[{"doi":"10.1093/evolinnean/kzae001","scopus_import":"1","oa":1,"day":"16","abstract":[{"text":"Speciation research—the scientific field focused on understanding the origin and diversity of species—has a long and complex history. While relevant to one another, the specific goals and activities of speciation researchers are highly diverse, and scattered across a collection of different perspectives. Thus, our understanding of speciation will benefit from efforts to bridge scientific findings and the diverse people who do the work. In this paper, we outline two ways of integrating speciation research: (i) scientific integration, through the bringing together of ideas, data, and approaches; and (ii) social integration, by creating ways for a diversity of researchers to participate in the scientific process. We then discuss five challenges to integration: (i) the multidisciplinary nature of speciation research, (ii) the complex language of speciation; (iii) a bias toward certain study systems; (iv) the challenges of working across scales; and (v) inconsistent measures and reporting standards. We provide practical steps that individuals and groups can take to help overcome these challenges, and argue that integration is a team effort in which we all have a role to play.","lang":"eng"}],"date_created":"2025-01-29T10:38:17Z","issue":"1","ddc":["570"],"file":[{"file_name":"2024_EvolJourLinneanSoc_Stankowski.pdf","success":1,"date_updated":"2025-01-29T10:52:40Z","content_type":"application/pdf","file_id":"18950","checksum":"db08120a92527acaef476bd93f2b87f9","file_size":3935454,"date_created":"2025-01-29T10:52:40Z","creator":"dernst","access_level":"open_access","relation":"main_file"}],"publication":"Evolutionary Journal of the Linnean Society","corr_author":"1","year":"2024","type":"journal_article","article_number":"kzae001","citation":{"apa":"Stankowski, S., Cutter, A. D., Satokangas, I., Lerch, B. A., Rolland, J., Smadja, C. M., … Kulmuni, J. (2024). Toward the integration of speciation research. <i>Evolutionary Journal of the Linnean Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evolinnean/kzae001\">https://doi.org/10.1093/evolinnean/kzae001</a>","chicago":"Stankowski, Sean, Asher D Cutter, Ina Satokangas, Brian A Lerch, Jonathan Rolland, Carole M Smadja, J Carolina Segami Marzal, et al. “Toward the Integration of Speciation Research.” <i>Evolutionary Journal of the Linnean Society</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/evolinnean/kzae001\">https://doi.org/10.1093/evolinnean/kzae001</a>.","mla":"Stankowski, Sean, et al. “Toward the Integration of Speciation Research.” <i>Evolutionary Journal of the Linnean Society</i>, vol. 3, no. 1, kzae001, Oxford University Press, 2024, doi:<a href=\"https://doi.org/10.1093/evolinnean/kzae001\">10.1093/evolinnean/kzae001</a>.","ieee":"S. Stankowski <i>et al.</i>, “Toward the integration of speciation research,” <i>Evolutionary Journal of the Linnean Society</i>, vol. 3, no. 1. Oxford University Press, 2024.","short":"S. Stankowski, A.D. Cutter, I. Satokangas, B.A. Lerch, J. Rolland, C.M. Smadja, J.C. Segami Marzal, C.R. Cooney, P.G.D. Feulner, F.M.C.B. Domingos, H.L. North, R. Yamaguchi, R.K. Butlin, J.B.W. Wolf, J. Coughlan, P. Heidbreder, R. Hernández-Gutiérrez, K.B. Barnard-Kubow, D. Peede, L. Rancilhac, R.B. Salvador, K.A. Thompson, E.A. Stacy, L.C. Moyle, M.D. Garlovsky, A. Maulana, A. Kantelinen, N.I. Cacho, H. Schneemann, M. Domínguez, E.B. Dopman, K. Lohse, S.J. Rometsch, A.A. Comeault, R.M. Merrill, E.S.C. Scordato, S. Singhal, V. Pärssinen, A.C.R. Lackey, S. Kumar, J.I. Meier, N.H. Barton, C. Fraisse, M. Ravinet, J. Kulmuni, Evolutionary Journal of the Linnean Society 3 (2024).","ama":"Stankowski S, Cutter AD, Satokangas I, et al. Toward the integration of speciation research. <i>Evolutionary Journal of the Linnean Society</i>. 2024;3(1). doi:<a href=\"https://doi.org/10.1093/evolinnean/kzae001\">10.1093/evolinnean/kzae001</a>","ista":"Stankowski S, Cutter AD, Satokangas I, Lerch BA, Rolland J, Smadja CM, Segami Marzal JC, Cooney CR, Feulner PGD, Domingos FMCB, North HL, Yamaguchi R, Butlin RK, Wolf JBW, Coughlan J, Heidbreder P, Hernández-Gutiérrez R, Barnard-Kubow KB, Peede D, Rancilhac L, Salvador RB, Thompson KA, Stacy EA, Moyle LC, Garlovsky MD, Maulana A, Kantelinen A, Cacho NI, Schneemann H, Domínguez M, Dopman EB, Lohse K, Rometsch SJ, Comeault AA, Merrill RM, Scordato ESC, Singhal S, Pärssinen V, Lackey ACR, Kumar S, Meier JI, Barton NH, Fraisse C, Ravinet M, Kulmuni J. 2024. Toward the integration of speciation research. Evolutionary Journal of the Linnean Society. 3(1), kzae001."},"OA_place":"publisher","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","publication_status":"published","date_updated":"2025-01-29T10:55:54Z","oa_version":"Published Version","date_published":"2024-02-16T00:00:00Z","publication_identifier":{"issn":["2752-938X"]},"department":[{"_id":"NiBa"}],"article_processing_charge":"Yes","publisher":"Oxford University Press","title":"Toward the integration of speciation research","volume":3,"month":"02","quality_controlled":"1","status":"public","acknowledgement":"We thank the staff of the Tvärminne Zoological Station (University of Helsinki) for their hospitality during the workshop. We are also grateful to everyone who applied to attend the workshop.\r\nFunding for the workshop was provided by the European Society for Evolutionary Biology through the Special Topic Network (STN) funding scheme.","tmp":{"image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"article_type":"original","OA_type":"gold","language":[{"iso":"eng"}],"intvolume":"         3","file_date_updated":"2025-01-29T10:52:40Z","author":[{"first_name":"Sean","full_name":"Stankowski, Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"last_name":"Cutter","full_name":"Cutter, Asher D","first_name":"Asher D"},{"first_name":"Ina","full_name":"Satokangas, Ina","last_name":"Satokangas"},{"last_name":"Lerch","full_name":"Lerch, Brian A","first_name":"Brian A"},{"last_name":"Rolland","first_name":"Jonathan","full_name":"Rolland, Jonathan"},{"last_name":"Smadja","first_name":"Carole M","full_name":"Smadja, Carole M"},{"last_name":"Segami Marzal","full_name":"Segami Marzal, J Carolina","first_name":"J Carolina"},{"first_name":"Christopher R","full_name":"Cooney, Christopher R","last_name":"Cooney"},{"last_name":"Feulner","first_name":"Philine G D","full_name":"Feulner, Philine G D"},{"first_name":"Fabricius Maia Chaves Bicalho","full_name":"Domingos, Fabricius Maia Chaves Bicalho","last_name":"Domingos"},{"full_name":"North, Henry L","first_name":"Henry L","last_name":"North"},{"full_name":"Yamaguchi, Ryo","first_name":"Ryo","last_name":"Yamaguchi"},{"last_name":"Butlin","first_name":"Roger K","full_name":"Butlin, Roger K"},{"last_name":"Wolf","full_name":"Wolf, Jochen B W","first_name":"Jochen B W"},{"full_name":"Coughlan, Jenn","first_name":"Jenn","last_name":"Coughlan"},{"last_name":"Heidbreder","first_name":"Patrick","full_name":"Heidbreder, Patrick"},{"last_name":"Hernández-Gutiérrez","first_name":"Rebeca","full_name":"Hernández-Gutiérrez, Rebeca"},{"last_name":"Barnard-Kubow","full_name":"Barnard-Kubow, Karen B","first_name":"Karen B"},{"first_name":"David","full_name":"Peede, David","last_name":"Peede"},{"full_name":"Rancilhac, Loïs","first_name":"Loïs","last_name":"Rancilhac"},{"full_name":"Salvador, Rodrigo Brincalepe","first_name":"Rodrigo Brincalepe","last_name":"Salvador"},{"full_name":"Thompson, Ken A","first_name":"Ken A","last_name":"Thompson"},{"last_name":"Stacy","full_name":"Stacy, Elizabeth A","first_name":"Elizabeth A"},{"last_name":"Moyle","full_name":"Moyle, Leonie C","first_name":"Leonie C"},{"full_name":"Garlovsky, Martin D","first_name":"Martin D","last_name":"Garlovsky"},{"last_name":"Maulana","first_name":"Arif","full_name":"Maulana, Arif"},{"last_name":"Kantelinen","full_name":"Kantelinen, Annina","first_name":"Annina"},{"full_name":"Cacho, N Ivalú","first_name":"N Ivalú","last_name":"Cacho"},{"first_name":"Hilde","full_name":"Schneemann, Hilde","last_name":"Schneemann"},{"full_name":"Domínguez, Marisol","first_name":"Marisol","last_name":"Domínguez"},{"first_name":"Erik B","full_name":"Dopman, Erik B","last_name":"Dopman"},{"full_name":"Lohse, Konrad","first_name":"Konrad","last_name":"Lohse"},{"first_name":"Sina J","full_name":"Rometsch, Sina J","last_name":"Rometsch"},{"last_name":"Comeault","first_name":"Aaron A","full_name":"Comeault, Aaron A"},{"first_name":"Richard M","full_name":"Merrill, Richard M","last_name":"Merrill"},{"last_name":"Scordato","full_name":"Scordato, Elizabeth S C","first_name":"Elizabeth S C"},{"first_name":"Sonal","full_name":"Singhal, Sonal","last_name":"Singhal"},{"last_name":"Pärssinen","first_name":"Varpu","full_name":"Pärssinen, Varpu"},{"full_name":"Lackey, Alycia C R","first_name":"Alycia C R","last_name":"Lackey"},{"first_name":"Sanghamitra","full_name":"Kumar, Sanghamitra","last_name":"Kumar"},{"last_name":"Meier","first_name":"Joana I","full_name":"Meier, Joana I"},{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","orcid":"0000-0001-8441-5075","first_name":"Christelle","full_name":"Fraisse, Christelle"},{"last_name":"Ravinet","first_name":"Mark","full_name":"Ravinet, Mark"},{"last_name":"Kulmuni","full_name":"Kulmuni, Jonna","first_name":"Jonna"}],"_id":"18949"},{"oa_version":"Published Version","publication_identifier":{"eissn":["1752-4571"]},"department":[{"_id":"NiBa"},{"_id":"BeVi"}],"date_published":"2023-02-01T00:00:00Z","publication_status":"published","date_updated":"2025-04-23T08:49:14Z","external_id":{"pmid":["36793688"],"isi":["000815663700001"]},"publisher":"Wiley","title":"Ten years of demographic modelling of divergence and speciation in the sea","article_processing_charge":"No","month":"02","volume":16,"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).","quality_controlled":"1","status":"public","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_type":"original","author":[{"full_name":"De Jode, Aurélien","first_name":"Aurélien","last_name":"De Jode"},{"full_name":"Le Moan, Alan","first_name":"Alan","last_name":"Le Moan"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"first_name":"Sean","full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski"},{"last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M","first_name":"Anja M","orcid":"0000-0003-1050-4969"},{"first_name":"Roger K.","full_name":"Butlin, Roger K.","last_name":"Butlin"},{"first_name":"Marina","full_name":"Rafajlović, Marina","last_name":"Rafajlović"},{"orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse"}],"intvolume":"        16","file_date_updated":"2023-02-27T07:10:17Z","_id":"11479","day":"01","page":"542-559","isi":1,"doi":"10.1111/eva.13428","scopus_import":"1","oa":1,"pmid":1,"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"],"date_created":"2022-07-03T22:01:33Z","issue":"2","publication":"Evolutionary Applications","file":[{"creator":"dernst","relation":"main_file","access_level":"open_access","date_created":"2023-02-27T07:10:17Z","checksum":"d4d6fa9ddf36643af994a6a757919afb","file_size":2269822,"content_type":"application/pdf","file_id":"12685","date_updated":"2023-02-27T07:10:17Z","file_name":"2023_EvolutionaryApplications_DeJode.pdf","success":1}],"year":"2023","type":"journal_article","citation":{"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>.","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.","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>","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>.","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.","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.","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>"},"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"quality_controlled":"1","status":"public","acknowledgement":"This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 715257) and by the Austrian Science Foundation (FWF SFB F88-10).