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Several livebearers within the genus Poecilia share a male-heterogametic sex chromosome system that is roughly 20\u00a0Myr old, with extreme variation in the degree of Y chromosome divergence. In Poecilia picta, the Y is highly degenerate and associated with complete X chromosome dosage compensation. In contrast, although recombination is restricted across almost the entire length of the sex chromosomes in Poecilia reticulata and Poecilia wingei, divergence between the X chromosome and the Y chromosome is very low. This clade therefore offers a unique opportunity to study the forces that accelerate or hinder sex chromosome divergence. We used RNA-seq data from multiple families of both P.\u00a0reticulata and P.\u00a0wingei, the species with low levels of sex chromosome divergence, to differentiate X and Y coding sequences based on sex-limited SNP inheritance. Phylogenetic tree analyses reveal that occasional recombination has persisted between the sex chromosomes for much of their length, as X- and Y-linked sequences cluster by species instead of by gametolog. This incomplete recombination suppression maintains the extensive homomorphy observed in these systems. In addition, we see differences between the previously identified strata in the phylogenetic clustering of X\u2013Y orthologs, with those that cluster by chromosome located in the older stratum, the region previously associated with the sex-determining locus. However, recombination arrest appears to have expanded throughout the sex chromosomes more gradually instead of through a stepwise process associated with inversions.<\/jats:p>","DOI":"10.1093\/gbe\/evaa099","type":"journal-article","created":{"date-parts":[[2020,5,13]],"date-time":"2020-05-13T23:31:04Z","timestamp":1589412664000},"page":"965-977","source":"Crossref","is-referenced-by-count":42,"title":["Guppy Y Chromosome Integrity Maintained by Incomplete Recombination Suppression"],"prefix":"10.1093","volume":"12","author":[{"given":"Iulia","family":"Darolti","sequence":"first","affiliation":[{"name":"Biodiversity Research Centre and Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alison E","family":"Wright","sequence":"first","affiliation":[{"name":"Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United 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