Mitogenomic characterization of South African leopards (Panthera pardus), and the effect of past climatic events

Abstract

Abstract Revealing phylogeographic structure is important for accurate subspecies delineation and understanding a species’ evolutionary history. In leopards (Panthera pardus), there are currently nine subspecies recognized. On the African continent, only one subspecies occurs (P. p. pardus), although historic mitochondrial DNA suggests the presence of three putative continental lineages: (1) West Africa (WA), (2) Central Africa (CA), and (3) Southern Africa (SA). So far, genome-wide data did not recover this phylogeographic structure, although leopards in the southern periphery of their distribution range in Africa have not yet been investigated in detail. The Mpumalanga province of South Africa is of particular interest, as here the CA and the SA clade possibly meet. The aim of this study was to characterize the first mitogenomes of African leopards from Mpumalanga, to help clarifying how South African leopards fit into continental patterns of genetic differentiation. Complete mitogenomes from six leopards were assembled de novo and included in phylogenetic analysis, in combination with other publicly available mitogenomes. Bayesian inference and Maximum Likelihood analyses identified two deeply diverged putative lineages within South Africa, which are more genetically distinct than two subspecies in Asia. The lineages dated back to 0.73–0.87 million years ago, indicating that they originated during the climatically unstable Mid-Pleistocene, as seen in other large mammals. The Pleistocene refuge theory states that the maintenance of savanna refugia in South Africa promoted the divergence between populations. As such, leopards may reflect the unique climatic history of South Africa, which has resulted in eminent and endemic genetic diversity.