Genomic divergence of leopards in the Cape Floristic Region of South Africa: potential drivers for local adaptation.

The adaptive value of intraspecific phenotypic variability, as well as the extent to which this is balanced by selection and genetic drift, is still relatively poorly explored. An intriguing population of leopard (Panthera pardus) occurs in the Cape Floristic Region, South Africa, where body mass is almost half that of leopards occurring in the savanna biome. In this study, we used whole-genome resequencing data of 43 leopards, including 10 from the Western Cape province (WCP). We explored spatial population structure and measured genome-wide diversity, including runs of homozygosity and genetic load. We compared their population demographic history to 'savanna leopards' in northern South Africa, and tested for signatures of selection that drive genomic and phenotypic differences. We found that WCP is distinct from other leopards in Africa, and that it diverged 20-24 thousand years ago from northern South Africa, which is in contrast to a lack of genome-wide differentiation found in previous studies. Because we found no obvious signs of genetic drift in WCP, the divergence is likely to have been caused by their population demographic history. We also found enriched genes that may relate to the local phenotype, possibly as an evolutionary response to food-scarce conditions. Leopards in the Cape Floristic Region utilize a unique landscape, which varies biologically in prey availability and vegetation structure, and anthropogenically with the province's rapidly growing human population. Considering the local adaptation and divergence found in both mitochondrial and nuclear genomes, leopards in the Cape can be considered an evolutionary significant unit (ESU).