[{"abstract":[{"text":"Understanding population divergence that eventually leads to speciation is essential for evolutionary biology. High species diversity in the sea was regarded as a paradox when strict allopatry was considered necessary for most speciation events because geographical barriers seemed largely absent in the sea, and many marine species have high dispersal capacities. Combining genome-wide data with demographic modelling to infer the demographic history of divergence has introduced new ways to address this classical issue. These models assume an ancestral population that splits into two subpopulations diverging according to different scenarios that allow tests for periods of gene flow. Models can also test for heterogeneities in population sizes and migration rates along the genome to account, respectively, for background selection and selection against introgressed ancestry. To investigate how barriers to gene flow arise in the sea, we compiled studies modelling the demographic history of divergence in marine organisms and extracted preferred demographic scenarios together with estimates of demographic parameters. These studies show that geographical barriers to gene flow do exist in the sea but that divergence can also occur without strict isolation. Heterogeneity of gene flow was detected in most population pairs suggesting the predominance of semipermeable barriers during divergence. We found a weak positive relationship between the fraction of the genome experiencing reduced gene flow and levels of genome-wide differentiation. Furthermore, we found that the upper bound of the ‘grey zone of speciation’ for our dataset extended beyond that found before, implying that gene flow between diverging taxa is possible at higher levels of divergence than previously thought. Finally, we list recommendations for further strengthening the use of demographic modelling in speciation research. These include a more balanced representation of taxa, more consistent and comprehensive modelling, clear reporting of results and simulation studies to rule out nonbiological explanations for general results.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"02","intvolume":" 16","publication_identifier":{"eissn":["1752-4571"]},"publication_status":"published","file":[{"file_name":"2023_EvolutionaryApplications_DeJode.pdf","date_created":"2023-02-27T07:10:17Z","creator":"dernst","file_size":2269822,"date_updated":"2023-02-27T07:10:17Z","success":1,"file_id":"12685","checksum":"d4d6fa9ddf36643af994a6a757919afb","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"volume":16,"issue":"2","_id":"11479","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-08-01T12:25:44Z","ddc":["576"],"department":[{"_id":"NiBa"},{"_id":"BeVi"}],"file_date_updated":"2023-02-27T07:10:17Z","acknowledgement":"We greatly thank all the corresponding authors of the studies that were included in our synthesis for the sharing of additional data: Thomas Broquet, Dmitry Filatov, Quentin Rougemont, Paolo Momigliano, Pierre-Alexandre Gagnaire, Carlos Prada, Ahmed Souissi, Michael Møller Hansen, Sylvie Lapègue, Joseph Di Battista, Michael Hellberg and Carlos Prada. RKB and ADJ were supported by the European Research Council. MR was supported by the Swedish Research Council Vetenskapsrådet (grant number 2021-05243; to MR) and Formas (grant number 2019-00882; to KJ and MR), and by additional grants from the European Research Council (to RKB) and Vetenskapsrådet (to KJ) through the Centre for Marine Evolutionary Biology (https://www.gu.se/en/cemeb-marine-evolutionary-biology).","publisher":"Wiley","quality_controlled":"1","oa":1,"has_accepted_license":"1","isi":1,"year":"2023","day":"01","publication":"Evolutionary Applications","page":"542-559","date_published":"2023-02-01T00:00:00Z","doi":"10.1111/eva.13428","date_created":"2022-07-03T22:01:33Z","citation":{"ista":"De Jode A, Le Moan A, Johannesson K, Faria R, Stankowski S, Westram AM, Butlin RK, Rafajlović M, Fraisse C. 2023. Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. 16(2), 542–559.","chicago":"De Jode, Aurélien, Alan Le Moan, Kerstin Johannesson, Rui Faria, Sean Stankowski, Anja M Westram, Roger K. Butlin, Marina Rafajlović, and Christelle Fraisse. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” Evolutionary Applications. Wiley, 2023. https://doi.org/10.1111/eva.13428.","apa":"De Jode, A., Le Moan, A., Johannesson, K., Faria, R., Stankowski, S., Westram, A. M., … Fraisse, C. (2023). Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. Wiley. https://doi.org/10.1111/eva.13428","ama":"De Jode A, Le Moan A, Johannesson K, et al. Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. 