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.

Seroprevalence studies indicate that FIV Ple is endemic in eight of the 11 populations but absent from the Asian GIR lions in India and in Namibia and southern Botswana/Kalahari regions (NAM/ BOT-I) in Southwest Africa ( Figure 1B ). Phylogenetic analysis of the conserved pol-RT region in 117 FIV-infected lions depicted monophyletic lineages [15, 18] that affirm six distinct subtypes (A-F) that are distributed geographically in three distinct patterns ( Figure 4B ; Figure S4 ). First, multiple subtypes may circulate within the same population as exemplified by subtypes A, B and C all ubiquitous within the three Serengeti lion populations (SER-I, SER-II and SER-III) and subtypes A and E within lions of Botswana (BOT-II) ( Figure 4B and 4C and Figure S4 ). Second, unique FIV Ple subtypes may be restricted to one location as subtype F in Kenya, subtype E in Botswana (BOT-II), subtype C in Serengeti, and subtype D in Krugar Park ( Figure 4B and 4C and Figure S4 ). Third, intra-subtype strains cluster geographically, as shown by distinct clades within subtype A that were restricted to lions within Krugar Park, Botswana and Serengeti and within subtype B that corresponded to Uganda, Serengeti and Ngorongoro Crater lions ( Figure 4B and 4C and Figure S4 ).