[{"publication_identifier":{"issn":["20411723"]},"pubrep_id":"791","doi":"10.1038/ncomms14251","quality_controlled":"1","isi":1,"language":[{"iso":"eng"}],"author":[{"full_name":"Wright, Alison","last_name":"Wright","first_name":"Alison"},{"full_name":"Darolti, Iulia","last_name":"Darolti","first_name":"Iulia"},{"full_name":"Bloch, Natasha","first_name":"Natasha","last_name":"Bloch"},{"first_name":"Vicencio","last_name":"Oostra","full_name":"Oostra, Vicencio"},{"full_name":"Sandkam, Benjamin","first_name":"Benjamin","last_name":"Sandkam"},{"first_name":"Séverine","last_name":"Buechel","full_name":"Buechel, Séverine"},{"last_name":"Kolm","first_name":"Niclas","full_name":"Kolm, Niclas"},{"first_name":"Felix","last_name":"Breden","full_name":"Breden, Felix"},{"first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306"},{"full_name":"Mank, Judith","last_name":"Mank","first_name":"Judith"}],"file":[{"content_type":"application/pdf","relation":"main_file","file_size":955256,"creator":"system","file_name":"IST-2017-791-v1+1_ncomms14251.pdf","date_created":"2018-12-12T10:15:22Z","access_level":"open_access","date_updated":"2018-12-12T10:15:22Z","file_id":"5141"}],"day":"31","title":"Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation","article_number":"14251","publist_id":"6292","publisher":"Nature Publishing Group","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"BeVi"}],"publication":"Nature Communications","article_processing_charge":"No","scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication_status":"published","oa":1,"has_accepted_license":"1","date_published":"2017-01-31T00:00:00Z","ddc":["570","576"],"status":"public","external_id":{"isi":["000392953700001"]},"intvolume":"         8","citation":{"apa":"Wright, A., Darolti, I., Bloch, N., Oostra, V., Sandkam, B., Buechel, S., … Mank, J. (2017). Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms14251\">https://doi.org/10.1038/ncomms14251</a>","mla":"Wright, Alison, et al. “Convergent Recombination Suppression Suggests Role of Sexual Selection in Guppy Sex Chromosome Formation.” <i>Nature Communications</i>, vol. 8, 14251, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/ncomms14251\">10.1038/ncomms14251</a>.","ista":"Wright A, Darolti I, Bloch N, Oostra V, Sandkam B, Buechel S, Kolm N, Breden F, Vicoso B, Mank J. 2017. Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation. Nature Communications. 8, 14251.","ama":"Wright A, Darolti I, Bloch N, et al. Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation. <i>Nature Communications</i>. 2017;8. doi:<a href=\"https://doi.org/10.1038/ncomms14251\">10.1038/ncomms14251</a>","short":"A. Wright, I. Darolti, N. Bloch, V. Oostra, B. Sandkam, S. Buechel, N. Kolm, F. Breden, B. Vicoso, J. Mank, Nature Communications 8 (2017).","chicago":"Wright, Alison, Iulia Darolti, Natasha Bloch, Vicencio Oostra, Benjamin Sandkam, Séverine Buechel, Niclas Kolm, Felix Breden, Beatriz Vicoso, and Judith Mank. “Convergent Recombination Suppression Suggests Role of Sexual Selection in Guppy Sex Chromosome Formation.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/ncomms14251\">https://doi.org/10.1038/ncomms14251</a>.","ieee":"A. Wright <i>et al.</i>, “Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation,” <i>Nature Communications</i>, vol. 8. Nature Publishing Group, 2017."},"date_updated":"2023-09-20T11:48:16Z","abstract":[{"lang":"eng","text":"Sex chromosomes evolve once recombination is halted between a homologous pair of chromosomes. The dominant model of sex chromosome evolution posits that recombination is suppressed between emerging X and Y chromosomes in order to resolve sexual conflict. Here we test this model using whole genome and transcriptome resequencing data in the guppy, a model for sexual selection with many Y-linked colour traits. We show that although the nascent Y chromosome encompasses nearly half of the linkage group, there has been no perceptible degradation of Y chromosome gene content or activity. Using replicate wild populations with differing levels of sexually antagonistic selection for colour, we also show that sexual selection leads to greater expansion of the non-recombining region and increased Y chromosome divergence. These results provide empirical support for longstanding models of sex chromosome catalysis, and suggest an important role for sexual selection and sexual conflict in genome evolution."}],"type":"journal_article","oa_version":"Published Version","month":"01","volume":8,"date_created":"2018-12-11T11:50:04Z","file_date_updated":"2018-12-12T10:15:22Z","year":"2017","_id":"1085"},{"project":[{"grant_number":"P28842-B22","_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Sex chromosome evolution under male- and female- heterogamety"}],"status":"public","related_material":{"record":[{"id":"614","status":"public","relation":"research_paper"}]},"citation":{"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.","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>.","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>","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>.","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>.","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>"},"oa":1,"has_accepted_license":"1","doi":"10.15479/AT:ISTA:7163","ddc":["576"],"date_published":"2017-12-01T00:00:00Z","contributor":[{"last_name":"Fraisse","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075"},{"id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8101-2518","last_name":"Picard","first_name":"Marion A L"},{"last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"year":"2017","_id":"7163","article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"author":[{"first_name":"Christelle","last_name":"Fraisse","full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075"}],"date_updated":"2024-02-21T13:47:47Z","abstract":[{"text":"The de novo genome assemblies generated for this study, and the associated metadata.","lang":"eng"}],"day":"01","file":[{"file_name":"Vicoso_Cohridella_Ndegeerella_Tsylvina_genome_assemblies.zip","content_type":"application/zip","relation":"main_file","file_size":841375478,"creator":"cfraisse","date_updated":"2020-07-14T12:47:50Z","file_id":"7164","checksum":"3cae8a2e3cbf8703399b9c483aaba7f3","date_created":"2019-12-10T08:46:46Z","access_level":"open_access"}],"oa_version":"Published Version","type":"research_data","month":"12","title":"Supplementary Files for \"The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W\"","file_date_updated":"2020-07-14T12:47:50Z","date_created":"2019-12-09T23:03:03Z"},{"related_material":{"record":[{"status":"public","id":"542","relation":"research_paper"}]},"citation":{"chicago":"Vicoso, Beatriz. “Data for ‘The Genomic Characterization of the t-Haplotype, a Mouse Meiotic Driver, Highlights Its Complex History and Specialized Biology.’” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:78\">https://doi.org/10.15479/AT:ISTA:78</a>.","ieee":"B. Vicoso, “Data for ‘The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology.’” Institute of Science and Technology Austria, 2017.","short":"B. Vicoso, (2017).","ama":"Vicoso B. Data for “The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology.” 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:78\">10.15479/AT:ISTA:78</a>","apa":"Vicoso, B. (2017). Data for “The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:78\">https://doi.org/10.15479/AT:ISTA:78</a>","ista":"Vicoso B. 2017. Data for ‘The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:78\">10.15479/AT:ISTA:78</a>.","mla":"Vicoso, Beatriz. <i>Data for “The Genomic Characterization of the t-Haplotype, a Mouse Meiotic Driver, Highlights Its Complex History and Specialized Biology.”</i> Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:78\">10.15479/AT:ISTA:78</a>."},"status":"public","date_published":"2017-11-06T00:00:00Z","ddc":["576"],"doi":"10.15479/AT:ISTA:78","contributor":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","contributor_type":"contact_person","first_name":"Beatriz"}],"oa":1,"has_accepted_license":"1","_id":"5571","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"article_processing_charge":"No","datarep_id":"78","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","department":[{"_id":"BeVi"}],"year":"2017","title":"Data for \"The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology\"","date_created":"2018-12-12T12:31:36Z","file_date_updated":"2020-07-14T12:47:04Z","author":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","first_name":"Beatriz","last_name":"Vicoso"}],"month":"11","oa_version":"Submitted Version","type":"research_data","abstract":[{"text":"This folder contains all the data used in each of the main figures of \"The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology\" (Kelemen, R., Vicoso, B.), as well as in the supplementary figures. \r\n","lang":"eng"}],"license":"https://creativecommons.org/publicdomain/zero/1.0/","day":"06","date_updated":"2024-02-21T13:48:16Z","file":[{"date_created":"2018-12-12T13:03:00Z","access_level":"open_access","file_id":"5618","date_updated":"2020-07-14T12:47:04Z","checksum":"4520eb2b8379417ee916995719158f16","file_size":143697895,"relation":"main_file","content_type":"application/zip","creator":"system","file_name":"IST-2017-78-v1+1_Data.zip"}]},{"related_material":{"record":[{"relation":"research_paper","id":"542","status":"public"}]},"citation":{"ieee":"B. Vicoso, “Code for ‘The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology.’” Institute of Science and Technology Austria, 2017.","chicago":"Vicoso, Beatriz. “Code for ‘The Genomic Characterization of the t-Haplotype, a Mouse Meiotic Driver, Highlights Its Complex History and Specialized Biology.’” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:79 \">https://doi.org/10.15479/AT:ISTA:79 </a>.","short":"B. Vicoso, (2017).","ama":"Vicoso B. Code for “The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology.” 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:79 \">10.15479/AT:ISTA:79 </a>","mla":"Vicoso, Beatriz. <i>Code for “The Genomic Characterization of the t-Haplotype, a Mouse Meiotic Driver, Highlights Its Complex History and Specialized Biology.”</i> Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:79 \">10.15479/AT:ISTA:79 </a>.","ista":"Vicoso B. 2017. Code for ‘The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:79 \">10.15479/AT:ISTA:79 </a>.","apa":"Vicoso, B. (2017). Code for “The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:79 \">https://doi.org/10.15479/AT:ISTA:79 </a>"},"status":"public","doi":"10.15479/AT:ISTA:79 ","date_published":"2017-11-06T00:00:00Z","ddc":["576"],"oa":1,"has_accepted_license":"1","_id":"5572","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"article_processing_charge":"No","datarep_id":"79","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","year":"2017","department":[{"_id":"BeVi"}],"title":"Code for \"The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology\"","file_date_updated":"2020-07-14T12:47:05Z","date_created":"2018-12-12T12:31:36Z","author":[{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso"}],"month":"11","type":"research_data","oa_version":"Submitted Version","date_updated":"2024-02-21T13:48:28Z","file":[{"checksum":"3e70a7bcd6ff0c38b79e4c8a7d137034","file_id":"5643","date_updated":"2020-07-14T12:47:05Z","access_level":"open_access","date_created":"2018-12-12T13:05:15Z","file_name":"IST-2017-79-v1+1_Code.zip","creator":"system","file_size":49823,"content_type":"application/zip","relation":"main_file"}],"abstract":[{"text":"Code described in the Supplementary Methods of \"The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology\" (Kelemen, R., Vicoso, B.)","lang":"eng"}],"day":"06"},{"oa":1,"publication_status":"published","has_accepted_license":"1","date_published":"2017-12-01T00:00:00Z","ddc":["570","576"],"external_id":{"pmid":["29133797"]},"status":"public","related_material":{"record":[{"status":"public","id":"7163","relation":"popular_science"}]},"intvolume":"         8","citation":{"ieee":"C. Fraisse, M. A. L. Picard, and B. Vicoso, “The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W,” <i>Nature Communications</i>, vol. 8, no. 1. Nature Publishing Group, 2017.","chicago":"Fraisse, Christelle, Marion A L Picard, and Beatriz Vicoso. “The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/s41467-017-01663-5\">https://doi.org/10.1038/s41467-017-01663-5</a>.","short":"C. Fraisse, M.A.L. Picard, B. Vicoso, Nature Communications 8 (2017).","ama":"Fraisse C, Picard MAL, Vicoso B. The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W. <i>Nature Communications</i>. 