The Evolutionary Dynamics of the Lion Panthera leo Revealed by Host and Viral Population Genomics

Antunes, Agostinho; Troyer, Jennifer L.; Roelke, Melody E.; Pecon-Slattery, Jill; Packer, Craig; Winterbach, Christiaan; Winterbach, Hanlie; Hemson, Graham; Frank, Laurence; Stander, Philip; Siefert, Ludwig; Driciru, Margaret; Funston, Paul J.; Alexander, Kathy A.; Prager, Katherine C.; Mills, Gus; Wildt, David; Bush, Mitch; O'Brien, Stephen J.; Johnson, Warren E.

If we had restricted our inferences to mtDNA, we might have concluded that East African lion populations, which are fixed or nearly fixed for haplotype H11, went extinct during the Pleistocene/Holocene transition (similar to the well known mega-fauna extinctions of the Late Pleistocene [34] ) and were then colonized by Southern populations. However, our population genomics data better fit a scenario of lion population expansion and interbreeding rather than simple replacement. First, genetic diversity and allelic richness at nDNA are slightly higher in East Africa populations relatively to those in Southern Africa. This is contrary to the expected pattern of population expansion in which there is usually a progressive decline in genetic diversity and allelic richness. Second, SER lions carry two diverse FIV Ple subtypes found only in East Africa (B-C), and not only FIV Ple subtype A, which was presumably introduced in East Africa coincidently with the mtDNA expansion event northwards from South. Third, the East African FIV Ple subtype B found in UGA/SER-I/SER-II/SER-III/NGC showed evidence of a population expansion (raggedness, r = 0.004; P,0.01; F s = 220.37; P,0.00001) and the highest nucleotide diversity observed within FIV Ple subtypes (p = 0.09). Four, the FIV Ple subtype diversity is higher in East African clades (four out of the six viral strains).