title: 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 (FIV(Ple)), 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 Phi(ST) = 0.92; nDNA F(ST) = 0.18), and reduced gene flow, which, along with large differences in sero-prevalence of six distinct FIV(Ple) 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 ( approximately 324,000-169,000 years ago), which expanded during the Late Pleistocene ( approximately 100,000 years ago) into Central and North Africa and into Asia. During the Pleistocene/Holocene transition ( approximately 14,000-7,000 years), another expansion occurred from southern refugia northwards towards East Africa, causing population interbreeding. In particular, lion and FIV(Ple) variation affirms that the large, well-studied lion population occupying the greater Serengeti Ecosystem is derived from three distinct populations that admixed recently.
authors.affiliation: Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland, United States of America.
authors.forename: Agostinho
authors.initials: A
authors.lastname: Antunes
authors.forename: Jennifer L
authors.initials: JL
authors.lastname: Troyer
authors.forename: Melody E
authors.initials: ME
authors.lastname: Roelke
authors.forename: Jill
authors.initials: J
authors.lastname: Pecon-Slattery
authors.forename: Craig
authors.initials: C
authors.lastname: Packer
authors.forename: Christiaan
authors.initials: C
authors.lastname: Winterbach
authors.forename: Hanlie
authors.initials: H
authors.lastname: Winterbach
authors.forename: Graham
authors.initials: G
authors.lastname: Hemson
authors.forename: Laurence
authors.initials: L
authors.lastname: Frank
authors.forename: Philip
authors.initials: P
authors.lastname: Stander
authors.forename: Ludwig
authors.initials: L
authors.lastname: Siefert
authors.forename: Margaret
authors.initials: M
authors.lastname: Driciru
authors.forename: Paul J
authors.initials: PJ
authors.lastname: Funston
authors.forename: Kathy A
authors.initials: KA
authors.lastname: Alexander
authors.forename: Katherine C
authors.initials: KC
authors.lastname: Prager
authors.forename: Gus
authors.initials: G
authors.lastname: Mills
authors.forename: David
authors.initials: D
authors.lastname: Wildt
authors.forename: Mitch
authors.initials: M
authors.lastname: Bush
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: O'Brien
authors.forename: Warren E
authors.initials: WE
authors.lastname: Johnson
mesh_terms: D000349:Africa; D025041:Animal Migration; D000818:Animals; D001208:Asia; D004272:DNA, Mitochondrial / Q000235:genetics; D004279:DNA, Viral / Q000235:genetics; D019143:Evolution, Molecular; D014644:Genetic Variation; D023281:Genomics; D054884:Host-Pathogen Interactions; D016089:Immunodeficiency Virus, Feline / Q000145:classification / Q000235:genetics*; D008045:Lions / Q000145:classification / Q000235:genetics* / Q000821:virology*; D018895:Microsatellite Repeats; D008969:Molecular Sequence Data; D010802:Phylogeny; D011153:Population / Q000235:genetics
chemical_list: D004272:DNA, Mitochondrial; D004279:DNA, Viral