[{"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).","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"01","isi":1,"author":[{"full_name":"De Jode, Aurélien","last_name":"De Jode","first_name":"Aurélien"},{"full_name":"Le Moan, Alan","first_name":"Alan","last_name":"Le Moan"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"full_name":"Stankowski, Sean","first_name":"Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"},{"last_name":"Rafajlović","first_name":"Marina","full_name":"Rafajlović, Marina"},{"full_name":"Fraisse, Christelle","first_name":"Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse"}],"file":[{"date_updated":"2023-02-27T07:10:17Z","file_name":"2023_EvolutionaryApplications_DeJode.pdf","date_created":"2023-02-27T07:10:17Z","creator":"dernst","checksum":"d4d6fa9ddf36643af994a6a757919afb","file_id":"12685","access_level":"open_access","content_type":"application/pdf","relation":"main_file","success":1,"file_size":2269822}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Wiley","title":"Ten years of demographic modelling of divergence and speciation in the sea","has_accepted_license":"1","publication":"Evolutionary Applications","page":"542-559","date_created":"2022-07-03T22:01:33Z","type":"journal_article","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"language":[{"iso":"eng"}],"article_processing_charge":"No","article_type":"original","quality_controlled":"1","volume":16,"external_id":{"isi":["000815663700001"]},"abstract":[{"lang":"eng","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."}],"issue":"2","date_updated":"2023-08-01T12:25:44Z","year":"2023","_id":"11479","status":"public","publication_identifier":{"eissn":["1752-4571"]},"oa":1,"month":"02","doi":"10.1111/eva.13428","publication_status":"published","oa_version":"Published Version","date_published":"2023-02-01T00:00:00Z","scopus_import":"1","file_date_updated":"2023-02-27T07:10:17Z","ddc":["576"],"intvolume":"        16","citation":{"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>.","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>.","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>","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.","ieee":"A. De Jode <i>et al.</i>, “Ten years of demographic modelling of divergence and speciation in the sea,” <i>Evolutionary Applications</i>, vol. 16, no. 2. Wiley, pp. 542–559, 2023.","ama":"De Jode A, Le Moan A, Johannesson K, et al. Ten years of demographic modelling of divergence and speciation in the sea. <i>Evolutionary Applications</i>. 2023;16(2):542-559. doi:<a href=\"https://doi.org/10.1111/eva.13428\">10.1111/eva.13428</a>"}},{"file":[{"relation":"main_file","content_type":"application/pdf","success":1,"file_size":1347136,"checksum":"f79ff5383e882ea3f95f3da47a78029d","creator":"dernst","file_id":"12440","access_level":"open_access","file_name":"2022_Genetics_Elkrewi.pdf","date_updated":"2023-01-30T08:59:58Z","date_created":"2023-01-30T08:59:58Z"}],"project":[{"grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","call_identifier":"H2020"},{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction"}],"isi":1,"author":[{"full_name":"Elkrewi, Marwan N","last_name":"Elkrewi","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231","first_name":"Marwan N"},{"first_name":"Uladzislava","last_name":"Khauratovich","id":"5eba06f4-97d8-11ed-9f8f-d826ebdd9434","full_name":"Khauratovich, Uladzislava"},{"full_name":"Toups, Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups","orcid":"0000-0002-9752-7380","first_name":"Melissa A"},{"full_name":"Bett, Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425","last_name":"Bett","first_name":"Vincent K"},{"full_name":"Mrnjavac, Andrea","first_name":"Andrea","last_name":"Mrnjavac","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425"},{"full_name":"Macon, Ariana","last_name":"Macon","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","orcid":"0000-0001-8441-5075","first_name":"Christelle","full_name":"Fraisse, Christelle"},{"full_name":"Sax, Luca","first_name":"Luca","id":"701c5602-97d8-11ed-96b5-b52773c70189","last_name":"Sax"},{"orcid":"0000-0001-8871-4961","first_name":"Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","last_name":"Huylmans","full_name":"Huylmans, Ann K"},{"full_name":"Hontoria, Francisco","last_name":"Hontoria","first_name":"Francisco"},{"full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"01","pmid":1,"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.","title":"ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp","publisher":"Oxford University Press","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"department":[{"_id":"BeVi"}],"type":"journal_article","date_created":"2023-01-16T09:56:10Z","publication":"Genetics","has_accepted_license":"1","related_material":{"record":[{"status":"public","relation":"research_data","id":"11653"}]},"external_id":{"pmid":["35977389"],"isi":["000850270300001"]},"keyword":["Genetics"],"volume":222,"quality_controlled":"1","article_processing_charge":"No","article_type":"original","_id":"12248","article_number":"iyac123","acknowledged_ssus":[{"_id":"ScienComp"}],"year":"2022","date_updated":"2024-03-25T23:30:26Z","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"}],"issue":"2","ec_funded":1,"month":"10","oa":1,"publication_identifier":{"issn":["1943-2631"]},"status":"public","date_published":"2022-10-01T00:00:00Z","oa_version":"Published Version","publication_status":"published","doi":"10.1093/genetics/iyac123","citation":{"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>","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>.","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.","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>","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>."