[{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"quality_controlled":"1","article_type":"original","issue":"2","volume":225,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"01","article_number":"iyad133","ddc":["570"],"citation":{"ista":"Barton NH, Etheridge AM, Véber A. 2023. The infinitesimal model with dominance. Genetics. 225(2), iyad133.","chicago":"Barton, Nicholas H, Alison M. Etheridge, and Amandine Véber. “The Infinitesimal Model with Dominance.” Genetics. Oxford University Press, 2023. https://doi.org/10.1093/genetics/iyad133.","short":"N.H. Barton, A.M. Etheridge, A. Véber, Genetics 225 (2023).","ieee":"N. H. Barton, A. M. Etheridge, and A. Véber, “The infinitesimal model with dominance,” Genetics, vol. 225, no. 2. Oxford University Press, 2023.","mla":"Barton, Nicholas H., et al. “The Infinitesimal Model with Dominance.” Genetics, vol. 225, no. 2, iyad133, Oxford University Press, 2023, doi:10.1093/genetics/iyad133.","apa":"Barton, N. H., Etheridge, A. M., & Véber, A. (2023). The infinitesimal model with dominance. Genetics. Oxford University Press. https://doi.org/10.1093/genetics/iyad133","ama":"Barton NH, Etheridge AM, Véber A. The infinitesimal model with dominance. Genetics. 2023;225(2). doi:10.1093/genetics/iyad133"},"publication":"Genetics","status":"public","scopus_import":"1","ec_funded":1,"has_accepted_license":"1","file":[{"file_name":"2023_Genetics_Barton.pdf","creator":"dernst","file_id":"14469","relation":"main_file","file_size":1439032,"checksum":"3f65b1fbe813e2f4dbb5d2b5e891844a","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-10-30T12:57:53Z","success":1,"date_created":"2023-10-30T12:57:53Z"}],"publisher":"Oxford University Press","date_updated":"2025-09-09T13:07:07Z","year":"2023","author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton"},{"full_name":"Etheridge, Alison M.","first_name":"Alison M.","last_name":"Etheridge"},{"last_name":"Véber","first_name":"Amandine","full_name":"Véber, Amandine"}],"acknowledgement":"NHB was supported in part by ERC Grants 250152 and 101055327. AV was partly supported by the chaire Modélisation Mathématique et Biodiversité of Veolia Environment—Ecole Polytechnique—Museum National d’Histoire Naturelle—Fondation X.","publication_identifier":{"eissn":["1943-2631"],"issn":["0016-6731"]},"project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"},{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327","name":"Understanding the evolution of continuous genomes"}],"external_id":{"arxiv":["2211.03515"],"isi":["001148042000008"]},"abstract":[{"text":"The classical infinitesimal model is a simple and robust model for the inheritance of quantitative traits. In this model, a quantitative trait is expressed as the sum of a genetic and an environmental component, and the genetic component of offspring traits within a family follows a normal distribution around the average of the parents’ trait values, and has a variance that is independent of the parental traits. In previous work, we showed that when trait values are determined by the sum of a large number of additive Mendelian factors, each of small effect, one can justify the infinitesimal model as a limit of Mendelian inheritance. In this paper, we show that this result extends to include dominance. We define the model in terms of classical quantities of quantitative genetics, before justifying it as a limit of Mendelian inheritance as the number, M, of underlying loci tends to infinity. As in the additive case, the multivariate normal distribution of trait values across the pedigree can be expressed in terms of variance components in an ancestral population and probabilities of identity by descent determined by the pedigree. Now, with just first-order dominance effects, we require two-, three-, and four-way identities. We also show that, even if we condition on parental trait values, the “shared” and “residual” components of trait values within each family will be asymptotically normally distributed as the number of loci tends to infinity, with an error of order 1/M−−√. We illustrate our results with some numerical examples.","lang":"eng"}],"month":"10","type":"journal_article","file_date_updated":"2023-10-30T12:57:53Z","arxiv":1,"article_processing_charge":"Yes (in subscription journal)","date_created":"2023-10-29T23:01:15Z","doi":"10.1093/genetics/iyad133","oa_version":"Published Version","title":"The infinitesimal model with dominance","department":[{"_id":"NiBa"}],"publication_status":"published","intvolume":" 225","language":[{"iso":"eng"}],"date_published":"2023-10-01T00:00:00Z","_id":"14452","isi":1,"related_material":{"record":[{"relation":"research_data","id":"12949","status":"public"}]}},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"quality_controlled":"1","article_type":"original","issue":"36","volume":119,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"29","article_number":"e2123152119","ddc":["570"],"citation":{"chicago":"Hledik, Michal, Nicholas H Barton, and Gašper Tkačik. “Accumulation and Maintenance of Information in Evolution.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2123152119.","ista":"Hledik M, Barton NH, Tkačik G. 2022. Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences of the United States of America. 119(36), e2123152119.","short":"M. Hledik, N.H. Barton, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","mla":"Hledik, Michal, et al. “Accumulation and Maintenance of Information in Evolution.” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 36, e2123152119, National Academy of Sciences, 2022, doi:10.1073/pnas.2123152119.","apa":"Hledik, M., Barton, N. H., & Tkačik, G. (2022). Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2123152119","ama":"Hledik M, Barton NH, Tkačik G. Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences of the United States of America. 2022;119(36). doi:10.1073/pnas.2123152119","ieee":"M. Hledik, N. H. Barton, and G. Tkačik, “Accumulation and maintenance of information in evolution,” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 36. National Academy of Sciences, 2022."},"status":"public","publication":"Proceedings of the National Academy of Sciences of the United States of America","has_accepted_license":"1","ec_funded":1,"scopus_import":"1","file":[{"access_level":"open_access","date_updated":"2022-09-12T08:08:12Z","date_created":"2022-09-12T08:08:12Z","success":1,"checksum":"6dec51f6567da9039982a571508a8e4d","file_size":2165752,"content_type":"application/pdf","file_name":"2022_PNAS_Hledik.pdf","creator":"dernst","file_id":"12091","relation":"main_file"}],"publisher":"National Academy of Sciences","date_updated":"2026-04-07T12:59:24Z","year":"2022","author":[{"id":"4171253A-F248-11E8-B48F-1D18A9856A87","full_name":"Hledik, Michal","last_name":"Hledik","first_name":"Michal"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"1","last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper"}],"corr_author":"1","acknowledgement":"We thank Ksenia Khudiakova, Wiktor Młynarski, Sean Stankowski, and two anonymous reviewers for discussions and comments on the manuscript. G.T. and M.H. acknowledge funding from the Human Frontier Science Program Grant RGP0032/2018. N.B. acknowledges funding from ERC Grant 250152 “Information and Evolution.”","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"project":[{"call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"grant_number":"RGP0034/2018","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","_id":"2665AAFE-B435-11E9-9278-68D0E5697425"}],"external_id":{"pmid":["36037343"],"isi":["000889278400014"]},"abstract":[{"lang":"eng","text":"Selection accumulates information in the genome—it guides stochastically evolving populations toward states (genotype frequencies) that would be unlikely under neutrality. This can be quantified as the Kullback–Leibler (KL) divergence between the actual distribution of genotype frequencies and the corresponding neutral distribution. First, we show that this population-level information sets an upper bound on the information at the level of genotype and phenotype, limiting how precisely they can be specified by selection. Next, we study how the accumulation and maintenance of information is limited by the cost of selection, measured as the genetic load or the relative fitness variance, both of which we connect to the control-theoretic KL cost of control. The information accumulation rate is upper bounded by the population size times the cost of selection. This bound is very general, and applies across models (Wright–Fisher, Moran, diffusion) and to arbitrary forms of selection, mutation, and recombination. Finally, the cost of maintaining information depends on how it is encoded: Specifying a single allele out of two is expensive, but one bit encoded among many weakly specified loci (as in a polygenic trait) is cheap."}],"file_date_updated":"2022-09-12T08:08:12Z","month":"08","type":"journal_article","article_processing_charge":"No","doi":"10.1073/pnas.2123152119","date_created":"2022-09-11T22:01:55Z","oa_version":"Published Version","title":"Accumulation and maintenance of information in evolution","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"pmid":1,"publication_status":"published","intvolume":" 119","language":[{"iso":"eng"}],"date_published":"2022-08-29T00:00:00Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"15020"}]},"_id":"12081","isi":1},{"publication":"Biology letters","status":"public","article_number":"20200913","citation":{"chicago":"Lagator, Mato, Hildegard Uecker, and Paul Neve. “Adaptation at Different Points along Antibiotic Concentration Gradients.” Biology Letters. Royal Society of London, 2021. https://doi.org/10.1098/rsbl.2020.0913.","ista":"Lagator M, Uecker H, Neve P. 2021. Adaptation at different points along antibiotic concentration gradients. Biology letters. 17(5), 20200913.","short":"M. Lagator, H. Uecker, P. Neve, Biology Letters 17 (2021).","ama":"Lagator M, Uecker H, Neve P. Adaptation at different points along antibiotic concentration gradients. Biology letters. 2021;17(5). doi:10.1098/rsbl.2020.0913","apa":"Lagator, M., Uecker, H., & Neve, P. (2021). Adaptation at different points along antibiotic concentration gradients. Biology Letters. Royal Society of London. https://doi.org/10.1098/rsbl.2020.0913","mla":"Lagator, Mato, et al. “Adaptation at Different Points along Antibiotic Concentration Gradients.” Biology Letters, vol. 17, no. 5, 20200913, Royal Society of London, 2021, doi:10.1098/rsbl.2020.0913.","ieee":"M. Lagator, H. Uecker, and P. Neve, “Adaptation at different points along antibiotic concentration gradients,” Biology letters, vol. 17, no. 5. Royal Society of London, 2021."