{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T15:42:18Z","timestamp":1791387738875,"version":"4.3.3"},"reference-count":89,"publisher":"Wiley","issue":"3","license":[{"start":{"date-parts":[[2024,1,3]],"date-time":"2024-01-03T00:00:00Z","timestamp":1704240000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001711","name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","doi-asserted-by":"publisher","award":["310030_200420"],"award-info":[{"award-number":["310030_200420"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Molecular Ecology Resources"],"published-print":{"date-parts":[[2024,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    The identification of sex\u2010linked scaffolds and the genetic sex of individuals, i.e. their sex karyotype, is a fundamental step in population genomic studies. If sex\u2010linked scaffolds are known, single individuals may be sexed based on read counts of next\u2010generation sequencing data. If both sex\u2010linked scaffolds as well as sex karyotypes are unknown, as is often the case for non\u2010model organisms, they have to be jointly inferred. For both cases, current methods rely on arbitrary thresholds, which limits their power for low\u2010depth data. In addition, most current methods are limited to euploid sex karyotypes (XX and XY). Here we develop\n                    <jats:styled-content>BeXY<\/jats:styled-content>\n                    , a fully Bayesian method to jointly infer the posterior probabilities for each scaffold to be autosomal, X\u2010 or Y\u2010linked and for each individual to be any of the sex karyotypes XX, XY, X0, XXX, XXY, XYY and XXYY. If the sex\u2010linked scaffolds are known, it also identifies autosomal trisomies and estimates the sex karyotype posterior probabilities for single individuals. As we show with downsampling experiments,\n                    <jats:styled-content>BeXY<\/jats:styled-content>\n                    has higher power than all existing methods. It accurately infers the sex karyotype of ancient human samples with as few as 20,000 reads and accurately infers sex\u2010linked scaffolds from data sets of just a handful of samples or with highly imbalanced sex ratios, also in the case of low\u2010quality reference assemblies. We illustrate the power of\n                    <jats:styled-content>BeXY<\/jats:styled-content>\n                    by applying it to both whole\u2010genome shotgun and target enrichment sequencing data of ancient and modern humans, as well as several non\u2010model organisms.\n                  <\/jats:p>","DOI":"10.1111\/1755-0998.13913","type":"journal-article","created":{"date-parts":[[2024,1,4]],"date-time":"2024-01-04T01:13:44Z","timestamp":1704330824000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Accurate Bayesian inference of sex chromosome karyotypes and sex\u2010linked scaffolds from low\u2010depth sequencing data"],"prefix":"10.1111","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8941-4274","authenticated-orcid":false,"given":"Madleina","family":"Caduff","sequence":"first","affiliation":[{"name":"Department of Biology University of Fribourg  Fribourg Switzerland"},{"name":"Swiss Institute of Bioinformatics  Fribourg Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Raphael","family":"Eckel","sequence":"additional","affiliation":[{"name":"Department of Biology University of Fribourg  Fribourg Switzerland"},{"name":"Swiss Institute of Bioinformatics  Fribourg Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christoph","family":"Leuenberger","sequence":"additional","affiliation":[{"name":"Department of Biology University of Fribourg  Fribourg Switzerland"},{"name":"Swiss Institute of Bioinformatics  Fribourg Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2866-6739","authenticated-orcid":false,"given":"Daniel","family":"Wegmann","sequence":"additional","affiliation":[{"name":"Department of Biology University of Fribourg  Fribourg Switzerland"},{"name":"Swiss Institute of Bioinformatics  Fribourg Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2024,1,3]]},"reference":[{"key":"e_1_2_8_2_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature14507"},{"key":"e_1_2_8_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-45839-z"},{"key":"e_1_2_8_4_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.aay6826"},{"key":"e_1_2_8_5_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.1001899"},{"key":"e_1_2_8_6_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.14217"},{"key":"e_1_2_8_7_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.aay5012"},{"key":"e_1_2_8_8_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msu109"},{"key":"e_1_2_8_9_1","doi-asserted-by":"publisher","DOI":"10.1016\/B978-0-12-820140-4.00002-8"},{"key":"e_1_2_8_10_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.aaf7943"},{"key":"e_1_2_8_11_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-020-68550-w"},{"key":"e_1_2_8_12_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cub.2020.08.033"},{"key":"e_1_2_8_13_1","doi-asserted-by":"publisher","DOI":"10.1002\/ece3.9185"},{"key":"e_1_2_8_14_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-018-0094-2"},{"key":"e_1_2_8_15_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.aar7711"},{"key":"e_1_2_8_16_1","doi-asserted-by":"publisher","DOI":"10.1086\/587642"},{"key":"e_1_2_8_17_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.aar2625"},{"key":"e_1_2_8_18_1","doi-asserted-by":"publisher","DOI":"10.1098\/rspb.2006.3720"},{"key":"e_1_2_8_19_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tig.2009.04.005"},{"key":"e_1_2_8_20_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tree.2013.09.008"},{"key":"e_1_2_8_21_1","doi-asserted-by":"publisher","DOI":"10.1093\/acprof:oso\/9780199208784.001.0001"},{"key":"e_1_2_8_22_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41559-020-1102-0"},{"key":"e_1_2_8_23_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-04241-4"},{"key":"e_1_2_8_24_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature17993"},{"key":"e_1_2_8_25_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-15560-x"},{"key":"e_1_2_8_26_1","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms6257"},{"key":"e_1_2_8_27_1","doi-asserted-by":"publisher","DOI":"10.1093\/jhered\/esv059"},{"key":"e_1_2_8_28_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755-0998.12264"},{"key":"e_1_2_8_29_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1903275116"},{"key":"e_1_2_8_30_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq102"},{"key":"e_1_2_8_31_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-genet-120215-035429"},{"key":"e_1_2_8_32_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.genet.42.110807.091714"},{"key":"e_1_2_8_33_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.2003703"},{"key":"e_1_2_8_34_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.267534.120"},{"key":"e_1_2_8_35_1","doi-asserted-by":"publisher","DOI":"10.1101\/2022.06.12.495320"},{"key":"e_1_2_8_36_1","doi-asserted-by":"publisher","DOI":"10.1002\/ajpa.23308"},{"key":"e_1_2_8_37_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0246833"},{"key":"e_1_2_8_38_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1523951113"},{"key":"e_1_2_8_39_1","doi-asserted-by":"publisher","DOI":"10.1002\/9781118150719"},{"key":"e_1_2_8_40_1","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms9912"},{"key":"e_1_2_8_41_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cub.2016.12.060"},{"key":"e_1_2_8_42_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-29158-y"},{"key":"e_1_2_8_43_1","first-page":"145","article-title":"Sex\u2010typing 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