"},{"full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","first_name":"Tiago","last_name":"Paixao"},{"first_name":"Tuan","last_name":"Pham","full_name":"Pham, Tuan"},{"full_name":"Pham, Stephanie","last_name":"Pham","first_name":"Stephanie"},{"full_name":"Zufall, Rebecca","first_name":"Rebecca","last_name":"Zufall"}],"intvolume":" 105","department":[{"_id":"NiBa"}],"publisher":"Oxford University Press","title":"Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila","status":"public","publication_status":"published","year":"2014","_id":"2252","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","publication_identifier":{"issn":["00221503"]},"month":"01","day":"01","scopus_import":"1","language":[{"iso":"eng"}],"date_published":"2014-01-01T00:00:00Z","doi":"10.1093/jhered/est063","page":"130 - 135","quality_controlled":"1","citation":{"ama":"Phadke S, Paixao T, Pham T, Pham S, Zufall R. Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila. Journal of Heredity. 2014;105(1):130-135. doi:10.1093/jhered/est063","ista":"Phadke S, Paixao T, Pham T, Pham S, Zufall R. 2014. Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila. Journal of Heredity. 105(1), 130–135.","ieee":"S. Phadke, T. Paixao, T. Pham, S. Pham, and R. Zufall, “Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila,” Journal of Heredity, vol. 105, no. 1. Oxford University Press, pp. 130–135, 2014.","apa":"Phadke, S., Paixao, T., Pham, T., Pham, S., & Zufall, R. (2014). Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila. Journal of Heredity. Oxford University Press. https://doi.org/10.1093/jhered/est063","mla":"Phadke, Sujal, et al. “Genetic Background Alters Dominance Relationships between Mat Alleles in the Ciliate Tetrahymena Thermophila.” Journal of Heredity, vol. 105, no. 1, Oxford University Press, 2014, pp. 130–35, doi:10.1093/jhered/est063.","short":"S. Phadke, T. Paixao, T. Pham, S. Pham, R. Zufall, Journal of Heredity 105 (2014) 130–135.","chicago":"Phadke, Sujal, Tiago Paixao, Tuan Pham, Stephanie Pham, and Rebecca Zufall. “Genetic Background Alters Dominance Relationships between Mat Alleles in the Ciliate Tetrahymena Thermophila.” Journal of Heredity. Oxford University Press, 2014. https://doi.org/10.1093/jhered/est063."},"publication":"Journal of Heredity"},{"abstract":[{"lang":"eng","text":"Transgenerational effects are broader than only parental relationships. Despite mounting evidence that multigenerational effects alter phenotypic and life-history traits, our understanding of how they combine to determine fitness is not well developed because of the added complexity necessary to study them. Here, we derive a quantitative genetic model of adaptation to an extraordinary new environment by an additive genetic component, phenotypic plasticity, maternal and grandmaternal effects. We show how, at equilibrium, negative maternal and negative grandmaternal effects maximize expected population mean fitness. We define negative transgenerational effects as those that have a negative effect on trait expression in the subsequent generation, that is, they slow, or potentially reverse, the expected evolutionary dynamic. When maternal effects are positive, negative grandmaternal effects are preferred. As expected under Mendelian inheritance, the grandmaternal effects have a lower impact on fitness than the maternal effects, but this dual inheritance model predicts a more complex relationship between maternal and grandmaternal effects to constrain phenotypic variance and so maximize expected population mean fitness in the offspring."}],"issue":"15","type":"journal_article","pubrep_id":"934","file":[{"file_id":"4886","relation":"main_file","date_updated":"2020-07-14T12:46:38Z","date_created":"2018-12-12T10:11:31Z","checksum":"e32abf75a248e7a11811fd7f60858769","file_name":"IST-2018-934-v1+1_Prizak_et_al-2014-Ecology_and_Evolution.pdf","access_level":"open_access","creator":"system","file_size":621582,"content_type":"application/pdf"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"537","title":"Fitness consequences of maternal and grandmaternal effects","ddc":["530","571"],"status":"public","intvolume":" 4","day":"19","has_accepted_license":"1","scopus_import":1,"date_published":"2014-07-19T00:00:00Z","publication":"Ecology and Evolution","citation":{"chicago":"Prizak, Roshan, Thomas Ezard, and Rebecca Hoyle. “Fitness Consequences of Maternal and Grandmaternal Effects.” Ecology and Evolution. Wiley-Blackwell, 2014. https://doi.org/10.1002/ece3.1150.","short":"R. Prizak, T. Ezard, R. Hoyle, Ecology and Evolution 4 (2014) 3139–3145.","mla":"Prizak, Roshan, et al. “Fitness Consequences of Maternal and Grandmaternal Effects.” Ecology and Evolution, vol. 4, no. 15, Wiley-Blackwell, 2014, pp. 3139–45, doi:10.1002/ece3.1150.","apa":"Prizak, R., Ezard, T., & Hoyle, R. (2014). Fitness consequences of maternal and grandmaternal effects. Ecology and Evolution. Wiley-Blackwell. https://doi.org/10.1002/ece3.1150","ieee":"R. Prizak, T. Ezard, and R. Hoyle, “Fitness consequences of maternal and grandmaternal effects,” Ecology and Evolution, vol. 4, no. 15. Wiley-Blackwell, pp. 3139–3145, 2014.","ista":"Prizak R, Ezard T, Hoyle R. 2014. Fitness consequences of maternal and grandmaternal effects. Ecology and Evolution. 4(15), 3139–3145.","ama":"Prizak R, Ezard T, Hoyle R. Fitness consequences of maternal and grandmaternal effects. Ecology and Evolution. 2014;4(15):3139-3145. doi:10.1002/ece3.1150"},"page":"3139 - 3145","file_date_updated":"2020-07-14T12:46:38Z","publist_id":"7280","author":[{"full_name":"Prizak, Roshan","last_name":"Prizak","first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ezard, Thomas","first_name":"Thomas","last_name":"Ezard"},{"full_name":"Hoyle, Rebecca","first_name":"Rebecca","last_name":"Hoyle"}],"date_created":"2018-12-11T11:47:02Z","date_updated":"2021-01-12T08:01:30Z","volume":4,"year":"2014","publication_status":"published","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"publisher":"Wiley-Blackwell","month":"07","doi":"10.1002/ece3.1150","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1},{"related_material":{"record":[{"status":"public","relation":"research_data","id":"9754"}]},"author":[{"last_name":"Hearn","first_name":"Jack","full_name":"Hearn, Jack"},{"full_name":"Stone, Graham","last_name":"Stone","first_name":"Graham"},{"full_name":"Bunnefeld, Lynsey","first_name":"Lynsey","last_name":"Bunnefeld"},{"full_name":"Nicholls, James","first_name":"James","last_name":"Nicholls"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"full_name":"Lohse, Konrad","first_name":"Konrad","last_name":"Lohse"}],"volume":23,"date_updated":"2023-02-23T14:07:09Z","date_created":"2018-12-11T11:56:07Z","year":"2014","acknowledgement":"This work was funded by NERC grants to G Stone, J Nicholls, K Lohse and N Barton (NE/J010499, NBAF375, NE/E014453/1 and NER/B/S2003/00856).","department":[{"_id":"NiBa"}],"publisher":"Wiley-Blackwell","publication_status":"published","publist_id":"4814","file_date_updated":"2020-07-14T12:45:31Z","doi":"10.1111/mec.12578","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","month":"01","pubrep_id":"559","file":[{"creator":"system","file_size":807444,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2016-559-v1+1_Hearn_et_al.pdf","checksum":"4de1ab255976a8ae77eb0e55ad62ecc9","date_updated":"2020-07-14T12:45:31Z","date_created":"2018-12-12T10:07:52Z","file_id":"4651","relation":"main_file"},{"checksum":"01a8073e071c088500425f910b0f1f71","date_created":"2018-12-12T10:07:53Z","date_updated":"2020-07-14T12:45:31Z","relation":"main_file","file_id":"4652","content_type":"application/pdf","file_size":1518088,"creator":"system","access_level":"open_access","file_name":"IST-2016-559-v1+2_Hearn_et_al_Suppl.pdf"}],"oa_version":"Submitted Version","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"2170","intvolume":" 23","status":"public","title":"Likelihood-based inference of population history from low-coverage de novo genome assemblies","ddc":["570"],"issue":"1","abstract":[{"text":" Short-read sequencing technologies have in principle made it feasible to draw detailed inferences about the recent history of any organism. In practice, however, this remains challenging due to the difficulty of genome assembly in most organisms and the lack of statistical methods powerful enough to discriminate between recent, nonequilibrium histories. We address both the assembly and inference challenges. We develop a bioinformatic pipeline for generating outgroup-rooted alignments of orthologous sequence blocks from de novo low-coverage short-read data for a small number of genomes, and show how such sequence blocks can be used to fit explicit models of population divergence and admixture in a likelihood framework. To illustrate our approach, we reconstruct the Pleistocene history of an oak-feeding insect (the oak gallwasp Biorhiza pallida), which, in common with many other taxa, was restricted during Pleistocene ice ages to a longitudinal series of southern refugia spanning the Western Palaearctic. Our analysis of sequence blocks sampled from a single genome from each of three major glacial refugia reveals support for an unexpected history dominated by recent admixture. Despite the fact that 80% of the genome is affected by admixture during the last glacial cycle, we are able to infer the deeper divergence history of these populations. These inferences are robust to variation in block length, mutation model and the sampling location of individual genomes within refugia. This combination of de novo assembly and numerical likelihood calculation provides a powerful framework for estimating recent population history that can be applied to any organism without the need for prior genetic resources.","lang":"eng"}],"type":"journal_article","date_published":"2014-01-01T00:00:00Z","citation":{"short":"J. Hearn, G. Stone, L. Bunnefeld, J. Nicholls, N.H. Barton, K. Lohse, Molecular Ecology 23 (2014) 198–211.","mla":"Hearn, Jack, et al. “Likelihood-Based Inference of Population History from Low-Coverage de Novo Genome Assemblies.” Molecular Ecology, vol. 23, no. 1, Wiley-Blackwell, 2014, pp. 198–211, doi:10.1111/mec.12578.","chicago":"Hearn, Jack, Graham Stone, Lynsey Bunnefeld, James Nicholls, Nicholas H Barton, and Konrad Lohse. “Likelihood-Based Inference of Population History from Low-Coverage de Novo Genome Assemblies.” Molecular Ecology. Wiley-Blackwell, 2014. https://doi.org/10.1111/mec.12578.","ama":"Hearn J, Stone G, Bunnefeld L, Nicholls J, Barton NH, Lohse K. Likelihood-based inference of population history from low-coverage de novo genome assemblies. Molecular Ecology. 2014;23(1):198-211. doi:10.1111/mec.12578","apa":"Hearn, J., Stone, G., Bunnefeld, L., Nicholls, J., Barton, N. H., & Lohse, K. (2014). Likelihood-based inference of population history from low-coverage de novo genome assemblies. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/mec.12578","ieee":"J. Hearn, G. Stone, L. Bunnefeld, J. Nicholls, N. H. Barton, and K. Lohse, “Likelihood-based inference of population history from low-coverage de novo genome assemblies,” Molecular Ecology, vol. 23, no. 1. Wiley-Blackwell, pp. 198–211, 2014.","ista":"Hearn J, Stone G, Bunnefeld L, Nicholls J, Barton NH, Lohse K. 2014. Likelihood-based inference of population history from low-coverage de novo genome assemblies. Molecular Ecology. 23(1), 198–211."},"publication":"Molecular Ecology","page":"198 - 211","has_accepted_license":"1","day":"01","scopus_import":1},{"oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:45:25Z","date_created":"2018-12-12T10:12:28Z","checksum":"9ab43db1b0fede7bfe560ed77e177b76","file_id":"4946","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":118813,"file_name":"IST-2016-462-v1+1_Novak-2014-Ecology_and_Evolution.pdf","access_level":"open_access"}],"pubrep_id":"462","intvolume":" 4","status":"public","title":"Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution","ddc":["570"],"_id":"2023","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","issue":"24","abstract":[{"lang":"eng","text":"Understanding the evolution of dispersal is essential for understanding and predicting the dynamics of natural populations. Two main factors are known to influence dispersal evolution: spatio-temporal variation in the environment and relatedness between individuals. However, the relation between these factors is still poorly understood, and they are usually treated separately. In this article, I present a theoretical framework that contains and connects effects of both environmental variation and relatedness, and reproduces and extends their known features. Spatial habitat variation selects for balanced dispersal strategies, whereby the population is kept at an ideal free distribution. Within this class of dispersal strategies, I explain how increased dispersal is promoted by perturbations to the dispersal type frequencies. An explicit formula shows the magnitude of the selective advantage of increased dispersal in terms of the spatial variability in the frequencies of the different dispersal strategies present. These variances are capable of capturing various sources of stochasticity and hence establish a common scale for their effects on the evolution of dispersal. The results furthermore indicate an alternative approach to identifying effects of relatedness on dispersal evolution."}],"type":"journal_article","date_published":"2014-11-27T00:00:00Z","page":"4589 - 4597","citation":{"chicago":"Novak, Sebastian. “Habitat Heterogeneities versus Spatial Type Frequency Variances as Driving Forces of Dispersal Evolution.” Ecology and Evolution. Wiley-Blackwell, 2014. https://doi.org/10.1002/ece3.1289.","mla":"Novak, Sebastian. “Habitat Heterogeneities versus Spatial Type Frequency Variances as Driving Forces of Dispersal Evolution.” Ecology and Evolution, vol. 4, no. 24, Wiley-Blackwell, 2014, pp. 4589–97, doi:10.1002/ece3.1289.","short":"S. Novak, Ecology and Evolution 4 (2014) 4589–4597.","ista":"Novak S. 2014. Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution. Ecology and Evolution. 4(24), 4589–4597.","apa":"Novak, S. (2014). Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution. Ecology and Evolution. Wiley-Blackwell. https://doi.org/10.1002/ece3.1289","ieee":"S. Novak, “Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution,” Ecology and Evolution, vol. 4, no. 24. Wiley-Blackwell, pp. 4589–4597, 2014.","ama":"Novak S. Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution. Ecology and Evolution. 2014;4(24):4589-4597. doi:10.1002/ece3.1289"},"publication":"Ecology and Evolution","has_accepted_license":"1","day":"27","scopus_import":1,"volume":4,"date_created":"2018-12-11T11:55:16Z","date_updated":"2023-09-07T11:55:53Z","related_material":{"record":[{"id":"1125","relation":"dissertation_contains","status":"public"}]},"author":[{"last_name":"Novak","first_name":"Sebastian","orcid":"0000-0002-2519-824X","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian"}],"publisher":"Wiley-Blackwell","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2014","publist_id":"5049","ec_funded":1,"file_date_updated":"2020-07-14T12:45:25Z","language":[{"iso":"eng"}],"doi":"10.1002/ece3.1289","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"11"},{"oa_version":"None","date_created":"2022-03-21T07:46:22Z","date_updated":"2022-06-20T09:18:06Z","edition":"2","author":[{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"NiBa"}],"publisher":"Elsevier","publication_status":"published","title":"Differentiation","status":"public","year":"2013","_id":"10899","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"book_chapter","language":[{"iso":"eng"}],"doi":"10.1016/b978-0-12-384719-5.00031-9","date_published":"2013-01-01T00:00:00Z","page":"508-515","quality_controlled":"1","citation":{"ista":"Barton NH. 2013.Differentiation. In: Encyclopedia of Biodiversity. , 508–515.","apa":"Barton, N. H. (2013). Differentiation. In Encyclopedia of Biodiversity (2nd ed., pp. 508–515). Elsevier. https://doi.org/10.1016/b978-0-12-384719-5.00031-9","ieee":"N. H. Barton, “Differentiation,” in Encyclopedia of Biodiversity, 2nd ed., Elsevier, 2013, pp. 508–515.","ama":"Barton NH. Differentiation. In: Encyclopedia of Biodiversity. 2nd ed. Elsevier; 2013:508-515. doi:10.1016/b978-0-12-384719-5.00031-9","chicago":"Barton, Nicholas H. “Differentiation.” In Encyclopedia of Biodiversity, 2nd ed., 508–15. Elsevier, 2013. https://doi.org/10.1016/b978-0-12-384719-5.00031-9.","mla":"Barton, Nicholas H. “Differentiation.” Encyclopedia of Biodiversity, 2nd ed., Elsevier, 2013, pp. 508–15, doi:10.1016/b978-0-12-384719-5.00031-9.","short":"N.H. Barton, in:, Encyclopedia of Biodiversity, 2nd ed., Elsevier, 2013, pp. 508–515."},"publication":"Encyclopedia of Biodiversity","publication_identifier":{"isbn":["978-0-12-384720-1"]},"article_processing_charge":"No","month":"01","day":"01","keyword":["Adaptive landscape","Cline","Coalescent process","Gene flow","Hybrid zone","Local adaptation","Natural selection","Neutral theory","Population structure","Speciation"],"scopus_import":"1"},{"publist_id":"4644","file_date_updated":"2020-07-14T12:45:37Z","author":[{"full_name":"Pickup, Melinda","first_name":"Melinda","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541"},{"first_name":"Spencer","last_name":"Barrett","full_name":"Barrett, Spencer"}],"volume":3,"date_created":"2018-12-11T11:56:47Z","date_updated":"2021-01-12T06:56:32Z","year":"2013","department":[{"_id":"NiBa"}],"publisher":"Wiley-Blackwell","publication_status":"published","month":"03","doi":"10.1002/ece3.465","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","issue":"3","abstract":[{"text":"Negative frequency-dependent selection should result in equal sex ratios in large populations of dioecious flowering plants, but deviations from equality are commonly reported. A variety of ecological and genetic factors can explain biased sex ratios, although the mechanisms involved are not well understood. Most dioecious species are long-lived and/or clonal complicating efforts to identify stages during the life cycle when biases develop. We investigated the demographic correlates of sex-ratio variation in two chromosome races of Rumex hastatulus, an annual, wind-pollinated colonizer of open habitats from the southern USA. We examined sex ratios in 46 populations and evaluated the hypothesis that the proximity of males in the local mating environment, through its influence on gametophytic selection, is the primary cause of female-biased sex ratios. Female-biased sex ratios characterized most populations of R. hastatulus (mean sex ratio = 0.62), with significant female bias in 89% of populations. Large, high-density populations had the highest proportion of females, whereas smaller, low-density populations had sex ratios closer to equality. Progeny sex ratios were more female biased when males were in closer proximity to females, a result consistent with the gametophytic selection hypothesis. Our results suggest that interactions between demographic and genetic factors are probably the main cause of female-biased sex ratios in R. hastatulus. The annual life cycle of this species may limit the scope for selection against males and may account for the weaker degree of bias in comparison with perennial Rumex species.","lang":"eng"}],"type":"journal_article","pubrep_id":"416","file":[{"creator":"system","file_size":626949,"content_type":"application/pdf","file_name":"IST-2016-416-v1+1_Pickup_et_al-2013-Ecology_and_Evolution.pdf","access_level":"open_access","date_created":"2018-12-12T10:17:35Z","date_updated":"2020-07-14T12:45:37Z","checksum":"b5531bab4c0dec396bf5c8497fe178bf","file_id":"5290","relation":"main_file"}],"oa_version":"Published Version","_id":"2287","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 3","status":"public","title":"The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant","ddc":["576"],"has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2013-03-01T00:00:00Z","citation":{"chicago":"Pickup, Melinda, and Spencer Barrett. “The Influence of Demography and Local Mating Environment on Sex Ratios in a Wind-Pollinated Dioecious Plant.” Ecology and Evolution. Wiley-Blackwell, 2013. https://doi.org/10.1002/ece3.465.","mla":"Pickup, Melinda, and Spencer Barrett. “The Influence of Demography and Local Mating Environment on Sex Ratios in a Wind-Pollinated Dioecious Plant.” Ecology and Evolution, vol. 3, no. 3, Wiley-Blackwell, 2013, pp. 629–39, doi:10.1002/ece3.465.","short":"M. Pickup, S. Barrett, Ecology and Evolution 3 (2013) 629–639.","ista":"Pickup M, Barrett S. 2013. The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant. Ecology and Evolution. 3(3), 629–639.","ieee":"M. Pickup and S. Barrett, “The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant,” Ecology and Evolution, vol. 3, no. 3. Wiley-Blackwell, pp. 629–639, 2013.","apa":"Pickup, M., & Barrett, S. (2013). The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant. Ecology and Evolution. Wiley-Blackwell. https://doi.org/10.1002/ece3.465","ama":"Pickup M, Barrett S. The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant. Ecology and Evolution. 2013;3(3):629-639. doi:10.1002/ece3.465"},"publication":"Ecology and Evolution","page":"629 - 639"},{"issue":"8","abstract":[{"text":"When a mutation with selective advantage s spreads through a panmictic population, it may cause two lineages at a linked locus to coalesce; the probability of coalescence is exp(−2rT), where T∼log(2Ns)/s is the time to fixation, N is the number of haploid individuals, and r is the recombination rate. Population structure delays fixation, and so weakens the effect of a selective sweep. However, favourable alleles spread through a spatially continuous population behind a narrow wavefront; ancestral lineages are confined at the tip of this front, and so coalesce rapidly. In extremely dense populations, coalescence is dominated by rare fluctuations ahead of the front. However, we show that for moderate densities, a simple quasi-deterministic approximation applies: the rate of coalescence within the front is λ∼2g(η)/(ρℓ), where ρ is the population density and is the characteristic scale of the wavefront; g(η) depends only on the strength of random drift, . The net effect of a sweep on coalescence also depends crucially on whether two lineages are ever both within the wavefront at the same time: even in the extreme case when coalescence within the front is instantaneous, the net rate of coalescence may be lower than in a single panmictic population. Sweeps can also have a substantial impact on the rate of gene flow. A single lineage will jump to a new location when it is hit by a sweep, with mean square displacement ; this can be substantial if the species’ range, L, is large, even if the species-wide rate of sweeps per map length, Λ/R, is small. This effect is half as strong in two dimensions. In contrast, the rate of coalescence between lineages, at random locations in space and on the genetic map, is proportional to (c/L)(Λ/R), where c is the wavespeed: thus, on average, one-dimensional structure is likely to reduce coalescence due to sweeps, relative to panmixis. In two dimensions, genes must move along the front before they can coalesce; this process is rapid, being dominated by rare fluctuations. This leads to a dramatically higher rate of coalescence within the wavefront than if lineages simply diffused along the front. Nevertheless, the net rate of coalescence due to a sweep through a two-dimensional population is likely to be lower than it would be with panmixis.","lang":"eng"}],"type":"journal_article","pubrep_id":"118","file":[{"content_type":"application/pdf","file_size":1706282,"creator":"system","access_level":"open_access","file_name":"IST-2013-118-v1+1_bartonetalRevision.pdf","checksum":"4274ec1f433b838a7d5b941cc9684ca7","date_created":"2018-12-12T10:18:54Z","date_updated":"2020-07-14T12:45:41Z","relation":"main_file","file_id":"5376"}],"oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2473","intvolume":" 87","title":"Genetic hitch-hiking in spatially extended populations","status":"public","ddc":["570"],"has_accepted_license":"1","day":"03","scopus_import":1,"date_published":"2013-01-03T00:00:00Z","citation":{"ama":"Barton NH, Etheridge A, Kelleher J, Véber A. Genetic hitch-hiking in spatially extended populations. Theoretical Population Biology. 2013;87(8):75-89. doi:10.1016/j.tpb.2012.12.001","ista":"Barton NH, Etheridge A, Kelleher J, Véber A. 2013. Genetic hitch-hiking in spatially extended populations. Theoretical Population Biology. 87(8), 75–89.","ieee":"N. H. Barton, A. Etheridge, J. Kelleher, and A. Véber, “Genetic hitch-hiking in spatially extended populations,” Theoretical Population Biology, vol. 87, no. 8. Elsevier, pp. 75–89, 2013.","apa":"Barton, N. H., Etheridge, A., Kelleher, J., & Véber, A. (2013). Genetic hitch-hiking in spatially extended populations. Theoretical Population Biology. Elsevier. https://doi.org/10.1016/j.tpb.2012.12.001","mla":"Barton, Nicholas H., et al. “Genetic Hitch-Hiking in Spatially Extended Populations.” Theoretical Population Biology, vol. 87, no. 8, Elsevier, 2013, pp. 75–89, doi:10.1016/j.tpb.2012.12.001.","short":"N.H. Barton, A. Etheridge, J. Kelleher, A. Véber, Theoretical Population Biology 87 (2013) 75–89.","chicago":"Barton, Nicholas H, Alison Etheridge, Jerome Kelleher, and Amandine Véber. “Genetic Hitch-Hiking in Spatially Extended Populations.” Theoretical Population Biology. Elsevier, 2013. https://doi.org/10.1016/j.tpb.2012.12.001."},"publication":"Theoretical Population Biology","page":"75 - 89","ec_funded":1,"publist_id":"4428","file_date_updated":"2020-07-14T12:45:41Z","author":[{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"last_name":"Etheridge","first_name":"Alison","full_name":"Etheridge, Alison"},{"last_name":"Kelleher","first_name":"Jerome","full_name":"Kelleher, Jerome"},{"full_name":"Véber, Amandine","first_name":"Amandine","last_name":"Véber"}],"volume":87,"date_created":"2018-12-11T11:57:52Z","date_updated":"2021-01-12T06:57:42Z","year":"2013","publisher":"Elsevier","department":[{"_id":"NiBa"}],"publication_status":"published","month":"01","doi":"10.1016/j.tpb.2012.12.001","language":[{"iso":"eng"}],"oa":1,"project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"quality_controlled":"1"},{"file_date_updated":"2020-07-14T12:45:45Z","ec_funded":1,"publist_id":"4174","date_updated":"2021-01-12T06:59:15Z","date_created":"2018-12-11T11:59:14Z","author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","first_name":"Tiago"}],"publication_status":"published","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publisher":"ACM","year":"2013","month":"07","language":[{"iso":"eng"}],"conference":{"location":"Amsterdam, Netherlands","start_date":"2013-07-06","end_date":"2013-07-10","name":"GECCO: Genetic and evolutionary computation conference"},"doi":"10.1145/2463372.2463568","quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"oa":1,"abstract":[{"text":"Even though both population and quantitative genetics, and evolutionary computation, deal with the same questions, they have developed largely independently of each other. I review key results from each field, emphasising those that apply independently of the (usually unknown) relation between genotype and phenotype. The infinitesimal model provides a simple framework for predicting the response of complex traits to selection, which in biology has proved remarkably successful. This allows one to choose the schedule of population sizes and selection intensities that will maximise the response to selection, given that the total number of individuals realised, C = ∑t Nt, is constrained. This argument shows that for an additive trait (i.e., determined by the sum of effects of the genes), the optimum population size and the maximum possible response (i.e., the total change in trait mean) are both proportional to √C.","lang":"eng"}],"type":"conference","file":[{"content_type":"application/pdf","file_size":475844,"creator":"system","access_level":"open_access","file_name":"IST-2016-564-v1+1_NickGECCO_2013_1_-1.pdf","checksum":"9d9be9090ce5c20766e0eb076ace5b98","date_updated":"2020-07-14T12:45:45Z","date_created":"2018-12-12T10:15:38Z","relation":"main_file","file_id":"5159"}],"oa_version":"Submitted Version","pubrep_id":"564","title":"Can quantitative and population genetics help us understand evolutionary computation?","status":"public","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2718","day":"01","has_accepted_license":"1","scopus_import":1,"date_published":"2013-07-01T00:00:00Z","page":"1573 - 1580","publication":"Proceedings of the 15th annual conference on Genetic and evolutionary computation","citation":{"apa":"Barton, N. H., & Paixao, T. (2013). Can quantitative and population genetics help us understand evolutionary computation? In Proceedings of the 15th annual conference on Genetic and evolutionary computation (pp. 1573–1580). Amsterdam, Netherlands: ACM. https://doi.org/10.1145/2463372.2463568","ieee":"N. H. Barton and T. Paixao, “Can quantitative and population genetics help us understand evolutionary computation?,” in Proceedings of the 15th annual conference on Genetic and evolutionary computation, Amsterdam, Netherlands, 2013, pp. 1573–1580.","ista":"Barton NH, Paixao T. 2013. Can quantitative and population genetics help us understand evolutionary computation? Proceedings of the 15th annual conference on Genetic and evolutionary computation. GECCO: Genetic and evolutionary computation conference, 1573–1580.","ama":"Barton NH, Paixao T. Can quantitative and population genetics help us understand evolutionary computation? In: Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation. ACM; 2013:1573-1580. doi:10.1145/2463372.2463568","chicago":"Barton, Nicholas H, and Tiago Paixao. “Can Quantitative and Population Genetics Help Us Understand Evolutionary Computation?” In Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, 1573–80. ACM, 2013. https://doi.org/10.1145/2463372.2463568.","short":"N.H. Barton, T. Paixao, in:, Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 1573–1580.","mla":"Barton, Nicholas H., and Tiago Paixao. “Can Quantitative and Population Genetics Help Us Understand Evolutionary Computation?” Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 1573–80, doi:10.1145/2463372.2463568."