[{"type":"research_data_reference","related_material":{"record":[{"id":"1158","relation":"used_in_publication","status":"public"}]},"author":[{"full_name":"Roux, Camille","last_name":"Roux","first_name":"Camille"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","first_name":"Christelle","last_name":"Fraisse","full_name":"Fraisse, Christelle"},{"last_name":"Romiguier","first_name":"Jonathan","full_name":"Romiguier, Jonathan"},{"full_name":"Anciaux, Youann","first_name":"Youann","last_name":"Anciaux"},{"first_name":"Nicolas","last_name":"Galtier","full_name":"Galtier, Nicolas"},{"last_name":"Bierne","first_name":"Nicolas","full_name":"Bierne, Nicolas"}],"oa_version":"Published Version","date_created":"2021-08-10T08:20:17Z","date_updated":"2023-02-21T16:21:20Z","year":"2016","_id":"9862","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publisher":"Public Library of Science","title":"Simulation study to test the robustness of ABC in face of recent times of divergence","status":"public","article_processing_charge":"No","month":"12","day":"27","doi":"10.1371/journal.pbio.2000234.s016","citation":{"ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Simulation study to test the robustness of ABC in face of recent times of divergence. 2016. doi:10.1371/journal.pbio.2000234.s016","apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne, N. (2016). Simulation study to test the robustness of ABC in face of recent times of divergence. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234.s016","ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Simulation study to test the robustness of ABC in face of recent times of divergence.” Public Library of Science, 2016.","ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Simulation study to test the robustness of ABC in face of recent times of divergence, Public Library of Science, 10.1371/journal.pbio.2000234.s016.","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).","mla":"Roux, Camille, et al. Simulation Study to Test the Robustness of ABC in Face of Recent Times of Divergence. Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234.s016.","chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Simulation Study to Test the Robustness of ABC in Face of Recent Times of Divergence.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pbio.2000234.s016."}},{"article_processing_charge":"No","month":"12","day":"27","citation":{"mla":"Roux, Camille, et al. Accessions of Surveyed Individuals, Geographic Locations and Summary Statistics. Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234.s017.","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).","chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Accessions of Surveyed Individuals, Geographic Locations and Summary Statistics.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pbio.2000234.s017.","ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Accessions of surveyed individuals, geographic locations and summary statistics. 2016. doi:10.1371/journal.pbio.2000234.s017","ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Accessions of surveyed individuals, geographic locations and summary statistics, Public Library of Science, 10.1371/journal.pbio.2000234.s017.","apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne, N. (2016). Accessions of surveyed individuals, geographic locations and summary statistics. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234.s017","ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Accessions of surveyed individuals, geographic locations and summary statistics.” Public Library of Science, 2016."},"doi":"10.1371/journal.pbio.2000234.s017","type":"research_data_reference","year":"2016","_id":"9863","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publisher":"Public Library of Science","title":"Accessions of surveyed individuals, geographic locations and summary statistics","status":"public","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1158"}]},"author":[{"first_name":"Camille","last_name":"Roux","full_name":"Roux, Camille"},{"last_name":"Fraisse","first_name":"Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle"},{"last_name":"Romiguier","first_name":"Jonathan","full_name":"Romiguier, Jonathan"},{"first_name":"Youann","last_name":"Anciaux","full_name":"Anciaux, Youann"},{"first_name":"Nicolas","last_name":"Galtier","full_name":"Galtier, Nicolas"},{"last_name":"Bierne","first_name":"Nicolas","full_name":"Bierne, Nicolas"}],"oa_version":"Published Version","date_updated":"2023-02-21T16:21:20Z","date_created":"2021-08-10T08:22:52Z"},{"day":"01","article_processing_charge":"No","has_accepted_license":"1","page":"124","citation":{"ista":"Novak S. 2016. Evolutionary proccesses in variable emvironments. Institute of Science and Technology Austria.","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.","ama":"Novak S. Evolutionary proccesses in variable emvironments. 