},"intvolume":"       222","ddc":["570"],"file_date_updated":"2023-01-30T08:59:58Z","scopus_import":"1"},{"external_id":{"isi":["000579599700001"],"pmid":["33045123"]},"volume":34,"quality_controlled":"1","related_material":{"record":[{"id":"13073","relation":"research_data","status":"public"}]},"article_type":"original","article_processing_charge":"No","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"page":"208-223","date_created":"2020-10-25T23:01:20Z","publication":"Journal of Evolutionary Biology","publisher":"Wiley","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels","isi":1,"author":[{"first_name":"Alexis","last_name":"Simon","full_name":"Simon, Alexis"},{"first_name":"Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","full_name":"Fraisse, Christelle"},{"first_name":"Tahani","last_name":"El Ayari","full_name":"El Ayari, Tahani"},{"first_name":"Cathy","last_name":"Liautard‐Haag","full_name":"Liautard‐Haag, Cathy"},{"first_name":"Petr","last_name":"Strelkov","full_name":"Strelkov, Petr"},{"last_name":"Welch","first_name":"John J","full_name":"Welch, John J"},{"full_name":"Bierne, Nicolas","last_name":"Bierne","first_name":"Nicolas"}],"pmid":1,"acknowledgement":"Data used in this work were partly produced through the genotyping and sequencing facilities of ISEM and LabEx CeMEB, an ANR ‘Investissements d'avenir’ program (ANR‐10‐LABX‐04‐01) This project benefited from the Montpellier Bioinformatics Biodiversity platform supported by the LabEx CeMEB. We thank Norah Saarman, Grant Pogson, Célia Gosset and Pierre‐Alexandre Gagnaire for providing samples. This work was funded by a Languedoc‐Roussillon ‘Chercheur(se)s d'Avenir’ grant (Connect7 project). P. Strelkov was supported by the Russian Science Foundation project 19‐74‐20024. This is article 2020‐240 of Institut des Sciences de l'Evolution de Montpellier.","day":"01","intvolume":"        34","citation":{"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.","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.","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>.","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>.","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>","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."},"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/818559"}],"oa_version":"Preprint","date_published":"2021-01-01T00:00:00Z","publication_status":"published","doi":"10.1111/jeb.13709","month":"01","status":"public","publication_identifier":{"eissn":["14209101"],"issn":["1010061X"]},"oa":1,"_id":"8708","date_updated":"2023-08-04T11:04:11Z","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"}],"issue":"1","year":"2021"},{"language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"type":"journal_article","date_created":"2020-12-06T23:01:16Z","page":"270-283","publication":"Journal of Evolutionary Biology","related_material":{"record":[{"status":"public","relation":"research_data","id":"13065"}]},"external_id":{"pmid":["33107098"],"isi":["000587769700001"]},"quality_controlled":"1","volume":34,"article_processing_charge":"No","article_type":"original","project":[{"_id":"2662AADE-B435-11E9-9278-68D0E5697425","grant_number":"M02463","call_identifier":"FWF","name":"Sex chromosomes and species barriers"}],"author":[{"first_name":"Stéphanie","last_name":"Arnoux","full_name":"Arnoux, Stéphanie"},{"last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle"},{"last_name":"Sauvage","first_name":"Christopher","full_name":"Sauvage, Christopher"}],"isi":1,"day":"01","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.","pmid":1,"title":"Genomic inference of complex domestication histories in three Solanaceae species","publisher":"Wiley","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-02-01T00:00:00Z","oa_version":"Published Version","publication_status":"published","doi":"10.1111/jeb.13723","intvolume":"        34","citation":{"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>","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.","short":"S. Arnoux, C. Fraisse, C. Sauvage, Journal of Evolutionary Biology 34 (2021) 270–283.","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>.","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>.","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>","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."},"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1111/jeb.13723","open_access":"1"}],"_id":"8928","year":"2021","date_updated":"2023-08-04T11:19:26Z","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."}],"issue":"2","month":"02","oa":1,"publication_identifier":{"eissn":["14209101"],"issn":["1010061X"]},"status":"public"},{"month":"01","status":"public","oa":1,"publication_identifier":{"issn":["1755098X"],"eissn":["17550998"]},"_id":"9119","date_updated":"2023-08-07T13:45:18Z","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"}],"year":"2021","intvolume":"        21","citation":{"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>.","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>","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.","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."