}},{"month":"10","doi":"10.1534/genetics.113.153536","language":[{"iso":"eng"}],"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3781978/","open_access":"1"}],"external_id":{"pmid":["23934880"]},"oa":1,"quality_controlled":"1","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"ec_funded":1,"publist_id":"4172","author":[{"last_name":"Long","first_name":"Hongan","full_name":"Long, Hongan"},{"full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","first_name":"Tiago"},{"full_name":"Azevedo, Ricardo","last_name":"Azevedo","first_name":"Ricardo"},{"last_name":"Zufall","first_name":"Rebecca","full_name":"Zufall, Rebecca"}],"date_created":"2018-12-11T11:59:15Z","date_updated":"2021-01-12T06:59:16Z","volume":195,"year":"2013","pmid":1,"publication_status":"published","publisher":"Genetics Society of America","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"day":"01","article_processing_charge":"No","scopus_import":1,"date_published":"2013-10-01T00:00:00Z","publication":"Genetics","citation":{"ieee":"H. Long, T. Paixao, R. Azevedo, and R. Zufall, “Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila,” Genetics, vol. 195, no. 2. Genetics Society of America, pp. 527–540, 2013.","apa":"Long, H., Paixao, T., Azevedo, R., & Zufall, R. (2013). Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.113.153536","ista":"Long H, Paixao T, Azevedo R, Zufall R. 2013. Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics. 195(2), 527–540.","ama":"Long H, Paixao T, Azevedo R, Zufall R. Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics. 2013;195(2):527-540. doi:10.1534/genetics.113.153536","chicago":"Long, Hongan, Tiago Paixao, Ricardo Azevedo, and Rebecca Zufall. “Accumulation of Spontaneous Mutations in the Ciliate Tetrahymena Thermophila.” Genetics. Genetics Society of America, 2013. https://doi.org/10.1534/genetics.113.153536.","short":"H. Long, T. Paixao, R. Azevedo, R. Zufall, Genetics 195 (2013) 527–540.","mla":"Long, Hongan, et al. “Accumulation of Spontaneous Mutations in the Ciliate Tetrahymena Thermophila.” Genetics, vol. 195, no. 2, Genetics Society of America, 2013, pp. 527–40, doi:10.1534/genetics.113.153536."},"page":"527-540","abstract":[{"lang":"eng","text":"Knowledge of the rate and fitness effects of mutations is essential for understanding the process of evolution. Mutations are inherently difficult to study because they are rare and are frequently eliminated by natural selection. In the ciliate Tetrahymena thermophila, mutations can accumulate in the germline genome without being exposed to selection. We have conducted a mutation accumulation (MA) experiment in this species. Assuming that all mutations are deleterious and have the same effect, we estimate that the deleterious mutation rate per haploid germline genome per generation is U = 0.0047 (95% credible interval: 0.0015, 0.0125), and that germline mutations decrease fitness by s = 11% when expressed in a homozygous state (95% CI: 4.4%, 27%). We also estimate that deleterious mutations are partially recessive on average (h = 0.26; 95% CI: –0.022, 0.62) and that the rate of lethal mutations is <10% of the deleterious mutation rate. Comparisons between the observed evolutionary responses in the germline and somatic genomes and the results from individual-based simulations of MA suggest that the two genomes have similar mutational parameters. These are the first estimates of the deleterious mutation rate and fitness effects from the eukaryotic supergroup Chromalveolata and are within the range of those of other eukaryotes."}],"issue":"2","type":"journal_article","oa_version":"Submitted Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2720","title":"Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila","status":"public","intvolume":" 195"},{"ec_funded":1,"publist_id":"4173","abstract":[{"text":"Prediction of the evolutionary process is a long standing problem both in the theory of evolutionary biology and evolutionary computation (EC). It has long been realized that heritable variation is crucial to both the response to selection and the success of genetic algorithms. However, not all variation contributes in the same way to the response. Quantitative genetics has developed a large body of work trying to estimate and understand how different components of the variance in fitness in the population contribute to the response to selection. We illustrate how to apply some concepts of quantitative genetics to the analysis of genetic algorithms. In particular, we derive estimates for the short term prediction of the response to selection and we use variance decomposition to gain insight on local aspects of the landscape. Finally, we propose a new population based genetic algorithm that uses these methods to improve its operation.","lang":"eng"}],"type":"conference","author":[{"last_name":"Paixao","first_name":"Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"oa_version":"None","date_created":"2018-12-11T11:59:15Z","date_updated":"2021-01-12T06:59:15Z","_id":"2719","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2013","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publisher":"ACM","title":"A variance decomposition approach to the analysis of genetic algorithms","status":"public","publication_status":"published","day":"01","month":"07","scopus_import":1,"doi":"10.1145/2463372.2463470","date_published":"2013-07-01T00:00:00Z","conference":{"start_date":"2013-07-06","location":"Amsterdam, Netherlands","end_date":"2013-07-10","name":"GECCO: Genetic and evolutionary computation conference"},"language":[{"iso":"eng"}],"citation":{"short":"T. Paixao, N.H. Barton, in:, Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 845–852.","mla":"Paixao, Tiago, and Nicholas H. Barton. “A Variance Decomposition Approach to the Analysis of Genetic Algorithms.” Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 845–52, doi:10.1145/2463372.2463470.","chicago":"Paixao, Tiago, and Nicholas H Barton. “A Variance Decomposition Approach to the Analysis of Genetic Algorithms.” In Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, 845–52. ACM, 2013. https://doi.org/10.1145/2463372.2463470.","ama":"Paixao T, Barton NH. A variance decomposition approach to the analysis of genetic algorithms. In: Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation. ACM; 2013:845-852. doi:10.1145/2463372.2463470","apa":"Paixao, T., & Barton, N. H. (2013). A variance decomposition approach to the analysis of genetic algorithms. In Proceedings of the 15th annual conference on Genetic and evolutionary computation (pp. 845–852). Amsterdam, Netherlands: ACM. https://doi.org/10.1145/2463372.2463470","ieee":"T. Paixao and N. H. Barton, “A variance decomposition approach to the analysis of genetic algorithms,” in Proceedings of the 15th annual conference on Genetic and evolutionary computation, Amsterdam, Netherlands, 2013, pp. 845–852.","ista":"Paixao T, Barton NH. 2013. A variance decomposition approach to the analysis of genetic algorithms. Proceedings of the 15th annual conference on Genetic and evolutionary computation. GECCO: Genetic and evolutionary computation conference, 845–852."},"publication":"Proceedings of the 15th annual conference on Genetic and evolutionary computation","page":"845 - 852","project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"quality_controlled":"1"},{"month":"10","language":[{"iso":"eng"}],"doi":"10.1016/j.jtbi.2013.05.029","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF","name":"Game Theory"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"ec_funded":1,"publist_id":"3984","file_date_updated":"2020-07-14T12:45:49Z","volume":334,"date_updated":"2021-01-12T06:59:55Z","date_created":"2018-12-11T11:59:45Z","author":[{"last_name":"Novak","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"department":[{"_id":"NiBa"},{"_id":"KrCh"}],"publisher":"Elsevier","publication_status":"published","year":"2013","has_accepted_license":"1","day":"07","scopus_import":1,"date_published":"2013-10-07T00:00:00Z","page":"26 - 34","citation":{"mla":"Novak, Sebastian, et al. “Density Games.” Journal of Theoretical Biology, vol. 334, Elsevier, 2013, pp. 26–34, doi:10.1016/j.jtbi.2013.05.029.","short":"S. Novak, K. Chatterjee, M. Nowak, Journal of Theoretical Biology 334 (2013) 26–34.","chicago":"Novak, Sebastian, Krishnendu Chatterjee, and Martin Nowak. “Density Games.” Journal of Theoretical Biology. Elsevier, 2013. https://doi.org/10.1016/j.jtbi.2013.05.029.","ama":"Novak S, Chatterjee K, Nowak M. Density games. Journal of Theoretical Biology. 2013;334:26-34. doi:10.1016/j.jtbi.2013.05.029","ista":"Novak S, Chatterjee K, Nowak M. 2013. Density games. Journal of Theoretical Biology. 334, 26–34.","ieee":"S. Novak, K. Chatterjee, and M. Nowak, “Density games,” Journal of Theoretical Biology, vol. 334. Elsevier, pp. 26–34, 2013.","apa":"Novak, S., Chatterjee, K., & Nowak, M. (2013). Density games. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2013.05.029"},"publication":"Journal of Theoretical Biology","abstract":[{"lang":"eng","text":"The basic idea of evolutionary game theory is that payoff determines reproductive rate. Successful individuals have a higher payoff and produce more offspring. But in evolutionary and ecological situations there is not only reproductive rate but also carrying capacity. Individuals may differ in their exposure to density limiting effects. Here we explore an alternative approach to evolutionary game theory by assuming that the payoff from the game determines the carrying capacity of individual phenotypes. Successful strategies are less affected by density limitation (crowding) and reach higher equilibrium abundance. We demonstrate similarities and differences between our framework and the standard replicator equation. Our equation is defined on the positive orthant, instead of the simplex, but has the same equilibrium points as the replicator equation. Linear stability analysis produces the classical conditions for asymptotic stability of pure strategies, but the stability properties of internal equilibria can differ in the two frameworks. For example, in a two-strategy game with an internal equilibrium that is always stable under the replicator equation, the corresponding equilibrium can be unstable in the new framework resulting in a limit cycle."}],"type":"journal_article","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2016-400-v1+1_1-s2.0-S0022519313002609-main.pdf","file_size":834604,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5110","checksum":"3c29059ab03a4b8f97a07646b817ddbb","date_updated":"2020-07-14T12:45:49Z","date_created":"2018-12-12T10:14:54Z"}],"pubrep_id":"400","intvolume":" 334","ddc":["000"],"status":"public","title":"Density games","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2817"},{"year":"2013","_id":"2823","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Post-fire recovery of revegetated woodland communities in south-eastern Australia","publication_status":"published","intvolume":" 38","publisher":"Wiley-Blackwell","department":[{"_id":"NiBa"}],"author":[{"full_name":"Pickup, Melinda","first_name":"Melinda","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541"},{"full_name":"Wilson, Susie","first_name":"Susie","last_name":"Wilson"},{"full_name":"Freudenberger, David","first_name":"David","last_name":"Freudenberger"},{"first_name":"Nick","last_name":"Nicholls","full_name":"Nicholls, Nick"},{"last_name":"Gould","first_name":"Lori","full_name":"Gould, Lori"},{"first_name":"Sarah","last_name":"Hnatiuk","full_name":"Hnatiuk, Sarah"},{"full_name":"Delandre, Jeni","first_name":"Jeni","last_name":"Delandre"}],"date_created":"2018-12-11T11:59:47Z","date_updated":"2021-01-12T06:59:58Z","volume":38,"oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","text":"The primary goal of restoration is to create self-sustaining ecological communities that are resilient to periodic disturbance. Currently, little is known about how restored communities respond to disturbance events such as fire and how this response compares to remnant vegetation. Following the 2003 fires in south-eastern Australia we examined the post-fire response of revegetation plantings and compared this to remnant vegetation. Ten burnt and 10 unburnt (control) sites were assessed for each of three types of vegetation (direct seeding revegetation, revegetation using nursery seedlings (tubestock) and remnant woodland). Sixty sampling sites were surveyed 6months after fire to quantify the initial survival of mid- and overstorey plant species in each type of vegetation. Three and 5years after fire all sites were resurveyed to assess vegetation structure, species diversity and vigour, as well as indicators of soil function. Overall, revegetation showed high (>60%) post-fire survival, but this varied among species depending on regeneration strategy (obligate seeder or resprouter). The native ground cover, mid- and overstorey in both types of plantings showed rapid recovery of vegetation structure and cover within 3years of fire. This recovery was similar to the burnt remnant woodlands. Non-native (exotic) ground cover initially increased after fire, but was no different in burnt and unburnt sites 5years after fire. Fire had no effect on species richness, but burnt direct seeding sites had reduced species diversity (Simpson's Diversity Index) while diversity was higher in burnt remnant woodlands. Indices of soil function in all types of vegetation had recovered to levels found in unburnt sites 5years after fire. These results indicate that even young revegetation (stands <10years old) showed substantial recovery from disturbance by fire. This suggests that revegetation can provide an important basis for restoring woodland communities in the fire-prone Australian environment."}],"issue":"3","publist_id":"3978","publication":"Austral Ecology","citation":{"chicago":"Pickup, Melinda, Susie Wilson, David Freudenberger, Nick Nicholls, Lori Gould, Sarah Hnatiuk, and Jeni Delandre. “Post-Fire Recovery of Revegetated Woodland Communities in South-Eastern Australia.” Austral Ecology. Wiley-Blackwell, 2013. https://doi.org/10.1111/j.1442-9993.2012.02404.x.","mla":"Pickup, Melinda, et al. “Post-Fire Recovery of Revegetated Woodland Communities in South-Eastern Australia.” Austral Ecology, vol. 38, no. 3, Wiley-Blackwell, 2013, pp. 300–12, doi:10.1111/j.1442-9993.2012.02404.x.","short":"M. Pickup, S. Wilson, D. Freudenberger, N. Nicholls, L. Gould, S. Hnatiuk, J. Delandre, Austral Ecology 38 (2013) 300–312.","ista":"Pickup M, Wilson S, Freudenberger D, Nicholls N, Gould L, Hnatiuk S, Delandre J. 2013. Post-fire recovery of revegetated woodland communities in south-eastern Australia. Austral Ecology. 38(3), 300–312.","ieee":"M. Pickup et al., “Post-fire recovery of revegetated woodland communities in south-eastern Australia,” Austral Ecology, vol. 38, no. 3. Wiley-Blackwell, pp. 300–312, 2013.","apa":"Pickup, M., Wilson, S., Freudenberger, D., Nicholls, N., Gould, L., Hnatiuk, S., & Delandre, J. (2013). Post-fire recovery of revegetated woodland communities in south-eastern Australia. Austral Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1442-9993.2012.02404.x","ama":"Pickup M, Wilson S, Freudenberger D, et al. Post-fire recovery of revegetated woodland communities in south-eastern Australia. Austral Ecology. 2013;38(3):300-312. doi:10.1111/j.1442-9993.2012.02404.x"},"quality_controlled":"1","page":"300 - 312","date_published":"2013-05-01T00:00:00Z","doi":"10.1111/j.1442-9993.2012.02404.x","language":[{"iso":"eng"}],"scopus_import":1,"month":"05","day":"01"},{"type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"We outline two approaches to inference of neighbourhood size, N, and dispersal rate, σ2, based on either allele frequencies or on the lengths of sequence blocks that are shared between genomes. Over intermediate timescales (10-100 generations, say), populations that live in two dimensions approach a quasi-equilibrium that is independent of both their local structure and their deeper history. Over such scales, the standardised covariance of allele frequencies (i.e. pairwise FS T) falls with the logarithm of distance, and depends only on neighbourhood size, N, and a 'local scale', κ; the rate of gene flow, σ2, cannot be inferred. We show how spatial correlations can be accounted for, assuming a Gaussian distribution of allele frequencies, giving maximum likelihood estimates of N and κ. Alternatively, inferences can be based on the distribution of the lengths of sequence that are identical between blocks of genomes: long blocks (>0.1 cM, say) tell us about intermediate timescales, over which we assume a quasi-equilibrium. For large neighbourhood size, the distribution of long blocks is given directly by the classical Wright-Malécot formula; this relationship can be used to infer both N and σ2. With small neighbourhood size, there is an appreciable chance that recombinant lineages will coalesce back before escaping into the distant past. For this case, we show that if genomes are sampled from some distance apart, then the distribution of lengths of blocks that are identical in state is geometric, with a mean that depends on N and σ2."}],"_id":"2842","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 87","status":"public","title":"Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks","ddc":["570"],"pubrep_id":"558","oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"5288","checksum":"9bf9d9a6fd03dd9df50906891f393bf8","date_created":"2018-12-12T10:17:33Z","date_updated":"2020-07-14T12:45:50Z","access_level":"open_access","file_name":"IST-2016-558-v1+1_inference_revised3101NB.pdf","file_size":1554712,"content_type":"application/pdf","creator":"system"},{"checksum":"2bceddb76edacd0cd5fad73051e2a928","date_created":"2018-12-12T10:17:34Z","date_updated":"2020-07-14T12:45:50Z","file_id":"5289","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":822964,"access_level":"open_access","file_name":"IST-2016-558-v1+2_inference_revised3101NBApp.pdf"}],"scopus_import":1,"has_accepted_license":"1","day":"01","citation":{"ista":"Barton NH, Etheridge A, Kelleher J, Véber A. 2013. Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks. Theoretical Population Biology. 87(1), 105–119.","apa":"Barton, N. H., Etheridge, A., Kelleher, J., & Véber, A. (2013). Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks. Theoretical Population Biology. Elsevier. https://doi.org/10.1016/j.tpb.2013.03.001","ieee":"N. H. Barton, A. Etheridge, J. Kelleher, and A. Véber, “Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks,” Theoretical Population Biology, vol. 87, no. 1. Elsevier, pp. 105–119, 2013.","ama":"Barton NH, Etheridge A, Kelleher J, Véber A. Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks. Theoretical Population Biology. 2013;87(1):105-119. doi:10.1016/j.tpb.2013.03.001","chicago":"Barton, Nicholas H, Alison Etheridge, Jerome Kelleher, and Amandine Véber. “Inference in Two Dimensions: Allele Frequencies versus Lengths of Shared Sequence Blocks.” Theoretical Population Biology. Elsevier, 2013. https://doi.org/10.1016/j.tpb.2013.03.001.","mla":"Barton, Nicholas H., et al. “Inference in Two Dimensions: Allele Frequencies versus Lengths of Shared Sequence Blocks.” Theoretical Population Biology, vol. 87, no. 1, Elsevier, 2013, pp. 105–19, doi:10.1016/j.tpb.2013.03.001.","short":"N.H. Barton, A. Etheridge, J. Kelleher, A. Véber, Theoretical Population Biology 87 (2013) 105–119."},"publication":"Theoretical Population Biology","page":"105 - 119","date_published":"2013-08-01T00:00:00Z","ec_funded":1,"publist_id":"3953","file_date_updated":"2020-07-14T12:45:50Z","year":"2013","department":[{"_id":"NiBa"}],"publisher":"Elsevier","publication_status":"published","author":[{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"first_name":"Alison","last_name":"Etheridge","full_name":"Etheridge, Alison"},{"full_name":"Kelleher, Jerome","first_name":"Jerome","last_name":"Kelleher"},{"last_name":"Véber","first_name":"Amandine","full_name":"Véber, Amandine"}],"volume":87,"date_created":"2018-12-11T11:59:53Z","date_updated":"2021-01-12T07:00:09Z","month":"08","oa":1,"project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"quality_controlled":"1","doi":"10.1016/j.tpb.2013.03.001","language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"doi":"10.1093/bioinformatics/btt067","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"quality_controlled":"1","oa":1,"month":"02","volume":29,"date_updated":"2021-01-12T07:00:38Z","date_created":"2018-12-11T12:00:17Z","author":[{"full_name":"Kelleher, Jerome","first_name":"Jerome","last_name":"Kelleher"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"first_name":"Alison","last_name":"Etheridge","full_name":"Etheridge, Alison"}],"department":[{"_id":"NiBa"}],"publisher":"Oxford University Press","publication_status":"published","year":"2013","ec_funded":1,"publist_id":"3833","file_date_updated":"2020-07-14T12:45:52Z","date_published":"2013-02-07T00:00:00Z","page":"955 - 956","citation":{"ama":"Kelleher J, Barton NH, Etheridge A. Coalescent simulation in continuous space. Bioinformatics. 2013;29(7):955-956. doi:10.1093/bioinformatics/btt067","ista":"Kelleher J, Barton NH, Etheridge A. 2013. Coalescent simulation in continuous space. Bioinformatics. 29(7), 955–956.","ieee":"J. Kelleher, N. H. Barton, and A. Etheridge, “Coalescent simulation in continuous space,” Bioinformatics, vol. 29, no. 7. Oxford University Press, pp. 955–956, 2013.","apa":"Kelleher, J., Barton, N. H., & Etheridge, A. (2013). Coalescent simulation in continuous space. Bioinformatics. Oxford University Press. https://doi.org/10.1093/bioinformatics/btt067","mla":"Kelleher, Jerome, et al. “Coalescent Simulation in Continuous Space.” Bioinformatics, vol. 29, no. 7, Oxford University Press, 2013, pp. 955–56, doi:10.1093/bioinformatics/btt067.","short":"J. Kelleher, N.H. Barton, A. Etheridge, Bioinformatics 29 (2013) 955–956.","chicago":"Kelleher, Jerome, Nicholas H Barton, and Alison Etheridge. “Coalescent Simulation in Continuous Space.” Bioinformatics. Oxford University Press, 2013. https://doi.org/10.1093/bioinformatics/btt067."},"publication":"Bioinformatics","has_accepted_license":"1","day":"07","scopus_import":1,"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2016-556-v1+1_bioinformatics-2013.pdf","creator":"system","file_size":170197,"content_type":"application/pdf","file_id":"5189","relation":"main_file","checksum":"a3b54d7477fac923815ac082403d9bd0","date_updated":"2020-07-14T12:45:52Z","date_created":"2018-12-12T10:16:04Z"}],"pubrep_id":"556","intvolume":" 29","status":"public","title":"Coalescent simulation in continuous space","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2910","issue":"7","abstract":[{"lang":"eng","text":"Coalescent simulation has become an indispensable tool in population genetics and many complex evolutionary scenarios have been incorporated into the basic algorithm. Despite many years of intense interest in spatial structure, however, there are no available methods to simulate the ancestry of a sample of genes that occupy a spatial continuum. This is mainly due to the severe technical problems encountered by the classical model of isolation\r\nby distance. A recently introduced model solves these technical problems and provides a solid theoretical basis for the study of populations evolving in continuous space. We present a detailed algorithm to simulate the coalescent process in this model, and provide an efficient implementation of a generalised version of this algorithm as a freely available Python module."}],"type":"journal_article"},{"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1088/1742-5468/2013/01/P01002","month":"01","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"IOP Publishing Ltd.","year":"2013","date_created":"2018-12-11T12:00:17Z","date_updated":"2021-01-12T07:00:37Z","volume":2013,"author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"},{"first_name":"Alison","last_name":"Etheridge","full_name":"Etheridge, Alison"},{"first_name":"Amandine","last_name":"Véber","full_name":"Véber, Amandine"}],"file_date_updated":"2020-07-14T12:45:52Z","publist_id":"3834","ec_funded":1,"publication":"Journal of Statistical Mechanics Theory and Experiment","citation":{"ama":"Barton NH, Etheridge A, Véber A. Modelling evolution in a spatial continuum. Journal of Statistical Mechanics Theory and Experiment. 2013;2013(1). doi:10.1088/1742-5468/2013/01/P01002","ista":"Barton NH, Etheridge A, Véber A. 2013. Modelling evolution in a spatial continuum. Journal of Statistical Mechanics Theory and Experiment. 2013(1).","apa":"Barton, N. H., Etheridge, A., & Véber, A. (2013). Modelling evolution in a spatial continuum. Journal of Statistical Mechanics Theory and Experiment. IOP Publishing Ltd. https://doi.org/10.1088/1742-5468/2013/01/P01002","ieee":"N. H. Barton, A. Etheridge, and A. Véber, “Modelling evolution in a spatial continuum,” Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 1. IOP Publishing Ltd., 2013.","mla":"Barton, Nicholas H., et al. “Modelling Evolution in a Spatial Continuum.” Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 1, IOP Publishing Ltd., 2013, doi:10.1088/1742-5468/2013/01/P01002.","short":"N.H. Barton, A. Etheridge, A. Véber, Journal of Statistical Mechanics Theory and Experiment 2013 (2013).","chicago":"Barton, Nicholas H, Alison Etheridge, and Amandine Véber. “Modelling Evolution in a Spatial Continuum.” Journal of Statistical Mechanics Theory and Experiment. IOP Publishing Ltd., 2013. https://doi.org/10.1088/1742-5468/2013/01/P01002."},"date_published":"2013-01-16T00:00:00Z","scopus_import":1,"day":"16","article_processing_charge":"No","has_accepted_license":"1","ddc":["570"],"status":"public","title":"Modelling evolution in a spatial continuum","intvolume":" 2013","_id":"2909","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","file":[{"date_created":"2018-12-12T10:16:52Z","date_updated":"2020-07-14T12:45:52Z","checksum":"ce8a4424385b3086138a1e054e16e0e3","file_id":"5242","relation":"main_file","creator":"system","file_size":702583,"content_type":"application/pdf","file_name":"IST-2016-557-v1+1_BEVrevised.pdf","access_level":"open_access"}],"pubrep_id":"557","type":"journal_article","abstract":[{"text":"We survey a class of models for spatially structured populations\r\nwhich we have called spatial Λ-Fleming–Viot processes. They arise from a flexible\r\nframework for modelling in which the key innovation is that random genetic drift\r\nis driven by a Poisson point process of spatial ‘events’. We demonstrate how this\r\novercomes some of the obstructions to modelling populations which evolve in two-\r\n(and higher-) dimensional spatial continua, how its predictions match phenomena\r\nobserved in data and how it fits with classical models. Finally we outline some\r\ndirections for future research.","lang":"eng"}],"issue":"1"},{"page":"267 - 269","publication":"Journal of Evolutionary Biology","citation":{"ama":"Barton NH. Does hybridisation influence speciation? . Journal of Evolutionary Biology. 2013;26(2):267-269. doi:10.1111/jeb.12015","apa":"Barton, N. H. (2013). Does hybridisation influence speciation? . Journal of Evolutionary Biology. Wiley-Blackwell. https://doi.org/10.1111/jeb.12015","ieee":"N. H. Barton, “Does hybridisation influence speciation? ,” Journal of Evolutionary Biology, vol. 26, no. 2. Wiley-Blackwell, pp. 267–269, 2013.","ista":"Barton NH. 2013. Does hybridisation influence speciation? . Journal of Evolutionary Biology. 26(2), 267–269.","short":"N.H. Barton, Journal of Evolutionary Biology 26 (2013) 267–269.","mla":"Barton, Nicholas H. “Does Hybridisation Influence Speciation? .” Journal of Evolutionary Biology, vol. 26, no. 2, Wiley-Blackwell, 2013, pp. 267–69, doi:10.1111/jeb.12015.","chicago":"Barton, Nicholas H. “Does Hybridisation Influence Speciation? .” Journal of Evolutionary Biology. Wiley-Blackwell, 2013. https://doi.org/10.1111/jeb.12015."},"date_published":"2013-01-17T00:00:00Z","scopus_import":1,"day":"17","has_accepted_license":"1","title":"Does hybridisation influence speciation? ","status":"public","ddc":["576"],"intvolume":" 26","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2908","file":[{"relation":"main_file","file_id":"4762","checksum":"716e88714c3411cd0bd70928b14ea692","date_updated":"2020-07-14T12:45:52Z","date_created":"2018-12-12T10:09:38Z","access_level":"open_access","file_name":"IST-2013-111-v1+1_Hybridisation_and_speciation_revised.rtf","file_size":13339,"content_type":"text/rtf","creator":"system"},{"file_id":"4763","relation":"main_file","date_created":"2018-12-12T10:09:39Z","date_updated":"2020-07-14T12:45:52Z","checksum":"957fd07c71c1b1eac2c65ae3311aca78","file_name":"IST-2017-111-v1+2_Hybridisation_and_speciation_revised.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":103437}],"oa_version":"Submitted Version","pubrep_id":"111","type":"journal_article","abstract":[{"text":"Hybridization is an almost inevitable component of speciation, and its study can tell us much about that process. However, hybridization itself may have a negligible influence on the origin of species: on the one hand, universally favoured alleles spread readily across hybrid zones, whilst on the other, spatially heterogeneous selection causes divergence despite gene flow. Thus, narrow hybrid zones or occasional hybridisation may hardly affect the process of divergence.","lang":"eng"}],"issue":"2","quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/jeb.12015","month":"01","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley-Blackwell","year":"2013","date_updated":"2021-01-12T07:00:37Z","date_created":"2018-12-11T12:00:17Z","volume":26,"author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"file_date_updated":"2020-07-14T12:45:52Z","publist_id":"3835"},{"month":"11","day":"04","publication_identifier":{"isbn":["9780691149776"]},"has_accepted_license":"1","date_published":"2013-11-04T00:00:00Z","language":[{"iso":"eng"}],"publication":"The Princeton Guide to Evolution","citation":{"short":"N.H. Barton, in:, The Princeton Guide to Evolution, Princeton University Press, 2013, pp. 328–333.","mla":"Barton, Nicholas H. “Recombination and Sex.” The Princeton Guide to Evolution, Princeton University Press, 2013, pp. 328–33.","chicago":"Barton, Nicholas H. “Recombination and Sex.” In The Princeton Guide to Evolution, 328–33. Princeton University Press, 2013.","ama":"Barton NH. Recombination and sex. In: The Princeton Guide to Evolution. Princeton University Press; 2013:328-333.","apa":"Barton, N. H. (2013). Recombination and sex. In The Princeton Guide to Evolution (pp. 328–333). Princeton University Press.","ieee":"N. H. Barton, “Recombination and sex,” in The Princeton Guide to Evolution, Princeton University Press, 2013, pp. 328–333.","ista":"Barton NH. 2013.Recombination and sex. In: The Princeton Guide to Evolution. , 328–333."