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.

Methods
DNA extractions of molecular weight >100 kb were sequenced on an Illumina HiSeq 2500 platform by a commercial provider using paired-end (2 x 150 bp) chemistry following the manufacturer’s instruction. We targeted 10X depth of coverage and generated whole-genome sequencing data for two leopards that each have unique traits: the red / strawberry leopard, and the melanistic / black leopard. Two other whole genomes were generated of Wildtype leopards belonging to the SA and CA mitochondrial clades, which were merged with another dataset of South African leopards (see #).