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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.","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.","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.","short":"G. Puixeu Sala, (2023).","ista":"Puixeu Sala G. 2023. 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In this model, a quantitative trait is expressed as the sum of a genetic and a non-genetic (environmental) component and the genetic component of offspring traits within a family follows a normal distribution around the average of the parents’ trait values, and has a variance that is independent of the trait values of the parents. Although the trait distribution across the whole population can be far from normal, the trait distributions within families are normally distributed with a variance-covariance matrix that is determined entirely by that in the ancestral population and the probabilities of identity determined by the pedigree. Moreover, conditioning on some of the trait values within the pedigree has predictable effects on the mean and variance within and between families. In previous work, Barton et al. (2017), we showed that when trait values are determined by the sum of a large number of Mendelian factors, each of small effect, one can justify the infinitesimal model as limit of Mendelian inheritance. It was also shown that under some forms of epistasis, trait values within a family are still normally distributed."}],"project":[{"grant_number":"101055327","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes"}],"status":"public","corr_author":"1","oa_version":"Published Version","article_processing_charge":"No","year":"2023","_id":"12949","type":"research_data","related_material":{"record":[{"status":"public","id":"14452","relation":"used_in_publication"}]},"date_updated":"2025-09-09T13:07:07Z","date_published":"2023-05-13T00:00:00Z","publisher":"Institute of Science and Technology Austria","date_created":"2023-05-13T09:49:09Z","department":[{"_id":"NiBa"}],"has_accepted_license":"1","file":[{"date_created":"2023-05-13T09:36:33Z","date_updated":"2023-05-13T09:36:33Z","content_type":"application/octet-stream","relation":"main_file","creator":"nbarton","checksum":"b0ce7d4b1ee7e7265430ceed36fc3336","file_name":"Neutral identities 16th 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dominance"},{"_id":"14058","date_updated":"2026-04-07T13:25:34Z","related_material":{"record":[{"status":"public","id":"9803","relation":"research_data"},{"id":"12933","status":"public","relation":"research_data"},{"status":"public","id":"6831","relation":"part_of_dissertation"},{"id":"14077","status":"public","relation":"part_of_dissertation"}]},"ec_funded":1,"OA_place":"publisher","oa":1,"month":"08","ddc":["576"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation","degree_awarded":"PhD","publication_status":"published","citation":{"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.","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.","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","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.","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.","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."},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-035-0"]},"file_date_updated":"2023-08-18T10:47:55Z","author":[{"id":"33AB266C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8330-1754","first_name":"Gemma","last_name":"Puixeu Sala","full_name":"Puixeu Sala, Gemma"}],"page":"230","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385"},{"name":"Sexual conflict: resolution, constraints and biomedical implications","_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A","grant_number":"25817"}],"oa_version":"Published Version","corr_author":"1","article_processing_charge":"No","year":"2023","type":"dissertation","date_published":"2023-08-15T00:00:00Z","publisher":"Institute of Science and Technology Austria","date_created":"2023-08-15T10:20:40Z","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"BeVi"}],"has_accepted_license":"1","file":[{"date_created":"2023-08-16T18:15:17Z","content_type":"application/zip","date_updated":"2023-08-17T06:55:24Z","checksum":"4e44e169f2724ee8c9324cd60bcc2b71","file_name":"Thesis_latex_forpdfa.zip","creator":"gpuixeus","relation":"source_file","access_level":"closed","file_id":"14075","file_size":10891454},{"file_name":"PhDThesis_PuixeuG.pdf","checksum":"e10b04cd8f3fecc0d9ef6e6868b6e1e8","creator":"gpuixeus","relation":"main_file","file_id":"14079","file_size":19856686,"access_level":"open_access","success":1,"date_created":"2023-08-18T10:47:55Z","content_type":"application/pdf","date_updated":"2023-08-18T10:47:55Z"}],"doi":"10.15479/at:ista:14058","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"15","supervisor":[{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton"}],"abstract":[{"lang":"eng","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."}],"status":"public","alternative_title":["ISTA Thesis"]},{"year":"2023","article_processing_charge":"Yes","oa_version":"Published Version","corr_author":"1","project":[{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"},{"_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A","name":"Sexual conflict: resolution, constraints and biomedical implications","grant_number":"25817"}],"author":[{"last_name":"Puixeu Sala","full_name":"Puixeu Sala, Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8330-1754","first_name":"Gemma"},{"full_name":"Macon, Ariana","last_name":"Macon","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"file_date_updated":"2023-11-07T09:00:19Z","publication_identifier":{"issn":["2160-1836"]},"language":[{"iso":"eng"}],"publication":"G3: Genes, Genomes, Genetics","citation":{"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.","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","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.","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).","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","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.","short":"G. Puixeu Sala, A. Macon, B. Vicoso, G3: Genes, Genomes, Genetics 13 (2023)."},"publication_status":"published","intvolume":" 13","acknowledged_ssus":[{"_id":"ScienComp"}],"title":"Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"month":"08","volume":13,"oa":1,"external_id":{"pmid":["37259621"],"isi":["001002997200001"]},"pmid":1,"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).","ec_funded":1,"related_material":{"record":[{"status":"public","id":"12933","relation":"research_data"},{"relation":"dissertation_contains","id":"14058","status":"public"}]},"date_updated":"2026-04-07T13:25:34Z","_id":"14077","status":"public","abstract":[{"lang":"eng","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."}],"isi":1,"keyword":["Genetics (clinical)","Genetics","Molecular Biology"],"day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1093/g3journal/jkad121","file":[{"access_level":"open_access","file_size":845642,"file_id":"14498","success":1,"checksum":"c62e29fc7c5efbf8356f4c60cab4a2d1","file_name":"2023_G3_Puixeu.pdf","creator":"dernst","relation":"main_file","content_type":"application/pdf","date_updated":"2023-11-07T09:00:19Z","date_created":"2023-11-07T09:00:19Z"}],"article_type":"original","department":[{"_id":"BeVi"},{"_id":"NiBa"},{"_id":"GradSch"}],"has_accepted_license":"1","scopus_import":"1","date_created":"2023-08-18T06:52:14Z","publisher":"Oxford University Press","quality_controlled":"1","date_published":"2023-08-01T00:00:00Z","issue":"8","type":"journal_article"},{"department":[{"_id":"NiBa"}],"has_accepted_license":"1","article_type":"original","file":[{"checksum":"3f65b1fbe813e2f4dbb5d2b5e891844a","file_name":"2023_Genetics_Barton.pdf","creator":"dernst","relation":"main_file","access_level":"open_access","file_id":"14469","file_size":1439032,"success":1,"date_created":"2023-10-30T12:57:53Z","content_type":"application/pdf","date_updated":"2023-10-30T12:57:53Z"}],"doi":"10.1093/genetics/iyad133","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2023-10-01T00:00:00Z","quality_controlled":"1","date_created":"2023-10-29T23:01:15Z","publisher":"Oxford University Press","scopus_import":"1","type":"journal_article","issue":"2","abstract":[{"text":"The classical infinitesimal model is a simple and robust model for the inheritance of quantitative traits. In this model, a quantitative trait is expressed as the sum of a genetic and an environmental component, and the genetic component of offspring traits within a family follows a normal distribution around the average of the parents’ trait values, and has a variance that is independent of the parental traits. In previous work, we showed that when trait values are determined by the sum of a large number of additive Mendelian factors, each of small effect, one can justify the infinitesimal model as a limit of Mendelian inheritance. In this paper, we show that this result extends to include dominance. We define the model in terms of classical quantities of quantitative genetics, before justifying it as a limit of Mendelian inheritance as the number, M, of underlying loci tends to infinity. As in the additive case, the multivariate normal distribution of trait values across the pedigree can be expressed in terms of variance components in an ancestral population and probabilities of identity by descent determined by the pedigree. Now, with just first-order dominance effects, we require two-, three-, and four-way identities. We also show that, even if we condition on parental trait values, the “shared” and “residual” components of trait values within each family will be asymptotically normally distributed as the number of loci tends to infinity, with an error of order 1/M−−√. We illustrate our results with some numerical examples.","lang":"eng"}],"status":"public","isi":1,"day":"01","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"The infinitesimal model with dominance","intvolume":" 