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The Christmas Island blue\u2010tailed skink (<jats:italic>Cryptoblepharus egeriae<\/jats:italic>) and Lister's gecko (<jats:italic>Lepidodactylus listeri<\/jats:italic>) are two endemic reptile species that went extinct in the wild shortly after the introduction of a predatory snake. After a decade of management, captive populations have expanded from 66 skinks and 43 geckos to several thousand individuals; however, little is known about patterns of genetic variation in these species. Here, we use PacBio HiFi long\u2010read and Hi\u2010C sequencing to generate highly contiguous reference genomes for both reptiles, including the XY chromosome pair in the skink. We then analyse patterns of genetic diversity to infer ancient demography and more recent histories of inbreeding. We observe high genome\u2010wide heterozygosity in the skink (0.007 heterozygous sites per base\u2010pair) and gecko (0.005), consistent with large historical population sizes. However, nearly 10% of the blue\u2010tailed skink reference genome falls within long (&gt;1\u00a0Mb) runs of homozygosity (ROH), resulting in homozygosity at all major histocompatibility complex (MHC) loci. In contrast, we detect a single ROH in Lister's gecko. We infer from the ROH lengths that related skinks may have established the captive populations. Despite a shared recent extinction in the wild, our results suggest important differences in these species' histories and implications for management. We show how reference genomes can contribute evolutionary and conservation insights, and we provide resources for future population\u2010level and comparative genomic studies in reptiles.<\/jats:p>","DOI":"10.1111\/1755-0998.13780","type":"journal-article","created":{"date-parts":[[2023,3,6]],"date-time":"2023-03-06T04:53:23Z","timestamp":1678078403000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":16,"title":["Genomes of two Extinct\u2010in\u2010the\u2010Wild reptiles from Christmas Island reveal distinct evolutionary histories and conservation insights"],"prefix":"10.1111","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8382-431X","authenticated-orcid":false,"given":"Tristram O.","family":"Dodge","sequence":"first","affiliation":[{"name":"School of Life and Environmental Sciences The University of Sydney  Sydney New South Wales Australia"},{"name":"Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Sydney  Sydney New South Wales Australia"},{"name":"Department of Biology Stanford University  Stanford California USA"},{"name":"Australian\u2010American Fulbright Commission  Deakin Australian Capital Territory Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9009-7453","authenticated-orcid":false,"given":"Katherine A.","family":"Farquharson","sequence":"additional","affiliation":[{"name":"School of Life and Environmental Sciences The University of Sydney  Sydney New South Wales Australia"},{"name":"Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Sydney  Sydney New South Wales Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claire","family":"Ford","sequence":"additional","affiliation":[{"name":"Taronga Conservation Society Australia  Mosman New South Wales Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lisa","family":"Cavanagh","sequence":"additional","affiliation":[{"name":"Taronga Conservation Society Australia  Mosman New South Wales Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kristen","family":"Schubert","sequence":"additional","affiliation":[{"name":"Parks Australia  Christmas Island Indian Ocean Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2075-5668","authenticated-orcid":false,"given":"Molly","family":"Schumer","sequence":"additional","affiliation":[{"name":"Department of Biology Stanford University  Stanford California USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katherine","family":"Belov","sequence":"additional","affiliation":[{"name":"School of Life and Environmental Sciences The University of Sydney  Sydney New South Wales Australia"},{"name":"Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Sydney  Sydney New South Wales Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6328-398X","authenticated-orcid":false,"given":"Carolyn J.","family":"Hogg","sequence":"additional","affiliation":[{"name":"School of Life and Environmental Sciences The University of Sydney  Sydney New South Wales Australia"},{"name":"Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Sydney  Sydney New South Wales Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2023,3,21]]},"reference":[{"key":"e_1_2_11_2_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2021.635208"},{"key":"e_1_2_11_3_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.palaeo.2019.109396"},{"key":"e_1_2_11_4_1","doi-asserted-by":"publisher","DOI":"10.1017\/S0030605316001071"},{"key":"e_1_2_11_5_1","doi-asserted-by":"publisher","DOI":"10.2307\/1774789"},{"key":"e_1_2_11_6_1","unstructured":"Andrews S.(2010).FastQC: A quality control tool for high throughput sequence 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G. &Sadlier R.(1999).The terrestrial reptiles of Christmas Island: A reappraisal of their status. Unpublished report to Parks Australia Canberra (Australian Museum Sydney)."},{"key":"e_1_2_11_17_1","volume-title":"The terrestrial reptiles of Australia's Island territories","author":"Cogger H. G.","year":"1983"},{"key":"e_1_2_11_18_1","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evaa104"},{"key":"e_1_2_11_19_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586\u2010022\u201004664\u20107"},{"key":"e_1_2_11_20_1","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giab008"},{"key":"e_1_2_11_21_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty149"},{"key":"e_1_2_11_22_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12864\u2010016\u20102774\u20103"},{"key":"e_1_2_11_23_1","unstructured":"Director of National Parks. 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