[{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"intvolume":" 6","publication_status":"published","publication_identifier":{"eissn":["2056-3744"]},"month":"10","year":"2022","quality_controlled":"1","citation":{"chicago":"Hearn, Katherine E., Eva L. Koch, Sean Stankowski, Roger K. Butlin, Rui Faria, Kerstin Johannesson, and Anja M Westram. “Differing Associations between Sex Determination and Sex-Linked Inversions in Two Ecotypes of Littorina Saxatilis.” Evolution Letters. Oxford University Press, 2022. https://doi.org/10.1002/evl3.295.","ieee":"K. E. Hearn et al., “Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis,” Evolution Letters, vol. 6, no. 5. Oxford University Press, pp. 358–374, 2022.","ista":"Hearn KE, Koch EL, Stankowski S, Butlin RK, Faria R, Johannesson K, Westram AM. 2022. Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis. Evolution Letters. 6(5), 358–374.","mla":"Hearn, Katherine E., et al. “Differing Associations between Sex Determination and Sex-Linked Inversions in Two Ecotypes of Littorina Saxatilis.” Evolution Letters, vol. 6, no. 5, Oxford University Press, 2022, pp. 358–74, doi:10.1002/evl3.295.","short":"K.E. Hearn, E.L. Koch, S. Stankowski, R.K. Butlin, R. Faria, K. Johannesson, A.M. Westram, Evolution Letters 6 (2022) 358–374.","apa":"Hearn, K. E., Koch, E. L., Stankowski, S., Butlin, R. K., Faria, R., Johannesson, K., & Westram, A. M. (2022). Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis. Evolution Letters. Oxford University Press. https://doi.org/10.1002/evl3.295","ama":"Hearn KE, Koch EL, Stankowski S, et al. Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis. Evolution Letters. 2022;6(5):358-374. doi:10.1002/evl3.295"},"abstract":[{"lang":"eng","text":"Sexual antagonism is a common hypothesis for driving the evolution of sex chromosomes, whereby recombination suppression is favored between sexually antagonistic loci and the sex-determining locus to maintain beneficial combinations of alleles. This results in the formation of a sex-determining region. Chromosomal inversions may contribute to recombination suppression but their precise role in sex chromosome evolution remains unclear. Because local adaptation is frequently facilitated through the suppression of recombination between adaptive loci by chromosomal inversions, there is potential for inversions that cover sex-determining regions to be involved in local adaptation as well, particularly if habitat variation creates environment-dependent sexual antagonism. With these processes in mind, we investigated sex determination in a well-studied example of local adaptation within a species: the intertidal snail, Littorina saxatilis. Using SNP data from a Swedish hybrid zone, we find novel evidence for a female-heterogametic sex determination system that is restricted to one ecotype. Our results suggest that four putative chromosomal inversions, two previously described and two newly discovered, span the putative sex chromosome pair. We determine their differing associations with sex, which suggest distinct strata of differing ages. The same inversions are found in the second ecotype but do not show any sex association. The striking disparity in inversion-sex associations between ecotypes that are connected by gene flow across a habitat transition that is just a few meters wide indicates a difference in selective regime that has produced a distinct barrier to the spread of the newly discovered sex-determining region between ecotypes. Such sex chromosome-environment interactions have not previously been uncovered in L. saxatilis and are known in few other organisms. A combination of both sex-specific selection and divergent natural selection is required to explain these highly unusual patterns."}],"date_created":"2022-08-28T22:02:02Z","type":"journal_article","publication":"Evolution Letters","page":"358-374","department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"ddc":["570"],"day":"01","author":[{"first_name":"Katherine E.","full_name":"Hearn, Katherine E.","last_name":"Hearn"},{"first_name":"Eva L.","full_name":"Koch, Eva L.","last_name":"Koch"},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","full_name":"Stankowski, Sean","first_name":"Sean"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"orcid":"0000-0003-1050-4969","first_name":"Anja M","full_name":"Westram, Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","doi":"10.1002/evl3.295","scopus_import":"1","license":"https://creativecommons.org/licenses/by/4.0/","date_updated":"2025-06-12T06:22:56Z","title":"Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis","file_date_updated":"2023-02-27T07:17:42Z","article_type":"original","oa_version":"Published Version","volume":6,"_id":"12001","date_published":"2022-10-01T00:00:00Z","oa":1,"issue":"5","article_processing_charge":"Yes","acknowledgement":"We thank A. Wright and four anonymous reviewers for valuable comments on an earlier draft of this manuscript and all members of the Littorina group for helpful discussions. This work was supported by a European Research Council grant to RKB and by a Natural Environment Research Council studentship to KEH through the ACCE doctoral training program. KJ acknowledges support from the Swedish Science Research Council VR (Vetenskaprådet) (2017-03798). RF was supported by an FCT CEEC (Fundação para a Ciênca e a Tecnologia, Concurso Estímulo ao Emprego Científico) contract (2020.00275.CEECIND).","publisher":"Oxford University Press","pmid":1,"file":[{"checksum":"2dcd06186a11b7d1be4cddc6b189f8fb","access_level":"open_access","content_type":"application/pdf","creator":"dernst","success":1,"file_size":2368965,"date_updated":"2023-02-27T07:17:42Z","relation":"main_file","date_created":"2023-02-27T07:17:42Z","file_name":"2022_EvolutionLetters_Hearn.pdf","file_id":"12686"}],"external_id":{"isi":["000839621100001"],"pmid":["36254259"]},"status":"public"},{"publication_status":"published","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"intvolume":" 119","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Proceedings of the National Academy of Sciences of the United States of America","type":"journal_article","year":"2022","citation":{"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.","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.","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","short":"M. Hledik, N.H. Barton, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","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","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."},"quality_controlled":"1","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."}],"date_created":"2022-09-11T22:01:55Z","month":"08","file_date_updated":"2022-09-12T08:08:12Z","article_type":"original","article_number":"e2123152119","oa_version":"Published Version","volume":119,"project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"},{"name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","grant_number":"RGP0034/2018","_id":"2665AAFE-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"date_updated":"2026-04-07T12:59:24Z","title":"Accumulation and maintenance of information in evolution","day":"29","ddc":["570"],"author":[{"first_name":"Michal","id":"4171253A-F248-11E8-B48F-1D18A9856A87","last_name":"Hledik","full_name":"Hledik, Michal"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","full_name":"Tkačik, Gašper","first_name":"Gašper","orcid":"1"}],"has_accepted_license":"1","scopus_import":"1","doi":"10.1073/pnas.2123152119","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"related_material":{"record":[{"status":"public","id":"15020","relation":"dissertation_contains"}]},"language":[{"iso":"eng"}],"pmid":1,"status":"public","file":[{"success":1,"access_level":"open_access","content_type":"application/pdf","creator":"dernst","checksum":"6dec51f6567da9039982a571508a8e4d","file_id":"12091","relation":"main_file","date_created":"2022-09-12T08:08:12Z","date_updated":"2022-09-12T08:08:12Z","file_name":"2022_PNAS_Hledik.pdf","file_size":2165752}],"external_id":{"pmid":["36037343"],"isi":["000889278400014"]},"oa":1,"issue":"36","article_processing_charge":"No","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.”","publisher":"National Academy of Sciences","corr_author":"1","_id":"12081","date_published":"2022-08-29T00:00:00Z"},{"external_id":{"isi":["000890735600001"]},"file":[{"content_type":"application/pdf","access_level":"open_access","creator":"dernst","success":1,"checksum":"28de155b231ac1c8d4501c98b2fb359a","relation":"main_file","date_updated":"2023-01-24T12:21:32Z","date_created":"2023-01-24T12:21:32Z","file_name":"2022_eLife_Hayward.pdf","file_id":"12363","file_size":18935612}],"status":"public","publisher":"eLife Sciences Publications","oa":1,"acknowledgement":"We thank Guy Amster, Jeremy Berg, Nick Barton, Yuval Simons and Molly Przeworski for many helpful discussions, and Jeremy Berg, Graham Coop, Joachim Hermisson, Guillaume Martin, Will Milligan, Peter Ralph, Yuval Simons, Leo Speidel and Molly Przeworski for comments on the manuscript.\r\nNational Institutes of Health GM115889 Laura Katharine Hayward Guy Sella \r\nNational Institutes of Health GM121372 Laura Katharine Hayward","article_processing_charge":"No","corr_author":"1","date_published":"2022-09-26T00:00:00Z","_id":"12157","article_number":"66697","volume":11,"oa_version":"Published Version","file_date_updated":"2023-01-24T12:21:32Z","article_type":"original","title":"Polygenic adaptation after a sudden change in environment","date_updated":"2024-10-09T21:03:38Z","has_accepted_license":"1","scopus_import":"1","doi":"10.7554/elife.66697","ddc":["570"],"day":"26","author":[{"id":"fc885ee5-24bf-11eb-ad7b-bcc5104c0c1b","full_name":"Hayward, Laura","last_name":"Hayward","first_name":"Laura"},{"full_name":"Sella, Guy","last_name":"Sella","first_name":"Guy"}],"language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"type":"journal_article","publication":"eLife","abstract":[{"text":"Polygenic adaptation is thought to be ubiquitous, yet remains poorly understood. Here, we model this process analytically, in the plausible setting of a highly polygenic, quantitative trait that experiences a sudden shift in the fitness optimum. We show how the mean phenotype changes over time, depending on the effect sizes of loci that contribute to variance in the trait, and characterize the allele dynamics at these loci. Notably, we describe the two phases of the allele dynamics: The first is a rapid phase, in which directional selection introduces small frequency differences between alleles whose effects are aligned with or opposed to the shift, ultimately leading to small differences in their probability of fixation during a second, longer phase, governed by stabilizing selection. As we discuss, key results should hold in more general settings and have important implications for efforts to identify the genetic basis of adaptation in humans and other species.","lang":"eng"}],"date_created":"2023-01-12T12:09:00Z","citation":{"chicago":"Hayward, Laura, and Guy Sella. “Polygenic Adaptation after a Sudden Change in Environment.” ELife. eLife Sciences Publications, 2022. https://doi.org/10.7554/elife.66697.","ieee":"L. Hayward and G. Sella, “Polygenic adaptation after a sudden change in environment,” eLife, vol. 11. eLife Sciences Publications, 2022.","ista":"Hayward L, Sella G. 2022. Polygenic adaptation after a sudden change in environment. eLife. 