},"oa":1,"quality_controlled":"1","page":"328 - 333","file_date_updated":"2020-07-14T12:45:52Z","abstract":[{"text":"Sex and recombination are among the most striking features of the living world, and they play a crucial role in allowing the evolution of complex adaptation. The sharing of genomes through the sexual union of different individuals requires elaborate behavioral and physiological adaptations. At the molecular level, the alignment of two DNA double helices, followed by their precise cutting and rejoining, is an extraordinary feat. Sex and recombination have diverse—and often surprising—evolutionary consequences: distinct sexes, elaborate mating displays, selfish genetic elements, and so on.","lang":"eng"}],"publist_id":"3839","type":"book_chapter","author":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"pubrep_id":"119","date_updated":"2021-01-12T07:00:37Z","date_created":"2018-12-11T12:00:16Z","oa_version":"Submitted Version","file":[{"file_id":"5237","relation":"main_file","date_created":"2018-12-12T10:16:47Z","date_updated":"2020-07-14T12:45:52Z","checksum":"8332ca9cb40f7e66d1006b175ce36b60","file_name":"IST-2013-119-v1+1_IV.4_Recombination_and_Sex_Barton_1-13-13-e.docx","access_level":"open_access","creator":"system","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":79838},{"file_name":"IST-2017-119-v1+2_Barton_Recombination_Sex.pdf","access_level":"open_access","content_type":"application/pdf","file_size":144131,"creator":"system","relation":"main_file","file_id":"5238","date_created":"2018-12-12T10:16:48Z","date_updated":"2020-07-14T12:45:52Z","checksum":"849f418620fb78d6ba23bb4f488ee93f"}],"_id":"2907","year":"2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["576"],"publication_status":"published","title":"Recombination and sex","status":"public","department":[{"_id":"NiBa"}],"publisher":"Princeton University Press"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Understanding the relative importance of heterosis and outbreeding depression over multiple generations is a key question in evolutionary biology and is essential for identifying appropriate genetic sources for population and ecosystem restoration. Here we use 2455 experimental crosses between 12 population pairs of the rare perennial plant Rutidosis leptorrhynchoides (Asteraceae) to investigate the multi-generational (F1, F2, F3) fitness outcomes of inter-population hybridization. We detected no evidence of outbreeding depression, with inter-population hybrids and backcrosses showing either similar fitness or significant heterosis for fitness components across the three generations. Variation in heterosis among population pairs was best explained by characteristics of the foreign source or home population, and was greatest when the source population was large, with high genetic diversity and low inbreeding, and the home population was small and inbred. Our results indicate that the primary consideration for maximizing progeny fitness following population augmentation or restoration is the use of seed from large, genetically diverse populations."}],"issue":"1750","status":"public","title":"Source population characteristics affect heterosis following genetic rescue of fragmented plant populations","intvolume":" 280","_id":"450","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","day":"07","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","citation":{"ieee":"M. Pickup, D. Field, D. Rowell, and A. Young, “Source population characteristics affect heterosis following genetic rescue of fragmented plant populations,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 280, no. 1750. Royal Society, The, 2013.","apa":"Pickup, M., Field, D., Rowell, D., & Young, A. (2013). Source population characteristics affect heterosis following genetic rescue of fragmented plant populations. Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2012.2058","ista":"Pickup M, Field D, Rowell D, Young A. 2013. Source population characteristics affect heterosis following genetic rescue of fragmented plant populations. Proceedings of the Royal Society of London Series B Biological Sciences. 280(1750), 2058.","ama":"Pickup M, Field D, Rowell D, Young A. Source population characteristics affect heterosis following genetic rescue of fragmented plant populations. Proceedings of the Royal Society of London Series B Biological Sciences. 2013;280(1750). doi:10.1098/rspb.2012.2058","chicago":"Pickup, Melinda, David Field, David Rowell, and Andrew Young. “Source Population Characteristics Affect Heterosis Following Genetic Rescue of Fragmented Plant Populations.” Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The, 2013. https://doi.org/10.1098/rspb.2012.2058.","short":"M. Pickup, D. Field, D. Rowell, A. Young, Proceedings of the Royal Society of London Series B Biological Sciences 280 (2013).","mla":"Pickup, Melinda, et al. “Source Population Characteristics Affect Heterosis Following Genetic Rescue of Fragmented Plant Populations.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 280, no. 1750, 2058, Royal Society, The, 2013, doi:10.1098/rspb.2012.2058."},"date_published":"2013-01-07T00:00:00Z","article_number":"2058","publist_id":"7372","publication_status":"published","publisher":"Royal Society, The","department":[{"_id":"NiBa"}],"year":"2013","pmid":1,"date_updated":"2021-01-12T07:57:25Z","date_created":"2018-12-11T11:46:32Z","volume":280,"author":[{"last_name":"Pickup","first_name":"Melinda","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","full_name":"Pickup, Melinda"},{"full_name":"Field, David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David"},{"full_name":"Rowell, David","last_name":"Rowell","first_name":"David"},{"full_name":"Young, Andrew","first_name":"Andrew","last_name":"Young"}],"month":"01","quality_controlled":"1","external_id":{"pmid":["23173202"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3574427/"}],"language":[{"iso":"eng"}],"doi":"10.1098/rspb.2012.2058"},{"type":"journal_article","issue":"4","abstract":[{"text":"We propose a two-step procedure for estimating multiple migration rates in an approximate Bayesian computation (ABC) framework, accounting for global nuisance parameters. The approach is not limited to migration, but generally of interest for inference problems with multiple parameters and a modular structure (e.g. independent sets of demes or loci). We condition on a known, but complex demographic model of a spatially subdivided population, motivated by the reintroduction of Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters ancestral mutation rate and male mating skew have been estimated for the whole population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step, we estimate in this study the migration rates independently for clusters of demes putatively connected by migration. For large clusters (many migration rates), ABC faces the problem of too many summary statistics. We therefore assess by simulation if estimation per pair of demes is a valid alternative. We find that the trade-off between reduced dimensionality for the pairwise estimation on the one hand and lower accuracy due to the assumption of pairwise independence on the other depends on the number of migration rates to be inferred: the accuracy of the pairwise approach increases with the number of parameters, relative to the joint estimation approach. To distinguish between low and zero migration, we perform ABC-type model comparison between a model with migration and one without. Applying the approach to microsatellite data from Alpine ibex, we find no evidence for substantial gene flow via migration, except for one pair of demes in one direction.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2944","intvolume":" 22","title":"Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. ","status":"public","oa_version":"None","scopus_import":1,"day":"01","citation":{"ieee":"S. Aeschbacher, A. Futschik, and M. Beaumont, “Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. ,” Molecular Ecology, vol. 22, no. 4. Wiley-Blackwell, pp. 987–1002, 2013.","apa":"Aeschbacher, S., Futschik, A., & Beaumont, M. (2013). Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/mec.12165","ista":"Aeschbacher S, Futschik A, Beaumont M. 2013. Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . Molecular Ecology. 22(4), 987–1002.","ama":"Aeschbacher S, Futschik A, Beaumont M. Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . Molecular Ecology. 2013;22(4):987-1002. doi:10.1111/mec.12165","chicago":"Aeschbacher, Simon, Andreas Futschik, and Mark Beaumont. “Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates. .” Molecular Ecology. Wiley-Blackwell, 2013. https://doi.org/10.1111/mec.12165.","short":"S. Aeschbacher, A. Futschik, M. Beaumont, Molecular Ecology 22 (2013) 987–1002.","mla":"Aeschbacher, Simon, et al. “Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates. .” Molecular Ecology, vol. 22, no. 4, Wiley-Blackwell, 2013, pp. 987–1002, doi:10.1111/mec.12165."},"publication":"Molecular Ecology","page":"987 - 1002","date_published":"2013-02-01T00:00:00Z","publist_id":"3788","acknowledgement":"This study has made use of the computational resources provided by IST Austria and the Edinburgh Compute and Data Facility (ECDF; http://www.ecdf.ed.ac.uk). The ECDF is partially supported by the eDIKT initiative (http://www.edikt.org.uk). S.A. acknowledges financial support by IST Austria, the Janggen-Pöhn Foundation, St. Gallen, the Roche Research Foundation, Basel, the University of Edinburgh in the form of a Torrance Studentship, and the Austrian Science Fund (FWF P21305-N13).","year":"2013","publisher":"Wiley-Blackwell","department":[{"_id":"NiBa"}],"publication_status":"published","related_material":{"record":[{"id":"9758","status":"public","relation":"research_data"}]},"author":[{"id":"2D35326E-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Aeschbacher","full_name":"Aeschbacher, Simon"},{"full_name":"Futschik, Andreas","first_name":"Andreas","last_name":"Futschik"},{"last_name":"Beaumont","first_name":"Mark","full_name":"Beaumont, Mark"}],"volume":22,"date_created":"2018-12-11T12:00:28Z","date_updated":"2023-02-23T14:07:19Z","month":"02","quality_controlled":"1","doi":"10.1111/mec.12165","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}]},{"type":"research_data_reference","abstract":[{"text":"Short-read sequencing technologies have in principle made it feasible to draw detailed inferences about the recent history of any organism. In practice, however, this remains challenging due to the difficulty of genome assembly in most organisms and the lack of statistical methods powerful enough to discriminate among recent, non-equilibrium histories. We address both the assembly and inference challenges. We develop a bioinformatic pipeline for generating outgroup-rooted alignments of orthologous sequence blocks from de novo low-coverage short-read data for a small number of genomes, and show how such sequence blocks can be used to fit explicit models of population divergence and admixture in a likelihood framework. To illustrate our approach, we reconstruct the Pleistocene history of an oak-feeding insect (the oak gallwasp Biorhiza pallida) which, in common with many other taxa, was restricted during Pleistocene ice ages to a longitudinal series of southern refugia spanning theWestern Palaearctic. Our analysis of sequence blocks sampled from a single genome from each of three major glacial refugia reveals support for an unexpected history dominated by recent admixture. Despite the fact that 80% of the genome is affected by admixture during the last glacial cycle, we are able to infer the deeper divergence history of these populations. These inferences are robust to variation in block length, mutation model, and the sampling location of individual genomes within refugia. This combination of de novo assembly and numerical likelihood calculation provides a powerful framework for estimating recent population history that can be applied to any organism without the need for prior genetic resources.","lang":"eng"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9754","year":"2013","status":"public","title":"Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies","department":[{"_id":"NiBa"}],"publisher":"Dryad","author":[{"first_name":"Jack","last_name":"Hearn","full_name":"Hearn, Jack"},{"first_name":"Graham","last_name":"Stone","full_name":"Stone, Graham"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"},{"last_name":"Lohse","first_name":"Konrad","full_name":"Lohse, Konrad"},{"last_name":"Bunnefeld","first_name":"Lynsey","full_name":"Bunnefeld, Lynsey"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"2170"}]},"date_updated":"2023-02-23T10:31:17Z","date_created":"2021-07-30T08:31:22Z","oa_version":"Published Version","month":"10","day":"01","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.5061/dryad.r3r60","open_access":"1"}],"citation":{"chicago":"Hearn, Jack, Graham Stone, Nicholas H Barton, Konrad Lohse, and Lynsey Bunnefeld. “Data from: Likelihood-Based Inference of Population History from Low Coverage de Novo Genome Assemblies.” Dryad, 2013. https://doi.org/10.5061/dryad.r3r60.","short":"J. Hearn, G. Stone, N.H. Barton, K. Lohse, L. Bunnefeld, (2013).","mla":"Hearn, Jack, et al. Data from: Likelihood-Based Inference of Population History from Low Coverage de Novo Genome Assemblies. Dryad, 2013, doi:10.5061/dryad.r3r60.","apa":"Hearn, J., Stone, G., Barton, N. H., Lohse, K., & Bunnefeld, L. (2013). Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies. Dryad. https://doi.org/10.5061/dryad.r3r60","ieee":"J. Hearn, G. Stone, N. H. Barton, K. Lohse, and L. Bunnefeld, “Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies.” Dryad, 2013.","ista":"Hearn J, Stone G, Barton NH, Lohse K, Bunnefeld L. 2013. Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies, Dryad, 10.5061/dryad.r3r60.","ama":"Hearn J, Stone G, Barton NH, Lohse K, Bunnefeld L. Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies. 2013. doi:10.5061/dryad.r3r60"},"oa":1,"doi":"10.5061/dryad.r3r60","date_published":"2013-10-01T00:00:00Z"},{"type":"journal_article","abstract":[{"text":"The search for extra-terrestrial intelligence (SETI) has been performed principally as a one-way survey, listening of radio frequencies across the Milky Way and other galaxies. However, scientists have engaged in an active messaging only rarely. This suggests the simple rationale that if other civilizations exist and take a similar approach to ours, namely listening but not broadcasting, the result is a silent universe. A simple game theoretical model, the prisoner's dilemma, explains this situation: each player (civilization) can passively search (defect), or actively search and broadcast (cooperate). In order to maximize the payoff (or, equivalently, minimize the risks) the best strategy is not to broadcast. In fact, the active search has been opposed on the basis that it might be dangerous to expose ourselves. However, most of these ideas have not been based on objective arguments, and ignore accounting of the possible gains and losses. Thus, the question stands: should we perform an active search? I develop a game-theoretical framework where civilizations can be of different types, and explicitly apply it to a situation where societies are either interested in establishing a two-way communication or belligerent and in urge to exploit ours. The framework gives a quantitative solution (a mixed-strategy), which is how frequent we should perform the active SETI. This frequency is roughly proportional to the inverse of the risk, and can be extremely small. However, given the immense amount of stars being scanned, it supports active SETI. The model is compared with simulations, and the possible actions are evaluated through the San Marino scale, measuring the risks of messaging.","lang":"eng"}],"issue":"1","publist_id":"3821","publication_status":"published","title":"The game of active search for extra terrestrial intelligence Breaking the Great Silence ","status":"public","department":[{"_id":"NiBa"}],"publisher":"Cambridge University Press","intvolume":" 12","_id":"2917","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2012","date_updated":"2021-01-12T07:00:41Z","date_created":"2018-12-11T12:00:19Z","oa_version":"None","volume":12,"author":[{"last_name":"Vladar","first_name":"Harold","orcid":"0000-0002-5985-7653","id":"2A181218-F248-11E8-B48F-1D18A9856A87","full_name":"Vladar, Harold"}],"scopus_import":1,"month":"11","day":"06","quality_controlled":"1","page":"53 - 62","publication":"International Journal of Astrobiology","citation":{"mla":"de Vladar, Harold. “The Game of Active Search for Extra Terrestrial Intelligence Breaking the Great Silence .” International Journal of Astrobiology, vol. 12, no. 1, Cambridge University Press, 2012, pp. 53–62, doi:10.1017/S1473550412000407.","short":"H. de Vladar, International Journal of Astrobiology 12 (2012) 53–62.","chicago":"Vladar, Harold de. “The Game of Active Search for Extra Terrestrial Intelligence Breaking the Great Silence .” International Journal of Astrobiology. Cambridge University Press, 2012. https://doi.org/10.1017/S1473550412000407.","ama":"de Vladar H. The game of active search for extra terrestrial intelligence Breaking the Great Silence . International Journal of Astrobiology. 2012;12(1):53-62. doi:10.1017/S1473550412000407","ista":"de Vladar H. 2012. The game of active search for extra terrestrial intelligence Breaking the Great Silence . International Journal of Astrobiology. 12(1), 53–62.","apa":"de Vladar, H. (2012). The game of active search for extra terrestrial intelligence Breaking the Great Silence . International Journal of Astrobiology. Cambridge University Press. https://doi.org/10.1017/S1473550412000407","ieee":"H. de Vladar, “The game of active search for extra terrestrial intelligence Breaking the Great Silence ,” International Journal of Astrobiology, vol. 12, no. 1. Cambridge University Press, pp. 53–62, 2012."},"language":[{"iso":"eng"}],"doi":"10.1017/S1473550412000407","date_published":"2012-11-06T00:00:00Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2962","title":"A novel approach for choosing summary statistics in approximate Bayesian computation","status":"public","intvolume":" 192","oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"The choice of summary statistics is a crucial step in approximate Bayesian computation (ABC). Since statistics are often not sufficient, this choice involves a trade-off between loss of information and reduction of dimensionality. The latter may increase the efficiency of ABC. Here, we propose an approach for choosing summary statistics based on boosting, a technique from the machine learning literature. We consider different types of boosting and compare them to partial least squares regression as an alternative. To mitigate the lack of sufficiency, we also propose an approach for choosing summary statistics locally, in the putative neighborhood of the true parameter value. We study a demographic model motivated by the re-introduction of Alpine ibex (Capra ibex) into the Swiss Alps. The parameters of interest are the mean and standard deviation across microsatellites of the scaled ancestral mutation rate (θanc = 4 Ne u), and the proportion of males obtaining access to matings per breeding season (ω). By simulation, we assess the properties of the posterior distribution obtained with the various methods. According to our criteria, ABC with summary statistics chosen locally via boosting with the L2-loss performs best. Applying that method to the ibex data, we estimate θanc ≈ 1.288, and find that most of the variation across loci of the ancestral mutation rate u is between 7.7×10−4 and 3.5×10−3 per locus per generation. The proportion of males with access to matings is estimated to ω ≈ 0.21, which is in good agreement with recent independent estimates.","lang":"eng"}],"issue":"3","publication":"Genetics","citation":{"ama":"Aeschbacher S, Beaumont M, Futschik A. A novel approach for choosing summary statistics in approximate Bayesian computation. Genetics. 2012;192(3):1027-1047. doi:10.1534/genetics.112.143164","ista":"Aeschbacher S, Beaumont M, Futschik A. 2012. A novel approach for choosing summary statistics in approximate Bayesian computation. Genetics. 192(3), 1027–1047.","ieee":"S. Aeschbacher, M. Beaumont, and A. Futschik, “A novel approach for choosing summary statistics in approximate Bayesian computation,” Genetics, vol. 192, no. 3. Genetics Society of America, pp. 1027–1047, 2012.","apa":"Aeschbacher, S., Beaumont, M., & Futschik, A. (2012). A novel approach for choosing summary statistics in approximate Bayesian computation. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.112.143164","mla":"Aeschbacher, Simon, et al. “A Novel Approach for Choosing Summary Statistics in Approximate Bayesian Computation.” Genetics, vol. 192, no. 3, Genetics Society of America, 2012, pp. 1027–47, doi:10.1534/genetics.112.143164.","short":"S. Aeschbacher, M. Beaumont, A. Futschik, Genetics 192 (2012) 1027–1047.","chicago":"Aeschbacher, Simon, Mark Beaumont, and Andreas Futschik. “A Novel Approach for Choosing Summary Statistics in Approximate Bayesian Computation.” Genetics. Genetics Society of America, 2012. https://doi.org/10.1534/genetics.112.143164."},"page":"1027 - 1047","date_published":"2012-11-01T00:00:00Z","scopus_import":1,"day":"01","year":"2012","pmid":1,"publication_status":"published","publisher":"Genetics Society of America","department":[{"_id":"NiBa"}],"author":[{"full_name":"Aeschbacher, Simon","id":"2D35326E-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Aeschbacher"},{"full_name":"Beaumont, Mark","last_name":"Beaumont","first_name":"Mark"},{"last_name":"Futschik","first_name":"Andreas","full_name":"Futschik, Andreas"}],"date_created":"2018-12-11T12:00:34Z","date_updated":"2021-01-12T07:40:05Z","volume":192,"publist_id":"3763","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3522150/","open_access":"1"}],"oa":1,"external_id":{"pmid":["22960215"]},"quality_controlled":"1","doi":"10.1534/genetics.112.143164","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"month":"11"},{"status":"public","publication_status":"published","title":"Disassortative mating and the maintenance of sexual polymorphism in painted maple","publisher":"Wiley-Blackwell","department":[{"_id":"NiBa"}],"intvolume":" 21","_id":"3122","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2012","date_created":"2018-12-11T12:01:31Z","date_updated":"2021-01-12T07:41:13Z","volume":21,"oa_version":"None","author":[{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","first_name":"David","last_name":"Field","full_name":"Field, David"},{"first_name":"Spencer","last_name":"Barrett","full_name":"Barrett, Spencer"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Since Darwin's pioneering research on plant reproductive biology (e.g. Darwin 1877), understanding the mechanisms maintaining the diverse sexual strategies of plants has remained an important challenge for evolutionary biologists. In some species, populations are sexually polymorphic and contain two or more mating morphs (sex phenotypes). Differences in morphology or phenology among the morphs influence patterns of non-random mating. In these populations, negative frequency-dependent selection arising from disassortative (intermorph) mating is usually required for the evolutionary maintenance of sexual polymorphism, but few studies have demonstrated the required patterns of non-random mating. In the current issue of Molecular Ecology, Shang (2012) make an important contribution to our understanding of how disassortative mating influences sex phenotype ratios in Acer pictum subsp. mono (painted maple), a heterodichogamous, deciduous tree of eastern China. They monitored sex expression in 97 adults and used paternity analysis of open-pollinated seed to examine disassortative mating among three sex phenotypes. Using a deterministic 'pollen transfer' model, Shang et al. present convincing evidence that differences in the degree of disassortative mating in progeny arrays of the sex phenotypes can explain their uneven frequencies in the adult population. This study provides a useful example of how the deployment of genetic markers, demographic monitoring and modelling can be integrated to investigate the maintenance of sexual diversity in plants. "}],"issue":"15","publist_id":"3577","quality_controlled":"1","page":"3640 - 3643","publication":"Molecular Ecology","citation":{"ama":"Field D, Barrett S. Disassortative mating and the maintenance of sexual polymorphism in painted maple. Molecular Ecology. 2012;21(15):3640-3643. doi:10.1111/j.1365-294X.2012.05643.x","ieee":"D. Field and S. Barrett, “Disassortative mating and the maintenance of sexual polymorphism in painted maple,” Molecular Ecology, vol. 21, no. 15. Wiley-Blackwell, pp. 3640–3643, 2012.","apa":"Field, D., & Barrett, S. (2012). Disassortative mating and the maintenance of sexual polymorphism in painted maple. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2012.05643.x","ista":"Field D, Barrett S. 2012. Disassortative mating and the maintenance of sexual polymorphism in painted maple. Molecular Ecology. 21(15), 3640–3643.","short":"D. Field, S. Barrett, Molecular Ecology 21 (2012) 3640–3643.","mla":"Field, David, and Spencer Barrett. “Disassortative Mating and the Maintenance of Sexual Polymorphism in Painted Maple.” Molecular Ecology, vol. 21, no. 15, Wiley-Blackwell, 2012, pp. 3640–43, doi:10.1111/j.1365-294X.2012.05643.x.","chicago":"Field, David, and Spencer Barrett. “Disassortative Mating and the Maintenance of Sexual Polymorphism in Painted Maple.” Molecular Ecology. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1365-294X.2012.05643.x."},"language":[{"iso":"eng"}],"doi":"10.1111/j.1365-294X.2012.05643.x","date_published":"2012-08-01T00:00:00Z","scopus_import":1,"month":"08","day":"01"},{"scopus_import":1,"day":"07","has_accepted_license":"1","publication":"PLoS Genetics","citation":{"apa":"Weissman, D., & Barton, N. H. (2012). Limits to the rate of adaptive substitution in sexual populations. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002740","ieee":"D. Weissman and N. H. Barton, “Limits to the rate of adaptive substitution in sexual populations,” PLoS Genetics, vol. 8, no. 6. Public Library of Science, 2012.","ista":"Weissman D, Barton NH. 2012. Limits to the rate of adaptive substitution in sexual populations. PLoS Genetics. 8(6), e1002740.","ama":"Weissman D, Barton NH. Limits to the rate of adaptive substitution in sexual populations. PLoS Genetics. 2012;8(6). doi:10.1371/journal.pgen.1002740","chicago":"Weissman, Daniel, and Nicholas H Barton. “Limits to the Rate of Adaptive Substitution in Sexual Populations.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002740.","short":"D. Weissman, N.H. Barton, PLoS Genetics 8 (2012).","mla":"Weissman, Daniel, and Nicholas H. Barton. “Limits to the Rate of Adaptive Substitution in Sexual Populations.” PLoS Genetics, vol. 8, no. 6, e1002740, Public Library of Science, 2012, doi:10.1371/journal.pgen.1002740."},"date_published":"2012-06-07T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"In large populations, many beneficial mutations may be simultaneously available and may compete with one another, slowing adaptation. By finding the probability of fixation of a favorable allele in a simple model of a haploid sexual population, we find limits to the rate of adaptive substitution, Λ, that depend on simple parameter combinations. When variance in fitness is low and linkage is loose, the baseline rate of substitution is Λ 0=2NU〈s〉 is the population size, U is the rate of beneficial mutations per genome, and 〈s〉 is their mean selective advantage. Heritable variance ν in log fitness due to unlinked loci reduces Λ by e -4ν under polygamy and e -8ν under monogamy. With a linear genetic map of length R Morgans, interference is yet stronger. We use a scaling argument to show that the density of adaptive substitutions depends on s, N, U, and R only through the baseline density: Λ/R=F(Λ 0/R). Under the approximation that the interference due to different sweeps adds up, we show that Λ/R~(Λ 0/R)/(1+2Λ 0/R), implying that interference prevents the rate of adaptive substitution from exceeding one per centimorgan per 200 generations. Simulations and numerical calculations confirm the scaling argument and confirm the additive approximation for Λ 0/R 1; for higher Λ 0/R, the rate of adaptation grows above R/2, but only very slowly. We also consider the effect of sweeps on neutral diversity and show that, while even occasional sweeps can greatly reduce neutral diversity, this effect saturates as sweeps become more common-diversity can be maintained even in populations experiencing very strong interference. Our results indicate that for some organisms the rate of adaptive substitution may be primarily recombination-limited, depending only weakly on the mutation supply and the strength of selection."}],"issue":"6","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3131","ddc":["570","576"],"title":"Limits to the rate of adaptive substitution in sexual populations","status":"public","intvolume":" 8","pubrep_id":"114","file":[{"checksum":"729a4becda7d786c4c3db8f9a1f77953","date_updated":"2020-07-14T12:46:01Z","date_created":"2018-12-12T10:08:00Z","relation":"main_file","file_id":"4659","file_size":1284801,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2013-114-v1+1_WeissmanBarton2012.pdf"}],"oa_version":"Published Version","month":"06","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"doi":"10.1371/journal.pgen.1002740","language":[{"iso":"eng"}],"article_number":"e1002740","file_date_updated":"2020-07-14T12:46:01Z","ec_funded":1,"publist_id":"3566","acknowledgement":"The work was funded by ERC grant 250152.