J Med Primatol 2000: 29: 57–62 Printed in Ireland - all rights resered. Microsatellite DNA variation in Bornean orangutans (Pongo pygmaeus ) Warren KS, Nijman IJ, Lenstra JA, Swan RA, Heriyanto, den Boer M. Microsatellite DNA variation in Bornean orangutans (Pongo pyg - maeus ). J Med Primatol 2000; 29:57–62. © Munksgaard, Copenhagen Abstract: Orangutans (Pongo pygmaeus ) on the islands of Borneo and Sumatra are considered two separate subspecies. However, the genetic relationships between isolated populations on Borneo are not clear. This study determined the extent of variation within the Bornean sub- species of orangutan, using microsatellite DNA analysis. Blood samples were collected from 96 individuals of known origin from East, West and Central Kalimantan. Human microsatellite primer pairs located at human map position D2S141, D4S431, D11S925, D16S420 and D17S791 were suitable for use in primates. D4S431 appeared monomorphic for all orangutans. In three cases (D2S141 East and West and D16S420 West), a highly significant excess of homozygous allele frequencies was detected, but with other primer pairs no signifi- cant difference in allele frequencies occurred. We conclude that the divergence between the different populations on Borneo is less than the variation within the populations. There was also evidence that inbreed- ing occurred within the populations. K.S. Warren 1,2 , I.J. Nijmian 3 , J.A. Lenstra 3 , R.A. Swan 1 , Heriyanto 2,4 , M. den Boer 5 1 Division of Veterinary and Biomedical Science, Murdoch University, Perth, Australia, 2 Wanariset Orangutan Reintroduction Project, P.O. Box 319, Balikpapan, 76103, East Kalimantan, Indonesia, 3 Institute of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Yalelaan 1, 3584 CL, Utrecht University, The Netherlands, 4 Department of Animal Quarantine, P.O. Box 423, Balikpapan, 76103 East Kalimantan, Indonesia, 5 Weverstraat 124, 6862, DT, Oosterbeek, The Netherlands Key words: conservation – genetic variation – primates Accepted October 4, 1999. Dr. Kristin Warren, c/- Division of Veterinary and Biomedical Sciences, Murdoch Univer- sity, South Street, 6150, Western Australia, Australia Funding: The financial support provided by BHP-Minerals Melbourne and the Merck Foundation is greatly appreciated. Introduction Orangutans (Pongo pygmaeus ) are found in the wild only on the islands of Borneo and Sumatra. Wild populations have declined in the past three decades and orangutans are now classified as an endangered species. Bornean and Sumatran orangutans are considered as different subspecies and perhaps even different species [18, 19]. The subspecies classification is based on a pericentric inversion of chromosome 2 [5, 15]. More recently, this was substantiated by mitochondrial DNA re- striction fragment length polymorphisms, nuclear minisatellite and mitochondrial 16S ribosomal RNA sequence analysis [19]. It has been argued that local populations have their own genetic iden- tities that have been created by long periods of isolation [4, 6, 10]. Rijksen [10] identified two types of Sumatran orangutans and Selenka [14] de- scribed eight Bornean subtypes. However, early descriptions of morphological variations may have reflected different age groups or clines in the popu- lation. On the other hand, Groves et al. [6] iden- tified significant differences in anatomical skull structure between three of Borneo’s geographically isolated populations and concluded that orangutans from Southwest Kalimantan were more similar to orangutans from Sumatra than to other populations in Borneo. The Bornean orangutan is found throughout Borneo in Kali- mantan, Sabah and Sarawak, but no wild orangutans are found in Brunei. The extent of intra-subspecific variation within the Bornean population has been identified as re- quiring further study [6, 8, 12, 16]. An initial study by Zhi et al. [19] concluded that there was little genetic variation among isolated populations of orangutans in Borneo. However, this study used samples from only five individuals from Kaliman- tan, where most of the wild Bornean orangutan population occurs. In the present study, we examined samples using microsatellite analysis from orangutans confiscated in different provinces of Kalimantan. Microsatel- 57