11, 66697.","apa":"Hayward, L., & Sella, G. (2022). Polygenic adaptation after a sudden change in environment. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.66697","short":"L. Hayward, G. Sella, ELife 11 (2022).","mla":"Hayward, Laura, and Guy Sella. “Polygenic Adaptation after a Sudden Change in Environment.” ELife, vol. 11, 66697, eLife Sciences Publications, 2022, doi:10.7554/elife.66697.","ama":"Hayward L, Sella G. Polygenic adaptation after a sudden change in environment. eLife. 2022;11. doi:10.7554/elife.66697"},"year":"2022","quality_controlled":"1","month":"09","publication_status":"published","publication_identifier":{"eissn":["2050-084X"]},"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"intvolume":" 11","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"doi":"10.1111/evo.14632","scopus_import":"1","has_accepted_license":"1","author":[{"full_name":"Stankowski, Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean"}],"day":"01","ddc":["570"],"title":"Digest: On the origin of a possible hybrid species","date_updated":"2025-06-11T13:40:40Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","oa_version":"Published Version","volume":76,"article_type":"original","file_date_updated":"2023-01-27T11:28:38Z","date_published":"2022-11-01T00:00:00Z","_id":"12234","corr_author":"1","publisher":"Wiley","article_processing_charge":"Yes (via OA deal)","oa":1,"issue":"11","file":[{"checksum":"4c0f05083b414ac0323a1b9ee1abc275","access_level":"open_access","content_type":"application/pdf","creator":"dernst","success":1,"file_size":287282,"relation":"main_file","date_updated":"2023-01-27T11:28:38Z","date_created":"2023-01-27T11:28:38Z","file_name":"2022_Evolution_Stankowski.pdf","file_id":"12425"}],"external_id":{"isi":["000855751600001"],"pmid":["36112597"]},"status":"public","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"intvolume":" 76","publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"publication_status":"published","keyword":["General Agricultural and Biological Sciences","Genetics","Ecology","Evolution","Behavior and Systematics"],"month":"11","date_created":"2023-01-16T09:50:48Z","abstract":[{"lang":"eng","text":"Hybrid speciation—the origin of new species resulting from the hybridization of genetically divergent lineages—was once considered rare, but genomic data suggest that it may occur more often than once thought. In this study, Noguerales and Ortego found genomic evidence supporting the hybrid origin of a grasshopper that is able to exploit a broader range of host plants than either of its putative parents."}],"citation":{"ista":"Stankowski S. 2022. Digest: On the origin of a possible hybrid species. Evolution. 76(11), 2784–2785.","ama":"Stankowski S. Digest: On the origin of a possible hybrid species. Evolution. 2022;76(11):2784-2785. doi:10.1111/evo.14632","apa":"Stankowski, S. (2022). Digest: On the origin of a possible hybrid species. Evolution. Wiley. https://doi.org/10.1111/evo.14632","mla":"Stankowski, Sean. “Digest: On the Origin of a Possible Hybrid Species.” Evolution, vol. 76, no. 11, Wiley, 2022, pp. 2784–85, doi:10.1111/evo.14632.","short":"S. Stankowski, Evolution 76 (2022) 2784–2785.","chicago":"Stankowski, Sean. “Digest: On the Origin of a Possible Hybrid Species.” Evolution. Wiley, 2022. https://doi.org/10.1111/evo.14632.","ieee":"S. Stankowski, “Digest: On the origin of a possible hybrid species,” Evolution, vol. 76, no. 11. Wiley, pp. 2784–2785, 2022."},"quality_controlled":"1","year":"2022","page":"2784-2785","type":"journal_article","publication":"Evolution"},{"intvolume":" 76","keyword":["General Agricultural and Biological Sciences","Genetics","Ecology","Evolution","Behavior and Systematics"],"publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","citation":{"chicago":"Koch, Eva L., Mark Ravinet, Anja M Westram, Kerstin Johannesson, and Roger K. Butlin. “Genetic Architecture of Repeated Phenotypic Divergence in Littorina Saxatilis Evolution.” Evolution. Wiley, 2022. https://doi.org/10.1111/evo.14602.","ieee":"E. L. Koch, M. Ravinet, A. M. Westram, K. Johannesson, and R. K. Butlin, “Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution,” Evolution, vol. 76, no. 10. Wiley, pp. 2332–2346, 2022.","ista":"Koch EL, Ravinet M, Westram AM, Johannesson K, Butlin RK. 2022. Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution. Evolution. 76(10), 2332–2346.","apa":"Koch, E. L., Ravinet, M., Westram, A. M., Johannesson, K., & Butlin, R. K. (2022). Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution. Evolution. Wiley. https://doi.org/10.1111/evo.14602","mla":"Koch, Eva L., et al. “Genetic Architecture of Repeated Phenotypic Divergence in Littorina Saxatilis Evolution.” Evolution, vol. 76, no. 10, Wiley, 2022, pp. 2332–46, doi:10.1111/evo.14602.","short":"E.L. Koch, M. Ravinet, A.M. Westram, K. Johannesson, R.K. Butlin, Evolution 76 (2022) 2332–2346.","ama":"Koch EL, Ravinet M, Westram AM, Johannesson K, Butlin RK. Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution. Evolution. 2022;76(10):2332-2346. doi:10.1111/evo.14602"},"year":"2022","abstract":[{"lang":"eng","text":"Chromosomal inversions have been shown to play a major role in a local adaptation by suppressing recombination between alternative arrangements and maintaining beneficial allele combinations. However, so far, their importance relative to the remaining genome remains largely unknown. Understanding the genetic architecture of adaptation requires better estimates of how loci of different effect sizes contribute to phenotypic variation. Here, we used three Swedish islands where the marine snail Littorina saxatilis has repeatedly evolved into two distinct ecotypes along a habitat transition. We estimated the contribution of inversion polymorphisms to phenotypic divergence while controlling for polygenic effects in the remaining genome using a quantitative genetics framework. We confirmed the importance of inversions but showed that contributions of loci outside inversions are of similar magnitude, with variable proportions dependent on the trait and the population. Some inversions showed consistent effects across all sites, whereas others exhibited site-specific effects, indicating that the genomic basis for replicated phenotypic divergence is only partly shared. The contributions of sexual dimorphism as well as environmental factors to phenotypic variation were significant but minor compared to inversions and polygenic background. Overall, this integrated approach provides insight into the multiple mechanisms contributing to parallel phenotypic divergence."}],"date_created":"2023-01-16T09:54:15Z","publication":"Evolution","type":"journal_article","page":"2332-2346","month":"10","title":"Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution","date_updated":"2023-08-04T09:42:11Z","file_date_updated":"2023-01-30T08:45:35Z","article_type":"original","volume":76,"oa_version":"Published Version","department":[{"_id":"NiBa"}],"related_material":{"record":[{"relation":"research_data","id":"13066","status":"public"}]},"language":[{"iso":"eng"}],"ddc":["570"],"day":"01","author":[{"last_name":"Koch","full_name":"Koch, Eva L.","first_name":"Eva L."},{"last_name":"Ravinet","full_name":"Ravinet, Mark","first_name":"Mark"},{"first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","full_name":"Westram, Anja M"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"first_name":"Roger K.","full_name":"Butlin, Roger K.","last_name":"Butlin"}],"has_accepted_license":"1","doi":"10.1111/evo.14602","scopus_import":"1","issue":"10","oa":1,"article_processing_charge":"No","acknowledgement":"We thank everyone who helped with fieldwork, snail processing, and DNA extractions, particularly Laura Brettell, Mårten Duvetorp, Juan Galindo, Anne-Lise Liabot, Irena Senčić, and Zuzanna Zagrodzka. We also thank Rui Faria and Jenny Larsson for their contributions, with inversions and shell shape respectively. KJ was funded by the Swedish research council Vetenskapsrådet, grant number 2017-03798. R.K.B. and E.K. were funded by the European Research Council (ERC-2015-AdG-693030-BARRIERS). R.K.B. was also funded by the Natural Environment Research Council and the Swedish Research Council Vetenskapsrådet.","publisher":"Wiley","pmid":1,"status":"public","external_id":{"pmid":["35994296"],"isi":["000848449100001"]},"file":[{"file_id":"12439","file_name":"2022_Evolution_Koch.pdf","date_created":"2023-01-30T08:45:35Z","date_updated":"2023-01-30T08:45:35Z","relation":"main_file","file_size":2990581,"success":1,"creator":"dernst","content_type":"application/pdf","access_level":"open_access","checksum":"defd8a4bea61cf00a3c88d4a30e2728c"}],"_id":"12247","date_published":"2022-10-01T00:00:00Z"},{"month":"09","publication":"Journal of Evolutionary Biology","type":"journal_article","page":"1143-1164","citation":{"ieee":"A. M. Westram, S. Stankowski, P. Surendranadh, and N. H. Barton, “What is reproductive isolation?,” Journal of Evolutionary Biology, vol. 35, no. 9. Wiley, pp. 1143–1164, 2022.","chicago":"Westram, Anja M, Sean Stankowski, Parvathy Surendranadh, and Nicholas H Barton. “What Is Reproductive Isolation?” Journal of Evolutionary Biology. Wiley, 2022. https://doi.org/10.1111/jeb.14005.","ama":"Westram AM, Stankowski S, Surendranadh P, Barton NH. What is reproductive isolation? Journal of Evolutionary Biology. 2022;35(9):1143-1164. doi:10.1111/jeb.14005","apa":"Westram, A. M., Stankowski, S., Surendranadh, P., & Barton, N. H. (2022). What is reproductive isolation? Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.14005","mla":"Westram, Anja M., et al. “What Is Reproductive Isolation?” Journal of Evolutionary Biology, vol. 35, no. 9, Wiley, 2022, pp. 1143–64, doi:10.1111/jeb.14005.","short":"A.M. Westram, S. Stankowski, P. Surendranadh, N.H. Barton, Journal of Evolutionary Biology 35 (2022) 1143–1164.","ista":"Westram AM, Stankowski S, Surendranadh P, Barton NH. 2022. What is reproductive isolation? Journal of Evolutionary Biology. 35(9), 1143–1164."