},"ddc":["570"],"scopus_import":"1","has_accepted_license":"1","ec_funded":1,"file":[{"date_created":"2021-05-25T14:09:03Z","success":1,"access_level":"open_access","date_updated":"2021-05-25T14:09:03Z","file_size":726759,"checksum":"9c13c1f5af7609c97c741f11d293188a","content_type":"application/pdf","file_id":"9425","relation":"main_file","file_name":"2021_BiologyLetters_Lagator.pdf","creator":"kschuh"}],"publisher":"Royal Society of London","date_updated":"2026-04-02T14:02:44Z","year":"2021","author":[{"id":"345D25EC-F248-11E8-B48F-1D18A9856A87","full_name":"Lagator, Mato","first_name":"Mato","last_name":"Lagator"},{"full_name":"Uecker, Hildegard","first_name":"Hildegard","last_name":"Uecker","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9435-2813"},{"last_name":"Neve","first_name":"Paul","full_name":"Neve, Paul"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"quality_controlled":"1","oa":1,"volume":17,"issue":"5","day":"12","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_status":"published","intvolume":" 17","pmid":1,"language":[{"iso":"eng"}],"date_published":"2021-05-12T00:00:00Z","_id":"9410","isi":1,"publication_identifier":{"eissn":["1744-957X"]},"corr_author":"1","acknowledgement":"We would like to thank Martin Ackermann, Camilo Barbosa, Nick Barton, Jonathan Bollback, Sebastian Bonhoeffer, Nick Colegrave, Calin Guet, Alex Hall, Sally Otto, Tiago Paixao, Srdjan Sarikas, Hinrich Schulenburg, Marjon de Vos and Michael Whitlock for insightful support.","abstract":[{"text":"Antibiotic concentrations vary dramatically in the body and the environment. Hence, understanding the dynamics of resistance evolution along antibiotic concentration gradients is critical for predicting and slowing the emergence and spread of resistance. While it has been shown that increasing the concentration of an antibiotic slows resistance evolution, how adaptation to one antibiotic concentration correlates with fitness at other points along the gradient has not received much attention. Here, we selected populations of Escherichia coli at several points along a concentration gradient for three different antibiotics, asking how rapidly resistance evolved and whether populations became specialized to the antibiotic concentration they were selected on. Populations selected at higher concentrations evolved resistance more slowly but exhibited equal or higher fitness across the whole gradient. Populations selected at lower concentrations evolved resistance rapidly, but overall fitness in the presence of antibiotics was lower. However, these populations readily adapted to higher concentrations upon subsequent selection. Our results indicate that resistance management strategies must account not only for the rates of resistance evolution but also for the fitness of evolved strains.","lang":"eng"}],"file_date_updated":"2021-05-25T14:09:03Z","month":"05","type":"journal_article","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"external_id":{"pmid":[" 33975485"],"isi":["000651501400001"]},"title":"Adaptation at different points along antibiotic concentration gradients","article_processing_charge":"No","date_created":"2021-05-23T22:01:43Z","oa_version":"Published Version","doi":"10.1098/rsbl.2020.0913","department":[{"_id":"NiBa"}]},{"article_processing_charge":"No","date_created":"2018-12-11T11:45:37Z","doi":"10.1111/1755-0998.12782","oa_version":"None","title":"Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering","department":[{"_id":"NiBa"}],"acknowledgement":"ERC, Grant/Award Number: 250152","project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"external_id":{"isi":["000441753000007"]},"abstract":[{"lang":"eng","text":"Pedigree and sibship reconstruction are important methods in quantifying relationships and fitness of individuals in natural populations. Current methods employ a Markov chain-based algorithm to explore plausible possible pedigrees iteratively. This provides accurate results, but is time-consuming. Here, we develop a method to infer sibship and paternity relationships from half-sibling arrays of known maternity using hierarchical clustering. Given 50 or more unlinked SNP markers and empirically derived error rates, the method performs as well as the widely used package Colony, but is faster by two orders of magnitude. Using simulations, we show that the method performs well across contrasting mating scenarios, even when samples are large. We then apply the method to open-pollinated arrays of the snapdragon Antirrhinum majus and find evidence for a high degree of multiple mating. Although we focus on diploid SNP data, the method does not depend on marker type and as such has broad applications in nonmodel systems. "}],"month":"09","type":"journal_article","date_published":"2018-09-01T00:00:00Z","related_material":{"record":[{"status":"public","id":"5583","relation":"popular_science"}]},"_id":"286","isi":1,"publication_status":"published","intvolume":" 18","language":[{"iso":"eng"}],"issue":"5","volume":18,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"01","quality_controlled":"1","date_updated":"2025-04-15T07:11:03Z","year":"2018","author":[{"id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254","first_name":"Thomas","last_name":"Ellis","full_name":"Ellis, Thomas"},{"full_name":"Field, David","first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478"},{"first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"page":"988 - 999","citation":{"ama":"Ellis T, Field D, Barton NH. Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. 2018;18(5):988-999. doi:10.1111/1755-0998.12782","mla":"Ellis, Thomas, et al. “Efficient Inference of Paternity and Sibship Inference given Known Maternity via Hierarchical Clustering.” Molecular Ecology Resources, vol. 18, no. 5, Wiley, 2018, pp. 988–99, doi:10.1111/1755-0998.12782.","ieee":"T. Ellis, D. Field, and N. H. Barton, “Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering,” Molecular Ecology Resources, vol. 18, no. 5. Wiley, pp. 988–999, 2018.","apa":"Ellis, T., Field, D., & Barton, N. H. (2018). Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.12782","chicago":"Ellis, Thomas, David Field, and Nicholas H Barton. “Efficient Inference of Paternity and Sibship Inference given Known Maternity via Hierarchical Clustering.” Molecular Ecology Resources. Wiley, 2018. https://doi.org/10.1111/1755-0998.12782.","short":"T. Ellis, D. Field, N.H. Barton, Molecular Ecology Resources 18 (2018) 988–999.","ista":"Ellis T, Field D, Barton NH. 2018. Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. 18(5), 988–999."},"publication":"Molecular Ecology Resources","status":"public","ec_funded":1,"scopus_import":"1","publisher":"Wiley"},{"abstract":[{"lang":"eng","text":"Self-incompatibility (SI) is a genetically based recognition system that functions to prevent self-fertilization and mating among related plants. An enduring puzzle in SI is how the high diversity observed in nature arises and is maintained. Based on the underlying recognition mechanism, SI can be classified into two main groups: self- and non-self recognition. Most work has focused on diversification within self-recognition systems despite expected differences between the two groups in the evolutionary pathways and outcomes of diversification. Here, we use a deterministic population genetic model and stochastic simulations to investigate how novel S-haplotypes evolve in a gametophytic non-self recognition (SRNase/S Locus F-box (SLF)) SI system. For this model the pathways for diversification involve either the maintenance or breakdown of SI and can vary in the order of mutations of the female (SRNase) and male (SLF) components. We show analytically that diversification can occur with high inbreeding depression and self-pollination, but this varies with evolutionary pathway and level of completeness (which determines the number of potential mating partners in the population), and in general is more likely for lower haplotype number. The conditions for diversification are broader in stochastic simulations of finite population size. However, the number of haplotypes observed under high inbreeding and moderate to high self-pollination is less than that commonly observed in nature. Diversification was observed through pathways that maintain SI as well as through self-compatible intermediates. Yet the lifespan of diversified haplotypes was sensitive to their level of completeness. By examining diversification in a non-self recognition SI system, this model extends our understanding of the evolution and maintenance of haplotype diversity observed in a self recognition system common in flowering plants."}],"type":"journal_article","month":"07","project":[{"call_identifier":"FP7","_id":"25B36484-B435-11E9-9278-68D0E5697425","name":"Mating system and the evolutionary dynamics of hybrid zones","grant_number":"329960"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7"}],"external_id":{"isi":["000437171700017"]},"department":[{"_id":"NiBa"},{"_id":"GaTk"}],"title":"Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system","main_file_link":[{"url":"https://www.biorxiv.org/node/80098.abstract","open_access":"1"}],"article_processing_charge":"No","oa_version":"Preprint","doi":"10.1534/genetics.118.300748","date_created":"2018-12-11T11:45:47Z","language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 209","_id":"316","isi":1,"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/recognizing-others-but-not-yourself-new-insights-into-the-evolution-of-plant-mating/","relation":"press_release"}],"record":[{"status":"public","id":"9813","relation":"research_data"}]},"date_published":"2018-07-01T00:00:00Z","quality_controlled":"1","article_type":"original","oa":1,"day":"01","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":209,"issue":"3","ec_funded":1,"scopus_import":"1","publisher":"Genetics Society of America","publication":"Genetics","status":"public","citation":{"mla":"Bodova, Katarina, et al. “Evolutionary Pathways for the Generation of New Self-Incompatibility Haplotypes in a Non-Self Recognition System.” Genetics, vol. 209, no. 3, Genetics Society of America, 2018, pp. 861–83, doi:10.1534/genetics.118.300748.","ama":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. 