2016.","chicago":"Novak, Sebastian. “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.","short":"S. Novak, Evolutionary Proccesses in Variable Emvironments, Institute of Science and Technology Austria, 2016."},"date_published":"2016-07-01T00:00:00Z","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"}],"ddc":["576"],"status":"public","title":"Evolutionary proccesses in variable emvironments","_id":"1125","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"file_name":"Novak_thesis.pdf","access_level":"closed","creator":"dernst","content_type":"application/pdf","file_size":3564901,"file_id":"6811","relation":"main_file","date_updated":"2019-08-13T09:01:00Z","date_created":"2019-08-13T09:01:00Z","checksum":"81dcc838dfcf7aa0b1a27ecf4fe2da4e"},{"access_level":"open_access","file_name":"2016_Novak_Thesis.pdf","file_size":2814384,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"9186","checksum":"30808d2f7ca920e09f63a95cdc49bffd","success":1,"date_updated":"2021-02-22T13:42:47Z","date_created":"2021-02-22T13:42:47Z"}],"month":"07","publication_identifier":{"issn":["2663-337X"]},"oa":1,"degree_awarded":"PhD","supervisor":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"language":[{"iso":"eng"}],"file_date_updated":"2021-02-22T13:42:47Z","publist_id":"6235","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","year":"2016","date_created":"2018-12-11T11:50:17Z","date_updated":"2023-09-07T11:55:53Z","author":[{"full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-824X","first_name":"Sebastian","last_name":"Novak"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"2023"}]}},{"_id":"1358","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 7","ddc":["576"],"status":"public","title":"Intrinsic limits to gene regulation by global crosstalk","pubrep_id":"627","oa_version":"Published Version","file":[{"file_name":"IST-2016-627-v1+1_ncomms12307.pdf","access_level":"open_access","creator":"system","file_size":861805,"content_type":"application/pdf","file_id":"4919","relation":"main_file","date_created":"2018-12-12T10:12:01Z","date_updated":"2020-07-14T12:44:46Z","checksum":"fe3f3a1526d180b29fe691ab11435b78"},{"access_level":"open_access","file_name":"IST-2016-627-v1+2_ncomms12307-s1.pdf","creator":"system","content_type":"application/pdf","file_size":1084703,"file_id":"4920","relation":"main_file","checksum":"164864a1a675f3ad80e9917c27aba07f","date_created":"2018-12-12T10:12:02Z","date_updated":"2020-07-14T12:44:46Z"}],"type":"journal_article","abstract":[{"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.","lang":"eng"}],"citation":{"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).","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.","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","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."},"publication":"Nature Communications","date_published":"2016-08-04T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"04","year":"2016","department":[{"_id":"GaTk"},{"_id":"NiBa"},{"_id":"CaGu"}],"publisher":"Nature Publishing Group","publication_status":"published","related_material":{"record":[{"id":"6071","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Friedlander, Tamar","last_name":"Friedlander","first_name":"Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Prizak, Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","first_name":"Roshan","last_name":"Prizak"},{"full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"},{"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":"Tkacik, Gasper","last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"volume":7,"date_updated":"2023-09-07T12:53:49Z","date_created":"2018-12-11T11:51:34Z","article_number":"12307","publist_id":"5887","ec_funded":1,"file_date_updated":"2020-07-14T12:44:46Z","license":"https://creativecommons.org/licenses/by/4.0/","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,"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"},{"call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27"}],"quality_controlled":"1","doi":"10.1038/ncomms12307","language":[{"iso":"eng"}],"month":"08"},{"type":"research_data_reference","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"}],"publisher":"Dryad","department":[{"_id":"NiBa"}],"title":"Data from: How does epistasis