225","external_id":{"isi":["001148042000008"],"arxiv":["2211.03515"]},"oa":1,"volume":225,"month":"10","ec_funded":1,"acknowledgement":"NHB was supported in part by ERC Grants 250152 and 101055327. AV was partly supported by the chaire Modélisation Mathématique et Biodiversité of Veolia Environment—Ecole Polytechnique—Museum National d’Histoire Naturelle—Fondation X.","_id":"14452","related_material":{"record":[{"relation":"research_data","id":"12949","status":"public"}]},"date_updated":"2025-09-09T13:07:07Z","article_processing_charge":"Yes (in subscription journal)","year":"2023","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7"},{"grant_number":"101055327","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes"}],"arxiv":1,"oa_version":"Published Version","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0016-6731"],"eissn":["1943-2631"]},"file_date_updated":"2023-10-30T12:57:53Z","author":[{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton"},{"first_name":"Alison M.","full_name":"Etheridge, Alison M.","last_name":"Etheridge"},{"first_name":"Amandine","last_name":"Véber","full_name":"Véber, Amandine"}],"article_number":"iyad133","publication_status":"published","citation":{"ieee":"N. H. Barton, A. M. Etheridge, and A. Véber, “The infinitesimal model with dominance,” Genetics, vol. 225, no. 2. Oxford University Press, 2023.","short":"N.H. Barton, A.M. Etheridge, A. Véber, Genetics 225 (2023).","apa":"Barton, N. H., Etheridge, A. M., & Véber, A. (2023). The infinitesimal model with dominance. Genetics. Oxford University Press. https://doi.org/10.1093/genetics/iyad133","ista":"Barton NH, Etheridge AM, Véber A. 2023. The infinitesimal model with dominance. Genetics. 225(2), iyad133.","chicago":"Barton, Nicholas H, Alison M. Etheridge, and Amandine Véber. “The Infinitesimal Model with Dominance.” Genetics. Oxford University Press, 2023. https://doi.org/10.1093/genetics/iyad133.","ama":"Barton NH, Etheridge AM, Véber A. The infinitesimal model with dominance. Genetics. 2023;225(2). doi:10.1093/genetics/iyad133","mla":"Barton, Nicholas H., et al. “The Infinitesimal Model with Dominance.” Genetics, vol. 225, no. 2, iyad133, Oxford University Press, 2023, doi:10.1093/genetics/iyad133."},"publication":"Genetics"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1126/science.adh8830","article_type":"original","department":[{"_id":"NiBa"}],"issue":"6671","type":"journal_article","scopus_import":"1","publisher":"AAAS","date_created":"2023-11-19T23:00:54Z","date_published":"2023-11-09T00:00:00Z","quality_controlled":"1","status":"public","main_file_link":[{"url":"https://centaur.reading.ac.uk/113962/1/adh8830_CombinedPDF_v6.pdf","open_access":"1"}],"abstract":[{"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.","lang":"eng"}],"day":"09","isi":1,"month":"11","volume":382,"oa":1,"external_id":{"isi":["001138596500033"],"pmid":["37943897"]},"intvolume":" 382","title":"Plant size, latitude, and phylogeny explain within-population variability in herbivory","date_updated":"2025-09-09T13:23:56Z","related_material":{"record":[{"relation":"research_data","id":"14579","status":"public"}]},"_id":"14552","pmid":1,"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.","OA_place":"repository","OA_type":"green","oa_version":"Submitted Version","page":"679-683","year":"2023","article_processing_charge":"No","publication":"Science","citation":{"ista":"Robinson ML et al. 2023. Plant size, latitude, and phylogeny explain within-population variability in herbivory. Science. 382(6671), 679–683.","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","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.","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.","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.","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","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."},"publication_status":"published","author":[{"first_name":"M. L.","last_name":"Robinson","full_name":"Robinson, M. L."},{"last_name":"Hahn","full_name":"Hahn, P. G.","first_name":"P. G."},{"full_name":"Inouye, B. D.","last_name":"Inouye","first_name":"B. D."},{"first_name":"N.","last_name":"Underwood","full_name":"Underwood, N."},{"last_name":"Whitehead","full_name":"Whitehead, S. R.","first_name":"S. R."},{"full_name":"Abbott, K. C.","last_name":"Abbott","first_name":"K. C."},{"full_name":"Bruna, E. M.","last_name":"Bruna","first_name":"E. M."},{"last_name":"Cacho","full_name":"Cacho, N. I.","first_name":"N. I."},{"first_name":"L. A.","last_name":"Dyer","full_name":"Dyer, L. A."},{"first_name":"L.","full_name":"Abdala-Roberts, L.","last_name":"Abdala-Roberts"},{"full_name":"Allen, W. J.","last_name":"Allen","first_name":"W. J."},{"first_name":"J. F.","last_name":"Andrade","full_name":"Andrade, J. F."},{"last_name":"Angulo","full_name":"Angulo, D. F.","first_name":"D. F."},{"first_name":"D.","last_name":"Anjos","full_name":"Anjos, D."},{"first_name":"D. N.","full_name":"Anstett, D. N.","last_name":"Anstett"},{"last_name":"Bagchi","full_name":"Bagchi, R.","first_name":"R."},{"last_name":"Bagchi","full_name":"Bagchi, S.","first_name":"S."},{"last_name":"Barbosa","full_name":"Barbosa, M.","first_name":"M."},{"full_name":"Barrett, S.","last_name":"Barrett","first_name":"S."},{"id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carina","orcid":"0000-0002-7354-8574","last_name":"Baskett","full_name":"Baskett, Carina"},{"first_name":"E.","full_name":"Ben-Simchon, E.","last_name":"Ben-Simchon"},{"last_name":"Bloodworth","full_name":"Bloodworth, K. J.","first_name":"K. J."},{"first_name":"J. L.","full_name":"Bronstein, J. L.","last_name":"Bronstein"},{"first_name":"Y. M.","last_name":"Buckley","full_name":"Buckley, Y. M."},{"first_name":"K. T.","last_name":"Burghardt","full_name":"Burghardt, K. T."},{"first_name":"C.","full_name":"Bustos-Segura, C.","last_name":"Bustos-Segura"},{"first_name":"E. S.","last_name":"Calixto","full_name":"Calixto, E. S."},{"first_name":"R. L.","last_name":"Carvalho","full_name":"Carvalho, R. L."},{"full_name":"Castagneyrol, B.","last_name":"Castagneyrol","first_name":"B."},{"last_name":"Chiuffo","full_name":"Chiuffo, M. C.","first_name":"M. C."},{"last_name":"Cinoğlu","full_name":"Cinoğlu, D.","first_name":"D."},{"last_name":"Cinto Mejía","full_name":"Cinto Mejía, E.","first_name":"E."},{"first_name":"M. C.","full_name":"Cock, M. C.","last_name":"Cock"},{"first_name":"R.","full_name":"Cogni, R.","last_name":"Cogni"},{"first_name":"O. L.","full_name":"Cope, O. L.","last_name":"Cope"},{"last_name":"Cornelissen","full_name":"Cornelissen, T.","first_name":"T."},{"first_name":"D. R.","last_name":"Cortez","full_name":"Cortez, D. R."},{"first_name":"D. W.","last_name":"Crowder","full_name":"Crowder, D. W."},{"first_name":"C.","last_name":"Dallstream","full_name":"Dallstream, C."},{"first_name":"W.","last_name":"Dáttilo","full_name":"Dáttilo, W."},{"first_name":"J. K.","full_name":"Davis, J. K.","last_name":"Davis"},{"last_name":"Dimarco","full_name":"Dimarco, R. D.","first_name":"R. D."},{"first_name":"H. E.","last_name":"Dole","full_name":"Dole, H. E."},{"first_name":"I. N.","full_name":"Egbon, I. N.","last_name":"Egbon"},{"first_name":"M.","full_name":"Eisenring, M.","last_name":"Eisenring"},{"first_name":"A.","full_name":"Ejomah, A.","last_name":"Ejomah"},{"full_name":"Elderd, B. D.","last_name":"Elderd","first_name":"B. D."},{"last_name":"Endara","full_name":"Endara, M. J.","first_name":"M. J."},{"full_name":"Eubanks, M. D.","last_name":"Eubanks","first_name":"M. D."},{"first_name":"S. E.","full_name":"Everingham, S. E.","last_name":"Everingham"},{"first_name":"K. N.","last_name":"Farah","full_name":"Farah, K. N."},{"full_name":"Farias, R. P.","last_name":"Farias","first_name":"R. P."},{"last_name":"Fernandes","full_name":"Fernandes, A. P.","first_name":"A. P."},{"last_name":"Fernandes","full_name":"Fernandes, G. W.","first_name":"G. W."},{"last_name":"Ferrante","full_name":"Ferrante, M.","first_name":"M."},{"first_name":"A.","full_name":"Finn, A.","last_name":"Finn"},{"first_name":"G. A.","full_name":"Florjancic, G. A.","last_name":"Florjancic"},{"last_name":"Forister","full_name":"Forister, M. L.","first_name":"M. L."},{"first_name":"Q. N.","full_name":"Fox, Q. N.","last_name":"Fox"},{"first_name":"E.","last_name":"Frago","full_name":"Frago, E."},{"first_name":"F. M.","last_name":"França","full_name":"França, F. M."},{"full_name":"Getman-Pickering, A. S.","last_name":"Getman-Pickering","first_name":"A. S."},{"full_name":"Getman-Pickering, Z.","last_name":"Getman-Pickering","first_name":"Z."},{"first_name":"E.","full_name":"Gianoli, E.","last_name":"Gianoli"},{"last_name":"Gooden","full_name":"Gooden, B.","first_name":"B."},{"full_name":"Gossner, M. M.","last_name":"Gossner","first_name":"M. M."},{"last_name":"Greig","full_name":"Greig, K. A.","first_name":"K. A."},{"first_name":"S.","full_name":"Gripenberg, S.","last_name":"Gripenberg"},{"full_name":"Groenteman, R.","last_name":"Groenteman","first_name":"R."},{"last_name":"Grof-Tisza","full_name":"Grof-Tisza, P.","first_name":"P."},{"first_name":"N.","full_name":"Haack, N.","last_name":"Haack"},{"full_name":"Hahn, L.","last_name":"Hahn","first_name":"L."},{"first_name":"S. M.","last_name":"Haq","full_name":"Haq, S. M."},{"last_name":"Helms","full_name":"Helms, A. M.","first_name":"A. M."},{"full_name":"Hennecke, J.","last_name":"Hennecke","first_name":"J."},{"first_name":"S. L.","last_name":"Hermann","full_name":"Hermann, S. L."},{"first_name":"L. M.","last_name":"Holeski","full_name":"Holeski, L. M."},{"first_name":"S.","last_name":"Holm","full_name":"Holm, S."},{"full_name":"Hutchinson, M. C.","last_name":"Hutchinson","first_name":"M. C."},{"last_name":"Jackson","full_name":"Jackson, E. E.","first_name":"E. E."},{"last_name":"Kagiya","full_name":"Kagiya, S.","first_name":"S."},{"full_name":"Kalske, A.","last_name":"Kalske","first_name":"A."},{"first_name":"M.","full_name":"Kalwajtys, M.","last_name":"Kalwajtys"},{"first_name":"R.","full_name":"Karban, R.","last_name":"Karban"},{"first_name":"R.","full_name":"Kariyat, R.","last_name":"Kariyat"},{"first_name":"T.","last_name":"Keasar","full_name":"Keasar, T."