2023;16(2):542-559. doi:10.1111/eva.13428","short":"A. De Jode, A. Le Moan, K. Johannesson, R. Faria, S. Stankowski, A.M. Westram, R.K. Butlin, M. Rafajlović, C. Fraisse, Evolutionary Applications 16 (2023) 542–559.","ieee":"A. De Jode et al., “Ten years of demographic modelling of divergence and speciation in the sea,” Evolutionary Applications, vol. 16, no. 2. Wiley, pp. 542–559, 2023.","mla":"De Jode, Aurélien, et al. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” Evolutionary Applications, vol. 16, no. 2, Wiley, 2023, pp. 542–59, doi:10.1111/eva.13428."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"De Jode, Aurélien","last_name":"De Jode","first_name":"Aurélien"},{"full_name":"Le Moan, Alan","last_name":"Le Moan","first_name":"Alan"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"full_name":"Stankowski, Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."},{"first_name":"Marina","last_name":"Rafajlović","full_name":"Rafajlović, Marina"},{"last_name":"Fraisse","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000815663700001"]},"title":"Ten years of demographic modelling of divergence and speciation in the sea"},{"author":[{"first_name":"Daniel I.","full_name":"Bolnick, Daniel I.","last_name":"Bolnick"},{"last_name":"Hund","full_name":"Hund, Amanda K.","first_name":"Amanda K."},{"last_name":"Nosil","full_name":"Nosil, Patrik","first_name":"Patrik"},{"last_name":"Peng","full_name":"Peng, Foen","first_name":"Foen"},{"first_name":"Mark","last_name":"Ravinet","full_name":"Ravinet, Mark"},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","full_name":"Stankowski, Sean","last_name":"Stankowski"},{"full_name":"Subramanian, Swapna","last_name":"Subramanian","first_name":"Swapna"},{"first_name":"Jochen B.W.","full_name":"Wolf, Jochen B.W.","last_name":"Wolf"},{"first_name":"Roman","last_name":"Yukilevich","full_name":"Yukilevich, Roman"}],"article_processing_charge":"No","external_id":{"isi":["001021686300024"],"pmid":["36622661"]},"title":"A multivariate view of the speciation continuum","citation":{"ama":"Bolnick DI, Hund AK, Nosil P, et al. A multivariate view of the speciation continuum. Evolution: International journal of organic evolution. 2023;77(1):318-328. doi:10.1093/evolut/qpac004","apa":"Bolnick, D. I., Hund, A. K., Nosil, P., Peng, F., Ravinet, M., Stankowski, S., … Yukilevich, R. (2023). A multivariate view of the speciation continuum. Evolution: International Journal of Organic Evolution. Oxford University Press. https://doi.org/10.1093/evolut/qpac004","ieee":"D. I. Bolnick et al., “A multivariate view of the speciation continuum,” Evolution: International journal of organic evolution, vol. 77, no. 1. Oxford University Press, pp. 318–328, 2023.","short":"D.I. Bolnick, A.K. Hund, P. Nosil, F. Peng, M. Ravinet, S. Stankowski, S. Subramanian, J.B.W. Wolf, R. Yukilevich, Evolution: International Journal of Organic Evolution 77 (2023) 318–328.","mla":"Bolnick, Daniel I., et al. “A Multivariate View of the Speciation Continuum.” Evolution: International Journal of Organic Evolution, vol. 77, no. 1, Oxford University Press, 2023, pp. 318–28, doi:10.1093/evolut/qpac004.","ista":"Bolnick DI, Hund AK, Nosil P, Peng F, Ravinet M, Stankowski S, Subramanian S, Wolf JBW, Yukilevich R. 2023. A multivariate view of the speciation continuum. Evolution: International journal of organic evolution. 77(1), 318–328.","chicago":"Bolnick, Daniel I., Amanda K. Hund, Patrik Nosil, Foen Peng, Mark Ravinet, Sean Stankowski, Swapna Subramanian, Jochen B.W. Wolf, and Roman Yukilevich. “A Multivariate View of the Speciation Continuum.” Evolution: International Journal of Organic Evolution. Oxford University Press, 2023. https://doi.org/10.1093/evolut/qpac004."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Oxford University Press","quality_controlled":"1","oa":1,"acknowledgement":"The authors of this article were supported by LMU Munich (J.B.W.W.), a James S. McDonnell Foundation postdoctoral fellowship (A.K.H.). P.N. received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant agreement No. 770826 EE-Dynamics).\r\nWe thank participants in the 2019 Gordon Conference on Speciation for the extensive conversation on this topic. Thanks to Dan Funk for providing permission to use data from Funk et al. 2006, and for comments on the manuscript.","page":"318-328","date_published":"2023-01-01T00:00:00Z","doi":"10.1093/evolut/qpac004","date_created":"2023-02-05T23:00:59Z","isi":1,"year":"2023","day":"01","publication":"Evolution: International journal of organic evolution","article_type":"original","type":"journal_article","status":"public","_id":"12514","department":[{"_id":"NiBa"}],"date_updated":"2023-08-01T12:58:30Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/evolut/qpac004"}],"month":"01","intvolume":" 77","abstract":[{"text":"The concept of a “speciation continuum” has gained popularity in recent decades. It emphasizes speciation as a