\r\nWe thank B. Charlesworth, O. Hallatschek, W. G. Hill, R. A. Neher, S. P. Otto, and the anonymous reviewers for their helpful suggestions.","year":"2012","publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"NiBa"}],"author":[{"full_name":"Weissman, Daniel","last_name":"Weissman","first_name":"Daniel","id":"2D0CE020-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"date_updated":"2021-01-12T07:41:17Z","date_created":"2018-12-11T12:01:34Z","volume":8},{"author":[{"full_name":"Vladar, Harold","id":"2A181218-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5985-7653","first_name":"Harold","last_name":"Vladar"}],"date_created":"2018-12-11T12:01:46Z","date_updated":"2021-01-12T07:41:31Z","volume":7,"year":"2012","acknowledgement":"The author was supported by the ERC-2009-AdG Grant for project 250152 SELECTIONINFORMATION. ","publication_status":"published","publisher":"BioMed Central","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:46:02Z","publist_id":"3518","ec_funded":1,"article_number":"6","doi":"10.1186/1745-6150-7-6","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"month":"02","pubrep_id":"99","file":[{"file_id":"5166","relation":"main_file","checksum":"e511e401e239ef608a7fd79b21a06d78","date_created":"2018-12-12T10:15:44Z","date_updated":"2020-07-14T12:46:02Z","access_level":"open_access","file_name":"IST-2012-99-v1+1_1745-6150-7-6.pdf","creator":"system","content_type":"application/pdf","file_size":4099536}],"oa_version":"Published Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3166","ddc":["570","576"],"title":"Amino acid fermentation at the origin of the genetic code","status":"public","intvolume":" 7","abstract":[{"text":"There is evidence that the genetic code was established prior to the existence of proteins, when metabolism was powered by ribozymes. Also, early proto-organisms had to rely on simple anaerobic bioenergetic processes. In this work I propose that amino acid fermentation powered metabolism in the RNA world, and that this was facilitated by proto-adapters, the precursors of the tRNAs. Amino acids were used as carbon sources rather than as catalytic or structural elements. In modern bacteria, amino acid fermentation is known as the Stickland reaction. This pathway involves two amino acids: the first undergoes oxidative deamination, and the second acts as an electron acceptor through reductive deamination. This redox reaction results in two keto acids that are employed to synthesise ATP via substrate-level phosphorylation. The Stickland reaction is the basic bioenergetic pathway of some bacteria of the genus Clostridium. Two other facts support Stickland fermentation in the RNA world. First, several Stickland amino acid pairs are synthesised in abiotic amino acid synthesis. This suggests that amino acids that could be used as an energy substrate were freely available. Second, anticodons that have complementary sequences often correspond to amino acids that form Stickland pairs. The main hypothesis of this paper is that pairs of complementary proto-adapters were assigned to Stickland amino acids pairs. There are signatures of this hypothesis in the genetic code. Furthermore, it is argued that the proto-adapters formed double strands that brought amino acid pairs into proximity to facilitate their mutual redox reaction, structurally constraining the anticodon pairs that are assigned to these amino acid pairs. Significance tests which randomise the code are performed to study the extent of the variability of the energetic (ATP) yield. Random assignments can lead to a substantial yield of ATP and maintain enough variability, thus selection can act and refine the assignments into a proto-code that optimises the energetic yield. Monte Carlo simulations are performed to evaluate the establishment of these simple proto-codes, based on amino acid substitutions and codon swapping. In all cases, donor amino acids are assigned to anticodons composed of U+G, and have low redundancy (1-2 codons), whereas acceptor amino acids are assigned to the the remaining codons. These bioenergetic and structural constraints allow for a metabolic role for amino acids before their co-option as catalyst cofactors. Reviewers: this article was reviewed by Prof. William Martin, Prof. Eors Szathmary (nominated by Dr. Gaspar Jekely) and Dr. Adam Kun (nominated by Dr. Sandor Pongor)","lang":"eng"}],"type":"journal_article","date_published":"2012-02-10T00:00:00Z","publication":"Biology Direct","citation":{"short":"H. de Vladar, Biology Direct 7 (2012).","mla":"de Vladar, Harold. “Amino Acid Fermentation at the Origin of the Genetic Code.” Biology Direct, vol. 7, 6, BioMed Central, 2012, doi:10.1186/1745-6150-7-6.","chicago":"Vladar, Harold de. “Amino Acid Fermentation at the Origin of the Genetic Code.” Biology Direct. BioMed Central, 2012. https://doi.org/10.1186/1745-6150-7-6.","ama":"de Vladar H. Amino acid fermentation at the origin of the genetic code. Biology Direct. 2012;7. doi:10.1186/1745-6150-7-6","apa":"de Vladar, H. (2012). Amino acid fermentation at the origin of the genetic code. Biology Direct. BioMed Central. https://doi.org/10.1186/1745-6150-7-6","ieee":"H. de Vladar, “Amino acid fermentation at the origin of the genetic code,” Biology Direct, vol. 7. BioMed Central, 2012.","ista":"de Vladar H. 2012. Amino acid fermentation at the origin of the genetic code. Biology Direct. 7, 6."},"day":"10","has_accepted_license":"1"},{"alternative_title":["Cellular Origin, Life in Extreme Habitats and Astrobiology"],"type":"book_chapter","abstract":[{"text":"The problem of the origin of metazoa is becoming more urgent in the context of astrobiology. By now it is clear that clues to the understanding of this crucial transition in the evolution of life can arise in a fourth pathway besides the three possibilities in the quest for simplicity outlined by Bonner in his classical book. In other words, solar system exploration seems to be one way in the long-term to elucidate the simplicity of evolutionary development. We place these ideas in the context of different inheritance systems, namely the genotypic and phenotypic replicators with limited or unlimited heredity, and ask which of these can support multicellular development, and to which degree of complexity. However, the quest for evidence on the evolution of biotas from planets around other stars does not seem to be feasible with present technology with direct visualization of living organisms on exoplanets. But this may be attempted on the Galilean moons of Jupiter where there is a possibility of detecting reliable biomarkers in the next decade with the Europa Jupiter System Mission, in view of recent progress by landing micropenetrators on planetary, or satellite surfaces. Mars is a second possibility in the inner Solar System, in spite of the multiple difficulties faced by the fleet of past, present and future missions. We discuss a series of preliminary ideas for elucidating the origin of metazoan analogues with available instrumentation in potential payloads of feasible space missions to the Galilean moons.","lang":"eng"}],"publist_id":"3369","title":"Can the evolution of multicellularity be anticipated in the exploration of the solar system?","status":"public","publication_status":"published","publisher":"Springer","intvolume":" 24","department":[{"_id":"NiBa"}],"year":"2012","_id":"3277","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:42:20Z","date_created":"2018-12-11T12:02:25Z","volume":24,"oa_version":"None","author":[{"first_name":"Harold","last_name":"de Vladar","id":"2A181218-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5985-7653","full_name":"de Vladar, Harold"},{"full_name":"Chela Flores, Julian","first_name":"Julian","last_name":"Chela Flores"}],"month":"01","day":"01","quality_controlled":"1","page":"387 - 405","publication":"Life on Earth and other planetary bodies","citation":{"ama":"de Vladar H, Chela Flores J. Can the evolution of multicellularity be anticipated in the exploration of the solar system? In: Life on Earth and Other Planetary Bodies. Vol 24. Springer; 2012:387-405. doi:10.1007/978-94-007-4966-5_22","apa":"de Vladar, H., & Chela Flores, J. (2012). Can the evolution of multicellularity be anticipated in the exploration of the solar system? In Life on Earth and other planetary bodies (Vol. 24, pp. 387–405). Springer. https://doi.org/10.1007/978-94-007-4966-5_22","ieee":"H. de Vladar and J. Chela Flores, “Can the evolution of multicellularity be anticipated in the exploration of the solar system?,” in Life on Earth and other planetary bodies, vol. 24, Springer, 2012, pp. 387–405.","ista":"de Vladar H, Chela Flores J. 2012.Can the evolution of multicellularity be anticipated in the exploration of the solar system? In: Life on Earth and other planetary bodies. Cellular Origin, Life in Extreme Habitats and Astrobiology, vol. 24, 387–405.","short":"H. de Vladar, J. Chela Flores, in:, Life on Earth and Other Planetary Bodies, Springer, 2012, pp. 387–405.","mla":"de Vladar, Harold, and Julian Chela Flores. “Can the Evolution of Multicellularity Be Anticipated in the Exploration of the Solar System?” Life on Earth and Other Planetary Bodies, vol. 24, Springer, 2012, pp. 387–405, doi:10.1007/978-94-007-4966-5_22.","chicago":"Vladar, Harold de, and Julian Chela Flores. “Can the Evolution of Multicellularity Be Anticipated in the Exploration of the Solar System?” In Life on Earth and Other Planetary Bodies, 24:387–405. Springer, 2012. https://doi.org/10.1007/978-94-007-4966-5_22."},"language":[{"iso":"eng"}],"date_published":"2012-01-01T00:00:00Z","doi":"10.1007/978-94-007-4966-5_22"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"498","intvolume":" 5","status":"public","ddc":["576"],"title":"Predicting local adaptation in fragmented plant populations: Implications for restoration genetics","pubrep_id":"942","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2018-942-v1+1_Pickup_et_al-2012-Evolutionary_Applications.pdf","creator":"system","file_size":396136,"content_type":"application/pdf","file_id":"4821","relation":"main_file","checksum":"233007138606aca5a2f75f7ae1742f43","date_updated":"2020-07-14T12:46:35Z","date_created":"2018-12-12T10:10:33Z"}],"type":"journal_article","issue":"8","abstract":[{"lang":"eng","text":"Understanding patterns and correlates of local adaptation in heterogeneous landscapes can provide important information in the selection of appropriate seed sources for restoration. We assessed the extent of local adaptation of fitness components in 12 population pairs of the perennial herb Rutidosis leptorrhynchoides (Asteraceae) and examined whether spatial scale (0.7-600 km), environmental distance, quantitative (QST) and neutral (FST) genetic differentiation, and size of the local and foreign populations could predict patterns of adaptive differentiation. Local adaptation varied among populations and fitness components. Including all population pairs, local adaptation was observed for seedling survival, but not for biomass, while foreign genotype advantage was observed for reproduction (number of inflorescences). Among population pairs, local adaptation increased with QST and local population size for biomass. QST was associated with environmental distance, suggesting ecological selection for phenotypic divergence. However, low FST and variation in population structure in small populations demonstrates the interaction of gene flow and drift in constraining local adaptation in R. leptorrhynchoides. Our study indicates that for species in heterogeneous landscapes, collecting seed from large populations from similar environments to candidate sites is likely to provide the most appropriate seed sources for restoration."}],"citation":{"short":"M. Pickup, D. Field, D. Rowell, A. Young, Evolutionary Applications 5 (2012) 913–924.","mla":"Pickup, Melinda, et al. “Predicting Local Adaptation in Fragmented Plant Populations: Implications for Restoration Genetics.” Evolutionary Applications, vol. 5, no. 8, Wiley-Blackwell, 2012, pp. 913–24, doi:10.1111/j.1752-4571.2012.00284.x.","chicago":"Pickup, Melinda, David Field, David Rowell, and Andrew Young. “Predicting Local Adaptation in Fragmented Plant Populations: Implications for Restoration Genetics.” Evolutionary Applications. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1752-4571.2012.00284.x.","ama":"Pickup M, Field D, Rowell D, Young A. Predicting local adaptation in fragmented plant populations: Implications for restoration genetics. Evolutionary Applications. 2012;5(8):913-924. doi:10.1111/j.1752-4571.2012.00284.x","apa":"Pickup, M., Field, D., Rowell, D., & Young, A. (2012). Predicting local adaptation in fragmented plant populations: Implications for restoration genetics. Evolutionary Applications. Wiley-Blackwell. https://doi.org/10.1111/j.1752-4571.2012.00284.x","ieee":"M. Pickup, D. Field, D. Rowell, and A. Young, “Predicting local adaptation in fragmented plant populations: Implications for restoration genetics,” Evolutionary Applications, vol. 5, no. 8. Wiley-Blackwell, pp. 913–924, 2012.","ista":"Pickup M, Field D, Rowell D, Young A. 2012. Predicting local adaptation in fragmented plant populations: Implications for restoration genetics. Evolutionary Applications. 5(8), 913–924."},"publication":"Evolutionary Applications","page":"913 - 924","date_published":"2012-12-01T00:00:00Z","has_accepted_license":"1","day":"01","acknowledgement":"We thank Graham Pickup, David Steer, Linda Broadhurst, Lan Li and Carole Elliott for technical assistance. The New\r\nSouth Wales Department of Environment and Climate Change, ACT Parks, Conservation and Lands and the\r\nDepartment of Sustainability and Environment in Victoria provided permits for seed and soil collection. We thank\r\nSpencer C. H. Barrett for comments that improved the quality of the manuscript.\r\n","year":"2012","publisher":"Wiley-Blackwell","department":[{"_id":"NiBa"}],"publication_status":"published","author":[{"last_name":"Pickup","first_name":"Melinda","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","full_name":"Pickup, Melinda"},{"orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David","full_name":"Field, David"},{"full_name":"Rowell, David","first_name":"David","last_name":"Rowell"},{"last_name":"Young","first_name":"Andrew","full_name":"Young, Andrew"}],"volume":5,"date_created":"2018-12-11T11:46:48Z","date_updated":"2021-01-12T08:01:06Z","publist_id":"7322","file_date_updated":"2020-07-14T12:46:35Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"quality_controlled":"1","doi":"10.1111/j.1752-4571.2012.00284.x","language":[{"iso":"eng"}],"month":"12"},{"type":"research_data_reference","abstract":[{"text":"We propose a two-step procedure for estimating multiple migration rates in an approximate Bayesian computation (ABC) framework, accounting for global nuisance parameters. The approach is not limited to migration, but generally of interest for inference problems with multiple parameters and a modular structure (e.g. independent sets of demes or loci). We condition on a known, but complex demographic model of a spatially subdivided population, motivated by the reintroduction of Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters ancestral mutation rate and male mating skew have been estimated for the whole population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step, we estimate in this study the migration rates independently for clusters of demes putatively connected by migration. For large clusters (many migration rates), ABC faces the problem of too many summary statistics. We therefore assess by simulation if estimation per pair of demes is a valid alternative. We find that the trade-off between reduced dimensionality for the pairwise estimation on the one hand and lower accuracy due to the assumption of pairwise independence on the other depends on the number of migration rates to be inferred: the accuracy of the pairwise approach increases with the number of parameters, relative to the joint estimation approach. To distinguish between low and zero migration, we perform ABC-type model comparison between a model with migration and one without. Applying the approach to microsatellite data from Alpine ibex, we find no evidence for substantial gene flow via migration, except for one pair of demes in one direction.","lang":"eng"}],"title":"Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates","status":"public","publisher":"Dryad","department":[{"_id":"NiBa"}],"_id":"9758","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2012","date_created":"2021-07-30T12:36:39Z","date_updated":"2023-02-23T11:05:19Z","oa_version":"Published Version","author":[{"full_name":"Aeschbacher, Simon","id":"2D35326E-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Aeschbacher"},{"last_name":"Futschik","first_name":"Andreas","full_name":"Futschik, Andreas"},{"full_name":"Beaumont, Mark","last_name":"Beaumont","first_name":"Mark"}],"related_material":{"record":[{"id":"2944","relation":"used_in_publication","status":"public"}]},"day":"14","month":"11","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.5061/dryad.274b1","open_access":"1"}],"oa":1,"citation":{"ama":"Aeschbacher S, Futschik A, Beaumont M. Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. 2012. doi:10.5061/dryad.274b1","ieee":"S. Aeschbacher, A. Futschik, and M. Beaumont, “Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates.” Dryad, 2012.","apa":"Aeschbacher, S., Futschik, A., & Beaumont, M. (2012). Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. Dryad. https://doi.org/10.5061/dryad.274b1","ista":"Aeschbacher S, Futschik A, Beaumont M. 2012. Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates, Dryad, 10.5061/dryad.274b1.","short":"S. Aeschbacher, A. Futschik, M. Beaumont, (2012).","mla":"Aeschbacher, Simon, et al. Data from: Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates. Dryad, 2012, doi:10.5061/dryad.274b1.","chicago":"Aeschbacher, Simon, Andreas Futschik, and Mark Beaumont. “Data from: Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates.” Dryad, 2012. https://doi.org/10.5061/dryad.274b1."},"doi":"10.5061/dryad.274b1","date_published":"2012-11-14T00:00:00Z"},{"author":[{"full_name":"Lohse, Konrad","first_name":"Konrad","last_name":"Lohse"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"},{"first_name":"George","last_name":"Melika","full_name":"Melika, George"},{"full_name":"Stone, Graham","first_name":"Graham","last_name":"Stone"}],"related_material":{"record":[{"id":"13075","status":"public","relation":"research_data"}]},"date_created":"2018-12-11T12:00:36Z","date_updated":"2023-05-30T13:07:47Z","volume":21,"acknowledgement":"This work was supported by funding from the UK Natural Environment Research Council to KL (NE/I020288/1) and GS (NE/H000038/1, NE/E014453/1, NER/B/504406/1, NER/B/S2003/00856) and a grant from the European Research Council (250152) to NB.\r\nWe thank Majide Tavakoli, Juli Pujade-Villar and Pablo-Fuentes Utrilla for contributing specimens. Mike Hickerson and three anonymous reviewers gave helpful comments on earlier versions of the manuscript. ","year":"2012","publication_status":"published","publisher":"Wiley-Blackwell","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:45:57Z","ec_funded":1,"publist_id":"3746","doi":"10.1111/j.1365-294X.2012.05700.x","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"month":"09","pubrep_id":"296","oa_version":"Submitted Version","file":[{"file_name":"IST-2014-296-v1+1_4_wasps_revised3.pdf","access_level":"open_access","creator":"system","file_size":235820,"content_type":"application/pdf","file_id":"5304","relation":"main_file","date_created":"2018-12-12T10:17:47Z","date_updated":"2020-07-14T12:45:57Z","checksum":"c14ee4cb2a8ba9575bfd8a9bb7a883bb"},{"access_level":"open_access","file_name":"IST-2014-296-v1+2_4_wasps_Supporting2.pdf","creator":"system","file_size":41975,"content_type":"application/pdf","file_id":"5305","relation":"main_file","checksum":"f00afc5b887c8222014b57375b8caece","date_created":"2018-12-12T10:17:48Z","date_updated":"2020-07-14T12:45:57Z"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2968","status":"public","ddc":["570","579"],"title":"A likelihood based comparison of population histories in a parasitoid guild","intvolume":" 21","abstract":[{"text":"Little is known about the stability of trophic relationships in complex natural communities over evolutionary timescales. Here, we use sequence data from 18 nuclear loci to reconstruct and compare the intraspecific histories of major Pleistocene refugial populations in the Middle East, the Balkans and Iberia in a guild of four Chalcid parasitoids (Cecidostiba fungosa, Cecidostiba semifascia, Hobbya stenonota and Mesopolobus amaenus) all attacking Cynipid oak galls. We develop a likelihood method to numerically estimate models of divergence between three populations from multilocus data. We investigate the power of this framework on simulated data, and-using triplet alignments of intronic loci-quantify the support for all possible divergence relationships between refugial populations in the four parasitoids. Although an East to West order of population divergence has highest support in all but one species, we cannot rule out alternative population tree topologies. Comparing the estimated times of population splits between species, we find that one species, M. amaenus, has a significantly older history than the rest of the guild and must have arrived in central Europe at least one glacial cycle prior to other guild members. This suggests that although all four species may share a common origin in the East, they expanded westwards into Europe at different times. © 2012 Blackwell Publishing Ltd.","lang":"eng"}],"issue":"18","type":"journal_article","date_published":"2012-09-01T00:00:00Z","publication":"Molecular Ecology","citation":{"chicago":"Lohse, Konrad, Nicholas H Barton, George Melika, and Graham Stone. “A Likelihood Based Comparison of Population Histories in a Parasitoid Guild.” Molecular Ecology. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1365-294X.2012.05700.x.","short":"K. Lohse, N.H. Barton, G. Melika, G. Stone, Molecular Ecology 21 (2012) 4605–4617.","mla":"Lohse, Konrad, et al. “A Likelihood Based Comparison of Population Histories in a Parasitoid Guild.” Molecular Ecology, vol. 21, no. 18, Wiley-Blackwell, 2012, pp. 4605–17, doi:10.1111/j.1365-294X.2012.05700.x.","ieee":"K. Lohse, N. H. Barton, G. Melika, and G. Stone, “A likelihood based comparison of population histories in a parasitoid guild,” Molecular Ecology, vol. 21, no. 18. Wiley-Blackwell, pp. 4605–4617, 2012.","apa":"Lohse, K., Barton, N. H., Melika, G., & Stone, G. (2012). A likelihood based comparison of population histories in a parasitoid guild. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2012.05700.x","ista":"Lohse K, Barton NH, Melika G, Stone G. 2012. A likelihood based comparison of population histories in a parasitoid guild. Molecular Ecology. 21(18), 4605–4617.","ama":"Lohse K, Barton NH, Melika G, Stone G. A likelihood based comparison of population histories in a parasitoid guild. Molecular Ecology. 2012;21(18):4605-4617. doi:10.1111/j.1365-294X.2012.05700.x"},"page":"4605 - 4617","day":"01","has_accepted_license":"1","scopus_import":1},{"abstract":[{"lang":"eng","text":"Little is known about the stability of trophic relationships in complex natural communities over evolutionary timescales. Here, we use sequence data from 18 nuclear loci to reconstruct and compare the intraspecific histories of major Pleistocene refugial populations in the Middle East, the Balkans and Iberia in a guild of four Chalcid parasitoids (Cecidostiba fungosa, C. semifascia, Hobbya stenonota and Mesopolobus amaenus) all attacking Cynipid oak galls. We develop a likelihood method to numerically estimate models of divergence between three populations from multilocus data. We investigate the power of this framework on simulated data, and - using triplet alignments of intronic loci - quantify the support for all possible divergence relationships between refugial populations in the four parasitoids. Although an East to West order of population divergence has highest support in all but one species, we cannot rule out alternative population tree topologies. Comparing the estimated times of population splits between species, we find that one species, M. amaenus, has a significantly older history than the rest of the guild and must have arrived in central Europe at least one glacial cycle prior to other guild members. This suggests that although all four species may share a common origin in the East, they expanded westwards into Europe at different times."}],"type":"research_data_reference","author":[{"first_name":"Konrad","last_name":"Lohse","full_name":"Lohse, Konrad"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"},{"full_name":"Stone, Graham","first_name":"Graham","last_name":"Stone"},{"full_name":"Melika, George","first_name":"George","last_name":"Melika"}],"related_material":{"record":[{"id":"2968","relation":"used_in_publication","status":"public"}]},"date_created":"2023-05-23T17:01:02Z","date_updated":"2023-05-30T13:07:48Z","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13075","year":"2012","status":"public","ddc":["570"],"title":"Data from: A likelihood-based comparison of population histories in a parasitoid guild","department":[{"_id":"NiBa"}],"publisher":"Dryad","day":"08","month":"06","article_processing_charge":"No","date_published":"2012-06-08T00:00:00Z","doi":"10.5061/DRYAD.0G0FS","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"mla":"Lohse, Konrad, et al. Data from: A Likelihood-Based Comparison of Population Histories in a Parasitoid Guild. Dryad, 2012, doi:10.5061/DRYAD.0G0FS.","short":"K. Lohse, N.H. Barton, G. Stone, G. Melika, (2012).","chicago":"Lohse, Konrad, Nicholas H Barton, Graham Stone, and George Melika. “Data from: A Likelihood-Based Comparison of Population Histories in a Parasitoid Guild.” Dryad, 2012. https://doi.org/10.5061/DRYAD.0G0FS.","ama":"Lohse K, Barton NH, Stone G, Melika G. Data from: A likelihood-based comparison of population histories in a parasitoid guild. 2012. doi:10.5061/DRYAD.0G0FS","ista":"Lohse K, Barton NH, Stone G, Melika G. 2012. Data from: A likelihood-based comparison of population histories in a parasitoid guild, Dryad, 10.5061/DRYAD.0G0FS.","apa":"Lohse, K., Barton, N. H., Stone, G., & Melika, G. (2012). Data from: A likelihood-based comparison of population histories in a parasitoid guild. Dryad. https://doi.org/10.5061/DRYAD.0G0FS","ieee":"K. Lohse, N. H. Barton, G. Stone, and G. Melika, “Data from: A likelihood-based comparison of population histories in a parasitoid guild.” Dryad, 2012."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.0g0fs"}]},{"type":"journal_article","issue":"7339","abstract":[{"text":"Nowak et al.1 argue that inclusive fitness theory has been of little value in explaining the natural world, and that it has led to negligible progress in explaining the evolution of eusociality. However, we believe that their arguments are based upon a misunderstanding of evolutionary theory and a misrepresentation of the empirical literature. We will focus our comments on three general issues.","lang":"eng"}],"intvolume":" 471","status":"public","title":"Inclusive fitness theory and eusociality","_id":"3372","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","scopus_import":1,"day":"23","page":"E1 - E4","citation":{"ista":"Abbot P et al. 2011. Inclusive fitness theory and eusociality. Nature. 471(7339), E1–E4.","apa":"Abbot, P., Abe, J., Alcock, J., Alizon, S., Alpedrinha, J., Andersson, M., … Zink, A. (2011). Inclusive fitness theory and eusociality. Nature. Nature Publishing Group. https://doi.org/10.1038/nature09831","ieee":"P. Abbot et al., “Inclusive fitness theory and eusociality,” Nature, vol. 471, no. 7339. Nature Publishing Group, pp. E1–E4, 2011.","ama":"Abbot P, Abe J, Alcock J, et al. Inclusive fitness theory and eusociality. Nature. 2011;471(7339):E1-E4. doi:10.1038/nature09831","chicago":"Abbot, Patrick, Jun Abe, John Alcock, Samuel Alizon, Joao Alpedrinha, Malte Andersson, Jean Andre, et al. “Inclusive Fitness Theory and Eusociality.” Nature. Nature Publishing Group, 2011. https://doi.org/10.1038/nature09831.","mla":"Abbot, Patrick, et al. “Inclusive Fitness Theory and Eusociality.” Nature, vol. 471, no. 7339, Nature Publishing Group, 2011, pp. E1–4, doi:10.1038/nature09831.","short":"P. Abbot, J. Abe, J. Alcock, S. Alizon, J. Alpedrinha, M. Andersson, J. Andre, M. Van Baalen, F. Balloux, S. Balshine, N.H. Barton, L. Beukeboom, J. Biernaskie, T. Bilde, G. Borgia, M. Breed, S. Brown, R. Bshary, A. Buckling, N. Burley, M. Burton Chellew, M. Cant, M. Chapuisat, E. Charnov, T. Clutton Brock, A. Cockburn, B. Cole, N. Colegrave, L. Cosmides, I. Couzin, J. Coyne, S. Creel, B. Crespi, R. Curry, S. Dall, T. Day, J. Dickinson, L. Dugatkin, C. El Mouden, S. Emlen, J. Evans, R. Ferriere, J. Field, S. Foitzik, K. Foster, W. Foster, C. Fox, J. Gadau, S. Gandon, A. Gardner, M. Gardner, T. Getty, M. Goodisman, A. Grafen, R. Grosberg, C. Grozinger, P. Gouyon, D. Gwynne, P. Harvey, B. Hatchwell, J. Heinze, H. Helantera, K. Helms, K. Hill, N. Jiricny, R. Johnstone, A. Kacelnik, E.T. Kiers, H. Kokko, J. Komdeur, J. Korb, D. Kronauer, R. Kümmerli, L. Lehmann, T. Linksvayer, S. Lion, B. Lyon, J. Marshall, R. Mcelreath, Y. Michalakis, R. Michod, D. Mock, T. Monnin, R. Montgomerie, A. Moore, U. Mueller, R. Noë, S. Okasha, P. Pamilo, G. Parker, J. Pedersen, I. Pen, D. Pfennig, D. Queller, D. Rankin, S. Reece, H. Reeve, M. Reuter, G. Roberts, S. Robson, D. Roze, F. Rousset, O. Rueppell, J. Sachs, L. Santorelli, P. Schmid Hempel, M. Schwarz, T. Scott Phillips, J. Shellmann Sherman, P. Sherman, D. Shuker, J. Smith, J. Spagna, B. Strassmann, A. Suarez, L. Sundström, M. Taborsky, P. Taylor, G. Thompson, J. Tooby, N. Tsutsui, K. Tsuji, S. Turillazzi, F. Úbeda, E. Vargo, B. Voelkl, T. Wenseleers, S. West, M. West Eberhard, D. Westneat, D. Wiernasz, G. Wild, R. Wrangham, A. Young, D. Zeh, J. Zeh, A. Zink, Nature 471 (2011) E1–E4."},"publication":"Nature","date_published":"2011-03-23T00:00:00Z","publist_id":"3237","publisher":"Nature Publishing Group","department":[{"_id":"NiBa"}],"publication_status":"published","pmid":1,"year":"2011","volume":471,"date_updated":"2021-01-12T07:43:02Z","date_created":"2018-12-11T12:02:57Z","author":[{"full_name":"Abbot, Patrick","first_name":"Patrick","last_name":"Abbot"},{"first_name":"Jun","last_name":"Abe","full_name":"Abe, Jun"},{"full_name":"Alcock, John","last_name":"Alcock","first_name":"John"},{"full_name":"Alizon, Samuel","last_name":"Alizon","first_name":"Samuel"},{"full_name":"Alpedrinha, Joao","last_name":"Alpedrinha","first_name":"Joao"},{"first_name":"Malte","last_name":"Andersson","full_name":"Andersson, Malte"},{"last_name":"Andre","first_name":"Jean","full_name":"Andre, Jean"},{"full_name":"Van Baalen, Minus","first_name":"Minus","last_name":"Van Baalen"},{"last_name":"Balloux","first_name":"Francois","full_name":"Balloux, 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Edward","first_name":"Edward","last_name":"Vargo"},{"first_name":"Bernard","last_name":"Voelkl","full_name":"Voelkl, Bernard"},{"full_name":"Wenseleers, Tom","last_name":"Wenseleers","first_name":"Tom"},{"full_name":"West, Stuart","first_name":"Stuart","last_name":"West"},{"last_name":"West Eberhard","first_name":"Mary","full_name":"West Eberhard, Mary"},{"last_name":"Westneat","first_name":"David","full_name":"Westneat, David"},{"last_name":"Wiernasz","first_name":"Diane","full_name":"Wiernasz, Diane"},{"full_name":"Wild, Geoff","first_name":"Geoff","last_name":"Wild"},{"full_name":"Wrangham, Richard","last_name":"Wrangham","first_name":"Richard"},{"full_name":"Young, Andrew","last_name":"Young","first_name":"Andrew"},{"full_name":"Zeh, David","last_name":"Zeh","first_name":"David"},{"last_name":"Zeh","first_name":"Jeanne","full_name":"Zeh, Jeanne"},{"full_name":"Zink, Andrew","last_name":"Zink","first_name":"Andrew"}],"month":"03","quality_controlled":"1","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836173/","open_access":"1"}],"external_id":{"pmid":["21430721"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/nature09831"},{"date_updated":"2021-01-12T07:43:11Z","date_created":"2018-12-11T12:03:05Z","volume":189,"author":[{"last_name":"Polechova","first_name":"Jitka","orcid":"0000-0003-0951-3112","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","full_name":"Polechova, Jitka"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Genetics Society of America","year":"2011","publist_id":"3213","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1534/genetics.111.129817","quality_controlled":"1","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}],"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176109/"}],"oa":1,"month":"09","oa_version":"Submitted Version","status":"public","title":"Genetic drift widens the expected cline but narrows the expected cline width","intvolume":" 189","_id":"3394","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Random genetic drift shifts clines in space, alters their width, and distorts their shape. Such random fluctuations complicate inferences from cline width and position. Notably, the effect of genetic drift on the expected shape of the cline is opposite to the naive (but quite common) misinterpretation of classic results on the expected cline. While random drift on average broadens the overall cline in expected allele frequency, it narrows the width of any particular cline. The opposing effects arise because locally, drift drives alleles to fixation—but fluctuations in position widen the expected cline. The effect of genetic drift can be predicted from standardized variance in allele frequencies, averaged across the habitat: 〈F〉. A cline maintained by spatially varying selection (step change) is expected to be narrower by a factor of relative to the cline in the absence of drift. The expected cline is broader by the inverse of this factor. In a tension zone maintained by underdominance, the expected cline width is narrower by about 1 – 〈F〉relative to the width in the absence of drift. Individual clines can differ substantially from the expectation, and we give quantitative predictions for the variance in cline position and width. The predictions apply to clines in almost one-dimensional circumstances such as hybrid zones in rivers, deep valleys, or along a coast line and give a guide to what patterns to expect in two dimensions."