Reconstructing the demographic history of orang‐utans using Approximate B ayesian Computation

Abstract

Investigating how different evolutionary forces have shaped patterns of DNA variation within and among species requires detailed knowledge of their demographic history. O rang‐utans, whose distribution is currently restricted to the S outh‐ E ast A sian islands of B orneo ( P ongo pygmaeus ) and S umatra ( P ongo abelii ), have likely experienced a complex demographic history, influenced by recurrent changes in climate and sea levels, volcanic activities and anthropogenic pressures. Using the most extensive sample set of wild orang‐utans to date, we employed an Approximate B ayesian Computation ( ABC ) approach to test the fit of 12 different demographic scenarios to the observed patterns of variation in autosomal, X ‐chromosomal, mitochondrial and Y ‐chromosomal markers. In the best‐fitting model, Sumatran orang‐utans exhibit a deep split of populations north and south of L ake T oba, probably caused by multiple eruptions of the T oba volcano. In addition, we found signals for a strong decline in all S umatran populations ~24 ka, probably associated with hunting by human colonizers. In contrast, B ornean orang‐utans experienced a severe bottleneck ~135 ka, followed by a population expansion and substructuring starting ~82 ka, which we link to an expansion from a glacial refugium. We showed that orang‐utans went through drastic changes in population size and connectedness, caused by recurrent contraction and expansion of rainforest habitat during Pleistocene glaciations and probably hunting by early humans. Our findings emphasize the fact that important aspects of the evolutionary past of species with complex demographic histories might remain obscured when applying overly simplified models.

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