},"year":"2022","quality_controlled":"1","date_created":"2023-01-16T09:59:24Z","abstract":[{"lang":"eng","text":"Reproductive isolation (RI) is a core concept in evolutionary biology. It has been the central focus of speciation research since the modern synthesis and is the basis by which biological species are defined. Despite this, the term is used in seemingly different ways, and attempts to quantify RI have used very different approaches. After showing that the field lacks a clear definition of the term, we attempt to clarify key issues, including what RI is, how it can be quantified in principle, and how it can be measured in practice. Following other definitions with a genetic focus, we propose that RI is a quantitative measure of the effect that genetic differences between populations have on gene flow. Specifically, RI compares the flow of neutral alleles in the presence of these genetic differences to the flow without any such differences. RI is thus greater than zero when genetic differences between populations reduce the flow of neutral alleles between populations. We show how RI can be quantified in a range of scenarios. A key conclusion is that RI depends strongly on circumstances—including the spatial, temporal and genomic context—making it difficult to compare across systems. After reviewing methods for estimating RI from data, we conclude that it is difficult to measure in practice. We discuss our findings in light of the goals of speciation research and encourage the use of methods for estimating RI that integrate organismal and genetic approaches."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","keyword":["Ecology","Evolution","Behavior and Systematics"],"publication_identifier":{"eissn":["1420-9101"],"issn":["1010-061X"]},"publication_status":"published","intvolume":" 35","corr_author":"1","_id":"12264","date_published":"2022-09-01T00:00:00Z","external_id":{"pmid":["36063156"],"isi":["000849851100002"]},"file":[{"file_size":3146793,"file_name":"2022_JourEvoBiology_Westram.pdf","date_updated":"2023-01-30T10:05:31Z","date_created":"2023-01-30T10:05:31Z","relation":"main_file","file_id":"12448","checksum":"f08de57112330a7ee88d2e1b20576a1e","creator":"dernst","content_type":"application/pdf","access_level":"open_access","success":1}],"status":"public","pmid":1,"acknowledgement":"We are grateful to the participants of the ESEB satellite symposium ‘Understanding reproductive isolation: bridging conceptual barriers in speciation research’ in 2021 for the interesting discussions that helped us clarify the thoughts presented in this article. We thank Roger Butlin, Michael Turelli and two anonymous reviewers for their thoughtful comments on this manuscript. We are also very grateful to Roger Butlin and the Barton Group for the continued conversa-tions about RI. In addition, we thank all participants of the speciation survey. Part of this work was funded by the Austrian Science Fund FWF (grant P 32166)","article_processing_charge":"Yes (via OA deal)","issue":"9","oa":1,"publisher":"Wiley","author":[{"full_name":"Westram, Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","orcid":"0000-0003-1050-4969"},{"first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","last_name":"Stankowski"},{"last_name":"Surendranadh","full_name":"Surendranadh, Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87","first_name":"Parvathy","orcid":"0000-0001-6395-386X"},{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H"}],"day":"01","ddc":["570"],"scopus_import":"1","doi":"10.1111/jeb.14005","has_accepted_license":"1","related_material":{"record":[{"relation":"other","id":"12265","status":"public"}]},"department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"article_type":"review","file_date_updated":"2023-01-30T10:05:31Z","oa_version":"Published Version","volume":35,"project":[{"name":"Snapdragon Speciation","grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"}],"date_updated":"2025-04-15T08:20:40Z","title":"What is reproductive isolation?"},{"external_id":{"isi":["000849851100009"]},"file":[{"checksum":"27268009e5eec030bc10667a4ac5ed4c","success":1,"content_type":"application/pdf","access_level":"open_access","creator":"dernst","file_size":349603,"file_id":"12449","date_updated":"2023-01-30T10:14:09Z","date_created":"2023-01-30T10:14:09Z","relation":"main_file","file_name":"2022_JourEvoBiology_Westram_Response.pdf"}],"status":"public","publisher":"Wiley","acknowledgement":"We are very grateful to the authors of the commentaries for the interesting discussion and to Luke Holman for handling this set of manuscripts. Part of this work was funded by the Austrian Science Fund FWF (grant P 32166).","article_processing_charge":"Yes (via OA deal)","issue":"9","oa":1,"corr_author":"1","date_published":"2022-09-01T00:00:00Z","_id":"12265","oa_version":"Published Version","volume":35,"article_type":"letter_note","file_date_updated":"2023-01-30T10:14:09Z","date_updated":"2025-04-15T08:20:40Z","title":"Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’","project":[{"name":"Snapdragon Speciation","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","grant_number":"P32166"}],"doi":"10.1111/jeb.14082","scopus_import":"1","has_accepted_license":"1","author":[{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M","last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969"},{"first_name":"Sean","full_name":"Stankowski, Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"id":"455235B8-F248-11E8-B48F-1D18A9856A87","last_name":"Surendranadh","full_name":"Surendranadh, Parvathy","orcid":"0000-0001-6395-386X","first_name":"Parvathy"},{"last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"}],"ddc":["570"],"day":"01","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"other","id":"12264","status":"public"}]},"department":[{"_id":"NiBa"}],"page":"1200-1205","type":"journal_article","publication":"Journal of Evolutionary Biology","date_created":"2023-01-16T09:59:37Z","year":"2022","quality_controlled":"1","citation":{"ieee":"A. M. Westram, S. Stankowski, P. Surendranadh, and N. H. Barton, “Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?,’” Journal of Evolutionary Biology, vol. 35, no. 9. Wiley, pp. 1200–1205, 2022.","chicago":"Westram, Anja M, Sean Stankowski, Parvathy Surendranadh, and Nicholas H Barton. “Reproductive Isolation, Speciation, and the Value of Disagreement: A Reply to the Commentaries on ‘What Is Reproductive Isolation?’” Journal of Evolutionary Biology. Wiley, 2022. https://doi.org/10.1111/jeb.14082.","apa":"Westram, A. M., Stankowski, S., Surendranadh, P., & Barton, N. H. (2022). Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’ Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.14082","short":"A.M. Westram, S. Stankowski, P. Surendranadh, N.H. Barton, Journal of Evolutionary Biology 35 (2022) 1200–1205.","mla":"Westram, Anja M., et al. “Reproductive Isolation, Speciation, and the Value of Disagreement: A Reply to the Commentaries on ‘What Is Reproductive Isolation?’” Journal of Evolutionary Biology, vol. 35, no. 9, Wiley, 2022, pp. 1200–05, doi:10.1111/jeb.14082.","ama":"Westram AM, Stankowski S, Surendranadh P, Barton NH. Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’ Journal of Evolutionary Biology. 2022;35(9):1200-1205. doi:10.1111/jeb.14082","ista":"Westram AM, Stankowski S, Surendranadh P, Barton NH. 2022. Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’ Journal of Evolutionary Biology. 35(9), 1200–1205."},"month":"09","publication_status":"published","publication_identifier":{"eissn":["1420-9101"],"issn":["1010-061X"]},"keyword":["Ecology","Evolution","Behavior and Systematics"],"intvolume":" 35","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"date_created":"2023-05-23T16:33:12Z","publisher":"Dryad","abstract":[{"lang":"eng","text":"Chromosomal inversions have been shown to play a major role in local adaptation by suppressing recombination between alternative arrangements and maintaining beneficial allele combinations. However, so far, their importance relative to the remaining genome remains largely unknown. Understanding the genetic architecture of adaptation requires better estimates of how loci of different effect sizes contribute to phenotypic variation. Here, we used three Swedish islands where the marine snail Littorina saxatilis has repeatedly evolved into two distinct ecotypes along a habitat transition. We estimated the contribution of inversion polymorphisms to phenotypic divergence while controlling for polygenic effects in the remaining genome using a quantitative genetics framework. We confirmed the importance of inversions but showed that contributions of loci outside inversions are of similar magnitude, with variable proportions dependent on the trait and the population. Some inversions showed consistent effects across all sites, whereas others exhibited site-specific effects, indicating that the genomic basis for replicated phenotypic divergence is only partly shared. The contributions of sexual dimorphism as well as environmental factors to phenotypic variation were significant but minor compared to inversions and polygenic background. Overall, this integrated approach provides insight into the multiple mechanisms contributing to parallel phenotypic divergence."}],"article_processing_charge":"No","citation":{"ista":"Koch E, Ravinet M, Westram AM, Jonannesson K, Butlin R. 2022. Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution, Dryad, 10.5061/DRYAD.M905QFV4B.","ama":"Koch E, Ravinet M, Westram AM, Jonannesson K, Butlin R. Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution. 2022. doi:10.5061/DRYAD.M905QFV4B","apa":"Koch, E., Ravinet, M., Westram, A. M., Jonannesson, K., & Butlin, R. (2022). Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution. Dryad. https://doi.org/10.5061/DRYAD.M905QFV4B","short":"E. Koch, M. Ravinet, A.M. Westram, K. Jonannesson, R. Butlin, (2022).","mla":"Koch, Eva, et al. Data from: Genetic Architecture of Repeated Phenotypic Divergence in Littorina Saxatilis Ecotype Evolution. Dryad, 2022, doi:10.5061/DRYAD.M905QFV4B.","chicago":"Koch, Eva, Mark Ravinet, Anja M Westram, Kerstin Jonannesson, and Roger Butlin. “Data from: Genetic Architecture of Repeated Phenotypic Divergence in Littorina Saxatilis Ecotype Evolution.” Dryad, 2022. https://doi.org/10.5061/DRYAD.M905QFV4B.","ieee":"E. Koch, M. Ravinet, A. M. Westram, K. Jonannesson, and R. Butlin, “Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution.” Dryad, 2022."