},{"first_name":"M. F.","last_name":"Kersch-Becker","full_name":"Kersch-Becker, M. F."},{"full_name":"Kharouba, H. M.","last_name":"Kharouba","first_name":"H. M."},{"first_name":"T. N.","last_name":"Kim","full_name":"Kim, T. N."},{"last_name":"Kimuyu","full_name":"Kimuyu, D. M.","first_name":"D. M."},{"full_name":"Kluse, J.","last_name":"Kluse","first_name":"J."},{"last_name":"Koerner","full_name":"Koerner, S. E.","first_name":"S. E."},{"first_name":"K. J.","last_name":"Komatsu","full_name":"Komatsu, K. J."},{"full_name":"Krishnan, S.","last_name":"Krishnan","first_name":"S."},{"first_name":"M.","full_name":"Laihonen, M.","last_name":"Laihonen"},{"last_name":"Lamelas-López","full_name":"Lamelas-López, L.","first_name":"L."},{"first_name":"M. C.","full_name":"Lascaleia, M. C.","last_name":"Lascaleia"},{"full_name":"Lecomte, N.","last_name":"Lecomte","first_name":"N."},{"full_name":"Lehn, C. R.","last_name":"Lehn","first_name":"C. R."},{"full_name":"Li, X.","last_name":"Li","first_name":"X."},{"full_name":"Lindroth, R. L.","last_name":"Lindroth","first_name":"R. L."},{"last_name":"Lopresti","full_name":"Lopresti, E. F.","first_name":"E. F."},{"first_name":"M.","last_name":"Losada","full_name":"Losada, M."},{"last_name":"Louthan","full_name":"Louthan, A. M.","first_name":"A. 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H."},{"first_name":"A. T.","full_name":"Moles, A. T.","last_name":"Moles"},{"first_name":"C. M.","last_name":"Moore","full_name":"Moore, C. M."},{"full_name":"Moreira, X.","last_name":"Moreira","first_name":"X."},{"last_name":"Morrison","full_name":"Morrison, C. R.","first_name":"C. R."},{"first_name":"M. C.","full_name":"Moshobane, M. C.","last_name":"Moshobane"},{"first_name":"A.","full_name":"Muola, A.","last_name":"Muola"},{"first_name":"R.","full_name":"Nakadai, R.","last_name":"Nakadai"},{"first_name":"K.","full_name":"Nakajima, K.","last_name":"Nakajima"},{"last_name":"Novais","full_name":"Novais, S.","first_name":"S."},{"last_name":"Ogbebor","full_name":"Ogbebor, C. O.","first_name":"C. O."},{"full_name":"Ohsaki, H.","last_name":"Ohsaki","first_name":"H."},{"first_name":"V. S.","full_name":"Pan, V. S.","last_name":"Pan"},{"first_name":"N. A.","last_name":"Pardikes","full_name":"Pardikes, N. 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J.M.","full_name":"Tack, A. J.M.","last_name":"Tack"},{"full_name":"Tayal, M.","last_name":"Tayal","first_name":"M."},{"full_name":"Tooker, J. F.","last_name":"Tooker","first_name":"J. F."},{"last_name":"Torrico-Bazoberry","full_name":"Torrico-Bazoberry, D.","first_name":"D."},{"full_name":"Tougeron, K.","last_name":"Tougeron","first_name":"K."},{"first_name":"A. M.","full_name":"Trowbridge, A. M.","last_name":"Trowbridge"},{"first_name":"S.","full_name":"Utsumi, S.","last_name":"Utsumi"},{"last_name":"Uyi","full_name":"Uyi, O.","first_name":"O."},{"last_name":"Vaca-Uribe","full_name":"Vaca-Uribe, J. L.","first_name":"J. L."},{"full_name":"Valtonen, A.","last_name":"Valtonen","first_name":"A."},{"last_name":"Van Dijk","full_name":"Van Dijk, L. J.A.","first_name":"L. J.A."},{"full_name":"Vandvik, V.","last_name":"Vandvik","first_name":"V."},{"last_name":"Villellas","full_name":"Villellas, J.","first_name":"J."},{"last_name":"Waller","full_name":"Waller, L. P.","first_name":"L. P."},{"last_name":"Weber","full_name":"Weber, M. G.","first_name":"M. G."},{"full_name":"Yamawo, A.","last_name":"Yamawo","first_name":"A."},{"first_name":"S.","full_name":"Yim, S.","last_name":"Yim"},{"first_name":"P. L.","full_name":"Zarnetske, P. L.","last_name":"Zarnetske"},{"last_name":"Zehr","full_name":"Zehr, L. N.","first_name":"L. N."},{"last_name":"Zhong","full_name":"Zhong, Z.","first_name":"Z."},{"first_name":"W. C.","full_name":"Wetzel, W. C.","last_name":"Wetzel"}],"publication_identifier":{"eissn":["1095-9203"]},"language":[{"iso":"eng"}]},{"tmp":{"image":"/images/cc_by_nc.png","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","short":"CC BY-NC (4.0)"},"ddc":["570"],"intvolume":" 36","title":"How chromosomal inversions reorient the evolutionary process","external_id":{"pmid":["37942504"],"isi":["001098690500001"]},"volume":36,"month":"12","oa":1,"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.","pmid":1,"_id":"14556","date_updated":"2025-09-09T13:22:35Z","article_processing_charge":"Yes (in subscription journal)","year":"2023","oa_version":"Published Version","publication_identifier":{"issn":["1010-061X"],"eissn":["1420-9101"]},"language":[{"iso":"eng"}],"author":[{"last_name":"Berdan","full_name":"Berdan, Emma L.","first_name":"Emma L."},{"last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"},{"first_name":"Roger","last_name":"Butlin","full_name":"Butlin, Roger"},{"first_name":"Brian","last_name":"Charlesworth","full_name":"Charlesworth, Brian"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"first_name":"Inês","full_name":"Fragata, Inês","last_name":"Fragata"},{"first_name":"Kimberly J.","last_name":"Gilbert","full_name":"Gilbert, Kimberly J."},{"full_name":"Jay, Paul","last_name":"Jay","first_name":"Paul"},{"last_name":"Kapun","full_name":"Kapun, Martin","first_name":"Martin"},{"first_name":"Katie E.","last_name":"Lotterhos","full_name":"Lotterhos, Katie E."},{"full_name":"Mérot, Claire","last_name":"Mérot","first_name":"Claire"},{"full_name":"Durmaz Mitchell, Esra","last_name":"Durmaz Mitchell","first_name":"Esra"},{"first_name":"Marta","full_name":"Pascual, Marta","last_name":"Pascual"},{"first_name":"Catherine L.","full_name":"Peichel, Catherine L.","last_name":"Peichel"},{"full_name":"Rafajlović, Marina","last_name":"Rafajlović","first_name":"Marina"},{"orcid":"0000-0003-1050-4969","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M","last_name":"Westram"},{"first_name":"Stephen W.","full_name":"Schaeffer, Stephen W.","last_name":"Schaeffer"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"full_name":"Flatt, Thomas","last_name":"Flatt","first_name":"Thomas"}],"file_date_updated":"2024-07-16T08:16:31Z","citation":{"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","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. 36(12), 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 36 (2023).","ieee":"E. L. Berdan et al., “How chromosomal inversions reorient the evolutionary process,” Journal of Evolutionary Biology, vol. 36, no. 12. Wiley, 2023.","mla":"Berdan, Emma L., et al. “How Chromosomal Inversions Reorient the Evolutionary Process.” Journal of Evolutionary Biology, vol. 36, no. 12, 14242, Wiley, 2023, doi:10.1111/jeb.14242.","ama":"Berdan EL, Barton NH, Butlin R, et al. How chromosomal inversions reorient the evolutionary process. Journal of Evolutionary Biology. 2023;36(12). 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."},"publication_status":"published","article_number":"14242","publication":"Journal of Evolutionary Biology","file":[{"checksum":"93ae4fa700aab8646bc62f0adeed8f8f","file_name":"2023_JourEvolutionaryBio_Berdan.pdf","relation":"main_file","creator":"dernst","access_level":"open_access","file_id":"17253","file_size":1401726,"success":1,"date_created":"2024-07-16T08:16:31Z","content_type":"application/pdf","date_updated":"2024-07-16T08:16:31Z"}],"article_type":"review","has_accepted_license":"1","department":[{"_id":"NiBa"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1111/jeb.14242","quality_controlled":"1","date_published":"2023-12-01T00:00:00Z","scopus_import":"1","publisher":"Wiley","date_created":"2023-11-19T23:00:55Z","issue":"12","type":"journal_article","abstract":[{"lang":"eng","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."}],"status":"public","isi":1,"day":"01"},{"article_processing_charge":"No","year":"2023","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8133118","open_access":"1"}],"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"}],"status":"public","oa_version":"Published Version","author":[{"last_name":"Wetzel","full_name":"Wetzel, William","first_name":"William"}],"citation":{"short":"W. Wetzel, (2023).","ieee":"W. Wetzel, “HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0.” Zenodo, 2023.","ista":"Wetzel W. 2023. HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0, Zenodo, 10.5281/ZENODO.8133117.","apa":"Wetzel, W. (2023). HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0. Zenodo. https://doi.org/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.","ama":"Wetzel W. HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0. 2023. doi:10.5281/ZENODO.8133117","mla":"Wetzel, William. HerbVar-Network/HV-Large-Patterns-MS-Public: V1.0.0. Zenodo, 2023, doi:10.5281/ZENODO.8133117."},"day":"11","ddc":["570"],"title":"HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0","department":[{"_id":"NiBa"}],"oa":1,"doi":"10.5281/ZENODO.8133117","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","date_published":"2023-07-11T00:00:00Z","date_created":"2023-11-20T11:07:45Z","publisher":"Zenodo","_id":"14579","type":"research_data_reference","related_material":{"record":[{"status":"public","id":"14552","relation":"used_in_publication"}]},"date_updated":"2025-09-09T13:23:55Z"},{"oa":1,"month":"12","title":"Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus","acknowledged_ssus":[{"_id":"ScienComp"}],"degree_awarded":"PhD","ddc":["570"],"related_material":{"record":[{"id":"11411","status":"public","relation":"part_of_dissertation"}]},"date_updated":"2026-04-07T13:28:30Z","_id":"14651","ec_funded":1,"OA_place":"publisher","oa_version":"Published Version","corr_author":"1","page":"96","project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385"}],"year":"2023","article_processing_charge":"No","publication_status":"published","citation":{"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","ista":"Arathoon LS. 2023. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. Institute of Science and Technology Austria.","short":"L.S. Arathoon, Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus, Institute of Science and Technology Austria, 2023.","ieee":"L. S. Arathoon, “Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus,” Institute of Science and Technology Austria, 2023."