2017;8(1). doi:<a href=\"https://doi.org/10.1038/s41467-017-01663-5\">10.1038/s41467-017-01663-5</a>","ista":"Fraisse C, Picard MAL, Vicoso B. 2017. The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W. Nature Communications. 8(1), 1486.","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>.","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>"},"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."}],"oa_version":"Published Version","month":"12","type":"journal_article","volume":8,"date_created":"2018-12-11T11:47:30Z","file_date_updated":"2020-07-14T12:47:20Z","year":"2017","_id":"614","publication_identifier":{"issn":["20411723"]},"pubrep_id":"910","doi":"10.1038/s41467-017-01663-5","quality_controlled":"1","project":[{"call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425","name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22"}],"language":[{"iso":"eng"}],"issue":"1","author":[{"first_name":"Christelle","last_name":"Fraisse","full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075"},{"orcid":"0000-0002-8101-2518","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","full_name":"Picard, Marion A","last_name":"Picard","first_name":"Marion A"},{"first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"file":[{"file_name":"2017_NatureComm_Fraisse.pdf","file_size":1201520,"relation":"main_file","content_type":"application/pdf","creator":"dernst","file_id":"7562","date_updated":"2020-07-14T12:47:20Z","checksum":"4da2651303c8afc2f7fc419be42a2433","date_created":"2020-03-03T15:55:50Z","access_level":"open_access"}],"day":"01","title":"The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W","article_number":"1486","publist_id":"7190","publisher":"Nature Publishing Group","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publication":"Nature Communications","scopus_import":1,"article_processing_charge":"No","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"external_id":{"isi":["000411814800016"]},"status":"public","citation":{"ama":"Huylmans AK, Macon A, Vicoso B. Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. <i>Molecular Biology and Evolution</i>. 2017;34(10):2637-2649. doi:<a href=\"https://doi.org/10.1093/molbev/msx190\">10.1093/molbev/msx190</a>","mla":"Huylmans, Ann K., et al. “Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome.” <i>Molecular Biology and Evolution</i>, vol. 34, no. 10, Oxford University Press, 2017, pp. 2637–49, doi:<a href=\"https://doi.org/10.1093/molbev/msx190\">10.1093/molbev/msx190</a>.","ista":"Huylmans AK, Macon A, Vicoso B. 2017. Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. Molecular Biology and Evolution. 34(10), 2637–2649.","apa":"Huylmans, A. K., Macon, A., &#38; Vicoso, B. (2017). Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msx190\">https://doi.org/10.1093/molbev/msx190</a>","ieee":"A. K. Huylmans, A. Macon, and B. Vicoso, “Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome,” <i>Molecular Biology and Evolution</i>, vol. 34, no. 10. Oxford University Press, pp. 2637–2649, 2017.","chicago":"Huylmans, Ann K, Ariana Macon, and Beatriz Vicoso. “Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2017. <a href=\"https://doi.org/10.1093/molbev/msx190\">https://doi.org/10.1093/molbev/msx190</a>.","short":"A.K. Huylmans, A. Macon, B. Vicoso, Molecular Biology and Evolution 34 (2017) 2637–2649."},"intvolume":"        34","has_accepted_license":"1","oa":1,"publication_status":"published","date_published":"2017-07-06T00:00:00Z","ddc":["570","576"],"year":"2017","_id":"945","type":"journal_article","month":"07","oa_version":"Published Version","abstract":[{"lang":"eng","text":"While chromosome-wide dosage compensation of the X chromosome has been found in many species, studies in ZW clades have indicated that compensation of the Z is more localized and/or incomplete. In the ZW Lepidoptera, some species show complete compensation of the Z chromosome, while others lack full equalization, but what drives these inconsistencies is unclear. Here, we compare patterns of male and female gene expression on the Z chromosome of two closely related butterfly species, Papilio xuthus and Papilio machaon, and in multiple tissues of two moths species, Plodia interpunctella and Bombyx mori, which were previously found to differ in the extent to which they equalize Z-linked gene expression between the sexes. We find that, while some species and tissues seem to have incomplete dosage compensation, this is in fact due to the accumulation of male-biased genes and the depletion of female-biased genes on the Z chromosome. Once this is accounted for, the Z chromosome is fully compensated in all four species, through the up-regulation of Z expression in females and in some cases additional down-regulation in males. We further find that both sex-biased genes and Z-linked genes have increased rates of expression divergence in this clade, and that this can lead to fast shifts in patterns of gene expression even between closely related species. Taken together, these results show that the uneven distribution of sex-biased genes on sex chromosomes can confound conclusions about dosage compensation and that Z chromosome-wide dosage compensation is not only possible but ubiquitous among Lepidoptera."