},"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.06.15.151597v2","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","date_published":"2021-01-15T00:00:00Z","publication_status":"published","doi":"10.1111/1755-0998.13323","publisher":"Wiley","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"DILS: Demographic inferences with linked selection by using ABC","author":[{"full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Popovic, Iva","last_name":"Popovic","first_name":"Iva"},{"full_name":"Mazoyer, Clément","first_name":"Clément","last_name":"Mazoyer"},{"last_name":"Spataro","first_name":"Bruno","full_name":"Spataro, Bruno"},{"full_name":"Delmotte, Stéphane","first_name":"Stéphane","last_name":"Delmotte"},{"full_name":"Romiguier, Jonathan","first_name":"Jonathan","last_name":"Romiguier"},{"full_name":"Loire, Étienne","first_name":"Étienne","last_name":"Loire"},{"first_name":"Alexis","last_name":"Simon","full_name":"Simon, Alexis"},{"last_name":"Galtier","first_name":"Nicolas","full_name":"Galtier, Nicolas"},{"full_name":"Duret, Laurent","first_name":"Laurent","last_name":"Duret"},{"last_name":"Bierne","first_name":"Nicolas","full_name":"Bierne, Nicolas"},{"full_name":"Vekemans, Xavier","last_name":"Vekemans","first_name":"Xavier"},{"last_name":"Roux","first_name":"Camille","full_name":"Roux, Camille"}],"isi":1,"day":"15","external_id":{"isi":["000614183100001"]},"quality_controlled":"1","volume":21,"article_processing_charge":"No","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"page":"2629-2644","date_created":"2021-02-14T23:01:14Z","publication":"Molecular Ecology Resources"},{"publication":"Genetics","date_created":"2021-02-18T14:41:30Z","type":"journal_article","department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","volume":217,"quality_controlled":"1","external_id":{"isi":["000637218100005"]},"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).","day":"01","author":[{"orcid":"0000-0001-8441-5075","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","full_name":"Fraisse, Christelle"},{"last_name":"Sachdeva","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","full_name":"Sachdeva, Himani"}],"isi":1,"project":[{"name":"Sex chromosomes and species barriers","call_identifier":"FWF","grant_number":"M02463","_id":"2662AADE-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Genetics Society of America","title":"The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes","doi":"10.1093/genetics/iyaa025","publication_status":"published","oa_version":"Published Version","date_published":"2021-02-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/genetics/iyaa025"}],"citation":{"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>","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.","short":"C. Fraisse, H. Sachdeva, Genetics 217 (2021).","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.","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>","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>.","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>."},"intvolume":"       217","abstract":[{"lang":"eng","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."}],"issue":"2","date_updated":"2023-08-07T13:47:01Z","year":"2021","acknowledged_ssus":[{"_id":"ScienComp"}],"article_number":"iyaa025","_id":"9168","status":"public","oa":1,"publication_identifier":{"issn":["1943-2631"]},"month":"02"},{"month":"10","oa":1,"title":"VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Dryad","status":"public","_id":"13065","author":[{"full_name":"Arnoux, Stephanie","first_name":"Stephanie","last_name":"Arnoux"},{"last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","first_name":"Christelle","full_name":"Fraisse, Christelle"},{"first_name":"Christopher","last_name":"Sauvage","full_name":"Sauvage, Christopher"}],"year":"2020","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","image":"/images/cc_0.png"},"day":"19","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"}],"date_updated":"2023-08-04T11:19:26Z","related_material":{"link":[{"relation":"software","url":"https://github.com/starnoux/arnoux_et_al_2019"}],"record":[{"relation":"used_in_publication","status":"public","id":"8928"}]},"citation":{"short":"S. Arnoux, C. Fraisse, C. Sauvage, (2020).","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.","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>.","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>.","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>."},"ddc":["570"],"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.q2bvq83hd"}],"date_published":"2020-10-19T00:00:00Z","department":[{"_id":"NiBa"}],"type":"research_data_reference","oa_version":"Published Version","date_created":"2023-05-23T16:30:20Z","doi":"10.5061/DRYAD.Q2BVQ83HD"},{"date_created":"2023-05-23T16:48:27Z","doi":"10.5061/DRYAD.R4XGXD29N","date_published":"2020-09-22T00:00:00Z","department":[{"_id":"NiBa"}],"oa_version":"Published Version","type":"research_data_reference","ddc":["570"],"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.r4xgxd29n"}],"related_material":{"record":[{"id":"8708","relation":"used_in_publication","status":"public"}]},"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.","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>","short":"A. Simon, C. Fraisse, T. El Ayari, C. Liautard-Haag, P. Strelkov, J. Welch, N. Bierne, (2020).","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>","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>.","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>."