Effects of Pleistocene glaciations and rivers on the population structure of Bornean orangutans ( Pongo pygmaeus )

Abstract

Sundaland, a tropical hotspot of biodiversity comprising Borneo and Sumatra among other islands, the Malay Peninsula, and a shallow sea, has been subject to dramatic environmental processes. Thus, it presents an ideal opportunity to investigate the role of environmental mechanisms in shaping species distribution and diversity. We investigated the population structure and underlying mechanisms of an insular endemic, the Bornean orangutan (Pongo pygmaeus). Phylogenetic reconstructions based on mtDNA sequences from 211 wild orangutans covering the entire range of the species indicate an unexpectedly recent common ancestor of Bornean orangutans 176 ka (95% highest posterior density, 72-322 ka), pointing to a Pleistocene refugium. High mtDNA differentiation among populations and rare haplotype sharing is consistent with a pattern of strong female philopatry. This is corroborated by isolation by distance tests, which show a significant correlation between mtDNA divergence and distance and a strong effect of rivers as barriers for female movement. Both frequency-based and Bayesian clustering analyses using as many as 25 nuclear microsatellite loci revealed a significant separation among all populations, as well as a small degree of male-mediated gene flow. This study highlights the unique effects of environmental and biological features on the evolutionary history of Bornean orangutans, a highly endangered species particularly vulnerable to future climate and anthropogenic change as an insular endemic.Asian great ape | genetic structure | radiation | geographical barriers | sociobehavioral barriers

The costs and benefits of flexibility as an expression of behavioural plasticity: a primate perspective

“…Two processes may serve to limit meaningful genetic differentiation. First, the population on Borneo has faced a near-extinction during the last glacial maximum between 60 and 20 kya, followed by expansion and substructuring during the subsequent warming and expansion of closed forests [35,36]. It is therefore not clear whether there was enough time for adaptation to arise, given the slow generation time of orang-utans of around 25 years [37].…”

Orangutan tool use and the evolution of technology

“…They are commonly subdivided into two species, the Sumatran Pongo abelii, and the Bornean Pongo pygmaeus (Xu & Arnason, 1996;Warren et al, 2001). The existing taxonomic subdivision of the three Bornean subspecies (P. p. pygmaeus, P. p. wurmbii and P. p. morio), described on the basis of morphological characteristics (Groves, 2001), however, does not adequately capture the genetic variation within this species (Arora et al, 2010).…”

Biogeographic distribution and metric dental variation of fossil and living orangutans (Pongo spp.)

“…(Wich et al 2008) have long been the focus of study by wildlife and conservation biologists both in their natural habitats and in captivity (Payne and Prudente 2010). In response to the dramatic climatic oscillations and environmental changes during the Quaternary period, the genus has had a very complex and dynamic evolutionary history in Asia since Early Pleistocene times, about 2 million years ago (Ma), as demonstrated in its diverse genetic (Xu and Arnason 1996;Muir et al 2000;Goossens et al 2009;Arora et al 2010;Natel et al 2014) and morphological features (Rijksen 1978;Röhrer-Ertl 1988;Schwartz 1988;Uchida 1998;van Schaik et al 2009), and reflected in its biogeographical and taxonomic aspects (Schwartz et al 1995;Vu 2001, 2002;Wang et al 2009;Zhao et al 2009;Yasamin et al 2013;Harrison et al 2014;Takai et al 2014;Wang et al 2014a;Filoux et al 2015). In certain parts of its prehistoric distribution range, Pongo shared the same general habitats with two other hominids: Gigantopithecus and/or hominins (Homo sp.…”