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However, detecting sex\u2010linked loci can be challenging, and available scripts neglect some categories of sex\u2010linked variation. Here, we present new\n                    <jats:italic>R<\/jats:italic>\n                    functions to (1) identify and separate sex\u2010linked loci in ZW and XY sex determination systems and (2) infer the genetic sex of individuals based on these loci. We tested these functions on genomic data for two bird and one mammal species and compared the biological inferences made before and after removing sex\u2010linked loci using our function. We found that our function identified autosomal loci with \u226598.8% accuracy and sex\u2010linked loci with an average accuracy of 87.8%. We showed that standard filters, such as low read depth and call rate, failed to remove up to 54.7% of sex\u2010linked loci. This led to (i) overestimation of population\n                    <jats:italic>F<\/jats:italic>\n                    <jats:sub>IS<\/jats:sub>\n                    by up to 24%, and the number of private alleles by up to 8%; (ii) wrongly inferring significant sex differences in heterozygosity; (iii) obscuring genetic population structure and (iv) inferring ~11% fewer correct parentages. We discuss how failure to remove sex\u2010linked markers can lead to incorrect biological inferences (e.g. sex\u2010biased dispersal and cryptic population structure) and misleading management recommendations. For reduced\u2010representation datasets with at least 15 known\u2010sex individuals of each sex, our functions offer convenient resources to remove sex\u2010linked loci and to sex the remaining individuals (freely available at\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"https:\/\/github.com\/drobledoruiz\/conservation_genomics\">https:\/\/github.com\/drobledoruiz\/conservation_genomics<\/jats:ext-link>\n                    ).\n                  <\/jats:p>","DOI":"10.1111\/1755-0998.13844","type":"journal-article","created":{"date-parts":[[2023,8,1]],"date-time":"2023-08-01T10:45:12Z","timestamp":1690886712000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["Easy\u2010to\u2010use\n                    <i>R<\/i>\n                    functions to separate reduced\u2010representation genomic datasets into sex\u2010linked\u00a0and autosomal loci, and conduct sex assignment"],"prefix":"10.1111","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9752-9602","authenticated-orcid":false,"given":"Diana A.","family":"Robledo\u2010Ruiz","sequence":"first","affiliation":[{"name":"School of Biological Sciences Monash University  Clayton Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8204-9873","authenticated-orcid":false,"given":"Lana","family":"Austin","sequence":"additional","affiliation":[{"name":"School of Biological Sciences Monash University  Clayton Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1271-4767","authenticated-orcid":false,"given":"J. Nevil","family":"Amos","sequence":"additional","affiliation":[{"name":"School of Biological Sciences Monash University  Clayton Victoria Australia"},{"name":"Department of Energy, Environment and Climate Action Arthur Rylah Institute for Environmental Research  Heidelberg Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5067-508X","authenticated-orcid":false,"given":"Jes\u00fas","family":"Castrej\u00f3n\u2010Figueroa","sequence":"additional","affiliation":[{"name":"School of Biological Sciences Monash University  Clayton Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9664-1624","authenticated-orcid":false,"given":"Daniel K. P.","family":"Harley","sequence":"additional","affiliation":[{"name":"Department of Wildlife Conservation and Science Zoos Victoria  Parkville Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8022-9627","authenticated-orcid":false,"given":"Michael J. L.","family":"Magrath","sequence":"additional","affiliation":[{"name":"Department of Wildlife Conservation and Science Zoos Victoria  Parkville Victoria Australia"},{"name":"School of BioSciences University of Melbourne  Parkville Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8139-7059","authenticated-orcid":false,"given":"Paul","family":"Sunnucks","sequence":"additional","affiliation":[{"name":"School of Biological Sciences Monash University  Clayton Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9455-4124","authenticated-orcid":false,"given":"Alexandra","family":"Pavlova","sequence":"additional","affiliation":[{"name":"School of Biological Sciences Monash University  Clayton Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2023,8]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755-0998.13351"},{"key":"e_1_2_10_3_1","doi-asserted-by":"publisher","DOI":"10.1093\/oso\/9780198856566.001.0001"},{"key":"e_1_2_10_4_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(05)80360-2"},{"key":"e_1_2_10_5_1","doi-asserted-by":"publisher","DOI":"10.1890\/13-1328.1"},{"key":"e_1_2_10_6_1","doi-asserted-by":"publisher","DOI":"10.1093\/jmammal\/gyv058"},{"key":"e_1_2_10_7_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0003376"},{"key":"e_1_2_10_8_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.2517-6161.1995.tb02031.x"},{"key":"e_1_2_10_9_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.14217"},{"key":"e_1_2_10_10_1","doi-asserted-by":"publisher","DOI":"10.1093\/acprof:oso\/9780199657148.001.0001"},{"key":"e_1_2_10_11_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0197364"},{"key":"e_1_2_10_12_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.biocon.2017.12.019"},{"key":"e_1_2_10_13_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.156034.113"},{"key":"e_1_2_10_14_1","doi-asserted-by":"publisher","DOI":"10.1046\/j.1420-9101.2001.00331.x"},{"key":"e_1_2_10_15_1","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.114.169052"},{"key":"e_1_2_10_16_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr330"},{"key":"e_1_2_10_17_1","doi-asserted-by":"publisher","DOI":"10.1093\/bfgp\/elq031"},{"key":"e_1_2_10_18_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755-0998.13339"},{"key":"e_1_2_10_19_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755-0998.13618"},{"key":"e_1_2_10_20_1","doi-asserted-by":"publisher","DOI":"10.1093\/jhered\/esx102"},{"key":"e_1_2_10_21_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.aal3327"},{"key":"e_1_2_10_22_1","doi-asserted-by":"crossref","unstructured":"Dudchenko O. 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