Analysis Of The Cat and Dog Y Chromosome Sequences

Although more than thirty mammalian genomes have been sequenced to draft quality, very few of these include the Y chromosome. This has severely limited our understanding of the evolutionary dynamics of Y chromosome gene persistence and loss, identification of conserved regulatory elements, as well the extent to which different types of selection act to maintain genes within this unique genomic environment. Here we present the first MSY (male-specific region of the Y chromosome) sequences from two carnivores, the domestic dog and cat. By combining these data with other available MSY sequences, our multiordinal comparison allows for the first accounting of levels of selection constraining the evolution of eutherian Y chromosomes, as well as the divergent and convergent evolutionary forces that allow for the retention of sequences in a non-recombining genomic environment. Despite gene gain and loss across the phylogeny, eutherian mammals retain a core set of genes that have been constrained by negative selection for the past 100 million years, and are partitioned into a discrete chromosomal domain that was radically restructured on the chimp/human lineage. By contrast, the acquisition and expansion of novel male-benefit gene families has been accompanied by signatures of positive selection in all examined eutherians.