\r\nWe thank the Vicoso group for comments on the manuscript and the ISTA Scientific computing team and the Vienna Biocenter Sequencing facility for technical support.","volume":222,"month":"10","article_processing_charge":"No","title":"ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp","publisher":"Oxford University Press","publication_status":"published","external_id":{"pmid":["35977389"],"isi":["000850270300001"]},"date_updated":"2026-09-06T22:30:29Z","oa_version":"Published Version","ec_funded":1,"publication_identifier":{"issn":["1943-2631"]},"department":[{"_id":"BeVi"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"date_published":"2022-10-01T00:00:00Z","_id":"12248","file_date_updated":"2023-01-30T08:59:58Z","intvolume":"       222","author":[{"orcid":"0000-0002-5328-7231","first_name":"Marwan N","full_name":"Elkrewi, Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi"},{"id":"5eba06f4-97d8-11ed-9f8f-d826ebdd9434","last_name":"Khauratovich","full_name":"Khauratovich, Uladzislava","first_name":"Uladzislava"},{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups","orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A","first_name":"Melissa A"},{"full_name":"Bett, Vincent K","first_name":"Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425","last_name":"Bett"},{"full_name":"Mrnjavac, Andrea","first_name":"Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","last_name":"Mrnjavac"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon","full_name":"Macon, Ariana","first_name":"Ariana"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","first_name":"Christelle"},{"first_name":"Luca","full_name":"Sax, Luca","id":"701c5602-97d8-11ed-96b5-b52773c70189","last_name":"Sax"},{"last_name":"Huylmans","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","first_name":"Ann K","full_name":"Huylmans, Ann K","orcid":"0000-0001-8871-4961"},{"last_name":"Hontoria","full_name":"Hontoria, Francisco","first_name":"Francisco"},{"last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_type":"original","language":[{"iso":"eng"}],"publication":"Genetics","file":[{"success":1,"file_name":"2022_Genetics_Elkrewi.pdf","date_updated":"2023-01-30T08:59:58Z","content_type":"application/pdf","file_id":"12440","file_size":1347136,"checksum":"f79ff5383e882ea3f95f3da47a78029d","date_created":"2023-01-30T08:59:58Z","relation":"main_file","access_level":"open_access","creator":"dernst"}],"issue":"2","date_created":"2023-01-16T09:56:10Z","ddc":["570"],"project":[{"call_identifier":"H2020","grant_number":"715257","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425"},{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction"}],"abstract":[{"text":"Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species Artemia sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species Artemia sp. Kazakhstan and several asexual lineages of Artemia parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality.","lang":"eng"}],"pmid":1,"doi":"10.1093/genetics/iyac123","scopus_import":"1","oa":1,"day":"01","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","keyword":["Genetics"],"has_accepted_license":"1","related_material":{"record":[{"status":"public","relation":"research_data","id":"11653"},{"id":"19386","relation":"dissertation_contains","status":"public"}]},"citation":{"mla":"Elkrewi, Marwan N., et al. “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.” <i>Genetics</i>, vol. 222, no. 2, iyac123, Oxford University Press, 2022, doi:<a href=\"https://doi.org/10.1093/genetics/iyac123\">10.1093/genetics/iyac123</a>.","ieee":"M. N. Elkrewi <i>et al.</i>, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp,” <i>Genetics</i>, vol. 222, no. 2. Oxford University Press, 2022.","chicago":"Elkrewi, Marwan N, Uladzislava Khauratovich, Melissa A Toups, Vincent K Bett, Andrea Mrnjavac, Ariana Macon, Christelle Fraisse, et al. “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.” <i>Genetics</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/genetics/iyac123\">https://doi.org/10.1093/genetics/iyac123</a>.","apa":"Elkrewi, M. N., Khauratovich, U., Toups, M. A., Bett, V. K., Mrnjavac, A., Macon, A., … Vicoso, B. (2022). ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp. <i>Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/genetics/iyac123\">https://doi.org/10.1093/genetics/iyac123</a>","ista":"Elkrewi MN, Khauratovich U, Toups MA, Bett VK, Mrnjavac A, Macon A, Fraisse C, Sax L, Huylmans AK, Hontoria F, Vicoso B. 2022. ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp. Genetics. 222(2), iyac123.","short":"M.N. Elkrewi, U. Khauratovich, M.A. Toups, V.K. Bett, A. Mrnjavac, A. Macon, C. Fraisse, L. Sax, A.K. Huylmans, F. Hontoria, B. Vicoso, Genetics 222 (2022).","ama":"Elkrewi MN, Khauratovich U, Toups MA, et al. ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp. <i>Genetics</i>. 2022;222(2). doi:<a href=\"https://doi.org/10.1093/genetics/iyac123\">10.1093/genetics/iyac123</a>"},"year":"2022","corr_author":"1","type":"journal_article","article_number":"iyac123"},{"related_material":{"record":[{"relation":"research_data","status":"public","id":"13073"}]},"citation":{"chicago":"Simon, Alexis, Christelle Fraisse, Tahani El Ayari, Cathy Liautard‐Haag, Petr Strelkov, John J Welch, and Nicolas Bierne. “How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels.” <i>Journal of Evolutionary Biology</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/jeb.13709\">https://doi.org/10.1111/jeb.13709</a>.","apa":"Simon, A., Fraisse, C., El Ayari, T., Liautard‐Haag, C., Strelkov, P., Welch, J. J., &#38; Bierne, N. (2021). How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels. <i>Journal of Evolutionary Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jeb.13709\">https://doi.org/10.1111/jeb.13709</a>","ieee":"A. Simon <i>et al.</i>, “How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels,” <i>Journal of Evolutionary Biology</i>, vol. 34, no. 1. Wiley, pp. 208–223, 2021.","mla":"Simon, Alexis, et al. “How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels.” <i>Journal of Evolutionary Biology</i>, vol. 34, no. 1, Wiley, 2021, pp. 208–23, doi:<a href=\"https://doi.org/10.1111/jeb.13709\">10.1111/jeb.13709</a>.","ista":"Simon A, Fraisse C, El Ayari T, Liautard‐Haag C, Strelkov P, Welch JJ, Bierne N. 2021. How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels. Journal of Evolutionary Biology. 34(1), 208–223.","ama":"Simon A, Fraisse C, El Ayari T, et al. How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels. <i>Journal of Evolutionary Biology</i>. 2021;34(1):208-223. doi:<a href=\"https://doi.org/10.1111/jeb.13709\">10.1111/jeb.13709</a>","short":"A. Simon, C. Fraisse, T. El Ayari, C. Liautard‐Haag, P. Strelkov, J.J. Welch, N. Bierne, Journal of Evolutionary Biology 34 (2021) 208–223."},"year":"2021","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://doi.org/10.1101/818559","open_access":"1"}],"abstract":[{"lang":"eng","text":"The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study ‘replicated’ instances of secondary contact between closely related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry‐informative panel of such SNPs. We then compared their frequencies in newly sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi‐stable variants (Dobzhansky‐Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact."}],"pmid":1,"doi":"10.1111/jeb.13709","scopus_import":"1","oa":1,"day":"01","page":"208-223","isi":1,"publication":"Journal of Evolutionary Biology","issue":"1","date_created":"2020-10-25T23:01:20Z","article_type":"original","language":[{"iso":"eng"}],"_id":"8708","intvolume":"        34","author":[{"first_name":"Alexis","full_name":"Simon, Alexis","last_name":"Simon"},{"orcid":"0000-0001-8441-5075","first_name":"Christelle","full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse"},{"first_name":"Tahani","full_name":"El Ayari, Tahani","last_name":"El Ayari"},{"full_name":"Liautard‐Haag, Cathy","first_name":"Cathy","last_name":"Liautard‐Haag"},{"first_name":"Petr","full_name":"Strelkov, Petr","last_name":"Strelkov"},{"first_name":"John J","full_name":"Welch, John J","last_name":"Welch"},{"last_name":"Bierne","first_name":"Nicolas","full_name":"Bierne, Nicolas"}],"article_processing_charge":"No","title":"How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels","publisher":"Wiley","publication_status":"published","external_id":{"isi":["000579599700001"],"pmid":["33045123"]},"date_updated":"2025-07-10T12:01:23Z","oa_version":"Preprint","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publication_identifier":{"eissn":["1420-9101"],"issn":["1010-061X"]},"date_published":"2021-01-01T00:00:00Z","quality_controlled":"1","status":"public","acknowledgement":"Data used in this work were partly produced through the genotyping and sequencing facilities of ISEM and LabEx CeMEB, an ANR ‘Investissements d'avenir’ program (ANR‐10‐LABX‐04‐01) This project benefited from the Montpellier Bioinformatics Biodiversity platform supported by the LabEx CeMEB. We thank Norah Saarman, Grant Pogson, Célia Gosset and Pierre‐Alexandre Gagnaire for providing samples. This work was funded by a Languedoc‐Roussillon ‘Chercheur(se)s d'Avenir’ grant (Connect7 project). P. Strelkov was supported by the Russian Science Foundation project 19‐74‐20024. This is article 2020‐240 of Institut des Sciences de l'Evolution de Montpellier.","volume":34,"month":"01"},{"volume":34,"month":"02","quality_controlled":"1","status":"public","acknowledgement":"This work was supported by the EU Marie Curie Career Integration grant (FP7‐PEOPLE‐2011‐CIG grant agreement PCIG10‐GA‐2011‐304164) attributed to CS. SA was supported by a PhD fellowship from the French Région PACA and the Plant Breeding division of INRA, in partnership with Gautier Semences. CF was supported by an Austrian Science Foundation FWF grant (Project M 2463‐B29). Authors thank Mathilde Causse and Beatriz Vicoso for their team leading. Thanks to the Italian Eggplant Genome Consortium, which includes the DISAFA, Plant Genetics and Breeding (University of Torino), the Biotechnology Department (University of Verona), the CREA‐ORL in Montanaso Lombardo (LO) and the ENEA in Rome for providing access to the eggplant genome reference. Thanks to CRB‐lég ( https://www6.paca.inra.fr/gafl_eng/Vegetables-GRC ) for managing and providing the genetic resources, to Marie‐Christine Daunay and Alain Palloix (INRA UR1052) for assistance in choosing the biological material used, to Muriel Latreille and Sylvain Santoni from the UMR AGAP (INRA Montpellier, France) for their help with RNAseq library preparation, to Jean‐Paul Bouchet and Jacques Lagnel (INRA UR1052) for their Bioinformatics assistance.","publication_status":"published","external_id":{"pmid":["33107098"],"isi":["000587769700001"]},"date_updated":"2026-06-18T19:37:17Z","oa_version":"Published Version","department":[{"_id":"NiBa"}],"date_published":"2021-02-01T00:00:00Z","publication_identifier":{"issn":["1010-061X"],"eissn":["1420-9101"]},"article_processing_charge":"No","publisher":"Wiley","title":"Genomic inference of complex domestication histories in three Solanaceae species","intvolume":"        34","author":[{"last_name":"Arnoux","first_name":"Stéphanie","full_name":"Arnoux, Stéphanie"},{"last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle","first_name":"Christelle","orcid":"0000-0001-8441-5075"},{"first_name":"Christopher","full_name":"Sauvage, Christopher","last_name":"Sauvage"}],"_id":"8928","article_type":"original","language":[{"iso":"eng"}],"date_created":"2020-12-06T23:01:16Z","issue":"2","ddc":["570"],"publication":"Journal of Evolutionary Biology","doi":"10.1111/jeb.13723","scopus_import":"1","oa":1,"page":"270-283","day":"01","isi":1,"project":[{"call_identifier":"FWF","grant_number":"M02463","name":"Sex chromosomes and species barriers","_id":"2662AADE-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jeb.13723"}],"abstract":[{"lang":"eng","text":"Domestication is a human‐induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species‐specific demographic processes between species. A convergent history of domestication with gene flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species‐specific and supported by the few historical records available."}],"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021","type":"journal_article","related_material":{"record":[{"status":"public","relation":"research_data","id":"13065"}]},"citation":{"apa":"Arnoux, S., Fraisse, C., &#38; Sauvage, C. (2021). Genomic inference of complex domestication histories in three Solanaceae species. <i>Journal of Evolutionary Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jeb.13723\">https://doi.org/10.1111/jeb.13723</a>","chicago":"Arnoux, Stéphanie, Christelle Fraisse, and Christopher Sauvage. “Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” <i>Journal of Evolutionary Biology</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/jeb.13723\">https://doi.org/10.1111/jeb.13723</a>.","ieee":"S. Arnoux, C. Fraisse, and C. Sauvage, “Genomic inference of complex domestication histories in three Solanaceae species,” <i>Journal of Evolutionary Biology</i>, vol. 34, no. 2. Wiley, pp. 270–283, 2021.","mla":"Arnoux, Stéphanie, et al. “Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” <i>Journal of Evolutionary Biology</i>, vol. 34, no. 2, Wiley, 2021, pp. 270–83, doi:<a href=\"https://doi.org/10.1111/jeb.13723\">10.1111/jeb.13723</a>.","ista":"Arnoux S, Fraisse C, Sauvage C. 2021. Genomic inference of complex domestication histories in three Solanaceae species. Journal of Evolutionary Biology. 34(2), 270–283.","short":"S. Arnoux, C. Fraisse, C. Sauvage, Journal of Evolutionary Biology 34 (2021) 270–283.","ama":"Arnoux S, Fraisse C, Sauvage C. Genomic inference of complex domestication histories in three Solanaceae species. <i>Journal of Evolutionary Biology</i>. 2021;34(2):270-283. doi:<a href=\"https://doi.org/10.1111/jeb.13723\">10.1111/jeb.13723</a>"}},{"citation":{"ista":"Fraisse C, Popovic I, Mazoyer C, Spataro B, Delmotte S, Romiguier J, Loire É, Simon A, Galtier N, Duret L, Bierne N, Vekemans X, Roux C. 2021. DILS: Demographic inferences with linked selection by using ABC. Molecular Ecology Resources. 21, 2629–2644.","ama":"Fraisse C, Popovic I, Mazoyer C, et al. DILS: Demographic inferences with linked selection by using ABC. <i>Molecular Ecology Resources</i>. 2021;21:2629-2644. doi:<a href=\"https://doi.org/10.1111/1755-0998.13323\">10.1111/1755-0998.13323</a>","short":"C. Fraisse, I. Popovic, C. Mazoyer, B. Spataro, S. Delmotte, J. Romiguier, É. Loire, A. Simon, N. Galtier, L. Duret, N. Bierne, X. Vekemans, C. Roux, Molecular Ecology Resources 21 (2021) 2629–2644.","chicago":"Fraisse, Christelle, Iva Popovic, Clément Mazoyer, Bruno Spataro, Stéphane Delmotte, Jonathan Romiguier, Étienne Loire, et al. “DILS: Demographic Inferences with Linked Selection by Using ABC.” <i>Molecular Ecology Resources</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/1755-0998.13323\">https://doi.org/10.1111/1755-0998.13323</a>.","apa":"Fraisse, C., Popovic, I., Mazoyer, C., Spataro, B., Delmotte, S., Romiguier, J., … Roux, C. (2021). DILS: Demographic inferences with linked selection by using ABC. <i>Molecular Ecology Resources</i>. Wiley. <a href=\"https://doi.org/10.1111/1755-0998.13323\">https://doi.org/10.1111/1755-0998.13323</a>","mla":"Fraisse, Christelle, et al. “DILS: Demographic Inferences with Linked Selection by Using ABC.” <i>Molecular Ecology Resources</i>, vol. 21, Wiley, 2021, pp. 2629–44, doi:<a href=\"https://doi.org/10.1111/1755-0998.13323\">10.1111/1755-0998.13323</a>.","ieee":"C. Fraisse <i>et al.</i>, “DILS: Demographic inferences with linked selection by using ABC,” <i>Molecular Ecology Resources</i>, vol. 21. Wiley, pp. 2629–2644, 2021."},"corr_author":"1","year":"2021","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.06.15.151597v2"}],"abstract":[{"text":"We present DILS, a deployable statistical analysis platform for conducting demographic inferences with linked selection from population genomic data using an Approximate Bayesian Computation framework. DILS takes as input single‐population or two‐population data sets (multilocus fasta sequences) and performs three types of analyses in a hierarchical manner, identifying: (a) the best demographic model to study the importance of gene flow and population size change on the genetic patterns of polymorphism and divergence, (b) the best genomic model to determine whether the effective size Ne and migration rate N, m are heterogeneously distributed along the genome (implying linked selection) and (c) loci in genomic regions most associated with barriers to gene flow. Also available via a Web interface, an objective of DILS is to facilitate collaborative research in speciation genomics. Here, we show the performance and limitations of DILS by using simulations and finally apply the method to published data on a divergence continuum composed by 28 pairs of Mytilus mussel populations/species.","lang":"eng"}],"isi":1,"day":"15","page":"2629-2644","doi":"10.1111/1755-0998.13323","scopus_import":"1","oa":1,"publication":"Molecular Ecology Resources","date_created":"2021-02-14T23:01:14Z","language":[{"iso":"eng"}],"article_type":"original","_id":"9119","author":[{"last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle","first_name":"Christelle","orcid":"0000-0001-8441-5075"},{"full_name":"Popovic, Iva","first_name":"Iva","last_name":"Popovic"},{"full_name":"Mazoyer, Clément","first_name":"Clément","last_name":"Mazoyer"},{"last_name":"Spataro","first_name":"Bruno","full_name":"Spataro, Bruno"},{"last_name":"Delmotte","first_name":"Stéphane","full_name":"Delmotte, Stéphane"},{"last_name":"Romiguier","full_name":"Romiguier, Jonathan","first_name":"Jonathan"},{"last_name":"Loire","first_name":"Étienne","full_name":"Loire, Étienne"},{"first_name":"Alexis","full_name":"Simon, Alexis","last_name":"Simon"},{"last_name":"Galtier","full_name":"Galtier, Nicolas","first_name":"Nicolas"},{"full_name":"Duret, Laurent","first_name":"Laurent","last_name":"Duret"},{"last_name":"Bierne","first_name":"Nicolas","full_name":"Bierne, Nicolas"},{"first_name":"Xavier","full_name":"Vekemans, Xavier","last_name":"Vekemans"},{"full_name":"Roux, Camille","first_name":"Camille","last_name":"Roux"}],"intvolume":"        21","title":"DILS: Demographic inferences with linked selection by using ABC","publisher":"Wiley","article_processing_charge":"No","oa_version":"Preprint","publication_identifier":{"issn":["1755-098X"],"eissn":["1755-0998"]},"department":[{"_id":"NiBa"}],"date_published":"2021-01-15T00:00:00Z","publication_status":"published","date_updated":"2025-06-12T06:34:23Z","external_id":{"isi":["000614183100001"],"pmid":["33448666"]},"quality_controlled":"1","status":"public","month":"01","volume":21},{"citation":{"ista":"Fraisse C, Sachdeva H. 2021. The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. Genetics. 217(2), iyaa025.","ama":"Fraisse C, Sachdeva H. The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. <i>Genetics</i>. 2021;217(2). doi:<a href=\"https://doi.org/10.1093/genetics/iyaa025\">10.1093/genetics/iyaa025</a>","short":"C. Fraisse, H. Sachdeva, Genetics 217 (2021).","apa":"Fraisse, C., &#38; Sachdeva, H. (2021). The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1093/genetics/iyaa025\">https://doi.org/10.1093/genetics/iyaa025</a>","chicago":"Fraisse, Christelle, and Himani Sachdeva. “The Rates of Introgression and Barriers to Genetic Exchange between Hybridizing Species: Sex Chromosomes vs Autosomes.” <i>Genetics</i>. Genetics Society of America, 2021. <a href=\"https://doi.org/10.1093/genetics/iyaa025\">https://doi.org/10.1093/genetics/iyaa025</a>.","mla":"Fraisse, Christelle, and Himani Sachdeva. “The Rates of Introgression and Barriers to Genetic Exchange between Hybridizing Species: Sex Chromosomes vs Autosomes.” <i>Genetics</i>, vol. 217, no. 2, iyaa025, Genetics Society of America, 2021, doi:<a href=\"https://doi.org/10.1093/genetics/iyaa025\">10.1093/genetics/iyaa025</a>.","ieee":"C. Fraisse and H. Sachdeva, “The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes,” <i>Genetics</i>, vol. 217, no. 2. Genetics Society of America, 2021."