}],"date_updated":"2023-09-26T15:36:34Z","page":"2637 - 2649","date_created":"2018-12-11T11:49:20Z","file_date_updated":"2020-07-14T12:48:15Z","volume":34,"project":[{"_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22"}],"issue":"10","language":[{"iso":"eng"}],"isi":1,"pubrep_id":"848","publication_identifier":{"issn":["07374038"]},"quality_controlled":"1","doi":"10.1093/molbev/msx190","department":[{"_id":"BeVi"}],"publisher":"Oxford University Press","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","publication":"Molecular Biology and Evolution","file":[{"file_name":"IST-2017-848-v1+1_2017_Vicoso_GlobalDosage.pdf","file_size":462863,"relation":"main_file","content_type":"application/pdf","creator":"system","file_id":"4810","date_updated":"2020-07-14T12:48:15Z","checksum":"009fd68043211d645ceb9d1de28274f2","date_created":"2018-12-12T10:10:23Z","access_level":"open_access"}],"day":"06","author":[{"first_name":"Ann K","last_name":"Huylmans","full_name":"Huylmans, Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8871-4961"},{"first_name":"Ariana","last_name":"Macon","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","full_name":"Macon, Ariana"},{"first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306"}],"publist_id":"6472","title":"Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome"},{"publication_identifier":{"issn":["0018067X"]},"doi":"10.1038/hdy.2017.12","quality_controlled":"1","isi":1,"issue":"1","language":[{"iso":"eng"}],"author":[{"full_name":"Argyridou, Eliza","last_name":"Argyridou","first_name":"Eliza"},{"full_name":"Huylmans, Ann K","orcid":"0000-0001-8871-4961","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","first_name":"Ann K","last_name":"Huylmans"},{"full_name":"Königer, Annabella","first_name":"Annabella","last_name":"Königer"},{"full_name":"Parsch, John","last_name":"Parsch","first_name":"John"}],"day":"01","title":"X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster","publist_id":"6374","publisher":"Nature Publishing Group","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"BeVi"}],"publication":"Heredity","scopus_import":"1","article_processing_charge":"No","publication_status":"published","date_published":"2017-07-01T00:00:00Z","external_id":{"isi":["000405397800004"]},"status":"public","related_material":{"record":[{"relation":"research_data","status":"public","id":"9861"}]},"intvolume":"       119","citation":{"short":"E. Argyridou, A.K. Huylmans, A. Königer, J. Parsch, Heredity 119 (2017) 27–34.","ieee":"E. Argyridou, A. K. Huylmans, A. Königer, and J. Parsch, “X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster,” <i>Heredity</i>, vol. 119, no. 1. Nature Publishing Group, pp. 27–34, 2017.","chicago":"Argyridou, Eliza, Ann K Huylmans, Annabella Königer, and John Parsch. “X-Linkage Is Not a General Inhibitor of Tissue-Specific Gene Expression in Drosophila Melanogaster.” <i>Heredity</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/hdy.2017.12\">https://doi.org/10.1038/hdy.2017.12</a>.","mla":"Argyridou, Eliza, et al. “X-Linkage Is Not a General Inhibitor of Tissue-Specific Gene Expression in Drosophila Melanogaster.” <i>Heredity</i>, vol. 119, no. 1, Nature Publishing Group, 2017, pp. 27–34, doi:<a href=\"https://doi.org/10.1038/hdy.2017.12\">10.1038/hdy.2017.12</a>.","ista":"Argyridou E, Huylmans AK, Königer A, Parsch J. 2017. X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster. Heredity. 119(1), 27–34.","apa":"Argyridou, E., Huylmans, A. K., Königer, A., &#38; Parsch, J. (2017). X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster. <i>Heredity</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/hdy.2017.12\">https://doi.org/10.1038/hdy.2017.12</a>","ama":"Argyridou E, Huylmans AK, Königer A, Parsch J. X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster. <i>Heredity</i>. 2017;119(1):27-34. doi:<a href=\"https://doi.org/10.1038/hdy.2017.12\">10.1038/hdy.2017.12</a>"},"page":"27 - 34","oa_version":"None","month":"07","type":"journal_article","abstract":[{"text":"As a consequence of its difference in copy number between males and females, the X chromosome is subject to unique evolutionary forces and gene regulatory mechanisms. Previous studies of Drosophila melanogaster have shown that the expression of X-linked, testis-specific reporter genes is suppressed in the male germline. However, it is not known whether this phenomenon is restricted to testis-expressed genes or if it is a more general property of genes with tissue-specific expression, which are also underrepresented on the X chromosome. To test this, we compared the expression of three tissue-specific reporter genes (ovary, accessory gland and Malpighian tubule) inserted at various autosomal and X-chromosomal locations. In contrast to testis-specific reporter genes, we found no reduction of X-linked expression in any of the other tissues. In accessory gland and Malpighian tubule, we detected higher expression of the X-linked reporter genes, which suggests that they are at least partially dosage compensated. We found no difference in the tissue-specificity of X-linked and autosomal reporter genes. These findings indicate that, in general, the X chromosome is not a detrimental environment for tissue-specific gene expression and that the suppression of X-linked expression is limited to the male germline.","lang":"eng"}],"date_updated":"2023-09-22T09:41:21Z","volume":119,"date_created":"2018-12-11T11:49:43Z","year":"2017","_id":"1019"},{"publisher":"Dryad","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"BeVi"}],"year":"2017","_id":"9861","article_processing_charge":"No","author":[{"last_name":"Argyridou","first_name":"Eliza","full_name":"Argyridou, Eliza"},{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8871-4961","full_name":"Huylmans, Ann K","last_name":"Huylmans","first_name":"Ann K"},{"first_name":"Annabella","last_name":"Königer","full_name":"Königer, Annabella"},{"full_name":"Parsch, John","last_name":"Parsch","first_name":"John"}],"abstract":[{"lang":"eng","text":"As a consequence of its difference in copy number between males and females, the X chromosome is subject to unique evolutionary forces and gene regulatory mechanisms. Previous studies of Drosophila melanogaster have shown that the expression of X-linked, testis-specific reporter genes is suppressed in the male germline. However, it is not known whether this phenomenon is