[{"oa_version":"Published Version","ddc":["570"],"title":"How chromosomal inversions reorient the evolutionary process","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14556","abstract":[{"text":"Inversions are structural mutations that reverse the sequence of a chromosome segment and reduce the effective rate of recombination in the heterozygous state. They play a major role in adaptation, as well as in other evolutionary processes such as speciation. Although inversions have been studied since the 1920s, they remain difficult to investigate because the reduced recombination conferred by them strengthens the effects of drift and hitchhiking, which in turn can obscure signatures of selection. Nonetheless, numerous inversions have been found to be under selection. Given recent advances in population genetic theory and empirical study, here we review how different mechanisms of selection affect the evolution of inversions. A key difference between inversions and other mutations, such as single nucleotide variants, is that the fitness of an inversion may be affected by a larger number of frequently interacting processes. This considerably complicates the analysis of the causes underlying the evolution of inversions. We discuss the extent to which these mechanisms can be disentangled, and by which approach.","lang":"eng"}],"type":"journal_article","date_published":"2023-11-08T00:00:00Z","article_type":"review","publication":"Journal of Evolutionary Biology","citation":{"ama":"Berdan EL, Barton NH, Butlin R, et al. How chromosomal inversions reorient the evolutionary process. Journal of Evolutionary Biology. 2023. doi:10.1111/jeb.14242","apa":"Berdan, E. L., Barton, N. H., Butlin, R., Charlesworth, B., Faria, R., Fragata, I., … Flatt, T. (2023). How chromosomal inversions reorient the evolutionary process. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.14242","ieee":"E. L. Berdan et al., “How chromosomal inversions reorient the evolutionary process,” Journal of Evolutionary Biology. Wiley, 2023.","ista":"Berdan EL, Barton NH, Butlin R, Charlesworth B, Faria R, Fragata I, Gilbert KJ, Jay P, Kapun M, Lotterhos KE, Mérot C, Durmaz Mitchell E, Pascual M, Peichel CL, Rafajlović M, Westram AM, Schaeffer SW, Johannesson K, Flatt T. 2023. How chromosomal inversions reorient the evolutionary process. Journal of Evolutionary Biology., 14242.","short":"E.L. Berdan, N.H. Barton, R. Butlin, B. Charlesworth, R. Faria, I. Fragata, K.J. Gilbert, P. Jay, M. Kapun, K.E. Lotterhos, C. Mérot, E. Durmaz Mitchell, M. Pascual, C.L. Peichel, M. Rafajlović, A.M. Westram, S.W. Schaeffer, K. Johannesson, T. Flatt, Journal of Evolutionary Biology (2023).","mla":"Berdan, Emma L., et al. “How Chromosomal Inversions Reorient the Evolutionary Process.” Journal of Evolutionary Biology, 14242, Wiley, 2023, doi:10.1111/jeb.14242.","chicago":"Berdan, Emma L., Nicholas H Barton, Roger Butlin, Brian Charlesworth, Rui Faria, Inês Fragata, Kimberly J. Gilbert, et al. “How Chromosomal Inversions Reorient the Evolutionary Process.” Journal of Evolutionary Biology. Wiley, 2023. https://doi.org/10.1111/jeb.14242."},"day":"08","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_updated":"2023-11-20T08:51:09Z","date_created":"2023-11-19T23:00:55Z","author":[{"last_name":"Berdan","first_name":"Emma L.","full_name":"Berdan, Emma L."},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"},{"full_name":"Butlin, Roger","first_name":"Roger","last_name":"Butlin"},{"full_name":"Charlesworth, Brian","first_name":"Brian","last_name":"Charlesworth"},{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"first_name":"Inês","last_name":"Fragata","full_name":"Fragata, Inês"},{"full_name":"Gilbert, Kimberly J.","last_name":"Gilbert","first_name":"Kimberly J."},{"full_name":"Jay, Paul","first_name":"Paul","last_name":"Jay"},{"last_name":"Kapun","first_name":"Martin","full_name":"Kapun, Martin"},{"full_name":"Lotterhos, Katie E.","first_name":"Katie E.","last_name":"Lotterhos"},{"last_name":"Mérot","first_name":"Claire","full_name":"Mérot, Claire"},{"last_name":"Durmaz Mitchell","first_name":"Esra","full_name":"Durmaz Mitchell, Esra"},{"full_name":"Pascual, Marta","last_name":"Pascual","first_name":"Marta"},{"last_name":"Peichel","first_name":"Catherine L.","full_name":"Peichel, Catherine L."},{"first_name":"Marina","last_name":"Rafajlović","full_name":"Rafajlović, Marina"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram","full_name":"Westram, Anja M"},{"last_name":"Schaeffer","first_name":"Stephen W.","full_name":"Schaeffer, Stephen W."},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"last_name":"Flatt","first_name":"Thomas","full_name":"Flatt, Thomas"}],"publication_status":"epub_ahead","department":[{"_id":"NiBa"}],"publisher":"Wiley","year":"2023","acknowledgement":"We are grateful to two referees and Luke Holman for valuable comments on a previous version of our manuscript. This paper was conceived at the ESEB Progress Meeting ‘Disentangling neutral versus adaptive evolution in chromosomal inversions’, organized by ELB, KJ and TF and held at Tjärnö Marine Laboratory (Sweden) between 28 February and 3 March 2022. We are indebted to ESEB for sponsoring our workshop and to the following funding bodies for supporting our research: ERC AdG 101055327 to NHB; Swedish Research Council (VR) 2018-03695 and Leverhulme Trust RPG-2021-141 to RKB; Fundação para a Ciência e a Tecnologia (FCT) contract 2020.00275.CEECIND and research project PTDC/BIA-1232 EVL/1614/2021 to RF; Fundação para a Ciência e a Tecnologia (FCT) junior researcher contract CEECIND/02616/2018 to IF; Swiss National Science Foundation (SNSF) Ambizione #PZ00P3_185952 to KJG; National Science Foundation NSF-OCE 2043905 and NSF-DEB 1655701 to KEL; Swiss National Science Foundation (SNSF) 310030_204681 to CLP; Swedish Research Council (VR) 2021-05243 to MR; Norwegian Research Council grant 315287 to AMW; Swiss National Science Foundation (SNSF) 31003A-182262 and