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The evolutionary dynamics of the lion Panthera leo revealed by host and viral population genomics.

Antunes A, Troyer JL, Roelke ME, Pecon-Slattery J, Packer C, Winterbach C, Winterbach H, Hemson G, Frank L, Stander P, Siefert L, Driciru M, Funston PJ, Alexander KA, Prager KC, Mills G, Wildt D, Bush M, O'Brien SJ, Johnson WE - PLoS Genet. (2008)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland, United States of America.

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.

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Population structure analyses in lions.(A) Bayesian population assignment test [22] of the 357 lions using 24 nDNA loci (ADA, TF, and 22 microsatellites) and mtDNA data, and considering K = 11 (11 populations). (B) Three-dimensional factorial correspondence analysis [23] (FCA) based on the 24 nDNA loci genotypes in the 357 lions. Axe 1, 2, and 3 represent 49.90% of the genetic variation observed. (C) FCA representation excluding the GIR lions. Axe 1, 2, and 3 represent 51.35% of the genetic variation observed. (D) FCA representation considering only the SER lions supportive of a three distinct population clusters subdivision (SER-I, SER-II, and SER-III).
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pgen-1000251-g002: Population structure analyses in lions.(A) Bayesian population assignment test [22] of the 357 lions using 24 nDNA loci (ADA, TF, and 22 microsatellites) and mtDNA data, and considering K = 11 (11 populations). (B) Three-dimensional factorial correspondence analysis [23] (FCA) based on the 24 nDNA loci genotypes in the 357 lions. Axe 1, 2, and 3 represent 49.90% of the genetic variation observed. (C) FCA representation excluding the GIR lions. Axe 1, 2, and 3 represent 51.35% of the genetic variation observed. (D) FCA representation considering only the SER lions supportive of a three distinct population clusters subdivision (SER-I, SER-II, and SER-III).

Mentions: Levels of population subdivision among lions were assessed using microsatellite and sequencing data. Eleven groups were identified using Bayesian analyses [22] and three-dimensional factorial correspondence analyses [23] (Figure 2; Table S3). Most clusters represented geographically circumscribed populations: Namibia (Nam), Kruger National Park (Kru), Ngorongoro Crater (Ngc), Kenya (Ken), Uganda (Uga), and Gir (Gir). Two distinct clusters were found in Botswana, Bot-I that included lions from southern Botswana and Kalahari (South Africa) (Fk = 0.24) and Bot-II found exclusively in northern Botswana (Fk = 0.18). Surprisingly, three distinct clusters were found in a single geographical locale (approximately 60×40 km square) in the large panmyctic population of the Serengeti National Park (Ser-I/Ser-II/Ser-III) (Fk = 0.18, 0.21, and 0.15, respectively).


The evolutionary dynamics of the lion Panthera leo revealed by host and viral population genomics.

Antunes A, Troyer JL, Roelke ME, Pecon-Slattery J, Packer C, Winterbach C, Winterbach H, Hemson G, Frank L, Stander P, Siefert L, Driciru M, Funston PJ, Alexander KA, Prager KC, Mills G, Wildt D, Bush M, O'Brien SJ, Johnson WE - PLoS Genet. (2008)

Population structure analyses in lions.(A) Bayesian population assignment test [22] of the 357 lions using 24 nDNA loci (ADA, TF, and 22 microsatellites) and mtDNA data, and considering K = 11 (11 populations). (B) Three-dimensional factorial correspondence analysis [23] (FCA) based on the 24 nDNA loci genotypes in the 357 lions. Axe 1, 2, and 3 represent 49.90% of the genetic variation observed. (C) FCA representation excluding the GIR lions. Axe 1, 2, and 3 represent 51.35% of the genetic variation observed. (D) FCA representation considering only the SER lions supportive of a three distinct population clusters subdivision (SER-I, SER-II, and SER-III).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2572142&req=5

pgen-1000251-g002: Population structure analyses in lions.(A) Bayesian population assignment test [22] of the 357 lions using 24 nDNA loci (ADA, TF, and 22 microsatellites) and mtDNA data, and considering K = 11 (11 populations). (B) Three-dimensional factorial correspondence analysis [23] (FCA) based on the 24 nDNA loci genotypes in the 357 lions. Axe 1, 2, and 3 represent 49.90% of the genetic variation observed. (C) FCA representation excluding the GIR lions. Axe 1, 2, and 3 represent 51.35% of the genetic variation observed. (D) FCA representation considering only the SER lions supportive of a three distinct population clusters subdivision (SER-I, SER-II, and SER-III).
Mentions: Levels of population subdivision among lions were assessed using microsatellite and sequencing data. Eleven groups were identified using Bayesian analyses [22] and three-dimensional factorial correspondence analyses [23] (Figure 2; Table S3). Most clusters represented geographically circumscribed populations: Namibia (Nam), Kruger National Park (Kru), Ngorongoro Crater (Ngc), Kenya (Ken), Uganda (Uga), and Gir (Gir). Two distinct clusters were found in Botswana, Bot-I that included lions from southern Botswana and Kalahari (South Africa) (Fk = 0.24) and Bot-II found exclusively in northern Botswana (Fk = 0.18). Surprisingly, three distinct clusters were found in a single geographical locale (approximately 60×40 km square) in the large panmyctic population of the Serengeti National Park (Ser-I/Ser-II/Ser-III) (Fk = 0.18, 0.21, and 0.15, respectively).

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland, United States of America.

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.

Show MeSH
Related in: MedlinePlus