},"year":"2020","day":"22","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","image":"/images/cc_0.png"},"abstract":[{"text":"The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study \"replicated\" instances of secondary contact between closely-related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry-informative panel of such SNPs. We then compared their frequencies in newly-sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi-stable variants (Dobzhansky-Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact.","lang":"eng"}],"date_updated":"2023-08-04T11:04:11Z","_id":"13073","author":[{"last_name":"Simon","first_name":"Alexis","full_name":"Simon, Alexis"},{"full_name":"Fraisse, Christelle","first_name":"Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse"},{"last_name":"El Ayari","first_name":"Tahani","full_name":"El Ayari, Tahani"},{"full_name":"Liautard-Haag, Cathy","first_name":"Cathy","last_name":"Liautard-Haag"},{"full_name":"Strelkov, Petr","first_name":"Petr","last_name":"Strelkov"},{"first_name":"John","last_name":"Welch","full_name":"Welch, John"},{"full_name":"Bierne, Nicolas","last_name":"Bierne","first_name":"Nicolas"}],"oa":1,"title":"How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"Dryad","month":"09"},{"month":"10","oa":1,"title":"Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Royal Society of London","status":"public","_id":"9798","author":[{"full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","orcid":"0000-0001-8441-5075","first_name":"Christelle"},{"first_name":"John J.","last_name":"Welch","full_name":"Welch, John J."}],"year":"2020","day":"15","abstract":[{"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.","lang":"eng"}],"date_updated":"2023-08-25T10:34:41Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"6467"}]},"citation":{"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>.","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>","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>.","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>.","short":"C. Fraisse, J.J. Welch, (2020).","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>","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."},"article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.7957472.v1","open_access":"1"}],"date_published":"2020-10-15T00:00:00Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"oa_version":"Published Version","type":"research_data_reference","date_created":"2021-08-06T11:18:15Z","doi":"10.6084/m9.figshare.7957472.v1"},{"article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.7957469.v1","open_access":"1"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6467"}]},"citation":{"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>.","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>","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>.","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>.","short":"C. Fraisse, J.J. Welch, (2020).","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.","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>"},"date_created":"2021-08-06T11:26:57Z","doi":"10.6084/m9.figshare.7957469.v1","date_published":"2020-10-15T00:00:00Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"type":"research_data_reference","oa_version":"Published Version","oa":1,"title":"Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Royal Society of London","status":"public","month":"10","year":"2020","day":"15","abstract":[{"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.","lang":"eng"}],"date_updated":"2023-08-25T10:34:41Z","_id":"9799","author":[{"full_name":"Fraisse, Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","orcid":"0000-0001-8441-5075"},{"full_name":"Welch, John J.","first_name":"John J.","last_name":"Welch"}]},{"project":[{"call_identifier":"FP7","name":"Mating system and the evolutionary dynamics of hybrid zones","_id":"25B36484-B435-11E9-9278-68D0E5697425","grant_number":"329960"},{"call_identifier":"FWF","name":"Sex chromosomes and species barriers","grant_number":"M02463","_id":"2662AADE-B435-11E9-9278-68D0E5697425"}],"author":[{"full_name":"Pickup, Melinda","first_name":"Melinda","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"first_name":"Yaniv","last_name":"Brandvain","full_name":"Brandvain, Yaniv"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","first_name":"Christelle","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle"},{"full_name":"Yakimowski, Sarah","last_name":"Yakimowski","first_name":"Sarah"},{"first_name":"Tanmay","last_name":"Dixit","full_name":"Dixit, Tanmay"},{"last_name":"Lexer","first_name":"Christian","full_name":"Lexer, Christian"},{"id":"71AA91B4-05ED-11EA-8BEB-F5833E63BD63","last_name":"Cereghetti","first_name":"Eva","full_name":"Cereghetti, Eva"},{"full_name":"Field, David","first_name":"David","orcid":"0000-0002-4014-8478","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87"}],"file":[{"date_updated":"2020-07-14T12:47:42Z","file_name":"2019_NewPhytologist_Pickup.pdf","date_created":"2019-11-13T08:15:05Z","creator":"dernst","file_id":"7011","checksum":"21e4c95599bbcaf7c483b89954658672","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_size":1511958}],"pmid":1,"day":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Wiley","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"has_accepted_license":"1","page":"1035-1047","date_created":"2019-09-07T14:35:40Z","publication":"New