{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,27]],"date-time":"2026-04-27T23:30:50Z","timestamp":1777332650196,"version":"3.51.4"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2022,5,4]],"date-time":"2022-05-04T00:00:00Z","timestamp":1651622400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010663","name":"H2020 European Research Council","doi-asserted-by":"publisher","award":["680951"],"award-info":[{"award-number":["680951"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["J of Evolutionary Biology"],"published-print":{"date-parts":[[2022,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Studies of sex chromosome systems at early stages of divergence are key to understanding the initial process and underlying causes of recombination suppression. However, identifying signatures of divergence in homomorphic sex chromosomes can be challenging due to high levels of sequence similarity between the X and the Y. Variations in methodological precision and underlying data can make all the difference between detecting subtle divergence patterns or missing them entirely. Recent efforts to test for X\u2010Y sequence differentiation in the guppy have led to contradictory results. Here, we apply different analytical methodologies to the same data set to test for the accuracy of different approaches in identifying patterns of sex chromosome divergence in the guppy. Our comparative analysis reveals that the most substantial source of variation in the results of the different analyses lies in the reference genome used. Analyses using custom\u2010made genome assemblies for the focal population or species successfully recover a signal of divergence across different methodological approaches. By contrast, using the distantly related\n                    <jats:italic>Xiphophorus<\/jats:italic>\n                    reference genome results in variable patterns, due to both sequence evolution and structural variations on the sex chromosomes between the guppy and\n                    <jats:italic>Xiphophorus<\/jats:italic>\n                    . Changes in mapping and filtering parameters can additionally introduce noise and obscure the signal. Our results illustrate how analytical differences can alter perceived results and we highlight best practices for the study of nascent sex chromosomes.\n                  <\/jats:p>","DOI":"10.1111\/jeb.14013","type":"journal-article","created":{"date-parts":[[2022,5,4]],"date-time":"2022-05-04T07:40:36Z","timestamp":1651650036000},"page":"1646-1658","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["Comparison of methodological approaches to the study of young sex chromosomes: A case study in\n                    <i>Poecilia<\/i>"],"prefix":"10.1093","volume":"35","author":[{"given":"Iulia","family":"Darolti","sequence":"first","affiliation":[{"name":"Department of Zoology and Biodiversity Research Centre University of British Columbia  Vancouver British Columbia Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pedro","family":"Almeida","sequence":"additional","affiliation":[{"name":"Department of Genetics, Evolution and Environment University College London  London UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alison E.","family":"Wright","sequence":"additional","affiliation":[{"name":"Ecology and Evolutionary Biology School of Biosciences University of Sheffield  Sheffield UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2450-513X","authenticated-orcid":false,"given":"Judith E.","family":"Mank","sequence":"additional","affiliation":[{"name":"Department of Zoology and Biodiversity Research Centre University of British Columbia  Vancouver British Columbia Canada"},{"name":"Centre for Ecology and Conservation College of Life and Environmental Sciences University of Exeter  Cornwall UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,5,4]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msaa257"},{"key":"e_1_2_10_3_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1818486116"},{"key":"e_1_2_10_4_1","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.113.150755"},{"key":"e_1_2_10_5_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"e_1_2_10_6_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.156034.113"},{"key":"e_1_2_10_7_1","doi-asserted-by":"publisher","DOI":"10.1534\/g3.120.401573"},{"key":"e_1_2_10_8_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr330"},{"key":"e_1_2_10_9_1","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evaa099"},{"key":"e_1_2_10_10_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1905298116"},{"key":"e_1_2_10_11_1","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evaa187"},{"key":"e_1_2_10_12_1","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evaa081"},{"key":"e_1_2_10_13_1","doi-asserted-by":"publisher","DOI":"10.1093\/genetics\/69.4.523"},{"key":"e_1_2_10_14_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.113985.110"},{"key":"e_1_2_10_15_1","doi-asserted-by":"publisher","DOI":"10.1093\/g3journal\/jkab435"},{"key":"e_1_2_10_16_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msx116"},{"key":"e_1_2_10_17_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0169087"},{"key":"e_1_2_10_18_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1923"},{"key":"e_1_2_10_19_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr509"},{"key":"e_1_2_10_20_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp324"},{"key":"e_1_2_10_21_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp352"},{"key":"e_1_2_10_22_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.16355"},{"key":"e_1_2_10_23_1","doi-asserted-by":"crossref","unstructured":"Metzger D. C. H. &Mank J. E.(2020).Conserved sex\u2010biased DNA methylation patterns target key developmental genes and non\u2010recombining region of the guppy sex chromosome. Biorxiv https:\/\/doi.org\/10.1101\/2020.08.21.261792","DOI":"10.1101\/2020.08.21.261792"},{"key":"e_1_2_10_24_1","doi-asserted-by":"publisher","DOI":"10.3390\/genes9050238"},{"key":"e_1_2_10_25_1","first-page":"301","article-title":"Primitive sex chromosomes in poecilid fishes harbour simple repetitive DNA sequences","volume":"265","author":"Nanda I.","year":"1993","journal-title":"Journal of Experimental Biology"},{"key":"e_1_2_10_26_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/mst035"},{"key":"e_1_2_10_27_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.15245"},{"key":"e_1_2_10_28_1","doi-asserted-by":"publisher","DOI":"10.1002\/jez.1400240202"},{"key":"e_1_2_10_29_1","doi-asserted-by":"publisher","DOI":"10.1101\/201178"},{"key":"e_1_2_10_30_1","doi-asserted-by":"crossref","unstructured":"Qiu S. Yong L. Wilson A. Croft D. P. Graham C. &Charlesworth D.(2022).Partial sex linkage and linkage disequilibrium on the guppy sex chromosome. Biorxiv https:\/\/doi.org\/10.1101\/2022.01.14.476360","DOI":"10.1101\/2022.01.14.476360"},{"key":"e_1_2_10_31_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq033"},{"key":"e_1_2_10_32_1","volume-title":"R: A language and environment for statistical computing","author":"R Core Team","year":"2019"},{"key":"e_1_2_10_33_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2015.10.071"},{"key":"e_1_2_10_34_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41559-021-01452-w"},{"key":"e_1_2_10_35_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng.2604"},{"key":"e_1_2_10_36_1","doi-asserted-by":"crossref","unstructured":"Sigeman H. Sinclair B. &Hansson B.(2021).FindZX: An automated pipeline for detecting and visualising sex chromosomes using whole\u2010genome sequencing data. 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