}],"issue":"1","type":"journal_article","date_published":"2011-09-01T00:00:00Z","page":"227 - 235","publication":"Genetics","citation":{"ama":"Polechova J, Barton NH. Genetic drift widens the expected cline but narrows the expected cline width. Genetics. 2011;189(1):227-235. doi:10.1534/genetics.111.129817","ista":"Polechova J, Barton NH. 2011. Genetic drift widens the expected cline but narrows the expected cline width. Genetics. 189(1), 227–235.","ieee":"J. Polechova and N. H. Barton, “Genetic drift widens the expected cline but narrows the expected cline width,” Genetics, vol. 189, no. 1. Genetics Society of America, pp. 227–235, 2011.","apa":"Polechova, J., & Barton, N. H. (2011). Genetic drift widens the expected cline but narrows the expected cline width. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.111.129817","mla":"Polechova, Jitka, and Nicholas H. Barton. “Genetic Drift Widens the Expected Cline but Narrows the Expected Cline Width.” Genetics, vol. 189, no. 1, Genetics Society of America, 2011, pp. 227–35, doi:10.1534/genetics.111.129817.","short":"J. Polechova, N.H. Barton, Genetics 189 (2011) 227–235.","chicago":"Polechova, Jitka, and Nicholas H Barton. “Genetic Drift Widens the Expected Cline but Narrows the Expected Cline Width.” Genetics. Genetics Society of America, 2011. https://doi.org/10.1534/genetics.111.129817."},"day":"01","scopus_import":1},{"month":"08","project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176105/","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1534/genetics.111.127555","publist_id":"3217","ec_funded":1,"department":[{"_id":"NiBa"}],"publisher":"Genetics Society of America","publication_status":"published","year":"2011","volume":188,"date_created":"2018-12-11T12:03:04Z","date_updated":"2021-01-12T07:43:09Z","author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"full_name":"Etheridge, Alison","last_name":"Etheridge","first_name":"Alison"}],"scopus_import":1,"day":"01","page":"953 - 973","citation":{"mla":"Barton, Nicholas H., and Alison Etheridge. “The Relation between Reproductive Value and Genetic Contribution.” Genetics, vol. 188, no. 4, Genetics Society of America, 2011, pp. 953–73, doi:10.1534/genetics.111.127555.","short":"N.H. Barton, A. Etheridge, Genetics 188 (2011) 953–973.","chicago":"Barton, Nicholas H, and Alison Etheridge. “The Relation between Reproductive Value and Genetic Contribution.” Genetics. Genetics Society of America, 2011. https://doi.org/10.1534/genetics.111.127555.","ama":"Barton NH, Etheridge A. The relation between reproductive value and genetic contribution. Genetics. 2011;188(4):953-973. doi:10.1534/genetics.111.127555","ista":"Barton NH, Etheridge A. 2011. The relation between reproductive value and genetic contribution. Genetics. 188(4), 953–973.","ieee":"N. H. Barton and A. Etheridge, “The relation between reproductive value and genetic contribution,” Genetics, vol. 188, no. 4. Genetics Society of America, pp. 953–973, 2011.","apa":"Barton, N. H., & Etheridge, A. (2011). The relation between reproductive value and genetic contribution. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.111.127555"},"publication":"Genetics","date_published":"2011-08-01T00:00:00Z","type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"What determines the genetic contribution that an individual makes to future generations? With biparental reproduction, each individual leaves a 'pedigree' of descendants, determined by the biparental relationships in the population. The pedigree of an individual constrains the lines of descent of each of its genes. An individual's reproductive value is the expected number of copies of each of its genes that is passed on to distant generations conditional on its pedigree. For the simplest model of biparental reproduction analogous to the Wright-Fisher model, an individual's reproductive value is determined within ~10 generations, independent of population size. Partial selfing and subdivision do not greatly slow this convergence. Our central result is that the probability that a gene will survive is proportional to the reproductive value of the individual that carries it, and that conditional on survival, after a few tens of generations, the distribution of the number of surviving copies is the same for all individuals, whatever their reproductive value. These results can be generalized to the joint distribution of surviving blocks of ancestral genome. Selection on unlinked loci in the genetic background may greatly increase the variance in reproductive value, but the above results nevertheless still hold. The almost linear relationship between survival probability and reproductive value also holds for weakly favored alleles. Thus, the influence of the complex pedigree of descendants on an individual's genetic contribution to the population can be summarized through a single number: its reproductive value."}],"intvolume":" 188","title":"The relation between reproductive value and genetic contribution","status":"public","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"3390","oa_version":"Submitted Version"},{"scopus_import":1,"day":"01","citation":{"mla":"de Vladar, Harold, and Nicholas H. Barton. “The Contribution of Statistical Physics to Evolutionary Biology.” Trends in Ecology and Evolution, vol. 26, no. 8, Cell Press, 2011, pp. 424–32, doi:10.1016/j.tree.2011.04.002.","short":"H. de Vladar, N.H. Barton, Trends in Ecology and Evolution 26 (2011) 424–432.","chicago":"Vladar, Harold de, and Nicholas H Barton. “The Contribution of Statistical Physics to Evolutionary Biology.” Trends in Ecology and Evolution. Cell Press, 2011. https://doi.org/10.1016/j.tree.2011.04.002.","ama":"de Vladar H, Barton NH. The contribution of statistical physics to evolutionary biology. Trends in Ecology and Evolution. 2011;26(8):424-432. doi:10.1016/j.tree.2011.04.002","ista":"de Vladar H, Barton NH. 2011. The contribution of statistical physics to evolutionary biology. Trends in Ecology and Evolution. 26(8), 424–432.","ieee":"H. de Vladar and N. H. Barton, “The contribution of statistical physics to evolutionary biology,” Trends in Ecology and Evolution, vol. 26, no. 8. Cell Press, pp. 424–432, 2011.","apa":"de Vladar, H., & Barton, N. H. (2011). The contribution of statistical physics to evolutionary biology. Trends in Ecology and Evolution. Cell Press. https://doi.org/10.1016/j.tree.2011.04.002"},"publication":"Trends in Ecology and Evolution","page":"424 - 432","date_published":"2011-08-01T00:00:00Z","type":"journal_article","issue":"8","abstract":[{"text":"Evolutionary biology shares many concepts with statistical physics: both deal with populations, whether of molecules or organisms, and both seek to simplify evolution in very many dimensions. Often, methodologies have undergone parallel and independent development, as with stochastic methods in population genetics. Here, we discuss aspects of population genetics that have embraced methods from physics: non-equilibrium statistical mechanics, travelling waves and Monte-Carlo methods, among others, have been used to study polygenic evolution, rates of adaptation and range expansions. These applications indicate that evolutionary biology can further benefit from interactions with other areas of statistical physics; for example, by following the distribution of paths taken by a population through time","lang":"eng"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"3391","intvolume":" 26","title":"The contribution of statistical physics to evolutionary biology","status":"public","oa_version":"Submitted Version","month":"08","main_file_link":[{"url":"http://arxiv.org/abs/1104.2854","open_access":"1"}],"oa":1,"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"quality_controlled":"1","doi":"10.1016/j.tree.2011.04.002","language":[{"iso":"eng"}],"publist_id":"3216","ec_funded":1,"year":"2011","publisher":"Cell Press","department":[{"_id":"NiBa"}],"publication_status":"published","author":[{"full_name":"de Vladar, Harold","id":"2A181218-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5985-7653","first_name":"Harold","last_name":"de Vladar"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"volume":26,"date_created":"2018-12-11T12:03:04Z","date_updated":"2021-01-12T07:43:10Z"},{"month":"03","main_file_link":[{"open_access":"1","url":"https://digital.csic.es/bitstream/10261/32783/3/Palero_et_al_2011.pdf"}],"oa":1,"quality_controlled":"1","doi":"10.1017/S0025315410000287","language":[{"iso":"eng"}],"publist_id":"2443","year":"2011","department":[{"_id":"NiBa"}],"publisher":"Cambridge University Press","publication_status":"published","author":[{"first_name":"Ferran","last_name":"Palero","id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0343-8329","full_name":"Palero, Ferran"},{"last_name":"Guerao","first_name":"Guillermo","full_name":"Guerao, Guillermo"},{"full_name":"Clark, Paul","last_name":"Clark","first_name":"Paul"},{"full_name":"Abello, Pere","first_name":"Pere","last_name":"Abello"}],"volume":91,"date_updated":"2021-01-12T07:52:10Z","date_created":"2018-12-11T12:05:09Z","scopus_import":1,"article_processing_charge":"No","day":"01","citation":{"apa":"Palero, F., Guerao, G., Clark, P., & Abello, P. (2011). Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description. Journal of the Marine Biological Association of the United Kingdom. Cambridge University Press. https://doi.org/10.1017/S0025315410000287","ieee":"F. Palero, G. Guerao, P. Clark, and P. Abello, “Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description,” Journal of the Marine Biological Association of the United Kingdom, vol. 91, no. 2. Cambridge University Press, pp. 485–492, 2011.","ista":"Palero F, Guerao G, Clark P, Abello P. 2011. Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description. Journal of the Marine Biological Association of the United Kingdom. 91(2), 485–492.","ama":"Palero F, Guerao G, Clark P, Abello P. Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description. Journal of the Marine Biological Association of the United Kingdom. 2011;91(2):485-492. doi:10.1017/S0025315410000287","chicago":"Palero, Ferran, Guillermo Guerao, Paul Clark, and Pere Abello. “Scyllarus Arctus (Crustacea: Decapoda: Scyllaridae) Final Stage Phyllosoma Identified by DNA Analysis, with Morphological Description.” Journal of the Marine Biological Association of the United Kingdom. Cambridge University Press, 2011. https://doi.org/10.1017/S0025315410000287.","short":"F. Palero, G. Guerao, P. Clark, P. Abello, Journal of the Marine Biological Association of the United Kingdom 91 (2011) 485–492.","mla":"Palero, Ferran, et al. “Scyllarus Arctus (Crustacea: Decapoda: Scyllaridae) Final Stage Phyllosoma Identified by DNA Analysis, with Morphological Description.” Journal of the Marine Biological Association of the United Kingdom, vol. 91, no. 2, Cambridge University Press, 2011, pp. 485–92, doi:10.1017/S0025315410000287."},"publication":"Journal of the Marine Biological Association of the United Kingdom","page":"485 - 492","article_type":"original","date_published":"2011-03-01T00:00:00Z","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"Advanced stages of Scyllarus phyllosoma larvae were collected by demersal trawling during fishery research surveys in the western Mediterranean Sea in 2003–2005. Nucleotide sequence analysis of the mitochondrial 16S rDNA gene allowed the final-stage phyllosoma of Scyllarus arctus to be identified among these larvae. Its morphology is described and illustrated. This constitutes the second complete description of a Scyllaridae phyllosoma with its specific identity being validated by molecular techniques (the first was S. pygmaeus). These results also solved a long lasting taxonomic anomaly of several species assigned to the ancient genus Phyllosoma Leach, 1814. Detailed examination indicated that the final-stage phyllosoma of S. arctus shows closer affinities with the American scyllarid Scyllarus depressus or with the Australian Scyllarus sp. b (sensu Phillips et al., 1981) than to its sympatric species S. pygmaeus."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3784","intvolume":" 91","title":"Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description","status":"public","oa_version":"Published Version"},{"type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"Analysis of genomic data requires an efficient way to calculate likelihoods across very large numbers of loci. We describe a general method for finding the distribution of genealogies: we allow migration between demes, splitting of demes [as in the isolation-with-migration (IM) model], and recombination between linked loci. These processes are described by a set of linear recursions for the generating function of branch lengths. Under the infinite-sites model, the probability of any configuration of mutations can be found by differentiating this generating function. Such calculations are feasible for small numbers of sampled genomes: as an example, we show how the generating function can be derived explicitly for three genes under the two-deme IM model. This derivation is done automatically, using Mathematica. Given data from a large number of unlinked and nonrecombining blocks of sequence, these results can be used to find maximum-likelihood estimates of model parameters by tabulating the probabilities of all relevant mutational configurations and then multiplying across loci. The feasibility of the method is demonstrated by applying it to simulated data and to a data set previously analyzed by Wang and Hey (2010) consisting of 26,141 loci sampled from Drosophila simulans and D. melanogaster. Our results suggest that such likelihood calculations are scalable to genomic data as long as the numbers of sampled individuals and mutations per sequence block are small."}],"intvolume":" 189","title":"A general method for calculating likelihoods under the coalescent process","status":"public","_id":"3290","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","scopus_import":1,"day":"01","page":"977 - 987","citation":{"ama":"Lohse K, Harrison R, Barton NH. A general method for calculating likelihoods under the coalescent process. Genetics. 2011;189(3):977-987. doi:10.1534/genetics.111.129569","apa":"Lohse, K., Harrison, R., & Barton, N. H. (2011). A general method for calculating likelihoods under the coalescent process. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.111.129569","ieee":"K. Lohse, R. Harrison, and N. H. Barton, “A general method for calculating likelihoods under the coalescent process,” Genetics, vol. 189, no. 3. Genetics Society of America, pp. 977–987, 2011.","ista":"Lohse K, Harrison R, Barton NH. 2011. A general method for calculating likelihoods under the coalescent process. Genetics. 189(3), 977–987.","short":"K. Lohse, R. Harrison, N.H. Barton, Genetics 189 (2011) 977–987.","mla":"Lohse, Konrad, et al. “A General Method for Calculating Likelihoods under the Coalescent Process.” Genetics, vol. 189, no. 3, Genetics Society of America, 2011, pp. 977–87, doi:10.1534/genetics.111.129569.","chicago":"Lohse, Konrad, Richard Harrison, and Nicholas H Barton. “A General Method for Calculating Likelihoods under the Coalescent Process.” Genetics. Genetics Society of America, 2011. https://doi.org/10.1534/genetics.111.129569."},"publication":"Genetics","date_published":"2011-11-01T00:00:00Z","publist_id":"3355","ec_funded":1,"department":[{"_id":"NiBa"}],"publisher":"Genetics Society of America","publication_status":"published","year":"2011","volume":189,"date_updated":"2021-01-12T07:42:26Z","date_created":"2018-12-11T12:02:29Z","author":[{"full_name":"Lohse, Konrad","last_name":"Lohse","first_name":"Konrad"},{"first_name":"Richard","last_name":"Harrison","full_name":"Harrison, Richard"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"month":"11","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3213358/"}],"language":[{"iso":"eng"}],"doi":"10.1534/genetics.111.129569"},{"oa_version":"Published Version","intvolume":" 93","status":"public","title":"Mapping Mendelian traits in asexual progeny using changes in marker allele frequency","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3380","issue":"3","abstract":[{"text":"Linkage between markers and genes that affect a phenotype of interest may be determined by examining differences in marker allele frequency in the extreme progeny of a cross between two inbred lines. This strategy is usually employed when pooling is used to reduce genotyping costs. When the cross progeny are asexual, the extreme progeny may be selected by multiple generations of asexual reproduction and selection. We analyse this method of measuring phenotype in asexual progeny and examine the changes in marker allele frequency due to selection over many generations. Stochasticity in marker frequency in the selected population arises due to the finite initial population size. We derive the distribution of marker frequency as a result of selection at a single major locus, and show that in order to avoid spurious changes in marker allele frequency in the selected population, the initial population size should be in the low to mid hundreds.","lang":"eng"}],"type":"journal_article","date_published":"2011-05-18T00:00:00Z","page":"221 - 232","article_type":"original","citation":{"ista":"Logeswaran S, Barton NH. 2011. Mapping Mendelian traits in asexual progeny using changes in marker allele frequency. Genetical Research. 93(3), 221–232.","ieee":"S. Logeswaran and N. H. Barton, “Mapping Mendelian traits in asexual progeny using changes in marker allele frequency,” Genetical Research, vol. 93, no. 3. Cambridge University Press, pp. 221–232, 2011.","apa":"Logeswaran, S., & Barton, N. H. (2011). Mapping Mendelian traits in asexual progeny using changes in marker allele frequency. Genetical Research. Cambridge University Press. https://doi.org/10.1017/S0016672311000115","ama":"Logeswaran S, Barton NH. Mapping Mendelian traits in asexual progeny using changes in marker allele frequency. Genetical Research. 2011;93(3):221-232. doi:10.1017/S0016672311000115","chicago":"Logeswaran, Sayanthan, and Nicholas H Barton. “Mapping Mendelian Traits in Asexual Progeny Using Changes in Marker Allele Frequency.” Genetical Research. Cambridge University Press, 2011. https://doi.org/10.1017/S0016672311000115.","mla":"Logeswaran, Sayanthan, and Nicholas H. Barton. “Mapping Mendelian Traits in Asexual Progeny Using Changes in Marker Allele Frequency.” Genetical Research, vol. 93, no. 3, Cambridge University Press, 2011, pp. 221–32, doi:10.1017/S0016672311000115.","short":"S. Logeswaran, N.H. Barton, Genetical Research 93 (2011) 221–232."},"publication":"Genetical Research","article_processing_charge":"No","day":"18","scopus_import":1,"volume":93,"date_created":"2018-12-11T12:03:00Z","date_updated":"2021-01-12T07:43:05Z","author":[{"full_name":"Logeswaran, Sayanthan","first_name":"Sayanthan","last_name":"Logeswaran"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"department":[{"_id":"NiBa"}],"publisher":"Cambridge University Press","publication_status":"published","year":"2011","publist_id":"3227","language":[{"iso":"eng"}],"doi":"10.1017/S0016672311000115","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.pure.ed.ac.uk/ws/files/8144621/GR_2011_Barton.pdf"}],"month":"05"},{"type":"journal_article","issue":"2","publist_id":"2449","_id":"3778","year":"2011","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","pmid":1,"status":"public","publication_status":"published","title":"Estimating linkage disequilibria","intvolume":" 106","department":[{"_id":"NiBa"}],"publisher":"Nature Publishing Group","author":[{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"date_updated":"2021-01-12T07:52:08Z","date_created":"2018-12-11T12:05:07Z","volume":106,"oa_version":"Submitted Version","scopus_import":1,"month":"02","day":"01","publication":"Heredity","external_id":{"pmid":["20502479"]},"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3183869/","open_access":"1"}],"oa":1,"citation":{"apa":"Barton, N. H. (2011). Estimating linkage disequilibria. Heredity. Nature Publishing Group. https://doi.org/10.1038/hdy.2010.67","ieee":"N. H. Barton, “Estimating linkage disequilibria,” Heredity, vol. 106, no. 2. Nature Publishing Group, pp. 205–206, 2011.","ista":"Barton NH. 2011. Estimating linkage disequilibria. Heredity. 106(2), 205–206.","ama":"Barton NH. Estimating linkage disequilibria. Heredity. 2011;106(2):205-206. doi:10.1038/hdy.2010.67","chicago":"Barton, Nicholas H. “Estimating Linkage Disequilibria.” Heredity. Nature Publishing Group, 2011. https://doi.org/10.1038/hdy.2010.67.","short":"N.H. Barton, Heredity 106 (2011) 205–206.","mla":"Barton, Nicholas H. “Estimating Linkage Disequilibria.” Heredity, vol. 106, no. 2, Nature Publishing Group, 2011, pp. 205–06, doi:10.1038/hdy.2010.67."},"page":"205 - 206","date_published":"2011-02-01T00:00:00Z","doi":"10.1038/hdy.2010.67","language":[{"iso":"eng"}]},{"publist_id":"3212","related_material":{"record":[{"id":"9762","relation":"research_data","status":"public"}]},"author":[{"id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0343-8329","first_name":"Ferran","last_name":"Palero","full_name":"Palero, Ferran"},{"last_name":"Abello","first_name":"Pere","full_name":"Abello, Pere"},{"first_name":"Enrique","last_name":"Macpherson","full_name":"Macpherson, Enrique"},{"full_name":"Beaumont, Mark","last_name":"Beaumont","first_name":"Mark"},{"full_name":"Pascual, Marta","last_name":"Pascual","first_name":"Marta"}],"volume":104,"date_created":"2018-12-11T12:03:06Z","date_updated":"2023-02-23T14:07:31Z","acknowledgement":"This work was supported by a pre-doctoral fellowship awarded by the Autonomous Government of Catalonia to F.P. (2006FIC-00082). Research was funded by projects FBBVA-BIOCON 08-187/09, CGL2006-13423, and CTM2007-66635. The authors are part of the research group 2009SGR-636, 2009SGR-655, and 2009SGR-1364 of the Generalitat de Catalunya. F.P. acknowledges EU-Synthesys grant (GB-TAF-4474).","year":"2011","publisher":"Wiley-Blackwell","department":[{"_id":"NiBa"}],"publication_status":"published","month":"09","doi":"10.1111/j.1095-8312.2011.01728.x","language":[{"iso":"eng"}],"quality_controlled":"1","issue":"2","abstract":[{"lang":"eng","text":"Defining population structure and genetic diversity levels is of the utmost importance for developing efficient conservation strategies. Overfishing has caused mean annual catches of the European spiny lobster (Palinurus elephas) to decrease alarmingly along its distribution area. In this context, there is a need for comprehensive studies aiming to evaluate the genetic health of the exploited populations. The present study is based on a set of ten nuclear markers amplified in 331 individuals from ten different localities covering most of P. elephas distribution area. Samples from Atlantic and Mediterranean basins showed small but significant differences, indicating that P. elephas populations do not behave as a single panmictic unit but form two partially-overlapping groups. Despite intense overfishing, our dataset did not recover a recent bottleneck signal, and instead showed a large and stable historical effective size. This result could be accounted for by specific life-history traits (reproduction and longevity) and the limitations of molecular markers in covering recent timescales for nontemporal samples. The findings of the present study emphasize the need to integrate information on effective population sizes and life-history parameters when evaluating population connectivity levels from genetic data."}],"type":"journal_article","oa_version":"None","_id":"3395","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","intvolume":" 104","status":"public","title":"Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster Palinurus elephas","article_processing_charge":"No","day":"14","scopus_import":"1","date_published":"2011-09-14T00:00:00Z","citation":{"ista":"Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. 2011. Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster Palinurus elephas. Biological Journal of the Linnean Society. 104(2), 407–418.","ieee":"F. Palero, P. Abello, E. Macpherson, M. Beaumont, and M. Pascual, “Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster Palinurus elephas,” Biological Journal of the Linnean Society, vol. 104, no. 2. Wiley-Blackwell, pp. 407–418, 2011.","apa":"Palero, F., Abello, P., Macpherson, E., Beaumont, M., & Pascual, M. (2011). Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster Palinurus elephas. Biological Journal of the Linnean Society. Wiley-Blackwell. https://doi.org/10.1111/j.1095-8312.2011.01728.x","ama":"Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster Palinurus elephas. Biological Journal of the Linnean Society. 2011;104(2):407-418. doi:10.1111/j.1095-8312.2011.01728.x","chicago":"Palero, Ferran, Pere Abello, Enrique Macpherson, Mark Beaumont, and Marta Pascual. “Effect of Oceanographic Barriers and Overfishing on the Population Genetic Structure of the European Spiny Lobster Palinurus Elephas.” Biological Journal of the Linnean Society. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1095-8312.2011.01728.x.","mla":"Palero, Ferran, et al. “Effect of Oceanographic Barriers and Overfishing on the Population Genetic Structure of the European Spiny Lobster Palinurus Elephas.” Biological Journal of the Linnean Society, vol. 104, no. 2, Wiley-Blackwell, 2011, pp. 407–18, doi:10.1111/j.1095-8312.2011.01728.x.","short":"F. Palero, P. Abello, E. Macpherson, M. Beaumont, M. Pascual, Biological Journal of the Linnean Society 104 (2011) 407–418."},"publication":"Biological Journal of the Linnean Society","page":"407 - 418"},{"oa_version":"Published Version","date_created":"2021-08-02T07:11:19Z","date_updated":"2023-02-23T11:25:25Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"3395"}]},"author":[{"full_name":"Palero, Ferran","first_name":"Ferran","last_name":"Palero","id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0343-8329"},{"full_name":"Abello, Pere","last_name":"Abello","first_name":"Pere"},{"last_name":"Macpherson","first_name":"Enrique","full_name":"Macpherson, Enrique"},{"full_name":"Beaumont, Mark","last_name":"Beaumont","first_name":"Mark"},{"last_name":"Pascual","first_name":"Marta","full_name":"Pascual, Marta"}],"publisher":"IST Austria","department":[{"_id":"NiBa"}],"title":"Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas)","status":"public","_id":"9762","year":"2011","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"lang":"eng","text":"Defining population structure and genetic diversity levels is of the utmost importance for developing efficient conservation strategies. Overfishing has caused mean annual catches of the European spiny lobster (Palinurus elephas) to decrease alarmingly along its distribution area. In this context, there is a need for comprehensive studies to evaluate the genetic health of the exploited populations. The present work is based on a set of 10 nuclear markers amplified in 331 individuals from 10 different localities covering most of P. elephas distribution area. Samples from Atlantic and Mediterranean basins showed small but significant differences, indicating that P. elephas populations do not behave as a single panmictic unit but form two partially-overlapping groups. Despite intense overfishing, our dataset did not recover a recent bottleneck signal, and showed a large and stable historical effective size instead. This result could be accounted for by specific life history traits (reproduction and longevity) and the limitations of molecular markers in covering very recent timescales for non temporal samples. Our study emphasizes the necessity of integrating information on effective population sizes and life history parameters when evaluating population connectivity levels from genetic data."}],"type":"research_data_reference","doi":"10.5061/dryad.299h8","date_published":"2011-05-12T00:00:00Z","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.299h8"}],"citation":{"ama":"Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas). 2011. doi:10.5061/dryad.299h8","apa":"Palero, F., Abello, P., Macpherson, E., Beaumont, M., & Pascual, M. (2011). Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas). IST Austria. https://doi.org/10.5061/dryad.299h8","ieee":"F. Palero, P. Abello, E. Macpherson, M. Beaumont, and M. Pascual, “Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas).” IST Austria, 2011.","ista":"Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. 2011. Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas), IST Austria, 10.5061/dryad.299h8.","short":"F. Palero, P. Abello, E. Macpherson, M. Beaumont, M. Pascual, (2011).","mla":"Palero, Ferran, et al. Data from: Effect of Oceanographic Barriers and Overfishing on the Population Genetic Structure of the European Spiny Lobster (Palinurus Elephas). IST Austria, 2011, doi:10.5061/dryad.299h8.","chicago":"Palero, Ferran, Pere Abello, Enrique Macpherson, Mark Beaumont, and Marta Pascual. “Data from: Effect of Oceanographic Barriers and Overfishing on the Population Genetic Structure of the European Spiny Lobster (Palinurus Elephas).” IST Austria, 2011. https://doi.org/10.5061/dryad.299h8."