[{"publication":"Journal of Evolutionary Biology","oa_version":"Published Version","project":[{"name":"Sex chromosomes and species barriers","grant_number":"M02463","_id":"2662AADE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"month":"02","language":[{"iso":"eng"}],"date_published":"2021-02-01T00:00:00Z","type":"journal_article","publication_identifier":{"issn":["1010061X"],"eissn":["14209101"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jeb.13723"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"13065"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","pmid":1,"_id":"8928","scopus_import":"1","author":[{"last_name":"Arnoux","first_name":"Stéphanie","full_name":"Arnoux, Stéphanie"},{"last_name":"Fraisse","first_name":"Christelle","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sauvage","first_name":"Christopher","full_name":"Sauvage, Christopher"}],"issue":"2","publication_status":"published","date_created":"2020-12-06T23:01:16Z","department":[{"_id":"NiBa"}],"article_processing_charge":"No","title":"Genomic inference of complex domestication histories in three Solanaceae species","intvolume":"        34","page":"270-283","quality_controlled":"1","publisher":"Wiley","article_type":"original","date_updated":"2023-08-04T11:19:26Z","citation":{"ista":"Arnoux S, Fraisse C, Sauvage C. 2021. Genomic inference of complex domestication histories in three Solanaceae species. Journal of Evolutionary Biology. 34(2), 270–283.","short":"S. Arnoux, C. Fraisse, C. Sauvage, Journal of Evolutionary Biology 34 (2021) 270–283.","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>.","chicago":"Arnoux, Stéphanie, Christelle Fraisse, and Christopher Sauvage. “Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” <i>Journal of Evolutionary Biology</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/jeb.13723\">https://doi.org/10.1111/jeb.13723</a>.","ieee":"S. Arnoux, C. Fraisse, and C. Sauvage, “Genomic inference of complex domestication histories in three Solanaceae species,” <i>Journal of Evolutionary Biology</i>, vol. 34, no. 2. Wiley, pp. 270–283, 2021.","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>","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>"},"year":"2021","isi":1,"external_id":{"pmid":["33107098"],"isi":["000587769700001"]},"doi":"10.1111/jeb.13723","day":"01","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"}],"volume":34,"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."},{"project":[{"grant_number":"M02463","name":"Sex chromosomes and species barriers","_id":"2662AADE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Published Version","article_number":"iyaa025","month":"02","publication":"Genetics","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1943-2631"]},"oa":1,"type":"journal_article","date_published":"2021-02-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/genetics/iyaa025"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","article_processing_charge":"No","date_created":"2021-02-18T14:41:30Z","department":[{"_id":"NiBa"}],"publication_status":"published","intvolume":"       217","title":"The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes","_id":"9168","issue":"2","author":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse","first_name":"Christelle"},{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","last_name":"Sachdeva","full_name":"Sachdeva, Himani"}],"publisher":"Genetics Society of America","article_type":"original","quality_controlled":"1","day":"01","doi":"10.1093/genetics/iyaa025","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."}],"year":"2021","citation":{"ista":"Fraisse C, Sachdeva H. 2021. The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. Genetics. 217(2), iyaa025.","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>.","short":"C. Fraisse, H. Sachdeva, Genetics 217 (2021).","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.","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>.","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>","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>"},"date_updated":"2023-08-07T13:47:01Z","external_id":{"isi":["000637218100005"]},"isi":1,"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).","volume":217},{"has_accepted_license":"1","publication":"New Phytologist","project":[{"call_identifier":"FP7","_id":"25B36484-B435-11E9-9278-68D0E5697425","name":"Mating system and the evolutionary dynamics of hybrid zones","grant_number":"329960"},{"grant_number":"M02463","name":"Sex chromosomes and species barriers","_id":"2662AADE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"oa_version":"Published Version","month":"11","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2019-11-01T00:00:00Z","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646X"]},"oa":1,"file":[{"checksum":"21e4c95599bbcaf7c483b89954658672","file_size":1511958,"date_created":"2019-11-13T08:15:05Z","content_type":"application/pdf","file_name":"2019_NewPhytologist_Pickup.pdf","date_updated":"2020-07-14T12:47:42Z","relation":"main_file","access_level":"open_access","creator":"dernst","file_id":"7011"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","pmid":1,"_id":"6856","issue":"3","author":[{"last_name":"Pickup","first_name":"Melinda","full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Brandvain","first_name":"Yaniv","full_name":"Brandvain, Yaniv"},{"first_name":"Christelle","last_name":"Fraisse","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sarah","last_name":"Yakimowski","full_name":"Yakimowski, Sarah"},{"first_name":"Tanmay","last_name":"Dixit","full_name":"Dixit, Tanmay"},{"first_name":"Christian","last_name":"Lexer","full_name":"Lexer, Christian"},{"id":"71AA91B4-05ED-11EA-8BEB-F5833E63BD63","full_name":"Cereghetti, Eva","first_name":"Eva","last_name":"Cereghetti"},{"first_name":"David","last_name":"Field","orcid":"0000-0002-4014-8478","full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","date_created":"2019-09-07T14:35:40Z","department":[{"_id":"NiBa"}],"publication_status":"published","intvolume":"       224","title":"Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow","quality_controlled":"1","ec_funded":1,"page":"1035-1047","file_date_updated":"2020-07-14T12:47:42Z","publisher":"Wiley","article_type":"original","citation":{"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>.","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>","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>","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.","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.","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>."},"year":"2019","date_updated":"2023-10-18T08:47:08Z","external_id":{"pmid":["31505037"]},"day":"01","doi":"10.1111/nph.16180","abstract":[{"lang":"eng","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."}],"volume":224,"ddc":["570"]}]