Data from: Red, gold and green: Comparative genomics of polymorphic leopards from South Africa

An important goal of comparative and functional genomics is to connect
genetic polymorphisms to phenotypic variation. Leopards (Panthera pardus)
from northern South Africa are particularly diverse, as here a unique
colour morph occurs, as well as two deeply diverged southern (SA) and
central African (CA) mitochondrial clades, stemming from two Pleistocene
refugia. Here, we present the first whole genomes of a red leopard and a
black (captive) leopard, and wildtypes belonging to the CA and SA
mitochondrial clades, to evaluate genome-wide diversity, divergence, and
high impact mutations that may relate to their phenotype. In the black
leopard, we found long runs of homozygosity (ROHs), low nucleotide
diversity across the genome, and a large number of homozygous structural
variants, likely resulting from inbreeding to maintain this colour morph
in captivity. In red leopards, ROHs were slightly longer compared to
wildtype leopards, with potential deleterious mutations relating to its
phenotype, including impaired vision. When assessing population structure,
we found no divergence between CA and SA leopards and the rest of Africa,
whether comparing single nucleotide or structural variants. This
illustrates the homogenizing effect of introgression, and highlights that
although leopards in northern South Africa may be phenotypically unique,
they are not genetically different.