},"article_number":"iyaa025","corr_author":"1","year":"2021","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher","pmid":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/genetics/iyaa025"}],"project":[{"call_identifier":"FWF","name":"Sex chromosomes and species barriers","grant_number":"M02463","_id":"2662AADE-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"Interspecific crossing experiments have shown that sex chromosomes play a major role in reproductive isolation between many pairs of species. However, their ability to act as reproductive barriers, which hamper interspecific genetic exchange, has rarely been evaluated quantitatively compared to Autosomes. This genome-wide limitation of gene flow is essential for understanding the complete separation of species, and thus speciation. Here, we develop a mainland-island model of secondary contact between hybridizing species of an XY (or ZW) sexual system. We obtain theoretical predictions for the frequency of introgressed alleles, and the strength of the barrier to neutral gene flow for the two types of chromosomes carrying multiple interspecific barrier loci. Theoretical predictions are obtained for scenarios where introgressed alleles are rare. We show that the same analytical expressions apply for sex chromosomes and autosomes, but with different sex-averaged effective parameters. The specific features of sex chromosomes (hemizygosity and absence of recombination in the heterogametic sex) lead to reduced levels of introgression on the X (or Z) compared to autosomes. This effect can be enhanced by certain types of sex-biased forces, but it remains overall small (except when alleles causing incompatibilities are recessive). We discuss these predictions in the light of empirical data comprising model-based tests of introgression and cline surveys in various biological systems.","lang":"eng"}],"isi":1,"day":"01","doi":"10.1093/genetics/iyaa025","scopus_import":"1","oa":1,"publication":"Genetics","ddc":["570"],"date_created":"2021-02-18T14:41:30Z","issue":"2","language":[{"iso":"eng"}],"OA_type":"free access","article_type":"original","_id":"9168","author":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","first_name":"Christelle"},{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","last_name":"Sachdeva","first_name":"Himani","full_name":"Sachdeva, Himani"}],"intvolume":"       217","publisher":"Genetics Society of America","title":"The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes","article_processing_charge":"No","oa_version":"Published Version","acknowledged_ssus":[{"_id":"ScienComp"}],"department":[{"_id":"NiBa"}],"publication_identifier":{"issn":["1943-2631"]},"date_published":"2021-02-01T00:00:00Z","publication_status":"published","external_id":{"pmid":["33724409"],"isi":["000637218100005"]},"date_updated":"2026-07-28T12:39:03Z","acknowledgement":"The computations were performed with the IST Austria High-Performance Computing (HPC) Cluster and the Institut Français de Bioinformatique (IFB) Core Cluster. We are grateful to Nick Barton and Beatriz Vicoso for critical comments on the model and the manuscript. We also thank Brian Charlesworth, Stuart Baird, and an anonymous reviewer for insightful comments.\r\nC.F. was supported by an Austrian Science Foundation FWF grant (Project M 2463-B29).","quality_controlled":"1","status":"public","month":"02","volume":217},{"oa_version":"Published Version","date_published":"2020-10-19T00:00:00Z","department":[{"_id":"NiBa"}],"day":"19","doi":"10.5061/DRYAD.Q2BVQ83HD","date_updated":"2026-06-18T19:37:16Z","oa":1,"publisher":"Dryad","title":"VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.q2bvq83hd"}],"article_processing_charge":"No","abstract":[{"text":"Domestication is a human-induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale, and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species-specific demographic processes between species. A convergent history of domestication with gene-flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species-specific and supported by the few historical records available.","lang":"eng"}],"month":"10","ddc":["570"],"date_created":"2023-05-23T16:30:20Z","status":"public","year":"2020","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"type":"research_data_reference","related_material":{"link":[{"url":"https://github.com/starnoux/arnoux_et_al_2019","relation":"software"}],"record":[{"relation":"used_in_publication","status":"public","id":"8928"}]},"citation":{"chicago":"Arnoux, Stephanie, Christelle Fraisse, and Christopher Sauvage. “VCF Files of Synonymous SNPs Related to: Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” Dryad, 2020. <a href=\"https://doi.org/10.5061/DRYAD.Q2BVQ83HD\">https://doi.org/10.5061/DRYAD.Q2BVQ83HD</a>.","apa":"Arnoux, S., Fraisse, C., &#38; Sauvage, C. (2020). VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species. Dryad. <a href=\"https://doi.org/10.5061/DRYAD.Q2BVQ83HD\">https://doi.org/10.5061/DRYAD.Q2BVQ83HD</a>","mla":"Arnoux, Stephanie, et al. <i>VCF Files of Synonymous SNPs Related to: Genomic Inference of Complex Domestication Histories in Three Solanaceae Species</i>. Dryad, 2020, doi:<a href=\"https://doi.org/10.5061/DRYAD.Q2BVQ83HD\">10.5061/DRYAD.Q2BVQ83HD</a>.","ieee":"S. Arnoux, C. Fraisse, and C. Sauvage, “VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species.” Dryad, 2020.","short":"S. Arnoux, C. Fraisse, C. Sauvage, (2020).","ama":"Arnoux S, Fraisse C, Sauvage C. VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species. 2020. doi:<a href=\"https://doi.org/10.5061/DRYAD.Q2BVQ83HD\">10.5061/DRYAD.Q2BVQ83HD</a>","ista":"Arnoux S, Fraisse C, Sauvage C. 2020. VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species, Dryad, <a href=\"https://doi.org/10.5061/DRYAD.Q2BVQ83HD\">10.5061/DRYAD.Q2BVQ83HD</a>."},"author":[{"last_name":"Arnoux","first_name":"Stephanie","full_name":"Arnoux, Stephanie"},{"orcid":"0000-0001-8441-5075","first_name":"Christelle","full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse"},{"full_name":"Sauvage, Christopher","first_name":"Christopher","last_name":"Sauvage"}],"license":"https://creativecommons.org/publicdomain/zero/1.0/","_id":"13065","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"year":"2020","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"type":"research_data_reference","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8708"}]},"citation":{"ieee":"A. Simon <i>et al.</i>, “How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels.” Dryad, 2020.","mla":"Simon, Alexis, et al. <i>How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels</i>. Dryad, 2020, doi:<a href=\"https://doi.org/10.5061/DRYAD.R4XGXD29N\">10.5061/DRYAD.R4XGXD29N</a>.","chicago":"Simon, Alexis, Christelle Fraisse, Tahani El Ayari, Cathy Liautard-Haag, Petr Strelkov, John Welch, and Nicolas Bierne. “How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels.” Dryad, 2020. <a href=\"https://doi.org/10.5061/DRYAD.R4XGXD29N\">https://doi.org/10.5061/DRYAD.R4XGXD29N</a>.","apa":"Simon, A., Fraisse, C., El Ayari, T., Liautard-Haag, C., Strelkov, P., Welch, J., &#38; Bierne, N. (2020). How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels. Dryad. <a href=\"https://doi.org/10.5061/DRYAD.R4XGXD29N\">https://doi.org/10.5061/DRYAD.R4XGXD29N</a>","short":"A. Simon, C. Fraisse, T. El Ayari, C. Liautard-Haag, P. Strelkov, J. Welch, N. Bierne, (2020).","ama":"Simon A, Fraisse C, El Ayari T, et al. How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels. 2020. doi:<a href=\"https://doi.org/10.5061/DRYAD.R4XGXD29N\">10.5061/DRYAD.R4XGXD29N</a>","ista":"Simon A, Fraisse C, El Ayari T, Liautard-Haag C, Strelkov P, Welch J, Bierne N. 2020. How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels, Dryad, <a href=\"https://doi.org/10.5061/DRYAD.R4XGXD29N\">10.5061/DRYAD.R4XGXD29N</a>."},"author":[{"last_name":"Simon","full_name":"Simon, Alexis","first_name":"Alexis"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","first_name":"Christelle"},{"first_name":"Tahani","full_name":"El Ayari, Tahani","last_name":"El Ayari"},{"full_name":"Liautard-Haag, Cathy","first_name":"Cathy","last_name":"Liautard-Haag"},{"last_name":"Strelkov","first_name":"Petr","full_name":"Strelkov, Petr"},{"first_name":"John","full_name":"Welch, John","last_name":"Welch"},{"full_name":"Bierne, Nicolas","first_name":"Nicolas","last_name":"Bierne"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13073","doi":"10.5061/DRYAD.R4XGXD29N","oa":1,"date_updated":"2025-07-10T12:01:22Z","oa_version":"Published Version","department":[{"_id":"NiBa"}],"day":"22","date_published":"2020-09-22T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.5061/dryad.r4xgxd29n","open_access":"1"}],"abstract":[{"text":"The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study \"replicated\" instances of secondary contact between closely-related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry-informative panel of such SNPs. We then compared their frequencies in newly-sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi-stable variants (Dobzhansky-Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact.","lang":"eng"}],"article_processing_charge":"No","title":"How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels","publisher":"Dryad","date_created":"2023-05-23T16:48:27Z","month":"09","ddc":["570"],"status":"public"},{"abstract":[{"lang":"eng","text":"Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA. Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations."}],"article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.7957472.v1","open_access":"1"}],"publisher":"Royal Society of London","title":"Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes","oa":1,"date_updated":"2026-06-18T19:05:02Z","doi":"10.6084/m9.figshare.7957472.v1","day":"15","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"date_published":"2020-10-15T00:00:00Z","oa_version":"Published Version","status":"public","date_created":"2021-08-06T11:18:15Z","month":"10","citation":{"ama":"Fraisse C, Welch JJ. Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes. 2020. doi:<a href=\"https://doi.org/10.6084/m9.figshare.7957472.v1\">10.6084/m9.figshare.7957472.v1</a>","short":"C. Fraisse, J.J. Welch, (2020).","ista":"Fraisse C, Welch JJ. 2020. Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes, Royal Society of London, <a href=\"https://doi.org/10.6084/m9.figshare.7957472.v1\">10.6084/m9.figshare.7957472.v1</a>.","mla":"Fraisse, Christelle, and John J. Welch. <i>Simulation Code for Fig S2 from the Distribution of Epistasis on Simple Fitness Landscapes</i>. Royal Society of London, 2020, doi:<a href=\"https://doi.org/10.6084/m9.figshare.7957472.v1\">10.6084/m9.figshare.7957472.v1</a>.","ieee":"C. Fraisse and J. J. Welch, “Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes.” Royal Society of London, 2020.","chicago":"Fraisse, Christelle, and John J. Welch. “Simulation Code for Fig S2 from the Distribution of Epistasis on Simple Fitness Landscapes.” Royal Society of London, 2020. <a href=\"https://doi.org/10.6084/m9.figshare.7957472.v1\">https://doi.org/10.6084/m9.figshare.7957472.v1</a>.","apa":"Fraisse, C., &#38; Welch, J. J. (2020). Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes. Royal Society of London. <a href=\"https://doi.org/10.6084/m9.figshare.7957472.v1\">https://doi.org/10.6084/m9.figshare.7957472.v1</a>"},"related_material":{"record":[{"id":"6467","status":"public","relation":"used_in_publication"}]},"type":"research_data_reference","OA_type":"hybrid","year":"2020","user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","_id":"9798","author":[{"full_name":"Fraisse, Christelle","first_name":"Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Welch, John J.","first_name":"John J.","last_name":"Welch"}],"OA_place":"publisher"},{"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"6467"}]},"citation":{"chicago":"Fraisse, Christelle, and John J. Welch. “Simulation Code for Fig S1 from the Distribution of Epistasis on Simple Fitness Landscapes.” Royal Society of London, 2020. <a href=\"https://doi.org/10.6084/m9.figshare.7957469.v1\">https://doi.org/10.6084/m9.figshare.7957469.v1</a>.","apa":"Fraisse, C., &#38; Welch, J. J. (2020). Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes. Royal Society of London. <a href=\"https://doi.org/10.6084/m9.figshare.7957469.v1\">https://doi.org/10.6084/m9.figshare.7957469.v1</a>","ieee":"C. Fraisse and J. J. Welch, “Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes.” Royal Society of London, 2020.","mla":"Fraisse, Christelle, and John J. Welch. <i>Simulation Code for Fig S1 from the Distribution of Epistasis on Simple Fitness Landscapes</i>. Royal Society of London, 2020, doi:<a href=\"https://doi.org/10.6084/m9.figshare.7957469.v1\">10.6084/m9.figshare.7957469.v1</a>.","ama":"Fraisse C, Welch JJ. Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes. 2020. doi:<a href=\"https://doi.org/10.6084/m9.figshare.7957469.v1\">10.6084/m9.figshare.7957469.v1</a>","short":"C. Fraisse, J.J. Welch, (2020).","ista":"Fraisse C, Welch JJ. 2020. Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes, Royal Society of London, <a href=\"https://doi.org/10.6084/m9.figshare.7957469.v1\">10.6084/m9.figshare.7957469.v1</a>."},"year":"2020","OA_type":"hybrid","type":"research_data_reference","user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","_id":"9799","OA_place":"publisher","author":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","orcid":"0000-0001-8441-5075","first_name":"Christelle","full_name":"Fraisse, Christelle"},{"full_name":"Welch, John J.","first_name":"John J.","last_name":"Welch"}],"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.7957469.v1","open_access":"1"}],"article_processing_charge":"No","abstract":[{"lang":"eng","text":"Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA. Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations."}],"publisher":"Royal Society of London","title":"Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes","doi":"10.6084/m9.figshare.7957469.v1","oa":1,"date_updated":"2026-06-18T19:05:02Z","oa_version":"Published Version","day":"15","date_published":"2020-10-15T00:00:00Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"status":"public","date_created":"2021-08-06T11:26:57Z","month":"10"},{"date_created":"2019-03-10T22:59:19Z","issue":"3","publication":"Molecular biology and evolution","scopus_import":"1","doi":"10.1093/molbev/msy246","oa":1,"day":"01","isi":1,"page":"500-515","project":[{"call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425","grant_number":"P28842-B22","name":"Sex chromosome evolution under male- and female- heterogamety"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30590559","open_access":"1"}],"abstract":[{"text":"Pleiotropy is the well-established idea that a single mutation affects multiple phenotypes. If a mutation has opposite effects on fitness when expressed in different contexts, then genetic conflict arises. Pleiotropic conflict is expected to reduce the efficacy of selection by limiting the fixation of beneficial mutations through adaptation, and the removal of deleterious mutations through purifying selection. Although this has been widely discussed, in particular in the context of a putative “gender load,” it has yet to be systematically quantified. In this work, we empirically estimate to which extent different pleiotropic regimes impede the efficacy of selection in Drosophila melanogaster. We use whole-genome polymorphism data from a single African population and divergence data from D. simulans to estimate the fraction of adaptive fixations (α), the rate of adaptation (ωA), and the direction of selection (DoS). After controlling for confounding covariates, we find that the different pleiotropic regimes have a relatively small, but significant, effect on selection efficacy. Specifically, our results suggest that pleiotropic sexual antagonism may restrict the efficacy of selection, but that this conflict can be resolved by limiting the expression of genes to the sex where they are beneficial. Intermediate levels of pleiotropy across tissues and life stages can also lead to maladaptation in D. melanogaster, due to inefficient purifying selection combined with low frequency of mutations that confer a selective advantage. Thus, our study highlights the need to consider the efficacy of selection in the context of antagonistic pleiotropy, and of genetic conflict in general.","lang":"eng"}],"pmid":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2019","type":"journal_article","related_material":{"record":[{"relation":"popular_science","status":"public","id":"5757"}]},"citation":{"ista":"Fraisse C, Puixeu Sala G, Vicoso B. 2019. Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular biology and evolution. 36(3), 500–515.","ama":"Fraisse C, Puixeu Sala G, Vicoso B. Pleiotropy modulates the efficacy of selection in drosophila melanogaster. <i>Molecular biology and evolution</i>. 2019;36(3):500-515. doi:<a href=\"https://doi.org/10.1093/molbev/msy246\">10.1093/molbev/msy246</a>","short":"C. Fraisse, G. Puixeu Sala, B. Vicoso, Molecular Biology and Evolution 36 (2019) 500–515.","chicago":"Fraisse, Christelle, Gemma Puixeu Sala, and Beatriz Vicoso. “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2019. <a href=\"https://doi.org/10.1093/molbev/msy246\">https://doi.org/10.1093/molbev/msy246</a>.","apa":"Fraisse, C., Puixeu Sala, G., &#38; Vicoso, B. (2019). Pleiotropy modulates the efficacy of selection in drosophila melanogaster. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msy246\">https://doi.org/10.1093/molbev/msy246</a>","ieee":"C. Fraisse, G. Puixeu Sala, and B. Vicoso, “Pleiotropy modulates the efficacy of selection in drosophila melanogaster,” <i>Molecular biology and evolution</i>, vol. 36, no. 3. Oxford University Press, pp. 500–515, 2019.","mla":"Fraisse, Christelle, et al. “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” <i>Molecular Biology and Evolution</i>, vol. 36, no. 3, Oxford University Press, 2019, pp. 500–15, doi:<a href=\"https://doi.org/10.1093/molbev/msy246\">10.1093/molbev/msy246</a>."},"volume":36,"month":"03","quality_controlled":"1","status":"public","publication_status":"published","date_updated":"2025-04-15T08:18:38Z","external_id":{"isi":["000462585100006"],"pmid":["30590559"]},"oa_version":"Submitted Version","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"date_published":"2019-03-01T00:00:00Z","publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"article_processing_charge":"No","publisher":"Oxford University Press","title":"Pleiotropy modulates the efficacy of selection in drosophila melanogaster","intvolume":"        36","author":[{"orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse"},{"orcid":"0000-0001-8330-1754","first_name":"Gemma","full_name":"Puixeu Sala, Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","last_name":"Puixeu Sala"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","first_name":"Beatriz"}],"_id":"6089","language":[{"iso":"eng"}]},{"year":"2019","type":"journal_article","citation":{"ama":"Field D, Fraisse C. Breaking down barriers in morning glories. <i>Molecular ecology</i>. 2019;28(7):1579-1581. doi:<a href=\"https://doi.org/10.1111/mec.15048\">10.1111/mec.15048</a>","short":"D. Field, C. Fraisse, Molecular Ecology 28 (2019) 1579–1581.","ista":"Field D, Fraisse C. 2019. Breaking down barriers in morning glories. Molecular ecology. 28(7), 1579–1581.","apa":"Field, D., &#38; Fraisse, C. (2019). Breaking down barriers in morning glories. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.15048\">https://doi.org/10.1111/mec.15048</a>","chicago":"Field, David, and Christelle Fraisse. “Breaking down Barriers in Morning Glories.” <i>Molecular Ecology</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/mec.15048\">https://doi.org/10.1111/mec.15048</a>.","ieee":"D. Field and C. Fraisse, “Breaking down barriers in morning glories,” <i>Molecular ecology</i>, vol. 28, no. 7. Wiley, pp. 1579–1581, 2019.","mla":"Field, David, and Christelle Fraisse. “Breaking down Barriers in Morning Glories.” <i>Molecular Ecology</i>, vol. 28, no. 7, Wiley, 2019, pp. 1579–81, doi:<a href=\"https://doi.org/10.1111/mec.15048\">10.1111/mec.15048</a>."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","has_accepted_license":"1","scopus_import":"1","doi":"10.1111/mec.15048","oa":1,"isi":1,"day":"01","page":"1579-1581","abstract":[{"text":"One of the most striking and consistent results in speciation genomics is the heterogeneous divergence observed across the genomes of closely related species. This pattern was initially attributed to different levels of gene exchange—with divergence preserved at loci generating a barrier to gene flow but homogenized at unlinked neutral loci. Although there is evidence to support this model, it is now recognized that interpreting patterns of divergence across genomes is not so straightforward. One \r\nproblem is that heterogenous divergence between populations can also be generated by other processes (e.g. recurrent selective sweeps or background selection) without any involvement of differential gene flow. Thus, integrated studies that identify which loci are likely subject to divergent selection are required to shed light on the interplay between selection and gene flow during the early phases of speciation. In this issue of Molecular Ecology, Rifkin et al. (2019) confront this challenge using a pair of sister morning glory species. They wisely design their sampling to take the geographic context of individuals into account, including geographically isolated (allopatric) and co‐occurring (sympatric) populations. This enabled them to show that individuals are phenotypically less differentiated in sympatry. They also found that the loci that resist introgression are enriched for those most differentiated in allopatry and loci that exhibit signals of divergent selection. One great strength of the \r\nstudy is the combination of methods from population genetics and molecular evolution, including the development of a model to simultaneously infer admixture proportions and selfing rates.","lang":"eng"}],"issue":"7","date_created":"2019-05-19T21:59:15Z","ddc":["580","576"],"file":[{"date_created":"2019-05-20T11:49:06Z","file_size":367711,"checksum":"521e3aff3e9263ddf2ffbfe0b6157715","access_level":"open_access","relation":"main_file","creator":"dernst","date_updated":"2020-07-14T12:47:31Z","file_name":"2019_MolecularEcology_Field.pdf","content_type":"application/pdf","file_id":"6472"}],"publication":"Molecular ecology","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}],"intvolume":"        28","file_date_updated":"2020-07-14T12:47:31Z","author":[{"orcid":"0000-0002-4014-8478","first_name":"David","full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","orcid":"0000-0001-8441-5075","first_name":"Christelle","full_name":"Fraisse, Christelle"}],"_id":"6466","publication_status":"published","date_updated":"2026-04-16T08:33:17Z","external_id":{"isi":["000474808300001"]},"oa_version":"Published Version","department":[{"_id":"NiBa"}],"publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"date_published":"2019-04-01T00:00:00Z","article_processing_charge":"No","publisher":"Wiley","title":"Breaking down barriers in morning glories","volume":28,"month":"04","quality_controlled":"1","status":"public"},{"oa_version":"Published Version","ec_funded":1,"publication_identifier":{"eissn":["1744-957X"],"issn":["1744-9561"]},"date_published":"2019-04-03T00:00:00Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publication_status":"published","date_updated":"2026-06-18T19:05:03Z","external_id":{"isi":["000465405300010"],"pmid":["31014191"]},"title":"The distribution of epistasis on simple fitness landscapes","publisher":"Royal Society of London","article_processing_charge":"No","month":"04","volume":15,"quality_controlled":"1","status":"public","language":[{"iso":"eng"}],"article_type":"original","author":[{"last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075"},{"last_name":"Welch","full_name":"Welch, John J.","first_name":"John J."