FZEB-0-214654 to TF. We also thank Luca Ferretti for the discussion and Eliane Zinn (Flatt lab) for help with reference formatting.","article_number":"14242","language":[{"iso":"eng"}],"doi":"10.1111/jeb.14242","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"main_file_link":[{"url":"https://doi.org/10.1111/jeb.14242","open_access":"1"}],"month":"11","publication_identifier":{"eissn":["1420-9101"],"issn":["1010-061X"]}},{"month":"11","publication_identifier":{"eissn":["1095-9203"]},"external_id":{"pmid":["37943897"]},"quality_controlled":"1","doi":"10.1126/science.adh8830","language":[{"iso":"eng"}],"year":"2023","acknowledgement":"The authors acknowledge funding for central project coordination from NSF Research Coordination Network grant DEB-2203582; the Ecology, Evolution, and Behavior Program at Michigan State University; and AgBioResearch at Michigan State University. Site-specific funding is listed in the supplementary materials.","pmid":1,"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"AAAS","author":[{"full_name":"Robinson, M. L.","first_name":"M. L.","last_name":"Robinson"},{"last_name":"Hahn","first_name":"P. G.","full_name":"Hahn, P. G."},{"first_name":"B. D.","last_name":"Inouye","full_name":"Inouye, B. D."},{"full_name":"Underwood, N.","first_name":"N.","last_name":"Underwood"},{"last_name":"Whitehead","first_name":"S. R.","full_name":"Whitehead, S. R."},{"full_name":"Abbott, K. C.","first_name":"K. C.","last_name":"Abbott"},{"last_name":"Bruna","first_name":"E. M.","full_name":"Bruna, E. M."},{"first_name":"N. I.","last_name":"Cacho","full_name":"Cacho, N. I."},{"full_name":"Dyer, L. A.","first_name":"L. A.","last_name":"Dyer"},{"full_name":"Abdala-Roberts, L.","last_name":"Abdala-Roberts","first_name":"L."},{"last_name":"Allen","first_name":"W. J.","full_name":"Allen, W. J."},{"first_name":"J. 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P."},{"full_name":"Weber, M. G.","last_name":"Weber","first_name":"M. G."},{"full_name":"Yamawo, A.","first_name":"A.","last_name":"Yamawo"},{"full_name":"Yim, S.","first_name":"S.","last_name":"Yim"},{"first_name":"P. L.","last_name":"Zarnetske","full_name":"Zarnetske, P. L."},{"first_name":"L. N.","last_name":"Zehr","full_name":"Zehr, L. N."},{"full_name":"Zhong, Z.","last_name":"Zhong","first_name":"Z."},{"full_name":"Wetzel, W. C.","last_name":"Wetzel","first_name":"W. C."}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"14579"}]},"date_created":"2023-11-19T23:00:54Z","date_updated":"2023-11-20T11:17:34Z","volume":382,"scopus_import":"1","day":"09","article_processing_charge":"No","publication":"Science","citation":{"short":"M.L. Robinson, P.G. Hahn, B.D. Inouye, N. Underwood, S.R. Whitehead, K.C. Abbott, E.M. Bruna, N.I. Cacho, L.A. Dyer, L. Abdala-Roberts, W.J. Allen, J.F. Andrade, D.F. Angulo, D. Anjos, D.N. Anstett, R. Bagchi, S. Bagchi, M. Barbosa, S. Barrett, C. Baskett, E. Ben-Simchon, K.J. Bloodworth, J.L. Bronstein, Y.M. Buckley, K.T. Burghardt, C. Bustos-Segura, E.S. Calixto, R.L. Carvalho, B. Castagneyrol, M.C. Chiuffo, D. Cinoğlu, E. Cinto Mejía, M.C. Cock, R. Cogni, O.L. Cope, T. Cornelissen, D.R. Cortez, D.W. Crowder, C. Dallstream, W. Dáttilo, J.K. Davis, R.D. Dimarco, H.E. Dole, I.N. Egbon, M. Eisenring, A. Ejomah, B.D. Elderd, M.J. Endara, M.D. Eubanks, S.E. Everingham, K.N. Farah, R.P. Farias, A.P. Fernandes, G.W. Fernandes, M. Ferrante, A. Finn, G.A. Florjancic, M.L. Forister, Q.N. Fox, E. Frago, F.M. França, A.S. Getman-Pickering, Z. Getman-Pickering, E. Gianoli, B. Gooden, M.M. Gossner, K.A. Greig, S. Gripenberg, R. Groenteman, P. Grof-Tisza, N. Haack, L. Hahn, S.M. Haq, A.M. Helms, J. Hennecke, S.L. Hermann, L.M. Holeski, S. Holm, M.C. Hutchinson, E.E. Jackson, S. Kagiya, A. Kalske, M. Kalwajtys, R. Karban, R. Kariyat, T. Keasar, M.F. Kersch-Becker, H.M. Kharouba, T.N. Kim, D.M. Kimuyu, J. Kluse, S.E. Koerner, K.J. Komatsu, S. Krishnan, M. Laihonen, L. Lamelas-López, M.C. Lascaleia, N. Lecomte, C.R. Lehn, X. Li, R.L. Lindroth, E.F. Lopresti, M. Losada, A.M. Louthan, V.J. Luizzi, S.C. Lynch, J.S. Lynn, N.J. Lyon, L.F. Maia, R.A. Maia, T.L. Mannall, B.S. Martin, T.J. Massad, A.C. Mccall, K. Mcgurrin, A.C. Merwin, Z. Mijango-Ramos, C.H. Mills, A.T. Moles, C.M. Moore, X. Moreira, C.R. Morrison, M.C. Moshobane, A. Muola, R. Nakadai, K. Nakajima, S. Novais, C.O. Ogbebor, H. Ohsaki, V.S. Pan, N.A. Pardikes, M. Pareja, N. Parthasarathy, R.R. Pawar, Q. Paynter, I.S. Pearse, R.M. Penczykowski, A.A. Pepi, C.C. Pereira, S.S. Phartyal, F.I. Piper, K. Poveda, E.G. Pringle, J. Puy, T. Quijano, C. Quintero, S. Rasmann, C. Rosche, L.Y. Rosenheim, J.A. Rosenheim, J.B. Runyon, A. Sadeh, Y. Sakata, D.M. Salcido, C. Salgado-Luarte, B.A. Santos, Y. Sapir, Y. Sasal, Y. Sato, M. Sawant, H. Schroeder, I. Schumann, M. Segoli, H. Segre, O. Shelef, N. Shinohara, R.P. Singh, D.S. Smith, M. Sobral, G.C. Stotz, A.J.M. Tack, M. Tayal, J.F. Tooker, D. Torrico-Bazoberry, K. Tougeron, A.M. Trowbridge, S. Utsumi, O. Uyi, J.L. Vaca-Uribe, A. Valtonen, L.J.A. Van Dijk, V. Vandvik, J. Villellas, L.P. Waller, M.G. Weber, A. Yamawo, S. Yim, P.L. Zarnetske, L.N. Zehr, Z. Zhong, W.C. Wetzel, Science 382 (2023) 679–683.","mla":"Robinson, M. L., et al. “Plant Size, Latitude, and Phylogeny Explain within-Population Variability in Herbivory.” Science, vol. 382, no. 6671, AAAS, 2023, pp. 679–83, doi:10.1126/science.adh8830.","chicago":"Robinson, M. L., P. G. Hahn, B. D. Inouye, N. Underwood, S. R. Whitehead, K. C. Abbott, E. M. Bruna, et al. “Plant Size, Latitude, and Phylogeny Explain within-Population Variability in Herbivory.” Science. AAAS, 2023. https://doi.org/10.1126/science.adh8830.","ama":"Robinson ML, Hahn PG, Inouye BD, et al. Plant size, latitude, and phylogeny explain within-population variability in herbivory. Science. 