restricted to testis-expressed genes or if it is a more general property of genes with tissue-specific expression, which are also underrepresented on the X chromosome. To test this, we compared the expression of three tissue-specific reporter genes (ovary, accessory gland and Malpighian tubule) inserted at various autosomal and X-chromosomal locations. In contrast to testis-specific reporter genes, we found no reduction of X-linked expression in any of the other tissues. In accessory gland and Malpighian tubule, we detected higher expression of the X-linked reporter genes, which suggests that they are at least partially dosage compensated. We found no difference in the tissue-specificity of X-linked and autosomal reporter genes. These findings indicate that, in general, the X chromosome is not a detrimental environment for tissue-specific gene expression and that the suppression of X-linked expression is limited to the male germline."}],"day":"14","date_updated":"2023-09-22T09:41:20Z","month":"02","oa_version":"Published Version","type":"research_data_reference","title":"Data from: X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster","date_created":"2021-08-10T08:12:52Z","status":"public","related_material":{"record":[{"relation":"used_in_publication","id":"1019","status":"public"}]},"citation":{"short":"E. Argyridou, A.K. Huylmans, A. Königer, J. Parsch, (2017).","chicago":"Argyridou, Eliza, Ann K Huylmans, Annabella Königer, and John Parsch. “Data from: X-Linkage Is Not a General Inhibitor of Tissue-Specific Gene Expression in Drosophila Melanogaster.” Dryad, 2017. <a href=\"https://doi.org/10.5061/dryad.02f6r\">https://doi.org/10.5061/dryad.02f6r</a>.","ieee":"E. Argyridou, A. K. Huylmans, A. Königer, and J. Parsch, “Data from: X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster.” Dryad, 2017.","apa":"Argyridou, E., Huylmans, A. K., Königer, A., &#38; Parsch, J. (2017). Data from: X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster. Dryad. <a href=\"https://doi.org/10.5061/dryad.02f6r\">https://doi.org/10.5061/dryad.02f6r</a>","mla":"Argyridou, Eliza, et al. <i>Data from: X-Linkage Is Not a General Inhibitor of Tissue-Specific Gene Expression in Drosophila Melanogaster</i>. Dryad, 2017, doi:<a href=\"https://doi.org/10.5061/dryad.02f6r\">10.5061/dryad.02f6r</a>.","ista":"Argyridou E, Huylmans AK, Königer A, Parsch J. 2017. Data from: X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster, Dryad, <a href=\"https://doi.org/10.5061/dryad.02f6r\">10.5061/dryad.02f6r</a>.","ama":"Argyridou E, Huylmans AK, Königer A, Parsch J. Data from: X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster. 2017. doi:<a href=\"https://doi.org/10.5061/dryad.02f6r\">10.5061/dryad.02f6r</a>"},"oa":1,"doi":"10.5061/dryad.02f6r","date_published":"2017-02-14T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.5061/dryad.02f6r","open_access":"1"}]},{"author":[{"full_name":"Roux, Camille","last_name":"Roux","first_name":"Camille"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","first_name":"Christelle","last_name":"Fraisse"},{"last_name":"Romiguier","first_name":"Jonathan","full_name":"Romiguier, Jonathan"},{"last_name":"Anciaux","first_name":"Youann","full_name":"Anciaux, Youann"},{"last_name":"Galtier","first_name":"Nicolas","full_name":"Galtier, Nicolas"},{"full_name":"Bierne, Nicolas","first_name":"Nicolas","last_name":"Bierne"}],"day":"27","file":[{"file_id":"5164","date_updated":"2020-07-14T12:44:36Z","checksum":"2bab63b068a9840efd532b9ae583f9bb","date_created":"2018-12-12T10:15:42Z","access_level":"open_access","file_name":"IST-2017-742-v1+1_journal.pbio.2000234.pdf","file_size":2494348,"relation":"main_file","content_type":"application/pdf","creator":"system"}],"article_number":"e2000234","title":"Shedding light on the grey zone of speciation along a continuum of genomic divergence","publist_id":"6200","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Public Library of Science","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publication":"PLoS Biology","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"scopus_import":1,"pubrep_id":"742","doi":"10.1371/journal.pbio.2000234","quality_controlled":"1","issue":"12","language":[{"iso":"eng"}],"oa_version":"Published Version","month":"12","type":"journal_article","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"}],"date_updated":"2023-02-23T14:11:16Z","volume":14,"file_date_updated":"2020-07-14T12:44:36Z","date_created":"2018-12-11T11:50:28Z","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.","year":"2016","_id":"1158","publication_status":"published","oa":1,"has_accepted_license":"1","date_published":"2016-12-27T00:00:00Z","ddc":["576"],"status":"public","intvolume":"        14","related_material":{"record":[{"relation":"research_data","id":"9862","status":"public"},{"status":"public","id":"9863","relation":"research_data"}]},"citation":{"ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Shedding light on the grey zone of speciation along a continuum of genomic divergence. <i>PLoS Biology</i>. 2016;14(12). doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234\">10.1371/journal.pbio.2000234</a>","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.","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>.","apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., &#38; Bierne, N. (2016). Shedding light on the grey zone of speciation along a continuum of genomic divergence. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2000234\">https://doi.org/10.1371/journal.pbio.2000234</a>","ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Shedding light on the grey zone of speciation along a continuum of genomic divergence,” <i>PLoS Biology</i>, vol. 14, no. 12. Public Library of Science, 2016.","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>.","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, PLoS Biology 14 (2016)."