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

Riashna Sithaldeen,Rebecca Rogers Ackermann,Jacqueline M. Bishop,Robert Guralnick

doi:10.1371/journal.pone.0123207

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.

Highlights

Large-scale environmental change during the Plio-Pleistocene influenced the evolutionary history of many animal lineages in Africa
To explore our central tenet that chacma baboon populations were repeatedly restricted to refugia during periods of regional climate cycling through the late Pleistocene, we analysed the spatial distribution of genetic variation and inferred more recent demographic change in the PU and p-value griseipes (PG) clades using data from the mitochondrial D-loop
Patterns of diversification in many lineages suggest significant demographic changes that correspond with these cycles, closely approximating proposed habitat and landscape barriers to gene flow, with diverse taxa retreating into refugia until climate amelioration

Summary

Introduction

Large-scale environmental change during the Plio-Pleistocene influenced the evolutionary history of many animal lineages in Africa. Olivacea/obscura complex [1] and the forest robins, family Muscicapidae [2], Africa’s herpetofauna including chameleons e.g. the Bradypodion complex [3] and snakes e.g. Bitis arietans [4] and a large number of mammalian lineages including bovids e.g. Alcelaphus buselaphus [5], primates e.g. Gorilla gorilla [6]; rodents e.g.the Heliophobius argenteocinereus complex [7], afrotheria e.g. Elephantulus edwardii [8]; bats e.g. the Rhinolophus hildebrandtii complex [9] and Rhinolophus darlingi complex [10], and suids e.g. Phacochoerus africanus [11] These studies provide compelling evidence for the key roles of both climate and tectonics in the evolution of Africa’s vast faunal diversity. We use a large mitochondrial dataset sampled across the broad southern African range of chacma baboons sensu lato to evaluate the evolutionary history of this charismatic primate (Fig 1); we interpret our findings in light of current models of Pleistocene environmental change in the region. Our results recover different evolutionary histories for these lineages and highlight the formative role of the Kalahari Desert in shaping the genetic architecture and evolutionary trajectories of these taxa

Ethics statement

Results & Discussion

Conclusions and Taxonomic Implications