}],"intvolume":"        15","_id":"6467","isi":1,"day":"03","scopus_import":"1","doi":"10.1098/rsbl.2018.0881","oa":1,"pmid":1,"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"main_file_link":[{"url":"https://doi.org/10.1098/rsbl.2018.0881","open_access":"1"}],"abstract":[{"lang":"eng","text":"Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA (small nucleolar RNA). Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations."}],"ddc":["570"],"date_created":"2019-05-19T21:59:15Z","issue":"4","publication":"Biology Letters","article_number":"0881","year":"2019","type":"journal_article","related_material":{"link":[{"url":"https://dx.doi.org/10.6084/m9.figshare.c.4461008","relation":"supplementary_material"}],"record":[{"id":"9799","status":"public","relation":"research_data"},{"relation":"research_data","status":"public","id":"9798"}]},"citation":{"short":"C. Fraisse, J.J. Welch, Biology Letters 15 (2019).","ama":"Fraisse C, Welch JJ. The distribution of epistasis on simple fitness landscapes. <i>Biology Letters</i>. 2019;15(4). doi:<a href=\"https://doi.org/10.1098/rsbl.2018.0881\">10.1098/rsbl.2018.0881</a>","ista":"Fraisse C, Welch JJ. 2019. The distribution of epistasis on simple fitness landscapes. Biology Letters. 15(4), 0881.","apa":"Fraisse, C., &#38; Welch, J. J. (2019). The distribution of epistasis on simple fitness landscapes. <i>Biology Letters</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rsbl.2018.0881\">https://doi.org/10.1098/rsbl.2018.0881</a>","chicago":"Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple Fitness Landscapes.” <i>Biology Letters</i>. Royal Society of London, 2019. <a href=\"https://doi.org/10.1098/rsbl.2018.0881\">https://doi.org/10.1098/rsbl.2018.0881</a>.","ieee":"C. Fraisse and J. J. Welch, “The distribution of epistasis on simple fitness landscapes,” <i>Biology Letters</i>, vol. 15, no. 4. Royal Society of London, 2019.","mla":"Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple Fitness Landscapes.” <i>Biology Letters</i>, vol. 15, no. 4, 0881, Royal Society of London, 2019, doi:<a href=\"https://doi.org/10.1098/rsbl.2018.0881\">10.1098/rsbl.2018.0881</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"oa_version":"Published Version","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646X"]},"ec_funded":1,"date_published":"2019-11-01T00:00:00Z","department":[{"_id":"NiBa"}],"publication_status":"published","external_id":{"pmid":["31505037"]},"date_updated":"2026-07-28T13:22:14Z","publisher":"Wiley","title":"Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow","article_processing_charge":"Yes (via OA deal)","month":"11","volume":224,"quality_controlled":"1","status":"public","language":[{"iso":"eng"}],"article_type":"original","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"OA_type":"hybrid","author":[{"first_name":"Melinda","full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"},{"full_name":"Brandvain, Yaniv","first_name":"Yaniv","last_name":"Brandvain"},{"first_name":"Christelle","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Yakimowski","full_name":"Yakimowski, Sarah","first_name":"Sarah"},{"last_name":"Dixit","full_name":"Dixit, Tanmay","first_name":"Tanmay"},{"full_name":"Lexer, Christian","first_name":"Christian","last_name":"Lexer"},{"full_name":"Cereghetti, Eva","first_name":"Eva","id":"71AA91B4-05ED-11EA-8BEB-F5833E63BD63","last_name":"Cereghetti"},{"first_name":"David","full_name":"Field, David","orcid":"0000-0002-4014-8478","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87"}],"intvolume":"       224","file_date_updated":"2020-07-14T12:47:42Z","_id":"6856","day":"01","page":"1035-1047","scopus_import":"1","doi":"10.1111/nph.16180","oa":1,"pmid":1,"project":[{"call_identifier":"FP7","_id":"25B36484-B435-11E9-9278-68D0E5697425","grant_number":"329960","name":"Mating system and the evolutionary dynamics of hybrid zones"},{"call_identifier":"FWF","name":"Sex chromosomes and species barriers","grant_number":"M02463","_id":"2662AADE-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"Plant mating systems play a key role in structuring genetic variation both within and between species. In hybrid zones, the outcomes and dynamics of hybridization are usually interpreted as the balance between gene flow and selection against hybrids. Yet, mating systems can introduce selective forces that alter these expectations; with diverse outcomes for the level and direction of gene flow depending on variation in outcrossing and whether the mating systems of the species pair are the same or divergent. We present a survey of hybridization in 133 species pairs from 41 plant families and examine how patterns of hybridization vary with mating system. We examine if hybrid zone mode, level of gene flow, asymmetries in gene flow and the frequency of reproductive isolating barriers vary in relation to mating system/s of the species pair. We combine these results with a simulation model and examples from the literature to address two general themes: (i) the two‐way interaction between introgression and the evolution of reproductive systems, and (ii) how mating system can facilitate or restrict interspecific gene flow. We conclude that examining mating system with hybridization provides unique opportunities to understand divergence and the processes underlying reproductive isolation.","lang":"eng"}],"ddc":["570"],"date_created":"2019-09-07T14:35:40Z","issue":"3","publication":"New Phytologist","file":[{"file_size":1511958,"checksum":"21e4c95599bbcaf7c483b89954658672","date_created":"2019-11-13T08:15:05Z","access_level":"open_access","relation":"main_file","creator":"dernst","file_name":"2019_NewPhytologist_Pickup.pdf","date_updated":"2020-07-14T12:47:42Z","content_type":"application/pdf","file_id":"7011"}],"year":"2019","type":"journal_article","citation":{"ama":"Pickup M, Barton NH, Brandvain Y, et al. Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. <i>New Phytologist</i>. 2019;224(3):1035-1047. doi:<a href=\"https://doi.org/10.1111/nph.16180\">10.1111/nph.16180</a>","short":"M. Pickup, N.H. Barton, Y. Brandvain, C. Fraisse, S. Yakimowski, T. Dixit, C. Lexer, E. Cereghetti, D. Field, New Phytologist 224 (2019) 1035–1047.","ista":"Pickup M, Barton NH, Brandvain Y, Fraisse C, Yakimowski S, Dixit T, Lexer C, Cereghetti E, Field D. 2019. Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. 224(3), 1035–1047.","chicago":"Pickup, Melinda, Nicholas H Barton, Yaniv Brandvain, Christelle Fraisse, Sarah Yakimowski, Tanmay Dixit, Christian Lexer, Eva Cereghetti, and David Field. “Mating System Variation in Hybrid Zones: Facilitation, Barriers and Asymmetries to Gene Flow.” <i>New Phytologist</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/nph.16180\">https://doi.org/10.1111/nph.16180</a>.","apa":"Pickup, M., Barton, N. H., Brandvain, Y., Fraisse, C., Yakimowski, S., Dixit, T., … Field, D. (2019). Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.16180\">https://doi.org/10.1111/nph.16180</a>","mla":"Pickup, Melinda, et al. “Mating System Variation in Hybrid Zones: Facilitation, Barriers and Asymmetries to Gene Flow.” <i>New Phytologist</i>, vol. 224, no. 3, Wiley, 2019, pp. 1035–47, doi:<a href=\"https://doi.org/10.1111/nph.16180\">10.1111/nph.16180</a>.","ieee":"M. Pickup <i>et al.</i>, “Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow,” <i>New Phytologist</i>, vol. 224, no. 3. Wiley, pp. 1035–1047, 2019."},"OA_place":"publisher","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"year":"2018","type":"journal_article","article_number":"30083438","citation":{"ieee":"C. Fraisse <i>et al.</i>, “The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies,” <i>PeerJ</i>, vol. 2018, no. 7. PeerJ, 2018.","mla":"Fraisse, Christelle, et al. “The Divergence History of European Blue Mussel Species Reconstructed from Approximate Bayesian Computation: The Effects of Sequencing Techniques and Sampling Strategies.” <i>PeerJ</i>, vol. 2018, no. 7, 30083438, PeerJ, 2018, doi:<a href=\"https://doi.org/10.7717/peerj.5198\">10.7717/peerj.5198</a>.","chicago":"Fraisse, Christelle, Camille Roux, Pierre Gagnaire, Jonathan Romiguier, Nicolas Faivre, John Welch, and Nicolas Bierne. “The Divergence History of European Blue Mussel Species Reconstructed from Approximate Bayesian Computation: The Effects of Sequencing Techniques and Sampling Strategies.” <i>PeerJ</i>. PeerJ, 2018. <a href=\"https://doi.org/10.7717/peerj.5198\">https://doi.org/10.7717/peerj.5198</a>.","apa":"Fraisse, C., Roux, C., Gagnaire, P., Romiguier, J., Faivre, N., Welch, J., &#38; Bierne, N. (2018). The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. <i>PeerJ</i>. PeerJ. <a href=\"https://doi.org/10.7717/peerj.5198\">https://doi.org/10.7717/peerj.5198</a>","short":"C. Fraisse, C. Roux, P. Gagnaire, J. Romiguier, N. Faivre, J. Welch, N. Bierne, PeerJ 2018 (2018).","ama":"Fraisse C, Roux C, Gagnaire P, et al. The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. <i>PeerJ</i>. 2018;2018(7). doi:<a href=\"https://doi.org/10.7717/peerj.5198\">10.7717/peerj.5198</a>","ista":"Fraisse C, Roux C, Gagnaire P, Romiguier J, Faivre N, Welch J, Bierne N. 2018. The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. PeerJ. 2018(7), 30083438."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","scopus_import":"1","doi":"10.7717/peerj.5198","oa":1,"isi":1,"day":"30","abstract":[{"lang":"eng","text":"Genome-scale diversity data are increasingly available in a variety of biological systems, and can be used to reconstruct the past evolutionary history of species divergence. However, extracting the full demographic information from these data is not trivial, and requires inferential methods that account for the diversity of coalescent histories throughout the genome. Here, we evaluate the potential and limitations of one such approach. We reexamine a well-known system of mussel sister species, using the joint site frequency spectrum (jSFS) of synonymousmutations computed either fromexome capture or RNA-seq, in an Approximate Bayesian Computation (ABC) framework. We first assess the best sampling strategy (number of: individuals, loci, and bins in the jSFS), and show that model selection is robust to variation in the number of individuals and loci. In contrast, different binning choices when summarizing the jSFS, strongly affect the results: including classes of low and high frequency shared polymorphisms can more effectively reveal recent migration events. We then take advantage of the flexibility of ABC to compare more realistic models of speciation, including variation in migration rates through time (i.e., periodic connectivity) and across genes (i.e., genome-wide heterogeneity in migration rates). We show that these models were consistently selected as the most probable, suggesting that mussels have experienced a complex history of gene flow during divergence and that the species boundary is semi-permeable. Our work provides a comprehensive evaluation of ABC demographic inference in mussels based on the coding jSFS, and supplies guidelines for employing different sequencing techniques and sampling strategies. We emphasize, perhaps surprisingly, that inferences are less limited by the volume of data, than by the way in which they are analyzed."