A Novel SNP Genotyping Technique to Determine Orangutan Relatedness and Genetic Diversity at Camp Leakey in Tanjung Puting, Central Kalimantan

Genetic studies of dispersal patterns in wild populations of orangutans (Pongo spp.) have sought to confirm behavioral observations that female orangutans tend to stay near their natal range while males disperse. In order to genotype a previously unsampled wild population of endangered orangutans at Tanjung Puting National Park I developed novel application of a methyl based magnetic capture for enrichment of fecal DNA and commercial human targeted single nucleotide polymorphism (SNP) microarray technology. I confirmed results of this new genotyping technique through standard microsatellite short tandem repeat (STR) micro-capillary genotyping. I estimate genetic diversity and relatedness (r) for 32 (21 female and 9 male) wild orangutans at the Camp Leakey Study Site. I successfully isolated 125 known human SNP loci (0.08% of those targeted) which hybridized orangutan DNA on the human targeted Illumina Infinium QC array. Average relatedness within the population, estimated from our combo SNP/STR dataset using TrioML estimator, is at a level between half and first cousins (r = .082), and I found no significant difference of r between males and females. All males and females had relatives within the study site but paternity was not assigned to any potential fathers sampled. Results indicate all sampled males and females are from the local population. High and near equal relatedness for both sexes in this group, combined with a low number of males sampled, suggests conditions for the potential for deep inbreeding. This is a particular concern because the population is at risk from further isolation through habitat fragmentation