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.

A second, more recent lion expansion probably occurred at the Pleistocene/Holocene transition, this one from Southern Africa toward East Africa (M2- Figure 1A, Figure 3 ). This is reflected in the mtDNA linage IV, where haplotypes present in Southern lions are basal (older) to those found in the East. Overall, mtDNA population nucleotide diversity decreases from Southern to East Africa ( Figure 1B and 1C) , a finding supported by pairwise mismatch analysis [30] (raggedness, r = 0.086; P,0.001). The fixation of mtDNA haplotype H11 in BOT-I (otherwise fixed only in East Africa populations) suggests that the colonizing lions expanded northwards from the Kalahari Desert, which included bush, woodland and savannah habitats during the climatic fluctuations of the Pleistocene [31] . This expansion would have occurred relatively recently as the single rare tip mtDNA haplotype H12, found only in SER-I, is derived from the interior widespread haplotype H11 (,14,000-7,000 years; given one mtDNA substitution every 7,000 years; Table 1 ). This expansion is also supported by FIV Ple subtype A where haplotypes present in Southern lions (KRU and BOT-I) are basal to those found in the East (SER-I, SER-II and SER-III) and a decrease of nucleotidediversity of this FIV Ple subtype is observed from Southern (p = 0.15) to Eastern Africa (p = 0.03) ( Figure 3B ). Interestingly, a similar northward colonization process from Southern Africa has been suggested for some of the lion preys, namely the impala, greater kudu, and wildebeest [32, 33] .