}],"date_created":"2018-12-11T11:44:50Z","issue":"7","ddc":["576"],"file":[{"content_type":"application/pdf","file_id":"5739","file_name":"2018_PeerJ_Fraisse.pdf","date_updated":"2020-07-14T12:44:48Z","relation":"main_file","access_level":"open_access","creator":"dernst","file_size":1480792,"checksum":"7d55ae22598a1c70759cd671600cff53","date_created":"2018-12-18T09:42:11Z"}],"publication":"PeerJ","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:44:48Z","intvolume":"      2018","author":[{"orcid":"0000-0001-8441-5075","first_name":"Christelle","full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse"},{"last_name":"Roux","full_name":"Roux, Camille","first_name":"Camille"},{"last_name":"Gagnaire","first_name":"Pierre","full_name":"Gagnaire, Pierre"},{"full_name":"Romiguier, Jonathan","first_name":"Jonathan","last_name":"Romiguier"},{"full_name":"Faivre, Nicolas","first_name":"Nicolas","last_name":"Faivre"},{"full_name":"Welch, John","first_name":"John","last_name":"Welch"},{"last_name":"Bierne","first_name":"Nicolas","full_name":"Bierne, Nicolas"}],"_id":"139","publication_status":"published","external_id":{"isi":["000440484800002"]},"date_updated":"2023-10-17T12:25:28Z","oa_version":"Published Version","date_published":"2018-07-30T00:00:00Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"article_processing_charge":"No","publist_id":"7784","publisher":"PeerJ","title":"The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies","volume":2018,"month":"07","quality_controlled":"1","status":"public"},{"status":"public","file":[{"creator":"cfraisse","relation":"main_file","access_level":"open_access","date_created":"2018-12-19T14:19:52Z","checksum":"aed7ee9ca3f4dc07d8a66945f68e13cd","file_size":369837892,"file_id":"5758","content_type":"application/zip","date_updated":"2020-07-14T12:47:11Z","file_name":"FileS1.zip"},{"checksum":"3592e467b4d8206650860b612d6e12f3","file_size":84856909,"date_created":"2018-12-19T14:19:49Z","creator":"cfraisse","access_level":"open_access","relation":"main_file","file_name":"FileS2.zip","date_updated":"2020-07-14T12:47:11Z","content_type":"application/zip","file_id":"5759"},{"content_type":"text/plain","file_id":"5760","file_name":"FileS3.txt","date_updated":"2020-07-14T12:47:11Z","creator":"cfraisse","access_level":"open_access","relation":"main_file","checksum":"c37ac5d5437c457338afc128c1240655","file_size":881133,"date_created":"2018-12-19T14:19:49Z"},{"file_name":"FileS4.txt","date_updated":"2020-07-14T12:47:11Z","content_type":"text/plain","file_id":"5761","file_size":883742,"checksum":"943dfd14da61817441e33e3e3cb8cdb9","date_created":"2018-12-19T14:19:49Z","access_level":"open_access","relation":"main_file","creator":"cfraisse"},{"content_type":"text/plain","file_id":"5762","file_name":"FileS5.txt","date_updated":"2020-07-14T12:47:11Z","creator":"cfraisse","access_level":"open_access","relation":"main_file","checksum":"1c669b6c4690ec1bbca3e2da9f566d17","file_size":2495437,"date_created":"2018-12-19T14:19:49Z"},{"date_updated":"2020-07-14T12:47:11Z","file_name":"FileS6.txt","file_id":"5763","content_type":"text/plain","date_created":"2018-12-19T14:19:50Z","checksum":"f40f661b987ca6fb6b47f650cbbb04e6","file_size":15913457,"creator":"cfraisse","relation":"main_file","access_level":"open_access"},{"date_updated":"2020-07-14T12:47:11Z","file_name":"FileS7.txt","content_type":"text/plain","file_id":"5764","date_created":"2018-12-19T14:19:50Z","file_size":2584120,"checksum":"25f41e5b8a075669c6c88d4c6713bf6f","access_level":"open_access","relation":"main_file","creator":"cfraisse"},{"date_updated":"2020-07-14T12:47:11Z","file_name":"FileS8.txt","content_type":"text/plain","file_id":"5765","date_created":"2018-12-19T14:19:50Z","checksum":"f6c0bd3e63e14ddf5445bd69b43a9152","file_size":2446059,"creator":"cfraisse","relation":"main_file","access_level":"open_access"},{"file_name":"FileS9.txt","date_updated":"2020-07-14T12:47:11Z","content_type":"text/plain","file_id":"5766","file_size":100737,"checksum":"0fe7a58a030b11bf3b9c8ff7a7addcae","date_created":"2018-12-19T14:19:50Z","relation":"main_file","access_level":"open_access","creator":"cfraisse"}],"date_created":"2018-12-19T14:22:35Z","month":"12","ddc":["576"],"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"article_processing_charge":"No","abstract":[{"text":"File S1. Variant Calling Format file of the ingroup: 197 haploid sequences of D. melanogaster from Zambia (Africa) aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S2. Variant Calling Format file of the outgroup: 1 haploid sequence of D. simulans aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S3. Annotations of each transcript in coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pn (# of non-synonymous polymorphic sites); Ds (# of synonymous divergent sites); Dn (# of non-synonymous divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S4. Annotations of each transcript in non-coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pu (# of UTR polymorphic sites); Ds (# of synonymous divergent sites); Du (# of UTR divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S5. Annotations of each transcript in coding regions with SNPGenie: Ps (# of synonymous polymorphic sites); πs (synonymous diversity); Ss_p (total # of synonymous sites in the polymorphism data); Pn (# of non-synonymous polymorphic sites); πn (non-synonymous diversity); Sn_p (total # of non-synonymous sites in the polymorphism data); Ds (# of synonymous divergent sites); ks (synonymous evolutionary rate); Ss_d (total # of synonymous sites in the divergence data); Dn (# of non-synonymous divergent sites); kn (non-synonymous evolutionary rate); Sn_d (total # of non-\r\nsynonymous sites in the divergence data); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S6. Gene expression values (RPKM summed over all transcripts) for each sample. Values were quantile-normalized across all samples.\r\n\r\nFile S7. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for coding sites, excluding variants below 5% frequency.\r\n\r\nFile S8. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for non-coding sites, excluding variants below 5%\r\nfrequency.\r\n\r\nFile S9. Final dataset with all covariates, ⍺ EWK , ωA EWK and deleterious SFS for coding sites obtained with the Eyre-Walker and Keightley method on binned data and using all variants.","lang":"eng"}],"publisher":"Institute of Science and Technology Austria","title":"Supplementary Files for \"Pleiotropy modulates the efficacy of selection in Drosophila melanogaster\"","doi":"10.15479/at:ista:/5757","oa":1,"date_updated":"2025-04-15T08:18:38Z","oa_version":"Published Version","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"ec_funded":1,"date_published":"2018-12-19T00:00:00Z","day":"19","keyword":["(mal)adaptation","pleiotropy","selective constraint","evo-devo","gene expression","Drosophila melanogaster"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5757","contributor":[{"last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"},{"first_name":"Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","last_name":"Puixeu Sala"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz"}],"has_accepted_license":"1","file_date_updated":"2020-07-14T12:47:11Z","author":[{"full_name":"Fraisse, Christelle","first_name":"Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"6089","status":"public","relation":"research_paper"}]},"citation":{"ama":"Fraisse C. Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” 2018. doi:<a href=\"https://doi.org/10.15479/at:ista:/5757\">10.15479/at:ista:/5757</a>","short":"C. Fraisse, (2018).","ista":"Fraisse C. 2018. Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/at:ista:/5757\">10.15479/at:ista:/5757</a>.","apa":"Fraisse, C. (2018). Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:/5757\">https://doi.org/10.15479/at:ista:/5757</a>","chicago":"Fraisse, Christelle. “Supplementary Files for ‘Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.’” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/at:ista:/5757\">https://doi.org/10.15479/at:ista:/5757</a>.","mla":"Fraisse, Christelle. <i>Supplementary Files for “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.”</i> Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/at:ista:/5757\">10.15479/at:ista:/5757</a>.","ieee":"C. Fraisse, “Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.’” Institute of Science and Technology Austria, 2018."},"year":"2018","type":"research_data"},{"doi":"10.1038/s41467-017-01663-5","scopus_import":"1","oa":1,"isi":1,"day":"01","project":[{"grant_number":"P28842-B22","name":"Sex chromosome evolution under male- and female- heterogamety","_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"abstract":[{"text":"Moths and butterflies (Lepidoptera) usually have a pair of differentiated WZ sex chromosomes. However, in most lineages outside of the division Ditrysia, as well as in the sister order Trichoptera, females lack a W chromosome. The W is therefore thought to have been acquired secondarily. Here we compare the genomes of three Lepidoptera species (one Dytrisia and two non-Dytrisia) to test three models accounting for the origin of the W: (1) a Z-autosome fusion; (2) a sex chromosome turnover; and (3) a non-canonical mechanism (e.g., through the recruitment of a B chromosome). We show that the gene content of the Z is highly conserved across Lepidoptera (rejecting a sex chromosome turnover) and that very few genes moved onto the Z in the common ancestor of the Ditrysia (arguing against a Z-autosome fusion). Our comparative genomics analysis therefore supports the secondary acquisition of the Lepidoptera W by a non-canonical mechanism, and it confirms the extreme stability of well-differentiated sex chromosomes.","lang":"eng"}],"pmid":1,"issue":"1","date_created":"2018-12-11T11:47:30Z","ddc":["570","576"],"publication":"Nature Communications","file":[{"date_created":"2020-03-03T15:55:50Z","checksum":"4da2651303c8afc2f7fc419be42a2433","file_size":1201520,"creator":"dernst","relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:47:20Z","file_name":"2017_NatureComm_Fraisse.pdf","file_id":"7562","content_type":"application/pdf"}],"corr_author":"1","year":"2017","type":"journal_article","article_number":"1486","related_material":{"record":[{"relation":"popular_science","status":"public","id":"7163"}]},"citation":{"mla":"Fraisse, Christelle, et al. “The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.” <i>Nature Communications</i>, vol. 8, no. 1, 1486, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/s41467-017-01663-5\">10.1038/s41467-017-01663-5</a>.","ieee":"C. Fraisse, M. A. L. Picard, and B. Vicoso, “The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W,” <i>Nature Communications</i>, vol. 8, no. 1. Nature Publishing Group, 2017.","chicago":"Fraisse, Christelle, Marion A L Picard, and Beatriz Vicoso. “The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/s41467-017-01663-5\">https://doi.org/10.1038/s41467-017-01663-5</a>.","apa":"Fraisse, C., Picard, M. A. L., &#38; Vicoso, B. (2017). The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-017-01663-5\">https://doi.org/10.1038/s41467-017-01663-5</a>","short":"C. Fraisse, M.A.L. Picard, B. Vicoso, Nature Communications 8 (2017).","ama":"Fraisse C, Picard MAL, Vicoso B. The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W. <i>Nature Communications</i>. 