{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T14:18:15Z","timestamp":1787062695450,"version":"build-2736575974"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2021,8,18]],"date-time":"2021-08-18T00:00:00Z","timestamp":1629244800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Inbreeding depression and genetic purging are important processes shaping the survivability and evolution of small populations. However, detecting purging is challenging in practice, in part because there are limited tools dedicated to it. I present a new R package to assist population analyses on detection and quantification of the inbreeding depression and genetic purging of biological fitness in pedigreed populations. It includes a collection of methods to estimate different measurements of inbreeding (Wright\u2019s, partial and ancestral inbreeding coefficients) as well as purging parameters (purged inbreeding, and opportunity of purging coefficients). Additional functions are also included to estimate population parameters, allowing to contextualize inbreeding and purging these results in terms of the population demographic history. purgeR is a valuable tool to gain insight into processes related to inbreeding and purging, and to better understand fitness and inbreeding load evolution in small populations.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>purgeR is an R package available at CRAN, and can be installed via install.packages(\u201cpurgeR\u201d). Source code is maintained at a GitLab repository (https:\/\/gitlab.com\/elcortegano\/purgeR).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab599","type":"journal-article","created":{"date-parts":[[2021,8,16]],"date-time":"2021-08-16T07:15:41Z","timestamp":1629098141000},"page":"564-565","source":"Crossref","is-referenced-by-count":19,"title":["purgeR: inbreeding and purging in pedigreed populations"],"prefix":"10.1093","volume":"38","author":[{"given":"Eugenio","family":"L\u00f3pez-Cortegano","sequence":"first","affiliation":[{"name":"Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh , Edinburgh EH9 3FL, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,8,18]]},"reference":[{"key":"2023020108420570800_btab599-B1","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1093\/oxfordjournals.jhered.a023085","article-title":"Ancestral inbreeding only minimally affects inbreeding depression in mammalian populations","volume":"88","author":"Ballou","year":"1997","journal-title":"J. Hered"},{"key":"2023020108420570800_btab599-B2","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1111\/jbg.12145","article-title":"GRAIN: a computer program to calculate ancestral and partial inbreeding coefficients using a gene dropping approach","volume":"132","author":"Baumung","year":"2015","journal-title":"J. Anim. Breed. Genet"},{"key":"2023020108420570800_btab599-B3","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1017\/S001667230500772X","article-title":"A simulation study on detecting purging of inbreeding depression in captive populations","volume":"86","author":"Boakes","year":"2005","journal-title":"Genet. Res"},{"key":"2023020108420570800_btab599-B4","doi-asserted-by":"crossref","first-page":"4991","DOI":"10.1111\/mec.14933","article-title":"Mutational load, inbreeding depression and heterosis in subdivided populations","volume":"27","author":"Charlesworth","year":"2018","journal-title":"Mol. 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Drift versus nonrandom mating","volume":"57","author":"Gl\u00e9min","year":"2003","journal-title":"Evolution"},{"key":"2023020108420570800_btab599-B10","doi-asserted-by":"crossref","first-page":"1001","DOI":"10.1038\/s41467-020-14803-1","article-title":"Purging of highly deleterious mutations through severe bottlenecks in Alpine ibex","volume":"11","author":"Grossen","year":"2020","journal-title":"Nat. Commun"},{"key":"2023020108420570800_btab599-B11","doi-asserted-by":"crossref","first-page":"1043","DOI":"10.1111\/j.1558-5646.2007.00088.x","article-title":"Inferring purging from pedigree data","volume":"61","author":"Gulisija","year":"2007","journal-title":"Evolution"},{"key":"2023020108420570800_btab599-B12","doi-asserted-by":"crossref","first-page":"632","DOI":"10.1093\/molbev\/msy228","article-title":"SLiM 3: forward genetic simulations beyond the Wright-Fisher model","volume":"36","author":"Haller","year":"2019","journal-title":"Mol. Biol. 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Evol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btab599\/40323769\/btab599.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/2\/564\/49007474\/btab599.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/2\/564\/49007474\/btab599.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T15:00:18Z","timestamp":1675263618000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/2\/564\/6354352"}},"subtitle":[],"editor":[{"given":"Russell","family":"Schwartz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2021,8,18]]},"references-count":13,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2022,1,3]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btab599","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,1,15]]},"published":{"date-parts":[[2021,8,18]]}}}