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 (<em>Pongo </em>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 (<em>r</em>) 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 <em>Illumina Infinium QC</em> array. Average relatedness within the population, estimated from our combo SNP/STR dataset using <em>TrioML</em> estimator, is at a level between half and first cousins (r = .082), and I found no significant difference of <em>r</em> 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.<strong></strong>

Name thesis:degree_name

Master of Science (MS)

Discipline thesis:degree_discipline

Primate Behavior

Year dc:date.available

2019

Author dc:creator

• Linsky, Ruth Ella

Contributors dc:contributor

• Lori K. Sheeran
• Biruté Mary Galdikas
• Joeseph Lorenz

• pongo
• genotyping
• Tanjung Puting
• relatedness
• Borneo
• SNP
• Behavior and Ethology
• Genetics
• Natural Resources and Conservation
• Population Biology

Language dc:language

English

Repository record dc:identifier

https://digitalcommons.cwu.edu/etd/1218

OAI identifier oai:identifier

oai:digitalcommons.cwu.edu:etd-2187