2017;8(1). doi:<a href=\"https://doi.org/10.1038/s41467-017-01663-5\">10.1038/s41467-017-01663-5</a>","ista":"Fraisse C, Picard MAL, Vicoso B. 2017. The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W. Nature Communications. 8(1), 1486."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","has_accepted_license":"1","publication_status":"published","external_id":{"isi":["000415124000013"],"pmid":["29133797"]},"date_updated":"2025-09-11T07:33:34Z","oa_version":"Published Version","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"date_published":"2017-12-01T00:00:00Z","publication_identifier":{"issn":["2041-1723"]},"publist_id":"7190","article_processing_charge":"No","title":"The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W","publisher":"Nature Publishing Group","volume":8,"month":"12","quality_controlled":"1","status":"public","article_type":"original","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}],"intvolume":"         8","file_date_updated":"2020-07-14T12:47:20Z","author":[{"orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse"},{"first_name":"Marion A","full_name":"Picard, Marion A","orcid":"0000-0002-8101-2518","last_name":"Picard","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vicoso, Beatriz","first_name":"Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"pubrep_id":"910","_id":"614"},{"date_created":"2019-12-09T23:03:03Z","month":"12","ddc":["576"],"status":"public","file":[{"checksum":"3cae8a2e3cbf8703399b9c483aaba7f3","file_size":841375478,"date_created":"2019-12-10T08:46:46Z","creator":"cfraisse","access_level":"open_access","relation":"main_file","file_name":"Vicoso_Cohridella_Ndegeerella_Tsylvina_genome_assemblies.zip","date_updated":"2020-07-14T12:47:50Z","content_type":"application/zip","file_id":"7164"}],"doi":"10.15479/AT:ISTA:7163","date_updated":"2025-09-11T07:33:33Z","oa":1,"oa_version":"Published Version","day":"01","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"date_published":"2017-12-01T00:00:00Z","project":[{"grant_number":"P28842-B22","name":"Sex chromosome evolution under male- and female- heterogamety","_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_processing_charge":"No","abstract":[{"lang":"eng","text":"The de novo genome assemblies generated for this study, and the associated metadata."}],"publisher":"Institute of Science and Technology Austria","title":"Supplementary Files for \"The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W\"","file_date_updated":"2020-07-14T12:47:50Z","author":[{"full_name":"Fraisse, Christelle","first_name":"Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","contributor":[{"last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","orcid":"0000-0001-8441-5075"},{"last_name":"Picard","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","first_name":"Marion A L","orcid":"0000-0002-8101-2518"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz"}],"_id":"7163","has_accepted_license":"1","year":"2017","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"type":"research_data","related_material":{"record":[{"relation":"research_paper","status":"public","id":"614"}]},"citation":{"apa":"Fraisse, C. (2017). Supplementary Files for “The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7163\">https://doi.org/10.15479/AT:ISTA:7163</a>","chicago":"Fraisse, Christelle. “Supplementary Files for ‘The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.’” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:7163\">https://doi.org/10.15479/AT:ISTA:7163</a>.","mla":"Fraisse, Christelle. <i>Supplementary Files for “The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.”</i> Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7163\">10.15479/AT:ISTA:7163</a>.","ieee":"C. Fraisse, “Supplementary Files for ‘The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W.’” Institute of Science and Technology Austria, 2017.","ama":"Fraisse C. Supplementary Files for “The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W.” 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7163\">10.15479/AT:ISTA:7163</a>","short":"C. Fraisse, (2017).","ista":"Fraisse C. 2017. Supplementary Files for ‘The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:7163\">10.15479/AT:ISTA:7163</a>."}},{"abstract":[{"lang":"eng","text":"Speciation results from the progressive accumulation of mutations that decrease the probability of mating between parental populations or reduce the fitness of hybrids—the so-called species barriers. The speciation genomic literature, however, is mainly a collection of case studies, each with its own approach and specificities, such that a global view of the gradual process of evolution from one to two species is currently lacking. Of primary importance is the prevalence of gene flow between diverging entities, which is central in most species concepts and has been widely discussed in recent years. Here, we explore the continuum of speciation thanks to a comparative analysis of genomic data from 61 pairs of populations/species of animals with variable levels of divergence. Gene flow between diverging gene pools is assessed under an approximate Bayesian computation (ABC) framework. We show that the intermediate &quot;grey zone&quot; of speciation, in which taxonomy is often controversial, spans from 0.5% to 2% of net synonymous divergence, irrespective of species life history traits or ecology. Thanks to appropriate modeling of among-locus variation in genetic drift and introgression rate, we clarify the status of the majority of ambiguous cases and uncover a number of cryptic species. Our analysis also reveals the high incidence in animals of semi-isolated species (when some but not all loci are affected by barriers to gene flow) and highlights the intrinsic difficulty, both statistical and conceptual, of delineating species in the grey zone of speciation."}],"doi":"10.1371/journal.pbio.2000234","scopus_import":"1","oa":1,"day":"27","isi":1,"file":[{"file_name":"IST-2017-742-v1+1_journal.pbio.2000234.pdf","date_updated":"2020-07-14T12:44:36Z","content_type":"application/pdf","file_id":"5164","checksum":"2bab63b068a9840efd532b9ae583f9bb","file_size":2494348,"date_created":"2018-12-12T10:15:42Z","creator":"system","relation":"main_file","access_level":"open_access"}],"publication":"PLoS Biology","issue":"12","date_created":"2018-12-11T11:50:28Z","ddc":["576"],"related_material":{"record":[{"relation":"research_data","status":"public","id":"9862"},{"id":"9863","relation":"research_data","status":"public"}]},"citation":{"ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Shedding light on the grey zone of speciation along a continuum of genomic divergence. <i>PLoS Biology</i>. 2016;14(12). doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234\">10.1371/journal.pbio.2000234</a>","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, PLoS Biology 14 (2016).","ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLoS Biology. 14(12), e2000234.","chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence.” <i>PLoS Biology</i>. Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pbio.2000234\">https://doi.org/10.1371/journal.pbio.2000234</a>.","apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., &#38; Bierne, N. (2016). Shedding light on the grey zone of speciation along a continuum of genomic divergence. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2000234\">https://doi.org/10.1371/journal.pbio.2000234</a>","ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Shedding light on the grey zone of speciation along a continuum of genomic divergence,” <i>PLoS Biology</i>, vol. 14, no. 12. Public Library of Science, 2016.","mla":"Roux, Camille, et al. “Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence.” <i>PLoS Biology</i>, vol. 14, no. 12, e2000234, Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234\">10.1371/journal.pbio.2000234</a>."},"year":"2016","type":"journal_article","article_number":"e2000234","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","has_accepted_license":"1","publist_id":"6200","article_processing_charge":"No","title":"Shedding light on the grey zone of speciation along a continuum of genomic divergence","publisher":"Public Library of Science","publication_status":"published","external_id":{"isi":["000392120100008"]},"date_updated":"2025-09-22T09:55:10Z","oa_version":"Published Version","date_published":"2016-12-27T00:00:00Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"quality_controlled":"1","status":"public","acknowledgement":"European Research Council (ERC) https://erc.europa.eu/ (grant number ERC grant 232971). PopPhyl project. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. French National Research Agency (ANR) http://www.agence-nationale-recherche.fr/en/project-based-funding-to-advance-french-research/ (grant number ANR-12-BSV7- 0011). HYSEA project.\r\nWe thank Aude Darracq, Vincent Castric, Pierre-Alexandre Gagnaire, Xavier Vekemans, and John Welch for insightful discussions. The computations were performed at the Vital-IT (http://www.vital-it.ch) Center for high-performance computing of the SIB Swiss Institute of Bioinformatics and the ISEM computing cluster at the platform Montpellier Bioinformatique et Biodiversité.","volume":14,"month":"12","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}],"pubrep_id":"742","_id":"1158","file_date_updated":"2020-07-14T12:44:36Z","intvolume":"        14","author":[{"first_name":"Camille","full_name":"Roux, Camille","last_name":"Roux"},{"orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse"},{"last_name":"Romiguier","first_name":"Jonathan","full_name":"Romiguier, Jonathan"},{"last_name":"Anciaux","first_name":"Youann","full_name":"Anciaux, Youann"},{"last_name":"Galtier","first_name":"Nicolas","full_name":"Galtier, Nicolas"},{"last_name":"Bierne","full_name":"Bierne, Nicolas","first_name":"Nicolas"}]}]