},"article_processing_charge":"No","day":"12","month":"05"},{"date_published":"2011-05-01T00:00:00Z","page":"720 - 739","article_type":"original","citation":{"apa":"de Vladar, H., & Barton, N. H. (2011). The statistical mechanics of a polygenic character under stabilizing selection mutation and drift. Journal of the Royal Society Interface. The Royal Society. https://doi.org/10.1098/rsif.2010.0438","ieee":"H. de Vladar and N. H. Barton, “The statistical mechanics of a polygenic character under stabilizing selection mutation and drift,” Journal of the Royal Society Interface, vol. 8, no. 58. The Royal Society, pp. 720–739, 2011.","ista":"de Vladar H, Barton NH. 2011. The statistical mechanics of a polygenic character under stabilizing selection mutation and drift. Journal of the Royal Society Interface. 8(58), 720–739.","ama":"de Vladar H, Barton NH. The statistical mechanics of a polygenic character under stabilizing selection mutation and drift. Journal of the Royal Society Interface. 2011;8(58):720-739. doi:10.1098/rsif.2010.0438","chicago":"Vladar, Harold de, and Nicholas H Barton. “The Statistical Mechanics of a Polygenic Character under Stabilizing Selection Mutation and Drift.” Journal of the Royal Society Interface. The Royal Society, 2011. https://doi.org/10.1098/rsif.2010.0438.","short":"H. de Vladar, N.H. Barton, Journal of the Royal Society Interface 8 (2011) 720–739.","mla":"de Vladar, Harold, and Nicholas H. Barton. “The Statistical Mechanics of a Polygenic Character under Stabilizing Selection Mutation and Drift.” Journal of the Royal Society Interface, vol. 8, no. 58, The Royal Society, 2011, pp. 720–39, doi:10.1098/rsif.2010.0438."},"publication":"Journal of the Royal Society Interface","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Submitted Version","intvolume":" 8","title":"The statistical mechanics of a polygenic character under stabilizing selection mutation and drift","status":"public","_id":"3375","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"58","abstract":[{"lang":"eng","text":"By exploiting an analogy between population genetics and statistical mechanics, we study the evolution of a polygenic trait under stabilizing selection, mutation and genetic drift. This requires us to track only four macroscopic variables, instead of the distribution of all the allele frequencies that influence the trait. These macroscopic variables are the expectations of: the trait mean and its square, the genetic variance, and of a measure of heterozygosity, and are derived from a generating function that is in turn derived by maximizing an entropy measure. These four macroscopics are enough to accurately describe the dynamics of the trait mean and of its genetic variance (and in principle of any other quantity). Unlike previous approaches that were based on an infinite series of moments or cumulants, which had to be truncated arbitrarily, our calculations provide a well-defined approximation procedure. We apply the framework to abrupt and gradual changes in the optimum, as well as to changes in the strength of stabilizing selection. Our approximations are surprisingly accurate, even for systems with as few as five loci. We find that when the effects of drift are included, the expected genetic variance is hardly altered by directional selection, even though it fluctuates in any particular instance. We also find hysteresis, showing that even after averaging over the microscopic variables, the macroscopic trajectories retain a memory of the underlying genetic states."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1098/rsif.2010.0438","project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"quality_controlled":"1","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3061091/","open_access":"1"}],"external_id":{"pmid":["21084341"]},"oa":1,"month":"05","volume":8,"date_updated":"2023-10-18T06:39:05Z","date_created":"2018-12-11T12:02:58Z","author":[{"orcid":"0000-0002-5985-7653","id":"2A181218-F248-11E8-B48F-1D18A9856A87","last_name":"de Vladar","first_name":"Harold","full_name":"de Vladar, Harold"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"department":[{"_id":"NiBa"}],"publisher":"The Royal Society","publication_status":"published","pmid":1,"year":"2011","publist_id":"3232","ec_funded":1},{"has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2011-09-01T00:00:00Z","page":"E48 - E75","article_type":"original","citation":{"chicago":"Barton, Nicholas H, and Michael Turelli. “Spatial Waves of Advance with Bistable Dynamics: Cytoplasmic and Genetic Analogues of Allee Effects.” American Naturalist. The University of Chicago Press, 2011. https://doi.org/10.1086/661246.","mla":"Barton, Nicholas H., and Michael Turelli. “Spatial Waves of Advance with Bistable Dynamics: Cytoplasmic and Genetic Analogues of Allee Effects.” American Naturalist, vol. 178, no. 3, The University of Chicago Press, 2011, pp. E48–75, doi:10.1086/661246.","short":"N.H. Barton, M. Turelli, American Naturalist 178 (2011) E48–E75.","ista":"Barton NH, Turelli M. 2011. Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues of Allee effects. American Naturalist. 178(3), E48–E75.","ieee":"N. H. Barton and M. Turelli, “Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues of Allee effects,” American Naturalist, vol. 178, no. 3. The University of Chicago Press, pp. E48–E75, 2011.","apa":"Barton, N. H., & Turelli, M. (2011). Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues of Allee effects. American Naturalist. The University of Chicago Press. https://doi.org/10.1086/661246","ama":"Barton NH, Turelli M. Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues of Allee effects. American Naturalist. 2011;178(3):E48-E75. doi:10.1086/661246"},"publication":"American Naturalist","issue":"3","abstract":[{"text":"Unlike unconditionally advantageous “Fisherian” variants that tend to spread throughout a species range once introduced anywhere, “bistable” variants, such as chromosome translocations, have two alternative stable frequencies, absence and (near) fixation. Analogous to populations with Allee effects, bistable variants tend to increase locally only once they become sufficiently common, and their spread depends on their rate of increase averaged over all frequencies. Several proposed manipulations of insect populations, such as using Wolbachia or “engineered underdominance” to suppress vector-borne diseases, produce bistable rather than Fisherian dynamics. We synthesize and extend theoretical analyses concerning three features of their spatial behavior: rate of spread, conditions to initiate spread from a localized introduction, and wave stopping caused by variation in population densities or dispersal rates. Unlike Fisherian variants, bistable variants tend to spread spatially only for particular parameter combinations and initial conditions. Wave initiation requires introduction over an extended region, while subsequent spatial spread is slower than for Fisherian waves and can easily be halted by local spatial inhomogeneities. We present several new results, including robust sufficient conditions to initiate (and stop) spread, using a one-parameter cubic approximation applicable to several models. The results have both basic and applied implications.","lang":"eng"}],"type":"journal_article","file":[{"relation":"main_file","file_id":"4692","date_created":"2018-12-12T10:08:31Z","date_updated":"2020-07-14T12:46:11Z","checksum":"7fd22a2ef3321a6fca6a439b3be5d8f4","file_name":"IST-2016-554-v1+1_BartonTurelli2011_copy.pdf","access_level":"open_access","content_type":"application/pdf","file_size":629130,"creator":"system"}],"oa_version":"Submitted Version","pubrep_id":"554","intvolume":" 178","title":"Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues of Allee effects","status":"public","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3393","publication_identifier":{"issn":["0003-0147"],"eissn":["1537-5323"]},"month":"09","language":[{"iso":"eng"}],"doi":"10.1086/661246","quality_controlled":"1","oa":1,"publist_id":"3214","file_date_updated":"2020-07-14T12:46:11Z","volume":178,"date_created":"2018-12-11T12:03:05Z","date_updated":"2023-10-18T08:01:43Z","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"},{"full_name":"Turelli, Michael","first_name":"Michael","last_name":"Turelli"}],"department":[{"_id":"NiBa"}],"publisher":"The University of Chicago Press","publication_status":"published","year":"2011"},{"ec_funded":1,"publist_id":"3337","publisher":"Genetics Society of America","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2010","acknowledgement":"This work was supported in part by a Robert N. Noyce Stanford Graduate Fellowship and European Research Council grant 250152 (to D.B.W.) and by National Institutes of Health grant GM 28016 (to M.W.F.).\r\nWe thank Michael Desai for many ideas and discussions and are grateful to Joanna Masel and an anonymous reviewer for their helpful suggestions. ","volume":186,"date_created":"2018-12-11T12:02:33Z","date_updated":"2021-01-12T07:42:31Z","author":[{"id":"2D0CE020-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","last_name":"Weissman","full_name":"Weissman, Daniel"},{"last_name":"Feldman","first_name":"Marcus","full_name":"Feldman, Marcus"},{"full_name":"Fisher, Daniel","last_name":"Fisher","first_name":"Daniel"}],"month":"12","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2998319/"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1534/genetics.110.123240","type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"Biological traits result in part from interactions between different genetic loci. This can lead to sign epistasis, in which a beneficial adaptation involves a combination of individually deleterious or neutral mutations; in this case, a population must cross a “fitness valley” to adapt. Recombination can assist this process by combining mutations from different individuals or retard it by breaking up the adaptive combination. Here, we analyze the simplest fitness valley, in which an adaptation requires one mutation at each of two loci to provide a fitness benefit. We present a theoretical analysis of the effect of recombination on the valley-crossing process across the full spectrum of possible parameter regimes. We find that low recombination rates can speed up valley crossing relative to the asexual case, while higher recombination rates slow down valley crossing, with the transition between the two regimes occurring when the recombination rate between the loci is approximately equal to the selective advantage provided by the adaptation. In large populations, if the recombination rate is high and selection against single mutants is substantial, the time to cross the valley grows exponentially with population size, effectively meaning that the population cannot acquire the adaptation. Recombination at the optimal (low) rate can reduce the valley-crossing time by up to several orders of magnitude relative to that in an asexual population. "}],"intvolume":" 186","status":"public","title":"The rate of fitness-valley crossing in sexual populations","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3303","oa_version":"Submitted Version","scopus_import":1,"day":"01","page":"1389 - 1410","citation":{"ieee":"D. Weissman, M. Feldman, and D. Fisher, “The rate of fitness-valley crossing in sexual populations,” Genetics, vol. 186, no. 4. Genetics Society of America, pp. 1389–1410, 2010.","apa":"Weissman, D., Feldman, M., & Fisher, D. (2010). The rate of fitness-valley crossing in sexual populations. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.110.123240","ista":"Weissman D, Feldman M, Fisher D. 2010. The rate of fitness-valley crossing in sexual populations. Genetics. 186(4), 1389–1410.","ama":"Weissman D, Feldman M, Fisher D. The rate of fitness-valley crossing in sexual populations. Genetics. 2010;186(4):1389-1410. doi:10.1534/genetics.110.123240","chicago":"Weissman, Daniel, Marcus Feldman, and Daniel Fisher. “The Rate of Fitness-Valley Crossing in Sexual Populations.” Genetics. Genetics Society of America, 2010. https://doi.org/10.1534/genetics.110.123240.","short":"D. Weissman, M. Feldman, D. Fisher, Genetics 186 (2010) 1389–1410.","mla":"Weissman, Daniel, et al. “The Rate of Fitness-Valley Crossing in Sexual Populations.” Genetics, vol. 186, no. 4, Genetics Society of America, 2010, pp. 1389–410, doi:10.1534/genetics.110.123240."},"publication":"Genetics","date_published":"2010-12-01T00:00:00Z"},{"abstract":[{"text":"We investigated temporal changes in hybridization and introgression between native red deer (Cervus elaphus) and invasive Japanese sika (Cervus nippon) on the Kintyre Peninsula, Scotland, over 15 years, through analysis of 1513 samples of deer at 20 microsatellite loci and a mtDNA marker. We found no evidence that either the proportion of recent hybrids, or the levels of introgression had changed over the study period. Nevertheless, in one population where the two species have been in contact since ∼1970, 44% of individuals sampled during the study were hybrids. This suggests that hybridization between these species can proceed fairly rapidly. By analysing the number of alleles that have introgressed from polymorphic red deer into the genetically homogenous sika population, we reconstructed the haplotypes of red deer alleles introduced by backcrossing. Five separate hybridization events could account for all the recently hybridized sika-like individuals found across a large section of the Peninsula. Although we demonstrate that low rates of F1 hybridization can lead to substantial introgression, the progress of hybridization and introgression appears to be unpredictable over the short timescales.","lang":"eng"}],"publist_id":"2779","issue":"5","type":"journal_article","date_created":"2018-12-11T12:04:12Z","date_updated":"2021-01-12T07:44:36Z","oa_version":"None","volume":19,"author":[{"first_name":"Helen","last_name":"Senn","full_name":"Senn, Helen"},{"full_name":"Goodman, Simon","first_name":"Simon","last_name":"Goodman"},{"full_name":"Swanson, Graeme","first_name":"Graeme","last_name":"Swanson"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"full_name":"Pemberton, Josephine","first_name":"Josephine","last_name":"Pemberton"}],"publication_status":"published","title":"Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland","status":"public","intvolume":" 19","publisher":"Wiley-Blackwell","department":[{"_id":"NiBa"}],"_id":"3604","year":"2010","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"03","day":"01","scopus_import":1,"language":[{"iso":"eng"}],"date_published":"2010-03-01T00:00:00Z","doi":"10.1111/j.1365-294X.2009.04497.x","quality_controlled":"1","page":"910 - 924","publication":"Molecular Ecology","citation":{"ista":"Senn H, Goodman S, Swanson G, Barton NH, Pemberton J. 2010. Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland. Molecular Ecology. 19(5), 910–924.","ieee":"H. Senn, S. Goodman, G. Swanson, N. H. Barton, and J. Pemberton, “Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland,” Molecular Ecology, vol. 19, no. 5. Wiley-Blackwell, pp. 910–924, 2010.","apa":"Senn, H., Goodman, S., Swanson, G., Barton, N. H., & Pemberton, J. (2010). Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2009.04497.x","ama":"Senn H, Goodman S, Swanson G, Barton NH, Pemberton J. Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland. Molecular Ecology. 2010;19(5):910-924. doi:10.1111/j.1365-294X.2009.04497.x","chicago":"Senn, Helen, Simon Goodman, Graeme Swanson, Nicholas H Barton, and Josephine Pemberton. “Investigating Temporal Changes in Hybridisation and Introgression between Invasive Sika (Cervus Nippon) and Native Red Deer (Cervus Elaphus) on the Kintyre Peninsula, Scotland.” Molecular Ecology. Wiley-Blackwell, 2010. https://doi.org/10.1111/j.1365-294X.2009.04497.x.","mla":"Senn, Helen, et al. “Investigating Temporal Changes in Hybridisation and Introgression between Invasive Sika (Cervus Nippon) and Native Red Deer (Cervus Elaphus) on the Kintyre Peninsula, Scotland.” Molecular Ecology, vol. 19, no. 5, Wiley-Blackwell, 2010, pp. 910–24, doi:10.1111/j.1365-294X.2009.04497.x.","short":"H. Senn, S. Goodman, G. Swanson, N.H. Barton, J. Pemberton, Molecular Ecology 19 (2010) 910–924."}},{"doi":"10.1093/jhered/esq111","date_published":"2010-12-02T00:00:00Z","language":[{"iso":"eng"}],"publication":"Journal of Heredity","citation":{"chicago":"Palero, Ferran, Fernando González Candelas, and Marta Pascual. “Microsatelight – Pipeline to Expedite Microsatellite Analysis.” Journal of Heredity. Oxford University Press, 2010. https://doi.org/10.1093/jhered/esq111.","mla":"Palero, Ferran, et al. “Microsatelight – Pipeline to Expedite Microsatellite Analysis.” Journal of Heredity, vol. 102, no. 2, Oxford University Press, 2010, pp. 247–49, doi:10.1093/jhered/esq111.","short":"F. Palero, F. González Candelas, M. Pascual, Journal of Heredity 102 (2010) 247–249.","ista":"Palero F, González Candelas F, Pascual M. 2010. Microsatelight – Pipeline to expedite microsatellite analysis. Journal of Heredity. 102(2), 247–249.","ieee":"F. Palero, F. González Candelas, and M. Pascual, “Microsatelight – Pipeline to expedite microsatellite analysis,” Journal of Heredity, vol. 102, no. 2. Oxford University Press, pp. 247–249, 2010.","apa":"Palero, F., González Candelas, F., & Pascual, M. (2010). Microsatelight – Pipeline to expedite microsatellite analysis. Journal of Heredity. Oxford University Press. https://doi.org/10.1093/jhered/esq111","ama":"Palero F, González Candelas F, Pascual M. Microsatelight – Pipeline to expedite microsatellite analysis. Journal of Heredity. 2010;102(2):247-249. doi:10.1093/jhered/esq111"},"quality_controlled":"1","page":"247 - 249","day":"02","month":"12","scopus_import":1,"author":[{"full_name":"Palero, Ferran","id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0343-8329","first_name":"Ferran","last_name":"Palero"},{"full_name":"González Candelas, Fernando","first_name":"Fernando","last_name":"González Candelas"},{"full_name":"Pascual, Marta","last_name":"Pascual","first_name":"Marta"}],"date_updated":"2021-01-12T07:52:10Z","date_created":"2018-12-11T12:05:09Z","oa_version":"None","volume":102,"acknowledgement":"Ministerio de Educación y Ciencia (CGL2006-13423, CTM2007-66635). M.P. and FP are part of the research group 2009SGR-636 of the Generalitat de Catalunya. F.P. acknowledges an EU-Synthesys grant (GB-TAF-4474).\r\n\r\nThanks to José Gabriel Segarra-Moragues (Centro de Investigaciones sobre Desertificación) for sending us pictures with several types of stuttering and Pedro Simões and Gemma Calàbria (Universitat de Barcelona) for testing this software. Finally, thanks are due to 2 anonymous referees for their valuable comments. These comments certainly helped to improve the manuscript.","_id":"3783","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2010","status":"public","publication_status":"published","title":"Microsatelight – Pipeline to expedite microsatellite analysis","publisher":"Oxford University Press","department":[{"_id":"NiBa"}],"intvolume":" 102","abstract":[{"lang":"eng","text":"MICROSATELIGHT is a Perl/Tk pipeline with a graphical user interface that facilitates several tasks when scoring microsatellites. It implements new subroutines in R and PERL and takes advantage of features provided by previously developed freeware. MICROSATELIGHT takes raw genotype data and automates the peak identification through PeakScanner. The PeakSelect subroutine assigns peaks to different microsatellite markers according to their multiplex group, fluorochrome type, and size range. After peak selection, binning of alleles can be carried out 1) automatically through AlleloBin or 2) by manual bin definition through Binator. In both cases, several features for quality checking and further binning improvement are provided. The genotype table can then be converted into input files for several population genetics programs through CREATE. Finally, Hardy–Weinberg equilibrium tests and confidence intervals for null allele frequency can be obtained through GENEPOP. MICROSATELIGHT is the only freely available public-domain software that facilitates full multiplex microsatellite scoring, from electropherogram files to user-defined text files to be used with population genetics software. MICROSATELIGHT has been created for the Windows XP operating system and has been successfully tested under Windows 7. It is available at http://sourceforge.net/projects/microsatelight/."}],"publist_id":"2444","issue":"2","type":"journal_article"},{"scopus_import":1,"day":"15","publication":"Ecology Letters","citation":{"ista":"Bridle J, Polechova J, Kawata M, Butlin R. 2010. Why is adaptation prevented at ecological margins? New insights from individual-based simulations. Ecology Letters. 13(4), 485–494.","ieee":"J. Bridle, J. Polechova, M. Kawata, and R. Butlin, “Why is adaptation prevented at ecological margins? New insights from individual-based simulations,” Ecology Letters, vol. 13, no. 4. Wiley-Blackwell, pp. 485–494, 2010.","apa":"Bridle, J., Polechova, J., Kawata, M., & Butlin, R. (2010). Why is adaptation prevented at ecological margins? New insights from individual-based simulations. Ecology Letters. Wiley-Blackwell. https://doi.org/10.1111/j.1461-0248.2010.01442.x","ama":"Bridle J, Polechova J, Kawata M, Butlin R. Why is adaptation prevented at ecological margins? New insights from individual-based simulations. Ecology Letters. 2010;13(4):485-494. doi:10.1111/j.1461-0248.2010.01442.x","chicago":"Bridle, Jon, Jitka Polechova, Masakado Kawata, and Roger Butlin. “Why Is Adaptation Prevented at Ecological Margins? New Insights from Individual-Based Simulations.” Ecology Letters. Wiley-Blackwell, 2010. https://doi.org/10.1111/j.1461-0248.2010.01442.x.","mla":"Bridle, Jon, et al. “Why Is Adaptation Prevented at Ecological Margins? New Insights from Individual-Based Simulations.” Ecology Letters, vol. 13, no. 4, Wiley-Blackwell, 2010, pp. 485–94, doi:10.1111/j.1461-0248.2010.01442.x.","short":"J. Bridle, J. Polechova, M. Kawata, R. Butlin, Ecology Letters 13 (2010) 485–494."},"page":"485 - 494","date_published":"2010-03-15T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"All species are restricted in their distribution. Currently, ecological models can only explain such limits if patches vary in quality, leading to asymmetrical dispersal, or if genetic variation is too low at the margins for adaptation. However, population genetic models suggest that the increase in genetic variance resulting from dispersal should allow adaptation to almost any ecological gradient. Clearly therefore, these models miss something that prevents evolution in natural populations. We developed an individual-based simulation to explore stochastic effects in these models. At high carrying capacities, our simulations largely agree with deterministic predictions. However, when carrying capacity is low, the population fails to establish for a wide range of parameter values where adaptation was expected from previous models. Stochastic or transient effects appear critical around the boundaries in parameter space between simulation behaviours. Dispersal, gradient steepness, and population density emerge as key factors determining adaptation on an ecological gradient. "}],"issue":"4","_id":"4134","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","title":"Why is adaptation prevented at ecological margins? New insights from individual-based simulations","status":"public","intvolume":" 13","oa_version":"None","month":"03","quality_controlled":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"doi":"10.1111/j.1461-0248.2010.01442.x","language":[{"iso":"eng"}],"publist_id":"1987","ec_funded":1,"acknowledgement":"We are very grateful to Nick Barton.","year":"2010","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley-Blackwell","author":[{"full_name":"Bridle, Jon","last_name":"Bridle","first_name":"Jon"},{"last_name":"Polechova","first_name":"Jitka","orcid":"0000-0003-0951-3112","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","full_name":"Polechova, Jitka"},{"full_name":"Kawata, Masakado","first_name":"Masakado","last_name":"Kawata"},{"full_name":"Butlin, Roger","last_name":"Butlin","first_name":"Roger"}],"date_created":"2018-12-11T12:07:08Z","date_updated":"2021-01-12T07:54:45Z","volume":13},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.1214/EJP.v15-741","language":[{"iso":"eng"}],"month":"02","year":"2010","department":[{"_id":"NiBa"}],"publisher":"Institute of Mathematical Statistics","publication_status":"published","author":[{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"full_name":"Etheridge, Alison","first_name":"Alison","last_name":"Etheridge"},{"first_name":"Amandine","last_name":"Véber","full_name":"Véber, Amandine"}],"volume":15,"date_created":"2018-12-11T12:07:48Z","date_updated":"2021-01-12T07:55:34Z","publist_id":"1863","file_date_updated":"2020-07-14T12:46:26Z","citation":{"ama":"Barton NH, Etheridge A, Véber A. A new model for evolution in a spatial continuum. Electronic Journal of Probability. 2010;15(7):162-216. doi:10.1214/EJP.v15-741","ista":"Barton NH, Etheridge A, Véber A. 2010. A new model for evolution in a spatial continuum. Electronic Journal of Probability. 15(7), 162–216.","ieee":"N. H. Barton, A. Etheridge, and A. Véber, “A new model for evolution in a spatial continuum,” Electronic Journal of Probability, vol. 15, no. 7. Institute of Mathematical Statistics, pp. 162–216, 2010.","apa":"Barton, N. H., Etheridge, A., & Véber, A. (2010). A new model for evolution in a spatial continuum. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/EJP.v15-741","mla":"Barton, Nicholas H., et al. “A New Model for Evolution in a Spatial Continuum.” Electronic Journal of Probability, vol. 15, no. 7, Institute of Mathematical Statistics, 2010, pp. 162–216, doi:10.1214/EJP.v15-741.","short":"N.H. Barton, A. Etheridge, A. Véber, Electronic Journal of Probability 15 (2010) 162–216.","chicago":"Barton, Nicholas H, Alison Etheridge, and Amandine Véber. “A New Model for Evolution in a Spatial Continuum.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2010. https://doi.org/10.1214/EJP.v15-741."},"publication":"Electronic Journal of Probability","page":"162 - 216","date_published":"2010-02-03T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"03","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"4243","intvolume":" 15","title":"A new model for evolution in a spatial continuum","status":"public","ddc":["576"],"pubrep_id":"369","oa_version":"Published Version","file":[{"file_name":"IST-2015-369-v1+1_741-2535-1-PB.pdf","access_level":"open_access","content_type":"application/pdf","file_size":450171,"creator":"system","relation":"main_file","file_id":"5140","date_updated":"2020-07-14T12:46:26Z","date_created":"2018-12-12T10:15:21Z","checksum":"bab577546dd4e8f882e9a9dd645cd01e"}],"type":"journal_article","issue":"7","abstract":[{"lang":"eng","text":"We investigate a new model for populations evolving in a spatial continuum. This model can be thought of as a spatial version of the Lambda-Fleming-Viot process. It explicitly incorporates both small scale reproduction events and large scale extinction-recolonisation events. The lineages ancestral to a sample from a population evolving according to this model can be described in terms of a spatial version of the Lambda-coalescent. Using a technique of Evans (1997), we prove existence and uniqueness in law for the model. We then investigate the asymptotic behaviour of the genealogy of a finite number of individuals sampled uniformly at random (or more generally `far enough apart') from a two-dimensional torus of sidelength L as L tends to infinity. Under appropriate conditions (and on a suitable timescale) we can obtain as limiting genealogical processes a Kingman coalescent, a more general Lambda-coalescent or a system of coalescing Brownian motions (with a non-local coalescence mechanism)."}]},{"language":[{"iso":"eng"}],"doi":"10.1098/rstb.2010.0106","quality_controlled":"1","oa":1,"month":"08","volume":365,"date_updated":"2021-01-12T07:52:07Z","date_created":"2018-12-11T12:05:06Z","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"department":[{"_id":"NiBa"}],"publisher":"Royal Society","publication_status":"published","acknowledgement":"Royal Society and Wolfson Foundation for their support\r\nWe would like to thank Brian Charlesworth and Sally Otto for their helpful comments.","year":"2010","publist_id":"2450","file_date_updated":"2020-07-14T12:46:15Z","date_published":"2010-08-27T00:00:00Z","page":"2559 - 2569","citation":{"ista":"Barton NH. 2010. Genetic linkage and natural selection. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1552), 2559–2569.","ieee":"N. H. Barton, “Genetic linkage and natural selection,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1552. Royal Society, pp. 2559–2569, 2010.","apa":"Barton, N. H. (2010). Genetic linkage and natural selection. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society. https://doi.org/10.1098/rstb.2010.0106","ama":"Barton NH. Genetic linkage and natural selection. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences. 2010;365(1552):2559-2569. doi:10.1098/rstb.2010.0106","chicago":"Barton, Nicholas H. “Genetic Linkage and Natural Selection.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, 2010. https://doi.org/10.1098/rstb.2010.0106.","mla":"Barton, Nicholas H. “Genetic Linkage and Natural Selection.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1552, Royal Society, 2010, pp. 2559–69, doi:10.1098/rstb.2010.0106.","short":"N.H. Barton, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 2559–2569."},"publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","has_accepted_license":"1","day":"27","scopus_import":1,"file":[{"content_type":"application/pdf","file_size":250255,"creator":"system","access_level":"open_access","file_name":"IST-2016-555-v1+1_RS2009_revised.pdf","checksum":"4d8aade10db030124ab158b622e337e0","date_updated":"2020-07-14T12:46:15Z","date_created":"2018-12-12T10:14:40Z","relation":"main_file","file_id":"5093"}],"oa_version":"Submitted Version","pubrep_id":"555","intvolume":" 365","ddc":["570"],"title":"Genetic linkage and natural selection","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3776","issue":"1552","abstract":[{"lang":"eng","text":"The prevalence of recombination in eukaryotes poses one of the most puzzling questions in biology. The most compelling general explanation is that recombination facilitates selection by breaking down the negative associations generated by random drift (i.e. Hill-Robertson interference, HRI). I classify the effects of HRI owing to: deleterious mutation, balancing selection and selective sweeps on: neutral diversity, rates of adaptation and the mutation load. These effects are mediated primarily by the density of deleterious mutations and of selective sweeps. Sequence polymorphism and divergence suggest that these rates may be high enough to cause significant interference even in genomic regions of high recombination. However, neither seems able to generate enough variance in fitness to select strongly for high rates of recombination. It is plausible that spatial and temporal fluctuations in selection generate much more fitness variance, and hence selection for recombination, than can be explained by uniformly deleterious mutations or species-wide selective sweeps."