continuous process that may be studied by comparing contemporary population pairs that show differing levels of divergence. In their recent perspective article in Evolution, Stankowski and Ravinet provided a valuable service by formally defining the speciation continuum as a continuum of reproductive isolation, based on opinions gathered from a survey of speciation researchers. While we agree that the speciation continuum has been a useful concept to advance the understanding of the speciation process, some intrinsic limitations exist. Here, we advocate for a multivariate extension, the speciation hypercube, first proposed by Dieckmann et al. in 2004, but rarely used since. We extend the idea of the speciation cube and suggest it has strong conceptual and practical advantages over a one-dimensional model. We illustrate how the speciation hypercube can be used to visualize and compare different speciation trajectories, providing new insights into the processes and mechanisms of speciation. A key strength of the speciation hypercube is that it provides a unifying framework for speciation research, as it allows questions from apparently disparate subfields to be addressed in a single conceptual model.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","volume":77,"issue":"1","publication_identifier":{"eissn":["1558-5646"]},"publication_status":"published","language":[{"iso":"eng"}]},{"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"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 32","month":"03","publication_status":"published","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"b10e0f8fa3dc4d72aaf77a557200978a","file_id":"14062","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2023_MolecularEcology_Shipilina.pdf","date_created":"2023-08-16T08:15:41Z","creator":"dernst","file_size":7144607,"date_updated":"2023-08-16T08:15:41Z"}],"volume":32,"issue":"6","_id":"12159","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"status":"public","date_updated":"2023-08-16T08:18:47Z","ddc":["570"],"department":[{"_id":"NiBa"}],"file_date_updated":"2023-08-16T08:15:41Z","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).","oa":1,"quality_controlled":"1","publisher":"Wiley","year":"2023","isi":1,"has_accepted_license":"1","publication":"Molecular Ecology","day":"01","page":"1441-1457","date_created":"2023-01-12T12:09:17Z","date_published":"2023-03-01T00:00:00Z","doi":"10.1111/mec.16793","project":[{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"The maintenance of alternative adaptive peaks in snapdragons","grant_number":"P32166"},{"name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327","name":"Understanding the evolution of continuous genomes"}],"citation":{"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.","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","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","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["36433653"],"isi":["000900762000001"]},"article_processing_charge":"Yes (via OA deal)","author":[{"full_name":"Shipilina, Daria","orcid":"0000-0002-1145-9226","last_name":"Shipilina","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","first_name":"Daria"},{"last_name":"Pal","full_name":"Pal, Arka","orcid":"0000-0002-4530-8469","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","first_name":"Arka"},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","last_name":"Stankowski","full_name":"Stankowski, Sean"},{"first_name":"Yingguang Frank","full_name":"Chan, Yingguang Frank","last_name":"Chan"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"title":"On the origin and structure of haplotype blocks"},{"title":"The infinitesimal model with dominance","article_processing_charge":"Yes (in subscription journal)","external_id":{"arxiv":["2211.03515"]},"author":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"first_name":"Alison M.","last_name":"Etheridge","full_name":"Etheridge, Alison M."},{"first_name":"Amandine","full_name":"Véber, Amandine","last_name":"Véber"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Barton, Nicholas H., et al. “The Infinitesimal Model with Dominance.” Genetics, vol. 225, no. 2, iyad133, Oxford Academic, 2023, doi:10.1093/genetics/iyad133.","short":"N.H. Barton, A.M. Etheridge, A. Véber, Genetics 225 (2023).","ieee":"N. H. Barton, A. M. Etheridge, and A. Véber, “The infinitesimal model with dominance,” Genetics, vol. 225, no. 2. Oxford Academic, 2023.","ama":"Barton NH, Etheridge AM, Véber A. The infinitesimal model with dominance. Genetics. 2023;225(2). doi:10.1093/genetics/iyad133","apa":"Barton, N. H., Etheridge, A. M., & Véber, A. (2023). The infinitesimal model with dominance. Genetics. Oxford Academic. https://doi.org/10.1093/genetics/iyad133","chicago":"Barton, Nicholas H, Alison M. Etheridge, and Amandine Véber. “The Infinitesimal Model with Dominance.” Genetics. Oxford Academic, 2023. https://doi.org/10.1093/genetics/iyad133.","ista":"Barton NH, Etheridge AM, Véber A. 2023. The infinitesimal model with dominance. Genetics. 