[{"citation":{"apa":"Lucek, K., Giménez, M. D., Joron, M., Rafajlović, M., Searle, J. B., Walden, N., … Faria, R. (2023). The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/cshperspect.a041447\">https://doi.org/10.1101/cshperspect.a041447</a>","ieee":"K. Lucek <i>et al.</i>, “The impact of chromosomal rearrangements in speciation: From micro- to macroevolution,” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 15, no. 11. Cold Spring Harbor Laboratory, 2023.","ama":"Lucek K, Giménez MD, Joron M, et al. The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. <i>Cold Spring Harbor Perspectives in Biology</i>. 2023;15(11). doi:<a href=\"https://doi.org/10.1101/cshperspect.a041447\">10.1101/cshperspect.a041447</a>","short":"K. Lucek, M.D. Giménez, M. Joron, M. Rafajlović, J.B. Searle, N. Walden, A.M. Westram, R. Faria, Cold Spring Harbor Perspectives in Biology 15 (2023).","mla":"Lucek, Kay, et al. “The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution.” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 15, no. 11, a041447, Cold Spring Harbor Laboratory, 2023, doi:<a href=\"https://doi.org/10.1101/cshperspect.a041447\">10.1101/cshperspect.a041447</a>.","ista":"Lucek K, Giménez MD, Joron M, Rafajlović M, Searle JB, Walden N, Westram AM, Faria R. 2023. The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. Cold Spring Harbor Perspectives in Biology. 15(11), a041447.","chicago":"Lucek, Kay, Mabel D. Giménez, Mathieu Joron, Marina Rafajlović, Jeremy B. Searle, Nora Walden, Anja M Westram, and Rui Faria. “The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution.” <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory, 2023. <a href=\"https://doi.org/10.1101/cshperspect.a041447\">https://doi.org/10.1101/cshperspect.a041447</a>."},"date_created":"2024-01-08T12:43:48Z","keyword":["General Biochemistry","Genetics and Molecular Biology"],"acknowledgement":"K.L. was funded by a Swiss National Science Foundation Eccellenza project: The evolution of strong reproductive barriers towards the completion of speciation (PCEFP3_202869). R.F.\r\nwas funded by an FCT CEEC (Fundação para a Ciênca e a Tecnologia, Concurso Estímulo ao\r\nEmprego Científico) contract (2020.00275. CEECIND) and by an FCT research project\r\n(PTDC/BIA-EVL/1614/2021). M.R. was funded by the Swedish Research Council Vetenskapsrådet (grant number 2021-05243). A.M.W. was partly funded by the Norwegian Research Council RCN. We thank Luis Silva for his help preparing Figure 1. We are grateful to Maren Wellenreuther, Daniel Bolnick, and two anonymous reviewers for their constructive feedback on an earlier version of this paper.","year":"2023","article_number":"a041447","_id":"14742","article_type":"original","doi":"10.1101/cshperspect.a041447","publication_status":"published","external_id":{"pmid":["37604585"]},"abstract":[{"text":"Chromosomal rearrangements (CRs) have been known since almost the beginning of genetics.\r\nWhile an important role for CRs in speciation has been suggested, evidence primarily stems\r\nfrom theoretical and empirical studies focusing on the microevolutionary level (i.e., on taxon\r\npairs where speciation is often incomplete). Although the role of CRs in eukaryotic speciation at\r\na macroevolutionary level has been supported by associations between species diversity and\r\nrates of evolution of CRs across phylogenies, these findings are limited to a restricted range of\r\nCRs and taxa. Now that more broadly applicable and precise CR detection approaches have\r\nbecome available, we address the challenges in filling some of the conceptual and empirical\r\ngaps between micro- and macroevolutionary studies on the role of CRs in speciation. We\r\nsynthesize what is known about the macroevolutionary impact of CRs and suggest new research avenues to overcome the pitfalls of previous studies to gain a more comprehensive understanding of the evolutionary significance of CRs in speciation across the tree of life.","lang":"eng"}],"department":[{"_id":"NiBa"},{"_id":"BeVi"}],"volume":15,"quality_controlled":"1","publisher":"Cold Spring Harbor Laboratory","date_published":"2023-11-01T00:00:00Z","title":"The impact of chromosomal rearrangements in speciation: From micro- to macroevolution","oa":1,"date_updated":"2024-01-08T12:52:29Z","issue":"11","article_processing_charge":"No","intvolume":"        15","scopus_import":"1","language":[{"iso":"eng"}],"publication":"Cold Spring Harbor Perspectives in Biology","author":[{"last_name":"Lucek","full_name":"Lucek, Kay","first_name":"Kay"},{"full_name":"Giménez, Mabel D.","first_name":"Mabel D.","last_name":"Giménez"},{"full_name":"Joron, Mathieu","first_name":"Mathieu","last_name":"Joron"},{"last_name":"Rafajlović","first_name":"Marina","full_name":"Rafajlović, Marina"},{"full_name":"Searle, Jeremy B.","first_name":"Jeremy B.","last_name":"Searle"},{"full_name":"Walden, Nora","first_name":"Nora","last_name":"Walden"},{"orcid":"0000-0003-1050-4969","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M","first_name":"Anja M"},{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"}],"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/cshperspect.a041447"}],"day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["1943-0264"]},"month":"11","pmid":1,"type":"journal_article","status":"public"},{"page":"542-559","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"volume":16,"quality_controlled":"1","publisher":"Wiley","date_published":"2023-02-01T00:00:00Z","external_id":{"isi":["000815663700001"]},"abstract":[{"text":"Understanding population divergence that eventually leads to speciation is essential for evolutionary biology. High species diversity in the sea was regarded as a paradox when strict allopatry was considered necessary for most speciation events because geographical barriers seemed largely absent in the sea, and many marine species have high dispersal capacities. Combining genome-wide data with demographic modelling to infer the demographic history of divergence has introduced new ways to address this classical issue. These models assume an ancestral population that splits into two subpopulations diverging according to different scenarios that allow tests for periods of gene flow. Models can also test for heterogeneities in population sizes and migration rates along the genome to account, respectively, for background selection and selection against introgressed ancestry. To investigate how barriers to gene flow arise in the sea, we compiled studies modelling the demographic history of divergence in marine organisms and extracted preferred demographic scenarios together with estimates of demographic parameters. These studies show that geographical barriers to gene flow do exist in the sea but that divergence can also occur without strict isolation. Heterogeneity of gene flow was detected in most population pairs suggesting the predominance of semipermeable barriers during divergence. We found a weak positive relationship between the fraction of the genome experiencing reduced gene flow and levels of genome-wide differentiation. Furthermore, we found that the upper bound of the ‘grey zone of speciation’ for our dataset extended beyond that found before, implying that gene flow between diverging taxa is possible at higher levels of divergence than previously thought. Finally, we list recommendations for further strengthening the use of demographic modelling in speciation research. These include a more balanced representation of taxa, more consistent and comprehensive modelling, clear reporting of results and simulation studies to rule out nonbiological explanations for general results.","lang":"eng"}],"ddc":["576"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_status":"published","doi":"10.1111/eva.13428","file_date_updated":"2023-02-27T07:10:17Z","_id":"11479","article_type":"original","date_created":"2022-07-03T22:01:33Z","citation":{"ieee":"A. De Jode <i>et al.</i>, “Ten years of demographic modelling of divergence and speciation in the sea,” <i>Evolutionary Applications</i>, vol. 16, no. 2. Wiley, pp. 542–559, 2023.","ama":"De Jode A, Le Moan A, Johannesson K, et al. Ten years of demographic modelling of divergence and speciation in the sea. <i>Evolutionary Applications</i>. 2023;16(2):542-559. doi:<a href=\"https://doi.org/10.1111/eva.13428\">10.1111/eva.13428</a>","short":"A. De Jode, A. Le Moan, K. Johannesson, R. Faria, S. Stankowski, A.M. Westram, R.K. Butlin, M. Rafajlović, C. Fraisse, Evolutionary Applications 16 (2023) 542–559.","mla":"De Jode, Aurélien, et al. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” <i>Evolutionary Applications</i>, vol. 16, no. 2, Wiley, 2023, pp. 542–59, doi:<a href=\"https://doi.org/10.1111/eva.13428\">10.1111/eva.13428</a>.","ista":"De Jode A, Le Moan A, Johannesson K, Faria R, Stankowski S, Westram AM, Butlin RK, Rafajlović M, Fraisse C. 2023. Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. 16(2), 542–559.","chicago":"De Jode, Aurélien, Alan Le Moan, Kerstin Johannesson, Rui Faria, Sean Stankowski, Anja M Westram, Roger K. Butlin, Marina Rafajlović, and Christelle Fraisse. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” <i>Evolutionary Applications</i>. Wiley, 2023. <a href=\"https://doi.org/10.1111/eva.13428\">https://doi.org/10.1111/eva.13428</a>.","apa":"De Jode, A., Le Moan, A., Johannesson, K., Faria, R., Stankowski, S., Westram, A. M., … Fraisse, C. (2023). Ten years of demographic modelling of divergence and speciation in the sea. <i>Evolutionary Applications</i>. Wiley. <a href=\"https://doi.org/10.1111/eva.13428\">https://doi.org/10.1111/eva.13428</a>"},"acknowledgement":"We greatly thank all the corresponding authors of the studies that were included in our synthesis for the sharing of additional data: Thomas Broquet, Dmitry Filatov, Quentin Rougemont, Paolo Momigliano, Pierre-Alexandre Gagnaire, Carlos Prada, Ahmed Souissi, Michael Møller Hansen, Sylvie Lapègue, Joseph Di Battista, Michael Hellberg and Carlos Prada. RKB and ADJ were supported by the European Research Council. MR was supported by the Swedish Research Council Vetenskapsrådet (grant number 2021-05243; to MR) and Formas (grant number 2019-00882; to KJ and MR), and by additional grants from the European Research Council (to RKB) and Vetenskapsrådet (to KJ) through the Centre for Marine Evolutionary Biology (https://www.gu.se/en/cemeb-marine-evolutionary-biology).","year":"2023","type":"journal_article","status":"public","oa_version":"Published Version","day":"01","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"creator":"dernst","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_size":2269822,"success":1,"checksum":"d4d6fa9ddf36643af994a6a757919afb","file_name":"2023_EvolutionaryApplications_DeJode.pdf","file_id":"12685","date_created":"2023-02-27T07:10:17Z","date_updated":"2023-02-27T07:10:17Z"}],"month":"02","publication_identifier":{"eissn":["1752-4571"]},"author":[{"full_name":"De Jode, Aurélien","first_name":"Aurélien","last_name":"De Jode"},{"last_name":"Le Moan","first_name":"Alan","full_name":"Le Moan, Alan"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","first_name":"Sean"},{"last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","first_name":"Anja M"},{"last_name":"Butlin","first_name":"Roger K.","full_name":"Butlin, Roger K."},{"last_name":"Rafajlović","full_name":"Rafajlović, Marina","first_name":"Marina"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","orcid":"0000-0001-8441-5075","first_name":"Christelle","full_name":"Fraisse, Christelle"}],"publication":"Evolutionary Applications","language":[{"iso":"eng"}],"scopus_import":"1","has_accepted_license":"1","intvolume":"        16","isi":1,"title":"Ten years of demographic modelling of divergence and speciation in the sea","oa":1,"date_updated":"2023-08-01T12:25:44Z","article_processing_charge":"No","issue":"2"},{"publisher":"eLife Sciences Publications","date_published":"2022-09-26T00:00:00Z","department":[{"_id":"NiBa"}],"volume":11,"quality_controlled":"1","publication_status":"published","ddc":["570"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"isi":["000890735600001"]},"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"}],"file_date_updated":"2023-01-24T12:21:32Z","article_type":"original","_id":"12157","doi":"10.7554/elife.66697","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","year":"2022","date_created":"2023-01-12T12:09:00Z","citation":{"apa":"Hayward, L., &#38; Sella, G. (2022). Polygenic adaptation after a sudden change in environment. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.66697\">https://doi.org/10.7554/elife.66697</a>","ieee":"L. Hayward and G. Sella, “Polygenic adaptation after a sudden change in environment,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","ama":"Hayward L, Sella G. Polygenic adaptation after a sudden change in environment. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/elife.66697\">10.7554/elife.66697</a>","short":"L. Hayward, G. Sella, ELife 11 (2022).","ista":"Hayward L, Sella G. 2022. Polygenic adaptation after a sudden change in environment. eLife. 11, 66697.","chicago":"Hayward, Laura, and Guy Sella. “Polygenic Adaptation after a Sudden Change in Environment.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/elife.66697\">https://doi.org/10.7554/elife.66697</a>.","mla":"Hayward, Laura, and Guy Sella. “Polygenic Adaptation after a Sudden Change in Environment.” <i>ELife</i>, vol. 11, 66697, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/elife.66697\">10.7554/elife.66697</a>."},"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"article_number":"66697","status":"public","type":"journal_article","author":[{"full_name":"Hayward, Laura","first_name":"Laura","id":"fc885ee5-24bf-11eb-ad7b-bcc5104c0c1b","last_name":"Hayward"},{"last_name":"Sella","first_name":"Guy","full_name":"Sella, Guy"}],"publication_identifier":{"eissn":["2050-084X"]},"month":"09","oa_version":"Published Version","day":"26","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"checksum":"28de155b231ac1c8d4501c98b2fb359a","file_name":"2022_eLife_Hayward.pdf","file_id":"12363","success":1,"date_updated":"2023-01-24T12:21:32Z","date_created":"2023-01-24T12:21:32Z","creator":"dernst","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_size":18935612}],"language":[{"iso":"eng"}],"publication":"eLife","oa":1,"date_updated":"2023-08-04T09:04:58Z","article_processing_charge":"No","title":"Polygenic adaptation after a sudden change in environment","isi":1,"scopus_import":"1","intvolume":"        11","has_accepted_license":"1"},{"year":"2022","date_created":"2023-01-12T12:10:28Z","citation":{"mla":"Westram, Anja M., and Roger Butlin. “Professor Kerstin Johannesson–Winner of the 2022 Molecular Ecology Prize.” <i>Molecular Ecology</i>, vol. 32, no. 1, Wiley, 2022, pp. 26–29, doi:<a href=\"https://doi.org/10.1111/mec.16779\">10.1111/mec.16779</a>.","ista":"Westram AM, Butlin R. 2022. Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize. Molecular Ecology. 32(1), 26–29.","chicago":"Westram, Anja M, and Roger Butlin. “Professor Kerstin Johannesson–Winner of the 2022 Molecular Ecology Prize.” <i>Molecular Ecology</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/mec.16779\">https://doi.org/10.1111/mec.16779</a>.","ama":"Westram AM, Butlin R. Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize. <i>Molecular Ecology</i>. 2022;32(1):26-29. doi:<a href=\"https://doi.org/10.1111/mec.16779\">10.1111/mec.16779</a>","ieee":"A. M. Westram and R. Butlin, “Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize,” <i>Molecular Ecology</i>, vol. 32, no. 1. Wiley, pp. 26–29, 2022.","short":"A.M. Westram, R. Butlin, Molecular Ecology 32 (2022) 26–29.","apa":"Westram, A. M., &#38; Butlin, R. (2022). Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.16779\">https://doi.org/10.1111/mec.16779</a>"},"keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"doi":"10.1111/mec.16779","_id":"12166","article_type":"letter_note","external_id":{"isi":["000892168800001"]},"abstract":[{"text":"Kerstin Johannesson is a marine ecologist and evolutionary biologist based at the Tjärnö Marine Laboratory of the University of Gothenburg, which is situated in the beautiful Kosterhavet National Park on the Swedish west coast. Her work, using marine periwinkles (especially Littorina saxatilis and L. fabalis) as main model systems, has made a remarkable contribution to marine evolutionary biology and our understanding of local adaptation and its genetic underpinnings.","lang":"eng"}],"publication_status":"published","publisher":"Wiley","date_published":"2022-11-28T00:00:00Z","page":"26-29","department":[{"_id":"NiBa"}],"volume":32,"quality_controlled":"1","isi":1,"scopus_import":"1","intvolume":"        32","date_updated":"2023-08-04T09:09:15Z","oa":1,"issue":"1","article_processing_charge":"No","title":"Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize","publication":"Molecular Ecology","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"month":"11","oa_version":"Published Version","day":"28","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/mec.16779"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Westram, Anja M","first_name":"Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969"},{"last_name":"Butlin","full_name":"Butlin, Roger","first_name":"Roger"}],"type":"journal_article","status":"public"},{"type":"journal_article","status":"public","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"month":"11","day":"01","oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"date_updated":"2023-01-27T11:28:38Z","date_created":"2023-01-27T11:28:38Z","file_id":"12425","checksum":"4c0f05083b414ac0323a1b9ee1abc275","file_name":"2022_Evolution_Stankowski.pdf","success":1,"access_level":"open_access","content_type":"application/pdf","file_size":287282,"relation":"main_file","creator":"dernst"}],"author":[{"first_name":"Sean","full_name":"Stankowski, Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E"}],"publication":"Evolution","language":[{"iso":"eng"}],"isi":1,"intvolume":"        76","scopus_import":"1","has_accepted_license":"1","oa":1,"date_updated":"2023-08-04T09:35:48Z","issue":"11","article_processing_charge":"Yes (via OA deal)","title":"Digest: On the origin of a possible hybrid species","publisher":"Wiley","date_published":"2022-11-01T00:00:00Z","page":"2784-2785","department":[{"_id":"NiBa"}],"volume":76,"quality_controlled":"1","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"external_id":{"isi":["000855751600001"]},"abstract":[{"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.","lang":"eng"}],"publication_status":"published","doi":"10.1111/evo.14632","file_date_updated":"2023-01-27T11:28:38Z","_id":"12234","article_type":"original","year":"2022","citation":{"short":"S. Stankowski, Evolution 76 (2022) 2784–2785.","ama":"Stankowski S. Digest: On the origin of a possible hybrid species. <i>Evolution</i>. 2022;76(11):2784-2785. doi:<a href=\"https://doi.org/10.1111/evo.14632\">10.1111/evo.14632</a>","ieee":"S. Stankowski, “Digest: On the origin of a possible hybrid species,” <i>Evolution</i>, vol. 76, no. 11. Wiley, pp. 2784–2785, 2022.","ista":"Stankowski S. 2022. Digest: On the origin of a possible hybrid species. Evolution. 76(11), 2784–2785.","mla":"Stankowski, Sean. “Digest: On the Origin of a Possible Hybrid Species.” <i>Evolution</i>, vol. 76, no. 11, Wiley, 2022, pp. 2784–85, doi:<a href=\"https://doi.org/10.1111/evo.14632\">10.1111/evo.14632</a>.","chicago":"Stankowski, Sean. “Digest: On the Origin of a Possible Hybrid Species.” <i>Evolution</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/evo.14632\">https://doi.org/10.1111/evo.14632</a>.","apa":"Stankowski, S. (2022). Digest: On the origin of a possible hybrid species. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.14632\">https://doi.org/10.1111/evo.14632</a>"},"date_created":"2023-01-16T09:50:48Z","keyword":["General Agricultural and Biological Sciences","Genetics","Ecology","Evolution","Behavior and Systematics"]},{"keyword":["General Agricultural and Biological Sciences","Genetics","Ecology","Evolution","Behavior and Systematics"],"citation":{"apa":"Koch, E. L., Ravinet, M., Westram, A. M., Johannesson, K., &#38; Butlin, R. K. (2022). Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.14602\">https://doi.org/10.1111/evo.14602</a>","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. <i>Evolution</i>. 2022;76(10):2332-2346. doi:<a href=\"https://doi.org/10.1111/evo.14602\">10.1111/evo.14602</a>","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,” <i>Evolution</i>, vol. 76, no. 10. Wiley, pp. 2332–2346, 2022.","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.” <i>Evolution</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/evo.14602\">https://doi.org/10.1111/evo.14602</a>.","mla":"Koch, Eva L., et al. “Genetic Architecture of Repeated Phenotypic Divergence in Littorina Saxatilis Evolution.” <i>Evolution</i>, vol. 76, no. 10, Wiley, 2022, pp. 2332–46, doi:<a href=\"https://doi.org/10.1111/evo.14602\">10.1111/evo.14602</a>.","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."},"date_created":"2023-01-16T09:54:15Z","year":"2022","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.","related_material":{"record":[{"status":"public","id":"13066","relation":"research_data"}]},"article_type":"original","_id":"12247","file_date_updated":"2023-01-30T08:45:35Z","doi":"10.1111/evo.14602","publication_status":"published","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."}],"external_id":{"pmid":["35994296"],"isi":["000848449100001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"quality_controlled":"1","volume":76,"department":[{"_id":"NiBa"}],"page":"2332-2346","date_published":"2022-10-01T00:00:00Z","publisher":"Wiley","title":"Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution","issue":"10","article_processing_charge":"No","oa":1,"date_updated":"2023-08-04T09:42:11Z","scopus_import":"1","intvolume":"        76","has_accepted_license":"1","isi":1,"language":[{"iso":"eng"}],"publication":"Evolution","author":[{"last_name":"Koch","full_name":"Koch, Eva L.","first_name":"Eva L."},{"last_name":"Ravinet","full_name":"Ravinet, Mark","first_name":"Mark"},{"last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M","full_name":"Westram, Anja M"},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"last_name":"Butlin","first_name":"Roger K.","full_name":"Butlin, Roger K."}],"file":[{"success":1,"file_name":"2022_Evolution_Koch.pdf","checksum":"defd8a4bea61cf00a3c88d4a30e2728c","file_id":"12439","date_created":"2023-01-30T08:45:35Z","date_updated":"2023-01-30T08:45:35Z","creator":"dernst","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_size":2990581}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","day":"01","publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"month":"10","type":"journal_article","status":"public","pmid":1},{"doi":"10.1111/jeb.14005","file_date_updated":"2023-01-30T10:05:31Z","article_type":"review","_id":"12264","related_material":{"record":[{"status":"public","id":"12265","relation":"other"}]},"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)","year":"2022","date_created":"2023-01-16T09:59:24Z","citation":{"apa":"Westram, A. M., Stankowski, S., Surendranadh, P., &#38; Barton, N. H. (2022). What is reproductive isolation? <i>Journal of Evolutionary Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jeb.14005\">https://doi.org/10.1111/jeb.14005</a>","ama":"Westram AM, Stankowski S, Surendranadh P, Barton NH. What is reproductive isolation? <i>Journal of Evolutionary Biology</i>. 2022;35(9):1143-1164. doi:<a href=\"https://doi.org/10.1111/jeb.14005\">10.1111/jeb.14005</a>","ieee":"A. M. Westram, S. Stankowski, P. Surendranadh, and N. H. Barton, “What is reproductive isolation?,” <i>Journal of Evolutionary Biology</i>, vol. 35, no. 9. Wiley, pp. 1143–1164, 2022.","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.","mla":"Westram, Anja M., et al. “What Is Reproductive Isolation?” <i>Journal of Evolutionary Biology</i>, vol. 35, no. 9, Wiley, 2022, pp. 1143–64, doi:<a href=\"https://doi.org/10.1111/jeb.14005\">10.1111/jeb.14005</a>.","chicago":"Westram, Anja M, Sean Stankowski, Parvathy Surendranadh, and Nicholas H Barton. “What Is Reproductive Isolation?” <i>Journal of Evolutionary Biology</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/jeb.14005\">https://doi.org/10.1111/jeb.14005</a>."},"keyword":["Ecology","Evolution","Behavior and Systematics"],"publisher":"Wiley","date_published":"2022-09-01T00:00:00Z","page":"1143-1164","department":[{"_id":"NiBa"}],"volume":35,"quality_controlled":"1","project":[{"name":"The maintenance of alternative adaptive peaks in snapdragons","grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"}],"ddc":["570"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"pmid":["36063156"],"isi":["000849851100002"]},"abstract":[{"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.","lang":"eng"}],"publication_status":"published","publication":"Journal of Evolutionary Biology","language":[{"iso":"eng"}],"isi":1,"has_accepted_license":"1","scopus_import":"1","intvolume":"        35","date_updated":"2023-08-04T09:53:40Z","oa":1,"issue":"9","article_processing_charge":"Yes (via OA deal)","title":"What is reproductive isolation?","pmid":1,"status":"public","type":"journal_article","month":"09","publication_identifier":{"issn":["1010-061X"],"eissn":["1420-9101"]},"oa_version":"Published Version","day":"01","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"creator":"dernst","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_size":3146793,"success":1,"checksum":"f08de57112330a7ee88d2e1b20576a1e","file_id":"12448","file_name":"2022_JourEvoBiology_Westram.pdf","date_created":"2023-01-30T10:05:31Z","date_updated":"2023-01-30T10:05:31Z"}],"author":[{"orcid":"0000-0003-1050-4969","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M","first_name":"Anja M"},{"full_name":"Stankowski, Sean","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski"},{"id":"455235B8-F248-11E8-B48F-1D18A9856A87","last_name":"Surendranadh","first_name":"Parvathy","full_name":"Surendranadh, Parvathy"},{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}]},{"status":"public","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_name":"2022_JourEvoBiology_Westram_Response.pdf","checksum":"27268009e5eec030bc10667a4ac5ed4c","file_id":"12449","success":1,"date_updated":"2023-01-30T10:14:09Z","date_created":"2023-01-30T10:14:09Z","creator":"dernst","access_level":"open_access","content_type":"application/pdf","file_size":349603,"relation":"main_file"}],"oa_version":"Published Version","day":"01","month":"09","publication_identifier":{"eissn":["1420-9101"],"issn":["1010-061X"]},"author":[{"first_name":"Anja M","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram"},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","first_name":"Sean","full_name":"Stankowski, Sean"},{"last_name":"Surendranadh","id":"455235B8-F248-11E8-B48F-1D18A9856A87","first_name":"Parvathy","full_name":"Surendranadh, Parvathy"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H"}],"publication":"Journal of Evolutionary Biology","language":[{"iso":"eng"}],"scopus_import":"1","intvolume":"        35","has_accepted_license":"1","isi":1,"title":"Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’","issue":"9","article_processing_charge":"Yes (via OA deal)","date_updated":"2023-08-04T09:53:41Z","oa":1,"volume":35,"quality_controlled":"1","department":[{"_id":"NiBa"}],"page":"1200-1205","date_published":"2022-09-01T00:00:00Z","publisher":"Wiley","project":[{"name":"The maintenance of alternative adaptive peaks in snapdragons","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","grant_number":"P32166"}],"external_id":{"isi":["000849851100009"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"publication_status":"published","doi":"10.1111/jeb.14082","_id":"12265","article_type":"letter_note","file_date_updated":"2023-01-30T10:14:09Z","related_material":{"record":[{"status":"public","relation":"other","id":"12264"}]},"keyword":["Ecology","Evolution","Behavior and Systematics"],"date_created":"2023-01-16T09:59:37Z","citation":{"mla":"Westram, Anja M., et al. “Reproductive Isolation, Speciation, and the Value of Disagreement: A Reply to the Commentaries on ‘What Is Reproductive Isolation?’” <i>Journal of Evolutionary Biology</i>, vol. 35, no. 9, Wiley, 2022, pp. 1200–05, doi:<a href=\"https://doi.org/10.1111/jeb.14082\">10.1111/jeb.14082</a>.","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?’” <i>Journal of Evolutionary Biology</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/jeb.14082\">https://doi.org/10.1111/jeb.14082</a>.","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.","short":"A.M. Westram, S. Stankowski, P. Surendranadh, N.H. Barton, Journal of Evolutionary Biology 35 (2022) 1200–1205.","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?’ <i>Journal of Evolutionary Biology</i>. 2022;35(9):1200-1205. doi:<a href=\"https://doi.org/10.1111/jeb.14082\">10.1111/jeb.14082</a>","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?,’” <i>Journal of Evolutionary Biology</i>, vol. 35, no. 9. Wiley, pp. 1200–1205, 2022.","apa":"Westram, A. M., Stankowski, S., Surendranadh, P., &#38; Barton, N. H. (2022). Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’ <i>Journal of Evolutionary Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jeb.14082\">https://doi.org/10.1111/jeb.14082</a>"},"year":"2022","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)."},{"author":[{"full_name":"Koch, Eva","first_name":"Eva","last_name":"Koch"},{"last_name":"Ravinet","full_name":"Ravinet, Mark","first_name":"Mark"},{"last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","first_name":"Anja M"},{"last_name":"Jonannesson","first_name":"Kerstin","full_name":"Jonannesson, Kerstin"},{"first_name":"Roger","full_name":"Butlin, Roger","last_name":"Butlin"}],"abstract":[{"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.