}},{"oa_version":"Published Version","month":"10","type":"journal_article","abstract":[{"lang":"eng","text":"Daphnia species have become models for ecological genomics and exhibit interesting features, such as high phenotypic plasticity and a densely packed genome with many lineage-specific genes. They are also cyclic parthenogenetic, with alternating asexual and sexual cycles and environmental sex determination. Here, we present a de novo transcriptome assembly of over 32,000 D. galeata genes and use it to investigate gene expression in females and spontaneously produced males of two clonal lines derived from lakes in Germany and the Czech Republic. We find that only a low percentage (18%) of genes shows sex-biased expression and that there are many more female-biased gene (FBG) than male-biased gene (MBG). Furthermore, FBGs tend to be more conserved between species than MBGs in both sequence and expression. These patterns may be a consequence of cyclic parthenogenesis leading to a relaxation of purifying selection on MBGs. The two clonal lines show considerable differences in both number and identity of sex-biased genes, suggesting that they may have reproductive strategies differing in their investment in sexual reproduction. Orthologs of key genes in the sex determination and juvenile hormone pathways, which are thought to be important for the transition from asexual to sexual reproduction, are present in D. galeata and highly conserved among Daphnia species."}],"date_updated":"2021-01-12T06:49:55Z","page":"3120 - 3139","date_created":"2018-12-11T11:51:24Z","file_date_updated":"2020-07-14T12:44:44Z","volume":8,"year":"2016","acknowledgement":"This study was financially supported by individual grants from the Volkswagen Stiftung (to M.C.), the Deutsche Forschungsgemeinschaft (grant PA 903/6 to J.P.) and the DAAD (to A.K.H.). The authors would like to thank I. Schrank, L. Theodosiou, M. Kredler, C. Laforsch, J. Wolinska, J. Griebel, R. Jaenichen, and K. Otte for providing the necessary resources and help for maintaining Daphnia cultures in the laboratory. H. Lainer supported us for the molecular laboratory work. D. Gilbert and J. K. Colbourne contributed ideas for the bioinformatics analysis, and L. Hardulak did the orthology mapping including more insect species. This study was financially supported by individual grants from the Volkswagen Stiftung (to M.C.), the Deutsche Forschungsgemeinschaft (grant PA 903/6 to J.P.) and the DAAD (to A.K.H.). This work benefits from and contributes to the Daphnia Genomics Consortium.","_id":"1329","has_accepted_license":"1","publication_status":"published","oa":1,"date_published":"2016-10-01T00:00:00Z","ddc":["576"],"status":"public","citation":{"chicago":"Huylmans, Ann K, Alberto López Ezquerra, John Parsch, and Mathilde Cordellier. “De Novo Transcriptome Assembly and Sex-Biased Gene Expression in the Cyclical Parthenogenetic Daphnia Galeata.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1093/gbe/evw221\">https://doi.org/10.1093/gbe/evw221</a>.","ieee":"A. K. Huylmans, A. López Ezquerra, J. Parsch, and M. Cordellier, “De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata,” <i>Genome Biology and Evolution</i>, vol. 8, no. 10. Oxford University Press, pp. 3120–3139, 2016.","short":"A.K. Huylmans, A. López Ezquerra, J. Parsch, M. Cordellier, Genome Biology and Evolution 8 (2016) 3120–3139.","ama":"Huylmans AK, López Ezquerra A, Parsch J, Cordellier M. De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata. <i>Genome Biology and Evolution</i>. 2016;8(10):3120-3139. doi:<a href=\"https://doi.org/10.1093/gbe/evw221\">10.1093/gbe/evw221</a>","apa":"Huylmans, A. K., López Ezquerra, A., Parsch, J., &#38; Cordellier, M. (2016). De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evw221\">https://doi.org/10.1093/gbe/evw221</a>","ista":"Huylmans AK, López Ezquerra A, Parsch J, Cordellier M. 2016. De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata. Genome Biology and Evolution. 8(10), 3120–3139.","mla":"Huylmans, Ann K., et al. “De Novo Transcriptome Assembly and Sex-Biased Gene Expression in the Cyclical Parthenogenetic Daphnia Galeata.” <i>Genome Biology and Evolution</i>, vol. 8, no. 10, Oxford University Press, 2016, pp. 3120–39, doi:<a href=\"https://doi.org/10.1093/gbe/evw221\">10.1093/gbe/evw221</a>."},"intvolume":"         8","file":[{"file_name":"IST-2016-663-v1+1_Genome_Biol_Evol-2016-Huylmans-3120-39.pdf","creator":"system","relation":"main_file","content_type":"application/pdf","file_size":1406265,"checksum":"25c7adcb452d39d3b6343ff4b57a652d","date_updated":"2020-07-14T12:44:44Z","file_id":"4924","access_level":"open_access","date_created":"2018-12-12T10:12:06Z"}],"day":"01","author":[{"orcid":"0000-0001-8871-4961","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","full_name":"Huylmans, Ann K","last_name":"Huylmans","first_name":"Ann K"},{"first_name":"Alberto","last_name":"López Ezquerra","full_name":"López Ezquerra, Alberto"},{"full_name":"Parsch, John","last_name":"Parsch","first_name":"John"},{"first_name":"Mathilde","last_name":"Cordellier","full_name":"Cordellier, Mathilde"}],"publist_id":"5940","title":"De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata","department":[{"_id":"BeVi"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Oxford University Press","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"scopus_import":1,"publication":"Genome Biology and Evolution","pubrep_id":"663","quality_controlled":"1","doi":"10.1093/gbe/evw221","issue":"10","language":[{"iso":"eng"}]},{"date_created":"2021-08-10T08:20:17Z","title":"Simulation study to test the robustness of ABC in face of recent times of divergence","date_updated":"2023-02-21T16:21:20Z","day":"27","type":"research_data_reference","month":"12","oa_version":"Published Version","author":[{"full_name":"Roux, Camille","first_name":"Camille","last_name":"Roux"},{"last_name":"Fraisse","first_name":"Christelle","full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075"},{"full_name":"Romiguier, Jonathan","first_name":"Jonathan","last_name":"Romiguier"},{"last_name":"Anciaux","first_name":"Youann","full_name":"Anciaux, Youann"},{"full_name":"Galtier, Nicolas","last_name":"Galtier","first_name":"Nicolas"},{"full_name":"Bierne, Nicolas","last_name":"Bierne","first_name":"Nicolas"}],"article_processing_charge":"No","_id":"9862","year":"2016","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publisher":"Public Library of Science","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","doi":"10.1371/journal.pbio.2000234.s016","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>","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>.","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>","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.","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>.","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016)."