2023;382(6671):679-683. doi:10.1126/science.adh8830","apa":"Robinson, M. L., Hahn, P. G., Inouye, B. D., Underwood, N., Whitehead, S. R., Abbott, K. C., … Wetzel, W. C. (2023). Plant size, latitude, and phylogeny explain within-population variability in herbivory. Science. AAAS. https://doi.org/10.1126/science.adh8830","ieee":"M. L. Robinson et al., “Plant size, latitude, and phylogeny explain within-population variability in herbivory,” Science, vol. 382, no. 6671. AAAS, pp. 679–683, 2023.","ista":"Robinson ML et al. 2023. Plant size, latitude, and phylogeny explain within-population variability in herbivory. Science. 382(6671), 679–683."},"article_type":"original","page":"679-683","date_published":"2023-11-09T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Interactions between plants and herbivores are central in most ecosystems, but their strength is highly variable. The amount of variability within a system is thought to influence most aspects of plant-herbivore biology, from ecological stability to plant defense evolution. Our understanding of what influences variability, however, is limited by sparse data. We collected standardized surveys of herbivory for 503 plant species at 790 sites across 116° of latitude. With these data, we show that within-population variability in herbivory increases with latitude, decreases with plant size, and is phylogenetically structured. Differences in the magnitude of variability are thus central to how plant-herbivore biology varies across macroscale gradients. We argue that increased focus on interaction variability will advance understanding of patterns of life on Earth."}],"issue":"6671","_id":"14552","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Plant size, latitude, and phylogeny explain within-population variability in herbivory","status":"public","intvolume":" 382","oa_version":"None"},{"author":[{"first_name":"William","last_name":"Wetzel","full_name":"Wetzel, William"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"14552"}]},"date_created":"2023-11-20T11:07:45Z","date_updated":"2023-11-20T11:17:33Z","oa_version":"Published Version","_id":"14579","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","status":"public","title":"HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0","ddc":["570"],"publisher":"Zenodo","department":[{"_id":"NiBa"}],"abstract":[{"text":"This is associated with our paper \"Plant size, latitude, and phylogeny explain within-population variability in herbivory\" published in Science.\r\n","lang":"eng"}],"type":"research_data_reference","date_published":"2023-07-11T00:00:00Z","doi":"10.5281/ZENODO.8133117","citation":{"ieee":"W. Wetzel, “HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0.” Zenodo, 2023.","apa":"Wetzel, W. (2023). HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0. Zenodo. https://doi.org/10.5281/ZENODO.8133117","ista":"Wetzel W. 2023. HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0, Zenodo, 10.5281/ZENODO.8133117.","ama":"Wetzel W. HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0. 2023. doi:10.5281/ZENODO.8133117","chicago":"Wetzel, William. “HerbVar-Network/HV-Large-Patterns-MS-Public: V1.0.0.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8133117.","short":"W. Wetzel, (2023).","mla":"Wetzel, William. HerbVar-Network/HV-Large-Patterns-MS-Public: V1.0.0. Zenodo, 2023, doi:10.5281/ZENODO.8133117."},"oa":1,"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8133118","open_access":"1"}],"month":"07","day":"11","article_processing_charge":"No"},{"page":"230","citation":{"chicago":"Puixeu Sala, Gemma. “The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14058.","short":"G. Puixeu Sala, The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation, Institute of Science and Technology Austria, 2023.","mla":"Puixeu Sala, Gemma. The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14058.","ieee":"G. Puixeu Sala, “The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation,” Institute of Science and Technology Austria, 2023.","apa":"Puixeu Sala, G. (2023). The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14058","ista":"Puixeu Sala G. 2023. The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. Institute of Science and Technology Austria.","ama":"Puixeu Sala G. The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. 2023. doi:10.15479/at:ista:14058"},"date_published":"2023-08-15T00:00:00Z","day":"15","article_processing_charge":"No","has_accepted_license":"1","status":"public","ddc":["576"],"title":"The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation","_id":"14058","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"file_name":"Thesis_latex_forpdfa.zip","access_level":"closed","creator":"gpuixeus","content_type":"application/zip","file_size":10891454,"file_id":"14075","relation":"source_file","date_created":"2023-08-16T18:15:17Z","date_updated":"2023-08-17T06:55:24Z","checksum":"4e44e169f2724ee8c9324cd60bcc2b71"},{"content_type":"application/pdf","file_size":19856686,"creator":"gpuixeus","file_name":"PhDThesis_PuixeuG.pdf","access_level":"open_access","date_updated":"2023-08-18T10:47:55Z","date_created":"2023-08-18T10:47:55Z","checksum":"e10b04cd8f3fecc0d9ef6e6868b6e1e8","success":1,"relation":"main_file","file_id":"14079"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Females and males across species are subject to divergent selective pressures arising\r\nfrom di↵erent reproductive interests and ecological niches. This often translates into a\r\nintricate array of sex-specific natural and sexual selection on traits that have a shared\r\ngenetic basis between both sexes, causing a genetic sexual conflict. The resolution of\r\nthis conflict mostly relies on the evolution of sex-specific expression of the shared genes,\r\nleading to phenotypic sexual dimorphism. Such sex-specific gene expression is thought\r\nto evolve via modifications of the genetic networks ultimately linked to sex-determining\r\ntranscription factors. Although much empirical and theoretical evidence supports this\r\nstandard picture of the molecular basis of sexual conflict resolution, there still are a\r\nfew open questions regarding the complex array of selective forces driving phenotypic\r\ndi↵erentiation between the sexes, as well as the molecular mechanisms underlying sexspecific adaptation. I address some of these open questions in my PhD thesis.