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.m905qfv4b"}],"day":"28","oa_version":"Published Version","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"month":"07","ddc":["570"],"department":[{"_id":"NiBa"}],"date_published":"2022-07-28T00:00:00Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","type":"research_data_reference","status":"public","publisher":"Dryad","date_created":"2023-05-23T16:33:12Z","title":"Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution","citation":{"mla":"Koch, Eva, et al. <i>Data from: Genetic Architecture of Repeated Phenotypic Divergence in Littorina Saxatilis Ecotype Evolution</i>. Dryad, 2022, doi:<a href=\"https://doi.org/10.5061/DRYAD.M905QFV4B\">10.5061/DRYAD.M905QFV4B</a>.","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, <a href=\"https://doi.org/10.5061/DRYAD.M905QFV4B\">10.5061/DRYAD.M905QFV4B</a>.","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. <a href=\"https://doi.org/10.5061/DRYAD.M905QFV4B\">https://doi.org/10.5061/DRYAD.M905QFV4B</a>.","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:<a href=\"https://doi.org/10.5061/DRYAD.M905QFV4B\">10.5061/DRYAD.M905QFV4B</a>","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.","short":"E. Koch, M. Ravinet, A.M. Westram, K. Jonannesson, R. Butlin, (2022).","apa":"Koch, E., Ravinet, M., Westram, A. M., Jonannesson, K., &#38; Butlin, R. (2022). Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution. Dryad. <a href=\"https://doi.org/10.5061/DRYAD.M905QFV4B\">https://doi.org/10.5061/DRYAD.M905QFV4B</a>"},"year":"2022","article_processing_charge":"No","oa":1,"date_updated":"2023-08-04T09:42:10Z","related_material":{"record":[{"id":"12247","relation":"used_in_publication","status":"public"}]},"_id":"13066","doi":"10.5061/DRYAD.M905QFV4B"},{"publication":"Evolution Letters","language":[{"iso":"eng"}],"isi":1,"has_accepted_license":"1","intvolume":"         6","oa":1,"date_updated":"2023-08-02T13:50:09Z","article_processing_charge":"No","issue":"1","title":"Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics, and disease control","status":"public","type":"journal_article","month":"02","publication_identifier":{"eissn":["2056-3744"]},"oa_version":"Published Version","day":"01","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"access_level":"open_access","relation":"main_file","file_size":2435185,"content_type":"application/pdf","creator":"dernst","date_created":"2022-07-29T06:59:10Z","date_updated":"2022-07-29T06:59:10Z","success":1,"file_id":"11689","checksum":"7e9a37e3b65b480cd7014a6a4a7e460a","file_name":"2022_EvolutionLetters_Turelli.pdf"}],"author":[{"full_name":"Turelli, Michael","first_name":"Michael","last_name":"Turelli"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H"}],"doi":"10.1002/evl3.270","file_date_updated":"2022-07-29T06:59:10Z","_id":"10604","article_type":"original","related_material":{"record":[{"status":"public","relation":"research_data","id":"11686"}]},"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.","year":"2022","citation":{"ama":"Turelli M, Barton NH. Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics, and disease control. <i>Evolution Letters</i>. 2022;6(1):92-105. doi:<a href=\"https://doi.org/10.1002/evl3.270\">10.1002/evl3.270</a>","ieee":"M. Turelli and N. H. Barton, “Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics, and disease control,” <i>Evolution Letters</i>, vol. 6, no. 1. Wiley, pp. 92–105, 2022.","short":"M. Turelli, N.H. Barton, Evolution Letters 6 (2022) 92–105.","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.","chicago":"Turelli, Michael, and Nicholas H Barton. “Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics, and Disease Control.” <i>Evolution Letters</i>. Wiley, 2022. <a href=\"https://doi.org/10.1002/evl3.270\">https://doi.org/10.1002/evl3.270</a>.","mla":"Turelli, Michael, and Nicholas H. Barton. “Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics, and Disease Control.” <i>Evolution Letters</i>, vol. 6, no. 1, Wiley, 2022, pp. 92–105, doi:<a href=\"https://doi.org/10.1002/evl3.270\">10.1002/evl3.270</a>.","apa":"Turelli, M., &#38; Barton, N. H. (2022). Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics, and disease control. <i>Evolution Letters</i>. Wiley. <a href=\"https://doi.org/10.1002/evl3.270\">https://doi.org/10.1002/evl3.270</a>"},"date_created":"2022-01-09T09:45:17Z","keyword":["genetics","ecology","evolution","behavior and systematics"],"publisher":"Wiley","date_published":"2022-02-01T00:00:00Z","page":"92-105","department":[{"_id":"NiBa"}],"volume":6,"quality_controlled":"1","ddc":["570"],"external_id":{"isi":["000754412600008"]},"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"}],"publication_status":"published"},{"day":"24","oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_size":1845792,"relation":"main_file","access_level":"open_access","content_type":"application/pdf","creator":"oolusany","date_updated":"2022-01-24T10:34:45Z","date_created":"2022-01-24T10:34:45Z","file_id":"10659","checksum":"04ca9e2f0e344d680b947f2457df8d0a","file_name":"rstb.2021.0010.pdf"}],"month":"01","publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"author":[{"first_name":"Himani","full_name":"Sachdeva, Himani","last_name":"Sachdeva"},{"orcid":"0000-0003-1971-8314","last_name":"Olusanya","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87","full_name":"Olusanya, Oluwafunmilola O","first_name":"Oluwafunmilola O"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"}],"pmid":1,"status":"public","type":"journal_article","intvolume":"       377","has_accepted_license":"1","isi":1,"title":"Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity","oa":1,"date_updated":"2025-05-26T09:05:09Z","issue":"1846","article_processing_charge":"No","publication":"Philosophical Transactions of the Royal Society B","language":[{"iso":"eng"}],"external_id":{"isi":["000745854300008"],"pmid":["35067097"]},"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"}],"ddc":["576"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"quality_controlled":"1","volume":377,"publisher":"The Royal Society","date_published":"2022-01-24T00:00:00Z","project":[{"_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8","grant_number":"P32896","name":"Causes and consequences of population fragmentation"}],"article_number":"20210010","related_material":{"record":[{"id":"14711","relation":"dissertation_contains","status":"public"}],"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/2021.08.05.455207"}]},"citation":{"short":"H. Sachdeva, O.O. Olusanya, N.H. Barton, Philosophical Transactions of the Royal Society B 377 (2022).","ama":"Sachdeva H, Olusanya OO, Barton NH. Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity. <i>Philosophical Transactions of the Royal Society B</i>. 2022;377(1846). doi:<a href=\"https://doi.org/10.1098/rstb.2021.0010\">10.1098/rstb.2021.0010</a>","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,” <i>Philosophical Transactions of the Royal Society B</i>, vol. 377, no. 1846. The Royal Society, 2022.","mla":"Sachdeva, Himani, et al. “Genetic Load and Extinction in Peripheral Populations: The Roles of Migration, Drift and Demographic Stochasticity.” <i>Philosophical Transactions of the Royal Society B</i>, vol. 377, no. 1846, 20210010, The Royal Society, 2022, doi:<a href=\"https://doi.org/10.1098/rstb.2021.0010\">10.1098/rstb.2021.0010</a>.","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.","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.” <i>Philosophical Transactions of the Royal Society B</i>. The Royal Society, 2022. <a href=\"https://doi.org/10.1098/rstb.2021.0010\">https://doi.org/10.1098/rstb.2021.0010</a>.","apa":"Sachdeva, H., Olusanya, O. O., &#38; Barton, N. H. (2022). Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity. <i>Philosophical Transactions of the Royal Society B</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rstb.2021.0010\">https://doi.org/10.1098/rstb.2021.0010</a>"},"date_created":"2022-01-24T10:34:53Z","acknowledgement":"This research was partly funded by the Austrian Science Fund (FWF) (grant no. P-32896B).","year":"2022","doi":"10.1098/rstb.2021.0010","file_date_updated":"2022-01-24T10:34:45Z","article_type":"original","_id":"10658"},{"author":[{"id":"345D25EC-F248-11E8-B48F-1D18A9856A87","last_name":"Lagator","full_name":"Lagator, Mato","first_name":"Mato"},{"full_name":"Sarikas, Srdjan","first_name":"Srdjan","last_name":"Sarikas","id":"35F0286E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Steinrueck","full_name":"Steinrueck, Magdalena","first_name":"Magdalena"},{"last_name":"Toledo-Aparicio","first_name":"David","full_name":"Toledo-Aparicio, David"},{"full_name":"Bollback, Jonathan P","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","orcid":"0000-0002-4624-4612"},{"orcid":"0000-0001-6220-2052","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","full_name":"Guet, Calin C"},{"full_name":"Tkačik, Gašper","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik"}],"month":"01","publication_identifier":{"eissn":["2050-084X"]},"file":[{"content_type":"application/pdf","access_level":"open_access","file_size":5604343,"relation":"main_file","creator":"cchlebak","date_updated":"2022-02-07T07:14:09Z","date_created":"2022-02-07T07:14:09Z","file_name":"2022_ELife_Lagator.pdf","checksum":"decdcdf600ff51e9a9703b49ca114170","file_id":"10739","success":1}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"26","oa_version":"Published Version","type":"journal_article","status":"public","pmid":1,"article_processing_charge":"No","oa":1,"date_updated":"2023-08-02T14:09:02Z","title":"Predicting bacterial promoter function and evolution from random sequences","isi":1,"intvolume":"        11","scopus_import":"1","has_accepted_license":"1","language":[{"iso":"eng"}],"publication":"eLife","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["576"],"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"}],"external_id":{"pmid":["35080492"],"isi":["000751104400001"]},"project":[{"grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer"}],"date_published":"2022-01-26T00:00:00Z","publisher":"eLife Sciences Publications","quality_controlled":"1","volume":11,"department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"NiBa"}],"year":"2022","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.","date_created":"2022-02-06T23:01:32Z","citation":{"apa":"Lagator, M., Sarikas, S., Steinrueck, M., Toledo-Aparicio, D., Bollback, J. P., Guet, C. C., &#38; Tkačik, G. (2022). Predicting bacterial promoter function and evolution from random sequences. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.64543\">https://doi.org/10.7554/eLife.64543</a>","short":"M. Lagator, S. Sarikas, M. Steinrueck, D. Toledo-Aparicio, J.P. Bollback, C.C. Guet, G. Tkačik, ELife 11 (2022).","ieee":"M. Lagator <i>et al.</i>, “Predicting bacterial promoter function and evolution from random sequences,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","ama":"Lagator M, Sarikas S, Steinrueck M, et al. Predicting bacterial promoter function and evolution from random sequences. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/eLife.64543\">10.7554/eLife.64543</a>","ista":"Lagator M, Sarikas S, Steinrueck M, Toledo-Aparicio D, Bollback JP, Guet CC, Tkačik G. 2022. Predicting bacterial promoter function and evolution from random sequences. eLife. 11, e64543.","mla":"Lagator, Mato, et al. “Predicting Bacterial Promoter Function and Evolution from Random Sequences.” <i>ELife</i>, vol. 11, e64543, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/eLife.64543\">10.7554/eLife.64543</a>.","chicago":"Lagator, Mato, Srdjan Sarikas, Magdalena Steinrueck, David Toledo-Aparicio, Jonathan P Bollback, Calin C Guet, and Gašper Tkačik. “Predicting Bacterial Promoter Function and Evolution from Random Sequences.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/eLife.64543\">https://doi.org/10.7554/eLife.64543</a>."},"article_number":"e64543","ec_funded":1,"article_type":"original","_id":"10736","file_date_updated":"2022-02-07T07:14:09Z","doi":"10.7554/eLife.64543"},{"abstract":[{"lang":"eng","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)’."}],"external_id":{"pmid":["35184588"],"isi":["000758140300001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"publication_status":"published","quality_controlled":"1","volume":377,"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"date_published":"2022-04-11T00:00:00Z","publisher":"The Royal Society","project":[{"name":"Causes and consequences of population fragmentation","grant_number":"P32896","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"14711"}]},"keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"citation":{"apa":"Barton, N. H., &#38; Olusanya, O. O. (2022). The response of a metapopulation to a changing environment. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rstb.2021.0009\">https://doi.org/10.1098/rstb.2021.0009</a>","ieee":"N. H. Barton and O. O. Olusanya, “The response of a metapopulation to a changing environment,” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1848. The Royal Society, 2022.","ama":"Barton NH, Olusanya OO. The response of a metapopulation to a changing environment. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. 2022;377(1848). doi:<a href=\"https://doi.org/10.1098/rstb.2021.0009\">10.1098/rstb.2021.0009</a>","short":"N.H. Barton, O.O. Olusanya, Philosophical Transactions of the Royal Society B: Biological Sciences 377 (2022).","mla":"Barton, Nicholas H., and Oluwafunmilola O. Olusanya. “The Response of a Metapopulation to a Changing Environment.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1848, The Royal Society, 2022, doi:<a href=\"https://doi.org/10.1098/rstb.2021.0009\">10.1098/rstb.2021.0009</a>.","chicago":"Barton, Nicholas H, and Oluwafunmilola O Olusanya. “The Response of a Metapopulation to a Changing Environment.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. The Royal Society, 2022. <a href=\"https://doi.org/10.1098/rstb.2021.0009\">https://doi.org/10.1098/rstb.2021.0009</a>.","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)."},"date_created":"2022-02-21T16:08:10Z","year":"2022","acknowledgement":"This research was partly funded by the Austrian Science Fund (FWF) [FWF P-32896B].","doi":"10.1098/rstb.2021.0009","_id":"10787","article_type":"original","file_date_updated":"2022-08-02T06:14:32Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"creator":"dernst","access_level":"open_access","content_type":"application/pdf","file_size":1349672,"relation":"main_file","success":1,"file_name":"2022_PhilosophicalTransactionsRSB_Barton.pdf","file_id":"11719","checksum":"3b0243738f01bf3c07e0d7e8dc64f71d","date_created":"2022-08-02T06:14:32Z","date_updated":"2022-08-02T06:14:32Z"}],"day":"11","oa_version":"Published Version","month":"04","publication_identifier":{"eissn":["1471-2970"],"issn":["0962-8436"]},"author":[{"first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240"},{"full_name":"Olusanya, Oluwafunmilola O","first_name":"Oluwafunmilola O","last_name":"Olusanya","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1971-8314"}],"type":"journal_article","status":"public","pmid":1,"has_accepted_license":"1","intvolume":"       377","scopus_import":"1","isi":1,"title":"The response of a metapopulation to a changing environment","article_processing_charge":"No","issue":"1848","date_updated":"2025-05-26T09:05:09Z","oa":1,"publication":"Philosophical Transactions of the Royal Society B: Biological Sciences","language":[{"iso":"eng"}]},{"publication_identifier":{"isbn":["978-3-99078-016-9"],"issn":["2663-337X"]},"month":"04","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"access_level":"open_access","relation":"main_file","file_size":11906472,"content_type":"application/pdf","creator":"cchlebak","date_created":"2022-04-07T08:11:34Z","date_updated":"2022-04-07T08:11:34Z","file_name":"LenkaPhD_Official_PDFA.pdf","checksum":"e9609bc4e8f8e20146fc1125fd4f1bf7","file_id":"11129"},{"file_id":"11130","checksum":"99d67040432fd07a225643a212ee8588","file_name":"LenkaPhD Official_source.zip","date_updated":"2022-04-07T08:11:51Z","date_created":"2022-04-07T08:11:51Z","creator":"cchlebak","access_level":"closed","file_size":23036766,"relation":"source_file","content_type":"application/x-zip-compressed"}],"day":"06","oa_version":"Published Version","author":[{"id":"2DFDEC72-F248-11E8-B48F-1D18A9856A87","last_name":"Matejovicova","full_name":"Matejovicova, Lenka","first_name":"Lenka"}],"status":"public","type":"dissertation","alternative_title":["ISTA Thesis"],"has_accepted_license":"1","article_processing_charge":"No","oa":1,"date_updated":"2023-06-23T06:26:41Z","title":"Genetic basis of flower colour as a model for adaptive evolution","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["576","582"],"abstract":[{"text":"Although we often see studies focusing on simple or even discrete traits in studies of colouration,\r\nthe variation of “appearance” phenotypes found in nature is often more complex, continuous\r\nand high-dimensional. Therefore, we developed automated methods suitable for large datasets\r\nof genomes and images, striving to account for their complex nature, while minimising human\r\nbias. We used these methods on a dataset of more than 20, 000 plant SNP genomes and\r\ncorresponding fower images from a hybrid zone of two subspecies of Antirrhinum majus with\r\ndistinctly coloured fowers to improve our understanding of the genetic nature of the fower\r\ncolour in our study system.\r\nFirstly, we use the advantage of large numbers of genotyped plants to estimate the haplotypes in\r\nthe main fower colour regulating region. We study colour- and geography-related characteristics\r\nof the estimated haplotypes and how they connect to their relatedness. We show discrepancies\r\nfrom the expected fower colour distributions given the genotype and identify particular\r\nhaplotypes leading to unexpected phenotypes. We also confrm a signifcant defcit of the\r\ndouble recessive recombinant and quite surprisingly, we show that haplotypes of the most\r\nfrequent parental type are much less variable than others.\r\nSecondly, we introduce our pipeline capable of processing tens of thousands of full fower\r\nimages without human interaction and summarising each image into a set of informative scores.\r\nWe show the compatibility of these machine-measured fower colour scores with the previously\r\nused manual scores and study impact of external efect on the resulting scores. Finally, we use\r\nthe machine-measured fower colour scores to ft and examine a phenotype cline across the\r\nhybrid zone in Planoles using full fower images as opposed to discrete, manual scores and\r\ncompare it with the genotypic cline.","lang":"eng"}],"publication_status":"published","date_published":"2022-04-06T00:00:00Z","supervisor":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"page":"112","degree_awarded":"PhD","year":"2022","citation":{"apa":"Matejovicova, L. (2022). <i>Genetic basis of flower colour as a model for adaptive evolution</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11128\">https://doi.org/10.15479/at:ista:11128</a>","ama":"Matejovicova L. Genetic basis of flower colour as a model for adaptive evolution. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11128\">10.15479/at:ista:11128</a>","ieee":"L. Matejovicova, “Genetic basis of flower colour as a model for adaptive evolution,” Institute of Science and Technology Austria, 2022.","short":"L. Matejovicova, Genetic Basis of Flower Colour as a Model for Adaptive Evolution, Institute of Science and Technology Austria, 2022.","ista":"Matejovicova L. 2022. Genetic basis of flower colour as a model for adaptive evolution. Institute of Science and Technology Austria.","chicago":"Matejovicova, Lenka. “Genetic Basis of Flower Colour as a Model for Adaptive Evolution.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11128\">https://doi.org/10.15479/at:ista:11128</a>.","mla":"Matejovicova, Lenka. <i>Genetic Basis of Flower Colour as a Model for Adaptive Evolution</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11128\">10.15479/at:ista:11128</a>."