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Although Y-specific features have been characterized in sex chromosomes of various ages, the earliest stages of Y chromosome evolution remain elusive. In particular, we do not know whether early stages of Y chromosome evolution consist of changes to individual genes or happen via chromosome-scale divergence from the X. To address this question, we quantified divergence between young proto-X and proto-Y chromosomes in the house fly, Musca domestica. We compared proto-sex chromosome sequence and gene expression between genotypic (XY) and sex-reversed (XX) males. We find evidence for sequence divergence between genes on the proto-X and proto-Y, including five genes with mitochondrial functions. There is also an excess of genes with divergent expression between the proto-X and proto-Y, but the number of genes is small. This suggests that individual proto-Y genes, but not the entire proto-Y chromosome, have diverged from the proto-X. We identified one gene, encoding an axonemal dynein assembly factor (which functions in sperm motility), that has higher expression in XY males than XX males because of a disproportionate contribution of the proto-Y allele to gene expression. The upregulation of the proto-Y allele may be favored in males because of this gene\u2019s function in spermatogenesis. The evolutionary divergence between proto-X and proto-Y copies of this gene, as well as the mitochondrial genes, is consistent with selection in males affecting the evolution of individual genes during early Y chromosome evolution.<\/jats:p>","DOI":"10.1093\/molbev\/msaa250","type":"journal-article","created":{"date-parts":[[2020,9,25]],"date-time":"2020-09-25T07:11:51Z","timestamp":1601017911000},"page":"606-618","source":"Crossref","is-referenced-by-count":16,"title":["Gene-Level, but Not Chromosome-Wide, Divergence between a Very Young House Fly Proto-Y Chromosome and Its Homologous Proto-X Chromosome"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2054-0904","authenticated-orcid":false,"given":"Jae Hak","family":"Son","sequence":"first","affiliation":[{"name":"Department of Biology and Biochemistry, University of Houston, Houston, TX"},{"name":"Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7362-9307","authenticated-orcid":false,"given":"Richard P","family":"Meisel","sequence":"additional","affiliation":[{"name":"Department of Biology and Biochemistry, University of Houston, Houston, TX"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,9,28]]},"reference":[{"issue":"3","key":"2021012317494816100_msaa250-B1","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J Mol Biol"},{"issue":"2","key":"2021012317494816100_msaa250-B2","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1038\/nrg3366","article-title":"Y-chromosome evolution: emerging insights into processes of Y-chromosome degeneration","volume":"14","author":"Bachtrog","year":"2013","journal-title":"Nat Rev Genet"},{"issue":"11","key":"2021012317494816100_msaa250-B3","doi-asserted-by":"crossref","first-page":"1587","DOI":"10.1038\/s41559-019-1009-9","article-title":"Massive gene amplification on a recently formed Drosophila Y chromosome","volume":"3","author":"Bachtrog","year":"2019","journal-title":"Nat Ecol Evol"},{"issue":"7","key":"2021012317494816100_msaa250-B4","doi-asserted-by":"crossref","first-page":"e1001899","DOI":"10.1371\/journal.pbio.1001899","article-title":"Sex determination: why so many ways of doing it?","volume":"12","author":"Bachtrog","year":"2014","journal-title":"PLoS Biol"},{"issue":"8","key":"2021012317494816100_msaa250-B5","doi-asserted-by":"crossref","first-page":"1336","DOI":"10.1101\/gr.077065.108","article-title":"An MCMC algorithm for haplotype assembly from whole-genome sequence data","volume":"18","author":"Bansal","year":"2008","journal-title":"Genome Res"},{"issue":"3","key":"2021012317494816100_msaa250-B6","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1534\/genetics.113.150755","article-title":"Expansion of the pseudo-autosomal region and ongoing recombination suppression in the Silene latifolia sex chromosomes","volume":"194","author":"Bergero","year":"2013","journal-title":"Genetics"},{"key":"2021012317494816100_msaa250-B7","doi-asserted-by":"crossref","DOI":"10.1093\/acprof:oso\/9780199657148.001.0001","volume-title":"The evolution of sex determination","author":"Beukeboom","year":"2014"},{"issue":"6","key":"2021012317494816100_msaa250-B8","doi-asserted-by":"crossref","first-page":"1025","DOI":"10.1139\/z64-100","article-title":"Somatic chromosomes of higher Diptera: IX. 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