\r\nFirst, how do patterns of phenotypic sexual dimorphism vary within populations,\r\nas a response to the temporal and spatial changes in sex-specific selective forces? To\r\ntackle this question, I analyze the patterns of sex-specific phenotypic variation along\r\nthree life stages and across populations spanning the whole geographical range of Rumex\r\nhastatulus, a wind-pollinated angiosperm, in the first Chapter of the thesis.\r\nSecond, how do gene expression patterns lead to phenotypic dimorphism, and what\r\nare the molecular mechanisms underlying the observed transcriptomic variation? I\r\naddress this question by examining the sex- and tissue-specific expression variation in\r\nnewly-generated datasets of sex-specific expression in heads and gonads of Drosophila\r\nmelanogaster. I additionally used two complementary approaches for the study of the\r\ngenetic basis of sex di↵erences in gene expression in the second and third Chapters of\r\nthe thesis.\r\nThird, how does intersex correlation, thought to be one of the main aspects constraining the ability for the two sexes to decouple, interact with the evolution of sexual\r\ndimorphism? I develop models of sex-specific stabilizing selection, mutation and drift\r\nto formalize common intuition regarding the patterns of covariation between intersex\r\ncorrelation and sexual dimorphism in the fourth Chapter of the thesis.\r\nAlltogether, the work described in this PhD thesis provides useful insights into the\r\nlinks between genetic, transcriptomic and phenotypic layers of sex-specific variation,\r\nand contributes to our general understanding of the dynamics of sexual dimorphism\r\nevolution.","lang":"eng"}],"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A","grant_number":"25817","name":"Sexual conflict: resolution, constraints and biomedical implications"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"supervisor":[{"first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:14058","month":"08","publication_identifier":{"isbn":["978-3-99078-035-0"],"issn":["2663-337X"]},"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"BeVi"}],"publisher":"Institute of Science and Technology Austria","year":"2023","date_created":"2023-08-15T10:20:40Z","date_updated":"2023-12-13T12:15:36Z","author":[{"full_name":"Puixeu Sala, Gemma","orcid":"0000-0001-8330-1754","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","last_name":"Puixeu Sala","first_name":"Gemma"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"9803"},{"status":"public","relation":"research_data","id":"12933"},{"id":"6831","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"14077"}]},"file_date_updated":"2023-08-18T10:47:55Z","ec_funded":1},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001002997200001"]},"oa":1,"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"},{"_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A","grant_number":"25817","name":"Sexual conflict: resolution, constraints and biomedical implications"}],"isi":1,"quality_controlled":"1","doi":"10.1093/g3journal/jkad121","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"publication_identifier":{"issn":["2160-1836"]},"month":"08","acknowledgement":"We thank members of the Vicoso Group for comments on the manuscript, the Scientific Computing Unit at ISTA for technical support, and 2 anonymous reviewers for useful feedback. GP is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology Austria (DOC 25817) and received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant (agreement no. 665385).","year":"2023","publisher":"Oxford University Press","department":[{"_id":"BeVi"},{"_id":"NiBa"},{"_id":"GradSch"}],"publication_status":"published","related_material":{"record":[{"status":"public","relation":"research_data","id":"12933"},{"relation":"dissertation_contains","status":"public","id":"14058"}]},"author":[{"orcid":"0000-0001-8330-1754","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","last_name":"Puixeu Sala","first_name":"Gemma","full_name":"Puixeu Sala, Gemma"},{"full_name":"Macon, Ariana","last_name":"Macon","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"volume":13,"date_updated":"2023-12-13T12:15:37Z","date_created":"2023-08-18T06:52:14Z","ec_funded":1,"file_date_updated":"2023-11-07T09:00:19Z","citation":{"ama":"Puixeu Sala G, Macon A, Vicoso B. Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. G3: Genes, Genomes, Genetics. 2023;13(8). doi:10.1093/g3journal/jkad121","ista":"Puixeu Sala G, Macon A, Vicoso B. 2023. Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. G3: Genes, Genomes, Genetics. 13(8).","ieee":"G. Puixeu Sala, A. Macon, and B. Vicoso, “Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster,” G3: Genes, Genomes, Genetics, vol. 13, no. 8. Oxford University Press, 2023.","apa":"Puixeu Sala, G., Macon, A., & Vicoso, B. (2023). Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. G3: Genes, Genomes, Genetics. Oxford University Press. https://doi.org/10.1093/g3journal/jkad121","mla":"Puixeu Sala, Gemma, et al. “Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” G3: Genes, Genomes, Genetics, vol. 13, no. 8, Oxford University Press, 2023, doi:10.1093/g3journal/jkad121.","short":"G. Puixeu Sala, A. Macon, B. Vicoso, G3: Genes, Genomes, Genetics 13 (2023).","chicago":"Puixeu Sala, Gemma, Ariana Macon, and Beatriz Vicoso. “Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” G3: Genes, Genomes, Genetics. Oxford University Press, 2023. https://doi.org/10.1093/g3journal/jkad121."