2018;209(3):861-883. doi:10.1534/genetics.118.300748","ieee":"K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system,” Genetics, vol. 209, no. 3. Genetics Society of America, pp. 861–883, 2018.","apa":"Bodova, K., Priklopil, T., Field, D., Barton, N. H., & Pickup, M. (2018). Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.300748","ista":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. 209(3), 861–883.","chicago":"Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and Melinda Pickup. “Evolutionary Pathways for the Generation of New Self-Incompatibility Haplotypes in a Non-Self Recognition System.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.300748.","short":"K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, Genetics 209 (2018) 861–883."},"page":"861-883","year":"2018","author":[{"full_name":"Bodova, Katarina","first_name":"Katarina","last_name":"Bodova","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7214-0171"},{"id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","full_name":"Priklopil, Tadeas","last_name":"Priklopil","first_name":"Tadeas"},{"first_name":"David","last_name":"Field","full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda","last_name":"Pickup","full_name":"Pickup, Melinda"}],"date_updated":"2025-04-15T06:50:00Z"},{"type":"journal_article","file_date_updated":"2020-07-14T12:47:09Z","month":"07","abstract":[{"lang":"eng","text":"Maladapted individuals can only colonise a new habitat if they can evolve a\r\npositive growth rate fast enough to avoid extinction, a process known as evolutionary\r\nrescue. We treat log fitness at low density in the new habitat as a\r\nsingle polygenic trait and thus use the infinitesimal model to follow the evolution\r\nof the growth rate; this assumes that the trait values of offspring of a\r\nsexual union are normally distributed around the mean of the parents’ trait\r\nvalues, with variance that depends only on the parents’ relatedness. The\r\nprobability that a single migrant can establish depends on just two parameters:\r\nthe mean and genetic variance of the trait in the source population.\r\nThe chance of success becomes small if migrants come from a population\r\nwith mean growth rate in the new habitat more than a few standard deviations\r\nbelow zero; this chance depends roughly equally on the probability\r\nthat the initial founder is unusually fit, and on the subsequent increase in\r\ngrowth rate of its offspring as a result of selection. The loss of genetic variation\r\nduring the founding event is substantial, but highly variable. With\r\ncontinued migration at rate M, establishment is inevitable; when migration\r\nis rare, the expected time to establishment decreases inversely with M.\r\nHowever, above a threshold migration rate, the population may be trapped\r\nin a ‘sink’ state, in which adaptation is held back by gene flow; above this\r\nthreshold, the expected time to establishment increases exponentially with M. This threshold behaviour is captured by a deterministic approximation,\r\nwhich assumes a Gaussian distribution of the trait in the founder population\r\nwith mean and variance evolving deterministically. By assuming a constant\r\ngenetic variance, we also develop a diffusion approximation for the joint distribution\r\nof population size and trait mean, which extends to include stabilising\r\nselection and density regulation. Divergence of the population from its\r\nancestors causes partial reproductive isolation, which we measure through\r\nthe reproductive value of migrants into the newly established population."}],"external_id":{"isi":["000440392900014"]},"project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"title":"Establishment in a new habitat by polygenic adaptation","date_created":"2018-12-11T11:47:12Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","oa_version":"Submitted Version","doi":"10.1016/j.tpb.2017.11.007","article_processing_charge":"No","department":[{"_id":"NiBa"}],"intvolume":" 122","publication_status":"published","publist_id":"7250","language":[{"iso":"eng"}],"date_published":"2018-07-01T00:00:00Z","_id":"564","related_material":{"record":[{"relation":"research_data","id":"9842","status":"public"}]},"isi":1,"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)"},"article_type":"original","quality_controlled":"1","oa":1,"volume":122,"issue":"7","day":"01","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication":"Theoretical Population Biology","status":"public","citation":{"mla":"Barton, Nicholas H., and Alison Etheridge. “Establishment in a New Habitat by Polygenic Adaptation.” Theoretical Population Biology, vol. 122, no. 7, Academic Press, 2018, pp. 110–27, doi:10.1016/j.tpb.2017.11.007.","ieee":"N. H. Barton and A. Etheridge, “Establishment in a new habitat by polygenic adaptation,” Theoretical Population Biology, vol. 122, no. 7. Academic Press, pp. 110–127, 2018.","apa":"Barton, N. H., & Etheridge, A. (2018). Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2017.11.007","ama":"Barton NH, Etheridge A. Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. 2018;122(7):110-127. doi:10.1016/j.tpb.2017.11.007","chicago":"Barton, Nicholas H, and Alison Etheridge. “Establishment in a New Habitat by Polygenic Adaptation.” Theoretical Population Biology. Academic Press, 2018. https://doi.org/10.1016/j.tpb.2017.11.007.","ista":"Barton NH, Etheridge A. 2018. Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. 122(7), 110–127.","short":"N.H. Barton, A. Etheridge, Theoretical Population Biology 122 (2018) 110–127."},"page":"110-127","ddc":["519","576"],"file":[{"creator":"nbarton","file_name":"bartonetheridge.pdf","relation":"main_file","file_id":"7199","access_level":"open_access","date_updated":"2020-07-14T12:47:09Z","date_created":"2019-12-21T09:36:39Z","checksum":"0b96f6db47e3e91b5e7d103b847c239d","file_size":2287682,"content_type":"application/pdf"}],"publisher":"Academic Press","ec_funded":1,"has_accepted_license":"1","scopus_import":"1","date_updated":"2025-04-15T07:11:04Z","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton"},{"last_name":"Etheridge","first_name":"Alison","full_name":"Etheridge, Alison"}],"year":"2018"},{"external_id":{"isi":["000393677300025"]},"project":[{"grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"file_date_updated":"2020-07-14T12:44:37Z","type":"journal_article","month":"01","abstract":[{"text":"Dispersal is a crucial factor in natural evolution, since it determines the habitat experienced by any population and defines the spatial scale of interactions between individuals. There is compelling evidence for systematic differences in dispersal characteristics within the same population, i.e., genotype-dependent dispersal. The consequences of genotype-dependent dispersal on other evolutionary phenomena, however, are poorly understood. In this article we investigate the effect of genotype-dependent dispersal on spatial gene frequency patterns, using a generalization of the classical diffusion model of selection and dispersal. Dispersal is characterized by the variance of dispersal (diffusion coefficient) and the mean displacement (directional advection term). We demonstrate that genotype-dependent dispersal may change the qualitative behavior of Fisher waves, which change from being “pulled” to being “pushed” wave fronts as the discrepancy in dispersal between genotypes increases. The speed of any wave is partitioned into components due to selection, genotype-dependent variance of dispersal, and genotype-dependent mean displacement. We apply our findings to wave fronts maintained by selection against heterozygotes. Furthermore, we identify a benefit of increased variance of dispersal, quantify its effect on the speed of the wave, and discuss the implications for the evolution of dispersal strategies.","lang":"eng"}],"pubrep_id":"727","publication_identifier":{"issn":["0016-6731"]},"department":[{"_id":"NiBa"}],"oa_version":"Submitted Version","doi":"10.1534/genetics.116.193946","date_created":"2018-12-11T11:50:31Z","article_processing_charge":"No","title":"Spatial gene frequency waves under genotype dependent dispersal","language":[{"iso":"eng"}],"publist_id":"6188","intvolume":" 205","publication_status":"published","isi":1,"_id":"1169","date_published":"2017-01-01T00:00:00Z","oa":1,"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","issue":"1","volume":205,"file":[{"creator":"system","file_name":"IST-2016-727-v1+1_SFC_Genetics_final.pdf","relation":"main_file","file_id":"4833","access_level":"open_access","date_updated":"2020-07-14T12:44:37Z","date_created":"2018-12-12T10:10:43Z","content_type":"application/pdf","checksum":"7c8ab79cda1f92760bbbbe0f53175bfc","file_size":361500}],"publisher":"Genetics Society of America","has_accepted_license":"1","scopus_import":"1","ec_funded":1,"citation":{"ama":"Novak S, Kollár R. Spatial gene frequency waves under genotype dependent dispersal. Genetics. 2017;205(1):367-374. doi:10.1534/genetics.116.193946","mla":"Novak, Sebastian, and Richard Kollár. “Spatial Gene Frequency Waves under Genotype Dependent Dispersal.” Genetics, vol. 205, no. 1, Genetics Society of America, 2017, pp. 367–74, doi:10.1534/genetics.116.193946.","apa":"Novak, S., & Kollár, R. (2017). Spatial gene frequency waves under genotype dependent dispersal. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.193946","ieee":"S. Novak and R. Kollár, “Spatial gene frequency waves under genotype dependent dispersal,” Genetics, vol. 205, no. 1. Genetics Society of America, pp. 367–374, 2017.","ista":"Novak S, Kollár R. 2017. Spatial gene frequency waves under genotype dependent dispersal. Genetics. 205(1), 367–374.","chicago":"Novak, Sebastian, and Richard Kollár. “Spatial Gene Frequency Waves under Genotype Dependent Dispersal.” Genetics. Genetics Society of America, 2017. https://doi.org/10.1534/genetics.116.193946.","short":"S. Novak, R. Kollár, Genetics 205 (2017) 367–374."