Whole genome sequencing and the application of a SNP panel reveal primary evolutionary lineages and genomic diversity in the lion (Panthera leo)

Previous phylogeographic studies of the lion (Panthera leo) have offered increased insight into the distribution of genetic diversity, as well as a revised taxonomy which now distinguishes between a northern (Panthera leo leo) and a southern (Panthera leo melanochaita) subspecies. However, existing whole range phylogeographic studies on lions focused on mitochondrial DNA and/or a limited set of microsatellites. The geographic extent of genetic lineages and their phylogenetic relationships remain uncertain, clouded by incomplete lineage sorting and sex-biased dispersal. In this study we present results of whole genome sequencing and subsequent variant calling in ten lions sampled throughout the geographic range. This resulted in the discovery of >150,000 Single Nucleotide Polymorphisms (SNPs), of which ~100,000 SNPs had sufficient coverage in at least half of the individuals. Phylogenetic analyses revealed the same basal split between northern and southern populations as had previously been reported using other genetic markers. Further, we designed a SNP panel, including 125 nuclear and 14 mitochondrial SNPs, which was subsequently tested on >200 lions from across their range. Results allow us to assign individuals to one of the four major clades: West & Central Africa, India, East Africa, or Southern Africa. This SNP panel can have important applications, not only for studying populations on a local geographic scale, but also for guiding conservation management of ex situ populations, and for tracing samples of unknown origin for forensic purposes. These genomic resources should not only contribute to our understanding of the evolutionary history of the lion, but may also play a crucial role in conservation efforts aimed at protecting the species in its full diversity.