[{"intvolume":"       225","article_number":"iyad133","status":"public","month":"10","date_created":"2023-10-29T23:01:15Z","issue":"2","volume":225,"article_type":"original","publisher":"Oxford Academic","file_date_updated":"2023-10-30T12:57:53Z","_id":"14452","related_material":{"record":[{"id":"12949","relation":"research_data","status":"public"}]},"ddc":["570"],"oa":1,"title":"The infinitesimal model with dominance","publication":"Genetics","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."}],"publication_status":"published","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"},{"grant_number":"101055327","name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00"}],"author":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton"},{"first_name":"Alison M.","last_name":"Etheridge","full_name":"Etheridge, Alison M."},{"full_name":"Véber, Amandine","last_name":"Véber","first_name":"Amandine"}],"quality_controlled":"1","citation":{"apa":"Barton, N. H., Etheridge, A. M., &#38; Véber, A. (2023). The infinitesimal model with dominance. <i>Genetics</i>. Oxford Academic. <a href=\"https://doi.org/10.1093/genetics/iyad133\">https://doi.org/10.1093/genetics/iyad133</a>","mla":"Barton, Nicholas H., et al. “The Infinitesimal Model with Dominance.” <i>Genetics</i>, vol. 225, no. 2, iyad133, Oxford Academic, 2023, doi:<a href=\"https://doi.org/10.1093/genetics/iyad133\">10.1093/genetics/iyad133</a>.","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.” <i>Genetics</i>. Oxford Academic, 2023. <a href=\"https://doi.org/10.1093/genetics/iyad133\">https://doi.org/10.1093/genetics/iyad133</a>.","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,” <i>Genetics</i>, vol. 225, no. 2. Oxford Academic, 2023.","ama":"Barton NH, Etheridge AM, Véber A. The infinitesimal model with dominance. <i>Genetics</i>. 2023;225(2). doi:<a href=\"https://doi.org/10.1093/genetics/iyad133\">10.1093/genetics/iyad133</a>"},"year":"2023","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","publication_identifier":{"issn":["0016-6731"],"eissn":["1943-2631"]},"arxiv":1,"file":[{"file_size":1439032,"content_type":"application/pdf","creator":"dernst","relation":"main_file","date_created":"2023-10-30T12:57:53Z","checksum":"3f65b1fbe813e2f4dbb5d2b5e891844a","file_name":"2023_Genetics_Barton.pdf","access_level":"open_access","success":1,"file_id":"14469","date_updated":"2023-10-30T12:57:53Z"}],"external_id":{"arxiv":["2211.03515"]},"date_published":"2023-10-01T00:00:00Z","department":[{"_id":"NiBa"}],"has_accepted_license":"1","doi":"10.1093/genetics/iyad133","language":[{"iso":"eng"}],"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.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (in subscription journal)","day":"01","oa_version":"Published Version","date_updated":"2025-05-28T11:42:48Z","type":"journal_article"},{"isi":1,"intvolume":"       221","status":"public","article_number":"iyac083","month":"07","date_created":"2022-05-26T13:44:50Z","volume":221,"issue":"3","article_type":"original","publisher":"Oxford University Press","file_date_updated":"2022-05-26T12:48:21Z","_id":"11411","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14651"},{"id":"11321","relation":"research_data","status":"public"},{"relation":"research_data","status":"public","id":"9192"}]},"ddc":["576"],"oa":1,"pmid":1,"publication":"Genetics","title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","abstract":[{"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.","lang":"eng"}],"publication_status":"published","project":[{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","grant_number":"P32166","name":"The maintenance of alternative adaptive peaks in snapdragons"}],"quality_controlled":"1","author":[{"id":"455235B8-F248-11E8-B48F-1D18A9856A87","full_name":"Surendranadh, Parvathy","first_name":"Parvathy","last_name":"Surendranadh"},{"last_name":"Arathoon","first_name":"Louise S","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1771-714X","full_name":"Arathoon, Louise S"},{"id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","full_name":"Baskett, Carina","orcid":"0000-0002-7354-8574","last_name":"Baskett","first_name":"Carina"},{"orcid":"0000-0002-4014-8478","full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David"},{"full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda","last_name":"Pickup"},{"last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"citation":{"apa":"Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., &#38; Barton, N. H. (2022). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. <i>Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/genetics/iyac083\">https://doi.org/10.1093/genetics/iyac083</a>","mla":"Surendranadh, Parvathy, et al. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” <i>Genetics</i>, vol. 221, no. 3, iyac083, Oxford University Press, 2022, doi:<a href=\"https://doi.org/10.1093/genetics/iyac083\">10.1093/genetics/iyac083</a>.","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.","short":"P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, Genetics 221 (2022).","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.” <i>Genetics</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/genetics/iyac083\">https://doi.org/10.1093/genetics/iyac083</a>.","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,” <i>Genetics</i>, vol. 221, no. 3. Oxford University Press, 2022.","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. <i>Genetics</i>. 2022;221(3). doi:<a href=\"https://doi.org/10.1093/genetics/iyac083\">10.1093/genetics/iyac083</a>"},"year":"2022","scopus_import":"1","publication_identifier":{"eissn":["1943-2631"]},"external_id":{"isi":["000803735800001"],"pmid":["35639938"]},"file":[{"file_size":885374,"content_type":"application/pdf","creator":"larathoo","date_created":"2022-05-26T12:48:15Z","relation":"main_file","access_level":"open_access","checksum":"cc2d56deb608bd53c5cc02f03a875107","file_name":"Manuscript.pdf","file_id":"11412","date_updated":"2022-05-26T12:48:15Z","success":1},{"file_size":1401704,"content_type":"application/pdf","creator":"larathoo","relation":"main_file","date_created":"2022-05-26T12:48:21Z","file_name":"SupplementalMaterial.pdf","checksum":"693742595b6c7ed809423be01460d083","access_level":"open_access","success":1,"date_updated":"2022-05-26T12:48:21Z","file_id":"11413"}],"date_published":"2022-07-01T00:00:00Z","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"doi":"10.1093/genetics/iyac083","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"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).","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"01","oa_version":"Submitted Version","date_updated":"2024-02-21T12:38:33Z","type":"journal_article"},{"intvolume":"       212","isi":1,"date_created":"2020-01-29T16:15:44Z","month":"07","status":"public","issue":"3","volume":212,"article_type":"original","publisher":"Genetics Society of America","publication":"Genetics","title":"Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua","pmid":1,"oa":1,"_id":"7400","project":[{"grant_number":"715257","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"publication_status":"published","abstract":[{"lang":"eng","text":"Suppressed recombination allows divergence between homologous sex chromosomes and the functionality of their genes. Here, we reveal patterns of the earliest stages of sex-chromosome evolution in the diploid dioecious herb Mercurialis annua on the basis of cytological analysis, de novo genome assembly and annotation, genetic mapping, exome resequencing of natural populations, and transcriptome analysis. The genome assembly contained 34,105 expressed genes, of which 10,076 were assigned to linkage groups. Genetic mapping and exome resequencing of individuals across the species range both identified the largest linkage group, LG1, as the sex chromosome. Although the sex chromosomes of M. annua are karyotypically homomorphic, we estimate that about one-third of the Y chromosome, containing 568 transcripts and spanning 22.3 cM in the corresponding female map, has ceased recombining. Nevertheless, we found limited evidence for Y-chromosome degeneration in terms of