},"date_created":"2022-04-07T08:19:54Z","doi":"10.15479/at:ista:11128","_id":"11128","file_date_updated":"2022-04-07T08:11:51Z","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"}]},{"file_date_updated":"2022-04-22T09:39:03Z","_id":"11321","doi":"10.15479/at:ista:11321","oa":1,"date_updated":"2024-02-21T12:41:09Z","article_processing_charge":"No","year":"2022","date_created":"2022-04-22T09:42:24Z","title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","citation":{"apa":"Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., &#38; Barton, N. H. (2022). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11321\">https://doi.org/10.15479/at:ista:11321</a>","chicago":"Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field, Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11321\">https://doi.org/10.15479/at:ista:11321</a>.","mla":"Surendranadh, Parvathy, et al. <i>Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11321\">10.15479/at:ista:11321</a>.","ista":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2022. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/at:ista:11321\">10.15479/at:ista:11321</a>.","ama":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11321\">10.15479/at:ista:11321</a>","ieee":"P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H. Barton, “Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus.” Institute of Science and Technology Austria, 2022.","short":"P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, (2022)."},"has_accepted_license":"1","related_material":{"record":[{"id":"11411","relation":"used_in_publication","status":"public"},{"status":"public","id":"9192","relation":"earlier_version"},{"status":"public","relation":"earlier_version","id":"8254"}]},"publisher":"Institute of Science and Technology Austria","status":"public","date_published":"2022-04-28T00:00:00Z","type":"research_data","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"author":[{"id":"455235B8-F248-11E8-B48F-1D18A9856A87","last_name":"Surendranadh","first_name":"Parvathy","full_name":"Surendranadh, Parvathy"},{"first_name":"Louise S","full_name":"Arathoon, Louise S","orcid":"0000-0003-1771-714X","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","last_name":"Arathoon"},{"first_name":"Carina","full_name":"Baskett, Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","last_name":"Baskett","orcid":"0000-0002-7354-8574"},{"last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","first_name":"David","full_name":"Field, David"},{"full_name":"Pickup, Melinda","first_name":"Melinda","orcid":"0000-0001-6118-0541","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"ddc":["570"],"month":"04","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"28","oa_version":"Published Version","contributor":[{"contributor_type":"project_member","last_name":"Arathoon","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S"},{"orcid":"0000-0002-7354-8574","last_name":"Baskett","contributor_type":"project_member","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carina"},{"first_name":"David","contributor_type":"project_member","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","orcid":"0000-0002-4014-8478"},{"first_name":"Melinda","last_name":"Pickup","contributor_type":"project_member","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","contributor_type":"project_member","first_name":"Nicholas H"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Here are the research data underlying the publication \"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus\" Further information are summed up in the README document. "}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/x-zip-compressed","file_size":13260571,"creator":"larathoo","date_created":"2022-04-22T09:39:03Z","date_updated":"2022-04-22T09:39:03Z","success":1,"checksum":"96c1b86cdf25481f2a52972fcc45ca7f","file_id":"11326","file_name":"Data_Code.zip"}]},{"isi":1,"has_accepted_license":"1","intvolume":"        76","scopus_import":"1","issue":"5","article_processing_charge":"No","date_updated":"2023-08-03T07:00:28Z","oa":1,"title":"Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization","publication":"Evolution","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"month":"05","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"creator":"dernst","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_size":2855214,"success":1,"file_id":"11729","checksum":"c27c025ae9afcf6c804d46a909775ee5","file_name":"2022_Evolution_Freitas.pdf","date_created":"2022-08-05T06:19:28Z","date_updated":"2022-08-05T06:19:28Z"}],"day":"01","oa_version":"Published Version","author":[{"first_name":"Susana","full_name":"Freitas, Susana","last_name":"Freitas"},{"first_name":"Anja M","full_name":"Westram, Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969"},{"last_name":"Schwander","full_name":"Schwander, Tanja","first_name":"Tanja"},{"full_name":"Arakelyan, Marine","first_name":"Marine","last_name":"Arakelyan"},{"full_name":"Ilgaz, Çetin","first_name":"Çetin","last_name":"Ilgaz"},{"first_name":"Yusuf","full_name":"Kumlutas, Yusuf","last_name":"Kumlutas"},{"last_name":"Harris","first_name":"David James","full_name":"Harris, David James"},{"last_name":"Carretero","full_name":"Carretero, Miguel A.","first_name":"Miguel A."},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"}],"type":"journal_article","status":"public","pmid":1,"ec_funded":1,"year":"2022","acknowledgement":"The authors thank A. van der Meijden and F. Ahmadzadeh for providing specimens and tissue samples, and A. Vardanyan, C. Corti, F. Jorge, and S. Drovetski for support during field work. The authors also thank S. Qiu for assistance with python scripting, S. Rocha for her support in BEAST analysis, and B. Wielstra for his comments on\r\na previous version of the manuscript. SF was funded by FCT grant SFRH/BD/81483/2011 (a PhD individual grant). AMW was funded by the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement no. 797747. TS acknowledges funding from the Swiss National Science Foundation (grants\r\nPP00P3_170627 and 31003A_182495). The work was carried out under financial support of the projects “Preserving Armenian biodiversity: Joint Portuguese – Armenian program for training in modern conservation biology” of Gulbenkian Foundation (Portugal) and PTDC/BIABEC/101256/2008 of Fundação para a Ciência e a Tecnologia (FCT, Portugal).","date_created":"2022-04-24T22:01:44Z","citation":{"short":"S. Freitas, A.M. Westram, T. Schwander, M. Arakelyan, Ç. Ilgaz, Y. Kumlutas, D.J. Harris, M.A. Carretero, R.K. Butlin, Evolution 76 (2022) 899–914.","ama":"Freitas S, Westram AM, Schwander T, et al. Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization. <i>Evolution</i>. 2022;76(5):899-914. doi:<a href=\"https://doi.org/10.1111/evo.14462\">10.1111/evo.14462</a>","ieee":"S. Freitas <i>et al.</i>, “Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization,” <i>Evolution</i>, vol. 76, no. 5. Wiley, pp. 899–914, 2022.","mla":"Freitas, Susana, et al. “Parthenogenesis in Darevskia Lizards: A Rare Outcome of Common Hybridization, Not a Common Outcome of Rare Hybridization.” <i>Evolution</i>, vol. 76, no. 5, Wiley, 2022, pp. 899–914, doi:<a href=\"https://doi.org/10.1111/evo.14462\">10.1111/evo.14462</a>.","ista":"Freitas S, Westram AM, Schwander T, Arakelyan M, Ilgaz Ç, Kumlutas Y, Harris DJ, Carretero MA, Butlin RK. 2022. Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization. Evolution. 76(5), 899–914.","chicago":"Freitas, Susana, Anja M Westram, Tanja Schwander, Marine Arakelyan, Çetin Ilgaz, Yusuf Kumlutas, David James Harris, Miguel A. Carretero, and Roger K. Butlin. “Parthenogenesis in Darevskia Lizards: A Rare Outcome of Common Hybridization, Not a Common Outcome of Rare Hybridization.” <i>Evolution</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/evo.14462\">https://doi.org/10.1111/evo.14462</a>.","apa":"Freitas, S., Westram, A. M., Schwander, T., Arakelyan, M., Ilgaz, Ç., Kumlutas, Y., … Butlin, R. K. (2022). Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.14462\">https://doi.org/10.1111/evo.14462</a>"},"doi":"10.1111/evo.14462","article_type":"original","_id":"11334","file_date_updated":"2022-08-05T06:19:28Z","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"ddc":["570"],"abstract":[{"lang":"eng","text":"Hybridization is a common evolutionary process with multiple possible outcomes. In vertebrates, interspecific hybridization has repeatedly generated parthenogenetic hybrid species. However, it is unknown whether the generation of parthenogenetic hybrids is a rare outcome of frequent hybridization between sexual species within a genus or the typical outcome of rare hybridization events. Darevskia is a genus of rock lizards with both hybrid parthenogenetic and sexual species. Using capture sequencing, we estimate phylogenetic relationships and gene flow among the sexual species, to determine how introgressive hybridization relates to the origins of parthenogenetic hybrids. We find evidence for widespread hybridization with gene flow, both between recently diverged species and deep branches. Surprisingly, we find no signal of gene flow between parental species of the parthenogenetic hybrids, suggesting that the parental pairs were either reproductively or geographically isolated early in their divergence. The generation of parthenogenetic hybrids in Darevskia is, then, a rare outcome of the total occurrence of hybridization within the genus, but the typical outcome when specific species pairs hybridize. Our results question the conventional view that parthenogenetic lineages are generated by hybridization in a window of divergence. Instead, they suggest that some lineages possess specific properties that underpin successful parthenogenetic reproduction."