},"ddc":["576"],"page":"367 - 374","status":"public","publication":"Genetics","author":[{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-824X","last_name":"Novak","first_name":"Sebastian","full_name":"Novak, Sebastian"},{"full_name":"Kollár, Richard","last_name":"Kollár","first_name":"Richard"}],"year":"2017","date_updated":"2025-07-10T11:50:13Z"},{"scopus_import":"1","ec_funded":1,"publisher":"Springer","status":"public","publication":"Bulletin of Mathematical Biology","page":"525-559","citation":{"mla":"Kollár, Richard, and Sebastian Novak. “Existence of Traveling Waves for the Generalized F–KPP Equation.” Bulletin of Mathematical Biology, vol. 79, no. 3, Springer, 2017, pp. 525–59, doi:10.1007/s11538-016-0244-3.","ieee":"R. Kollár and S. Novak, “Existence of traveling waves for the generalized F–KPP equation,” Bulletin of Mathematical Biology, vol. 79, no. 3. Springer, pp. 525–559, 2017.","apa":"Kollár, R., & Novak, S. (2017). Existence of traveling waves for the generalized F–KPP equation. Bulletin of Mathematical Biology. Springer. https://doi.org/10.1007/s11538-016-0244-3","ama":"Kollár R, Novak S. Existence of traveling waves for the generalized F–KPP equation. Bulletin of Mathematical Biology. 2017;79(3):525-559. doi:10.1007/s11538-016-0244-3","chicago":"Kollár, Richard, and Sebastian Novak. “Existence of Traveling Waves for the Generalized F–KPP Equation.” Bulletin of Mathematical Biology. Springer, 2017. https://doi.org/10.1007/s11538-016-0244-3.","short":"R. Kollár, S. Novak, Bulletin of Mathematical Biology 79 (2017) 525–559.","ista":"Kollár R, Novak S. 2017. Existence of traveling waves for the generalized F–KPP equation. Bulletin of Mathematical Biology. 79(3), 525–559."},"year":"2017","author":[{"first_name":"Richard","last_name":"Kollár","full_name":"Kollár, Richard"},{"full_name":"Novak, Sebastian","last_name":"Novak","first_name":"Sebastian","orcid":"0000-0002-2519-824X","id":"461468AE-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2025-09-22T09:44:54Z","quality_controlled":"1","oa":1,"day":"01","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":79,"issue":"3","language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 79","publist_id":"6160","isi":1,"_id":"1191","date_published":"2017-03-01T00:00:00Z","abstract":[{"text":"Variation in genotypes may be responsible for differences in dispersal rates, directional biases, and growth rates of individuals. These traits may favor certain genotypes and enhance their spatiotemporal spreading into areas occupied by the less advantageous genotypes. We study how these factors influence the speed of spreading in the case of two competing genotypes under the assumption that spatial variation of the total population is small compared to the spatial variation of the frequencies of the genotypes in the population. In that case, the dynamics of the frequency of one of the genotypes is approximately described by a generalized Fisher–Kolmogorov–Petrovskii–Piskunov (F–KPP) equation. This generalized F–KPP equation with (nonlinear) frequency-dependent diffusion and advection terms admits traveling wave solutions that characterize the invasion of the dominant genotype. Our existence results generalize the classical theory for traveling waves for the F–KPP with constant coefficients. Moreover, in the particular case of the quadratic (monostable) nonlinear growth–decay rate in the generalized F–KPP we study in detail the influence of the variance in diffusion and mean displacement rates of the two genotypes on the minimal wave propagation speed.","lang":"eng"}],"type":"journal_article","arxiv":1,"month":"03","project":[{"call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7"}],"external_id":{"isi":["000395156200005"],"arxiv":["1607.00944"]},"acknowledgement":"We thank Nick Barton, Katarína Bod’ová, and Sr\r\n-\r\ndan Sarikas for constructive feed-\r\nback and support. Furthermore, we would like to express our deep gratitude to the anonymous referees (one\r\nof whom, Jimmy Garnier, agreed to reveal his identity) and the editor Max Souza, for very helpful and\r\ndetailed comments and suggestions that significantly helped us to improve the manuscript. This project has\r\nreceived funding from the European Union’s Seventh Framework Programme for research, technological\r\ndevelopment and demonstration under Grant Agreement 618091 Speed of Adaptation in Population Genet-\r\nics and Evolutionary Computation (SAGE) and the European Research Council (ERC) Grant No. 250152\r\n(SN), from the Scientific Grant Agency of the Slovak Republic under the Grant 1/0459/13 and by the Slovak\r\nResearch and Development Agency under the Contract No. APVV-14-0378 (RK). RK would also like to\r\nthank IST Austria for its hospitality during the work on this project.","department":[{"_id":"NiBa"}],"title":"Existence of traveling waves for the generalized F–KPP equation","article_processing_charge":"No","main_file_link":[{"url":"https://arxiv.org/abs/1607.00944","open_access":"1"}],"oa_version":"Preprint","date_created":"2018-12-11T11:50:38Z","doi":"10.1007/s11538-016-0244-3"},{"date_published":"2017-01-01T00:00:00Z","_id":"1199","isi":1,"related_material":{"record":[{"relation":"research_data","id":"9710","status":"public"}]},"publist_id":"6151","publication_status":"published","intvolume":" 118","language":[{"iso":"eng"}],"article_processing_charge":"No","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5176114/","open_access":"1"}],"oa_version":"Submitted Version","date_created":"2018-12-11T11:50:40Z","doi":"10.1038/hdy.2016.109","title":"How does epistasis influence the response to selection?","department":[{"_id":"NiBa"}],"project":[{"call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000392229100011"]},"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":"journal_article","month":"01","date_updated":"2025-04-15T07:11:02Z","year":"2017","author":[{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"citation":{"ista":"Barton NH. 2017. How does epistasis influence the response to selection? Heredity. 118, 96–109.","chicago":"Barton, Nicholas H. “How Does Epistasis Influence the Response to Selection?” Heredity. Nature Publishing Group, 2017. https://doi.org/10.1038/hdy.2016.109.","short":"N.H. Barton, Heredity 118 (2017) 96–109.","ama":"Barton NH. How does epistasis influence the response to selection? Heredity. 2017;118:96-109. doi:10.1038/hdy.2016.109","mla":"Barton, Nicholas H. “How Does Epistasis Influence the Response to Selection?” Heredity, vol. 118, Nature Publishing Group, 2017, pp. 96–109, doi:10.1038/hdy.2016.109.","ieee":"N. H. Barton, “How does epistasis influence the response to selection?,” Heredity, vol. 118. Nature Publishing Group, pp. 96–109, 2017.","apa":"Barton, N. H. (2017). How does epistasis influence the response to selection? Heredity. Nature Publishing Group. https://doi.org/10.1038/hdy.2016.109"},"page":"96 - 109","status":"public","publication":"Heredity","scopus_import":"1","ec_funded":1,"publisher":"Nature Publishing Group","volume":118,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"01","oa":1,"quality_controlled":"1"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"quality_controlled":"1","issue":"8","volume":54,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","ddc":["006","576"],"page":"765 - 787","citation":{"ama":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking the evolution of gene regulatory networks. Acta Informatica. 2017;54(8):765-787. doi:10.1007/s00236-016-0278-x","mla":"Giacobbe, Mirco, et al. “Model Checking the Evolution of Gene Regulatory Networks.” Acta Informatica, vol. 54, no. 8, Springer, 2017, pp. 765–87, doi:10.1007/s00236-016-0278-x.","apa":"Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., & Petrov, T. (2017). Model checking the evolution of gene regulatory networks. Acta Informatica. Springer. https://doi.org/10.1007/s00236-016-0278-x","ieee":"M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov, “Model checking the evolution of gene regulatory networks,” Acta Informatica, vol. 54, no. 8. Springer, pp. 765–787, 2017.","chicago":"Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago Paixao, and Tatjana Petrov. “Model Checking the Evolution of Gene Regulatory Networks.” Acta Informatica. Springer, 2017. https://doi.org/10.1007/s00236-016-0278-x.","short":"M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, Acta Informatica 54 (2017) 765–787.","ista":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2017. Model checking the evolution of gene regulatory networks. Acta Informatica. 54(8), 765–787."},"status":"public","publication":"Acta Informatica","has_accepted_license":"1","ec_funded":1,"scopus_import":"1","file":[{"checksum":"4e661d9135d7f8c342e8e258dee76f3e","content_type":"application/pdf","file_size":755241,"access_level":"open_access","date_updated":"2020-07-14T12:44:46Z","date_created":"2019-01-17T15:57:29Z","file_name":"2017_ActaInformatica_Giacobbe.pdf","creator":"dernst","file_id":"5841","relation":"main_file"}],"publisher":"Springer","date_updated":"2025-07-10T11:50:42Z","year":"2017","author":[{"orcid":"0000-0001-8180-0904","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","full_name":"Giacobbe, Mirco","first_name":"Mirco","last_name":"Giacobbe"},{"full_name":"Guet, Calin C","last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"id":"335E5684-F248-11E8-B48F-1D18A9856A87","first_name":"Ashutosh","last_name":"Gupta","full_name":"Gupta, Ashutosh"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A"},{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","first_name":"Tiago","last_name":"Paixao","full_name":"Paixao, Tiago"},{"first_name":"Tatjana","last_name":"Petrov","full_name":"Petrov, Tatjana","orcid":"0000-0002-9041-0905","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87"}],"pubrep_id":"649","corr_author":"1","publication_identifier":{"issn":["0001-5903"]},"project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091","call_identifier":"FP7"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7"}],"external_id":{"isi":["000414343200003"]},"abstract":[{"lang":"eng","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 logic. 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."}],"type":"journal_article","month":"12","file_date_updated":"2020-07-14T12:44:46Z","article_processing_charge":"No","date_created":"2018-12-11T11:51:32Z","doi":"10.1007/s00236-016-0278-x","oa_version":"Published Version","title":"Model checking the evolution of gene regulatory networks","department":[{"_id":"ToHe"},{"_id":"CaGu"},{"_id":"NiBa"}],"publist_id":"5898","publication_status":"published","intvolume":" 54","language":[{"iso":"eng"}],"date_published":"2017-12-01T00:00:00Z","_id":"1351","related_material":{"record":[{"relation":"earlier_version","id":"1835","status":"public"}]},"isi":1},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","issue":"4","volume":71,"oa":1,"quality_controlled":"1","author":[{"id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9435-2813","last_name":"Uecker","first_name":"Hildegard","full_name":"Uecker, Hildegard"}],"year":"2017","date_updated":"2025-07-10T11:49:52Z","publisher":"Wiley-Blackwell","ec_funded":1,"scopus_import":"1","page":"845 - 858","citation":{"short":"H. Uecker, Evolution 71 (2017) 845–858.","chicago":"Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal Populations.” Evolution. Wiley-Blackwell, 2017. https://doi.org/10.1111/evo.13191.","ista":"Uecker H. 2017. Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. 71(4), 845–858.","mla":"Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal Populations.” Evolution, vol. 71, no. 4, Wiley-Blackwell, 2017, pp. 845–58, doi:10.1111/evo.13191.","apa":"Uecker, H. (2017). Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. Wiley-Blackwell. https://doi.org/10.1111/evo.13191","ama":"Uecker H. Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. 2017;71(4):845-858. doi:10.1111/evo.13191","ieee":"H. Uecker, “Evolutionary rescue in randomly mating, selfing, and clonal populations,” Evolution, vol. 71, no. 4. Wiley-Blackwell, pp. 845–858, 2017."},"publication":"Evolution","status":"public","department":[{"_id":"NiBa"}],"oa_version":"Submitted Version","doi":"10.1111/evo.13191","date_created":"2018-12-11T11:49:57Z","main_file_link":[{"url":"http://biorxiv.org/content/early/2016/10/14/081042","open_access":"1"}],"article_processing_charge":"No","title":"Evolutionary rescue in randomly mating, selfing, and clonal populations","external_id":{"isi":["000398545200003"]},"project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"type":"journal_article","month":"04","abstract":[{"lang":"eng","text":"Severe environmental change can drive a population extinct unless the population adapts in time to the new conditions (“evolutionary rescue”). How does biparental sexual reproduction influence the chances of population persistence compared to clonal reproduction or selfing? In this article, we set up a one‐locus two‐allele model for adaptation in diploid species, where rescue is contingent on the establishment of the mutant homozygote. Reproduction can occur by random mating, selfing, or clonally. Random mating generates and destroys the rescue mutant; selfing is efficient at generating it but at the same time depletes the heterozygote, which can lead to a low mutant frequency in the standing genetic variation. Due to these (and other) antagonistic effects, we find a nontrivial dependence of population survival on the rate of sex/selfing, which is strongly influenced by the dominance coefficient of the mutation before and after the environmental change. Importantly, since mating with the wild‐type breaks the mutant homozygote up, a slow decay of the wild‐type population size can impede rescue in randomly mating populations."}],"publication_identifier":{"issn":["0014-3820"]},"_id":"1063","isi":1,"date_published":"2017-04-01T00:00:00Z","language":[{"iso":"eng"}],"publist_id":"6327","intvolume":" 71","publication_status":"published"},{"department":[{"_id":"NiBa"},{"_id":"JoBo"}],"title":"Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family","oa_version":"Published Version","date_created":"2018-12-11T11:50:01Z","doi":"10.1098/rsif.2016.0139","article_processing_charge":"Yes (in subscription journal)","month":"01","type":"journal_article","file_date_updated":"2019-01-18T09:14:02Z","abstract":[{"lang":"eng","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 fX174 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."}],"external_id":{"isi":["000393380400001"]},"project":[{"call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440","name":"Selective Barriers to Horizontal Gene Transfer"}],"publication_identifier":{"issn":["1742-5689"]},"_id":"1077","isi":1,"related_material":{"record":[{"relation":"research_data","id":"9864","status":"public"}]},"date_published":"2017-01-04T00:00:00Z","language":[{"iso":"eng"}],"intvolume":" 14","publication_status":"published","publist_id":"6303","day":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":14,"issue":"126","quality_controlled":"1","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"last_name":"Fernandes Redondo","first_name":"Rodrigo A","full_name":"Fernandes Redondo, Rodrigo A","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5837-2793"},{"last_name":"Vladar","first_name":"Harold","full_name":"Vladar, Harold","orcid":"0000-0002-5985-7653","id":"2A181218-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Włodarski, Tomasz","last_name":"Włodarski","first_name":"Tomasz"},{"orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","first_name":"Jonathan P","full_name":"Bollback, Jonathan P"}],"year":"2017","date_updated":"2025-07-10T11:49:59Z","file":[{"access_level":"open_access","date_updated":"2019-01-18T09:14:02Z","success":1,"date_created":"2019-01-18T09:14:02Z","file_size":1092015,"content_type":"application/pdf","file_name":"2017_JRSI_Redondo.pdf","creator":"dernst","file_id":"5843","relation":"main_file"}],"publisher":"Royal Society of London","has_accepted_license":"1","scopus_import":"1","ec_funded":1,"status":"public","publication":"Journal of the Royal Society Interface","article_number":"20160139","citation":{"ama":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. 2017;14(126). doi:10.1098/rsif.2016.0139","ieee":"R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family,” Journal of the Royal Society Interface, vol. 14, no. 126. Royal Society of London, 2017.","apa":"Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., & Bollback, J. P. (2017). Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. Royal Society of London. https://doi.org/10.1098/rsif.2016.0139","mla":"Fernandes Redondo, Rodrigo A., et al. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” Journal of the Royal Society Interface, vol. 14, no. 126, 20160139, Royal Society of London, 2017, doi:10.1098/rsif.2016.0139.","short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, Journal of the Royal Society Interface 14 (2017).","chicago":"Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan P Bollback. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” Journal of the Royal Society Interface. Royal Society of London, 2017. https://doi.org/10.1098/rsif.2016.0139.","ista":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2017. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. 14(126), 20160139."},"ddc":["570"]},{"pubrep_id":"908","corr_author":"1","publication_identifier":{"issn":["0040-5809"]},"project":[{"call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000417668700005"]},"abstract":[{"text":"Our focus here is on the infinitesimal model. In this model, one or several quantitative traits are described as the sum of a genetic and a non-genetic component, the first being distributed within families as a normal random variable centred at the average of the parental genetic components, and with a variance independent of the parental traits. Thus, the variance that segregates within families is not perturbed by selection, and can be predicted from the variance components. This does not necessarily imply that the trait distribution across the whole population should be Gaussian, and indeed selection or population structure may have a substantial effect on the overall trait distribution. One of our main aims is to identify some general conditions on the allelic effects for the infinitesimal model to be accurate. We first review the long history of the infinitesimal model in quantitative genetics. Then we formulate the model at the phenotypic level in terms of individual trait values and relationships between individuals, but including different evolutionary processes: genetic drift, recombination, selection, mutation, population structure, …. We give a range of examples of its application to evolutionary questions related to stabilising selection, assortative mating, effective population size and response to selection, habitat preference and speciation. We provide a mathematical justification of the model as the limit as the number M of underlying loci tends to infinity of a model with Mendelian inheritance, mutation and environmental noise, when the genetic component of the trait is purely additive. We also show how the model generalises to include epistatic effects. We prove in particular that, within each family, the genetic components of the individual trait values in the current generation are indeed normally distributed with a variance independent of ancestral traits, up to an error of order 1∕M. Simulations suggest that in some cases the convergence may be as fast as 1∕M.","lang":"eng"}],"type":"journal_article","month":"12","file_date_updated":"2020-07-14T12:47:25Z","article_processing_charge":"No","oa_version":"Published Version","date_created":"2018-12-11T11:47:34Z","doi":"10.1016/j.tpb.2017.06.001","title":"The infinitesimal model: Definition derivation and implications","department":[{"_id":"NiBa"}],"publist_id":"7169","publication_status":"published","intvolume":" 118","language":[{"iso":"eng"}],"date_published":"2017-12-01T00:00:00Z","isi":1,"_id":"626","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"quality_controlled":"1","volume":118,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"01","page":"50 - 73","citation":{"ista":"Barton NH, Etheridge A, Véber A. 2017. The infinitesimal model: Definition derivation and implications. Theoretical Population Biology. 118, 50–73.","chicago":"Barton, Nicholas H, Alison Etheridge, and Amandine Véber. “The Infinitesimal Model: Definition Derivation and Implications.” Theoretical Population Biology. Academic Press, 2017. https://doi.org/10.1016/j.tpb.2017.06.001.","short":"N.H. Barton, A. Etheridge, A. Véber, Theoretical Population Biology 118 (2017) 50–73.","apa":"Barton, N. H., Etheridge, A., & Véber, A. (2017). The infinitesimal model: Definition derivation and implications. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2017.06.001","ieee":"N. H. Barton, A. Etheridge, and A. Véber, “The infinitesimal model: Definition derivation and implications,” Theoretical Population Biology, vol. 118. Academic Press, pp. 50–73, 2017.","mla":"Barton, Nicholas H., et al. “The Infinitesimal Model: Definition Derivation and Implications.” Theoretical Population Biology, vol. 118, Academic Press, 2017, pp. 50–73, doi:10.1016/j.tpb.2017.06.001.","ama":"Barton NH, Etheridge A, Véber A. The infinitesimal model: Definition derivation and implications. Theoretical Population Biology. 