},"related_material":{"record":[{"status":"public","id":"1158","relation":"used_in_publication"}]},"status":"public"},{"related_material":{"record":[{"relation":"used_in_publication","id":"1158","status":"public"}]},"citation":{"ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Accessions of surveyed individuals, geographic locations and summary statistics. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">10.1371/journal.pbio.2000234.s017</a>","mla":"Roux, Camille, et al. <i>Accessions of Surveyed Individuals, Geographic Locations and Summary Statistics</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">10.1371/journal.pbio.2000234.s017</a>.","ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Accessions of surveyed individuals, geographic locations and summary statistics, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">10.1371/journal.pbio.2000234.s017</a>.","apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., &#38; Bierne, N. (2016). Accessions of surveyed individuals, geographic locations and summary statistics. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">https://doi.org/10.1371/journal.pbio.2000234.s017</a>","ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Accessions of surveyed individuals, geographic locations and summary statistics.” Public Library of Science, 2016.","chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Accessions of Surveyed Individuals, Geographic Locations and Summary Statistics.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">https://doi.org/10.1371/journal.pbio.2000234.s017</a>.","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016)."},"status":"public","doi":"10.1371/journal.pbio.2000234.s017","_id":"9863","article_processing_charge":"No","publisher":"Public Library of Science","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"year":"2016","title":"Accessions of surveyed individuals, geographic locations and summary statistics","date_created":"2021-08-10T08:22:52Z","author":[{"last_name":"Roux","first_name":"Camille","full_name":"Roux, Camille"},{"first_name":"Christelle","last_name":"Fraisse","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle"},{"full_name":"Romiguier, Jonathan","first_name":"Jonathan","last_name":"Romiguier"},{"full_name":"Anciaux, Youann","first_name":"Youann","last_name":"Anciaux"},{"first_name":"Nicolas","last_name":"Galtier","full_name":"Galtier, Nicolas"},{"first_name":"Nicolas","last_name":"Bierne","full_name":"Bierne, Nicolas"}],"day":"27","date_updated":"2023-02-21T16:21:20Z","oa_version":"Published Version","type":"research_data_reference","month":"12"},{"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"issue":"12","language":[{"iso":"eng"}],"pubrep_id":"496","doi":"10.1093/gbe/evv215","quality_controlled":"1","publisher":"Oxford University Press","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"BeVi"}],"publication":"Genome Biology and Evolution","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"scopus_import":1,"article_processing_charge":"No","author":[{"full_name":"Pal, Arka","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","last_name":"Pal","first_name":"Arka"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso","first_name":"Beatriz"}],"file":[{"file_name":"IST-2016-496-v1+1_Genome_Biol_Evol-2015-Pal-3259-68.pdf","file_size":858027,"content_type":"application/pdf","relation":"main_file","creator":"system","file_id":"5284","date_updated":"2020-07-14T12:45:00Z","checksum":"2b56b8c2e2a1d4cc3c9cb8daba26dd9b","date_created":"2018-12-12T10:17:29Z","access_level":"open_access"}],"day":"01","title":"The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression","publist_id":"5664","status":"public","intvolume":"         7","citation":{"ama":"Pal A, Vicoso B. The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression. <i>Genome Biology and Evolution</i>. 2015;7(12):3259-3268. doi:<a href=\"https://doi.org/10.1093/gbe/evv215\">10.1093/gbe/evv215</a>","ista":"Pal A, Vicoso B. 2015. The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression. Genome Biology and Evolution. 7(12), 3259–3268.","mla":"Pal, Arka, and Beatriz Vicoso. “The X Chromosome of Hemipteran Insects: Conservation, Dosage Compensation and Sex-Biased Expression.” <i>Genome Biology and Evolution</i>, vol. 7, no. 12, Oxford University Press, 2015, pp. 3259–68, doi:<a href=\"https://doi.org/10.1093/gbe/evv215\">10.1093/gbe/evv215</a>.","apa":"Pal, A., &#38; Vicoso, B. (2015). The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evv215\">https://doi.org/10.1093/gbe/evv215</a>","ieee":"A. Pal and B. Vicoso, “The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression,” <i>Genome Biology and Evolution</i>, vol. 7, no. 12. Oxford University Press, pp. 3259–3268, 2015.","chicago":"Pal, Arka, and Beatriz Vicoso. “The X Chromosome of Hemipteran Insects: Conservation, Dosage Compensation and Sex-Biased Expression.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2015. <a href=\"https://doi.org/10.1093/gbe/evv215\">https://doi.org/10.1093/gbe/evv215</a>.","short":"A. Pal, B. Vicoso, Genome Biology and Evolution 7 (2015) 3259–3268."