},"file_date_updated":"2023-12-14T08:58:18Z","author":[{"id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S","orcid":"0000-0003-1771-714X","last_name":"Arathoon","full_name":"Arathoon, Louise S"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:14651","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"file":[{"content_type":"application/pdf","date_updated":"2023-12-13T15:37:55Z","date_created":"2023-12-13T15:37:55Z","file_id":"14684","file_size":34101468,"access_level":"open_access","success":1,"checksum":"520bdb61e95e66070e02824947d2c5fa","file_name":"Phd_Thesis_LA.pdf","relation":"main_file","creator":"larathoo"},{"date_created":"2023-12-13T15:42:23Z","content_type":"application/zip","date_updated":"2023-12-14T08:58:18Z","file_name":"Phd_Thesis_LA.zip","checksum":"d8e59afd0817c98fba2564a264508e5c","relation":"source_file","creator":"larathoo","access_level":"closed","file_size":31052872,"file_id":"14685"},{"access_level":"closed","file_size":10713896,"file_id":"14681","file_name":"Supplementary_Materials.zip","checksum":"9a778c949932286f4519e1f1fca2820d","creator":"larathoo","relation":"supplementary_material","content_type":"application/zip","date_updated":"2023-12-14T08:58:18Z","date_created":"2023-12-11T19:24:59Z"}],"type":"dissertation","date_created":"2023-12-11T19:30:37Z","publisher":"Institute of Science and Technology Austria","date_published":"2023-12-12T00:00:00Z","status":"public","supervisor":[{"last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"}],"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"}],"alternative_title":["ISTA Thesis"],"day":"12"},{"_id":"14732","related_material":{"record":[{"relation":"later_version","status":"public","id":"21322"},{"id":"14711","status":"public","relation":"dissertation_contains"}]},"date_updated":"2026-04-07T12:54:28Z","type":"preprint","OA_place":"repository","date_published":"2023-12-04T00:00:00Z","date_created":"2024-01-04T09:35:54Z","department":[{"_id":"NiBa"},{"_id":"JaMa"}],"month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"doi":"10.1101/2023.12.02.569702","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"title":"Genetic load, eco-evolutionary feedback and extinction in a metapopulation","citation":{"ista":"Olusanya OO, Khudiakova K, Sachdeva H. Genetic load, eco-evolutionary feedback and extinction in a metapopulation. bioRxiv, 10.1101/2023.12.02.569702.","apa":"Olusanya, O. O., Khudiakova, K., & Sachdeva, H. (n.d.). Genetic load, eco-evolutionary feedback and extinction in a metapopulation. bioRxiv. https://doi.org/10.1101/2023.12.02.569702","ieee":"O. O. Olusanya, K. Khudiakova, and H. Sachdeva, “Genetic load, eco-evolutionary feedback and extinction in a metapopulation,” bioRxiv. .","short":"O.O. Olusanya, K. Khudiakova, H. Sachdeva, BioRxiv (n.d.).","mla":"Olusanya, Oluwafunmilola O., et al. “Genetic Load, Eco-Evolutionary Feedback and Extinction in a Metapopulation.” BioRxiv, doi:10.1101/2023.12.02.569702.","chicago":"Olusanya, Oluwafunmilola O, Kseniia Khudiakova, and Himani Sachdeva. “Genetic Load, Eco-Evolutionary Feedback and Extinction in a Metapopulation.” BioRxiv, n.d. https://doi.org/10.1101/2023.12.02.569702.","ama":"Olusanya OO, Khudiakova K, Sachdeva H. Genetic load, eco-evolutionary feedback and extinction in a metapopulation. bioRxiv. doi:10.1101/2023.12.02.569702"},"publication_status":"draft","day":"04","publication":"bioRxiv","language":[{"iso":"eng"}],"author":[{"first_name":"Oluwafunmilola O","orcid":"0000-0003-1971-8314","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87","full_name":"Olusanya, Oluwafunmilola O","last_name":"Olusanya"},{"last_name":"Khudiakova","full_name":"Khudiakova, Kseniia","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","orcid":"0000-0002-6246-1465","first_name":"Kseniia"},{"first_name":"Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","full_name":"Sachdeva, Himani","last_name":"Sachdeva"}],"abstract":[{"lang":"eng","text":"Fragmented landscapes pose a significant threat to the persistence of species as they are highly susceptible to heightened risk of extinction due to the combined effects of genetic and demographic factors such as genetic drift and demographic stochasticity. This paper explores the intricate interplay between genetic load and extinction risk within metapopulations with a focus on understanding the impact of eco-evolutionary feedback mechanisms. We distinguish between two models of selection: soft selection, characterised by subpopulations maintaining carrying capacity despite load, and hard selection, where load can significantly affect population size. Within the soft selection framework, we investigate the impact of gene flow on genetic load at a single locus, while also considering the effect of selection strength and dominance coefficient. We subsequently build on this to examine how gene flow influences both population size and load under hard selection as well as identify critical thresholds for metapopulation persistence. Our analysis employs the diffusion, semi-deterministic and effective migration approximations. Our findings reveal that under soft selection, even modest levels of migration can significantly alleviate the burden of load. In sharp contrast, with hard selection, a much higher degree of gene flow is required to mitigate load and prevent the collapse of the metapopulation. Overall, this study sheds light into the crucial role migration plays in shaping the dynamics of genetic load and extinction risk in fragmented landscapes, offering valuable insights for conservation strategies and the preservation of diversity in a changing world."}],"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2023.12.02.569702v1","open_access":"1"}],"project":[{"_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8","name":"Causes and consequences of population fragmentation","grant_number":"P32896"},{"name":"The impact of deleterious mutations on small populations","_id":"34d33d68-11ca-11ed-8bc3-ec13763c0ca8","grant_number":"26293"},{"_id":"34c872fe-11ca-11ed-8bc3-8534b82131e6","name":"Polygenic Adaptation in a Metapopulation","grant_number":"26380"}],"corr_author":"1","oa_version":"Preprint","status":"public","article_processing_charge":"No","year":"2023"},{"isi":1,"day":"01","keyword":["General Biochemistry","Genetics and Molecular Biology"],"status":"public","main_file_link":[{"url":"https://doi.org/10.1101/cshperspect.a041447","open_access":"1"}],"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."}],"publisher":"Cold Spring Harbor Laboratory Press","date_created":"2024-01-08T12:43:48Z","scopus_import":"1","quality_controlled":"1","date_published":"2023-11-01T00:00:00Z","type":"journal_article","issue":"11","doi":"10.1101/cshperspect.a041447","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"article_type":"original","author":[{"full_name":"Lucek, Kay","last_name":"Lucek","first_name":"Kay"},{"first_name":"Mabel D.","last_name":"Giménez","full_name":"Giménez, Mabel D."},{"first_name":"Mathieu","full_name":"Joron, Mathieu","last_name":"Joron"},{"full_name":"Rafajlović, Marina","last_name":"Rafajlović","first_name":"Marina"},{"last_name":"Searle","full_name":"Searle, Jeremy B.","first_name":"Jeremy B."},{"full_name":"Walden, Nora","last_name":"Walden","first_name":"Nora"},{"last_name":"Westram","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","orcid":"0000-0003-1050-4969"},{"last_name":"Faria","full_name":"Faria, Rui","first_name":"Rui"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1943-0264"]},"publication":"Cold Spring Harbor Perspectives in Biology","publication_status":"published","article_number":"a041447","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 Press. 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 Press, 2023.","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).","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 Press, 2023, doi:10.1101/cshperspect.a041447.","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 Press, 2023. https://doi.org/10.1101/cshperspect.a041447."},"year":"2023","article_processing_charge":"No","oa_version":"Published Version","pmid":1,"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.","date_updated":"2026-06-18T17:37:44Z","_id":"14742","title":"The impact of chromosomal rearrangements in speciation: From micro- to macroevolution","intvolume":" 15","ddc":["570"],"oa":1,"volume":15,"month":"11","external_id":{"pmid":["37604585"],"isi":["001096272600001"]}},{"year":"2023","article_processing_charge":"No","oa_version":"Preprint","page":"2041-2054","author":[{"last_name":"Stankowski","full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean"},{"first_name":"Madeline A.","last_name":"Chase","full_name":"Chase, Madeline A."},{"full_name":"McIntosh, Hanna","last_name":"McIntosh","first_name":"Hanna"},{"full_name":"Streisfeld, Matthew A.","last_name":"Streisfeld","first_name":"Matthew A."}],"publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"language":[{"iso":"eng"}],"publication":"Molecular Ecology","citation":{"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.","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.","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","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.","short":"S. Stankowski, M.A. Chase, H. McIntosh, M.A. Streisfeld, Molecular Ecology 32 (2023) 2041–2054.","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."