},"publication":"G3: Genes, Genomes, Genetics","article_type":"original","date_published":"2023-08-01T00:00:00Z","scopus_import":"1","keyword":["Genetics (clinical)","Genetics","Molecular Biology"],"article_processing_charge":"Yes","has_accepted_license":"1","day":"01","_id":"14077","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 13","status":"public","title":"Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster","ddc":["570"],"oa_version":"Published Version","file":[{"file_id":"14498","relation":"main_file","success":1,"checksum":"c62e29fc7c5efbf8356f4c60cab4a2d1","date_updated":"2023-11-07T09:00:19Z","date_created":"2023-11-07T09:00:19Z","access_level":"open_access","file_name":"2023_G3_Puixeu.pdf","creator":"dernst","content_type":"application/pdf","file_size":845642}],"type":"journal_article","issue":"8","abstract":[{"text":"The regulatory architecture of gene expression is known to differ substantially between sexes in Drosophila, but most studies performed\r\nso far used whole-body data and only single crosses, which may have limited their scope to detect patterns that are robust across tissues\r\nand biological replicates. Here, we use allele-specific gene expression of parental and reciprocal hybrid crosses between 6 Drosophila\r\nmelanogaster inbred lines to quantify cis- and trans-regulatory variation in heads and gonads of both sexes separately across 3 replicate\r\ncrosses. Our results suggest that female and male heads, as well as ovaries, have a similar regulatory architecture. On the other hand,\r\ntestes display more and substantially different cis-regulatory effects, suggesting that sex differences in the regulatory architecture that\r\nhave been previously observed may largely derive from testis-specific effects. We also examine the difference in cis-regulatory variation\r\nof genes across different levels of sex bias in gonads and heads. Consistent with the idea that intersex correlations constrain expression\r\nand can lead to sexual antagonism, we find more cis variation in unbiased and moderately biased genes in heads. In ovaries, reduced cis\r\nvariation is observed for male-biased genes, suggesting that cis variants acting on these genes in males do not lead to changes in ovary\r\nexpression. Finally, we examine the dominance patterns of gene expression and find that sex- and tissue-specific patterns of inheritance\r\nas well as trans-regulatory variation are highly variable across biological crosses, although these were performed in highly controlled\r\nexperimental conditions. This highlights the importance of using various genetic backgrounds to infer generalizable patterns.","lang":"eng"}]},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"citation":{"ieee":"G. Puixeu Sala, “Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster.” Institute of Science and Technology Austria, 2023.","apa":"Puixeu Sala, G. (2023). Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12933","ista":"Puixeu Sala G. 2023. Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12933.","ama":"Puixeu Sala G. Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. 2023. doi:10.15479/AT:ISTA:12933","chicago":"Puixeu Sala, Gemma. “Data from: Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12933.","short":"G. Puixeu Sala, (2023).","mla":"Puixeu Sala, Gemma. Data from: Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12933."},"date_published":"2023-05-15T00:00:00Z","doi":"10.15479/AT:ISTA:12933","has_accepted_license":"1","article_processing_charge":"No","day":"15","month":"05","year":"2023","_id":"12933","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"BeVi"}],"ddc":["570"],"title":"Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster","status":"public","related_material":{"record":[{"id":"14058","relation":"used_in_publication","status":"public"},{"relation":"used_in_publication","status":"public","id":"14077"}]},"contributor":[{"first_name":"Ariana","last_name":"Macon","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz"}],"author":[{"orcid":"0000-0001-8330-1754","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","last_name":"Puixeu Sala","first_name":"Gemma","full_name":"Puixeu Sala, Gemma"}],"oa_version":"Published Version","file":[{"file_id":"12934","relation":"main_file","date_created":"2023-05-10T09:41:43Z","date_updated":"2023-05-10T09:41:43Z","success":1,"checksum":"0ba0bcd0bb8b18d84792136a4370df90","file_name":"Dataset_S1.csv","access_level":"open_access","creator":"gpuixeus","file_size":8029982,"content_type":"text/csv"},{"file_name":"Dataset_S2.csv","access_level":"open_access","file_size":13667640,"content_type":"text/csv","creator":"gpuixeus","relation":"main_file","file_id":"12935","date_updated":"2023-05-10T09:41:43Z","date_created":"2023-05-10T09:41:43Z","checksum":"a62aa9a6d4904e0fdb699cf752640863","success":1},{"creator":"gpuixeus","content_type":"text/csv","file_size":8369141,"access_level":"open_access","file_name":"Dataset_S3.csv","success":1,"checksum":"e20ea7f4f8a9bdf1b3849a44664ae58b","date_updated":"2023-05-10T09:41:48Z","date_created":"2023-05-10T09:41:48Z","file_id":"12936","relation":"main_file"},{"file_id":"12937","relation":"main_file","date_updated":"2023-05-10T09:41:50Z","date_created":"2023-05-10T09:41:50Z","success":1,"checksum":"f6156e5fc44446c907ddd0d7289d4cf8","file_name":"Dataset_S4.csv","access_level":"open_access","creator":"gpuixeus","file_size":19543247,"content_type":"text/csv"},{"file_name":"readme.txt","access_level":"open_access","file_size":4566,"content_type":"text/plain","creator":"gpuixeus","relation":"main_file","file_id":"12944","date_updated":"2023-05-11T12:50:18Z","date_created":"2023-05-11T12:50:18Z","checksum":"ae9f54c77a1c42b666ae6c1dfd33ac86","success":1}],"date_updated":"2023-12-13T12:15:36Z","date_created":"2023-05-10T10:00:49Z","type":"research_data","file_date_updated":"2023-05-11T12:50:18Z","abstract":[{"lang":"eng","text":"Datasets of the publication \"Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster\"."