},"publication_status":"published","oa":1,"has_accepted_license":"1","date_published":"2015-12-01T00:00:00Z","ddc":["570"],"year":"2015","_id":"1513","page":"3259 - 3268","type":"journal_article","month":"12","oa_version":"Published Version","date_updated":"2021-01-12T06:51:18Z","abstract":[{"lang":"eng","text":"Insects of the order Hemiptera (true bugs) use a wide range of mechanisms of sex determination, including genetic sex determination, paternal genome elimination, and haplodiploidy. Genetic sex determination, the prevalent mode, is generally controlled by a pair of XY sex chromosomes or by an XX/X0 system, but different configurations that include additional sex chromosomes are also present. Although this diversity of sex determining systems has been extensively studied at the cytogenetic level, only the X chromosome of the model pea aphid Acyrthosiphon pisum has been analyzed at the genomic level, and little is known about X chromosome biology in the rest of the order.\r\n\r\nIn this study, we take advantage of published DNA- and RNA-seq data from three additional Hemiptera species to perform a comparative analysis of the gene content and expression of the X chromosome throughout this clade. We find that, despite showing evidence of dosage compensation, the X chromosomes of these species show female-biased expression, and a deficit of male-biased genes, in direct contrast to the pea aphid X. We further detect an excess of shared gene content between these very distant species, suggesting that despite the diversity of sex determining systems, the same chromosomal element is used as the X throughout a large portion of the order. "}],"volume":7,"date_created":"2018-12-11T11:52:27Z","file_date_updated":"2020-07-14T12:45:00Z"},{"article_type":"original","article_processing_charge":"No","scopus_import":1,"publication":"PNAS","department":[{"_id":"BeVi"}],"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"National Academy of Sciences","publist_id":"5594","title":"Birth of a new gene on the Y chromosome of Drosophila melanogaster","day":"06","author":[{"full_name":"Carvalho, Antonio","first_name":"Antonio","last_name":"Carvalho"},{"first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Russo, Claudia","first_name":"Claudia","last_name":"Russo"},{"full_name":"Swenor, Bonnielin","last_name":"Swenor","first_name":"Bonnielin"},{"last_name":"Clark","first_name":"Andrew","full_name":"Clark, Andrew"}],"issue":"40","language":[{"iso":"eng"}],"quality_controlled":"1","doi":"10.1073/pnas.1516543112","_id":"1577","year":"2015","acknowledgement":"This work was supported by grants from Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), FAPERJ, and CAPES (to A.B.C.), and National Institutes of Health Grant R01 GM64590 (to A.G.C. and A.B.C.).\r\nWe thank M. Vibranovski, C. Bergman, and the Berkeley Drosophila Genome Project for access to unpublished data; M. Vibranovski, R. Hoskins, S. Celniker, C. Kennedy, J. Carlson, S. Galasinski, B. Wakimoto, J. Yasuhara, G. Sutton, M. Kuhner, J. Felsenstein, and C. Santos for help in various steps of the work; and B. Bitner-Mathe, R. Ventura, the members of the A.B.C. and A.G.C. laboratories, and two reviewers for many valuable comments on the manuscript.","date_created":"2018-12-11T11:52:49Z","volume":112,"month":"10","type":"journal_article","oa_version":"Published Version","date_updated":"2021-01-12T06:51:43Z","abstract":[{"lang":"eng","text":"Contrary to the pattern seen in mammalian sex chromosomes, where most Y-linked genes have X-linked homologs, the Drosophila X and Y chromosomes appear to be unrelated. Most of the Y-linked genes have autosomal paralogs, so autosome-to-Y transposition must be the main source of Drosophila Y-linked genes. Here we show how these genes were acquired. We found a previously unidentified gene (flagrante delicto Y, FDY) that originated from a recent duplication of the autosomal gene vig2 to the Y chromosome of Drosophila melanogaster. Four contiguous genes were duplicated along with vig2, but they became pseudogenes through the accumulation of deletions and transposable element insertions, whereas FDY remained functional, acquired testis-specific expression, and now accounts for ∼20% of the vig2-like mRNA in testis. FDY is absent in the closest relatives of D. melanogaster, and DNA sequence divergence indicates that the duplication to the Y chromosome occurred ∼2 million years ago. Thus, FDY provides a snapshot of the early stages of the establishment of a Y-linked gene and demonstrates how the Drosophila Y has been accumulating autosomal genes."}],"page":"12450 - 12455","citation":{"short":"A. Carvalho, B. Vicoso, C. Russo, B. Swenor, A. Clark, PNAS 112 (2015) 12450–12455.","ieee":"A. Carvalho, B. Vicoso, C. Russo, B. Swenor, and A. Clark, “Birth of a new gene on the Y chromosome of Drosophila melanogaster,” <i>PNAS</i>, vol. 112, no. 40. National Academy of Sciences, pp. 12450–12455, 2015.","chicago":"Carvalho, Antonio, Beatriz Vicoso, Claudia Russo, Bonnielin Swenor, and Andrew Clark. “Birth of a New Gene on the Y Chromosome of Drosophila Melanogaster.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1516543112\">https://doi.org/10.1073/pnas.1516543112</a>.","ista":"Carvalho A, Vicoso B, Russo C, Swenor B, Clark A. 2015. Birth of a new gene on the Y chromosome of Drosophila melanogaster. PNAS. 112(40), 12450–12455.","mla":"Carvalho, Antonio, et al. “Birth of a New Gene on the Y Chromosome of Drosophila Melanogaster.” <i>PNAS</i>, vol. 112, no. 40, National Academy of Sciences, 2015, pp. 12450–55, doi:<a href=\"https://doi.org/10.1073/pnas.1516543112\">10.1073/pnas.1516543112</a>.","apa":"Carvalho, A., Vicoso, B., Russo, C., Swenor, B., &#38; Clark, A. (2015). Birth of a new gene on the Y chromosome of Drosophila melanogaster. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1516543112\">https://doi.org/10.1073/pnas.1516543112</a>","ama":"Carvalho A, Vicoso B, Russo C, Swenor B, Clark A. Birth of a new gene on the Y chromosome of Drosophila melanogaster. <i>PNAS</i>. 2015;112(40):12450-12455. doi:<a href=\"https://doi.org/10.1073/pnas.1516543112\">10.1073/pnas.1516543112</a>"},"intvolume":"       112","external_id":{"pmid":["26385968"]},"status":"public","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4603513/","open_access":"1"}],"date_published":"2015-10-06T00:00:00Z","publication_status":"published","oa":1}]