225(2), iyad133."},"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"},{"grant_number":"101055327","name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00"}],"article_number":"iyad133","date_created":"2023-10-29T23:01:15Z","doi":"10.1093/genetics/iyad133","date_published":"2023-10-01T00:00:00Z","publication":"Genetics","day":"01","year":"2023","has_accepted_license":"1","oa":1,"publisher":"Oxford Academic","quality_controlled":"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.","department":[{"_id":"NiBa"}],"file_date_updated":"2023-10-30T12:57:53Z","ddc":["570"],"date_updated":"2023-10-30T13:04:11Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"14452","ec_funded":1,"related_material":{"record":[{"status":"public","id":"12949","relation":"research_data"}]},"issue":"2","volume":225,"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":1439032,"date_updated":"2023-10-30T12:57:53Z","file_name":"2023_Genetics_Barton.pdf","date_created":"2023-10-30T12:57:53Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"14469","checksum":"3f65b1fbe813e2f4dbb5d2b5e891844a"}],"publication_status":"published","publication_identifier":{"issn":["0016-6731"],"eissn":["1943-2631"]},"intvolume":" 225","month":"10","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","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."}]},{"_id":"12949","type":"research_data","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"project":[{"name":"Understanding the evolution of continuous genomes","grant_number":"101055327","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00"}],"status":"public","keyword":["Quantitative genetics","infinitesimal model"],"citation":{"ista":"Barton NH. 2023. The infinitesimal model with dominance, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12949.","chicago":"Barton, Nicholas H. “The Infinitesimal Model with Dominance.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12949.","short":"N.H. Barton, (2023).","ieee":"N. H. Barton, “The infinitesimal model with dominance.” Institute of Science and Technology Austria, 2023.","ama":"Barton NH. The infinitesimal model with dominance. 2023. doi:10.15479/AT:ISTA:12949","apa":"Barton, N. H. (2023). The infinitesimal model with dominance. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12949","mla":"Barton, Nicholas H. The Infinitesimal Model with Dominance. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12949."},"date_updated":"2023-10-30T13:04:11Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["576"],"author":[{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"The infinitesimal model with dominance","file_date_updated":"2023-05-16T04:09:08Z","department":[{"_id":"NiBa"}],"abstract":[{"lang":"eng","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 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."}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"05","has_accepted_license":"1","year":"2023","day":"13","file":[{"file_size":13662,"date_updated":"2023-05-13T09:36:33Z","creator":"nbarton","file_name":"Neutral identities 16th Jan","date_created":"2023-05-13T09:36:33Z","content_type":"application/octet-stream","relation":"main_file","access_level":"open_access","success":1,"checksum":"b0ce7d4b1ee7e7265430ceed36fc3336","file_id":"12950"},{"file_name":"p, zA, zD, N=30 neutral III","date_created":"2023-05-13T09:38:17Z","file_size":181619928,"date_updated":"2023-05-13T09:38:17Z","creator":"nbarton","success":1,"file_id":"12951","checksum":"ad5035ad4f7d3b150a252c79884f6a83","content_type":"application/octet-stream","relation":"main_file","access_level":"open_access"},{"success":1,"checksum":"62182a1de796256edd6f4223704312ef","file_id":"12952","relation":"main_file","access_level":"open_access","content_type":"application/octet-stream","file_name":"p, zA, zD, N=30 neutral IV","date_created":"2023-05-13T09:41:59Z","creator":"nbarton","file_size":605902074,"date_updated":"2023-05-13T09:41:59Z"},{"date_updated":"2023-05-13T09:46:52Z","file_size":1018238746,"creator":"nbarton","date_created":"2023-05-13T09:46:52Z","file_name":"p, zA, zD, N=30 selected k=5","content_type":"application/octet-stream","access_level":"open_access","relation":"main_file","file_id":"12953","checksum":"af775dda5c4f6859cb1e5a81ec40a667","success":1},{"file_name":"Pairwise F N=30 neutral II","date_created":"2023-05-13T09:42:05Z","file_size":3197160,"date_updated":"2023-05-13T09:42:05Z","creator":"nbarton","success":1,"checksum":"af26f3394c387d3ada14b434cd68b1e5","file_id":"12954","content_type":"application/octet-stream","relation":"main_file","access_level":"open_access"},{"file_name":"Pedigrees