},"year":"2022","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.m905qfv4b"}],"status":"public","type":"research_data_reference","date_published":"2022-07-28T00:00:00Z","_id":"13066","month":"07","title":"Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution","date_updated":"2023-08-04T09:42:10Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"12247","relation":"used_in_publication"}]},"department":[{"_id":"NiBa"}],"doi":"10.5061/DRYAD.M905QFV4B","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Eva","full_name":"Koch, Eva","last_name":"Koch"},{"first_name":"Mark","last_name":"Ravinet","full_name":"Ravinet, Mark"},{"last_name":"Westram","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M"},{"full_name":"Jonannesson, Kerstin","last_name":"Jonannesson","first_name":"Kerstin"},{"first_name":"Roger","full_name":"Butlin, Roger","last_name":"Butlin"}],"ddc":["570"],"tmp":{"short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"day":"28"},{"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"11686","status":"public","relation":"research_data"}]},"department":[{"_id":"NiBa"}],"scopus_import":"1","doi":"10.1002/evl3.270","has_accepted_license":"1","author":[{"full_name":"Turelli, Michael","last_name":"Turelli","first_name":"Michael"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H"}],"ddc":["570"],"day":"01","title":"Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics, and disease control","date_updated":"2025-06-11T13:45:56Z","volume":6,"oa_version":"Published Version","article_type":"original","file_date_updated":"2022-07-29T06:59:10Z","date_published":"2022-02-01T00:00:00Z","_id":"10604","publisher":"Wiley","article_processing_charge":"No","acknowledgement":"We thank S. O'Neill, C. Simmons, and the World Mosquito Project for providing access to unpublished data. S. Ritchie provided valuable insights into Aedes aegypti biology and the literature describing A. aegypti populations near Cairns. We thank B. Cooper for help with the figures and D. Shropshire, S. O'Neill, S. Ritchie, A. Hoffmann, B. Cooper, and members of the Cooper lab for comments on an earlier draft. Comments from three reviewers greatly improved our presentation.","oa":1,"issue":"1","status":"public","external_id":{"pmid":["35127140"],"isi":["000754412600008"]},"file":[{"file_name":"2022_EvolutionLetters_Turelli.pdf","date_created":"2022-07-29T06:59:10Z","relation":"main_file","date_updated":"2022-07-29T06:59:10Z","file_id":"11689","file_size":2435185,"creator":"dernst","content_type":"application/pdf","access_level":"open_access","success":1,"checksum":"7e9a37e3b65b480cd7014a6a4a7e460a"}],"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"intvolume":" 6","publication_identifier":{"eissn":["2056-3744"]},"publication_status":"published","keyword":["genetics","ecology","evolution","behavior and systematics"],"month":"02","date_created":"2022-01-09T09:45:17Z","abstract":[{"text":"Maternally inherited Wolbachia transinfections are being introduced into natural mosquito populations to reduce the transmission of dengue, Zika, and other arboviruses. Wolbachia-induced cytoplasmic incompatibility provides a frequency-dependent reproductive advantage to infected females that can spread transinfections within and among populations. However, because transinfections generally reduce host fitness, they tend to spread within populations only after their frequency exceeds a critical threshold. This produces bistability with stable equilibrium frequencies at both 0 and 1, analogous to the bistability produced by underdominance between alleles or karyotypes and by population dynamics under Allee effects. Here, we analyze how stochastic frequency variation produced by finite population size can facilitate the local spread of variants with bistable dynamics into areas where invasion is unexpected from deterministic models. Our exemplar is the establishment of wMel Wolbachia in the Aedes aegypti population of Pyramid Estates (PE), a small community in far north Queensland, Australia. In 2011, wMel was stably introduced into Gordonvale, separated from PE by barriers to A. aegypti dispersal. After nearly 6 years during which wMel was observed only at low frequencies in PE, corresponding to an apparent equilibrium between immigration and selection, wMel rose to fixation by 2018. Using analytic approximations and statistical analyses, we demonstrate that the observed fixation of wMel at PE is consistent with both stochastic transition past an unstable threshold frequency and deterministic transformation produced by steady immigration at a rate just above the threshold required for deterministic invasion. The indeterminacy results from a delicate balance of parameters needed to produce the delayed transition observed. Our analyses suggest that once Wolbachia transinfections are established locally through systematic introductions, stochastic “threshold crossing” is likely to only minimally enhance spatial spread, providing a local ratchet that slightly—but systematically—aids area-wide transformation of disease-vector populations in heterogeneous landscapes.","lang":"eng"}],"quality_controlled":"1","citation":{"ama":"Turelli M, Barton NH. Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics, and disease control. Evolution Letters. 2022;6(1):92-105. doi:10.1002/evl3.270","short":"M. Turelli, N.H. Barton, Evolution Letters 6 (2022) 92–105.","apa":"Turelli, M., & Barton, N. H. (2022). Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics, and disease control. Evolution Letters. Wiley. https://doi.org/10.1002/evl3.270","mla":"Turelli, Michael, and Nicholas H. Barton. “Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics, and Disease Control.” Evolution Letters, vol. 6, no. 1, Wiley, 2022, pp. 92–105, doi:10.1002/evl3.270.","ista":"Turelli M, Barton NH. 2022. Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics, and disease control. Evolution Letters. 6(1), 92–105.","ieee":"M. Turelli and N. H. Barton, “Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics, and disease control,” Evolution Letters, vol. 6, no. 1. Wiley, pp. 92–105, 2022.","chicago":"Turelli, Michael, and Nicholas H Barton. “Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics, and Disease Control.” Evolution Letters. Wiley, 2022. https://doi.org/10.1002/evl3.270."},"year":"2022","page":"92-105","publication":"Evolution Letters","type":"journal_article"},{"article_number":"20210010","oa_version":"Published Version","volume":377,"file_date_updated":"2022-01-24T10:34:45Z","article_type":"original","title":"Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity","date_updated":"2026-04-07T12:54:28Z","project":[{"name":"Causes and consequences of population fragmentation","grant_number":"P32896","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8"}],"has_accepted_license":"1","scopus_import":"1","doi":"10.1098/rstb.2021.0010","day":"24","ddc":["576"],"author":[{"last_name":"Sachdeva","full_name":"Sachdeva, Himani","first_name":"Himani"},{"orcid":"0000-0003-1971-8314","first_name":"Oluwafunmilola O","full_name":"Olusanya, Oluwafunmilola O","last_name":"Olusanya","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"}],"language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"related_material":{"record":[{"id":"14711","status":"public","relation":"dissertation_contains"}],"link":[{"url":"https://doi.org/10.1101/2021.08.05.455207","relation":"earlier_version"}]},"pmid":1,"status":"public","external_id":{"isi":["000745854300008"],"pmid":["35067097"]},"file":[{"checksum":"04ca9e2f0e344d680b947f2457df8d0a","access_level":"open_access","content_type":"application/pdf","creator":"oolusany","file_size":1845792,"relation":"main_file","date_created":"2022-01-24T10:34:45Z","date_updated":"2022-01-24T10:34:45Z","file_name":"rstb.2021.0010.pdf","file_id":"10659"}],"publisher":"The Royal Society","oa":1,"issue":"1846","article_processing_charge":"No","acknowledgement":"This research was partly funded by the Austrian Science Fund (FWF) (grant no. P-32896B).","date_published":"2022-01-24T00:00:00Z","_id":"10658","publication_identifier":{"eissn":["1471-2970"],"issn":["0962-8436"]},"publication_status":"published","intvolume":" 377","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"type":"journal_article","publication":"Philosophical Transactions of the Royal Society B","abstract":[{"text":"We analyse how migration from a large mainland influences genetic load and population numbers on an island, in a scenario where fitness-affecting variants are unconditionally deleterious, and where numbers decline with increasing load. Our analysis shows that migration can have qualitatively different effects, depending on the total mutation target and fitness effects of deleterious variants. In particular, we find that populations exhibit a genetic Allee effect across a wide range of parameter combinations, when variants are partially recessive, cycling between low-load (large-population) and high-load (sink) states. Increased migration reduces load in the sink state (by increasing heterozygosity) but further inflates load in the large-population state (by hindering purging). We identify various critical parameter thresholds at which one or other stable state collapses, and discuss how these thresholds are influenced by the genetic versus demographic effects of migration. Our analysis is based on a ‘semi-deterministic’ analysis, which accounts for genetic drift but neglects demographic stochasticity. We also compare against simulations which account for both demographic stochasticity and drift. Our results clarify the importance of gene flow as a key determinant of extinction risk in peripheral populations, even in the absence of ecological gradients. This article is part of the theme issue ‘Species’ ranges in the face of changing environments (part I)’.","lang":"eng"}],"date_created":"2022-01-24T10:34:53Z","year":"2022","citation":{"ama":"Sachdeva H, Olusanya OO, Barton NH. Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity. Philosophical Transactions of the Royal Society B. 2022;377(1846). doi:10.1098/rstb.2021.0010","mla":"Sachdeva, Himani, et al. “Genetic Load and Extinction in Peripheral Populations: The Roles of Migration, Drift and Demographic Stochasticity.” Philosophical Transactions of the Royal Society B, vol. 377, no. 1846, 20210010, The Royal Society, 2022, doi:10.1098/rstb.2021.0010.","apa":"Sachdeva, H., Olusanya, O. O., & Barton, N. H. (2022). Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity. Philosophical Transactions of the Royal Society B. The Royal Society. https://doi.org/10.1098/rstb.2021.0010","short":"H. Sachdeva, O.O. Olusanya, N.H. Barton, Philosophical Transactions of the Royal Society B 377 (2022).","ista":"Sachdeva H, Olusanya OO, Barton NH. 2022. Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity. Philosophical Transactions of the Royal Society B. 377(1846), 20210010.","ieee":"H. Sachdeva, O. O. Olusanya, and N. H. Barton, “Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity,” Philosophical Transactions of the Royal Society B, vol. 377, no. 1846. The Royal Society, 2022.","chicago":"Sachdeva, Himani, Oluwafunmilola O Olusanya, and Nicholas H Barton. “Genetic Load and Extinction in Peripheral Populations: The Roles of Migration, Drift and Demographic Stochasticity.” Philosophical Transactions of the Royal Society B. The Royal Society, 2022. https://doi.org/10.1098/rstb.2021.0010."