Population genomics of Grant's gazelle
The Grant's gazelle complex (Nanger granti s.l.) in eastern Africa harbours rare autosome-sex chromosome translocations that have generated neo-sex chromosomes. Here, we sequenced 33 whole genomes from two principal lineages—Peter's gazelle (N. petersii) and Grant's gazelle (N. granti)—as well as a hybrid population, and performed population genetic analyses to understand how these neo-sex chromosomes influence variation within and between lineages. Strikingly, two regions on the neo-sex chromosomes, one ˜51 megabase (Mb) segment derived from ancestral chromosome 16 and another ˜12.5 Mb segment from ancestral chromosome 5, have stopped recombining and show relaxation of purifying selection in their neo-Y-linked homologs, both hallmarks of sex chromosome degeneration. The hybrid population carries approximately 59% genomic ancestry from Peter's gazelle and 41% from Grant's gazelle (N. granti), with admixture being both ancient and recent. Parental ancestry is unevenly distributed across the genome, with extensive “deserts” devoid of Grant's gazelle (N. granti) ancestry. These non-recombining regions constitute major barriers to gene flow: hybrid individuals from Mkomazi are fixed for Peter's gazelle alleles in the neo-Y linked homologs in both regions, and nearly fixed for Peter's gazelle in one of the corresponding neo-X regions. Overall, our results suggest that neo-sex chromosomes are helping to reinforce genetic barriers between these nascent species, providing a compelling example of their role in an ongoing mammalian speciation process.