N=30 neutral II","date_created":"2023-05-13T09:42:06Z","creator":"nbarton","file_size":55492,"date_updated":"2023-05-13T09:42:06Z","success":1,"file_id":"12955","checksum":"d5da7dc0e7282dd48222e26d12e34220","relation":"main_file","access_level":"open_access","content_type":"application/octet-stream"},{"file_name":"selected reps N=30 selected k=1,2 300 reps III","date_created":"2023-05-13T09:46:06Z","file_size":474003467,"date_updated":"2023-05-13T09:46:06Z","creator":"nbarton","success":1,"file_id":"12956","checksum":"00f386d80677590e29f6235d49cba58d","content_type":"application/octet-stream","relation":"main_file","access_level":"open_access"},{"success":1,"file_id":"12957","checksum":"658cef3eaea6136a4d24da4f074191d7","relation":"main_file","access_level":"open_access","content_type":"application/octet-stream","file_name":"Algorithm for caclulating identities.nb","date_created":"2023-05-13T09:46:08Z","creator":"nbarton","file_size":121209,"date_updated":"2023-05-13T09:46:08Z"},{"creator":"nbarton","date_updated":"2023-05-13T09:46:08Z","file_size":1803898,"date_created":"2023-05-13T09:46:08Z","file_name":"Infinitesimal with dominance.nb","access_level":"open_access","relation":"main_file","content_type":"application/octet-stream","checksum":"db9b6dddd7a596d974e25f5e78f5c45c","file_id":"12958","success":1},{"checksum":"91f80a9fb58cae8eef2d8bf59fe30189","file_id":"12967","success":1,"access_level":"open_access","relation":"main_file","content_type":"text/plain","date_created":"2023-05-16T04:09:08Z","file_name":"ReadMe.txt","creator":"nbarton","date_updated":"2023-05-16T04:09:08Z","file_size":990}],"related_material":{"record":[{"status":"public","id":"14452","relation":"used_in_publication"}]},"doi":"10.15479/AT:ISTA:12949","date_published":"2023-05-13T00:00:00Z","date_created":"2023-05-13T09:49:09Z","contributor":[{"first_name":"Amandine","contributor_type":"researcher","last_name":"Veber"},{"contributor_type":"researcher","first_name":"Alison","last_name":"Etheridge"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Berdan EL, Barton NH, Butlin R, Charlesworth B, Faria R, Fragata I, Gilbert KJ, Jay P, Kapun M, Lotterhos KE, Mérot C, Durmaz Mitchell E, Pascual M, Peichel CL, Rafajlović M, Westram AM, Schaeffer SW, Johannesson K, Flatt T. 2023. How chromosomal inversions reorient the evolutionary process. Journal of Evolutionary Biology., 14242.","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.","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","ama":"Berdan EL, Barton NH, Butlin R, et al. How chromosomal inversions reorient the evolutionary process. Journal of Evolutionary Biology. 2023. doi:10.1111/jeb.14242","short":"E.L. Berdan, N.H. Barton, R. Butlin, B. Charlesworth, R. Faria, I. Fragata, K.J. Gilbert, P. Jay, M. Kapun, K.E. Lotterhos, C. Mérot, E. Durmaz Mitchell, M. Pascual, C.L. Peichel, M. Rafajlović, A.M. Westram, S.W. Schaeffer, K. Johannesson, T. Flatt, Journal of Evolutionary Biology (2023).","ieee":"E. L. Berdan et al., “How chromosomal inversions reorient the evolutionary process,” Journal of Evolutionary Biology. Wiley, 2023.","mla":"Berdan, Emma L., et al. “How Chromosomal Inversions Reorient the Evolutionary Process.” Journal of Evolutionary Biology, 14242, Wiley, 2023, doi:10.1111/jeb.14242."},"title":"How chromosomal inversions reorient the evolutionary process","author":[{"full_name":"Berdan, Emma L.","last_name":"Berdan","first_name":"Emma L."},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"},{"first_name":"Roger","last_name":"Butlin","full_name":"Butlin, Roger"},{"first_name":"Brian","last_name":"Charlesworth","full_name":"Charlesworth, Brian"},{"last_name":"Faria","full_name":"Faria, Rui","first_name":"Rui"},{"first_name":"Inês","last_name":"Fragata","full_name":"Fragata, Inês"},{"full_name":"Gilbert, Kimberly J.","last_name":"Gilbert","first_name":"Kimberly J."},{"first_name":"Paul","full_name":"Jay, Paul","last_name":"Jay"},{"first_name":"Martin","last_name":"Kapun","full_name":"Kapun, Martin"},{"last_name":"Lotterhos","full_name":"Lotterhos, Katie E.","first_name":"Katie E."},{"full_name":"Mérot, Claire","last_name":"Mérot","first_name":"Claire"},{"full_name":"Durmaz Mitchell, Esra","last_name":"Durmaz Mitchell","first_name":"Esra"},{"full_name":"Pascual, Marta","last_name":"Pascual","first_name":"Marta"},{"full_name":"Peichel, Catherine L.","last_name":"Peichel","first_name":"Catherine L."},{"first_name":"Marina","last_name":"Rafajlović","full_name":"Rafajlović, Marina"},{"last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"},{"last_name":"Schaeffer","full_name":"Schaeffer, Stephen W.","first_name":"Stephen W."