},"quality_controlled":"1","month":"01"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":" 11","publication_identifier":{"eissn":["2050-084X"]},"publication_status":"published","month":"01","abstract":[{"text":"Predicting function from sequence is a central problem of biology. Currently, this is possible only locally in a narrow mutational neighborhood around a wildtype sequence rather than globally from any sequence. Using random mutant libraries, we developed a biophysical model that accounts for multiple features of σ70 binding bacterial promoters to predict constitutive gene expression levels from any sequence. We experimentally and theoretically estimated that 10–20% of random sequences lead to expression and ~80% of non-expressing sequences are one mutation away from a functional promoter. The potential for generating expression from random sequences is so pervasive that selection acts against σ70-RNA polymerase binding sites even within inter-genic, promoter-containing regions. This pervasiveness of σ70-binding sites implies that emergence of promoters is not the limiting step in gene regulatory evolution. Ultimately, the inclusion of novel features of promoter function into a mechanistic model enabled not only more accurate predictions of gene expression levels, but also identified that promoters evolve more rapidly than previously thought.","lang":"eng"}],"date_created":"2022-02-06T23:01:32Z","citation":{"ista":"Lagator M, Sarikas S, Steinrück M, Toledo-Aparicio D, Bollback JP, Guet CC, Tkačik G. 2022. Predicting bacterial promoter function and evolution from random sequences. eLife. 11, e64543.","ama":"Lagator M, Sarikas S, Steinrück M, et al. Predicting bacterial promoter function and evolution from random sequences. eLife. 2022;11. doi:10.7554/eLife.64543","apa":"Lagator, M., Sarikas, S., Steinrück, M., Toledo-Aparicio, D., Bollback, J. P., Guet, C. C., & Tkačik, G. (2022). Predicting bacterial promoter function and evolution from random sequences. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.64543","short":"M. Lagator, S. Sarikas, M. Steinrück, D. Toledo-Aparicio, J.P. Bollback, C.C. Guet, G. Tkačik, ELife 11 (2022).","mla":"Lagator, Mato, et al. “Predicting Bacterial Promoter Function and Evolution from Random Sequences.” ELife, vol. 11, e64543, eLife Sciences Publications, 2022, doi:10.7554/eLife.64543.","chicago":"Lagator, Mato, Srdjan Sarikas, Magdalena Steinrück, David Toledo-Aparicio, Jonathan P Bollback, Calin C Guet, and Gašper Tkačik. “Predicting Bacterial Promoter Function and Evolution from Random Sequences.” ELife. eLife Sciences Publications, 2022. https://doi.org/10.7554/eLife.64543.","ieee":"M. Lagator et al., “Predicting bacterial promoter function and evolution from random sequences,” eLife, vol. 11. eLife Sciences Publications, 2022."},"quality_controlled":"1","year":"2022","type":"journal_article","publication":"eLife","language":[{"iso":"eng"}],"department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"NiBa"}],"has_accepted_license":"1","scopus_import":"1","doi":"10.7554/eLife.64543","day":"26","ddc":["576"],"author":[{"id":"345D25EC-F248-11E8-B48F-1D18A9856A87","full_name":"Lagator, Mato","last_name":"Lagator","first_name":"Mato"},{"id":"35F0286E-F248-11E8-B48F-1D18A9856A87","full_name":"Sarikas, Srdjan","last_name":"Sarikas","first_name":"Srdjan"},{"last_name":"Steinrück","full_name":"Steinrück, Magdalena","id":"2C023F40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1229-9719","first_name":"Magdalena"},{"first_name":"David","last_name":"Toledo-Aparicio","full_name":"Toledo-Aparicio, David"},{"orcid":"0000-0002-4624-4612","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P","last_name":"Bollback"},{"orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tkačik","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","orcid":"0000-0002-6699-1455"}],"date_updated":"2025-03-31T16:00:23Z","title":"Predicting bacterial promoter function and evolution from random sequences","project":[{"call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer","grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"article_number":"e64543","oa_version":"Published Version","volume":11,"file_date_updated":"2022-02-07T07:14:09Z","article_type":"original","date_published":"2022-01-26T00:00:00Z","_id":"10736","corr_author":"1","publisher":"eLife Sciences Publications","oa":1,"acknowledgement":"We thank Hande Acar, Nicholas H Barton, Rok Grah, Tiago Paixao, Maros Pleska, Anna Staron, and Murat Tugrul for insightful comments and input on the manuscript. This work was supported by: Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (grant number 216779/Z/19/Z) to ML; IPC Grant from IST Austria to ML and SS; European Research Council Funding Programme 7 (2007–2013, grant agreement number 648440) to JPB.","article_processing_charge":"No","pmid":1,"status":"public","external_id":{"pmid":["35080492"],"isi":["000751104400001"]},"file":[{"file_id":"10739","file_name":"2022_ELife_Lagator.pdf","relation":"main_file","date_created":"2022-02-07T07:14:09Z","date_updated":"2022-02-07T07:14:09Z","file_size":5604343,"success":1,"creator":"cchlebak","content_type":"application/pdf","access_level":"open_access","checksum":"decdcdf600ff51e9a9703b49ca114170"}]},{"isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":" 377","publication_status":"published","publication_identifier":{"eissn":["1471-2970"],"issn":["0962-8436"]},"keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"month":"04","abstract":[{"text":"A species distributed across diverse environments may adapt to local conditions. We ask how quickly such a species changes its range in response to changed conditions. Szép et al. (Szép E, Sachdeva H, Barton NH. 2021 Polygenic local adaptation in metapopulations: a stochastic eco-evolutionary model. Evolution75, 1030–1045 (doi:10.1111/evo.14210)) used the infinite island model to find the stationary distribution of allele frequencies and deme sizes. We extend this to find how a metapopulation responds to changes in carrying capacity, selection strength, or migration rate when deme sizes are fixed. We further develop a ‘fixed-state’ approximation. Under this approximation, polymorphism is only possible for a narrow range of habitat proportions when selection is weak compared to drift, but for a much wider range otherwise. When rates of selection or migration relative to drift change in a single deme of the metapopulation, the population takes a time of order m−1 to reach the new equilibrium. However, even with many loci, there can be substantial fluctuations in net adaptation, because at each locus, alleles randomly get lost or fixed. Thus, in a finite metapopulation, variation may gradually be lost by chance, even if it would persist in an infinite metapopulation. When conditions change across the whole metapopulation, there can be rapid change, which is predicted well by the fixed-state approximation. This work helps towards an understanding of how metapopulations extend their range across diverse environments.\r\nThis article is part of the theme issue ‘Species’ ranges in the face of changing environments (Part II)’.","lang":"eng"}],"date_created":"2022-02-21T16:08:10Z","year":"2022","quality_controlled":"1","citation":{"ieee":"N. H. Barton and O. O. Olusanya, “The response of a metapopulation to a changing environment,” Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 377, no. 1848. The Royal Society, 2022.","chicago":"Barton, Nicholas H, and Oluwafunmilola O Olusanya. “The Response of a Metapopulation to a Changing Environment.” Philosophical Transactions of the Royal Society B: Biological Sciences. The Royal Society, 2022. https://doi.org/10.1098/rstb.2021.0009.","mla":"Barton, Nicholas H., and Oluwafunmilola O. Olusanya. “The Response of a Metapopulation to a Changing Environment.” Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 377, no. 1848, The Royal Society, 2022, doi:10.1098/rstb.2021.0009.","apa":"Barton, N. H., & Olusanya, O. O. (2022). The response of a metapopulation to a changing environment. Philosophical Transactions of the Royal Society B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2021.0009","short":"N.H. Barton, O.O. Olusanya, Philosophical Transactions of the Royal Society B: Biological Sciences 377 (2022).","ama":"Barton NH, Olusanya OO. The response of a metapopulation to a changing environment. Philosophical Transactions of the Royal Society B: Biological Sciences. 2022;377(1848). doi:10.1098/rstb.2021.0009","ista":"Barton NH, Olusanya OO. 2022. The response of a metapopulation to a changing environment. Philosophical Transactions of the Royal Society B: Biological Sciences. 377(1848)."},"publication":"Philosophical Transactions of the Royal Society B: Biological Sciences","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"14711","status":"public"}]},"has_accepted_license":"1","doi":"10.1098/rstb.2021.0009","scopus_import":"1","day":"11","ddc":["570"],"author":[{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Oluwafunmilola O","orcid":"0000-0003-1971-8314","last_name":"Olusanya","full_name":"Olusanya, Oluwafunmilola O","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87"}],"title":"The response of a metapopulation to a changing environment","date_updated":"2026-04-07T12:54:28Z","project":[{"grant_number":"P32896","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8","name":"Causes and consequences of population fragmentation"}],"volume":377,"oa_version":"Published Version","file_date_updated":"2022-08-02T06:14:32Z","article_type":"original","date_published":"2022-04-11T00:00:00Z","_id":"10787","corr_author":"1","publisher":"The Royal Society","issue":"1848","oa":1,"article_processing_charge":"No","acknowledgement":"This research was partly funded by the Austrian Science Fund (FWF) [FWF P-32896B].","pmid":1,"status":"public","file":[{"checksum":"3b0243738f01bf3c07e0d7e8dc64f71d","access_level":"open_access","content_type":"application/pdf","creator":"dernst","success":1,"file_size":1349672,"date_created":"2022-08-02T06:14:32Z","date_updated":"2022-08-02T06:14:32Z","relation":"main_file","file_name":"2022_PhilosophicalTransactionsRSB_Barton.pdf","file_id":"11719"}],"external_id":{"isi":["000758140300001"],"pmid":["35184588"]}},{"article_processing_charge":"No","oa":1,"publisher":"Institute of Science and Technology Austria","status":"public","file":[{"embargo":"2023-05-19","checksum":"4d75e6a619df7e8a9d6e840aee182380","content_type":"application/pdf","access_level":"open_access","creator":"sbelohla","file_size":8247240,"date_updated":"2023-05-20T22:30:03Z","relation":"main_file","date_created":"2022-05-19T13:03:13Z","file_name":"thesis_sb_final_pdfa.pdf","file_id":"11398"},{"creator":"sbelohla","access_level":"closed","content_type":"application/x-zip-compressed","checksum":"7a5d8b6dd0ca00784f860075b0a7d8f0","embargo_to":"open_access","file_id":"11399","file_name":"thesis_sb_final.zip","relation":"source_file","date_created":"2022-05-19T13:07:47Z","date_updated":"2023-05-20T22:30:03Z","file_size":7094}],"_id":"11388","date_published":"2022-05-18T00:00:00Z","corr_author":"1","title":"The genetic basis of complex traits studied via analysis of evolve and resequence experiments","date_updated":"2026-04-07T14:29:57Z","file_date_updated":"2023-05-20T22:30:03Z","oa_version":"Published Version","related_material":{"record":[{"id":"6713","status":"public","relation":"part_of_dissertation"}]},"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"language":[{"iso":"eng"}],"author":[{"full_name":"Belohlavy, Stefanie","last_name":"Belohlavy","id":"43FE426A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9849-498X","first_name":"Stefanie"}],"day":"18","ddc":["576"],"doi":"10.15479/at:ista:11388","has_accepted_license":"1","citation":{"ista":"Belohlavy S. 2022. