Identification of Diagnostic Mitochondrial DNA Single Nucleotide Polymorphisms Specific to Sumatran Orangutan (Pongo abelii) Populations

Puji Rianti (Primate Research Center, Bogor Agricultural University, Bogor 16151 Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Darmaga Campus, Bogor 16680)
Dyah Perwitasari-Farajallah (Primate Research Center, Bogor Agricultural University, Bogor 16151 Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Darmaga Campus, Bogor 16680)
Dondin Sajuthi (Primate Research Center, Bogor Agricultural University, Bogor 16151 Faculty of Veterinary, Bogor Agricultural University, Darmaga Campus, Bogor 16680)
Joko Pamungkas (Primate Research Center, Bogor Agricultural University, Bogor 16151 Faculty of Veterinary, Bogor Agricultural University, Darmaga Campus, Bogor 16680)
Alexander Nater (Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden Anthropological Institute and Museum, University of Zürich, CH-8057 Zürich, Switzerland)
Michael Krützen (Anthropological Institute and Museum, University of Zürich, CH-8057 Zürich, Switzerland)

HAYATI Journal of Biosciences
Vol. 22 No. 4 (2015): October 2015

The hypervariable region I of mitochondrial DNA has frequently been used to distinguish among populations, in particular in species with strong female philopatry. In such cases, populations are expected to diverge rapidly for hypervariable region I markers because of the smaller effective population size and thus increased genetic drift. This rapid divergence leads to the accumulation of mutations exclusively found in one population, which may serve as diagnostic single nucleotide polymorphisms (SNPs). To date, diagnostic SNPs distinctive to Sumatran orangutan populations have not yet been described. However, given the continuously declining numbers of Sumatran orangutans, this information can be vital for effective conservation measures, especially regarding reintroductions of orangutans in rehabilitation centers. Phylogenetic analyses of 54 samples of Sumatran orangutans from nine sampling sites with good provenance, we found five major clades and a total of 20 haplotypes. We propose a total of 52 diagnostic SNPs that are specific to Sumatran orangutan populations. Data can be used to develop restriction fragment length polymorphism assays to carry out genetic assignments using basic laboratory equipment to assign Sumatran orangutan to their population of origin.