}],"type":"journal_article"},{"month":"06","quality_controlled":"1","oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pubmed/20439284","open_access":"1"}],"external_id":{"pmid":["20439284"]},"language":[{"iso":"eng"}],"doi":"10.1098/rstb.2010.0001","publist_id":"2455","department":[{"_id":"NiBa"}],"publisher":"Royal Society","publication_status":"published","pmid":1,"acknowledgement":"The author thanks the Werner-Gren Foundation and the Royal Swedish Academy of Sciences for organizing the symposium on the ‘Origin of Species’. He also thanks Reinhard Bürger, and two anonymous referees, for their helpful comments.\r\n","year":"2010","volume":365,"date_created":"2018-12-11T12:05:05Z","date_updated":"2021-01-12T07:52:06Z","author":[{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"scopus_import":1,"day":"12","page":"1825 - 1840","citation":{"ama":"Barton NH. What role does natural selection play in speciation? Philosophical Transactions of the Royal Society of London Series B, Biological Sciences. 2010;365(1547):1825-1840. doi:10.1098/rstb.2010.0001","ieee":"N. H. Barton, “What role does natural selection play in speciation?,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1547. Royal Society, pp. 1825–1840, 2010.","apa":"Barton, N. H. (2010). What role does natural selection play in speciation? Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society. https://doi.org/10.1098/rstb.2010.0001","ista":"Barton NH. 2010. What role does natural selection play in speciation? Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1547), 1825–1840.","short":"N.H. Barton, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 1825–1840.","mla":"Barton, Nicholas H. “What Role Does Natural Selection Play in Speciation?” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1547, Royal Society, 2010, pp. 1825–40, doi:10.1098/rstb.2010.0001.","chicago":"Barton, Nicholas H. “What Role Does Natural Selection Play in Speciation?” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, 2010. https://doi.org/10.1098/rstb.2010.0001."},"publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","date_published":"2010-06-12T00:00:00Z","type":"journal_article","issue":"1547","abstract":[{"text":"If distinct biological species are to coexist in sympatry, they must be reproductively isolated and must exploit different limiting resources. A two-niche Levene model is analysed, in which habitat preference and survival depend on underlying additive traits. The population genetics of preference and viability are equivalent. However, there is a linear trade-off between the chances of settling in either niche, whereas viabilities may be constrained arbitrarily. With a convex trade-off, a sexual population evolves a single generalist genotype, whereas with a concave trade-off, disruptive selection favours maximal variance. A pure habitat preference evolves to global linkage equilibrium if mating occurs in a single pool, but remarkably, evolves to pairwise linkage equilibrium within niches if mating is within those niches--independent of the genetics. With a concave trade-off, the population shifts sharply between a unimodal distribution with high gene flow and a bimodal distribution with strong isolation, as the underlying genetic variance increases. However, these alternative states are only simultaneously stable for a narrow parameter range. A sharp threshold is only seen if survival in the 'wrong' niche is low; otherwise, strong isolation is impossible. Gene flow from divergent demes makes speciation much easier in parapatry than in sympatry.","lang":"eng"}],"intvolume":" 365","status":"public","title":"What role does natural selection play in speciation?","_id":"3773","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version"},{"pmid":1,"acknowledgement":"I would like to thank W. G. Hill and L. Loewe for organizing this special issue, and the Royal Society and Wolfson Foundation for their support. Also, A. Kondrashov and L. Loewe gave very helpful comments that helped improve the manuscript.","year":"2010","publisher":"Royal Society","department":[{"_id":"NiBa"}],"publication_status":"published","author":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"volume":365,"date_updated":"2021-01-12T07:52:07Z","date_created":"2018-12-11T12:05:07Z","publist_id":"2451","external_id":{"pmid":["20308104"]},"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pubmed/20308104"}],"oa":1,"quality_controlled":"1","doi":"10.1098/rstb.2009.0320","language":[{"iso":"eng"}],"month":"04","_id":"3777","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 365","title":"Mutation and the evolution of recombination","status":"public","oa_version":"Submitted Version","type":"journal_article","issue":"1544","abstract":[{"text":"Under the classical view, selection depends more or less directly on mutation: standing genetic variance is maintained by a balance between selection and mutation, and adaptation is fuelled by new favourable mutations. Recombination is favoured if it breaks negative associations among selected alleles, which interfere with adaptation. Such associations may be generated by negative epistasis, or by random drift (leading to the Hill-Robertson effect). Both deterministic and stochastic explanations depend primarily on the genomic mutation rate, U. This may be large enough to explain high recombination rates in some organisms, but seems unlikely to be so in general. Random drift is a more general source of negative linkage disequilibria, and can cause selection for recombination even in large populations, through the chance loss of new favourable mutations. The rate of species-wide substitutions is much too low to drive this mechanism, but local fluctuations in selection, combined with gene flow, may suffice. These arguments are illustrated by comparing the interaction between good and bad mutations at unlinked loci under the infinitesimal model.","lang":"eng"}],"citation":{"ista":"Barton NH. 2010. Mutation and the evolution of recombination. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1544), 1281–1294.","apa":"Barton, N. H. (2010). Mutation and the evolution of recombination. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society. https://doi.org/10.1098/rstb.2009.0320","ieee":"N. H. Barton, “Mutation and the evolution of recombination,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1544. Royal Society, pp. 1281–1294, 2010.","ama":"Barton NH. Mutation and the evolution of recombination. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences. 2010;365(1544):1281-1294. doi:10.1098/rstb.2009.0320","chicago":"Barton, Nicholas H. “Mutation and the Evolution of Recombination.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, 2010. https://doi.org/10.1098/rstb.2009.0320.","mla":"Barton, Nicholas H. “Mutation and the Evolution of Recombination.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1544, Royal Society, 2010, pp. 1281–94, doi:10.1098/rstb.2009.0320.","short":"N.H. Barton, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 1281–1294."},"publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","page":"1281 - 1294","date_published":"2010-04-27T00:00:00Z","scopus_import":1,"day":"27"},{"issue":"2","abstract":[{"lang":"eng","text":"1. Hybridisation with an invasive species has the potential to alter the phenotype and hence the ecology of a native counterpart. 2. Here data from populations of native red deer Cervus elaphus and invasive sika deer Cervus nippon in Scotland is used to assess the extent to which hybridisation between them is causing phenotypic change. This is done by regression of phenotypic traits against genetic hybrid scores. 3. Hybridisation is causing increases in the body weight of sika-like deer and decreases in the body weight of red-like females. Hybridisation is causing increases in jaw length and increases in incisor arcade breadth in sika-like females. Hybridisation is also causing decreases in incisor arcade breadth in red-like females. 4. There is currently no evidence that hybridisation is causing changes in the kidney fat weight or pregnancy rates of either population. 5. Increased phenotypic similarity between the two species is likely to lead to further hybridisation. The ecological consequences of this are difficult to predict."}],"type":"journal_article","oa_version":"None","intvolume":" 79","title":"Phenotypic correlates of hybridisation between red and sika deer (genus Cervus)","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3774","day":"01","scopus_import":1,"date_published":"2010-03-01T00:00:00Z","page":"414 - 425","citation":{"mla":"Senn, Helen, et al. “Phenotypic Correlates of Hybridisation between Red and Sika Deer (Genus Cervus).” Journal of Animal Ecology, vol. 79, no. 2, Wiley-Blackwell, 2010, pp. 414–25, doi:10.1111/j.1365-2656.2009.01633.x.","short":"H. Senn, G. Swanson, S. Goodman, N.H. Barton, J. Pemberton, Journal of Animal Ecology 79 (2010) 414–425.","chicago":"Senn, Helen, Graeme Swanson, Simon Goodman, Nicholas H Barton, and Josephine Pemberton. “Phenotypic Correlates of Hybridisation between Red and Sika Deer (Genus Cervus).” Journal of Animal Ecology. Wiley-Blackwell, 2010. https://doi.org/10.1111/j.1365-2656.2009.01633.x.","ama":"Senn H, Swanson G, Goodman S, Barton NH, Pemberton J. Phenotypic correlates of hybridisation between red and sika deer (genus Cervus). Journal of Animal Ecology. 2010;79(2):414-425. doi:10.1111/j.1365-2656.2009.01633.x","ista":"Senn H, Swanson G, Goodman S, Barton NH, Pemberton J. 2010. Phenotypic correlates of hybridisation between red and sika deer (genus Cervus). Journal of Animal Ecology. 79(2), 414–425.","apa":"Senn, H., Swanson, G., Goodman, S., Barton, N. H., & Pemberton, J. (2010). Phenotypic correlates of hybridisation between red and sika deer (genus Cervus). Journal of Animal Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-2656.2009.01633.x","ieee":"H. Senn, G. Swanson, S. Goodman, N. H. Barton, and J. Pemberton, “Phenotypic correlates of hybridisation between red and sika deer (genus Cervus),” Journal of Animal Ecology, vol. 79, no. 2. Wiley-Blackwell, pp. 414–425, 2010."},"publication":"Journal of Animal Ecology","publist_id":"2453","volume":79,"date_updated":"2021-01-12T07:52:06Z","date_created":"2018-12-11T12:05:06Z","author":[{"full_name":"Senn, Helen","last_name":"Senn","first_name":"Helen"},{"full_name":"Swanson, Graeme","first_name":"Graeme","last_name":"Swanson"},{"first_name":"Simon","last_name":"Goodman","full_name":"Goodman, Simon"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"last_name":"Pemberton","first_name":"Josephine","full_name":"Pemberton, Josephine"}],"publisher":"Wiley-Blackwell","department":[{"_id":"NiBa"}],"publication_status":"published","pmid":1,"year":"2010","acknowledgement":"This project was funded through a NERC studentship to HVS which was CASE partnered by the Macaulay Institute.\r\nWe thank the Forestry Commission Scotland rangers for all their help with providing the larder data for and samples from red and sika deer, Stephen Senn and Jarrod Hadfield for statistical advice and Steve Albon for helpful comments on the manuscript.","month":"03","language":[{"iso":"eng"}],"doi":"10.1111/j.1365-2656.2009.01633.x","quality_controlled":"1","external_id":{"pmid":["20002231"]}},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.1371/journal.pgen.1000987","language":[{"iso":"eng"}],"month":"06","year":"2010","publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"NiBa"}],"author":[{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"date_updated":"2021-01-12T07:52:05Z","date_created":"2018-12-11T12:05:05Z","volume":6,"article_number":"e1000987","file_date_updated":"2020-07-14T12:46:15Z","publist_id":"2454","publication":"PLoS Genetics","citation":{"chicago":"Barton, Nicholas H. “Understanding Adaptation in Large Populations.” PLoS Genetics. Public Library of Science, 2010. https://doi.org/10.1371/journal.pgen.1000987.","mla":"Barton, Nicholas H. “Understanding Adaptation in Large Populations.” PLoS Genetics, vol. 6, no. 6, e1000987, Public Library of Science, 2010, doi:10.1371/journal.pgen.1000987.","short":"N.H. Barton, PLoS Genetics 6 (2010).","ista":"Barton NH. 2010. Understanding adaptation in large populations. PLoS Genetics. 6(6), e1000987.","ieee":"N. H. Barton, “Understanding adaptation in large populations,” PLoS Genetics, vol. 6, no. 6. Public Library of Science, 2010.","apa":"Barton, N. H. (2010). Understanding adaptation in large populations. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1000987","ama":"Barton NH. Understanding adaptation in large populations. PLoS Genetics. 2010;6(6). doi:10.1371/journal.pgen.1000987"},"date_published":"2010-06-17T00:00:00Z","scopus_import":1,"day":"17","has_accepted_license":"1","_id":"3772","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Understanding adaptation in large populations","ddc":["570","576"],"status":"public","intvolume":" 6","pubrep_id":"524","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2016-524-v1+1_journal.pgen.1000987.PDF","creator":"system","content_type":"application/pdf","file_size":349965,"file_id":"5075","relation":"main_file","checksum":"5c14de2680ab483cb835096c99ee734d","date_updated":"2020-07-14T12:46:15Z","date_created":"2018-12-12T10:14:24Z"}],"type":"journal_article","issue":"6"},{"language":[{"iso":"eng"}],"doi":"10.3989/scimar.2010.74n3465","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://eprints.soton.ac.uk/68731/"}],"month":"09","volume":74,"date_created":"2018-12-11T12:05:10Z","date_updated":"2021-01-12T07:52:11Z","author":[{"full_name":"Palero, Ferran","id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0343-8329","first_name":"Ferran","last_name":"Palero"},{"full_name":"Hall, Sally","last_name":"Hall","first_name":"Sally"},{"last_name":"Clark","first_name":"Paul","full_name":"Clark, Paul"},{"last_name":"Johnston","first_name":"David","full_name":"Johnston, David"},{"full_name":"Mackenzie Dodds, Jackie","last_name":"Mackenzie Dodds","first_name":"Jackie"},{"full_name":"Thatje, Sven","first_name":"Sven","last_name":"Thatje"}],"publisher":"Consejo Superior de Investigaciones Científicas","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2010","acknowledgement":"The authors would like to thank two anonymous reviewers for their remarks, which helped to improve the manuscript. This project was supported by the Marine Biodiversity and Ecosystem Functioning Network of Excellence MarBEF (Contract no. GOCE-CT-2003-505446) of the 6th European Framework Programme(FP6), the Zoology Research Fund, Department of Zoology, NHM, London, a Research Grant from the Royal Society to S.T., and a pre-doctoral fellowship awarded by the Autonomous Government of Catalonia to F.P.(2006FIC-00082). This research received support from the SYNTHESYS Project http://www.synthesys. info/ which is financed by European Community Research Infrastructure Action under the FP6 “Structuring the European Research Area” Programme. Many thanks are due to J. Fortuño for suggesting TMS as an alternative to critical point drying, P.Crabb for helping with the UV-light photography setting and our colleagues/friends in the Whale Basement Molecular Laboratories, Department of Zoology NHM \r\n\r\n","publist_id":"2440","date_published":"2010-09-01T00:00:00Z","page":"465 - 470","citation":{"ama":"Palero F, Hall S, Clark P, Johnston D, Mackenzie Dodds J, Thatje S. DNA extraction from formalin-fixed tissue: new light from the deep sea. Scientia Marina. 2010;74(3):465-470. doi:10.3989/scimar.2010.74n3465","ista":"Palero F, Hall S, Clark P, Johnston D, Mackenzie Dodds J, Thatje S. 2010. DNA extraction from formalin-fixed tissue: new light from the deep sea. Scientia Marina. 74(3), 465–470.","apa":"Palero, F., Hall, S., Clark, P., Johnston, D., Mackenzie Dodds, J., & Thatje, S. (2010). DNA extraction from formalin-fixed tissue: new light from the deep sea. Scientia Marina. Consejo Superior de Investigaciones Científicas. https://doi.org/10.3989/scimar.2010.74n3465","ieee":"F. Palero, S. Hall, P. Clark, D. Johnston, J. Mackenzie Dodds, and S. Thatje, “DNA extraction from formalin-fixed tissue: new light from the deep sea,” Scientia Marina, vol. 74, no. 3. Consejo Superior de Investigaciones Científicas, pp. 465–470, 2010.","mla":"Palero, Ferran, et al. “DNA Extraction from Formalin-Fixed Tissue: New Light from the Deep Sea.” Scientia Marina, vol. 74, no. 3, Consejo Superior de Investigaciones Científicas, 2010, pp. 465–70, doi:10.3989/scimar.2010.74n3465.","short":"F. Palero, S. Hall, P. Clark, D. Johnston, J. Mackenzie Dodds, S. Thatje, Scientia Marina 74 (2010) 465–470.","chicago":"Palero, Ferran, Sally Hall, Paul Clark, David Johnston, Jackie Mackenzie Dodds, and Sven Thatje. “DNA Extraction from Formalin-Fixed Tissue: New Light from the Deep Sea.” Scientia Marina. Consejo Superior de Investigaciones Científicas, 2010. https://doi.org/10.3989/scimar.2010.74n3465."},"publication":"Scientia Marina","day":"01","scopus_import":1,"oa_version":"Submitted Version","intvolume":" 74","title":"DNA extraction from formalin-fixed tissue: new light from the deep sea","status":"public","_id":"3787","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"3","abstract":[{"text":"DNA samples were extracted from ethanol and formalin-fixed decapod crustacean tissue using a new method based on Tetramethylsilane (TMS)-Chelex. It is shown that neither an indigestible matrix of cross-linked protein nor soluble PCR inhibitors impede PCR success when dealing with formalin-fixed material. Instead, amplification success from formalin-fixed tissue appears to depend on the presence of unmodified DNA in the extracted sample. A staining method that facilitates the targeting of samples with a high content of unmodified DNA is provided.","lang":"eng"}],"type":"journal_article"},{"citation":{"ieee":"F. Palero, G. Guerao, P. Clark, and P. Abello, “Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first complete description,” Zootaxa, vol. 2403, no. 1. Magnolia Press, pp. 42–58, 2010.","apa":"Palero, F., Guerao, G., Clark, P., & Abello, P. (2010). Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first complete description. Zootaxa. Magnolia Press. https://doi.org/10.11646/zootaxa.2403.1.4","ista":"Palero F, Guerao G, Clark P, Abello P. 2010. Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first complete description. Zootaxa. 2403(1), 42–58.","ama":"Palero F, Guerao G, Clark P, Abello P. Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first complete description. Zootaxa. 2010;2403(1):42-58. doi:10.11646/zootaxa.2403.1.4","chicago":"Palero, Ferran, Guillermo Guerao, Paul Clark, and Pere Abello. “Final-Stage Phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The First Complete Description.” Zootaxa. Magnolia Press, 2010. https://doi.org/10.11646/zootaxa.2403.1.4.","short":"F. Palero, G. Guerao, P. Clark, P. Abello, Zootaxa 2403 (2010) 42–58.","mla":"Palero, Ferran, et al. “Final-Stage Phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The First Complete Description.” Zootaxa, vol. 2403, no. 1, Magnolia Press, 2010, pp. 42–58, doi:10.11646/zootaxa.2403.1.4."},"publication":"Zootaxa","page":"42 - 58","article_type":"original","quality_controlled":"1","date_published":"2010-03-19T00:00:00Z","doi":"10.11646/zootaxa.2403.1.4","language":[{"iso":"eng"}],"scopus_import":"1","article_processing_charge":"No","day":"19","month":"03","year":"2010","_id":"3786","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 2403","publisher":"Magnolia Press","department":[{"_id":"NiBa"}],"title":"Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first complete description","publication_status":"published","status":"public","author":[{"full_name":"Palero, Ferran","id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0343-8329","first_name":"Ferran","last_name":"Palero"},{"first_name":"Guillermo","last_name":"Guerao","full_name":"Guerao, Guillermo"},{"last_name":"Clark","first_name":"Paul","full_name":"Clark, Paul"},{"full_name":"Abello, Pere","first_name":"Pere","last_name":"Abello"}],"oa_version":"None","volume":2403,"date_created":"2018-12-11T12:05:10Z","date_updated":"2022-03-21T08:22:58Z","type":"journal_article","publist_id":"2441","issue":"1","abstract":[{"text":"Four rare palinurid phyllosoma larvae, one mid-stage and three final stage, were found among the unclassified collections in the Crustacea Section, Natural History Museum, London. Detailed morphological analysis of the larvae indicated that they belong to several Palinustus species given the presence of incipient blunt-horns, length of antennula, length ratio of segments of antennular peduncle, distribution of pereiopod spines, and shape of uropods and telson. Moreover, the size of the final-stage larvae agrees with that expected given the size of the recently described puerulus stage of Palinustus mossambicus. This constitutes the first description of a complete phyllosoma assigned to Palinustus species. The phyllosoma described in the present study include the largest Palinuridae larva ever found.","lang":"eng"}]},{"intvolume":" 64","department":[{"_id":"NiBa"}],"publisher":"Wiley-Blackwell","status":"public","publication_status":"published","title":"A new model for extinction and recolonization in two dimensions: Quantifying phylogeography","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"474","year":"2010","acknowledgement":"This work has made use of the resources provided by the Edinburgh Compute and Data Facility (ECDF). The ECDF is partially supported by the eDIKT initiative. NHB is supported in part by EPSRC Grant EP/E066070/1; JK is supported by EPSRC Grant EP/E066070/1; and AME is supported in part by EPSRC Grant EP/E065945/1.","oa_version":"None","volume":64,"date_created":"2018-12-11T11:46:40Z","date_updated":"2021-01-12T08:00:52Z","author":[{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"first_name":"Jerome","last_name":"Kelleher","full_name":"Kelleher, Jerome"},{"full_name":"Etheridge, Alison","last_name":"Etheridge","first_name":"Alison"}],"type":"journal_article","publist_id":"2780","issue":"9","abstract":[{"lang":"eng","text":"Classical models of gene flow fail in three ways: they cannot explain large-scale patterns; they predict much more genetic diversity than is observed; and they assume that loosely linked genetic loci evolve independently. We propose a new model that deals with these problems. Extinction events kill some fraction of individuals in a region. These are replaced by offspring from a small number of parents, drawn from the preexisting population. This model of evolution forwards in time corresponds to a backwards model, in which ancestral lineages jump to a new location if they are hit by an event, and may coalesce with other lineages that are hit by the same event. We derive an expression for the identity in allelic state, and show that, over scales much larger than the largest event, this converges to the classical value derived by Wright and Malécot. However, rare events that cover large areas cause low genetic diversity, large-scale patterns, and correlations in ancestry between unlinked loci."}],"page":"2701 - 2715","quality_controlled":"1","citation":{"chicago":"Barton, Nicholas H, Jerome Kelleher, and Alison Etheridge. “A New Model for Extinction and Recolonization in Two Dimensions: Quantifying Phylogeography.” Evolution. Wiley-Blackwell, 2010. https://doi.org/10.1111/j.1558-5646.2010.01019.x.","mla":"Barton, Nicholas H., et al. “A New Model for Extinction and Recolonization in Two Dimensions: Quantifying Phylogeography.” Evolution, vol. 64, no. 9, Wiley-Blackwell, 2010, pp. 2701–15, doi:10.1111/j.1558-5646.2010.01019.x.","short":"N.H. Barton, J. Kelleher, A. Etheridge, Evolution 64 (2010) 2701–2715.","ista":"Barton NH, Kelleher J, Etheridge A. 2010. A new model for extinction and recolonization in two dimensions: Quantifying phylogeography. Evolution. 64(9), 2701–2715.","ieee":"N. H. Barton, J. Kelleher, and A. Etheridge, “A new model for extinction and recolonization in two dimensions: Quantifying phylogeography,” Evolution, vol. 64, no. 9. Wiley-Blackwell, pp. 2701–2715, 2010.","apa":"Barton, N. H., Kelleher, J., & Etheridge, A. (2010). A new model for extinction and recolonization in two dimensions: Quantifying phylogeography. Evolution. Wiley-Blackwell. https://doi.org/10.1111/j.1558-5646.2010.01019.x","ama":"Barton NH, Kelleher J, Etheridge A. A new model for extinction and recolonization in two dimensions: Quantifying phylogeography. Evolution. 2010;64(9):2701-2715. doi:10.1111/j.1558-5646.2010.01019.x"},"publication":"Evolution","language":[{"iso":"eng"}],"doi":"10.1111/j.1558-5646.2010.01019.x","date_published":"2010-09-01T00:00:00Z","scopus_import":1,"day":"01","month":"09"},{"publication":"PLoS Biology","citation":{"ama":"Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. Cryptic variation between species and the basis of hybrid performance. PLoS Biology. 2010;8(7). doi:10.1371/journal.pbio.1000429","apa":"Rosas, U., Barton, N. H., Copsey, L., Barbier De Reuille, P., & Coen, E. (2010). Cryptic variation between species and the basis of hybrid performance. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1000429","ieee":"U. Rosas, N. H. Barton, L. Copsey, P. Barbier De Reuille, and E. Coen, “Cryptic variation between species and the basis of hybrid performance,” PLoS Biology, vol. 8, no. 7. Public Library of Science, 2010.","ista":"Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. 2010. Cryptic variation between species and the basis of hybrid performance. PLoS Biology. 8(7), e1000429.","short":"U. Rosas, N.H. Barton, L. Copsey, P. Barbier De Reuille, E. Coen, PLoS Biology 8 (2010).","mla":"Rosas, Ulises, et al. “Cryptic Variation between Species and the Basis of Hybrid Performance.” PLoS Biology, vol. 8, no. 7, e1000429, Public Library of Science, 2010, doi:10.1371/journal.pbio.1000429.","chicago":"Rosas, Ulises, Nicholas H Barton, Lucy Copsey, Pierre Barbier De Reuille, and Enrico Coen. “Cryptic Variation between Species and the Basis of Hybrid Performance.” PLoS Biology. Public Library of Science, 2010. https://doi.org/10.1371/journal.pbio.1000429."},"date_published":"2010-07-20T00:00:00Z","scopus_import":1,"day":"20","has_accepted_license":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3779","status":"public","ddc":["576"],"title":"Cryptic variation between species and the basis of hybrid performance","intvolume":" 8","pubrep_id":"366","oa_version":"Published Version","file":[{"creator":"system","content_type":"application/pdf","file_size":1089530,"access_level":"open_access","file_name":"IST-2015-366-v1+1_journal.pbio.1000429.pdf","checksum":"ee1ce2fb283a6b4127544ae532d0b4a1","date_created":"2018-12-12T10:14:11Z","date_updated":"2020-07-14T12:46:15Z","file_id":"5060","relation":"main_file"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Crosses between closely related species give two contrasting results. One result is that species hybrids may be inferior to their parents, for example, being less fertile [1]. The other is that F1 hybrids may display superior performance (heterosis), for example with increased vigour [2]. Although various hypotheses have been proposed to account for these two aspects of hybridisation, their biological basis is still poorly understood [3]. To gain further insights into this issue, we analysed the role that variation in gene expression may play. We took a conserved trait, flower asymmetry in Antirrhinum, and determined the extent to which the underlying regulatory genes varied in expression among closely related species. We show that expression of both genes analysed, CYC and RAD, varies significantly between species because of cis-acting differences. By making a quantitative genotype-phenotype map, using a range of mutant alleles, we demonstrate that the species lie on a plateau in gene expression-morphology space, so that the variation has no detectable phenotypic effect. However, phenotypic differences can be revealed by shifting genotypes off the plateau through genetic crosses. Our results can be readily explained if genomes are free to evolve within an effectively neutral zone in gene expression space. The consequences of this drift will be negligible for individual loci, but when multiple loci across the genome are considered, we show that the variation may have significant effects on phenotype and fitness, causing a significant drift load. By considering these consequences for various gene-expression-fitness landscapes, we conclude that F1 hybrids might be expected to show increased performance with regard to conserved traits, such as basic physiology, but reduced performance with regard to others. Thus, our study provides a new way of explaining how various aspects of hybrid performance may arise through natural variation in gene activity."}],"issue":"7","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.1371/journal.pbio.1000429","language":[{"iso":"eng"}],"month":"07","year":"2010","acknowledgement":"This was supported by a Marie Curie grant for early stage training and the BBSRC-John Innes Centre PhD Rotation Program.\r\nWe would like to thank X. Feng and A. Hudson for assistance with introgressions and genotyping; A. Green, A. Bangham and J. Pateman for advice and assistance on shape model procedures; F. Alderson and S.Mitchell from JIC horticultural services; P.J. Wittkopp for protocols and advice on pyrosequencing; and R. Sablowski for discussions and comments.\r\n","publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"NiBa"}],"author":[{"full_name":"Rosas, Ulises","first_name":"Ulises","last_name":"Rosas"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Copsey, Lucy","last_name":"Copsey","first_name":"Lucy"},{"full_name":"Barbier De Reuille, Pierre","last_name":"Barbier De Reuille","first_name":"Pierre"},{"full_name":"Coen, Enrico","first_name":"Enrico","last_name":"Coen"}],"related_material":{"record":[{"id":"9764","relation":"research_data","status":"public"}]},"date_updated":"2023-02-23T14:07:34Z","date_created":"2018-12-11T12:05:07Z","volume":8,"article_number":"e1000429","file_date_updated":"2020-07-14T12:46:15Z","publist_id":"2448"},{"date_published":"2010-07-20T00:00:00Z","doi":"10.1371/journal.pbio.1000429.s003","citation":{"ama":"Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. Heterosis and the drift load. 2010. doi:10.1371/journal.pbio.1000429.s003","ista":"Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. 