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

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 FST = 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

Standardised residuals for large prey biomass (LSU/100 km²) categories per Management Zone.

<p>Standardised residuals for large prey biomass (LSU/100 km²) categories per Management Zone.</p

Percentage small prey biomass.

<p>Map of the distribution of the percentage small prey biomass across the Conservation - and Agricultural Zones. The percentage was calculated from the total available biomass of small prey and small livestock consisting of sheep (<i>Ovis</i> spp.) and goats (<i>Capra hircus</i>).</p

Typical large African carnivore prey species occurring in Botswana used in the biomass analysis with their corresponding body weight (kg) and Large Stock Unit (LSU) conversion.

<p>Typical large African carnivore prey species occurring in Botswana used in the biomass analysis with their corresponding body weight (kg) and Large Stock Unit (LSU) conversion.</p

Land use zones in Botswana.

<p>Map of the two main land use zones: the Conservation Zones (green colours) consisting of protected areas and Wildlife Management Areas, and the Agricultural Zones (brown colours) consisting of communal grazing land, farms used mainly for livestock production and limited crop production, game ranches, and mining - and residential areas.</p

Standardised residuals for the presence/absence of large livestock (cattle, horses and donkeys) and small livestock (goats and sheep) per Management Zone.

<p>Standardised residuals for the presence/absence of large livestock (cattle, horses and donkeys) and small livestock (goats and sheep) per Management Zone.</p

Criteria applied to distinguish between the different categories of large – and small prey biomass.

<p>Criteria applied to distinguish between the different categories of large – and small prey biomass.</p

Large prey biomass.

<p>Map of the distribution of large prey biomass across the Conservation - and Agricultural Zones. Large prey species refers to wild ungulate species weighing >60 kg and occurring in Botswana that are typical prey for lions (<i>Panthera leo</i>), and includes warthog and ostrich but excludes atypical prey such as elephants.</p

Standardised residuals for small prey biomass (LSU/100 km²) categories per Management Zone.

<p>Standardised residuals for small prey biomass (LSU/100 km²) categories per Management Zone.</p

Calculated chi square value, degrees of freedom (df), adjusted α value and the chi square test statistic value for the six contingency tables.

<p>*The α value was adjusted for six comparisons following the Sequential Bonferroni procedure <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0100202#pone.0100202-Quinn1" target="_blank">[34]</a>.</p