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.

Based on patterns of genetic diversity and phylogenetic analysis of lion nDNA/mtDNA and FIV Ple markers, we propose a scenario of a period of refugia/isolation in the Late Pleistocene followed by two major lion expansions across Africa and Asia. The first expansion, supported by the mtDNA NCPA [27] (x 2 = 690.00, P#0.0001; Figure S5 ), was a long-distance colonization of mtDNA lineage-III (GIR/ATL/ANG/ZBW) around 118,000 years ago (95% CI: 28,000-208,000), with subsequent fragmentation of haplotypes H5-H6 into Central and North Africa and haplotypes H7-H8 into West Asia (M1- Figure 1A) . Support for this initial expansion is also found in nDNA. The ADA haplotype A5 fixed in GIR in also present in KEN, SER-II, and SER-III, suggesting that lions likely colonized West Asia from the East Africa refugia ( Figure 1B) . Such an expansion may have been favored by the start of a warmer and less arid period in Africa 130,000-70,000 years ago [29] . This ''out-of-Africa event'' would have occurred much later than the initial lion expansion through Eurasia based on fossils (,500,000 years ago) [3] . It is likely that multiple lion expansions occurred in the Pleistocene, as occurred with humans [21] .