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In the genomics era, this debate continues, with relatedness estimates being sensitive to the methods used to generate markers, marker quality, and levels of diversity in sampled individuals. Here, we compare six commonly used genome\u2010based relatedness estimators (kinship genetic distance [KGD], Wang maximum likelihood [TrioML], Queller and Goodnight [\n                    <jats:italic>R<\/jats:italic>\n                    <jats:sub>xy<\/jats:sub>\n                    ], Kinship INference for Genome\u2010wide association studies [KING\u2010robust), and pairwise relatedness [\n                    <jats:italic>R<\/jats:italic>\n                    <jats:sub>AB<\/jats:sub>\n                    ], allele\u2010sharing coancestry [AS]) across five species bred in captivity\u2013including three birds and two mammals\u2013with varying degrees of reliable pedigree data, using reduced\u2010representation and whole genome resequencing data. Genome\u2010based relatedness estimates varied widely across estimators, sequencing methods, and species, yet the most consistent results for known first order relationships were found using\n                    <jats:italic>R<\/jats:italic>\n                    <jats:sub>xy<\/jats:sub>\n                    ,\n                    <jats:italic>R<\/jats:italic>\n                    <jats:sub>AB<\/jats:sub>\n                    , and AS. However, AS was found to be less consistently correlated with known pedigree relatedness than either\n                    <jats:italic>R<\/jats:italic>\n                    <jats:sub>xy<\/jats:sub>\n                    or\n                    <jats:italic>R<\/jats:italic>\n                    <jats:sub>AB<\/jats:sub>\n                    . Our combined results indicate there is not a single genome\u2010based estimator that is ideal across different species and data types. To determine the most appropriate genome\u2010based relatedness estimator for each new data set, we recommend assessing the relative: (1) correlation of candidate estimators with known relationships in the pedigree and (2) precision of candidate estimators with known first\u2010order relationships. These recommendations are broadly applicable to conservation breeding programmes, particularly where genome\u2010based estimates of relatedness can complement and complete poorly pedigreed populations.\u00a0Given a growing interest in the application of wild pedigrees, our results are also applicable to in situ wildlife management.\n                  <\/jats:p>","DOI":"10.1111\/1755-0998.13630","type":"journal-article","created":{"date-parts":[[2022,5,5]],"date-time":"2022-05-05T07:59:25Z","timestamp":1651737565000},"page":"2546-2558","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":26,"title":["Comparing genome\u2010based estimates of relatedness for use in pedigree\u2010based conservation management"],"prefix":"10.1111","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3404-5253","authenticated-orcid":false,"given":"Samantha S.","family":"Hauser","sequence":"first","affiliation":[{"name":"Department of Biological Sciences University of Wisconsin\u2010Milwaukee  Milwaukee Wisconsin USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4650-8067","authenticated-orcid":false,"given":"Stephanie J.","family":"Galla","sequence":"additional","affiliation":[{"name":"School of Biological Sciences University of Canterbury  Christchurch New Zealand"},{"name":"Department of Biological Sciences Boise State University  Boise Idaho USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1795-6589","authenticated-orcid":false,"given":"Andrea S.","family":"Putnam","sequence":"additional","affiliation":[{"name":"Department of Exhibit\u2010Curators San Diego Zoo Wildlife Alliance  San Diego California USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2112-5761","authenticated-orcid":false,"given":"Tammy E.","family":"Steeves","sequence":"additional","affiliation":[{"name":"School of Biological Sciences University of Canterbury  Christchurch New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9892-1056","authenticated-orcid":false,"given":"Emily K.","family":"Latch","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences University of Wisconsin\u2010Milwaukee  Milwaukee Wisconsin USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2022,5,27]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755\u20100998.12739"},{"key":"e_1_2_10_3_1","first-page":"509","volume-title":"Genetics and conservation","author":"Ballou J. 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