}]},{"scopus_import":"1","article_processing_charge":"Yes (in subscription journal)","day":"16","article_type":"original","citation":{"short":"J. Reeve, R.K. Butlin, E.L. Koch, S. Stankowski, R. Faria, Molecular Ecology (2023).","mla":"Reeve, James, et al. “Chromosomal Inversion Polymorphisms Are Widespread across the Species Ranges of Rough Periwinkles (Littorina Saxatilis and L. Arcana).” Molecular Ecology, Wiley, 2023, doi:10.1111/mec.17160.","chicago":"Reeve, James, Roger K. Butlin, Eva L. Koch, Sean Stankowski, and Rui Faria. “Chromosomal Inversion Polymorphisms Are Widespread across the Species Ranges of Rough Periwinkles (Littorina Saxatilis and L. Arcana).” Molecular Ecology. Wiley, 2023. https://doi.org/10.1111/mec.17160.","ama":"Reeve J, Butlin RK, Koch EL, Stankowski S, Faria R. Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana). Molecular Ecology. 2023. doi:10.1111/mec.17160","ieee":"J. Reeve, R. K. Butlin, E. L. Koch, S. Stankowski, and R. Faria, “Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana),” Molecular Ecology. Wiley, 2023.","apa":"Reeve, J., Butlin, R. K., Koch, E. L., Stankowski, S., & Faria, R. (2023). Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana). Molecular Ecology. Wiley. https://doi.org/10.1111/mec.17160","ista":"Reeve J, Butlin RK, Koch EL, Stankowski S, Faria R. 2023. Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana). Molecular Ecology."},"publication":"Molecular Ecology","date_published":"2023-10-16T00:00:00Z","type":"journal_article","abstract":[{"text":"Inversions are thought to play a key role in adaptation and speciation, suppressing recombination between diverging populations. Genes influencing adaptive traits cluster in inversions, and changes in inversion frequencies are associated with environmental differences. However, in many organisms, it is unclear if inversions are geographically and taxonomically widespread. The intertidal snail, Littorina saxatilis, is one such example. Strong associations between putative polymorphic inversions and phenotypic differences have been demonstrated between two ecotypes of L. saxatilis in Sweden and inferred elsewhere, but no direct evidence for inversion polymorphism currently exists across the species range. Using whole genome data from 107 snails, most inversion polymorphisms were found to be widespread across the species range. The frequencies of some inversion arrangements were significantly different among ecotypes, suggesting a parallel adaptive role. Many inversions were also polymorphic in the sister species, L. arcana, hinting at an ancient origin.","lang":"eng"}],"status":"public","title":"Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14463","oa_version":"Published Version","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"month":"10","quality_controlled":"1","isi":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/mec.17160"}],"external_id":{"pmid":["37843465"],"isi":["001085119000001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/mec.17160","department":[{"_id":"NiBa"}],"publisher":"Wiley","publication_status":"epub_ahead","pmid":1,"acknowledgement":"We would like to thank members of the Littorina team for their advice and feedback during this project. In particular, we thank Alan Le Moan, who inspired us to look at heterozygosity differences to identify inversions, and Katherine Hearn for helping with the PCA scripts. We thank Edinburgh Genomics for library preparation and sequencing. Sample collections, sequencing and data preparation were supported by the European Research Council (ERC-2015-AdG-693030- BARRIERS) and the Natural Environment Research Council (NE/P001610/1). The analysis was supported by the Swedish Research Council (vetenskaprådet; 2018-03695_VR) and the Portuguese Foundation for Science and Technology (Fundación para a Ciência e Tecnologia) through a research project (PTDC/BIA-EVL/1614/2021) and CEEC contract (2020.00275.CEECIND).","year":"2023","date_created":"2023-10-29T23:01:17Z","date_updated":"2023-12-13T13:05:27Z","author":[{"full_name":"Reeve, James","last_name":"Reeve","first_name":"James"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."},{"full_name":"Koch, Eva L.","first_name":"Eva L.","last_name":"Koch"},{"last_name":"Stankowski","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"}]},{"author":[{"id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1771-714X","first_name":"Louise S","last_name":"Arathoon","full_name":"Arathoon, Louise S"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11411"}]},"date_updated":"2023-12-22T11:04:45Z","date_created":"2023-12-11T19:30:37Z","year":"2023","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"file_date_updated":"2023-12-14T08:58:18Z","ec_funded":1,"doi":"10.15479/at:ista:14651","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"ScienComp"}],"supervisor":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"language":[{"iso":"eng"}],"oa":1,"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"month":"12","publication_identifier":{"issn":["2663 - 337X"]},"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"14684","checksum":"520bdb61e95e66070e02824947d2c5fa","success":1,"date_created":"2023-12-13T15:37:55Z","date_updated":"2023-12-13T15:37:55Z","access_level":"open_access","file_name":"Phd_Thesis_LA.pdf","file_size":34101468,"content_type":"application/pdf","creator":"larathoo"},{"creator":"larathoo","file_size":31052872,"content_type":"application/zip","access_level":"closed","file_name":"Phd_Thesis_LA.zip","checksum":"d8e59afd0817c98fba2564a264508e5c","date_updated":"2023-12-14T08:58:18Z","date_created":"2023-12-13T15:42:23Z","file_id":"14685","relation":"source_file"},{"file_size":10713896,"content_type":"application/zip","creator":"larathoo","file_name":"Supplementary_Materials.zip","access_level":"closed","date_updated":"2023-12-14T08:58:18Z","date_created":"2023-12-11T19:24:59Z","checksum":"9a778c949932286f4519e1f1fca2820d","relation":"supplementary_material","file_id":"14681"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"14651","ddc":["570"],"status":"public","title":"Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus","abstract":[{"text":"For