},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"full_name":"Flatt, Thomas","last_name":"Flatt","first_name":"Thomas"}],"article_processing_charge":"No","article_number":"14242","day":"08","publication":"Journal of Evolutionary Biology","has_accepted_license":"1","year":"2023","date_published":"2023-11-08T00:00:00Z","doi":"10.1111/jeb.14242","date_created":"2023-11-19T23:00:55Z","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.","publisher":"Wiley","quality_controlled":"1","oa":1,"ddc":["570"],"date_updated":"2023-11-20T08:51:09Z","department":[{"_id":"NiBa"}],"_id":"14556","status":"public","article_type":"review","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1010-061X"],"eissn":["1420-9101"]},"publication_status":"epub_ahead","oa_version":"Published Version","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."}],"month":"11","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jeb.14242"}]},{"date_created":"2023-11-19T23:00:54Z","doi":"10.1126/science.adh8830","date_published":"2023-11-09T00:00:00Z","page":"679-683","publication":"Science","day":"09","year":"2023","publisher":"AAAS","quality_controlled":"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.","title":"Plant size, latitude, and phylogeny explain within-population variability in herbivory","external_id":{"pmid":["37943897"]},"article_processing_charge":"No","author":[{"full_name":"Robinson, M. 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A."},{"last_name":"Pareja","full_name":"Pareja, M.","first_name":"M."},{"first_name":"N.","last_name":"Parthasarathy","full_name":"Parthasarathy, N."},{"first_name":"R. R.","last_name":"Pawar","full_name":"Pawar, R. R."},{"last_name":"Paynter","full_name":"Paynter, Q.","first_name":"Q."},{"first_name":"I. S.","full_name":"Pearse, I. S.","last_name":"Pearse"},{"first_name":"R. M.","full_name":"Penczykowski, R. M.","last_name":"Penczykowski"},{"first_name":"A. A.","last_name":"Pepi","full_name":"Pepi, A. A."},{"first_name":"C. C.","full_name":"Pereira, C. C.","last_name":"Pereira"},{"first_name":"S. S.","full_name":"Phartyal, S. S.","last_name":"Phartyal"},{"last_name":"Piper","full_name":"Piper, F. I.","first_name":"F. I."},{"first_name":"K.","last_name":"Poveda","full_name":"Poveda, K."},{"first_name":"E. G.","full_name":"Pringle, E. G.","last_name":"Pringle"},{"first_name":"J.","full_name":"Puy, J.","last_name":"Puy"},{"first_name":"T.","full_name":"Quijano, T.","last_name":"Quijano"},{"first_name":"C.","full_name":"Quintero, C.","last_name":"Quintero"},{"last_name":"Rasmann","full_name":"Rasmann, S.","first_name":"S."},{"full_name":"Rosche, C.","last_name":"Rosche","first_name":"C."},{"last_name":"Rosenheim","full_name":"Rosenheim, L. Y.","first_name":"L. Y."},{"first_name":"J. A.","full_name":"Rosenheim, J. A.","last_name":"Rosenheim"},{"first_name":"J. B.","full_name":"Runyon, J. B.","last_name":"Runyon"},{"last_name":"Sadeh","full_name":"Sadeh, A.","first_name":"A."},{"first_name":"Y.","full_name":"Sakata, Y.","last_name":"Sakata"},{"first_name":"D. M.","last_name":"Salcido","full_name":"Salcido, D. M."},{"first_name":"C.","full_name":"Salgado-Luarte, C.","last_name":"Salgado-Luarte"},{"first_name":"B. A.","last_name":"Santos","full_name":"Santos, B. A."},{"first_name":"Y.","full_name":"Sapir, Y.","last_name":"Sapir"},{"first_name":"Y.","last_name":"Sasal","full_name":"Sasal, Y."},{"full_name":"Sato, Y.","last_name":"Sato","first_name":"Y."},{"first_name":"M.","last_name":"Sawant","full_name":"Sawant, M."},{"full_name":"Schroeder, H.","last_name":"Schroeder","first_name":"H."},{"first_name":"I.","full_name":"Schumann, I.","last_name":"Schumann"},{"last_name":"Segoli","full_name":"Segoli, M.","first_name":"M."},{"first_name":"H.","last_name":"Segre","full_name":"Segre, H."},{"first_name":"O.","full_name":"Shelef, O.","last_name":"Shelef"},{"first_name":"N.","full_name":"Shinohara, N.","last_name":"Shinohara"},{"first_name":"R. P.","full_name":"Singh, R. P.","last_name":"Singh"},{"first_name":"D. S.","full_name":"Smith, D. S.","last_name":"Smith"},{"last_name":"Sobral","full_name":"Sobral, M.","first_name":"M."},{"last_name":"Stotz","full_name":"Stotz, G. C.","first_name":"G. C."},{"last_name":"Tack","full_name":"Tack, A. J.M.","first_name":"A. J.M."},{"last_name":"Tayal","full_name":"Tayal, M.","first_name":"M."},{"first_name":"J. F.","last_name":"Tooker","full_name":"Tooker, J. F."},{"full_name":"Torrico-Bazoberry, D.","last_name":"Torrico-Bazoberry","first_name":"D."},{"last_name":"Tougeron","full_name":"Tougeron, K.","first_name":"K."},{"full_name":"Trowbridge, A. M.","last_name":"Trowbridge","first_name":"A. M."},{"full_name":"Utsumi, S.","last_name":"Utsumi","first_name":"S."},{"first_name":"O.","full_name":"Uyi, O.","last_name":"Uyi"},{"first_name":"J. L.","last_name":"Vaca-Uribe","full_name":"Vaca-Uribe, J. L."