The House Fly Y Chromosome is Young and Undifferentiated from its Ancient X Chromosome Partner

Ancient or canonical sex chromosome pairs consist of a gene rich X (or Z) chromosome and a male(or female-) limited Y (or W) chromosome that is gene poor. In contrast to highly differentiated sex chromosomes, nascent sex chromosome pairs are homomorphic or very similar in sequence content. Nascent sex chromosomes arise frequently over the course of evolution, as evidenced by differences in sex chromosomes between closely related species and sex chromosome polymorphisms within species. Sex chromosome turnover typically occurs when an existing sex chromosome becomes fused to an autosome or an autosome acquires a new sex-determining locus/allele. Previously documented sex chromosome transitions involve changes to both members of the sex chromosome pair (X and Y, or Z and W). The house fly has sex chromosomes that resembles the ancestral fly karyotype that originated 100 million years ago, and therefore house fly is expected to have differentiated X and Y chromosomes. We tested this hypothesis using whole genome sequencing and transcriptomic data, and we surprisingly discovered little evidence for X-Y differentiation in house fly. We propose that house fly has retained the ancient X chromosome, but the ancestral Y was replaced by an X chromosome carrying a male determining gene. In this evolutionary scenario, the house fly has an ancient X chromosome that is partnered with with a neo-Y chromosome. This example of sex chromosome recycling illustrates how one member of a sex chromosome pair can experience evolutionary turnover while the other member remains unaffected. 2 . CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/073023 doi: bioRxiv preprint first posted online Sep. 1, 2016;