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. Institute of Science and Technology Austria.","short":"S. Belohlavy, The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments, Institute of Science and Technology Austria, 2022.","mla":"Belohlavy, Stefanie. The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11388.","apa":"Belohlavy, S. (2022). The genetic basis of complex traits studied via analysis of evolve and resequence experiments. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11388","ama":"Belohlavy S. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. 2022. doi:10.15479/at:ista:11388","chicago":"Belohlavy, Stefanie. “The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11388.","ieee":"S. Belohlavy, “The genetic basis of complex traits studied via analysis of evolve and resequence experiments,” Institute of Science and Technology Austria, 2022."},"year":"2022","date_created":"2022-05-16T16:49:18Z","abstract":[{"lang":"eng","text":"In evolve and resequence experiments, a population is sequenced, subjected to selection and\r\nthen sequenced again, so that genetic changes before and after selection can be observed at\r\nthe genetic level. Here, I use these studies to better understand the genetic basis of complex\r\ntraits - traits which depend on more than a few genes.\r\nIn the first chapter, I discuss the first evolve and resequence experiment, in which a population\r\nof mice, the so-called \"Longshanks\" mice, were selected for tibia length while their body mass\r\nwas kept constant. The full pedigree is known. We observed a selection response on all\r\nchromosomes and used the infinitesimal model with linkage, a model which assumes an infinite\r\nnumber of genes with infinitesimally small effect sizes, as a null model. Results implied a very\r\npolygenic basis with a few loci of major effect standing out and changing in parallel. There\r\nwas large variability between the different chromosomes in this study, probably due to LD.\r\nIn chapter two, I go on to discuss the impact of LD, on the variability in an allele-frequency\r\nbased summary statistic, giving an equation based on the initial allele frequencies, average\r\npairwise LD, and the first four moments of the haplotype block copy number distribution. I\r\ndescribe this distribution by referring back to the founder generation. I then demonstrate\r\nhow to infer selection via a maximum likelihood scheme on the example of a single locus and\r\ndiscuss how to extend this to more realistic scenarios.\r\nIn chapter three, I discuss the second evolve and resequence experiment, in which a small\r\npopulation of Drosophila melanogaster was selected for increased pupal case size over 6\r\ngenerations. The experiment was highly replicated with 27 lines selected within family and a\r\nknown pedigree. We observed a phenotypic selection response of over one standard deviation.\r\nI describe the patterns in allele frequency data, including allele frequency changes and patterns\r\nof heterozygosity, and give ideas for future work."}],"degree_awarded":"PhD","type":"dissertation","page":"98","OA_place":"publisher","month":"05","alternative_title":["ISTA Thesis"],"publication_identifier":{"isbn":["978-3-99078-018-3"]},"publication_status":"published","supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd"},{"department":[{"_id":"NiBa"}],"related_material":{"record":[{"id":"9394","status":"public","relation":"used_in_publication"}]},"has_accepted_license":"1","doi":"10.5061/DRYAD.ZGMSBCCB4","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"10","tmp":{"short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"ddc":["570"],"author":[{"first_name":"Eva","last_name":"Koch","full_name":"Koch, Eva"},{"full_name":"Morales, Hernán E.","last_name":"Morales","first_name":"Hernán E."},{"first_name":"Jenny","last_name":"Larsson","full_name":"Larsson, Jenny"},{"last_name":"Westram","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M"},{"last_name":"Faria","full_name":"Faria, Rui","first_name":"Rui"},{"first_name":"Alan R.","full_name":"Lemmon, Alan R.","last_name":"Lemmon"},{"last_name":"Lemmon","full_name":"Lemmon, E. Moriarty","first_name":"E. Moriarty"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"last_name":"Butlin","full_name":"Butlin, Roger K.","first_name":"Roger K."}],"date_updated":"2026-04-07T14:01:30Z","title":"Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis","oa_version":"Published Version","date_published":"2021-04-10T00:00:00Z","OA_place":"publisher","_id":"12987","month":"04","publisher":"Dryad","abstract":[{"text":"Chromosomal inversion polymorphisms, segments of chromosomes that are flipped in orientation and occur in reversed order in some individuals, have long been recognized to play an important role in local adaptation. They can reduce recombination in heterozygous individuals and thus help to maintain sets of locally adapted alleles. In a wide range of organisms, populations adapted to different habitats differ in frequency of inversion arrangements. However, getting a full understanding of the importance of inversions for adaptation requires confirmation of their influence on traits under divergent selection. Here, we studied a marine snail, Littorina saxatilis, that has evolved ecotypes adapted to wave exposure or crab predation. These two types occur in close proximity on different parts of the shore. Gene flow between them exists in contact zones. However, they exhibit strong phenotypic divergence in several traits under habitat-specific selection, including size, shape and behaviour. We used crosses between these ecotypes to identify genomic regions that explain variation in these traits by using QTL analysis and variance partitioning across linkage groups. We could show that previously detected inversion regions contribute to adaptive divergence. Some inversions influenced multiple traits suggesting that they contain sets of locally adaptive alleles. Our study also identified regions without known inversions that are important for phenotypic divergence. Thus, we provide a more complete overview of the importance of inversions in relation to the remaining genome.","lang":"eng"}],"date_created":"2023-05-16T12:34:09Z","citation":{"ama":"Koch E, Morales HE, Larsson J, et al. Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. 2021. doi:10.5061/DRYAD.ZGMSBCCB4","mla":"Koch, Eva, et al. Data from: Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis. Dryad, 2021, doi:10.5061/DRYAD.ZGMSBCCB4.","apa":"Koch, E., Morales, H. E., Larsson, J., Westram, A. M., Faria, R., Lemmon, A. R., … Butlin, R. K. (2021). Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Dryad. https://doi.org/10.5061/DRYAD.ZGMSBCCB4","short":"E. Koch, H.E. Morales, J. Larsson, A.M. Westram, R. Faria, A.R. Lemmon, E.M. Lemmon, K. Johannesson, R.K. Butlin, (2021).","ista":"Koch E, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM, Johannesson K, Butlin RK. 2021. Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis, Dryad, 10.5061/DRYAD.ZGMSBCCB4.","ieee":"E. Koch et al., “Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis.” Dryad, 2021.","chicago":"Koch, Eva, Hernán E. Morales, Jenny Larsson, Anja M Westram, Rui Faria, Alan R. Lemmon, E. Moriarty Lemmon, Kerstin Johannesson, and Roger K. Butlin. “Data from: Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” Dryad, 2021. https://doi.org/10.5061/DRYAD.ZGMSBCCB4."},"oa":1,"year":"2021","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.5061/dryad.zgmsbccb4","open_access":"1"}],"status":"public","type":"research_data_reference"},{"main_file_link":[{"url":"https://doi.org/10.5061/dryad.8gtht76p1","open_access":"1"}],"status":"public","type":"research_data_reference","abstract":[{"text":"This paper analyzes the conditions for local adaptation in a metapopulation with infinitely many islands under a model of hard selection, where population size depends on local fitness. Each island belongs to one of two distinct ecological niches or habitats. Fitness is influenced by an additive trait which is under habitat-dependent directional selection. Our analysis is based on the diffusion approximation and accounts for both genetic drift and demographic stochasticity. By neglecting linkage disequilibria, it yields the joint distribution of allele frequencies and population size on each island. We find that under hard selection, the conditions for local adaptation in a rare habitat are more restrictive for more polygenic traits: even moderate migration load per locus at very many loci is sufficient for population sizes to decline. This further reduces the efficacy of selection at individual loci due to increased drift and because smaller populations are more prone to swamping due to migration, causing a positive feedback between increasing maladaptation and declining population sizes. Our analysis also highlights the importance of demographic stochasticity, which exacerbates the decline in numbers of maladapted populations, leading to population collapse in the rare habitat at significantly lower migration than predicted by deterministic arguments.","lang":"eng"}],"publisher":"Dryad","date_created":"2023-05-23T16:17:02Z","year":"2021","citation":{"ieee":"E. Szep, H. Sachdeva, and N. H. Barton, “Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model.” Dryad, 2021.","chicago":"Szep, Eniko, Himani Sachdeva, and Nicholas H Barton. “Supplementary Code for: Polygenic Local Adaptation in Metapopulations: A Stochastic Eco-Evolutionary Model.” Dryad, 2021. https://doi.org/10.5061/DRYAD.8GTHT76P1.","short":"E. Szep, H. Sachdeva, N.H. Barton, (2021).","mla":"Szep, Eniko, et al. Supplementary Code for: Polygenic Local Adaptation in Metapopulations: A Stochastic Eco-Evolutionary Model. Dryad, 2021, doi:10.5061/DRYAD.8GTHT76P1.","apa":"Szep, E., Sachdeva, H., & Barton, N. H. (2021). Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model. Dryad. https://doi.org/10.5061/DRYAD.8GTHT76P1","ama":"Szep E, Sachdeva H, Barton NH. Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model. 2021. doi:10.5061/DRYAD.8GTHT76P1","ista":"Szep E, Sachdeva H, Barton NH. 2021. Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model, Dryad, 10.5061/DRYAD.8GTHT76P1."