influence the response to selection?","status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9710","year":"2016","oa_version":"Published Version","date_created":"2021-07-23T11:45:47Z","date_updated":"2023-09-20T11:17:47Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1199"}]},"author":[{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"article_processing_charge":"No","day":"23","month":"09","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.s5s7r"}],"citation":{"ista":"Barton NH. 2016. Data from: How does epistasis influence the response to selection?, Dryad, 10.5061/dryad.s5s7r.","apa":"Barton, N. H. (2016). Data from: How does epistasis influence the response to selection? Dryad. https://doi.org/10.5061/dryad.s5s7r","ieee":"N. H. Barton, “Data from: How does epistasis influence the response to selection?” Dryad, 2016.","ama":"Barton NH. Data from: How does epistasis influence the response to selection? 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.","mla":"Barton, Nicholas H. Data from: How Does Epistasis Influence the Response to Selection? Dryad, 2016, doi:10.5061/dryad.s5s7r.","short":"N.H. Barton, (2016)."},"oa":1,"date_published":"2016-09-23T00:00:00Z","doi":"10.5061/dryad.s5s7r"},{"publisher":"The Royal Society","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"title":"Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family","status":"public","_id":"9864","year":"2016","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","date_updated":"2023-09-20T11:56:33Z","date_created":"2021-08-10T08:29:47Z","related_material":{"record":[{"id":"1077","status":"public","relation":"used_in_publication"}]},"author":[{"full_name":"Fernandes Redondo, Rodrigo A","orcid":"0000-0002-5837-2793","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","last_name":"Fernandes Redondo","first_name":"Rodrigo A"},{"id":"2A181218-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5985-7653","first_name":"Harold","last_name":"de Vladar","full_name":"de Vladar, Harold"},{"full_name":"Włodarski, Tomasz","last_name":"Włodarski","first_name":"Tomasz"},{"last_name":"Bollback","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P"}],"type":"research_data_reference","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"}],"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.4315652.v1","open_access":"1"}],"citation":{"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","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)."},"oa":1,"doi":"10.6084/m9.figshare.4315652.v1","date_published":"2016-12-14T00:00:00Z","article_processing_charge":"No","month":"12","day":"14"},{"month":"06","day":"1","scopus_import":1,"language":[{"iso":"eng"}],"doi":"10.1093/aob/mcw043","date_published":"2016-06-01T00:00:00Z","quality_controlled":"1","page":"1133 - 1140","publication":"Annals of Botany","citation":{"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.","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"},"abstract":[{"lang":"eng","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."}],"issue":"7","publist_id":"5828","type":"journal_article","date_created":"2018-12-11T11:51:42Z","date_updated":"2024-02-21T13:49:53Z","oa_version":"None","volume":117,"author":[{"orcid":"0000-0002-8511-0254","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","last_name":"Ellis","first_name":"Thomas","full_name":"Ellis, Thomas"},{"last_name":"Field","first_name":"David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","full_name":"Field, David"}],"related_material":{"record":[{"status":"public","relation":"popular_science","id":"5550"}]},"publication_status":"published","status":"public","title":"Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae","publisher":"Oxford University Press","department":[{"_id":"NiBa"}],"intvolume":" 117","year":"2016","_id":"1382","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"},{"date_created":"2018-12-11T11:51:47Z","date_updated":"2024-02-21T13:51:39Z","author":[{"orcid":"0000-0002-8511-0254","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","last_name":"Ellis","first_name":"Thomas","full_name":"Ellis, Thomas"}],"related_material":{"record":[{"id":"5553","status":"public","relation":"popular_science"},{"id":"5551","relation":"popular_science","status":"public"},{"relation":"popular_science","status":"public","id":"5552"}]},"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","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. ","year":"2016","file_date_updated":"2020-07-14T12:44:48Z","publist_id":"5809","supervisor":[{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:TH_526 ","oa":1,"month":"02","publication_identifier":{"issn":["2663-337X"]},"file":[{"access_level":"open_access","file_name":"IST-2016-526-v1+1_Ellis_signed_thesis.pdf","creator":"system","file_size":11928241,"content_type":"application/pdf","file_id":"5106","relation":"main_file","checksum":"a89b17ff27cf92c9a15f6b3d46bd7e53","date_created":"2018-12-12T10:14:51Z","date_updated":"2020-07-14T12:44:48Z"}],"oa_version":"Published Version","pubrep_id":"526","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"],"_id":"1398","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_published":"2016-02-18T00:00:00Z","page":"130","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 ."