self-incompatibility (SI) to be stable in a population, theory predicts that sufficient inbreeding depression (ID) is required: the fitness of offspring from self-mated individuals must be low enough to prevent the spread of self-compatibility (SC). Reviews of natural plant populations have supported this theory, with SI species generally showing high levels of ID. However, there is thought to be an under-sampling of self-incompatible taxa in the current literature. In this thesis, I study inbreeding depression in the SI plant species Antirrhinum majus using both greenhouse crosses and a large collected field dataset. Additionally, the gametophytic S-locus of A. majus is highly heterozygous and polymorphic, thus making assembly and discovery of S-alleles very difficult. Here, 206 new alleles of the male component SLFs are presented, along with a phylogeny showing the high conservation with alleles from another Antirrhinum species. Lastly, selected sites within the protein structure of SLFs are investigated, with one site in particular highlighted as potentially being involved in the SI recognition mechanism.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2023-12-12T00:00:00Z","citation":{"short":"L.S. Arathoon, Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus, Institute of Science and Technology Austria, 2023.","mla":"Arathoon, Louise S. Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14651.","chicago":"Arathoon, Louise S. “Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14651.","ama":"Arathoon LS. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. 2023. doi:10.15479/at:ista:14651","apa":"Arathoon, L. S. (2023). Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14651","ieee":"L. S. Arathoon, “Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus,” Institute of Science and Technology Austria, 2023.","ista":"Arathoon LS. 2023. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. Institute of Science and Technology Austria."},"page":"96","day":"12","has_accepted_license":"1","article_processing_charge":"No"},{"date_published":"2023-11-01T00:00:00Z","article_type":"original","publication":"Cold Spring Harbor Perspectives in Biology","citation":{"ista":"Lucek K, Giménez MD, Joron M, Rafajlović M, Searle JB, Walden N, Westram AM, Faria R. 2023. The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. Cold Spring Harbor Perspectives in Biology. 15(11), a041447.","apa":"Lucek, K., Giménez, M. D., Joron, M., Rafajlović, M., Searle, J. B., Walden, N., … Faria, R. (2023). The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. Cold Spring Harbor Perspectives in Biology. Cold Spring Harbor Laboratory. https://doi.org/10.1101/cshperspect.a041447","ieee":"K. Lucek et al., “The impact of chromosomal rearrangements in speciation: From micro- to macroevolution,” Cold Spring Harbor Perspectives in Biology, vol. 15, no. 11. Cold Spring Harbor Laboratory, 2023.","ama":"Lucek K, Giménez MD, Joron M, et al. The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. Cold Spring Harbor Perspectives in Biology. 2023;15(11). doi:10.1101/cshperspect.a041447","chicago":"Lucek, Kay, Mabel D. Giménez, Mathieu Joron, Marina Rafajlović, Jeremy B. Searle, Nora Walden, Anja M Westram, and Rui Faria. “The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution.” Cold Spring Harbor Perspectives in Biology. Cold Spring Harbor Laboratory, 2023. https://doi.org/10.1101/cshperspect.a041447.","mla":"Lucek, Kay, et al. “The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution.” Cold Spring Harbor Perspectives in Biology, vol. 15, no. 11, a041447, Cold Spring Harbor Laboratory, 2023, doi:10.1101/cshperspect.a041447.","short":"K. Lucek, M.D. Giménez, M. Joron, M. Rafajlović, J.B. Searle, N. Walden, A.M. Westram, R. Faria, Cold Spring Harbor Perspectives in Biology 15 (2023)."},"day":"01","article_processing_charge":"No","keyword":["General Biochemistry","Genetics and Molecular Biology"],"scopus_import":"1","oa_version":"Published Version","title":"The impact of chromosomal rearrangements in speciation: From micro- to macroevolution","status":"public","intvolume":" 15","_id":"14742","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Chromosomal rearrangements (CRs) have been known since almost the beginning of genetics.\r\nWhile an important role for CRs in speciation has been suggested, evidence primarily stems\r\nfrom theoretical and empirical studies focusing on the microevolutionary level (i.e., on taxon\r\npairs where speciation is often incomplete). Although the role of CRs in eukaryotic speciation at\r\na macroevolutionary level has been supported by associations between species diversity and\r\nrates of evolution of CRs across phylogenies, these findings are limited to a restricted range of\r\nCRs and taxa. Now that more broadly applicable and precise CR detection approaches have\r\nbecome available, we address the challenges in filling some of the conceptual and empirical\r\ngaps between micro- and macroevolutionary studies on the role of CRs in speciation. We\r\nsynthesize what is known about the macroevolutionary impact of CRs and suggest new research avenues to overcome the pitfalls of previous studies to gain a more comprehensive understanding of the evolutionary significance of CRs in speciation across the tree of life."}],"issue":"11","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1101/cshperspect.a041447","quality_controlled":"1","external_id":{"pmid":["37604585"]},"main_file_link":[{"url":"https://doi.org/10.1101/cshperspect.a041447","open_access":"1"}],"oa":1,"month":"11","publication_identifier":{"issn":["1943-0264"]},"date_updated":"2024-01-08T12:52:29Z","date_created":"2024-01-08T12:43:48Z","volume":15,"author":[{"full_name":"Lucek, Kay","first_name":"Kay","last_name":"Lucek"},{"last_name":"Giménez","first_name":"Mabel D.","full_name":"Giménez, Mabel D."},{"last_name":"Joron","first_name":"Mathieu","full_name":"Joron, Mathieu"},{"full_name":"Rafajlović, Marina","first_name":"Marina","last_name":"Rafajlović"},{"last_name":"Searle","first_name":"Jeremy B.","full_name":"Searle, Jeremy B."