},"oa":1,"article_processing_charge":"No","month":"03","corr_author":"1","date_published":"2021-03-02T00:00:00Z","_id":"13062","oa_version":"Published Version","title":"Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model","date_updated":"2025-06-12T06:35:39Z","doi":"10.5061/DRYAD.8GTHT76P1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"ddc":["570"],"day":"02","author":[{"first_name":"Eniko","last_name":"Szep","full_name":"Szep, Eniko","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","last_name":"Sachdeva","full_name":"Sachdeva, Himani"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"}],"department":[{"_id":"NiBa"}],"related_material":{"record":[{"relation":"used_in_publication","id":"9252","status":"public"}]}},{"intvolume":" 2","date_updated":"2024-10-09T21:08:11Z","title":"Hybrid Zones","publication_identifier":{"eisbn":["9780470015902"],"isbn":["9780470016176"]},"publication_status":"published","oa_version":"None","volume":2,"language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"doi":"10.1002/9780470015902.a0029355","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"28","author":[{"first_name":"Sean","full_name":"Stankowski, Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"first_name":"Daria","orcid":"0000-0002-1145-9226","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","last_name":"Shipilina","full_name":"Shipilina, Daria"},{"first_name":"Anja M","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Wiley","abstract":[{"lang":"eng","text":"Hybrid zones are narrow geographic regions where different populations, races or interbreeding species meet and mate, producing mixed ‘hybrid’ offspring. They are relatively common and can be found in a diverse range of organisms and environments. The study of hybrid zones has played an important role in our understanding of the origin of species, with hybrid zones having been described as ‘natural laboratories’. This is because they allow us to study,in situ, the conditions and evolutionary forces that enable divergent taxa to remain distinct despite some ongoing gene exchange between them."}],"date_created":"2024-02-14T12:05:50Z","citation":{"chicago":"Stankowski, Sean, Daria Shipilina, and Anja M Westram. “Hybrid Zones.” In Encyclopedia of Life Sciences, Vol. 2. ELS. Wiley, 2021. https://doi.org/10.1002/9780470015902.a0029355.","ieee":"S. Stankowski, D. Shipilina, and A. M. Westram, “Hybrid Zones,” in Encyclopedia of Life Sciences, vol. 2, Wiley, 2021.","ista":"Stankowski S, Shipilina D, Westram AM. 2021.Hybrid Zones. In: Encyclopedia of Life Sciences. vol. 2.","ama":"Stankowski S, Shipilina D, Westram AM. Hybrid Zones. In: Encyclopedia of Life Sciences. Vol 2. eLS. Wiley; 2021. doi:10.1002/9780470015902.a0029355","apa":"Stankowski, S., Shipilina, D., & Westram, A. M. (2021). Hybrid Zones. In Encyclopedia of Life Sciences (Vol. 2). Wiley. https://doi.org/10.1002/9780470015902.a0029355","short":"S. Stankowski, D. Shipilina, A.M. Westram, in:, Encyclopedia of Life Sciences, Wiley, 2021.","mla":"Stankowski, Sean, et al. “Hybrid Zones.” Encyclopedia of Life Sciences, vol. 2, Wiley, 2021, doi:10.1002/9780470015902.a0029355."},"quality_controlled":"1","series_title":"eLS","year":"2021","article_processing_charge":"No","publication":"Encyclopedia of Life Sciences","status":"public","type":"book_chapter","date_published":"2021-05-28T00:00:00Z","_id":"14984","month":"05","corr_author":"1"},{"date_updated":"2024-10-09T21:01:16Z","title":"Dynamic maximum entropy provides accurate approximation of structured population dynamics","article_number":"e1009661","volume":17,"oa_version":"Published Version","file_date_updated":"2022-05-16T08:53:11Z","article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"},{"_id":"GaTk"}],"has_accepted_license":"1","doi":"10.1371/journal.pcbi.1009661","scopus_import":"1","ddc":["570"],"day":"01","author":[{"id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","last_name":"Bod'ová","full_name":"Bod'ová, Katarína","first_name":"Katarína","orcid":"0000-0002-7214-0171"},{"first_name":"Eniko","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","last_name":"Szep","full_name":"Szep, Eniko"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"}],"publisher":"Public Library of Science","oa":1,"issue":"12","article_processing_charge":"No","acknowledgement":"Computational resources for the study were provided by the Institute of Science and Technology, Austria.\r\nKB received funding from the Scientific Grant Agency of the Slovak Republic under the Grants Nos. 1/0755/19 and 1/0521/20.","pmid":1,"file":[{"file_size":2299486,"file_id":"11383","relation":"main_file","date_created":"2022-05-16T08:53:11Z","date_updated":"2022-05-16T08:53:11Z","file_name":"2021_PLOsComBio_Bodova.pdf","checksum":"dcd185d4f7e0acee25edf1d6537f447e","success":1,"content_type":"application/pdf","access_level":"open_access","creator":"dernst"}],"status":"public","external_id":{"pmid":["34851948"],"arxiv":["2102.03669"]},"date_published":"2021-12-01T00:00:00Z","_id":"10535","arxiv":1,"corr_author":"1","intvolume":" 17","publication_status":"published","publication_identifier":{"eissn":["1553-7358"],"issn":["1553-734X"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"abstract":[{"text":"Realistic models of biological processes typically involve interacting components on multiple scales, driven by changing environment and inherent stochasticity. Such models are often analytically and numerically intractable. We revisit a dynamic maximum entropy method that combines a static maximum entropy with a quasi-stationary approximation. This allows us to reduce stochastic non-equilibrium dynamics expressed by the Fokker-Planck equation to a simpler low-dimensional deterministic dynamics, without the need to track microscopic details. Although the method has been previously applied to a few (rather complicated) applications in population genetics, our main goal here is to explain and to better understand how the method works. We demonstrate the usefulness of the method for two widely studied stochastic problems, highlighting its accuracy in capturing important macroscopic quantities even in rapidly changing non-stationary conditions. For the Ornstein-Uhlenbeck process, the method recovers the exact dynamics whilst for a stochastic island model with migration from other habitats, the approximation retains high macroscopic accuracy under a wide range of scenarios in a dynamic environment.","lang":"eng"}],"date_created":"2021-12-12T23:01:27Z","year":"2021","citation":{"ieee":"K. Bodova, E. Szep, and N. H. Barton, “Dynamic maximum entropy provides accurate approximation of structured population dynamics,” PLoS Computational Biology, vol. 17, no. 12. Public Library of Science, 2021.","chicago":"Bodova, Katarina, Eniko Szep, and Nicholas H Barton. “Dynamic Maximum Entropy Provides Accurate Approximation of Structured Population Dynamics.” PLoS Computational Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1009661.","short":"K. Bodova, E. Szep, N.H. Barton, PLoS Computational Biology 17 (2021).","mla":"Bodova, Katarina, et al. “Dynamic Maximum Entropy Provides Accurate Approximation of Structured Population Dynamics.” PLoS Computational Biology, vol. 17, no. 12, e1009661, Public Library of Science, 2021, doi:10.1371/journal.pcbi.1009661.","apa":"Bodova, K., Szep, E., & Barton, N. H. (2021). Dynamic maximum entropy provides accurate approximation of structured population dynamics. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1009661","ama":"Bodova K, Szep E, Barton NH. Dynamic maximum entropy provides accurate approximation of structured population dynamics. PLoS Computational Biology. 2021;17(12). doi:10.1371/journal.pcbi.1009661","ista":"Bodova K, Szep E, Barton NH. 2021. Dynamic maximum entropy provides accurate approximation of structured population dynamics. PLoS Computational Biology. 17(12), e1009661."},"quality_controlled":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"type":"journal_article","publication":"PLoS Computational Biology","month":"12"},{"intvolume":" 34","publication_identifier":{"issn":["1010-061X"],"eissn":["1420-9101"]},"publication_status":"published","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Simon, Alexis, Christelle Fraisse, Tahani El Ayari, Cathy Liautard‐Haag, Petr Strelkov, John J Welch, and Nicolas Bierne. “How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels.” Journal of Evolutionary Biology. Wiley, 2021. https://doi.org/10.1111/jeb.13709.","ieee":"A. Simon et al., “How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels,” Journal of Evolutionary Biology, vol. 34, no. 1. Wiley, pp. 208–223, 2021.","ista":"Simon A, Fraisse C, El Ayari T, Liautard‐Haag C, Strelkov P, Welch JJ, Bierne N. 2021. How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels. Journal of Evolutionary Biology. 34(1), 208–223.","apa":"Simon, A., Fraisse, C., El Ayari, T., Liautard‐Haag, C., Strelkov, P., Welch, J. J., & Bierne, N. (2021). How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.13709","mla":"Simon, Alexis, et al. “How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels.” Journal of Evolutionary Biology, vol. 34, no. 1, Wiley, 2021, pp. 208–23, doi:10.1111/jeb.13709.","short":"A. Simon, C. Fraisse, T. El Ayari, C. Liautard‐Haag, P. Strelkov, J.J. Welch, N. Bierne, Journal of Evolutionary Biology 34 (2021) 208–223.","ama":"Simon A, Fraisse C, El Ayari T, et al. How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels. Journal of Evolutionary Biology. 