},"publication_status":"published","intvolume":" 32","title":"Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone","volume":32,"month":"04","oa":1,"external_id":{"pmid":["36651268"],"isi":["000919244600001"]},"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.","pmid":1,"date_updated":"2024-01-16T10:10:00Z","_id":"14787","status":"public","main_file_link":[{"url":"https://doi.org/10.1101/2022.01.28.478139","open_access":"1"}],"abstract":[{"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.","lang":"eng"}],"isi":1,"day":"01","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1111/mec.16849","article_type":"original","department":[{"_id":"NiBa"}],"publisher":"Wiley","date_created":"2024-01-10T10:44:45Z","date_published":"2023-04-01T00:00:00Z","quality_controlled":"1","issue":"8","type":"journal_article"},{"title":"Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["570"],"oa":1,"doi":"10.5281/ZENODO.8318995","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"09","has_accepted_license":"1","department":[{"_id":"NiBa"}],"date_created":"2024-01-16T10:23:01Z","publisher":"Zenodo","date_published":"2023-09-05T00:00:00Z","type":"research_data_reference","date_updated":"2025-09-04T11:38:30Z","related_material":{"record":[{"status":"public","id":"14796","relation":"used_in_publication"}]},"_id":"14812","year":"2023","article_processing_charge":"No","status":"public","corr_author":"1","oa_version":"Published Version","abstract":[{"text":"This repository contains the code and VCF files needed to conduct the analyses in our MS. Each folder contains a readMe document explaining the nature of each file and dataset and the results and analyses that they relate to. The same anlaysis code (but not VCF files) is also available at https://github.com/seanstankowski/Littorina_reproductive_mode","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.8318995"}],"author":[{"full_name":"Stankowski, Sean","last_name":"Stankowski","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"}],"contributor":[{"first_name":"Zusanna","last_name":"Zagrodzka"},{"last_name":"Garlovsky","first_name":"Martin"},{"orcid":"0000-0002-4530-8469","first_name":"Arka","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","last_name":"Pal"},{"first_name":"Daria","orcid":"0000-0002-1145-9226","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","last_name":"Shipilina"},{"last_name":"Garcia Castillo","id":"ae681a14-dc74-11ea-a0a7-c6ef18161701","first_name":"Diego Fernando"},{"first_name":"Hila","id":"d6ab5470-2fb3-11ed-8633-986a9b84edac","last_name":"Lifchitz"},{"first_name":"Alan","last_name":"Le Moan"},{"first_name":"Erica","last_name":"Leder"},{"last_name":"Reeve","first_name":"James"},{"last_name":"Johannesson","first_name":"Kerstin"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram"},{"last_name":"Butlin","first_name":"Roger"}],"day":"05","citation":{"short":"S. Stankowski, (2023).","ieee":"S. Stankowski, “Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails.” Zenodo, 2023.","apa":"Stankowski, S. (2023). Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails. Zenodo. https://doi.org/10.5281/ZENODO.8318995","ista":"Stankowski S. 2023. Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails, Zenodo, 10.5281/ZENODO.8318995.","ama":"Stankowski S. Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails. 2023. doi:10.5281/ZENODO.8318995","chicago":"Stankowski, Sean. “Data and Code for: The Genetic Architecture of a Recent Transition to Live-Bearing in Marine Snails.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8318995.","mla":"Stankowski, Sean. Data and Code for: The Genetic Architecture of a Recent Transition to Live-Bearing in Marine Snails. Zenodo, 2023, doi:10.5281/ZENODO.8318995."}},{"oa":1,"month":"08","volume":2,"ddc":["570"],"tmp":{"image":"/images/cc_by_nc.png","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","short":"CC BY-NC (4.0)"},"title":"Whole-genome phylogeography of the intertidal snail Littorina saxatilis","intvolume":" 2","_id":"14833","date_updated":"2024-10-09T21:07:54Z","acknowledgement":"Isobel Eyres, Richard Turney, Graciela Sotelo, Jenny Larson, and Stéphane Loisel helped with the collection and processing of samples. Petri Kemppainen kindly provided samples from Trondheim Fjord. Mark Dunning helped with the development of bioinformatic pipelines. The analysis of genomic data was conducted on the University of Sheffield high-performance computing cluster, ShARC. Funding was provided by the Natural Environment Research Council (NERC) and the European Research Council (ERC). J.G. was funded by a Juntas Industriales y Navales (JIN) project (Ministerio de Ciencia, Innovación y Universidades, code RTI2018-101274-J-I00).","corr_author":"1","oa_version":"Published Version","article_processing_charge":"Yes","year":"2023","publication_status":"published","article_number":"kzad002","citation":{"mla":"Stankowski, Sean, et al. “Whole-Genome Phylogeography of the Intertidal Snail Littorina Saxatilis.” Evolutionary Journal of the Linnean Society, vol. 2, no. 1, kzad002, Oxford University Press, 2023, doi:10.1093/evolinnean/kzad002.","ama":"Stankowski S, Zagrodzka ZB, Galindo J, et al. Whole-genome phylogeography of the intertidal snail Littorina saxatilis. Evolutionary Journal of the Linnean Society. 2023;2(1). doi:10.1093/evolinnean/kzad002","chicago":"Stankowski, Sean, Zuzanna B Zagrodzka, Juan Galindo, Mauricio Montaño-Rendón, Rui Faria, Natalia Mikhailova, April M H Blakeslee, et al. “Whole-Genome Phylogeography of the Intertidal Snail Littorina Saxatilis.” Evolutionary Journal of the Linnean Society. Oxford University Press, 2023. https://doi.org/10.1093/evolinnean/kzad002.","ista":"Stankowski S, Zagrodzka ZB, Galindo J, Montaño-Rendón M, Faria R, Mikhailova N, Blakeslee AMH, Arnason E, Broquet T, Morales HE, Grahame JW, Westram AM, Johannesson K, Butlin RK. 2023. Whole-genome phylogeography of the intertidal snail Littorina saxatilis. Evolutionary Journal of the Linnean Society. 2(1), kzad002.","apa":"Stankowski, S., Zagrodzka, Z. B., Galindo, J., Montaño-Rendón, M., Faria, R., Mikhailova, N., … Butlin, R. K. (2023). Whole-genome phylogeography of the intertidal snail Littorina saxatilis. Evolutionary Journal of the Linnean Society. Oxford University Press. https://doi.org/10.1093/evolinnean/kzad002","ieee":"S. Stankowski et al., “Whole-genome phylogeography of the intertidal snail Littorina saxatilis,” Evolutionary Journal of the Linnean Society, vol. 2, no. 1. Oxford University Press, 2023.","short":"S. Stankowski, Z.B. Zagrodzka, J. Galindo, M. Montaño-Rendón, R. Faria, N. Mikhailova, A.M.H. Blakeslee, E. Arnason, T. Broquet, H.E. Morales, J.W. Grahame, A.M. Westram, K. Johannesson, R.K. Butlin, Evolutionary Journal of the Linnean Society 2 (2023)."},"publication":"Evolutionary Journal of the Linnean Society","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2752-938X"]},"file_date_updated":"2024-01-23T08:10:00Z","author":[{"last_name":"Stankowski","full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean"},{"first_name":"Zuzanna B","last_name":"Zagrodzka","full_name":"Zagrodzka, Zuzanna B"},{"first_name":"Juan","last_name":"Galindo","full_name":"Galindo, Juan"},{"full_name":"Montaño-Rendón, Mauricio","last_name":"Montaño-Rendón","first_name":"Mauricio"},{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"first_name":"Natalia","last_name":"Mikhailova","full_name":"Mikhailova, Natalia"},{"first_name":"April M H","last_name":"Blakeslee","full_name":"Blakeslee, April M H"},{"last_name":"Arnason","full_name":"Arnason, Einar","first_name":"Einar"},{"first_name":"Thomas","full_name":"Broquet, Thomas","last_name":"Broquet"},{"first_name":"Hernán E","full_name":"Morales, Hernán E","last_name":"Morales"},{"last_name":"Grahame","full_name":"Grahame, John W","first_name":"John W"},{"full_name":"Westram, Anja M","last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"first_name":"Roger K","last_name":"Butlin","full_name":"Butlin, Roger K"}],"department":[{"_id":"NiBa"}],"has_accepted_license":"1","file":[{"file_id":"14875","file_size":3408944,"access_level":"open_access","success":1,"checksum":"ba6f9102d3a9fe6631c4fa398c5e4313","file_name":"2023_EvolJourLinneanSociety_Stankowski.pdf","creator":"dernst","relation":"main_file","content_type":"application/pdf","date_updated":"2024-01-23T08:10:00Z","date_created":"2024-01-23T08:10:00Z"}],"article_type":"original","doi":"10.1093/evolinnean/kzad002","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","issue":"1","quality_controlled":"1","date_published":"2023-08-17T00:00:00Z","date_created":"2024-01-18T07:54:10Z","publisher":"Oxford University Press","abstract":[{"lang":"eng","text":"Understanding the factors that have shaped the current distributions and diversity of species is a central and longstanding aim of evolutionary biology. The recent inclusion of genomic data into phylogeographic studies has dramatically improved our understanding in organisms where evolutionary relationships have been challenging to infer. We used whole-genome sequences to study the phylogeography of the intertidal snail Littorina saxatilis, which has successfully colonized and diversified across a broad range of coastal environments in the Northern Hemisphere amid repeated cycles of glaciation. Building on past studies based on short DNA sequences, we used genome-wide data to provide a clearer picture of the relationships among samples spanning most of the species natural range. Our results confirm the trans-Atlantic colonization of North America from Europe, and have allowed us to identify rough locations of glacial refugia and to infer likely routes of colonization within Europe. We also investigated the signals in different datasets to account for the effects of genomic architecture and non-neutral evolution, which provides new insights about diversification of four ecotypes of L. saxatilis (the crab, wave, barnacle, and brackish ecotypes) at different spatial scales. Overall, we provide a much clearer picture of the biogeography of L. saxatilis, providing a foundation for more detailed phylogenomic and demographic studies."