gene loss and pseudogenization, and most X- and Y-linked genes appear to have diverged in the period subsequent to speciation between M. annua and its sister species M. huetii, which shares the same sex-determining region. Taken together, our results suggest that the M. annua Y chromosome has at least two evolutionary strata: a small old stratum shared with M. huetii, and a more recent larger stratum that is probably unique to M. annua and that stopped recombining ∼1 MYA. Patterns of gene expression within the nonrecombining region are consistent with the idea that sexually antagonistic selection may have played a role in favoring suppressed recombination."}],"citation":{"apa":"Veltsos, P., Ridout, K. E., Toups, M. A., González-Martínez, S. C., Muyle, A., Emery, O., … Pannell, J. R. (2019). Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.119.302045\">https://doi.org/10.1534/genetics.119.302045</a>","mla":"Veltsos, Paris, et al. “Early Sex-Chromosome Evolution in the Diploid Dioecious Plant Mercurialis Annua.” <i>Genetics</i>, vol. 212, no. 3, Genetics Society of America, 2019, pp. 815–35, doi:<a href=\"https://doi.org/10.1534/genetics.119.302045\">10.1534/genetics.119.302045</a>.","chicago":"Veltsos, Paris, Kate E. Ridout, Melissa A Toups, Santiago C. González-Martínez, Aline Muyle, Olivier Emery, Pasi Rastas, et al. “Early Sex-Chromosome Evolution in the Diploid Dioecious Plant Mercurialis Annua.” <i>Genetics</i>. Genetics Society of America, 2019. <a href=\"https://doi.org/10.1534/genetics.119.302045\">https://doi.org/10.1534/genetics.119.302045</a>.","short":"P. Veltsos, K.E. Ridout, M.A. Toups, S.C. González-Martínez, A. Muyle, O. Emery, P. Rastas, V. Hudzieczek, R. Hobza, B. Vyskot, G.A.B. Marais, D.A. Filatov, J.R. Pannell, Genetics 212 (2019) 815–835.","ista":"Veltsos P, Ridout KE, Toups MA, González-Martínez SC, Muyle A, Emery O, Rastas P, Hudzieczek V, Hobza R, Vyskot B, Marais GAB, Filatov DA, Pannell JR. 2019. Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua. Genetics. 212(3), 815–835.","ieee":"P. Veltsos <i>et al.</i>, “Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua,” <i>Genetics</i>, vol. 212, no. 3. Genetics Society of America, pp. 815–835, 2019.","ama":"Veltsos P, Ridout KE, Toups MA, et al. Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua. <i>Genetics</i>. 2019;212(3):815-835. doi:<a href=\"https://doi.org/10.1534/genetics.119.302045\">10.1534/genetics.119.302045</a>"},"main_file_link":[{"url":"https://doi.org/10.1534/genetics.119.302045","open_access":"1"}],"author":[{"full_name":"Veltsos, Paris","first_name":"Paris","last_name":"Veltsos"},{"first_name":"Kate E.","last_name":"Ridout","full_name":"Ridout, Kate E."},{"first_name":"Melissa A","last_name":"Toups","full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"González-Martínez, Santiago C.","last_name":"González-Martínez","first_name":"Santiago C."},{"first_name":"Aline","last_name":"Muyle","full_name":"Muyle, Aline"},{"full_name":"Emery, Olivier","last_name":"Emery","first_name":"Olivier"},{"full_name":"Rastas, Pasi","last_name":"Rastas","first_name":"Pasi"},{"last_name":"Hudzieczek","first_name":"Vojtech","full_name":"Hudzieczek, Vojtech"},{"last_name":"Hobza","first_name":"Roman","full_name":"Hobza, Roman"},{"last_name":"Vyskot","first_name":"Boris","full_name":"Vyskot, Boris"},{"full_name":"Marais, Gabriel A. B.","first_name":"Gabriel A. B.","last_name":"Marais"},{"full_name":"Filatov, Dmitry A.","last_name":"Filatov","first_name":"Dmitry A."},{"last_name":"Pannell","first_name":"John R.","full_name":"Pannell, John R."}],"quality_controlled":"1","year":"2019","publication_identifier":{"eissn":["1943-2631"],"issn":["0016-6731"]},"scopus_import":"1","date_published":"2019-07-01T00:00:00Z","external_id":{"pmid":["31113811"],"isi":["000474809300015"]},"page":"815-835","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1534/genetics.119.302045","department":[{"_id":"BeVi"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","date_updated":"2023-09-07T14:49:29Z","type":"journal_article","oa_version":"Published Version","day":"01"}]