2017;118:50-73. doi:10.1016/j.tpb.2017.06.001"},"ddc":["576"],"status":"public","publication":"Theoretical Population Biology","scopus_import":"1","has_accepted_license":"1","ec_funded":1,"publisher":"Academic Press","file":[{"date_created":"2018-12-12T10:12:45Z","access_level":"open_access","date_updated":"2020-07-14T12:47:25Z","file_size":1133924,"content_type":"application/pdf","checksum":"7dd02bfcfe8f244f4a6c19091aedf2c8","relation":"main_file","file_id":"4964","creator":"system","file_name":"IST-2017-908-v1+1_1-s2.0-S0040580917300886-main_1_.pdf"}],"date_updated":"2025-09-11T07:29:31Z","year":"2017","author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H"},{"full_name":"Etheridge, Alison","last_name":"Etheridge","first_name":"Alison"},{"last_name":"Véber","first_name":"Amandine","full_name":"Véber, Amandine"}]},{"issue":"6","volume":71,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","oa":1,"quality_controlled":"1","date_updated":"2025-07-10T12:02:04Z","year":"2017","author":[{"full_name":"Sachdeva, Himani","last_name":"Sachdeva","first_name":"Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"ddc":["576"],"page":"1478 - 1493 ","citation":{"mla":"Sachdeva, Himani, and Nicholas H. Barton. “Divergence and Evolution of Assortative Mating in a Polygenic Trait Model of Speciation with Gene Flow.” Evolution; International Journal of Organic Evolution, vol. 71, no. 6, Wiley-Blackwell, 2017, pp. 1478–93, doi:10.1111/evo.13252.","apa":"Sachdeva, H., & Barton, N. H. (2017). Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow. Evolution; International Journal of Organic Evolution. Wiley-Blackwell. https://doi.org/10.1111/evo.13252","ama":"Sachdeva H, Barton NH. Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow. Evolution; International Journal of Organic Evolution. 2017;71(6):1478-1493. doi:10.1111/evo.13252","ieee":"H. Sachdeva and N. H. Barton, “Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow,” Evolution; International Journal of Organic Evolution, vol. 71, no. 6. Wiley-Blackwell, pp. 1478–1493, 2017.","chicago":"Sachdeva, Himani, and Nicholas H Barton. “Divergence and Evolution of Assortative Mating in a Polygenic Trait Model of Speciation with Gene Flow.” Evolution; International Journal of Organic Evolution. Wiley-Blackwell, 2017. https://doi.org/10.1111/evo.13252.","ista":"Sachdeva H, Barton NH. 2017. Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow. Evolution; International Journal of Organic Evolution. 71(6), 1478–1493.","short":"H. Sachdeva, N.H. Barton, Evolution; International Journal of Organic Evolution 71 (2017) 1478–1493."},"status":"public","publication":"Evolution; International Journal of Organic Evolution","has_accepted_license":"1","scopus_import":"1","ec_funded":1,"publisher":"Wiley-Blackwell","file":[{"file_name":"2017_Evolution_Sachdeva_supplement.pdf","creator":"dernst","file_id":"6329","relation":"main_file","file_size":625260,"checksum":"6d4c38cb1347fd43620d1736c6df5c79","content_type":"application/pdf","date_updated":"2020-07-14T12:48:18Z","access_level":"open_access","date_created":"2019-04-17T07:37:04Z"},{"file_name":"2017_Evolution_Sachdeva_article.pdf","creator":"dernst","file_id":"6330","relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:48:18Z","date_created":"2019-04-17T07:37:04Z","checksum":"f1d90dd8831b44baf49b4dd176f263af","content_type":"application/pdf","file_size":520110}],"article_processing_charge":"No","date_created":"2018-12-11T11:49:34Z","oa_version":"Submitted Version","doi":"10.1111/evo.13252","title":"Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow","department":[{"_id":"NiBa"}],"pubrep_id":"977","corr_author":"1","publication_identifier":{"issn":["0014-3820"]},"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7"},{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"external_id":{"isi":["000403014800005"],"pmid":["28419447"]},"abstract":[{"text":"Assortative mating is an important driver of speciation in populations with gene flow and is predicted to evolve under certain conditions in few-locus models. However, the evolution of assortment is less understood for mating based on quantitative traits, which are often characterized by high genetic variability and extensive linkage disequilibrium between trait loci. We explore this scenario for a two-deme model with migration, by considering a single polygenic trait subject to divergent viability selection across demes, as well as assortative mating and sexual selection within demes, and investigate how trait divergence is shaped by various evolutionary forces. Our analysis reveals the existence of sharp thresholds of assortment strength, at which divergence increases dramatically. We also study the evolution of assortment via invasion of modifiers of mate discrimination and show that the ES assortment strength has an intermediate value under a range of migration-selection parameters, even in diverged populations, due to subtle effects which depend sensitively on the extent of phenotypic variation within these populations. The evolutionary dynamics of the polygenic trait is studied using the hypergeometric and infinitesimal models. We further investigate the sensitivity of our results to the assumptions of the hypergeometric model, using individual-based simulations.","lang":"eng"}],"type":"journal_article","file_date_updated":"2020-07-14T12:48:18Z","month":"06","date_published":"2017-06-01T00:00:00Z","_id":"990","isi":1,"publist_id":"6409","pmid":1,"publication_status":"published","intvolume":" 71","language":[{"iso":"eng"}]},{"oa":1,"quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"09","issue":"1","volume":8,"publisher":"Nature Publishing Group","file":[{"creator":"system","file_name":"IST-2017-864-v1+1_s41467-017-00238-8.pdf","relation":"main_file","file_id":"5064","date_updated":"2020-07-14T12:48:16Z","access_level":"open_access","date_created":"2018-12-12T10:14:14Z","file_size":998157,"checksum":"29a1b5db458048d3bd5c67e0e2a56818","content_type":"application/pdf"},{"file_id":"5065","relation":"main_file","file_name":"IST-2017-864-v1+2_41467_2017_238_MOESM1_ESM.pdf","creator":"system","content_type":"application/pdf","file_size":9715993,"checksum":"7b78401e52a576cf3e6bbf8d0abadc17","date_created":"2018-12-12T10:14:15Z","access_level":"open_access","date_updated":"2020-07-14T12:48:16Z"}],"scopus_import":"1","has_accepted_license":"1","ec_funded":1,"citation":{"apa":"Friedlander, T., Prizak, R., Barton, N. H., & Tkačik, G. (2017). Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-00238-8","ama":"Friedlander T, Prizak R, Barton NH, Tkačik G. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-00238-8","mla":"Friedlander, Tamar, et al. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” Nature Communications, vol. 8, no. 1, 216, Nature Publishing Group, 2017, doi:10.1038/s41467-017-00238-8.","ieee":"T. Friedlander, R. Prizak, N. H. Barton, and G. Tkačik, “Evolution of new regulatory functions on biophysically realistic fitness landscapes,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017.","chicago":"Friedlander, Tamar, Roshan Prizak, Nicholas H Barton, and Gašper Tkačik. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-00238-8.","short":"T. Friedlander, R. Prizak, N.H. Barton, G. Tkačik, Nature Communications 8 (2017).","ista":"Friedlander T, Prizak R, Barton NH, Tkačik G. 2017. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. 8(1), 216."},"ddc":["539","576"],"article_number":"216","publication":"Nature Communications","status":"public","author":[{"id":"36A5845C-F248-11E8-B48F-1D18A9856A87","full_name":"Friedlander, Tamar","last_name":"Friedlander","first_name":"Tamar"},{"id":"4456104E-F248-11E8-B48F-1D18A9856A87","full_name":"Prizak, Roshan","first_name":"Roshan","last_name":"Prizak"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","first_name":"Gasper","last_name":"Tkacik"}],"year":"2017","date_updated":"2026-04-08T13:54:24Z","external_id":{"isi":["000407198800005"]},"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7"},{"call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27"}],"month":"08","file_date_updated":"2020-07-14T12:48:16Z","type":"journal_article","abstract":[{"text":"Gene expression is controlled by networks of regulatory proteins that interact specifically with external signals and DNA regulatory sequences. These interactions force the network components to co-evolve so as to continually maintain function. Yet, existing models of evolution mostly focus on isolated genetic elements. In contrast, we study the essential process by which regulatory networks grow: the duplication and subsequent specialization of network components. We synthesize a biophysical model of molecular interactions with the evolutionary framework to find the conditions and pathways by which new regulatory functions emerge. We show that specialization of new network components is usually slow, but can be drastically accelerated in the presence of regulatory crosstalk and mutations that promote promiscuous interactions between network components.","lang":"eng"}],"pubrep_id":"864","corr_author":"1","publication_identifier":{"issn":["2041-1723"]},"department":[{"_id":"GaTk"},{"_id":"NiBa"}],"date_created":"2018-12-11T11:49:23Z","doi":"10.1038/s41467-017-00238-8","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","title":"Evolution of new regulatory functions on biophysically realistic fitness landscapes","language":[{"iso":"eng"}],"publist_id":"6459","intvolume":" 8","publication_status":"published","_id":"955","related_material":{"record":[{"relation":"dissertation_contains","id":"6071","status":"public"}]},"isi":1,"date_published":"2017-08-09T00:00:00Z"},{"issue":"3","volume":205,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","oa":1,"quality_controlled":"1","date_updated":"2026-04-08T14:06:35Z","author":[{"orcid":"0000-0002-4884-9682","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","full_name":"Ringbauer, Harald","last_name":"Ringbauer","first_name":"Harald"},{"last_name":"Coop","first_name":"Graham","full_name":"Coop, Graham"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"year":"2017","page":"1335 - 1351","citation":{"ista":"Ringbauer H, Coop G, Barton NH. 2017. Inferring recent demography from isolation by distance of long shared sequence blocks. Genetics. 