{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T04:20:16Z","timestamp":1791778816677,"version":"4.3.4"},"posted":{"date-parts":[[2024,4,3]]},"group-title":"Genomics","reference-count":100,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2024,4,3]],"date-time":"2024-04-03T00:00:00Z","timestamp":1712102400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"name":"NIH","award":["R35GM151945"],"award-info":[{"award-number":["R35GM151945"]}]},{"name":"DOE","award":["SCR_025154"],"award-info":[{"award-number":["SCR_025154"]}]},{"DOI":"10.13039\/100008321","name":"Penn State University","doi-asserted-by":"crossref","award":["RRID:SCR_026424"],"award-info":[{"award-number":["RRID:SCR_026424"]}],"id":[{"id":"10.13039\/100008321","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,6,29]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>The mammalian Y chromosome is an evolutionary paradox: it cannot recombine across most of its length and has lost many genes, yet it retains multicopy gene families required for sperm production. How these genes survive has been difficult to resolve because their near-identical copies collapse in most genome assemblies and are difficult to analyze accurately with short RNA reads. Using telomere-to-telomere assemblies of seven ape genomes together with long-read testis transcriptomes, protein-structure predictions, and selection tests, we show that these gene families vary extensively but encode structurally conserved proteins. We demonstrate that, while copy number varies across and within species, palindromes and tandem arrays are equally effective in homogenizing copies via gene conversion\u2014a result we could obtain only with complete assemblies. We detect extensive transcript variation arising from alternative splicing and inter-copy sequence differences. Yet this variation collapses into only a few predicted protein-structure clusters per family. Furthermore, we find evidence of purifying selection acting on gene families (and domains) encoding ordered protein structures\u2014the majority of multicopy families on the human Y. Thus, copy number and (to a lesser degree) sequence, and transcript structure and sequence all vary, whereas protein structure, which is important for spermatogenic function, is held nearly constant. Together, our results show that palindrome- and array-mediated homogenization and purifying selection aimed at preserving protein structure jointly enable the survival of fertility-related genes on the non-recombining Y chromosome. These results will inform diagnostic approaches to human Y-linked infertility and studies of the conservation of non-human great apes.<\/jats:p>","DOI":"10.1101\/2024.04.02.587783","type":"posted-content","created":{"date-parts":[[2024,4,3]],"date-time":"2024-04-03T17:25:25Z","timestamp":1712165125000},"source":"Crossref","is-referenced-by-count":3,"title":["How and why multicopy genes survive on the human Y chromosome"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7726-4691","authenticated-orcid":false,"given":"Karol","family":"Pal","sequence":"first","affiliation":[{"name":"Pennsylvania State University, University Park, PA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9866-351X","authenticated-orcid":false,"given":"Aleksandra","family":"Greshnova","sequence":"additional","affiliation":[{"name":"Pennsylvania State University, University Park, PA, USA"},{"name":"University of Regensburg, Regensburg, Germany"},{"name":"Biozentrum, University of Basel, Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1623-6566","authenticated-orcid":false,"given":"Sukhwan","family":"Park","sequence":"additional","affiliation":[{"name":"Seoul National University, Seoul, South Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Byung June","family":"Ko","sequence":"additional","affiliation":[{"name":"Pennsylvania State University, University Park, PA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hana","family":"Palova","sequence":"additional","affiliation":[{"name":"Pennsylvania State University, University Park, PA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8781-9753","authenticated-orcid":false,"given":"Martin","family":"Steinegger","sequence":"additional","affiliation":[{"name":"Seoul National University, Seoul, South Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sergei L.","family":"Kosakovsky Pond","sequence":"additional","affiliation":[{"name":"Temple University, Philadelphia, PA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4719-8010","authenticated-orcid":false,"given":"Stefan","family":"Canzar","sequence":"additional","affiliation":[{"name":"University of Regensburg, Regensburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6212-9526","authenticated-orcid":false,"given":"Kateryna D.","family":"Makova","sequence":"additional","affiliation":[{"name":"Pennsylvania State University, University Park, PA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026070116050940000_2024.04.02.587783v3.1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1313759110"},{"key":"2026070116050940000_2024.04.02.587783v3.2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-023-05752-y"},{"issue":"July","key":"2026070116050940000_2024.04.02.587783v3.3","first-page":"207958","article-title":"Why Chromosome Palindromes?","volume":"2012","year":"2012","journal-title":"International Journal of Evolutionary Biology"},{"key":"2026070116050940000_2024.04.02.587783v3.4","doi-asserted-by":"publisher","DOI":"10.1101\/gr.5734907"},{"key":"2026070116050940000_2024.04.02.587783v3.5","doi-asserted-by":"publisher","DOI":"10.1093\/oxfordjournals.molbev.a003831"},{"key":"2026070116050940000_2024.04.02.587783v3.6","doi-asserted-by":"publisher","DOI":"10.1101\/gr.237586.118"},{"key":"2026070116050940000_2024.04.02.587783v3.7","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-10-421"},{"key":"2026070116050940000_2024.04.02.587783v3.8","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2001749117"},{"key":"2026070116050940000_2024.04.02.587783v3.9","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2003-4-9-226"},{"issue":"5","key":"2026070116050940000_2024.04.02.587783v3.10","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1111\/j.1442-2042.2007.01741.x","article-title":"Alu Sequence Variants of the BPY2 Gene in Proven Fertile and Infertile Men with Sertoli Cell-Only Phenotype: Alu Sequence Variants of BPY2","volume":"14","year":"2007","journal-title":"International Journal of Urology: Official Journal of the Japanese Urological Association"},{"issue":"7","key":"2026070116050940000_2024.04.02.587783v3.11","doi-asserted-by":"crossref","first-page":"512","DOI":"10.1038\/s41576-026-00935-5","article-title":"Evolutionary Causes and Consequences of Gene Duplication","volume":"27","year":"2026","journal-title":"Nature Reviews. 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