Genetic Divergence of Orangutan Subspecies (Pongo pygmaeus) Yun-wu Zhang, 1,2 Oliver A. Ryder, 1 Ya-ping Zhang 2 1 Center for Reproduction of Endangered Species, Zoological Society of San Diego, San Diego, CA 92112, USA 2 Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China Received: 13 June 2000 / Accepted: 30 January 2000 Abstract. Microsatellites and mitochondrial DNA se- quences were studied for the two subspecies of orangu- tans (Pongo pygmaeus), which are located in Borneo (P. p. pygmaeus) and Sumatra (P. p. abelii), respectively. Both subspecies possess marked genetic diversity. Ge- netic subdivision was identified within the Sumatran or- angutans. The genetic differentiation between the two subspecies is highly significant for ND5 region but not significant for 16s rRNA or microsatellite data by exact tests, although F ST estimates are highly significant for these markers. Divergence time between the two subspe- cies is approximately 2.3 ± 0.5 million years ago (MYA) estimated from our data, much earlier than the isolation of their geological distribution. Neither subspecies un- derwent a recent bottleneck, though the Sumatran sub- species might have experienced expansion approxi- mately 82,000 years ago. The estimated effective population sizes for both subspecies are on the order of 10 4 . Our results contribute additional information that may be interpreted in the context of orangutan conser- vation efforts. Key words: Orangutan — Genetic diversity — Ge- netic differentiation — mtDNA-Microsatellites. Introduction The orangutan, Pongo pygmaeus, is the only extant non- African great ape species. The current wild populations of orangutan exist only in the islands of Borneo and Sumatra, although the fossils of orangutans have been found in sites widespread throughout Southeast Asia (Smith and Pilbeam 1980), documenting a previously wider distribution. In the wild, the species has become severely threatened because of poaching and habitat de- struction. It is estimated that populations in the wild may have declined by as much as 30–50% between 1983 and 1993 (Sodaro 1997). Traditionally, the two island populations are regarded as two subspecies: Pongo pygmaeus pygmaeus (Lin- naeus, 1760) on Borneo and P. p. abelii (Lesson, 1827) on Sumatra, based primarily on their distinctive morpho- logical and behavioral characteristics (Groves 1971; Rijksen 1978; Nowak 1991; Demitros 1997). The two subspecies differ cytogenetically by a pericentric inver- sion of chromosome 2, and this difference has been used as an index of subspecies for captivity management (Seuanez et al. 1979; Ryder and Chemnick 1993). How- ever, molecular genetic data from protein electrophoresis (Bruce and Ayala 1979), DNA hybridization (Caccone and Powell 1989), isozyme, two-dimensional electropho- resis (Janczewski et al. 1990), mtDNA-RFLP, mtDNA sequences, and minisatellites (Ferris et al. 1981; Ryder and Chemnick 1993; Xu and Arnason 1996a; Zhi et al. 1996; Muir et al. 2000) have demonstrated that the dif- ferences between the two subspecies are almost the same as or even higher than those between recognized species, e.g., chimpanzee (Pan troglodytes) vs. bonobo (Pan pa- niscus), horse (Equus caballus) vs. donkey (Equus asi- nus), etc. Some authors suggest the two orangutan sub- species should be elevated to species status (Xu and Correspondence to: O. A. Ryder; E-mail: oryder@ucsd.edu J Mol Evol (2001) 52:516–526 DOI: 10.1007/s002390010182 © Springer-Verlag New York Inc. 2001