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.

Relative to East Africa, Southern lions have a slightly more recent mtDNA coalescence. Lineage II, found in NAM, BOT-II and KRU has an estimated coalescence of 169,000 years (95% CI: 34,000-304,000) and the more widespread lineage IV found in the Southern populations of BOT-I, BOT-II and KRU as well as the Eastern populations of SER (I, II, and III), NGC and UGA, coalesces ,101,000 years ago (95% CI: 11,000-191,000). However, the similar levels of nDNA genetic diversity, the occurrence of an exclusively Southern mtDNA lineage II and highly divergent FIV Ple subtypes, FIV Ple subtype D found only in KRU and subtype E exclusive to BOT-II, suggests that both East and Southern Africa were important refugia for lions during the Pleistocene. Therefore, the co-occurrence of divergent mtDNA haplotypes (6 to 10 mutations; Figure 1B and 1C) in southern populations may be the consequence of further isolation within refugia during colder climatic periods. Contemporary fragmentation of lion populations could further explain the results of nested-clade phylogeographical analysis (NCPA [27] ) ( Figure S5 ), which inferred restricted gene flow with isolation-by-distance between mtDNA haplotypes H9 (BOT-II) and H10 (KRU) (x 2 = 10.00, P = 0.0200), between haplotypes H1 (BOT-II/NAM) and H2 (KRU) (x 2 = 71.00, P#0.0001), and between haplotypes H9-H10 (BOT-II/KRU) and haplotypes H11-H12 (BOT-I/KRU/SER/NGC/UGA) (x 2 = 187.83, P#0.0001).