},{"first_name":"A.","full_name":"Valtonen, A.","last_name":"Valtonen"},{"first_name":"L. J.A.","full_name":"Van Dijk, L. J.A.","last_name":"Van Dijk"},{"last_name":"Vandvik","full_name":"Vandvik, V.","first_name":"V."},{"last_name":"Villellas","full_name":"Villellas, J.","first_name":"J."},{"first_name":"L. P.","last_name":"Waller","full_name":"Waller, L. P."},{"first_name":"M. G.","last_name":"Weber","full_name":"Weber, M. G."},{"first_name":"A.","last_name":"Yamawo","full_name":"Yamawo, A."},{"first_name":"S.","full_name":"Yim, S.","last_name":"Yim"},{"first_name":"P. L.","full_name":"Zarnetske, P. L.","last_name":"Zarnetske"},{"full_name":"Zehr, L. N.","last_name":"Zehr","first_name":"L. N."},{"last_name":"Zhong","full_name":"Zhong, Z.","first_name":"Z."},{"first_name":"W. C.","last_name":"Wetzel","full_name":"Wetzel, W. C."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Robinson ML et al. 2023. Plant size, latitude, and phylogeny explain within-population variability in herbivory. Science. 382(6671), 679–683.","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.","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.","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.","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","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","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."},"volume":382,"related_material":{"record":[{"id":"14579","status":"public","relation":"research_data"}]},"issue":"6671","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1095-9203"]},"intvolume":" 382","month":"11","scopus_import":"1","oa_version":"None","pmid":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"}],"department":[{"_id":"NiBa"}],"date_updated":"2023-11-20T11:17:34Z","status":"public","type":"journal_article","article_type":"original","_id":"14552"},{"month":"07","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8133118","open_access":"1"}],"oa":1,"publisher":"Zenodo","oa_version":"Published Version","abstract":[{"lang":"eng","text":"This is associated with our paper \"Plant size, latitude, and phylogeny explain within-population variability in herbivory\" published in Science.\r\n"}],"date_created":"2023-11-20T11:07:45Z","doi":"10.5281/ZENODO.8133117","related_material":{"record":[{"id":"14552","status":"public","relation":"used_in_publication"}]},"date_published":"2023-07-11T00:00:00Z","day":"11","year":"2023","status":"public","type":"research_data_reference","_id":"14579","title":"HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0","department":[{"_id":"NiBa"}],"article_processing_charge":"No","author":[{"last_name":"Wetzel","full_name":"Wetzel, William","first_name":"William"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"citation":{"apa":"Wetzel, W. (2023). HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0. Zenodo. 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","ieee":"W. Wetzel, “HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0.” Zenodo, 2023.","short":"W. Wetzel, (2023).","mla":"Wetzel, William. HerbVar-Network/HV-Large-Patterns-MS-Public: V1.0.0. Zenodo, 2023, doi:10.5281/ZENODO.8133117.","ista":"Wetzel W. 2023. HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0, Zenodo, 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."},"date_updated":"2023-11-20T11:17:33Z"},{"has_accepted_license":"1","year":"2023","day":"15","page":"230","doi":"10.15479/at:ista:14058","date_published":"2023-08-15T00:00:00Z","date_created":"2023-08-15T10:20:40Z","publisher":"Institute of Science and Technology Austria","oa":1,"citation":{"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","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","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.","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.","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.","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."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"last_name":"Puixeu Sala","orcid":"0000-0001-8330-1754","full_name":"Puixeu Sala, Gemma","first_name":"Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation","project":[{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A","name":"Sexual conflict: resolution, constraints and biomedical implications","grant_number":"25817"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-035-0"]},"publication_status":"published","degree_awarded":"PhD","file":[{"creator":"gpuixeus","date_updated":"2023-08-17T06:55:24Z","file_size":10891454,"date_created":"2023-08-16T18:15:17Z","file_name":"Thesis_latex_forpdfa.zip","access_level":"closed","relation":"source_file","content_type":"application/zip","file_id":"14075","checksum":"4e44e169f2724ee8c9324cd60bcc2b71"},{"date_created":"2023-08-18T10:47:55Z","file_name":"PhDThesis_PuixeuG.pdf","date_updated":"2023-08-18T10:47:55Z","file_size":19856686,"creator":"gpuixeus","file_id":"14079","checksum":"e10b04cd8f3fecc0d9ef6e6868b6e1e8","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"9803","status":"public","relation":"research_data"},{"id":"12933","status":"public","relation":"research_data"},{"relation":"part_of_dissertation","id":"6831","status":"public"},{"id":"14077","status":"public","relation":"part_of_dissertation"}]},"ec_funded":1,"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."