}],"status":"public","day":"17"},{"publisher":"Institute of Science and Technology Austria","date_created":"2023-04-04T18:57:11Z","date_published":"2023-04-05T00:00:00Z","type":"dissertation","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","doi":"10.15479/at:ista:12800","file":[{"date_created":"2023-04-06T06:09:40Z","date_updated":"2023-06-02T22:30:04Z","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","embargo_to":"open_access","relation":"supplementary_material","creator":"mjulseth","file_name":"Dispersaldata.xlsx","checksum":"b76cf6d69f2093d8248f6a3f9d4654a4","access_level":"closed","file_id":"12805","file_size":52795},{"date_created":"2023-04-06T06:11:27Z","content_type":"application/vnd.wolfram.nb","date_updated":"2023-06-02T22:30:04Z","checksum":"5a13b6d204371572e249f03795bc0d04","file_name":"2023_MSc_ThesisMaraJulseth_Notebook.nb","embargo":"2023-06-01","creator":"mjulseth","relation":"supplementary_material","file_id":"12806","file_size":787239,"access_level":"open_access"},{"relation":"source_file","creator":"mjulseth","checksum":"c3ec842839ed1e66bf2618ae33047df8","file_name":"ThesisMaraJulseth_04_23.docx","file_id":"12812","file_size":1061763,"access_level":"closed","date_created":"2023-04-06T08:26:12Z","date_updated":"2023-06-02T22:30:04Z","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"content_type":"application/pdf","date_updated":"2023-06-02T22:30:04Z","date_created":"2023-04-06T08:26:37Z","access_level":"open_access","file_id":"12813","file_size":1741364,"embargo":"2023-06-01","file_name":"ThesisMaraJulseth_04_23.pdf","checksum":"3132cc998fbe3ae2a3a83c2a69367f37","creator":"mjulseth","relation":"main_file"}],"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"has_accepted_license":"1","day":"05","alternative_title":["ISTA Master's Thesis"],"status":"public","abstract":[{"text":"The evolutionary processes that brought about today’s plethora of living species and the many billions more ancient ones all underlie biology. Evolutionary pathways are neither directed nor deterministic, but rather an interplay between selection, migration, mutation, genetic drift and other environmental factors. Hybrid zones, as natural crossing experiments, offer a great opportunity to use cline analysis to deduce different evolutionary processes - for example, selection strength. Theoretical cline models, largely assuming uniform distribution of individuals, often lack the capability of incorporating population structure. Since in reality organisms mostly live in patchy distributions and their dispersal is hardly ever Gaussian, it is necessary to unravel the effect of these different elements of population structure on cline parameters and shape. In this thesis, I develop a simulation inspired by the A. majus hybrid zone of a single selected locus under frequency dependent selection. This simulation enables us to untangle the effects of different elements of population structure as for example a low-density center and long-range dispersal. This thesis is therefore a first step towards theoretically untangling the effects of different elements of population structure on cline parameters and shape. ","lang":"eng"}],"supervisor":[{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"OA_place":"publisher","date_updated":"2026-04-07T14:01:51Z","_id":"12800","degree_awarded":"MS","title":"The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone","ddc":["576"],"month":"04","oa":1,"author":[{"id":"1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1","first_name":"Mara","last_name":"Julseth","full_name":"Julseth, Mara"}],"file_date_updated":"2023-06-02T22:30:04Z","publication_identifier":{"issn":["2791-4585"]},"language":[{"iso":"eng"}],"citation":{"short":"M. Julseth, The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone, Institute of Science and Technology Austria, 2023.","ieee":"M. Julseth, “The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone,” Institute of Science and Technology Austria, 2023.","ista":"Julseth M. 2023. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. Institute of Science and Technology Austria.","apa":"Julseth, M. (2023). The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12800","ama":"Julseth M. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. 2023. doi:10.15479/at:ista:12800","chicago":"Julseth, Mara. “The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12800.","mla":"Julseth, Mara. The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12800."},"publication_status":"published","year":"2023","article_processing_charge":"No","corr_author":"1","oa_version":"Published Version","page":"21"},{"citation":{"short":"D. Shipilina, A. Pal, S. Stankowski, Y.F. Chan, N.H. Barton, Molecular Ecology 32 (2023) 1441–1457.","ieee":"D. Shipilina, A. Pal, S. Stankowski, Y. F. Chan, and N. H. Barton, “On the origin and structure of haplotype blocks,” Molecular Ecology, vol. 32, no. 6. Wiley, pp. 1441–1457, 2023.","ista":"Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. 2023. On the origin and structure of haplotype blocks. Molecular Ecology. 32(6), 1441–1457.","apa":"Shipilina, D., Pal, A., Stankowski, S., Chan, Y. F., & Barton, N. H. (2023). On the origin and structure of haplotype blocks. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.16793","chicago":"Shipilina, Daria, Arka Pal, Sean Stankowski, Yingguang Frank Chan, and Nicholas H Barton. “On the Origin and Structure of Haplotype Blocks.” Molecular Ecology. Wiley, 2023. https://doi.org/10.1111/mec.16793.","ama":"Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. On the origin and structure of haplotype blocks. Molecular Ecology. 2023;32(6):1441-1457. doi:10.1111/mec.16793","mla":"Shipilina, Daria, et al. “On the Origin and Structure of Haplotype Blocks.” Molecular Ecology, vol. 32, no. 6, Wiley, 2023, pp. 1441–57, doi:10.1111/mec.16793."},"publication_status":"published","publication":"Molecular Ecology","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"language":[{"iso":"eng"}],"author":[{"id":"428A94B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1145-9226","first_name":"Daria","last_name":"Shipilina","full_name":"Shipilina, Daria"},{"orcid":"0000-0002-4530-8469","first_name":"Arka","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","full_name":"Pal, Arka","last_name":"Pal"},{"first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","last_name":"Stankowski"},{"last_name":"Chan","full_name":"Chan, Yingguang Frank","first_name":"Yingguang Frank"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"file_date_updated":"2023-08-16T08:15:41Z","page":"1441-1457","project":[{"grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"Snapdragon Speciation"},{"name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211"},{"name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327"}],"corr_author":"1","oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","year":"2023","_id":"12159","date_updated":"2026-08-30T22:30:44Z","related_material":{"record":[{"status":"public","id":"20694","relation":"dissertation_contains"}]},"pmid":1,"acknowledgement":"We thank the Barton group for useful discussion and feedback during the writing of this article. Comments from Roger Butlin, Molly Schumer's Group, the tskit development team, editors and three reviewers greatly improved the manuscript. Funding was provided by SCAS (Natural Sciences Programme, Knut and Alice Wallenberg Foundation), an FWF Wittgenstein grant (PT1001Z211), an FWF standalone grant (grant P 32166), and an ERC Advanced Grant. YFC was supported by the Max Planck Society and an ERC Proof of Concept Grant #101069216 (HAPLOTAGGING).","external_id":{"pmid":["36433653"],"isi":["000900762000001"]},"volume":32,"month":"03","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["570"],"intvolume":" 32","title":"On the origin and structure of haplotype blocks","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"day":"01","isi":1,"abstract":[{"text":"The term “haplotype block” is commonly used in the developing field of haplotype-based inference methods. We argue that the term should be defined based on the structure of the Ancestral Recombination Graph (ARG), which contains complete information on the ancestry of a sample. We use simulated examples to demonstrate key features of the relationship between haplotype blocks and ancestral structure, emphasizing the stochasticity of the processes that generate them. Even the simplest cases of neutrality or of a “hard” selective sweep produce a rich structure, often missed by commonly used statistics. We highlight a number of novel methods for inferring haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate how they can be used to define haplotype blocks using an empirical data set. While the advent of new, computationally efficient methods makes it possible to apply these concepts broadly, they (and additional new methods) could benefit from adding features to explore haplotype blocks, as we define them. Understanding and applying the concept of the haplotype block will be essential to fully exploit long and linked-read sequencing technologies.","lang":"eng"}],"status":"public","issue":"6","type":"journal_article","quality_controlled":"1","date_published":"2023-03-01T00:00:00Z","scopus_import":"1","publisher":"Wiley","date_created":"2023-01-12T12:09:17Z","file":[{"success":1,"access_level":"open_access","file_id":"14062","file_size":7144607,"relation":"main_file","creator":"dernst","file_name":"2023_MolecularEcology_Shipilina.pdf","checksum":"b10e0f8fa3dc4d72aaf77a557200978a","date_updated":"2023-08-16T08:15:41Z","content_type":"application/pdf","date_created":"2023-08-16T08:15:41Z"}],"article_type":"original","department":[{"_id":"NiBa"}],"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1111/mec.16793"},{"oa":1,"month":"04","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"}],"title":"Genetic basis of flower colour as a model for adaptive evolution","degree_awarded":"PhD","ddc":["576","582"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2026-04-07T14:12:19Z","_id":"11128","OA_place":"publisher","oa_version":"Published Version","corr_author":"1","page":"112","year":"2022","article_processing_charge":"No","publication_status":"published","citation":{"ieee":"L. Matejovicova, “Genetic basis of flower colour as a model for adaptive evolution,” Institute of Science and Technology Austria, 2022.","short":"L. Matejovicova, Genetic Basis of Flower Colour as a Model for Adaptive Evolution, Institute of Science and Technology Austria, 2022.","apa":"Matejovicova, L. (2022). Genetic basis of flower colour as a model for adaptive evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11128","ista":"Matejovicova L. 2022. Genetic basis of flower colour as a model for adaptive evolution. Institute of Science and Technology Austria.","ama":"Matejovicova L. Genetic basis of flower colour as a model for adaptive evolution. 