2010. Heterosis and the drift load, Public Library of Science, 10.1371/journal.pbio.1000429.s003.","apa":"Rosas, U., Barton, N. H., Copsey, L., Barbier De Reuille, P., & Coen, E. (2010). Heterosis and the drift load. Public Library of Science. https://doi.org/10.1371/journal.pbio.1000429.s003","ieee":"U. Rosas, N. H. Barton, L. Copsey, P. Barbier De Reuille, and E. Coen, “Heterosis and the drift load.” Public Library of Science, 2010.","mla":"Rosas, Ulises, et al. Heterosis and the Drift Load. Public Library of Science, 2010, doi:10.1371/journal.pbio.1000429.s003.","short":"U. Rosas, N.H. Barton, L. Copsey, P. Barbier De Reuille, E. Coen, (2010).","chicago":"Rosas, Ulises, Nicholas H Barton, Lucy Copsey, Pierre Barbier De Reuille, and Enrico Coen. “Heterosis and the Drift Load.” Public Library of Science, 2010. https://doi.org/10.1371/journal.pbio.1000429.s003."},"article_processing_charge":"No","month":"07","day":"20","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"3779"}]},"author":[{"full_name":"Rosas, Ulises","first_name":"Ulises","last_name":"Rosas"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"},{"last_name":"Copsey","first_name":"Lucy","full_name":"Copsey, Lucy"},{"first_name":"Pierre","last_name":"Barbier De Reuille","full_name":"Barbier De Reuille, Pierre"},{"last_name":"Coen","first_name":"Enrico","full_name":"Coen, Enrico"}],"oa_version":"Published Version","date_updated":"2023-02-23T11:42:17Z","date_created":"2021-08-02T09:45:39Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9764","year":"2010","publisher":"Public Library of Science","department":[{"_id":"NiBa"}],"status":"public","title":"Heterosis and the drift load","type":"research_data_reference"},{"author":[{"orcid":"0000-0002-0343-8329","id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","last_name":"Palero","first_name":"Ferran","full_name":"Palero, Ferran"},{"last_name":"Abello","first_name":"Pere","full_name":"Abello, Pere"},{"full_name":"Macpherson, E.","last_name":"Macpherson","first_name":"E."},{"first_name":"C.","last_name":"Matthee","full_name":"Matthee, C."},{"full_name":"Pascual, Marta","last_name":"Pascual","first_name":"Marta"}],"date_created":"2018-12-11T12:05:09Z","date_updated":"2023-10-16T09:51:05Z","oa_version":"None","volume":30,"year":"2010","_id":"3785","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","status":"public","title":"Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata)","department":[{"_id":"NiBa"}],"publisher":"Oxford University Press","intvolume":" 30","abstract":[{"lang":"eng","text":"Most fisheries involving spiny lobsters of the genus Palinurus have been over exploited during the last decades, so there is a raising concern about management decisions for these valuable resources. A total of 13 microsatellite DNA loci recently developed in Palinurus elephas were assayed in order to assess genetic diversity levels in every known species of the genus. Microsatellite markers gave amplifications and showed polymorphism in all species, with gene diversity values varying from 0.65060.077 SD (Palinurus barbarae) to 0.79260.051 SD (Palinurus elephas). Most importantly, when depth distribution was taken into account, shallower waters pecies consistently showed larger historical effective population sizes than their deeper-water counterparts. This could explain why deeper-water species are more sensitive to overfishing, and would indicate that overexploitation may have a larger impact on their long-term genetic diversity."}],"publist_id":"2442","issue":"4","type":"journal_article","doi":"10.1651/09-3192.1","date_published":"2010-10-01T00:00:00Z","language":[{"iso":"eng"}],"publication":"Journal of Crustacean Biology","citation":{"ista":"Palero F, Abello P, Macpherson E, Matthee C, Pascual M. 2010. Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata). Journal of Crustacean Biology. 30(4), 658–663.","ieee":"F. Palero, P. Abello, E. Macpherson, C. Matthee, and M. Pascual, “Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata),” Journal of Crustacean Biology, vol. 30, no. 4. Oxford University Press, pp. 658–663, 2010.","apa":"Palero, F., Abello, P., Macpherson, E., Matthee, C., & Pascual, M. (2010). Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata). Journal of Crustacean Biology. Oxford University Press. https://doi.org/10.1651/09-3192.1","ama":"Palero F, Abello P, Macpherson E, Matthee C, Pascual M. Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata). Journal of Crustacean Biology. 2010;30(4):658-663. doi:10.1651/09-3192.1","chicago":"Palero, Ferran, Pere Abello, E. Macpherson, C. Matthee, and Marta Pascual. “Genetic Diversity Levels in Fishery-Exploited Spiny Lobsters of the Genus Palinurus (Decapoda: Achelata).” Journal of Crustacean Biology. Oxford University Press, 2010. https://doi.org/10.1651/09-3192.1.","mla":"Palero, Ferran, et al. “Genetic Diversity Levels in Fishery-Exploited Spiny Lobsters of the Genus Palinurus (Decapoda: Achelata).” Journal of Crustacean Biology, vol. 30, no. 4, Oxford University Press, 2010, pp. 658–63, doi:10.1651/09-3192.1.","short":"F. Palero, P. Abello, E. Macpherson, C. Matthee, M. Pascual, Journal of Crustacean Biology 30 (2010) 658–663."},"quality_controlled":"1","page":"658 - 663","month":"10","day":"01","article_processing_charge":"No","publication_identifier":{"issn":["0278-0372"],"eissn":["1937-240X"]},"scopus_import":"1"},{"has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2009-08-01T00:00:00Z","citation":{"ama":"Davison A, Barton NH, Clarke B. The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails. Journal of Evolutionary Biology. 2009;22(8):1624-1635. doi:10.1111/j.1420-9101.2009.01770.x","ista":"Davison A, Barton NH, Clarke B. 2009. The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails. Journal of Evolutionary Biology. 22(8), 1624–1635.","apa":"Davison, A., Barton, N. H., & Clarke, B. (2009). The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/j.1420-9101.2009.01770.x","ieee":"A. Davison, N. H. Barton, and B. Clarke, “The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails,” Journal of Evolutionary Biology, vol. 22, no. 8. Wiley, pp. 1624–1635, 2009.","mla":"Davison, Angus, et al. “The Effect of Chirality Phenotype and Genotype on the Fecundity and Viability of Partula Suturalis and Lymnaea Stagnalis: Implications for the Evolution of Sinistral Snails.” Journal of Evolutionary Biology, vol. 22, no. 8, Wiley, 2009, pp. 1624–35, doi:10.1111/j.1420-9101.2009.01770.x.","short":"A. Davison, N.H. Barton, B. Clarke, Journal of Evolutionary Biology 22 (2009) 1624–1635.","chicago":"Davison, Angus, Nicholas H Barton, and Bryan Clarke. “The Effect of Chirality Phenotype and Genotype on the Fecundity and Viability of Partula Suturalis and Lymnaea Stagnalis: Implications for the Evolution of Sinistral Snails.” Journal of Evolutionary Biology. Wiley, 2009. https://doi.org/10.1111/j.1420-9101.2009.01770.x."},"publication":"Journal of Evolutionary Biology","page":"1624 - 1635","issue":"8","abstract":[{"text":"Why are sinistral snails so rare? Two main hypotheses are that selection acts against the establishment of new coiling morphs, because dextral and sinistral snails have trouble mating, or else a developmental constraint prevents the establishment of sinistrals. We therefore used an isolate of the snail Lymnaea stagnalis, in which sinistrals are rare, and populations of Partula suturalis, in which sinistrals are common, as well as a mathematical model, to understand the circumstances by which new morphs evolve. The main finding is that the sinistral genotype is associated with reduced egg viability in L. stagnalis, but in P. suturalis individuals of sinistral and dextral genotype appear equally fecund, implying a lack of a constraint. As positive frequency-dependent selection against the rare chiral morph in P. suturalis also operates over a narrow range (< 3%), the results suggest a model for chiral evolution in snails in which weak positive frequency-dependent selection may be overcome by a negative frequency-dependent selection, such as reproductive character displacement. In snails, there is not always a developmental constraint. As the direction of cleavage, and thus the directional asymmetry of the entire body, does not generally vary in other Spiralia (annelids, echiurans, vestimentiferans, sipunculids and nemerteans), it remains an open question as to whether this is because of a constraint and/or because most taxa do not have a conspicuous external asymmetry (like a shell) upon which selection can act.","lang":"eng"}],"type":"journal_article","pubrep_id":"553","file":[{"file_name":"Davison_JEB_v31_2009.pdf","access_level":"open_access","creator":"dernst","file_size":2583812,"content_type":"application/pdf","file_id":"6044","relation":"main_file","date_created":"2019-02-22T09:21:44Z","date_updated":"2020-07-14T12:46:15Z","checksum":"f70c15c6ab9306121d4153a3be0d2346"}],"oa_version":"Submitted Version","_id":"3780","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 22","title":"The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails","status":"public","ddc":["570"],"month":"08","doi":"10.1111/j.1420-9101.2009.01770.x","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","publist_id":"2447","file_date_updated":"2020-07-14T12:46:15Z","author":[{"last_name":"Davison","first_name":"Angus","full_name":"Davison, Angus"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"first_name":"Bryan","last_name":"Clarke","full_name":"Clarke, Bryan"}],"volume":22,"date_created":"2018-12-11T12:05:08Z","date_updated":"2021-01-12T07:52:09Z","acknowledgement":"We owe a great debt to Jim Murray for his many contributions to the study of Partula, in the field, in the laboratory, in the interpretation of data, and in generating new ideas about evolution. With pleasure and respect we dedicate this paper to him. Jim Murray played a leading role in making the collections used here. We are very grateful also to Ann Clarke and Elizabeth Murray for help with collecting, to Lorna Stewart for snail dissections, to Joris Koene for the gift of snails, to Natasha Constant for entering the data, and Takahiro Asami, Edmund Gittenberger and Gerhard Falkner for establishing the sinistral stock of L. stagnalis. Comments from an anonymous referee, A. Richard Palmer and the editorial board improved the manuscript. Work in the field was supported by the Royal Society, The Carnegie Trust, the Percy Sladen Trust and the National Science Foundation. The Science Research Council (B/SR/4144), the National Science Foundation (GB-4188), the Royal Society and the University of Nottingham supported work in the laboratory.","year":"2009","department":[{"_id":"NiBa"}],"publisher":"Wiley","publication_status":"published"},{"issue":"5","abstract":[{"text":"Populations living in a spatially and temporally changing environment can adapt to the changing optimum and/or migrate toward favorable habitats. Here we extend previous analyses with a static optimum to allow the environment to vary in time as well as in space. The model follows both population dynamics and the trait mean under stabilizing selection, and the outcomes can be understood by comparing the loads due to genetic variance, dispersal, and temporal change. With fixed genetic variance, we obtain two regimes: (1) adaptation that is uniform along the environmental gradient and that responds to the moving optimum as expected for panmictic populations and when the spatial gradient is sufficiently steep, and (2) a population with limited range that adapts more slowly than the environmental optimum changes in both time and space; the population therefore becomes locally extinct and migrates toward suitable habitat. We also use a population‐genetic model with many loci to allow genetic variance to evolve, and we show that the only solution now has uniform adaptation.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","pubrep_id":"552","intvolume":" 174","status":"public","title":"Species' range: Adaptation in space and time","ddc":["570"],"_id":"4136","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","day":"05","scopus_import":1,"date_published":"2009-11-05T00:00:00Z","page":"E186 - E204","article_type":"original","citation":{"chicago":"Polechova, Jitka, Nicholas H Barton, and Glenn Marion. “Species’ Range: Adaptation in Space and Time.” American Naturalist. University of Chicago Press, 2009. https://doi.org/10.1086/605958.","mla":"Polechova, Jitka, et al. “Species’ Range: Adaptation in Space and Time.” American Naturalist, vol. 174, no. 5, University of Chicago Press, 2009, pp. E186–204, doi:10.1086/605958.","short":"J. Polechova, N.H. Barton, G. Marion, American Naturalist 174 (2009) E186–E204.","ista":"Polechova J, Barton NH, Marion G. 2009. Species’ range: Adaptation in space and time. American Naturalist. 174(5), E186–E204.","ieee":"J. Polechova, N. H. Barton, and G. Marion, “Species’ range: Adaptation in space and time,” American Naturalist, vol. 174, no. 5. University of Chicago Press, pp. E186–E204, 2009.","apa":"Polechova, J., Barton, N. H., & Marion, G. (2009). Species’ range: Adaptation in space and time. American Naturalist. University of Chicago Press. https://doi.org/10.1086/605958","ama":"Polechova J, Barton NH, Marion G. Species’ range: Adaptation in space and time. American Naturalist. 2009;174(5):E186-E204. doi:10.1086/605958"},"publication":"American Naturalist","publist_id":"1986","volume":174,"date_created":"2018-12-11T12:07:09Z","date_updated":"2021-01-12T07:54:46Z","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1086/659642"}]},"author":[{"orcid":"0000-0003-0951-3112","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","last_name":"Polechova","first_name":"Jitka","full_name":"Polechova, Jitka"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"full_name":"Marion, Glenn","last_name":"Marion","first_name":"Glenn"}],"department":[{"_id":"NiBa"}],"publisher":"University of Chicago Press","publication_status":"published","pmid":1,"year":"2009","month":"11","language":[{"iso":"eng"}],"doi":"10.1086/605958","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.doi.org/10.1086/605958"}],"external_id":{"pmid":[" 19788353"]},"oa":1},{"acknowledgement":"This work was supported by a Royal Society/Wolfson Research Merit award, and by a grant from the Natural Environment Research Council.\r\nWe are very grateful for insightful comments from S. P. Otto, and for helpful suggestions from the referees and the Associate Editor, Maria Servedio.","year":"2009","publication_status":"published","publisher":"Wiley","department":[{"_id":"NiBa"}],"author":[{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"first_name":"Maria","last_name":"De Cara","full_name":"De Cara, Maria"}],"date_updated":"2021-01-12T07:55:33Z","date_created":"2018-12-11T12:07:48Z","volume":63,"file_date_updated":"2020-07-14T12:46:25Z","publist_id":"1866","oa":1,"quality_controlled":"1","doi":"10.1111/j.1558-5646.2009.00622.x","language":[{"iso":"eng"}],"month":"05","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"4242","status":"public","ddc":["570"],"title":"The evolution of strong reproductive isolation","intvolume":" 63","pubrep_id":"551","oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"4903","date_created":"2018-12-12T10:11:46Z","date_updated":"2020-07-14T12:46:25Z","checksum":"1920d2e25ef335833764256c1a47bbfb","file_name":"IST-2016-551-v1+1_BartonDeCaraRevNew.pdf","access_level":"open_access","content_type":"application/pdf","file_size":720913,"creator":"system"},{"file_size":290160,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2016-551-v1+2_BartonDeCaraRevNewSI.pdf","checksum":"c1c51bbc10d4f328fc96fc5b0e5dc25d","date_updated":"2020-07-14T12:46:25Z","date_created":"2018-12-12T10:11:47Z","relation":"main_file","file_id":"4904"}],"type":"journal_article","abstract":[{"text":"Felsenstein distinguished two ways by which selection can directly strengthen isolation. First, a modifier that strengthens prezygotic isolation can be favored everywhere. This fits with the traditional view of reinforcement as an adaptation to reduce deleterious hybridization by strengthening assortative mating. Second, selection can favor association between different incompatibilities, despite recombination. We generalize this “two allele” model to follow associations among any number of incompatibilities, which may include both assortment and hybrid inviability. Our key argument is that this process, of coupling between incompatibilities, may be quite different from the usual view of reinforcement: strong isolation can evolve through the coupling of any kind of incompatibility, whether prezygotic or postzygotic. Single locus incompatibilities become coupled because associations between them increase the variance in compatibility, which in turn increases mean fitness if there is positive epistasis. Multiple incompatibilities, each maintained by epistasis, can become coupled in the same way. In contrast, a single-locus incompatibility can become coupled with loci that reduce the viability of haploid hybrids because this reduces harmful recombination. We obtain simple approximations for the limits of tight linkage, and strong assortment, and show how assortment alleles can invade through associations with other components of reproductive isolation.","lang":"eng"}],"issue":"5","publication":"Evolution; International Journal of Organic Evolution","citation":{"chicago":"Barton, Nicholas H, and Maria De Cara. “The Evolution of Strong Reproductive Isolation.” Evolution; International Journal of Organic Evolution. Wiley, 2009. https://doi.org/10.1111/j.1558-5646.2009.00622.x.","short":"N.H. Barton, M. De Cara, Evolution; International Journal of Organic Evolution 63 (2009) 1171–1190.","mla":"Barton, Nicholas H., and Maria De Cara. “The Evolution of Strong Reproductive Isolation.” Evolution; International Journal of Organic Evolution, vol. 63, no. 5, Wiley, 2009, pp. 1171–90, doi:10.1111/j.1558-5646.2009.00622.x.","apa":"Barton, N. H., & De Cara, M. (2009). The evolution of strong reproductive isolation. Evolution; International Journal of Organic Evolution. Wiley. https://doi.org/10.1111/j.1558-5646.2009.00622.x","ieee":"N. H. Barton and M. De Cara, “The evolution of strong reproductive isolation,” Evolution; International Journal of Organic Evolution, vol. 63, no. 5. Wiley, pp. 1171–1190, 2009.","ista":"Barton NH, De Cara M. 2009. The evolution of strong reproductive isolation. Evolution; International Journal of Organic Evolution. 63(5), 1171–1190.","ama":"Barton NH, De Cara M. The evolution of strong reproductive isolation. Evolution; International Journal of Organic Evolution. 2009;63(5):1171-1190. doi:10.1111/j.1558-5646.2009.00622.x"},"page":"1171 - 1190","date_published":"2009-05-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1"},{"abstract":[{"text":"Sex and recombination have long been seen as adaptations that facilitate natural selection by generating favorable variations. If recombination is to aid selection, there must be negative linkage disequilibria—favorable alleles must be found together less often than expected by chance. These negative linkage disequilibria can be generated directly by selection, but this must involve negative epistasis of just the right strength, which is not expected, from either experiment or theory. Random drift provides a more general source of negative associations: Favorable mutations almost always arise on different genomes, and negative associations tend to persist, precisely because they shield variation from selection.\r\n\r\nWe can understand how recombination aids adaptation by determining the maximum possible rate of adaptation. With unlinked loci, this rate increases only logarithmically with the influx of favorable mutations. With a linear genome, a scaling argument shows that in a large population, the rate of adaptive substitution depends only on the expected rate in the absence of interference, divided by the total rate of recombination. A two-locus approximation predicts an upper bound on the rate of substitution, proportional to recombination rate.\r\n\r\nIf associations between linked loci do impede adaptation, there can be substantial selection for modifiers that increase recombination. Whether this can account for the maintenance of high rates of sex and recombination depends on the extent of selection. It is clear that the rate of species-wide substitutions is typically far too low to generate appreciable selection for recombination. However, local sweeps within a subdivided population may be effective.","lang":"eng"}],"publist_id":"2708","type":"book_chapter","author":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"date_created":"2018-12-11T12:04:33Z","date_updated":"2021-01-12T07:45:04Z","oa_version":"None","volume":74,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3675","year":"2009","acknowledgement":"Royal Society and the Engineering and Physical Sciences for support (GR/ T11753/01)","publication_status":"published","status":"public","title":"Why sex and recombination? ","intvolume":" 74","publisher":"Cold Spring Harbor Laboratory Press","department":[{"_id":"NiBa"}],"month":"11","day":"10","scopus_import":1,"doi":"10.1101/sqb.2009.74.030","date_published":"2009-11-10T00:00:00Z","language":[{"iso":"eng"}],"publication":"Cold Spring Harbor Symposia on Quantitative Biology","citation":{"ama":"Barton NH. Why sex and recombination? . In: Cold Spring Harbor Symposia on Quantitative Biology. Vol 74. Cold Spring Harbor Laboratory Press; 2009:187-195. doi:10.1101/sqb.2009.74.030","ista":"Barton NH. 2009.Why sex and recombination? . In: Cold Spring Harbor Symposia on Quantitative Biology. vol. 74, 187–195.","apa":"Barton, N. H. (2009). Why sex and recombination? . In Cold Spring Harbor Symposia on Quantitative Biology (Vol. 74, pp. 187–195). Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/sqb.2009.74.030","ieee":"N. H. Barton, “Why sex and recombination? ,” in Cold Spring Harbor Symposia on Quantitative Biology, vol. 74, Cold Spring Harbor Laboratory Press, 2009, pp. 187–195.","mla":"Barton, Nicholas H. “Why Sex and Recombination? .” Cold Spring Harbor Symposia on Quantitative Biology, vol. 74, Cold Spring Harbor Laboratory Press, 2009, pp. 187–95, doi:10.1101/sqb.2009.74.030.","short":"N.H. Barton, in:, Cold Spring Harbor Symposia on Quantitative Biology, Cold Spring Harbor Laboratory Press, 2009, pp. 187–195.","chicago":"Barton, Nicholas H. “Why Sex and Recombination? .” In Cold Spring Harbor Symposia on Quantitative Biology, 74:187–95. Cold Spring Harbor Laboratory Press, 2009. https://doi.org/10.1101/sqb.2009.74.030."},"quality_controlled":"1","page":"187 - 195"},{"publisher":"Elsevier","department":[{"_id":"NiBa"}],"publication_status":"published","acknowledgement":"This work was supported by a Royal Society/Wolfson Award, and by grants EP/T11753/01, EP/C546318/01 from the EPSRC.\r\nWe are grateful to M. Cates, H.P. de Vladar and G. Sella, and to two anonymous referees, for their helpful comments.","year":"2009","volume":259,"date_created":"2018-12-11T12:05:06Z","date_updated":"2021-01-12T07:52:06Z","author":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"},{"last_name":"Coe","first_name":"Jason","full_name":"Coe, Jason"}],"publist_id":"2452","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-00554594/document","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.jtbi.2009.03.019","month":"07","intvolume":" 259","status":"public","title":"On the application of statistical physics to evolutionary biology","_id":"3775","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"There is a close analogy between statistical thermodynamics and the evolution of allele frequencies under mutation, selection and random drift. Wright's formula for the stationary distribution of allele frequencies is analogous to the Boltzmann distribution in statistical physics. Population size, 2N, plays the role of the inverse temperature, 1/kT, and determines the magnitude of random fluctuations. Log mean fitness, View the MathML source, tends to increase under selection, and is analogous to a (negative) energy; a potential function, U, increases under mutation in a similar way. An entropy, SH, can be defined which measures the deviation from the distribution of allele frequencies expected under random drift alone; the sum View the MathML source gives a free fitness that increases as the population evolves towards its stationary distribution. Usually, we observe the distribution of a few quantitative traits that depend on the frequencies of very many alleles. The mean and variance of such traits are analogous to observable quantities in statistical thermodynamics. Thus, we can define an entropy, SΩ, which measures the volume of allele frequency space that is consistent with the observed trait distribution. The stationary distribution of the traits is View the MathML source; this applies with arbitrary epistasis and dominance. The entropies SΩ, SH are distinct, but converge when there are so many alleles that traits fluctuate close to their expectations. Populations tend to evolve towards states that can be realised in many ways (i.e., large SΩ), which may lead to a substantial drop below the adaptive peak; we illustrate this point with a simple model of genetic redundancy. This analogy with statistical thermodynamics brings together previous ideas in a general framework, and justifies a maximum entropy approximation to the dynamics of quantitative traits."}],"page":"317 - 324","citation":{"apa":"Barton, N. H., & Coe, J. (2009). On the application of statistical physics to evolutionary biology. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2009.03.019","ieee":"N. H. Barton and J. Coe, “On the application of statistical physics to evolutionary biology,” Journal of Theoretical Biology, vol. 259, no. 2. Elsevier, pp. 317–324, 2009.","ista":"Barton NH, Coe J. 2009. On the application of statistical physics to evolutionary biology. Journal of Theoretical Biology. 259(2), 317–324.","ama":"Barton NH, Coe J. On the application of statistical physics to evolutionary biology. Journal of Theoretical Biology. 2009;259(2):317-324. doi:10.1016/j.jtbi.2009.03.019","chicago":"Barton, Nicholas H, and Jason Coe. “On the Application of Statistical Physics to Evolutionary Biology.” Journal of Theoretical Biology. Elsevier, 2009. https://doi.org/10.1016/j.jtbi.2009.03.019.","short":"N.H. Barton, J. Coe, Journal of Theoretical Biology 259 (2009) 317–324.","mla":"Barton, Nicholas H., and Jason Coe. “On the Application of Statistical Physics to Evolutionary Biology.” Journal of Theoretical Biology, vol. 259, no. 2, Elsevier, 2009, pp. 317–24, doi:10.1016/j.jtbi.2009.03.019."},"publication":"Journal of Theoretical Biology","date_published":"2009-07-21T00:00:00Z","scopus_import":1,"day":"21"},{"page":"997 - 1011","quality_controlled":"1","citation":{"short":"N.H. Barton, H. De Vladar, Genetics 181 (2009) 997–1011.","mla":"Barton, Nicholas H., and Harold De Vladar. “Statistical Mechanics and the Evolution of Polygenic Quantitative Traits.” Genetics, vol. 181, no. 3, Genetics Society of America, 2009, pp. 997–1011, doi:10.1534/genetics.108.099309.","chicago":"Barton, Nicholas H, and Harold De Vladar. “Statistical Mechanics and the Evolution of Polygenic Quantitative Traits.” Genetics. Genetics Society of America, 2009. https://doi.org/10.1534/genetics.108.099309.","ama":"Barton NH, De Vladar H. Statistical mechanics and the evolution of polygenic quantitative traits. Genetics. 2009;181(3):997-1011. doi:10.1534/genetics.108.099309","ieee":"N. H. Barton and H. De Vladar, “Statistical mechanics and the evolution of polygenic quantitative traits,” Genetics, vol. 181, no. 3. Genetics Society of America, pp. 997–1011, 2009.","apa":"Barton, N. H., & De Vladar, H. (2009). Statistical mechanics and the evolution of polygenic quantitative traits. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.108.099309","ista":"Barton NH, De Vladar H. 2009. Statistical mechanics and the evolution of polygenic quantitative traits. Genetics. 181(3), 997–1011."},"publication":"Genetics","language":[{"iso":"eng"}],"date_published":"2009-03-01T00:00:00Z","doi":"10.1534/genetics.108.099309","scopus_import":1,"day":"01","month":"03","department":[{"_id":"NiBa"}],"intvolume":" 181","publisher":"Genetics Society of America","title":"Statistical mechanics and the evolution of polygenic quantitative traits","publication_status":"published","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"4231","acknowledgement":"N.B. was supported by the Engineering and Physical Sciences Research Council (GR/T11753 and GR/T19537) and by the Royal Society.\r\nWe are grateful to Ellen Baake for helping to initiate this project and for her comments on this manuscript. We also thank Michael Turelli for his comments on the manuscript and I. Pen for discussions and support in this project. This project was a result of a collaboration supported by the European Science Foundation grant “Integrating population genetics and conservation biology.” ","year":"2009","volume":181,"oa_version":"None","date_created":"2018-12-11T12:07:44Z","date_updated":"2021-01-12T07:55:29Z","author":[{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"De Vladar, Harold","last_name":"De Vladar","first_name":"Harold"}],"type":"journal_article","issue":"3","publist_id":"1882","abstract":[{"text":"The evolution of quantitative characters depends on the frequencies of the alleles involved, yet these frequencies cannot usually be measured. Previous groups have proposed an approximation to the dynamics of quantitative traits, based on an analogy with statistical mechanics. We present a modified version of that approach, which makes the analogy more precise and applies quite generally to describe the evolution of allele frequencies. We calculate explicitly how the macroscopic quantities (i.e., quantities that depend on the quantitative trait) depend on evolutionary forces, in a way that is independent of the microscopic details. We first show that the stationary distribution of allele frequencies under drift, selection, and mutation maximizes a certain measure of entropy, subject to constraints on the expectation of observable quantities. We then approximate the dynamical changes in these expectations, assuming that the distribution of allele frequencies always maximizes entropy, conditional on the expected values. When applied to directional selection on an additive trait, this gives a very good approximation to the evolution of the trait mean and the genetic variance, when the number of mutations per generation is sufficiently high (4Nμ > 1). We show how the method can be modified for small mutation rates (4Nμ → 0). We outline how this method describes epistatic interactions as, for example, with stabilizing selection.","lang":"eng"}]}]