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

Abstract

The lion Panthera leo is one of the world's most charismatic carnivores and is one of Africa's key predators. Here, we used a large dataset from 357 lions comprehending 1.13 megabases of sequence data and genotypes from 22 microsatellite loci to characterize its recent evolutionary history. Patterns of molecular genetic variation in multiple maternal (mtDNA), paternal (Y-chromosome), and biparental nuclear (nDNA) genetic markers were compared with patterns of sequence and subtype variation of the lion feline immunodeficiency virus (FIVPle), a lentivirus analogous to human immunodeficiency virus (HIV). In spite of the ability of lions to disperse long distances, patterns of lion genetic diversity suggest substantial population subdivision (mtDNA ΦST = 0.92; nDNA F ST = 0.18), and reduced gene flow, which, along with large differences in sero-prevalence of six distinct FIVPle subtypes among lion populations, refute the hypothesis that African lions consist of a single panmictic population. Our results suggest that extant lion populations derive from several Pleistocene refugia in East and Southern Africa (∼324,000–169,000 years ago), which expanded during the Late Pleistocene (∼100,000 years ago) into Central and North Africa and into Asia. During the Pleistocene/Holocene transition (∼14,000–7,000 years), another expansion occurred from southern refugia northwards towards East Africa, causing population interbreeding. In particular, lion and FIVPle variation affirms that the large, well-studied lion population occupying the greater Serengeti Ecosystem is derived from three distinct populations that admixed recently.

A genetically distinct lion (Panthera leo) population from Ethiopia

“…However, given the limited information on the phenotypes and especially genetics of now extinct populations, appreciable genetic diversity may already have been lost in the lion. A substantial loss of genetic diversity is in fact quite likely for lions as patterns of lion genetic diversity suggest substantial population subdivision and reduced gene flow (Antunes et al 2008), highlighting the importance of preserving local lion populations in decline.…”

“…In this study, we compared, based on microsatellite and mitochondrial DNA data, the lions from Addis Ababa to several well-characterized lion populations representative of their extant range in the wild. Both mitochondrial DNA and microsatellite data tend to cluster lions geographically and therefore allow to some extent for approximation of their geographical origin (Driscoll 1998;Dubach et al 2005;Barnett et al 2006a;Antunes et al 2008;Bertola et al 2011). However, mitochondrial data as a single, strictly maternally inherited locus are easily affected by genetic introgression from translocated females and are, as shown by the network analysis (Fig.…”

The size of savannah Africa: a lion’s (Panthera leo) view

“…In view of reported declines, it still does not qualify as a stronghold. Populations in these regions are genetically distinct (Antunes et al 2008;Bertola et al 2011). Keeping these populations from extinction will require conservation efforts well beyond the dismal performance of the region's other protected areas.…”

Three-dimensional cranial ontogeny in pantherines (Panthera leo,P. onca,P. pardus,P. tigris; Carnivora:, Felidae)

“…P. leo was present in Africa from the Late Pliocene, in the Middle Pleistocene it migrated to Europe and by the Late Pleistocene had a wide intercontinental distribution (Antunes et al, 2008). The P. onca fossil record is limited to the Pleistocene of North and South America.…”