205(3), 1335–1351.","chicago":"Ringbauer, Harald, Graham Coop, and Nicholas H Barton. “Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks.” Genetics. Genetics Society of America, 2017. https://doi.org/10.1534/genetics.116.196220.","short":"H. Ringbauer, G. Coop, N.H. Barton, Genetics 205 (2017) 1335–1351.","ama":"Ringbauer H, Coop G, Barton NH. Inferring recent demography from isolation by distance of long shared sequence blocks. Genetics. 2017;205(3):1335-1351. doi:10.1534/genetics.116.196220","ieee":"H. Ringbauer, G. Coop, and N. H. Barton, “Inferring recent demography from isolation by distance of long shared sequence blocks,” Genetics, vol. 205, no. 3. Genetics Society of America, pp. 1335–1351, 2017.","apa":"Ringbauer, H., Coop, G., & Barton, N. H. (2017). Inferring recent demography from isolation by distance of long shared sequence blocks. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.196220","mla":"Ringbauer, Harald, et al. “Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks.” Genetics, vol. 205, no. 3, Genetics Society of America, 2017, pp. 1335–51, doi:10.1534/genetics.116.196220."},"status":"public","publication":"Genetics","publisher":"Genetics Society of America","scopus_import":"1","ec_funded":1,"date_created":"2018-12-11T11:50:00Z","oa_version":"Preprint","doi":"10.1534/genetics.116.196220","main_file_link":[{"url":"http://www.biorxiv.org/content/early/2016/09/23/076810","open_access":"1"}],"article_processing_charge":"No","title":"Inferring recent demography from isolation by distance of long shared sequence blocks","department":[{"_id":"NiBa"}],"publication_identifier":{"issn":["0016-6731"]},"external_id":{"isi":["000395807200023"]},"project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"type":"journal_article","month":"03","abstract":[{"text":"Recently it has become feasible to detect long blocks of nearly identical sequence shared between pairs of genomes. These IBD blocks are direct traces of recent coalescence events and, as such, contain ample signal to infer recent demography. Here, we examine sharing of such blocks in two-dimensional populations with local migration. Using a diffusion approximation to trace genetic ancestry, we derive analytical formulae for patterns of isolation by distance of IBD blocks, which can also incorporate recent population density changes. We introduce an inference scheme that uses a composite likelihood approach to fit these formulae. We then extensively evaluate our theory and inference method on a range of scenarios using simulated data. We first validate the diffusion approximation by showing that the theoretical results closely match the simulated block sharing patterns. We then demonstrate that our inference scheme can accurately and robustly infer dispersal rate and effective density, as well as bounds on recent dynamics of population density. To demonstrate an application, we use our estimation scheme to explore the fit of a diffusion model to Eastern European samples in the POPRES data set. We show that ancestry diffusing with a rate of σ ≈ 50–100 km/√gen during the last centuries, combined with accelerating population growth, can explain the observed exponential decay of block sharing with increasing pairwise sample distance.","lang":"eng"}],"date_published":"2017-03-01T00:00:00Z","_id":"1074","related_material":{"record":[{"status":"public","id":"200","relation":"dissertation_contains"}]},"isi":1,"publist_id":"6307","intvolume":" 205","publication_status":"published","language":[{"iso":"eng"}]},{"author":[{"full_name":"Franssen, Susan","first_name":"Susan","last_name":"Franssen"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton"},{"last_name":"Schlötterer","first_name":"Christian","full_name":"Schlötterer, Christian"}],"year":"2016","date_updated":"2025-09-22T09:43:41Z","file":[{"relation":"main_file","file_id":"5223","creator":"system","file_name":"IST-2017-770-v1+1_FranssenEtAl_nofigs-1.pdf","content_type":"application/pdf","file_size":295274,"checksum":"1e78d3aaffcb40dc8b02b7b4666019e0","date_created":"2018-12-12T10:16:35Z","date_updated":"2020-07-14T12:44:38Z","access_level":"open_access"},{"creator":"system","file_name":"IST-2017-770-v1+2_Fig1.pdf","relation":"main_file","file_id":"5224","access_level":"open_access","date_updated":"2020-07-14T12:44:38Z","date_created":"2018-12-12T10:16:36Z","checksum":"e13171843283774404c936c581b4543e","file_size":10902625,"content_type":"application/pdf"},{"access_level":"open_access","date_updated":"2020-07-14T12:44:38Z","date_created":"2018-12-12T10:16:37Z","content_type":"application/pdf","checksum":"63bc6e6e61f347594d8c00c37f874a0b","file_size":21437,"creator":"system","file_name":"IST-2017-770-v1+3_Fig2.pdf","relation":"main_file","file_id":"5225"},{"relation":"main_file","file_id":"5226","creator":"system","file_name":"IST-2017-770-v1+4_Fig3.pdf","content_type":"application/pdf","checksum":"da87cc7c78808837f22a3dae1c8397f9","file_size":1172194,"date_created":"2018-12-12T10:16:38Z","access_level":"open_access","date_updated":"2020-07-14T12:44:38Z"},{"content_type":"application/pdf","checksum":"e47b2a0c32142f423b3100150c0294f8","file_size":50045,"access_level":"open_access","date_updated":"2020-07-14T12:44:38Z","date_created":"2018-12-12T10:16:38Z","file_name":"IST-2017-770-v1+5_Fig4.pdf","creator":"system","file_id":"5227","relation":"main_file"},{"file_name":"IST-2017-770-v1+6_Fig5.pdf","creator":"system","file_id":"5228","relation":"main_file","content_type":"application/pdf","checksum":"a5a7d6b32e7e17d35d337d7ec2a9f6c9","file_size":50705,"access_level":"open_access","date_updated":"2020-07-14T12:44:38Z","date_created":"2018-12-12T10:16:39Z"}],"publisher":"Oxford University Press","scopus_import":"1","ec_funded":1,"has_accepted_license":"1","ddc":["576"],"page":"174 - 184","citation":{"short":"S. Franssen, N.H. Barton, C. Schlötterer, Molecular Biology and Evolution 34 (2016) 174–184.","ista":"Franssen S, Barton NH, Schlötterer C. 2016. Reconstruction of haplotype-blocks selected during experimental evolution. Molecular Biology and Evolution. 34(1), 174–184.","chicago":"Franssen, Susan, Nicholas H Barton, and Christian Schlötterer. “Reconstruction of Haplotype-Blocks Selected during Experimental Evolution.” Molecular Biology and Evolution. Oxford University Press, 2016. https://doi.org/10.1093/molbev/msw210.","apa":"Franssen, S., Barton, N. H., & Schlötterer, C. (2016). Reconstruction of haplotype-blocks selected during experimental evolution. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msw210","ama":"Franssen S, Barton NH, Schlötterer C. Reconstruction of haplotype-blocks selected during experimental evolution. Molecular Biology and Evolution. 2016;34(1):174-184. doi:10.1093/molbev/msw210","ieee":"S. Franssen, N. H. Barton, and C. Schlötterer, “Reconstruction of haplotype-blocks selected during experimental evolution.,” Molecular Biology and Evolution, vol. 34, no. 1. Oxford University Press, pp. 174–184, 2016.","mla":"Franssen, Susan, et al. “Reconstruction of Haplotype-Blocks Selected during Experimental Evolution.” Molecular Biology and Evolution, vol. 34, no. 1, Oxford University Press, 2016, pp. 174–84, doi:10.1093/molbev/msw210."},"status":"public","publication":"Molecular Biology and Evolution","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"03","issue":"1","volume":34,"oa":1,"quality_controlled":"1","_id":"1195","isi":1,"date_published":"2016-10-03T00:00:00Z","language":[{"iso":"eng"}],"publist_id":"6155","intvolume":" 34","publication_status":"published","department":[{"_id":"NiBa"}],"doi":"10.1093/molbev/msw210","oa_version":"Submitted Version","date_created":"2018-12-11T11:50:39Z","article_processing_charge":"No","title":"Reconstruction of haplotype-blocks selected during experimental evolution.","external_id":{"isi":["000396772000009"]},"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7"}],"type":"journal_article","month":"10","file_date_updated":"2020-07-14T12:44:38Z","abstract":[{"lang":"eng","text":"The genetic analysis of experimentally evolving populations typically relies on short reads from pooled individuals (Pool-Seq). While this method provides reliable allele frequency estimates, the underlying haplotype structure remains poorly characterized. With small population sizes and adaptive variants that start from low frequencies, the interpretation of selection signatures in most Evolve and Resequencing studies remains challenging. To facilitate the characterization of selection targets, we propose a new approach that reconstructs selected haplotypes from replicated time series, using Pool-Seq data. We identify selected haplotypes through the correlated frequencies of alleles carried by them. Computer simulations indicate that selected haplotype-blocks of several Mb can be reconstructed with high confidence and low error rates, even when allele frequencies change only by 20% across three replicates. Applying this method to real data from D. melanogaster populations adapting to a hot environment, we identify a selected haplotype-block of 6.93 Mb. We confirm the presence of this haplotype-block in evolved populations by experimental haplotyping, demonstrating the power and accuracy of our haplotype reconstruction from Pool-Seq data. We propose that the combination of allele frequency estimates with haplotype information will provide the key to understanding the dynamics of adaptive alleles. "}],"acknowledgement":"The authors thank all members of the Institute of Population\r\nGenetics for discussion and support on the project and par-\r\nticularly N. Barghi for helpful comments on earlier versions of\r\nthe manuscript. This work was supported by the European\r\nResearch Council (ERC) grants “ArchAdapt” and “250152”.","pubrep_id":"770"},{"publisher":"National Academy of Sciences","scopus_import":"1","ec_funded":1,"status":"public","publication":"PNAS","citation":{"ista":"Paixao T, Barton NH. 2016. The effect of gene interactions on the long-term response to selection. PNAS. 113(16), 4422–4427.","chicago":"Paixao, Tiago, and Nicholas H Barton. “The Effect of Gene Interactions on the Long-Term Response to Selection.” PNAS. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1518830113.","short":"T. Paixao, N.H. Barton, PNAS 113 (2016) 4422–4427.","mla":"Paixao, Tiago, and Nicholas H. Barton. “The Effect of Gene Interactions on the Long-Term Response to Selection.” PNAS, vol. 113, no. 16, National Academy of Sciences, 2016, pp. 4422–27, doi:10.1073/pnas.1518830113.","apa":"Paixao, T., & Barton, N. H. (2016). The effect of gene interactions on the long-term response to selection. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1518830113","ieee":"T. Paixao and N. H. Barton, “The effect of gene interactions on the long-term response to selection,” PNAS, vol. 113, no. 16. National Academy of Sciences, pp. 4422–4427, 2016.","ama":"Paixao T, Barton NH. The effect of gene interactions on the long-term response to selection. PNAS. 2016;113(16):4422-4427. doi:10.1073/pnas.1518830113"},"page":"4422 - 4427","author":[{"last_name":"Paixao","first_name":"Tiago","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton"}],"year":"2016","date_updated":"2025-09-22T07:45:33Z","article_type":"original","quality_controlled":"1","oa":1,"day":"19","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":113,"issue":"16","language":[{"iso":"eng"}],"intvolume":" 113","publication_status":"published","pmid":1,"publist_id":"5886","_id":"1359","isi":1,"date_published":"2016-04-19T00:00:00Z","type":"journal_article","month":"04","abstract":[{"text":"The role of gene interactions in the evolutionary process has long\r\nbeen controversial. Although some argue that they are not of\r\nimportance, because most variation is additive, others claim that\r\ntheir effect in the long term can be substantial. Here, we focus on\r\nthe long-term effects of genetic interactions under directional\r\nselection assuming no mutation or dominance, and that epistasis is\r\nsymmetrical overall. We ask by how much the mean of a complex\r\ntrait can be increased by selection and analyze two extreme\r\nregimes, in which either drift or selection dominate the dynamics\r\nof allele frequencies. In both scenarios, epistatic interactions affect\r\nthe long-term response to selection by modulating the additive\r\ngenetic variance. When drift dominates, we extend Robertson\r\n’\r\ns\r\n[Robertson A (1960)\r\nProc R Soc Lond B Biol Sci\r\n153(951):234\r\n−\r\n249]\r\nargument to show that, for any form of epistasis, the total response\r\nof a haploid population is proportional to the initial total genotypic\r\nvariance. In contrast, the total response of a diploid population is\r\nincreased by epistasis, for a given initial genotypic variance. When\r\nselection dominates, we show that the total selection response can\r\nonly be increased by epistasis when s\r\nome initially deleterious alleles\r\nbecome favored as the genetic background changes. We find a sim-\r\nple approximation for this effect and show that, in this regime, it is\r\nthe structure of the genotype - phenotype map that matters and not\r\nthe variance components of the population.","lang":"eng"}],"external_id":{"pmid":["27044080"],"isi":["000374393800056"]},"project":[{"call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7"}],"corr_author":"1","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"title":"The effect of gene interactions on the long-term response to selection","date_created":"2018-12-11T11:51:34Z","oa_version":"Published Version","doi":"10.1073/pnas.1518830113","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4843425/"}]},{"date_updated":"2025-09-18T14:22:05Z","author":[{"full_name":"Bod'ová, Katarína","first_name":"Katarína","last_name":"Bod'ová","orcid":"0000-0002-7214-0171","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","last_name":"Tkacik","first_name":"Gasper"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton"}],"year":"2016","citation":{"short":"K. Bodova, G. Tkačik, N.H. Barton, Genetics 202 (2016) 1523–1548.","ista":"Bodova K, Tkačik G, Barton NH. 2016. A general approximation for the dynamics of quantitative traits. Genetics. 202(4), 1523–1548.","chicago":"Bodova, Katarina, Gašper Tkačik, and Nicholas H Barton. “A General Approximation for the Dynamics of Quantitative Traits.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.184127.","mla":"Bodova, Katarina, et al. “A General Approximation for the Dynamics of Quantitative Traits.” Genetics, vol. 202, no. 4, Genetics Society of America, 2016, pp. 1523–48, doi:10.1534/genetics.115.184127.","apa":"Bodova, K., Tkačik, G., & Barton, N. H. (2016). A general approximation for the dynamics of quantitative traits. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.184127","ieee":"K. Bodova, G. Tkačik, and N. H. Barton, “A general approximation for the dynamics of quantitative traits,” Genetics, vol. 202, no. 4. Genetics Society of America, pp. 1523–1548, 2016.","ama":"Bodova K, Tkačik G, Barton NH. A general approximation for the dynamics of quantitative traits. Genetics. 2016;202(4):1523-1548. doi:10.1534/genetics.115.184127"},"page":"1523 - 1548","publication":"Genetics","status":"public","publisher":"Genetics Society of America","scopus_import":"1","ec_funded":1,"issue":"4","volume":202,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"06","oa":1,"quality_controlled":"1","date_published":"2016-04-06T00:00:00Z","_id":"1420","isi":1,"publist_id":"5787","intvolume":" 202","publication_status":"published","language":[{"iso":"eng"}],"oa_version":"Preprint","date_created":"2018-12-11T11:51:55Z","doi":"10.1534/genetics.115.184127","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1510.08344"}],"title":"A general approximation for the dynamics of quantitative traits","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"corr_author":"1","external_id":{"isi":["000373959100022"],"arxiv":["1510.08344"]},"project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"},{"_id":"255008E4-B435-11E9-9278-68D0E5697425","grant_number":"RGP0065/2012","name":"Information processing and computation in fish groups"}],"arxiv":1,"type":"journal_article","month":"04","abstract":[{"text":"Selection, mutation, and random drift affect the dynamics of allele frequencies and consequently of quantitative traits. While the macroscopic dynamics of quantitative traits can be measured, the underlying allele frequencies are typically unobserved. Can we understand how the macroscopic observables evolve without following these microscopic processes? This problem has been studied previously by analogy with statistical mechanics: the allele frequency distribution at each time point is approximated by the stationary form, which maximizes entropy. We explore the limitations of this method when mutation is small (4Nμ < 1) so that populations are typically close to fixation, and we extend the theory in this regime to account for changes in mutation strength. We consider a single diallelic locus either under directional selection or with overdominance and then generalize to multiple unlinked biallelic loci with unequal effects. We find that the maximum-entropy approximation is remarkably accurate, even when mutation and selection change rapidly. ","lang":"eng"}]},{"oa":1,"quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"01","issue":"2","volume":202,"scopus_import":"1","ec_funded":1,"publisher":"Genetics Society of America","page":"721 - 732","citation":{"chicago":"Uecker, Hildegard, and Joachim Hermisson. “The Role of Recombination in Evolutionary Rescue.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.180299.","short":"H. Uecker, J. Hermisson, Genetics 202 (2016) 721–732.","ista":"Uecker H, Hermisson J. 2016. The role of recombination in evolutionary rescue. Genetics. 202(2), 721–732.","mla":"Uecker, Hildegard, and Joachim Hermisson. “The Role of Recombination in Evolutionary Rescue.” Genetics, vol. 202, no. 2, Genetics Society of America, 2016, pp. 721–32, doi:10.1534/genetics.115.180299.","ama":"Uecker H, Hermisson J. The role of recombination in evolutionary rescue. Genetics. 2016;202(2):721-732. doi:10.1534/genetics.115.180299","apa":"Uecker, H., & Hermisson, J. (2016). The role of recombination in evolutionary rescue. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.180299","ieee":"H. Uecker and J. Hermisson, “The role of recombination in evolutionary rescue,” Genetics, vol. 202, no. 2. Genetics Society of America, pp. 721–732, 2016."},"publication":"Genetics","status":"public","year":"2016","author":[{"orcid":"0000-0001-9435-2813","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","full_name":"Uecker, Hildegard","last_name":"Uecker","first_name":"Hildegard"},{"full_name":"Hermisson, Joachim","first_name":"Joachim","last_name":"Hermisson"}],"date_updated":"2025-09-22T09:17:06Z","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"name":"Evolutionary rescue","_id":"25B67606-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000371304600028"]},"abstract":[{"lang":"eng","text":"How likely is it that a population escapes extinction through adaptive evolution? The answer to this question is of great relevance in conservation biology, where we aim at species’ rescue and the maintenance of biodiversity, and in agriculture and medicine, where we seek to hamper the emergence of pesticide or drug resistance. By reshuffling the genome, recombination has two antagonistic effects on the probability of evolutionary rescue: It generates and it breaks up favorable gene combinations. Which of the two effects prevails depends on the fitness effects of mutations and on the impact of stochasticity on the allele frequencies. In this article, we analyze a mathematical model for rescue after a sudden environmental change when adaptation is contingent on mutations at two loci. The analysis reveals a complex nonlinear dependence of population survival on recombination. We moreover find that, counterintuitively, a fast eradication of the wild type can promote rescue in the presence of recombination. The model also shows that two-step rescue is not unlikely to happen and can even be more likely than single-step rescue (where adaptation relies on a single mutation), depending on the circumstances."}],"month":"02","type":"journal_article","acknowledgement":"This work was made possible by a “For Women in Science” fellowship (L’Oréal Österreich in cooperation with the Austrian Commission for the United Nations Educational, Scientific, and Cultural Organization and the Austrian Academy of Sciences with financial support from the Federal Ministry for Science and Research Austria) and European Research Council grant 250152 (to Nick Barton).","department":[{"_id":"NiBa"}],"article_processing_charge":"No","main_file_link":[{"url":"http://biorxiv.org/content/early/2015/07/06/022020.abstract","open_access":"1"}],"date_created":"2018-12-11T11:50:54Z","doi":"10.1534/genetics.115.180299","oa_version":"Preprint","title":"The role of recombination in evolutionary rescue","language":[{"iso":"eng"}],"publist_id":"6091","publication_status":"published","intvolume":" 202","_id":"1241","isi":1,"date_published":"2016-02-01T00:00:00Z"}]