2022. doi:10.15479/at:ista:11128","chicago":"Matejovicova, Lenka. “Genetic Basis of Flower Colour as a Model for Adaptive Evolution.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11128.","mla":"Matejovicova, Lenka. Genetic Basis of Flower Colour as a Model for Adaptive Evolution. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11128."},"file_date_updated":"2022-04-07T08:11:51Z","author":[{"first_name":"Lenka","id":"2DFDEC72-F248-11E8-B48F-1D18A9856A87","full_name":"Matejovicova, Lenka","last_name":"Matejovicova"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-99078-016-9"],"issn":["2663-337X"]},"doi":"10.15479/at:ista:11128","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"has_accepted_license":"1","file":[{"file_size":11906472,"file_id":"11129","access_level":"open_access","creator":"cchlebak","relation":"main_file","file_name":"LenkaPhD_Official_PDFA.pdf","checksum":"e9609bc4e8f8e20146fc1125fd4f1bf7","date_updated":"2022-04-07T08:11:34Z","content_type":"application/pdf","date_created":"2022-04-07T08:11:34Z"},{"access_level":"closed","file_id":"11130","file_size":23036766,"creator":"cchlebak","relation":"source_file","file_name":"LenkaPhD Official_source.zip","checksum":"99d67040432fd07a225643a212ee8588","date_updated":"2022-04-07T08:11:51Z","content_type":"application/x-zip-compressed","date_created":"2022-04-07T08:11:51Z"}],"type":"dissertation","publisher":"Institute of Science and Technology Austria","date_created":"2022-04-07T08:19:54Z","date_published":"2022-04-06T00:00:00Z","status":"public","supervisor":[{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"text":"Although we often see studies focusing on simple or even discrete traits in studies of colouration,\r\nthe variation of “appearance” phenotypes found in nature is often more complex, continuous\r\nand high-dimensional. Therefore, we developed automated methods suitable for large datasets\r\nof genomes and images, striving to account for their complex nature, while minimising human\r\nbias. We used these methods on a dataset of more than 20, 000 plant SNP genomes and\r\ncorresponding fower images from a hybrid zone of two subspecies of Antirrhinum majus with\r\ndistinctly coloured fowers to improve our understanding of the genetic nature of the fower\r\ncolour in our study system.\r\nFirstly, we use the advantage of large numbers of genotyped plants to estimate the haplotypes in\r\nthe main fower colour regulating region. We study colour- and geography-related characteristics\r\nof the estimated haplotypes and how they connect to their relatedness. We show discrepancies\r\nfrom the expected fower colour distributions given the genotype and identify particular\r\nhaplotypes leading to unexpected phenotypes. We also confrm a signifcant defcit of the\r\ndouble recessive recombinant and quite surprisingly, we show that haplotypes of the most\r\nfrequent parental type are much less variable than others.\r\nSecondly, we introduce our pipeline capable of processing tens of thousands of full fower\r\nimages without human interaction and summarising each image into a set of informative scores.\r\nWe show the compatibility of these machine-measured fower colour scores with the previously\r\nused manual scores and study impact of external efect on the resulting scores. Finally, we use\r\nthe machine-measured fower colour scores to ft and examine a phenotype cline across the\r\nhybrid zone in Planoles using full fower images as opposed to discrete, manual scores and\r\ncompare it with the genotypic cline.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"day":"06"},{"_id":"11321","date_updated":"2025-04-15T08:20:40Z","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"9192"},{"id":"8254","status":"public","relation":"earlier_version"},{"status":"public","id":"11411","relation":"used_in_publication"}]},"type":"research_data","date_published":"2022-04-28T00:00:00Z","date_created":"2022-04-22T09:42:24Z","publisher":"Institute of Science and Technology Austria","file":[{"file_id":"11326","file_size":13260571,"access_level":"open_access","success":1,"checksum":"96c1b86cdf25481f2a52972fcc45ca7f","file_name":"Data_Code.zip","relation":"main_file","creator":"larathoo","content_type":"application/x-zip-compressed","date_updated":"2022-04-22T09:39:03Z","date_created":"2022-04-22T09:39:03Z"}],"has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"04","doi":"10.15479/at:ista:11321","oa":1,"ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","citation":{"ista":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2022. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus, Institute of Science and Technology Austria, 10.15479/at:ista:11321.","apa":"Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., & Barton, N. H. (2022). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11321","short":"P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, (2022).","ieee":"P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H. Barton, “Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus.” Institute of Science and Technology Austria, 2022.","mla":"Surendranadh, Parvathy, et al. Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11321.","chicago":"Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field, Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11321.","ama":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. 2022. doi:10.15479/at:ista:11321"},"day":"28","contributor":[{"last_name":"Arathoon","contributor_type":"project_member","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S"},{"last_name":"Baskett","first_name":"Carina","orcid":"0000-0002-7354-8574","contributor_type":"project_member","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Field","contributor_type":"project_member","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","orcid":"0000-0002-4014-8478"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","orcid":"0000-0001-6118-0541","first_name":"Melinda","last_name":"Pickup"},{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","contributor_type":"project_member","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"}],"author":[{"full_name":"Surendranadh, Parvathy","last_name":"Surendranadh","orcid":"0000-0001-6395-386X","first_name":"Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Louise S","orcid":"0000-0003-1771-714X","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","full_name":"Arathoon, Louise S","last_name":"Arathoon"},{"id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7354-8574","first_name":"Carina","last_name":"Baskett","full_name":"Baskett, Carina"},{"first_name":"David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","full_name":"Field, David","last_name":"Field"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda","orcid":"0000-0001-6118-0541","last_name":"Pickup","full_name":"Pickup, Melinda"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H"}],"file_date_updated":"2022-04-22T09:39:03Z","abstract":[{"lang":"eng","text":"Here are the research data underlying the publication \"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus\" Further information are summed up in the README document. "}],"corr_author":"1","oa_version":"Published Version","status":"public","article_processing_charge":"No","year":"2022"},{"title":"Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization","intvolume":" 76","ddc":["570"],"tmp":{"image":"/images/cc_by_nc.png","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","short":"CC BY-NC (4.0)"},"oa":1,"month":"05","volume":76,"external_id":{"pmid":["35323995"],"isi":["000781632500001"]},"pmid":1,"acknowledgement":"The authors thank A. van der Meijden and F. Ahmadzadeh for providing specimens and tissue samples, and A. Vardanyan, C. Corti, F. Jorge, and S. Drovetski for support during field work. The authors also thank S. Qiu for assistance with python scripting, S. Rocha for her support in BEAST analysis, and B. Wielstra for his comments on\r\na previous version of the manuscript. SF was funded by FCT grant SFRH/BD/81483/2011 (a PhD individual grant). AMW was funded by the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement no. 797747. TS acknowledges funding from the Swiss National Science Foundation (grants\r\nPP00P3_170627 and 31003A_182495). The work was carried out under financial support of the projects “Preserving Armenian biodiversity: Joint Portuguese – Armenian program for training in modern conservation biology” of Gulbenkian Foundation (Portugal) and PTDC/BIABEC/101256/2008 of Fundação para a Ciência e a Tecnologia (FCT, Portugal).","ec_funded":1,"date_updated":"2025-04-14T07:48:21Z","_id":"11334","year":"2022","article_processing_charge":"No","oa_version":"Published Version","project":[{"grant_number":"797747","call_identifier":"H2020","_id":"265B41B8-B435-11E9-9278-68D0E5697425","name":"Theoretical and empirical approaches to understanding Parallel Adaptation"}],"page":"899-914","file_date_updated":"2022-08-05T06:19:28Z","author":[{"first_name":"Susana","last_name":"Freitas","full_name":"Freitas, Susana"},{"orcid":"0000-0003-1050-4969","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M","last_name":"Westram"},{"last_name":"Schwander","full_name":"Schwander, Tanja","first_name":"Tanja"},{"full_name":"Arakelyan, Marine","last_name":"Arakelyan","first_name":"Marine"},{"full_name":"Ilgaz, Çetin","last_name":"Ilgaz","first_name":"Çetin"},{"first_name":"Yusuf","last_name":"Kumlutas","full_name":"Kumlutas, Yusuf"},{"first_name":"David James","last_name":"Harris","full_name":"Harris, David James"},{"last_name":"Carretero","full_name":"Carretero, Miguel A.","first_name":"Miguel A."