},{"last_name":"Walden","first_name":"Nora","full_name":"Walden, Nora"},{"full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"}],"publication_status":"published","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"publisher":"Cold Spring Harbor Laboratory","acknowledgement":"K.L. was funded by a Swiss National Science Foundation Eccellenza project: The evolution of strong reproductive barriers towards the completion of speciation (PCEFP3_202869). R.F.\r\nwas funded by an FCT CEEC (Fundação para a Ciênca e a Tecnologia, Concurso Estímulo ao\r\nEmprego Científico) contract (2020.00275. CEECIND) and by an FCT research project\r\n(PTDC/BIA-EVL/1614/2021). M.R. was funded by the Swedish Research Council Vetenskapsrådet (grant number 2021-05243). A.M.W. was partly funded by the Norwegian Research Council RCN. We thank Luis Silva for his help preparing Figure 1. We are grateful to Maren Wellenreuther, Daniel Bolnick, and two anonymous reviewers for their constructive feedback on an earlier version of this paper.","year":"2023","pmid":1,"article_number":"a041447"},{"isi":1,"quality_controlled":"1","external_id":{"pmid":["36651268"],"isi":["000919244600001"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1101/2022.01.28.478139","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1111/mec.16849","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"month":"04","publisher":"Wiley","department":[{"_id":"NiBa"}],"publication_status":"published","pmid":1,"acknowledgement":"We thank Julian Catchen for making modifications to Stacks to aid this project. Peter L. Ralph, Thomas Nelson, Roger K. Butlin, Anja M. Westram and Nicholas H. Barton provided advice, stimulating discussion and critical feedback. The project was supported by National Science Foundation grant DEB-1258199.","year":"2023","volume":32,"date_updated":"2024-01-16T10:10:00Z","date_created":"2024-01-10T10:44:45Z","author":[{"id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","last_name":"Stankowski","full_name":"Stankowski, Sean"},{"full_name":"Chase, Madeline A.","last_name":"Chase","first_name":"Madeline A."},{"full_name":"McIntosh, Hanna","first_name":"Hanna","last_name":"McIntosh"},{"first_name":"Matthew A.","last_name":"Streisfeld","full_name":"Streisfeld, Matthew A."}],"page":"2041-2054","article_type":"original","citation":{"chicago":"Stankowski, Sean, Madeline A. Chase, Hanna McIntosh, and Matthew A. Streisfeld. “Integrating Top‐down and Bottom‐up Approaches to Understand the Genetic Architecture of Speciation across a Monkeyflower Hybrid Zone.” Molecular Ecology. Wiley, 2023. https://doi.org/10.1111/mec.16849.","short":"S. Stankowski, M.A. Chase, H. McIntosh, M.A. Streisfeld, Molecular Ecology 32 (2023) 2041–2054.","mla":"Stankowski, Sean, et al. “Integrating Top‐down and Bottom‐up Approaches to Understand the Genetic Architecture of Speciation across a Monkeyflower Hybrid Zone.” Molecular Ecology, vol. 32, no. 8, Wiley, 2023, pp. 2041–54, doi:10.1111/mec.16849.","ieee":"S. Stankowski, M. A. Chase, H. McIntosh, and M. A. Streisfeld, “Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone,” Molecular Ecology, vol. 32, no. 8. Wiley, pp. 2041–2054, 2023.","apa":"Stankowski, S., Chase, M. A., McIntosh, H., & Streisfeld, M. A. (2023). Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.16849","ista":"Stankowski S, Chase MA, McIntosh H, Streisfeld MA. 2023. Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone. Molecular Ecology. 32(8), 2041–2054.","ama":"Stankowski S, Chase MA, McIntosh H, Streisfeld MA. Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone. Molecular Ecology. 2023;32(8):2041-2054. doi:10.1111/mec.16849"},"publication":"Molecular Ecology","date_published":"2023-04-01T00:00:00Z","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"article_processing_charge":"No","day":"01","intvolume":" 32","title":"Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone","status":"public","_id":"14787","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"journal_article","issue":"8","abstract":[{"lang":"eng","text":"Understanding the phenotypic and genetic architecture of reproductive isolation is a long‐standing goal of speciation research. In several systems, large‐effect loci contributing to barrier phenotypes have been characterized, but such causal connections are rarely known for more complex genetic architectures. In this study, we combine “top‐down” and “bottom‐up” approaches with demographic modelling toward an integrated understanding of speciation across a monkeyflower hybrid zone. Previous work suggests that pollinator visitation acts as a primary barrier to gene flow between two divergent red‐ and yellow‐flowered ecotypes ofMimulus aurantiacus. Several candidate isolating traits and anonymous single nucleotide polymorphism loci under divergent selection have been identified, but their genomic positions remain unknown. Here, we report findings from demographic analyses that indicate this hybrid zone formed by secondary contact, but that subsequent gene flow was restricted by widespread barrier loci across the genome. Using a novel, geographic cline‐based genome scan, we demonstrate that candidate barrier loci are broadly distributed across the genome, rather than mapping to one or a few “islands of speciation.” Quantitative trait locus (QTL) mapping reveals that most floral traits are highly polygenic, with little evidence that QTL colocalize, indicating that most traits are genetically independent. Finally, we find little evidence that QTL and candidate barrier loci overlap, suggesting that some loci contribute to other forms of reproductive isolation. Our findings highlight the challenges of understanding the genetic architecture of reproductive isolation and reveal that barriers to gene flow other than pollinator isolation may play an important role in this system."}]}]