2021;34(1):208-223. doi:10.1111/jeb.13709"},"quality_controlled":"1","year":"2021","abstract":[{"text":"The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study ‘replicated’ instances of secondary contact between closely related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry‐informative panel of such SNPs. We then compared their frequencies in newly sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi‐stable variants (Dobzhansky‐Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact.","lang":"eng"}],"date_created":"2020-10-25T23:01:20Z","type":"journal_article","publication":"Journal of Evolutionary Biology","main_file_link":[{"url":"https://doi.org/10.1101/818559","open_access":"1"}],"page":"208-223","month":"01","title":"How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels","date_updated":"2025-07-10T12:01:23Z","article_type":"original","volume":34,"oa_version":"Preprint","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"related_material":{"record":[{"id":"13073","status":"public","relation":"research_data"}]},"language":[{"iso":"eng"}],"day":"01","author":[{"last_name":"Simon","full_name":"Simon, Alexis","first_name":"Alexis"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","first_name":"Christelle"},{"first_name":"Tahani","last_name":"El Ayari","full_name":"El Ayari, Tahani"},{"first_name":"Cathy","last_name":"Liautard‐Haag","full_name":"Liautard‐Haag, Cathy"},{"last_name":"Strelkov","full_name":"Strelkov, Petr","first_name":"Petr"},{"first_name":"John J","last_name":"Welch","full_name":"Welch, John J"},{"full_name":"Bierne, Nicolas","last_name":"Bierne","first_name":"Nicolas"}],"scopus_import":"1","doi":"10.1111/jeb.13709","oa":1,"issue":"1","acknowledgement":"Data used in this work were partly produced through the genotyping and sequencing facilities of ISEM and LabEx CeMEB, an ANR ‘Investissements d'avenir’ program (ANR‐10‐LABX‐04‐01) This project benefited from the Montpellier Bioinformatics Biodiversity platform supported by the LabEx CeMEB. We thank Norah Saarman, Grant Pogson, Célia Gosset and Pierre‐Alexandre Gagnaire for providing samples. This work was funded by a Languedoc‐Roussillon ‘Chercheur(se)s d'Avenir’ grant (Connect7 project). P. Strelkov was supported by the Russian Science Foundation project 19‐74‐20024. This is article 2020‐240 of Institut des Sciences de l'Evolution de Montpellier.","article_processing_charge":"No","publisher":"Wiley","pmid":1,"status":"public","external_id":{"isi":["000579599700001"],"pmid":["33045123"]},"_id":"8708","date_published":"2021-01-01T00:00:00Z"},{"isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 75","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"publication_status":"published","month":"02","date_created":"2020-11-08T23:01:26Z","abstract":[{"lang":"eng","text":"Montane cloud forests are areas of high endemism, and are one of the more vulnerable terrestrial ecosystems to climate change. Thus, understanding how they both contribute to the generation of biodiversity, and will respond to ongoing climate change, are important and related challenges. The widely accepted model for montane cloud forest dynamics involves upslope forcing of their range limits with global climate warming. However, limited climate data provides some support for an alternative model, where range limits are forced downslope with climate warming. Testing between these two models is challenging, due to the inherent limitations of climate and pollen records. We overcome this with an alternative source of historical information, testing between competing model predictions using genomic data and demographic analyses for a species of beetle tightly associated to an oceanic island cloud forest. Results unequivocally support the alternative model: populations that were isolated at higher elevation peaks during the Last Glacial Maximum are now in contact and hybridizing at lower elevations. Our results suggest that genomic data are a rich source of information to further understand how montane cloud forest biodiversity originates, and how it is likely to be impacted by ongoing climate change."}],"quality_controlled":"1","year":"2021","citation":{"chicago":"Salces-Castellano, Antonia, Sean Stankowski, Paula Arribas, Jairo Patino, Dirk N. Karger, Roger Butlin, and Brent C. Emerson. “Long-Term Cloud Forest Response to Climate Warming Revealed by Insect Speciation History.” Evolution. Wiley, 2021. https://doi.org/10.1111/evo.14111.","ieee":"A. Salces-Castellano et al., “Long-term cloud forest response to climate warming revealed by insect speciation history,” Evolution, vol. 75, no. 2. Wiley, pp. 231–244, 2021.","ista":"Salces-Castellano A, Stankowski S, Arribas P, Patino J, Karger DN, Butlin R, Emerson BC. 2021. Long-term cloud forest response to climate warming revealed by insect speciation history. Evolution. 75(2), 231–244.","ama":"Salces-Castellano A, Stankowski S, Arribas P, et al. Long-term cloud forest response to climate warming revealed by insect speciation history. Evolution. 2021;75(2):231-244. doi:10.1111/evo.14111","apa":"Salces-Castellano, A., Stankowski, S., Arribas, P., Patino, J., Karger, D. N., Butlin, R., & Emerson, B. C. (2021). Long-term cloud forest response to climate warming revealed by insect speciation history. Evolution. Wiley. https://doi.org/10.1111/evo.14111","short":"A. Salces-Castellano, S. Stankowski, P. Arribas, J. Patino, D.N. Karger, R. Butlin, B.C. Emerson, Evolution 75 (2021) 231–244.","mla":"Salces-Castellano, Antonia, et al. “Long-Term Cloud Forest Response to Climate Warming Revealed by Insect Speciation History.” Evolution, vol. 75, no. 2, Wiley, 2021, pp. 231–44, doi:10.1111/evo.14111."},"page":"231-244","main_file_link":[{"url":"http://hdl.handle.net/10261/223937","open_access":"1"}],"publication":"Evolution","type":"journal_article","language":[{"iso":"eng"}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1111/evo.14225"}]},"department":[{"_id":"NiBa"}],"doi":"10.1111/evo.14111","scopus_import":"1","author":[{"last_name":"Salces-Castellano","full_name":"Salces-Castellano, Antonia","first_name":"Antonia"},{"first_name":"Sean","full_name":"Stankowski, Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"full_name":"Arribas, Paula","last_name":"Arribas","first_name":"Paula"},{"full_name":"Patino, Jairo","last_name":"Patino","first_name":"Jairo"},{"first_name":"Dirk N. ","last_name":"Karger","full_name":"Karger, Dirk N. "},{"full_name":"Butlin, Roger","last_name":"Butlin","first_name":"Roger"},{"full_name":"Emerson, Brent C.","last_name":"Emerson","first_name":"Brent C."}],"day":"01","date_updated":"2023-08-04T11:09:49Z","title":"Long-term cloud forest response to climate warming revealed by insect speciation history","oa_version":"Submitted Version","volume":75,"article_type":"original","date_published":"2021-02-01T00:00:00Z","_id":"8743","publisher":"Wiley","article_processing_charge":"No","acknowledgement":"This work was financed by the Spanish Agencia Estatal de Investigación (CGL2017‐85718‐P), awarded to BCE, and co‐financed by FEDER. It was also supported by the Spanish Ministerio de Ciencia, Innovación y Universidades (EQC2018‐004418‐P), awarded to BCE. AS‐C was funded by the Spanish Ministerio de Ciencia, Innovación y Universidades through an FPU PhD fellowship (FPU014/02948). The authors thank Instituto Tecnológico y de Energías Renovables (ITER), S.A for providing access to the Teide High‐Performance Computing facility (Teide‐HPC). Fieldwork was supported by collecting permit AFF 107/17 (sigma number 2017‐00572) kindly provided by the Cabildo of Tenerife. The authors wish to thank the following for field work and sample sorting and identification: A. J. Pérez‐Delgado, H. López, and C. Andújar. We also thank V. García‐Olivares for assistance with laboratory and bioinformatic work.","issue":"2","oa":1,"external_id":{"pmid":["33078844"],"isi":["000583190600001"]},"status":"public","pmid":1},{"author":[{"first_name":"Stéphanie","last_name":"Arnoux","full_name":"Arnoux, Stéphanie"},{"full_name":"Fraisse, Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","orcid":"0000-0001-8441-5075"},{"last_name":"Sauvage","full_name":"Sauvage, Christopher","first_name":"Christopher"}],"ddc":["570"],"day":"01","doi":"10.1111/jeb.13723","scopus_import":"1","related_material":{"record":[{"id":"13065","status":"public","relation":"research_data"}]},"department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"article_type":"original","oa_version":"Published Version","volume":34,"project":[{"name":"Sex chromosomes and species barriers","grant_number":"M02463","_id":"2662AADE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"date_updated":"2026-06-18T19:37:17Z","title":"Genomic inference of complex domestication histories in three Solanaceae species","_id":"8928","date_published":"2021-02-01T00:00:00Z","external_id":{"isi":["000587769700001"],"pmid":["33107098"]},"status":"public","pmid":1,"article_processing_charge":"No","acknowledgement":"This work was supported by the EU Marie Curie Career Integration grant (FP7‐PEOPLE‐2011‐CIG grant agreement PCIG10‐GA‐2011‐304164) attributed to CS. SA was supported by a PhD fellowship from the French Région PACA and the Plant Breeding division of INRA, in partnership with Gautier Semences. CF was supported by an Austrian Science Foundation FWF grant (Project M 2463‐B29). Authors thank Mathilde Causse and Beatriz Vicoso for their team leading. Thanks to the Italian Eggplant Genome Consortium, which includes the DISAFA, Plant Genetics and Breeding (University of Torino), the Biotechnology Department (University of Verona), the CREA‐ORL in Montanaso Lombardo (LO) and the ENEA in Rome for providing access to the eggplant genome reference. Thanks to CRB‐lég ( https://www6.paca.inra.fr/gafl_eng/Vegetables-GRC ) for managing and providing the genetic resources, to Marie‐Christine Daunay and Alain Palloix (INRA UR1052) for assistance in choosing the biological material used, to Muriel Latreille and Sylvain Santoni from the UMR AGAP (INRA Montpellier, France) for their help with RNAseq library preparation, to Jean‐Paul Bouchet and Jacques Lagnel (INRA UR1052) for their Bioinformatics assistance.","oa":1,"issue":"2","publisher":"Wiley","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"publication_status":"published","publication_identifier":{"issn":["1010-061X"],"eissn":["1420-9101"]},"intvolume":" 34","month":"02","publication":"Journal of Evolutionary Biology","type":"journal_article","page":"270-283","main_file_link":[{"url":"https://doi.org/10.1111/jeb.13723","open_access":"1"}],"year":"2021","quality_controlled":"1","citation":{"ieee":"S. Arnoux, C. Fraisse, and C. Sauvage, “Genomic inference of complex domestication histories in three Solanaceae species,” Journal of Evolutionary Biology, vol. 34, no. 2. Wiley, pp. 270–283, 2021.","chicago":"Arnoux, Stéphanie, Christelle Fraisse, and Christopher Sauvage. “Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” Journal of Evolutionary Biology. Wiley, 2021. https://doi.org/10.1111/jeb.13723.","ama":"Arnoux S, Fraisse C, Sauvage C. Genomic inference of complex domestication histories in three Solanaceae species. Journal of Evolutionary Biology. 2021;34(2):270-283. doi:10.1111/jeb.13723","mla":"Arnoux, Stéphanie, et al. “Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” Journal of Evolutionary Biology, vol. 34, no. 2, Wiley, 2021, pp. 270–83, doi:10.1111/jeb.13723.","short":"S. Arnoux, C. Fraisse, C. Sauvage, Journal of Evolutionary Biology 34 (2021) 270–283.","apa":"Arnoux, S., Fraisse, C., & Sauvage, C. (2021). Genomic inference of complex domestication histories in three Solanaceae species. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.13723","ista":"Arnoux S, Fraisse C, Sauvage C. 2021. Genomic inference of complex domestication histories in three Solanaceae species. Journal of Evolutionary Biology. 34(2), 270–283."},"date_created":"2020-12-06T23:01:16Z","abstract":[{"lang":"eng","text":"Domestication is a human‐induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species‐specific demographic processes between species. A convergent history of domestication with gene flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species‐specific and supported by the few historical records available."}]}]