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Pleistocene aridification cycles shaped the contemporary genetic architecture of Southern African baboons.

Sithaldeen R, Ackermann RR, Bishop JM - PLoS ONE (2015)

Bottom Line: Our analysis highlights a period of continuous population growth beginning in the Middle to Late Pleistocene in both the ursinus and the PG2 griseipes lineages.All three clades identified in the study then enter a state of declining population size (Nef) through to the Holocene; this is particularly marked in the last 20,000 years, most likely coincident with the Last Glacial Maximum.The pattern recovered here conforms to expectations based on the dynamic regional climate trends in southern Africa through the Pleistocene and provides further support for complex patterns of diversification in the region's biodiversity.

View Article: PubMed Central - PubMed

Affiliation: Department of Archaeology, University of Cape Town, Private Bag X3, Rondebosch 7701, South Africa.

ABSTRACT
Plio-Pleistocene environmental change influenced the evolutionary history of many animal lineages in Africa, highlighting key roles for both climate and tectonics in the evolution of Africa's faunal diversity. Here, we explore diversification in the southern African chacma baboon Papio ursinus sensu lato and reveal a dominant role for increasingly arid landscapes during past glacial cycles in shaping contemporary genetic structure. Recent work on baboons (Papio spp.) supports complex lineage structuring with a dominant pulse of diversification occurring 1-2Ma, and yet the link to palaeoenvironmental change remains largely untested. Phylogeographic reconstruction based on mitochondrial DNA sequence data supports a scenario where chacma baboon populations were likely restricted to refugia during periods of regional cooling and drying through the Late Pleistocene. The two lineages of chacma baboon, ursinus and griseipes, are strongly geographically structured, and demographic reconstruction together with spatial analysis of genetic variation point to possible climate-driven isolating events where baboons may have retreated to more optimum conditions during cooler, drier periods. Our analysis highlights a period of continuous population growth beginning in the Middle to Late Pleistocene in both the ursinus and the PG2 griseipes lineages. All three clades identified in the study then enter a state of declining population size (Nef) through to the Holocene; this is particularly marked in the last 20,000 years, most likely coincident with the Last Glacial Maximum. The pattern recovered here conforms to expectations based on the dynamic regional climate trends in southern Africa through the Pleistocene and provides further support for complex patterns of diversification in the region's biodiversity.

No MeSH data available.


Related in: MedlinePlus

Spatial genetic diversity and population structure in chacma baboons across southern Africa.(a) Rooted NeighbourNet network for ursinus and griseipes chacma lineages together with Papio cynacephalus and P. kindae. Numerous recent studies based on mtDNA reveal griseipes as sister to these two more northerly species. (b) Bayesian analysis of spatial genetic structure reveals distinct geographic clustering in both lineages. PG1—blue; PG2—green; PU1—red; PU2—yellow; PU3—orange. (c) Landscape plots of genetic diversity across the sampling distributions of the PG (left) and PU (right) clades in southern Africa; the plots are oriented north-south.
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pone.0123207.g005: Spatial genetic diversity and population structure in chacma baboons across southern Africa.(a) Rooted NeighbourNet network for ursinus and griseipes chacma lineages together with Papio cynacephalus and P. kindae. Numerous recent studies based on mtDNA reveal griseipes as sister to these two more northerly species. (b) Bayesian analysis of spatial genetic structure reveals distinct geographic clustering in both lineages. PG1—blue; PG2—green; PU1—red; PU2—yellow; PU3—orange. (c) Landscape plots of genetic diversity across the sampling distributions of the PG (left) and PU (right) clades in southern Africa; the plots are oriented north-south.

Mentions: Splitstree networks for the PG and PU D-loop lineages (Fig 5A) indicate two distinct clades in PG and three in PU. Estimates of genetic variation across these clades are reported in Table 1. Spatial analysis using BAPS (Fig 5B) together with AMOVA (Table 2) both support clear geographic structuring in chacma baboons and provide good support for strong regional phylogeographic structure. The AMOVA analysis revealed significant population genetic differentiation among clades, with ~45% of the variation distributed among ‘groups’ (PU and PG), and ~31% among ‘populations’ i.e. the five clades. Given the effects of climate cycling on vegetation in this region it is most likely that differentiation among chacma lineages occurred via drift, most likely via isolation and changing population sizes. Landscape visualization of genetic distance (reflecting underlying genetic diversity; Table 1) generated in Alleles in Space (Fig 5C) also suggest diverse histories in chacma baboons. In the PG lineage, high genetic distance (diversity) occurs in the west and east, associated with the distribution of the PG1 and 2 clades respectively, while in the PU lineage, the highest genetic diversity occurs in the PU1 and 2 clades, which together with PG1 border the Kalahari Desert. When considered together, these plots are most likely consistent with a model of contraction into vegetated refugia and subsequent recolonization of the surrounding landscape.