Phytologist","external_id":{"pmid":["31505037"]},"quality_controlled":"1","volume":224,"article_type":"original","article_processing_charge":"No","_id":"6856","date_updated":"2023-10-18T08:47:08Z","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"}],"issue":"3","year":"2019","month":"11","ec_funded":1,"status":"public","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646X"]},"oa":1,"oa_version":"Published Version","date_published":"2019-11-01T00:00:00Z","publication_status":"published","doi":"10.1111/nph.16180","citation":{"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.","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>.","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>","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>.","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.","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.","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>"},"intvolume":"       224","scopus_import":"1","file_date_updated":"2020-07-14T12:47:42Z","ddc":["570"]},{"_id":"6089","year":"2019","issue":"3","abstract":[{"lang":"eng","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."}],"date_updated":"2024-02-21T13:59:17Z","month":"03","publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"oa":1,"status":"public","date_published":"2019-03-01T00:00:00Z","oa_version":"Submitted Version","doi":"10.1093/molbev/msy246","publication_status":"published","intvolume":"        36","citation":{"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>.","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>","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.","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>.","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>","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.","short":"C. Fraisse, G. Puixeu Sala, B. Vicoso, Molecular Biology and Evolution 36 (2019) 500–515."},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30590559","open_access":"1"}],"scopus_import":"1","author":[{"last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","first_name":"Christelle","full_name":"Fraisse, Christelle"},{"last_name":"Puixeu Sala","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","first_name":"Gemma","orcid":"0000-0001-8330-1754","full_name":"Puixeu Sala, Gemma"},{"last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","full_name":"Vicoso, Beatriz"}],"isi":1,"project":[{"name":"Sex chromosome evolution under male- and female- heterogamety","call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425","grant_number":"P28842-B22"}],"day":"01","pmid":1,"title":"Pleiotropy modulates the efficacy of selection in drosophila melanogaster","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Oxford University Press","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"language":[{"iso":"eng"}],"type":"journal_article","publication":"Molecular biology and evolution","date_created":"2019-03-10T22:59:19Z","page":"500-515","related_material":{"record":[{"status":"public","relation":"popular_science","id":"5757"}]},"volume":36,"quality_controlled":"1","external_id":{"isi":["000462585100006"],"pmid":["30590559"]},"article_processing_charge":"No"},{"ddc":["580","576"],"file_date_updated":"2020-07-14T12:47:31Z","scopus_import":"1","intvolume":"        28","citation":{"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>.","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>","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>.","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.","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."},"doi":"10.1111/mec.15048","publication_status":"published","date_published":"2019-04-01T00:00:00Z","oa_version":"Published Version","oa":1,"publication_identifier":{"eissn":["1365294X"]},"status":"public","month":"04","year":"2019","issue":"7","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"}],"date_updated":"2023-08-25T10:37:30Z","_id":"6466","article_processing_charge":"No","quality_controlled":"1","volume":28,"external_id":{"isi":["000474808300001"]},"publication":"Molecular ecology","date_created":"2019-05-19T21:59:15Z","page":"1579-1581","has_accepted_license":"1","department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"type":"journal_article","title":"Breaking down barriers in morning glories","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Wiley","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"01","file":[{"file_size":367711,"content_type":"application/pdf","relation":"main_file","date_created":"2019-05-20T11:49:06Z","date_updated":"2020-07-14T12:47:31Z","file_name":"2019_MolecularEcology_Field.pdf","access_level":"open_access","creator":"dernst","file_id":"6472","checksum":"521e3aff3e9263ddf2ffbfe0b6157715"}],"author":[{"orcid":"0000-0002-4014-8478","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","full_name":"Field, David"},{"last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","first_name":"Christelle","full_name":"Fraisse, Christelle"}],"isi":1},{"doi":"10.1098/rsbl.2018.0881","publication_status":"published","date_published":"2019-04-03T00:00:00Z","oa_version":"Published Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1098/rsbl.2018.0881"}],"citation":{"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.","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>","short":"C. Fraisse, J.J. Welch, Biology Letters 15 (2019).","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>.","ista":"Fraisse C, Welch JJ. 2019. The distribution of epistasis on simple fitness landscapes. Biology Letters. 