[{"citation":{"ista":"Novak S. 2016. Evolutionary proccesses in variable emvironments. Institute of Science and Technology Austria.","chicago":"Novak, Sebastian. “Evolutionary Proccesses in Variable Emvironments.” Institute of Science and Technology Austria, 2016.","apa":"Novak, S. (2016). Evolutionary proccesses in variable emvironments. Institute of Science and Technology Austria.","ama":"Novak S. Evolutionary proccesses in variable emvironments. 2016.","short":"S. Novak, Evolutionary Proccesses in Variable Emvironments, Institute of Science and Technology Austria, 2016.","ieee":"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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","publist_id":"6235","author":[{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","full_name":"Novak, Sebastian","orcid":"0000-0002-2519-824X","last_name":"Novak"}],"title":"Evolutionary proccesses in variable emvironments","year":"2016","has_accepted_license":"1","day":"01","page":"124","date_created":"2018-12-11T11:50:17Z","date_published":"2016-07-01T00:00:00Z","oa":1,"publisher":"Institute of Science and Technology Austria","date_updated":"2023-09-07T11:55:53Z","supervisor":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"ddc":["576"],"department":[{"_id":"NiBa"}],"file_date_updated":"2021-02-22T13:42:47Z","_id":"1125","type":"dissertation","status":"public","publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2019-08-13T09:01:00Z","file_name":"Novak_thesis.pdf","creator":"dernst","date_updated":"2019-08-13T09:01:00Z","file_size":3564901,"file_id":"6811","checksum":"81dcc838dfcf7aa0b1a27ecf4fe2da4e","access_level":"closed","relation":"main_file","content_type":"application/pdf"},{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"9186","checksum":"30808d2f7ca920e09f63a95cdc49bffd","creator":"dernst","file_size":2814384,"date_updated":"2021-02-22T13:42:47Z","file_name":"2016_Novak_Thesis.pdf","date_created":"2021-02-22T13:42:47Z"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"2023"}]},"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"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"07"},{"has_accepted_license":"1","year":"2016","day":"04","publication":"Nature Communications","doi":"10.1038/ncomms12307","date_published":"2016-08-04T00:00:00Z","date_created":"2018-12-11T11:51:34Z","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"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.","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","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","short":"T. Friedlander, R. Prizak, C.C. Guet, N.H. Barton, G. Tkačik, Nature Communications 7 (2016).","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.","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.","ista":"Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. 2016. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 7, 12307."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5887","author":[{"first_name":"Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","last_name":"Friedlander","full_name":"Friedlander, Tamar"},{"first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","full_name":"Prizak, Roshan","last_name":"Prizak"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"title":"Intrinsic limits to gene regulation by global crosstalk","article_number":"12307","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"},{"call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation"}],"publication_status":"published","file":[{"checksum":"fe3f3a1526d180b29fe691ab11435b78","file_id":"4919","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:12:01Z","file_name":"IST-2016-627-v1+1_ncomms12307.pdf","date_updated":"2020-07-14T12:44:46Z","file_size":861805,"creator":"system"},{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"4920","checksum":"164864a1a675f3ad80e9917c27aba07f","file_size":1084703,"date_updated":"2020-07-14T12:44:46Z","creator":"system","file_name":"IST-2016-627-v1+2_ncomms12307-s1.pdf","date_created":"2018-12-12T10:12:02Z"}],"language":[{"iso":"eng"}],"volume":7,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6071"}]},"ec_funded":1,"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"}],"oa_version":"Published Version","scopus_import":1,"month":"08","intvolume":" 7","date_updated":"2023-09-07T12:53:49Z","ddc":["576"],"file_date_updated":"2020-07-14T12:44:46Z","department":[{"_id":"GaTk"},{"_id":"NiBa"},{"_id":"CaGu"}],"_id":"1358","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"627"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-20T11:17:47Z","citation":{"ista":"Barton NH. 2016. Data from: How does epistasis influence the response to selection?, Dryad, 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.","short":"N.H. Barton, (2016).","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","apa":"Barton, N. H. (2016). Data from: How does epistasis influence the response to selection? Dryad. 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."},"department":[{"_id":"NiBa"}],"title":"Data from: How does epistasis influence the response to selection?","author":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"article_processing_charge":"No","_id":"9710","status":"public","type":"research_data_reference","day":"23","year":"2016","date_published":"2016-09-23T00:00:00Z","doi":"10.5061/dryad.s5s7r","related_material":{"record":[{"relation":"used_in_publication","id":"1199","status":"public"}]},"date_created":"2021-07-23T11:45:47Z","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"month":"09","publisher":"Dryad","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.s5s7r"}]},{"status":"public","type":"research_data_reference","_id":"9864","title":"Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"article_processing_charge":"No","author":[{"orcid":"0000-0002-5837-2793","full_name":"Fernandes Redondo, Rodrigo A","last_name":"Fernandes Redondo","first_name":"Rodrigo A","id":"409D5C96-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-5985-7653","full_name":"de Vladar, Harold","last_name":"de Vladar","id":"2A181218-F248-11E8-B48F-1D18A9856A87","first_name":"Harold"},{"full_name":"Włodarski, Tomasz","last_name":"Włodarski","first_name":"Tomasz"},{"last_name":"Bollback","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-20T11:56:33Z","citation":{"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).","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","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","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.","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."},"month":"12","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.4315652.v1","open_access":"1"}],"oa":1,"publisher":"The Royal Society","oa_version":"Published Version","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"}],"date_created":"2021-08-10T08:29:47Z","doi":"10.6084/m9.figshare.4315652.v1","related_material":{"record":[{"id":"1077","status":"public","relation":"used_in_publication"}]},"date_published":"2016-12-14T00:00:00Z","day":"14","year":"2016"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T13:49:53Z","citation":{"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.","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.","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","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.","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."},"department":[{"_id":"NiBa"}],"title":"Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae","publist_id":"5828","author":[{"last_name":"Ellis","full_name":"Ellis, Thomas","orcid":"0000-0002-8511-0254","first_name":"Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","full_name":"Field, David","orcid":"0000-0002-4014-8478","last_name":"Field"}],"_id":"1382","status":"public","type":"journal_article","day":"1","publication":"Annals of Botany","language":[{"iso":"eng"}],"publication_status":"published","year":"2016","volume":117,"doi":"10.1093/aob/mcw043","date_published":"2016-06-01T00:00:00Z","issue":"7","related_material":{"record":[{"id":"5550","status":"public","relation":"popular_science"}]},"date_created":"2018-12-11T11:51:42Z","page":"1133 - 1140","oa_version":"None","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.","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"}],"month":"06","intvolume":" 117","publisher":"Oxford University Press","quality_controlled":"1","scopus_import":1}]