},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"publication":"Evolution","publication_status":"published","citation":{"mla":"Freitas, Susana, et al. “Parthenogenesis in Darevskia Lizards: A Rare Outcome of Common Hybridization, Not a Common Outcome of Rare Hybridization.” Evolution, vol. 76, no. 5, Wiley, 2022, pp. 899–914, doi:10.1111/evo.14462.","chicago":"Freitas, Susana, Anja M Westram, Tanja Schwander, Marine Arakelyan, Çetin Ilgaz, Yusuf Kumlutas, David James Harris, Miguel A. Carretero, and Roger K. Butlin. “Parthenogenesis in Darevskia Lizards: A Rare Outcome of Common Hybridization, Not a Common Outcome of Rare Hybridization.” Evolution. Wiley, 2022. https://doi.org/10.1111/evo.14462.","ama":"Freitas S, Westram AM, Schwander T, et al. Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization. Evolution. 2022;76(5):899-914. doi:10.1111/evo.14462","apa":"Freitas, S., Westram, A. M., Schwander, T., Arakelyan, M., Ilgaz, Ç., Kumlutas, Y., … Butlin, R. K. (2022). Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization. Evolution. Wiley. https://doi.org/10.1111/evo.14462","ista":"Freitas S, Westram AM, Schwander T, Arakelyan M, Ilgaz Ç, Kumlutas Y, Harris DJ, Carretero MA, Butlin RK. 2022. Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization. Evolution. 76(5), 899–914.","ieee":"S. Freitas et al., “Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization,” Evolution, vol. 76, no. 5. Wiley, pp. 899–914, 2022.","short":"S. Freitas, A.M. Westram, T. Schwander, M. Arakelyan, Ç. Ilgaz, Y. Kumlutas, D.J. Harris, M.A. Carretero, R.K. Butlin, Evolution 76 (2022) 899–914."},"doi":"10.1111/evo.14462","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"has_accepted_license":"1","file":[{"date_created":"2022-08-05T06:19:28Z","content_type":"application/pdf","date_updated":"2022-08-05T06:19:28Z","file_name":"2022_Evolution_Freitas.pdf","checksum":"c27c025ae9afcf6c804d46a909775ee5","creator":"dernst","relation":"main_file","file_id":"11729","file_size":2855214,"access_level":"open_access","success":1}],"article_type":"original","date_created":"2022-04-24T22:01:44Z","publisher":"Wiley","scopus_import":"1","quality_controlled":"1","date_published":"2022-05-01T00:00:00Z","type":"journal_article","issue":"5","status":"public","abstract":[{"lang":"eng","text":"Hybridization is a common evolutionary process with multiple possible outcomes. In vertebrates, interspecific hybridization has repeatedly generated parthenogenetic hybrid species. However, it is unknown whether the generation of parthenogenetic hybrids is a rare outcome of frequent hybridization between sexual species within a genus or the typical outcome of rare hybridization events. Darevskia is a genus of rock lizards with both hybrid parthenogenetic and sexual species. Using capture sequencing, we estimate phylogenetic relationships and gene flow among the sexual species, to determine how introgressive hybridization relates to the origins of parthenogenetic hybrids. We find evidence for widespread hybridization with gene flow, both between recently diverged species and deep branches. Surprisingly, we find no signal of gene flow between parental species of the parthenogenetic hybrids, suggesting that the parental pairs were either reproductively or geographically isolated early in their divergence. The generation of parthenogenetic hybrids in Darevskia is, then, a rare outcome of the total occurrence of hybridization within the genus, but the typical outcome when specific species pairs hybridize. Our results question the conventional view that parthenogenetic lineages are generated by hybridization in a window of divergence. Instead, they suggest that some lineages possess specific properties that underpin successful parthenogenetic reproduction."}],"isi":1,"day":"01"},{"publication_status":"published","article_number":"iyac083","citation":{"short":"P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, Genetics 221 (2022).","ieee":"P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H. Barton, “Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus,” Genetics, vol. 221, no. 3. Oxford University Press, 2022.","ista":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2022. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Genetics. 221(3), iyac083.","apa":"Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., & Barton, N. H. (2022). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Genetics. Oxford University Press. https://doi.org/10.1093/genetics/iyac083","chicago":"Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field, Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Genetics. Oxford University Press, 2022. https://doi.org/10.1093/genetics/iyac083.","ama":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Genetics. 2022;221(3). doi:10.1093/genetics/iyac083","mla":"Surendranadh, Parvathy, et al. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Genetics, vol. 221, no. 3, iyac083, Oxford University Press, 2022, doi:10.1093/genetics/iyac083."},"publication":"Genetics","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1943-2631"]},"file_date_updated":"2022-05-26T12:48:21Z","author":[{"first_name":"Parvathy","orcid":"0000-0001-6395-386X","id":"455235B8-F248-11E8-B48F-1D18A9856A87","full_name":"Surendranadh, Parvathy","last_name":"Surendranadh"},{"first_name":"Louise S","orcid":"0000-0003-1771-714X","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","full_name":"Arathoon, Louise S","last_name":"Arathoon"},{"full_name":"Baskett, Carina","last_name":"Baskett","orcid":"0000-0002-7354-8574","first_name":"Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Field, David","last_name":"Field","orcid":"0000-0002-4014-8478","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","first_name":"Melinda","last_name":"Pickup","full_name":"Pickup, Melinda"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H"}],"project":[{"name":"Snapdragon Speciation","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","grant_number":"P32166"}],"oa_version":"Submitted Version","corr_author":"1","article_processing_charge":"No","year":"2022","_id":"11411","related_material":{"record":[{"relation":"research_data","id":"9192","status":"public"},{"status":"public","id":"11321","relation":"research_data"},{"id":"14651","status":"public","relation":"dissertation_contains"}]},"date_updated":"2026-04-07T13:28:29Z","pmid":1,"acknowledgement":"Part of this work was funded by Marie Curie COFUND Doctoral Fellowship and Austrian Science Fund FWF (grant P32166).\r\nWe thank the many volunteers and friends who have contributed to data collection in the field site over the years, in particular those who have managed field seasons: Barbora Trubenova, Maria Clara Melo, Tom Ellis, Eva Cereghetti, Lenka Matejovicova, Beatriz Pablo Carmona. Frederic Ferrer and Eva Salmerón Mateu have been immensely helpful with logistics at our informal field station, El Serrat de Planoles. We thank Sean Stankowski for technical help in\r\nproducing figure 1. This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).","external_id":{"isi":["000803735800001"],"pmid":["35639938"]},"oa":1,"volume":221,"month":"07","ddc":["576"],"acknowledged_ssus":[{"_id":"ScienComp"}],"title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","intvolume":" 221","day":"01","isi":1,"abstract":[{"lang":"eng","text":"Many studies have quantified the distribution of heterozygosity and relatedness in natural populations, but few have examined the demographic processes driving these patterns. In this study, we take a novel approach by studying how population structure affects both pairwise identity and the distribution of heterozygosity in a natural population of the self-incompatible plant Antirrhinum majus. Excess variance in heterozygosity between individuals is due to identity disequilibrium, which reflects the variance in inbreeding between individuals; it is measured by the statistic g2. We calculated g2 together with FST and pairwise relatedness (Fij) using 91 SNPs in 22,353 individuals collected over 11 years. We find that pairwise Fij declines rapidly over short spatial scales, and the excess variance in heterozygosity between individuals reflects significant variation in inbreeding. Additionally, we detect an excess of individuals with around half the average heterozygosity, indicating either selfing or matings between close relatives. We use 2 types of simulation to ask whether variation in heterozygosity is consistent with fine-scale spatial population structure. First, by simulating offspring using parents drawn from a range of spatial scales, we show that the known pollen dispersal kernel explains g2. Second, we simulate a 1,000-generation pedigree using the known dispersal and spatial distribution and find that the resulting g2 is consistent with that observed from the field data. In contrast, a simulated population with uniform density underestimates g2, indicating that heterogeneous density promotes identity disequilibrium. Our study shows that heterogeneous density and leptokurtic dispersal can together explain the distribution of heterozygosity."}],"status":"public","type":"journal_article","issue":"3","date_published":"2022-07-01T00:00:00Z","quality_controlled":"1","date_created":"2022-05-26T13:44:50Z","publisher":"Oxford University Press","scopus_import":"1","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"article_type":"original","file":[{"success":1,"access_level":"open_access","file_size":885374,"file_id":"11412","relation":"main_file","creator":"larathoo","checksum":"cc2d56deb608bd53c5cc02f03a875107","file_name":"Manuscript.pdf","date_updated":"2022-05-26T12:48:15Z","content_type":"application/pdf","date_created":"2022-05-26T12:48:15Z"},{"creator":"larathoo","relation":"main_file","file_name":"SupplementalMaterial.pdf","checksum":"693742595b6c7ed809423be01460d083","success":1,"access_level":"open_access","file_size":1401704,"file_id":"11413","date_created":"2022-05-26T12:48:21Z","date_updated":"2022-05-26T12:48:21Z","content_type":"application/pdf"}],"doi":"10.1093/genetics/iyac083","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"}]