}],"external_id":{"pmid":["35323995"],"isi":["000781632500001"]},"publication_status":"published","date_published":"2022-05-01T00:00:00Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","publisher":"Wiley","volume":76,"quality_controlled":"1","page":"899-914","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"project":[{"name":"Theoretical and empirical approaches to understanding Parallel Adaptation","call_identifier":"H2020","grant_number":"797747","_id":"265B41B8-B435-11E9-9278-68D0E5697425"}]},{"publication_status":"published","abstract":[{"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.","lang":"eng"}],"ddc":["576"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"page":"98","publisher":"Institute of Science and Technology Austria","date_published":"2022-05-18T00:00:00Z","supervisor":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H"}],"date_created":"2022-05-16T16:49:18Z","citation":{"mla":"Belohlavy, Stefanie. <i>The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11388\">10.15479/at:ista:11388</a>.","chicago":"Belohlavy, Stefanie. “The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11388\">https://doi.org/10.15479/at:ista:11388</a>.","ista":"Belohlavy S. 2022. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. Institute of Science and Technology Austria.","ieee":"S. Belohlavy, “The genetic basis of complex traits studied via analysis of evolve and resequence experiments,” Institute of Science and Technology Austria, 2022.","ama":"Belohlavy S. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11388\">10.15479/at:ista:11388</a>","short":"S. Belohlavy, The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments, Institute of Science and Technology Austria, 2022.","apa":"Belohlavy, S. (2022). <i>The genetic basis of complex traits studied via analysis of evolve and resequence experiments</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11388\">https://doi.org/10.15479/at:ista:11388</a>"},"year":"2022","related_material":{"record":[{"relation":"part_of_dissertation","id":"6713","status":"public"}]},"degree_awarded":"PhD","file_date_updated":"2023-05-20T22:30:03Z","_id":"11388","doi":"10.15479/at:ista:11388","author":[{"full_name":"Belohlavy, Stefanie","first_name":"Stefanie","id":"43FE426A-F248-11E8-B48F-1D18A9856A87","last_name":"Belohlavy","orcid":"0000-0002-9849-498X"}],"day":"18","oa_version":"Published Version","file":[{"checksum":"4d75e6a619df7e8a9d6e840aee182380","file_id":"11398","file_name":"thesis_sb_final_pdfa.pdf","embargo":"2023-05-19","date_updated":"2023-05-20T22:30:03Z","date_created":"2022-05-19T13:03:13Z","creator":"sbelohla","access_level":"open_access","content_type":"application/pdf","file_size":8247240,"relation":"main_file"},{"embargo_to":"open_access","creator":"sbelohla","file_size":7094,"relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed","checksum":"7a5d8b6dd0ca00784f860075b0a7d8f0","file_id":"11399","file_name":"thesis_sb_final.zip","date_updated":"2023-05-20T22:30:03Z","date_created":"2022-05-19T13:07:47Z"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"05","publication_identifier":{"isbn":["978-3-99078-018-3"]},"alternative_title":["ISTA Thesis"],"type":"dissertation","status":"public","title":"The genetic basis of complex traits studied via analysis of evolve and resequence experiments","date_updated":"2023-08-29T06:41:51Z","oa":1,"article_processing_charge":"No","has_accepted_license":"1","language":[{"iso":"eng"}]},{"ddc":["576"],"abstract":[{"lang":"eng","text":"Many studies have quantified the distribution of heterozygosity and relatedness in natural populations, but few have examined the demographic processes driving these patterns. In this study, we take a novel approach by studying how population structure affects both pairwise identity and the distribution of heterozygosity in a natural population of the self-incompatible plant Antirrhinum majus. Excess variance in heterozygosity between individuals is due to identity disequilibrium, which reflects the variance in inbreeding between individuals; it is measured by the statistic g2. We calculated g2 together with FST and pairwise relatedness (Fij) using 91 SNPs in 22,353 individuals collected over 11 years. We find that pairwise Fij declines rapidly over short spatial scales, and the excess variance in heterozygosity between individuals reflects significant variation in inbreeding. Additionally, we detect an excess of individuals with around half the average heterozygosity, indicating either selfing or matings between close relatives. We use 2 types of simulation to ask whether variation in heterozygosity is consistent with fine-scale spatial population structure. First, by simulating offspring using parents drawn from a range of spatial scales, we show that the known pollen dispersal kernel explains g2. Second, we simulate a 1,000-generation pedigree using the known dispersal and spatial distribution and find that the resulting g2 is consistent with that observed from the field data. In contrast, a simulated population with uniform density underestimates g2, indicating that heterogeneous density promotes identity disequilibrium. Our study shows that heterogeneous density and leptokurtic dispersal can together explain the distribution of heterozygosity."}],"external_id":{"isi":["000803735800001"],"pmid":["35639938"]},"publication_status":"published","date_published":"2022-07-01T00:00:00Z","publisher":"Oxford University Press","quality_controlled":"1","volume":221,"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"project":[{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","grant_number":"P32166","name":"The maintenance of alternative adaptive peaks in snapdragons"}],"article_number":"iyac083","related_material":{"record":[{"status":"public","id":"14651","relation":"dissertation_contains"},{"status":"public","relation":"research_data","id":"11321"},{"status":"public","relation":"research_data","id":"9192"}]},"year":"2022","acknowledgement":"Part of this work was funded by Marie Curie COFUND Doctoral Fellowship and Austrian Science Fund FWF (grant P32166).\r\nWe thank the many volunteers and friends who have contributed to data collection in the field site over the years, in particular those who have managed field seasons: Barbora Trubenova, Maria Clara Melo, Tom Ellis, Eva Cereghetti, Lenka Matejovicova, Beatriz Pablo Carmona. Frederic Ferrer and Eva Salmerón Mateu have been immensely helpful with logistics at our informal field station, El Serrat de Planoles. We thank Sean Stankowski for technical help in\r\nproducing figure 1. This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).","citation":{"short":"P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, Genetics 221 (2022).","ama":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. <i>Genetics</i>. 2022;221(3). doi:<a href=\"https://doi.org/10.1093/genetics/iyac083\">10.1093/genetics/iyac083</a>","ieee":"P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H. Barton, “Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus,” <i>Genetics</i>, vol. 221, no. 3. Oxford University Press, 2022.","mla":"Surendranadh, Parvathy, et al. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” <i>Genetics</i>, vol. 221, no. 3, iyac083, Oxford University Press, 2022, doi:<a href=\"https://doi.org/10.1093/genetics/iyac083\">10.1093/genetics/iyac083</a>.","chicago":"Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field, Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” <i>Genetics</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/genetics/iyac083\">https://doi.org/10.1093/genetics/iyac083</a>.","ista":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2022. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Genetics. 221(3), iyac083.","apa":"Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., &#38; Barton, N. H. (2022). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. <i>Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/genetics/iyac083\">https://doi.org/10.1093/genetics/iyac083</a>"},"date_created":"2022-05-26T13:44:50Z","doi":"10.1093/genetics/iyac083","article_type":"original","_id":"11411","file_date_updated":"2022-05-26T12:48:21Z","acknowledged_ssus":[{"_id":"ScienComp"}],"publication_identifier":{"eissn":["1943-2631"]},"month":"07","file":[{"creator":"larathoo","relation":"main_file","file_size":885374,"content_type":"application/pdf","access_level":"open_access","success":1,"checksum":"cc2d56deb608bd53c5cc02f03a875107","file_id":"11412","file_name":"Manuscript.pdf","date_created":"2022-05-26T12:48:15Z","date_updated":"2022-05-26T12:48:15Z"},{"date_updated":"2022-05-26T12:48:21Z","date_created":"2022-05-26T12:48:21Z","checksum":"693742595b6c7ed809423be01460d083","file_id":"11413","file_name":"SupplementalMaterial.pdf","success":1,"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":1401704,"creator":"larathoo"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"01","oa_version":"Submitted Version","author":[{"first_name":"Parvathy","full_name":"Surendranadh, Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87","last_name":"Surendranadh"},{"full_name":"Arathoon, Louise S","first_name":"Louise S","orcid":"0000-0003-1771-714X","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","last_name":"Arathoon"},{"orcid":"0000-0002-7354-8574","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","last_name":"Baskett","full_name":"Baskett, Carina","first_name":"Carina"},{"full_name":"Field, David","first_name":"David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field"},{"orcid":"0000-0001-6118-0541","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","full_name":"Pickup, Melinda","first_name":"Melinda"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"status":"public","type":"journal_article","pmid":1,"isi":1,"scopus_import":"1","has_accepted_license":"1","intvolume":"       221","issue":"3","article_processing_charge":"No","date_updated":"2024-02-21T12:38:33Z","oa":1,"title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","publication":"Genetics","language":[{"iso":"eng"}]},{"author":[{"full_name":"Saona Urmeneta, Raimundo J","first_name":"Raimundo J","orcid":"0000-0001-5103-038X","last_name":"Saona