15(4), 0881.","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>.","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>"},"intvolume":"        15","year":"2019","issue":"4","abstract":[{"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.","lang":"eng"}],"date_updated":"2023-08-25T10:34:41Z","_id":"6467","article_number":"0881","oa":1,"publication_identifier":{"issn":["17449561"],"eissn":["1744957X"]},"status":"public","ec_funded":1,"month":"04","publication":"Biology Letters","date_created":"2019-05-19T21:59:15Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","article_processing_charge":"No","related_material":{"link":[{"relation":"supplementary_material","url":"https://dx.doi.org/10.6084/m9.figshare.c.4461008"}],"record":[{"status":"public","relation":"research_data","id":"9798"},{"id":"9799","status":"public","relation":"research_data"}]},"quality_controlled":"1","volume":15,"external_id":{"isi":["000465405300010"],"pmid":["31014191"]},"day":"03","pmid":1,"isi":1,"author":[{"last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle"},{"full_name":"Welch, John J.","last_name":"Welch","first_name":"John J."}],"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"title":"The distribution of epistasis on simple fitness landscapes","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Royal Society of London"},{"date_updated":"2024-02-21T13:59:18Z","abstract":[{"lang":"eng","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."}],"day":"19","year":"2018","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"author":[{"full_name":"Fraisse, Christelle","first_name":"Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse"}],"file":[{"access_level":"open_access","file_id":"5758","checksum":"aed7ee9ca3f4dc07d8a66945f68e13cd","creator":"cfraisse","date_created":"2018-12-19T14:19:52Z","date_updated":"2020-07-14T12:47:11Z","file_name":"FileS1.zip","file_size":369837892,"content_type":"application/zip","relation":"main_file"},{"content_type":"application/zip","relation":"main_file","file_size":84856909,"file_name":"FileS2.zip","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:49Z","checksum":"3592e467b4d8206650860b612d6e12f3","creator":"cfraisse","file_id":"5759","access_level":"open_access"},{"content_type":"text/plain","relation":"main_file","file_size":881133,"file_id":"5760","checksum":"c37ac5d5437c457338afc128c1240655","creator":"cfraisse","access_level":"open_access","date_updated":"2020-07-14T12:47:11Z","file_name":"FileS3.txt","date_created":"2018-12-19T14:19:49Z"},{"content_type":"text/plain","relation":"main_file","file_size":883742,"date_updated":"2020-07-14T12:47:11Z","file_name":"FileS4.txt","date_created":"2018-12-19T14:19:49Z","file_id":"5761","creator":"cfraisse","checksum":"943dfd14da61817441e33e3e3cb8cdb9","access_level":"open_access"},{"file_size":2495437,"content_type":"text/plain","relation":"main_file","date_created":"2018-12-19T14:19:49Z","date_updated":"2020-07-14T12:47:11Z","file_name":"FileS5.txt","access_level":"open_access","file_id":"5762","creator":"cfraisse","checksum":"1c669b6c4690ec1bbca3e2da9f566d17"},{"file_name":"FileS6.txt","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:50Z","creator":"cfraisse","checksum":"f40f661b987ca6fb6b47f650cbbb04e6","file_id":"5763","access_level":"open_access","relation":"main_file","content_type":"text/plain","file_size":15913457},{"file_size":2584120,"relation":"main_file","content_type":"text/plain","date_created":"2018-12-19T14:19:50Z","date_updated":"2020-07-14T12:47:11Z","file_name":"FileS7.txt","access_level":"open_access","file_id":"5764","checksum":"25f41e5b8a075669c6c88d4c6713bf6f","creator":"cfraisse"},{"checksum":"f6c0bd3e63e14ddf5445bd69b43a9152","creator":"cfraisse","file_id":"5765","access_level":"open_access","file_name":"FileS8.txt","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:50Z","relation":"main_file","content_type":"text/plain","file_size":2446059},{"file_size":100737,"relation":"main_file","content_type":"text/plain","access_level":"open_access","creator":"cfraisse","file_id":"5766","checksum":"0fe7a58a030b11bf3b9c8ff7a7addcae","date_created":"2018-12-19T14:19:50Z","date_updated":"2020-07-14T12:47:11Z","file_name":"FileS9.txt"}],"_id":"5757","publisher":"Institute of Science and Technology Austria","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Supplementary Files for \"Pleiotropy modulates the efficacy of selection in Drosophila melanogaster\"","oa":1,"month":"12","ec_funded":1,"contributor":[{"last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"},{"last_name":"Puixeu Sala","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","first_name":"Gemma"},{"first_name":"Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","doi":"10.15479/at:ista:/5757","date_created":"2018-12-19T14:22:35Z","oa_version":"Published Version","type":"research_data","date_published":"2018-12-19T00:00:00Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:11Z","article_processing_charge":"No","ddc":["576"],"citation":{"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>.","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>","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>.","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>.","ieee":"C. Fraisse, “Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.’” Institute of Science and Technology Austria, 2018.","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)."