Pleistocene aridification cycles shaped the contemporary genetic architecture of Southern African baboons.

Sithaldeen R, Ackermann RR, Bishop JM - PLoS ONE (2015)

Spatial genetic diversity and population structure in chacma baboons across southern Africa.(a) Rooted NeighbourNet network for ursinus and griseipes chacma lineages together with Papio cynacephalus and P. kindae. Numerous recent studies based on mtDNA reveal griseipes as sister to these two more northerly species. (b) Bayesian analysis of spatial genetic structure reveals distinct geographic clustering in both lineages. PG1—blue; PG2—green; PU1—red; PU2—yellow; PU3—orange. (c) Landscape plots of genetic diversity across the sampling distributions of the PG (left) and PU (right) clades in southern Africa; the plots are oriented north-south.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4430493&req=5

pone.0123207.g005: Spatial genetic diversity and population structure in chacma baboons across southern Africa.(a) Rooted NeighbourNet network for ursinus and griseipes chacma lineages together with Papio cynacephalus and P. kindae. Numerous recent studies based on mtDNA reveal griseipes as sister to these two more northerly species. (b) Bayesian analysis of spatial genetic structure reveals distinct geographic clustering in both lineages. PG1—blue; PG2—green; PU1—red; PU2—yellow; PU3—orange. (c) Landscape plots of genetic diversity across the sampling distributions of the PG (left) and PU (right) clades in southern Africa; the plots are oriented north-south.
Mentions: Splitstree networks for the PG and PU D-loop lineages (Fig 5A) indicate two distinct clades in PG and three in PU. Estimates of genetic variation across these clades are reported in Table 1. Spatial analysis using BAPS (Fig 5B) together with AMOVA (Table 2) both support clear geographic structuring in chacma baboons and provide good support for strong regional phylogeographic structure. The AMOVA analysis revealed significant population genetic differentiation among clades, with ~45% of the variation distributed among ‘groups’ (PU and PG), and ~31% among ‘populations’ i.e. the five clades. Given the effects of climate cycling on vegetation in this region it is most likely that differentiation among chacma lineages occurred via drift, most likely via isolation and changing population sizes. Landscape visualization of genetic distance (reflecting underlying genetic diversity; Table 1) generated in Alleles in Space (Fig 5C) also suggest diverse histories in chacma baboons. In the PG lineage, high genetic distance (diversity) occurs in the west and east, associated with the distribution of the PG1 and 2 clades respectively, while in the PU lineage, the highest genetic diversity occurs in the PU1 and 2 clades, which together with PG1 border the Kalahari Desert. When considered together, these plots are most likely consistent with a model of contraction into vegetated refugia and subsequent recolonization of the surrounding landscape.

Bottom Line: Our analysis highlights a period of continuous population growth beginning in the Middle to Late Pleistocene in both the ursinus and the PG2 griseipes lineages.All three clades identified in the study then enter a state of declining population size (Nef) through to the Holocene; this is particularly marked in the last 20,000 years, most likely coincident with the Last Glacial Maximum.The pattern recovered here conforms to expectations based on the dynamic regional climate trends in southern Africa through the Pleistocene and provides further support for complex patterns of diversification in the region's biodiversity.

View Article: PubMed Central - PubMed

Affiliation: Department of Archaeology, University of Cape Town, Private Bag X3, Rondebosch 7701, South Africa.

ABSTRACT
Plio-Pleistocene environmental change influenced the evolutionary history of many animal lineages in Africa, highlighting key roles for both climate and tectonics in the evolution of Africa's faunal diversity. Here, we explore diversification in the southern African chacma baboon Papio ursinus sensu lato and reveal a dominant role for increasingly arid landscapes during past glacial cycles in shaping contemporary genetic structure. Recent work on baboons (Papio spp.) supports complex lineage structuring with a dominant pulse of diversification occurring 1-2Ma, and yet the link to palaeoenvironmental change remains largely untested. Phylogeographic reconstruction based on mitochondrial DNA sequence data supports a scenario where chacma baboon populations were likely restricted to refugia during periods of regional cooling and drying through the Late Pleistocene. The two lineages of chacma baboon, ursinus and griseipes, are strongly geographically structured, and demographic reconstruction together with spatial analysis of genetic variation point to possible climate-driven isolating events where baboons may have retreated to more optimum conditions during cooler, drier periods. Our analysis highlights a period of continuous population growth beginning in the Middle to Late Pleistocene in both the ursinus and the PG2 griseipes lineages. All three clades identified in the study then enter a state of declining population size (Nef) through to the Holocene; this is particularly marked in the last 20,000 years, most likely coincident with the Last Glacial Maximum. The pattern recovered here conforms to expectations based on the dynamic regional climate trends in southern Africa through the Pleistocene and provides further support for complex patterns of diversification in the region's biodiversity.

No MeSH data available.


Related in: MedlinePlus