}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"08","supervisor":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"date_updated":"2023-12-13T12:15:36Z","ddc":["576"],"file_date_updated":"2023-08-18T10:47:55Z","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"BeVi"}],"_id":"14058","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public"},{"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Genetics (clinical)","Genetics","Molecular Biology"],"_id":"14077","file_date_updated":"2023-11-07T09:00:19Z","department":[{"_id":"BeVi"},{"_id":"NiBa"},{"_id":"GradSch"}],"date_updated":"2023-12-13T12:15:37Z","ddc":["570"],"scopus_import":"1","month":"08","intvolume":" 13","acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"text":"The regulatory architecture of gene expression is known to differ substantially between sexes in Drosophila, but most studies performed\r\nso far used whole-body data and only single crosses, which may have limited their scope to detect patterns that are robust across tissues\r\nand biological replicates. Here, we use allele-specific gene expression of parental and reciprocal hybrid crosses between 6 Drosophila\r\nmelanogaster inbred lines to quantify cis- and trans-regulatory variation in heads and gonads of both sexes separately across 3 replicate\r\ncrosses. Our results suggest that female and male heads, as well as ovaries, have a similar regulatory architecture. On the other hand,\r\ntestes display more and substantially different cis-regulatory effects, suggesting that sex differences in the regulatory architecture that\r\nhave been previously observed may largely derive from testis-specific effects. We also examine the difference in cis-regulatory variation\r\nof genes across different levels of sex bias in gonads and heads. Consistent with the idea that intersex correlations constrain expression\r\nand can lead to sexual antagonism, we find more cis variation in unbiased and moderately biased genes in heads. In ovaries, reduced cis\r\nvariation is observed for male-biased genes, suggesting that cis variants acting on these genes in males do not lead to changes in ovary\r\nexpression. Finally, we examine the dominance patterns of gene expression and find that sex- and tissue-specific patterns of inheritance\r\nas well as trans-regulatory variation are highly variable across biological crosses, although these were performed in highly controlled\r\nexperimental conditions. This highlights the importance of using various genetic backgrounds to infer generalizable patterns.","lang":"eng"}],"oa_version":"Published Version","issue":"8","volume":13,"related_material":{"record":[{"id":"12933","status":"public","relation":"research_data"},{"relation":"dissertation_contains","status":"public","id":"14058"}]},"ec_funded":1,"publication_identifier":{"issn":["2160-1836"]},"publication_status":"published","file":[{"file_name":"2023_G3_Puixeu.pdf","date_created":"2023-11-07T09:00:19Z","file_size":845642,"date_updated":"2023-11-07T09:00:19Z","creator":"dernst","success":1,"checksum":"c62e29fc7c5efbf8356f4c60cab4a2d1","file_id":"14498","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"},{"name":"Sexual conflict: resolution, constraints and biomedical implications","grant_number":"25817","_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A"}],"author":[{"id":"33AB266C-F248-11E8-B48F-1D18A9856A87","first_name":"Gemma","last_name":"Puixeu Sala","full_name":"Puixeu Sala, Gemma","orcid":"0000-0001-8330-1754"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","full_name":"Macon, Ariana","last_name":"Macon"},{"last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["001002997200001"]},"article_processing_charge":"Yes","title":"Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster","citation":{"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).","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.","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).","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","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Oxford University Press","quality_controlled":"1","oa":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).","doi":"10.1093/g3journal/jkad121","date_published":"2023-08-01T00:00:00Z","date_created":"2023-08-18T06:52:14Z","isi":1,"has_accepted_license":"1","year":"2023","day":"01","publication":"G3: Genes, Genomes, Genetics"}]