},"keyword":["(mal)adaptation","pleiotropy","selective constraint","evo-devo","gene expression","Drosophila melanogaster"],"related_material":{"record":[{"id":"6089","status":"public","relation":"research_paper"}]}},{"month":"07","status":"public","oa":1,"article_number":"30083438","_id":"139","date_updated":"2023-10-17T12:25:28Z","issue":"7","abstract":[{"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.","lang":"eng"}],"year":"2018","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.","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>","short":"C. Fraisse, C. Roux, P. Gagnaire, J. Romiguier, N. Faivre, J. Welch, N. Bierne, PeerJ 2018 (2018).","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>","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.","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>."},"intvolume":"      2018","scopus_import":"1","file_date_updated":"2020-07-14T12:44:48Z","ddc":["576"],"oa_version":"Published Version","date_published":"2018-07-30T00:00:00Z","publication_status":"published","doi":"10.7717/peerj.5198","publisher":"PeerJ","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies","isi":1,"author":[{"orcid":"0000-0001-8441-5075","first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle"},{"last_name":"Roux","first_name":"Camille","full_name":"Roux, Camille"},{"full_name":"Gagnaire, Pierre","last_name":"Gagnaire","first_name":"Pierre"},{"full_name":"Romiguier, Jonathan","first_name":"Jonathan","last_name":"Romiguier"},{"last_name":"Faivre","first_name":"Nicolas","full_name":"Faivre, Nicolas"},{"full_name":"Welch, John","first_name":"John","last_name":"Welch"},{"first_name":"Nicolas","last_name":"Bierne","full_name":"Bierne, Nicolas"}],"file":[{"creator":"dernst","file_id":"5739","checksum":"7d55ae22598a1c70759cd671600cff53","access_level":"open_access","file_name":"2018_PeerJ_Fraisse.pdf","date_updated":"2020-07-14T12:44:48Z","date_created":"2018-12-18T09:42:11Z","relation":"main_file","content_type":"application/pdf","file_size":1480792}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"30","external_id":{"isi":["000440484800002"]},"volume":2018,"quality_controlled":"1","publist_id":"7784","article_processing_charge":"No","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"has_accepted_license":"1","date_created":"2018-12-11T11:44:50Z","publication":"PeerJ"},{"article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:50Z","ddc":["576"],"citation":{"short":"C. Fraisse, (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>","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.","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>.","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>","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>.","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>."},"related_material":{"record":[{"id":"614","relation":"research_paper","status":"public"}]},"doi":"10.15479/AT:ISTA:7163","has_accepted_license":"1","date_created":"2019-12-09T23:03:03Z","oa_version":"Published Version","type":"research_data","date_published":"2017-12-01T00:00:00Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","status":"public","oa":1,"title":"Supplementary Files for \"The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W\"","month":"12","contributor":[{"orcid":"0000-0001-8441-5075","first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8101-2518","first_name":"Marion A L","last_name":"Picard","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso"}],"abstract":[{"lang":"eng","text":"The de novo genome assemblies generated for this study, and the associated metadata."}],"date_updated":"2024-02-21T13:47:47Z","year":"2017","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"01","author":[{"full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"}],"project":[{"name":"Sex chromosome evolution under male- and female- heterogamety","call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425","grant_number":"P28842-B22"}],"_id":"7163","file":[{"date_created":"2019-12-10T08:46:46Z","file_name":"Vicoso_Cohridella_Ndegeerella_Tsylvina_genome_assemblies.zip","date_updated":"2020-07-14T12:47:50Z","access_level":"open_access","file_id":"7164","creator":"cfraisse","checksum":"3cae8a2e3cbf8703399b9c483aaba7f3","file_size":841375478,"content_type":"application/zip","relation":"main_file"}]},{"year":"2017","date_updated":"2024-02-21T13:47:47Z","abstract":[{"lang":"eng","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."}],"issue":"1","_id":"614","article_number":"1486","publication_identifier":{"issn":["20411723"]},"oa":1,"status":"public","month":"12","publication_status":"published","doi":"10.1038/s41467-017-01663-5","date_published":"2017-12-01T00:00:00Z","oa_version":"Published Version","ddc":["570","576"],"file_date_updated":"2020-07-14T12:47:20Z","scopus_import":1,"citation":{"short":"C. Fraisse, M.A.L. Picard, B. Vicoso, Nature Communications 8 (2017).","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.","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>","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>","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>.","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."