Urmeneta","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425"},{"full_name":"Kondrashov, Fyodor","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","orcid":"0000-0001-8243-4694"},{"orcid":"0000-0002-6246-1465","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","last_name":"Khudiakova","full_name":"Khudiakova, Kseniia","first_name":"Kseniia"}],"file":[{"creator":"dernst","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_size":463025,"checksum":"05a1fe7d10914a00c2bca9b447993a65","file_name":"2022_BulletinMathBiology_Saona.pdf","file_id":"11455","success":1,"date_updated":"2022-06-20T07:51:32Z","date_created":"2022-06-20T07:51:32Z"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"17","oa_version":"Published Version","publication_identifier":{"eissn":["1522-9602"],"issn":["0092-8240"]},"month":"06","type":"journal_article","status":"public","title":"Relation between the number of peaks and the number of reciprocal sign epistatic interactions","article_processing_charge":"Yes (via OA deal)","issue":"8","oa":1,"date_updated":"2023-08-03T07:20:53Z","has_accepted_license":"1","scopus_import":"1","intvolume":"        84","isi":1,"language":[{"iso":"eng"}],"publication":"Bulletin of Mathematical Biology","publication_status":"published","abstract":[{"lang":"eng","text":"Empirical essays of fitness landscapes suggest that they may be rugged, that is having multiple fitness peaks. Such fitness landscapes, those that have multiple peaks, necessarily have special local structures, called reciprocal sign epistasis (Poelwijk et al. in J Theor Biol 272:141–144, 2011). Here, we investigate the quantitative relationship between the number of fitness peaks and the number of reciprocal sign epistatic interactions. Previously, it has been shown (Poelwijk et al. in J Theor Biol 272:141–144, 2011) that pairwise reciprocal sign epistasis is a necessary but not sufficient condition for the existence of multiple peaks. Applying discrete Morse theory, which to our knowledge has never been used in this context, we extend this result by giving the minimal number of reciprocal sign epistatic interactions required to create a given number of peaks."}],"external_id":{"isi":["000812509800001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["510","570"],"project":[{"call_identifier":"H2020","name":"Characterizing the fitness landscape on population and global scales","grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425"},{"_id":"c098eddd-5a5b-11eb-8a69-abe27170a68f","grant_number":"I05127","name":"Evolutionary analysis of gene regulation"}],"volume":84,"quality_controlled":"1","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"JaMa"}],"date_published":"2022-06-17T00:00:00Z","publisher":"Springer Nature","keyword":["Computational Theory and Mathematics","General Agricultural and Biological Sciences","Pharmacology","General Environmental Science","General Biochemistry","Genetics and Molecular Biology","General Mathematics","Immunology","General Neuroscience"],"date_created":"2022-06-17T16:16:15Z","citation":{"mla":"Saona Urmeneta, Raimundo J., et al. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” <i>Bulletin of Mathematical Biology</i>, vol. 84, no. 8, 74, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/s11538-022-01029-z\">10.1007/s11538-022-01029-z</a>.","ista":"Saona Urmeneta RJ, Kondrashov F, Khudiakova K. 2022. Relation between the number of peaks and the number of reciprocal sign epistatic interactions. Bulletin of Mathematical Biology. 84(8), 74.","chicago":"Saona Urmeneta, Raimundo J, Fyodor Kondrashov, and Kseniia Khudiakova. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” <i>Bulletin of Mathematical Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s11538-022-01029-z\">https://doi.org/10.1007/s11538-022-01029-z</a>.","short":"R.J. Saona Urmeneta, F. Kondrashov, K. Khudiakova, Bulletin of Mathematical Biology 84 (2022).","ama":"Saona Urmeneta RJ, Kondrashov F, Khudiakova K. Relation between the number of peaks and the number of reciprocal sign epistatic interactions. <i>Bulletin of Mathematical Biology</i>. 2022;84(8). doi:<a href=\"https://doi.org/10.1007/s11538-022-01029-z\">10.1007/s11538-022-01029-z</a>","ieee":"R. J. Saona Urmeneta, F. Kondrashov, and K. Khudiakova, “Relation between the number of peaks and the number of reciprocal sign epistatic interactions,” <i>Bulletin of Mathematical Biology</i>, vol. 84, no. 8. Springer Nature, 2022.","apa":"Saona Urmeneta, R. J., Kondrashov, F., &#38; Khudiakova, K. (2022). Relation between the number of peaks and the number of reciprocal sign epistatic interactions. <i>Bulletin of Mathematical Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11538-022-01029-z\">https://doi.org/10.1007/s11538-022-01029-z</a>"},"year":"2022","acknowledgement":"We are grateful to Herbert Edelsbrunner and Jeferson Zapata for helpful discussions. Open access funding provided by Austrian Science Fund (FWF). Partially supported by the ERC Consolidator (771209–CharFL) and the FWF Austrian Science Fund (I5127-B) grants to FAK.","related_material":{"link":[{"url":"https://doi.org/10.1007/s11538-022-01118-z","relation":"erratum"}]},"article_number":"74","ec_funded":1,"_id":"11447","article_type":"original","file_date_updated":"2022-06-20T07:51:32Z","doi":"10.1007/s11538-022-01029-z"},{"publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"abstract":[{"text":"Local adaptation leads to differences between populations within a species. In many systems, similar environmental contrasts occur repeatedly, sometimes driving parallel phenotypic evolution. Understanding the genomic basis of local adaptation and parallel evolution is a major goal of evolutionary genomics. It is now known that by preventing the break-up of favourable combinations of alleles across multiple loci, genetic architectures that reduce recombination, like chromosomal inversions, can make an important contribution to local adaptation. However, little is known about whether inversions also contribute disproportionately to parallel evolution. Our aim here is to highlight this knowledge gap, to showcase existing studies, and to illustrate the differences between genomic architectures with and without inversions using simple models. We predict that by generating stronger effective selection, inversions can sometimes speed up the parallel adaptive process or enable parallel adaptation where it would be impossible otherwise, but this is highly dependent on the spatial setting. We highlight that further empirical work is needed, in particular to cover a broader taxonomic range and to understand the relative importance of inversions compared to genomic regions without inversions.","lang":"eng"}],"external_id":{"isi":["000812317300005"]},"project":[{"name":"The maintenance of alternative adaptive peaks in snapdragons","grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"}],"date_published":"2022-08-01T00:00:00Z","publisher":"Royal Society of London","quality_controlled":"1","volume":377,"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"year":"2022","acknowledgement":"We thank the editor and two anonymous reviewers for their helpful and interesting comments on this manuscript.","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"date_created":"2022-07-08T11:41:56Z","citation":{"mla":"Westram, Anja M., et al. “Inversions and Parallel Evolution.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1856, 20210203, Royal Society of London, 2022, doi:<a href=\"https://doi.org/10.1098/rstb.2021.0203\">10.1098/rstb.2021.0203</a>.","chicago":"Westram, Anja M, Rui Faria, Kerstin Johannesson, Roger Butlin, and Nicholas H Barton. “Inversions and Parallel Evolution.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. Royal Society of London, 2022. <a href=\"https://doi.org/10.1098/rstb.2021.0203\">https://doi.org/10.1098/rstb.2021.0203</a>.","ista":"Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. 2022. Inversions and parallel evolution. Philosophical Transactions of the Royal Society B: Biological Sciences. 377(1856), 20210203.","short":"A.M. Westram, R. Faria, K. Johannesson, R. Butlin, N.H. Barton, Philosophical Transactions of the Royal Society B: Biological Sciences 377 (2022).","ama":"Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. Inversions and parallel evolution. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. 2022;377(1856). doi:<a href=\"https://doi.org/10.1098/rstb.2021.0203\">10.1098/rstb.2021.0203</a>","ieee":"A. M. Westram, R. Faria, K. Johannesson, R. Butlin, and N. H. Barton, “Inversions and parallel evolution,” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1856. Royal Society of London, 2022.","apa":"Westram, A. M., Faria, R., Johannesson, K., Butlin, R., &#38; Barton, N. H. (2022). Inversions and parallel evolution. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rstb.2021.0203\">https://doi.org/10.1098/rstb.2021.0203</a>"},"article_number":"20210203","article_type":"original","_id":"11546","file_date_updated":"2023-02-02T08:20:29Z","doi":"10.1098/rstb.2021.0203","author":[{"first_name":"Anja M","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram"},{"last_name":"Faria","full_name":"Faria, Rui","first_name":"Rui"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"full_name":"Butlin, Roger","first_name":"Roger","last_name":"Butlin"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"month":"08","publication_identifier":{"eissn":["1471-2970"],"issn":["0962-8436"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_size":920304,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","creator":"dernst","date_created":"2023-02-02T08:20:29Z","date_updated":"2023-02-02T08:20:29Z","success":1,"checksum":"49f69428f3dcf5ce3ff281f7d199e9df","file_id":"12479","file_name":"2022_PhilosophicalTransactionsB_Westram.pdf"}],"oa_version":"Published Version","day":"01","type":"journal_article","status":"public","article_processing_charge":"Yes (via OA deal)","issue":"1856","oa":1,"date_updated":"2023-08-03T11:55:42Z","title":"Inversions and parallel evolution","isi":1,"has_accepted_license":"1","scopus_import":"1","intvolume":"       377","language":[{"iso":"eng"}],"publication":"Philosophical Transactions of the Royal Society B: Biological Sciences"}]