},"day":"18","has_accepted_license":"1","article_processing_charge":"No"},{"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"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.","lang":"eng"}],"status":"public","ddc":["576"],"title":"Evolution of transcriptional regulatory sequences","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"1131","oa_version":"Published Version","file":[{"creator":"dernst","file_size":3695257,"content_type":"application/pdf","access_level":"closed","file_name":"Tugrul_thesis_w_signature_page.pdf","checksum":"66cb61a59943e4fb7447c6a86be5ef51","date_updated":"2019-08-13T08:53:52Z","date_created":"2019-08-13T08:53:52Z","file_id":"6810","relation":"main_file"},{"access_level":"open_access","file_name":"2016_Tugrul_Thesis.pdf","content_type":"application/pdf","file_size":3880811,"creator":"dernst","relation":"main_file","file_id":"9182","checksum":"293e388d70563760f6b24c3e66283dda","success":1,"date_created":"2021-02-22T11:45:20Z","date_updated":"2021-02-22T11:45:20Z"}],"article_processing_charge":"No","has_accepted_license":"1","day":"01","page":"89","citation":{"ieee":"M. Tugrul, “Evolution of transcriptional regulatory sequences,” Institute of Science and Technology Austria, 2016.","apa":"Tugrul, M. (2016). Evolution of transcriptional regulatory sequences. Institute of Science and Technology Austria.","ista":"Tugrul M. 2016. Evolution of transcriptional regulatory sequences. Institute of Science and Technology Austria.","ama":"Tugrul M. Evolution of transcriptional regulatory sequences. 2016.","chicago":"Tugrul, Murat. “Evolution of Transcriptional Regulatory Sequences.” Institute of Science and Technology Austria, 2016.","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."},"date_published":"2016-07-01T00:00:00Z","publist_id":"6229","file_date_updated":"2021-02-22T11:45:20Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"}],"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":[{"relation":"part_of_dissertation","status":"public","id":"1666"},{"relation":"research_data","status":"public","id":"5554"}]},"author":[{"orcid":"0000-0002-8523-0758","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","last_name":"Tugrul","first_name":"Murat","full_name":"Tugrul, Murat"}],"publication_identifier":{"issn":["2663-337X"]},"month":"07","oa":1,"language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}]},{"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"}],"publist_id":"5768","ec_funded":1,"publication_status":"published","status":"public","title":"First steps towards a runtime comparison of natural and artificial evolution","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publisher":"ACM","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1430","year":"2015","date_updated":"2021-01-12T06:50:41Z","date_created":"2018-12-11T11:51:58Z","oa_version":"Preprint","author":[{"full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","first_name":"Tiago"},{"last_name":"Sudholt","first_name":"Dirk","full_name":"Sudholt, Dirk"},{"last_name":"Heredia","first_name":"Jorge","full_name":"Heredia, Jorge"},{"last_name":"Trubenova","first_name":"Barbora","orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87","full_name":"Trubenova, Barbora"}],"scopus_import":1,"day":"11","month":"07","quality_controlled":"1","page":"1455 - 1462","project":[{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091","call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"}],"publication":"Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1504.06260"}],"oa":1,"citation":{"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.","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."},"language":[{"iso":"eng"}],"conference":{"location":"Madrid, Spain","start_date":"2015-07-11","end_date":"2015-07-15","name":"GECCO: Genetic and evolutionary computation conference"},"date_published":"2015-07-11T00:00:00Z","doi":"10.1145/2739480.2754758"}]