},"intvolume":"         8","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"01","pmid":1,"file":[{"relation":"main_file","content_type":"application/pdf","file_size":1201520,"creator":"dernst","file_id":"7562","checksum":"4da2651303c8afc2f7fc419be42a2433","access_level":"open_access","file_name":"2017_NatureComm_Fraisse.pdf","date_updated":"2020-07-14T12:47:20Z","date_created":"2020-03-03T15:55:50Z"}],"project":[{"grant_number":"P28842-B22","_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Sex chromosome evolution under male- and female- heterogamety"}],"author":[{"full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","first_name":"Christelle","orcid":"0000-0001-8441-5075"},{"full_name":"Picard, Marion A","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","last_name":"Picard","orcid":"0000-0002-8101-2518","first_name":"Marion A"},{"first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","full_name":"Vicoso, Beatriz"}],"title":"The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W","publisher":"Nature Publishing Group","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:47:30Z","publication":"Nature Communications","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"type":"journal_article","publist_id":"7190","article_processing_charge":"No","article_type":"original","pubrep_id":"910","related_material":{"record":[{"status":"public","relation":"popular_science","id":"7163"}]},"external_id":{"pmid":["29133797"]},"quality_controlled":"1","volume":8},{"publist_id":"6200","pubrep_id":"742","related_material":{"record":[{"status":"public","relation":"research_data","id":"9862"},{"relation":"research_data","status":"public","id":"9863"}]},"volume":14,"quality_controlled":"1","date_created":"2018-12-11T11:50:28Z","publication":"PLoS Biology","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"type":"journal_article","title":"Shedding light on the grey zone of speciation along a continuum of genomic divergence","publisher":"Public Library of Science","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"27","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.","file":[{"access_level":"open_access","file_id":"5164","checksum":"2bab63b068a9840efd532b9ae583f9bb","creator":"system","date_created":"2018-12-12T10:15:42Z","date_updated":"2020-07-14T12:44:36Z","file_name":"IST-2017-742-v1+1_journal.pbio.2000234.pdf","file_size":2494348,"content_type":"application/pdf","relation":"main_file"}],"author":[{"full_name":"Roux, Camille","last_name":"Roux","first_name":"Camille"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","orcid":"0000-0001-8441-5075","first_name":"Christelle","full_name":"Fraisse, Christelle"},{"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"},{"full_name":"Bierne, Nicolas","last_name":"Bierne","first_name":"Nicolas"}],"ddc":["576"],"scopus_import":1,"file_date_updated":"2020-07-14T12:44:36Z","citation":{"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.","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).","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>.","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>.","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.","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>"},"intvolume":"        14","publication_status":"published","doi":"10.1371/journal.pbio.2000234","date_published":"2016-12-27T00:00:00Z","oa_version":"Published Version","oa":1,"status":"public","month":"12","year":"2016","date_updated":"2023-02-23T14:11:16Z","issue":"12","abstract":[{"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.","lang":"eng"}],"_id":"1158","article_number":"e2000234"},{"month":"12","title":"Simulation study to test the robustness of ABC in face of recent times of divergence","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","publisher":"Public Library of Science","_id":"9862","author":[{"first_name":"Camille","last_name":"Roux","full_name":"Roux, Camille"},{"full_name":"Fraisse, Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","first_name":"Christelle"},{"last_name":"Romiguier","first_name":"Jonathan","full_name":"Romiguier, Jonathan"},{"full_name":"Anciaux, Youann","first_name":"Youann","last_name":"Anciaux"},{"first_name":"Nicolas","last_name":"Galtier","full_name":"Galtier, Nicolas"},{"last_name":"Bierne","first_name":"Nicolas","full_name":"Bierne, Nicolas"}],"year":"2016","day":"27","date_updated":"2023-02-21T16:21:20Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1158"}]},"citation":{"ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Simulation study to test the robustness of ABC in face of recent times of divergence. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">10.1371/journal.pbio.2000234.s016</a>","ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Simulation study to test the robustness of ABC in face of recent times of divergence.” Public Library of Science, 2016.","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).","chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Simulation Study to Test the Robustness of ABC in Face of Recent Times of Divergence.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">https://doi.org/10.1371/journal.pbio.2000234.s016</a>.","apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., &#38; Bierne, N. (2016). Simulation study to test the robustness of ABC in face of recent times of divergence. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">https://doi.org/10.1371/journal.pbio.2000234.s016</a>","mla":"Roux, Camille, et al. <i>Simulation Study to Test the Robustness of ABC in Face of Recent Times of Divergence</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">10.1371/journal.pbio.2000234.s016</a>.","ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Simulation study to test the robustness of ABC in face of recent times of divergence, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">10.1371/journal.pbio.2000234.s016</a>."},"article_processing_charge":"No","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"oa_version":"Published Version","type":"research_data_reference","date_created":"2021-08-10T08:20:17Z","doi":"10.1371/journal.pbio.2000234.s016"}]