No abstract

Previous genetic studies of orangutans (Pongo spp.) have relied mainly upon mitochondrial DNA or microsatellite short tandem repeats (STR) for genomic genotyping analysis. Scientists have yet to take advantage of the genetic closeness of the great apes to humans for genomic analysis by using advanced techniques available for human genotyping. To genotype orangutans at Tanjung Puting National Park, we developed a novel combination of a methyl-based magnetic enrichment capture of genomic fecal DNA with genotyping on a human targeted single nucleotide polymorphism (SNP) microarray, and compared this to additional microsatellite (STR) micro-capillary genotyping. We successfully isolated 125 known human genomic SNP loci (0.08% of those targeted) which hybridized orangutan DNA on the human targeted Illumina Infinium QC array. We estimated genetic diversity and relatedness (r) using three estimators for a total of 32 (21 female and 9 male) wild orangutans at the Camp Leakey study site. Average TrioML relatedness within the sample, estimated from our combo SNP/STR dataset, was at a range consistent with half and first cousins (r = .082). All sampled males and females had relatives within the study site indicating we have verified a local, closely related community of wild orangutans at Camp Leakey.

Abstract. Galdikas BM, Linsky RE, Djojoasmoro R, Lorenz J, Wagner RS. 2023. A 50 year decennial survey of male Bornean orangutans (Pongo pygmaeus wurmbii) with supplemental genetic analysis in Tanjung Puting National Park, Indonesia. Biodiversitas 24: 2587-2595. This study investigates the declining presence of adult males in a protected wild population of Bornean orangutans (Pongo pygmaeus wurmbii) at the Camp Leakey study area in Tanjung Puting National Park (TPNP), Central Kalimantan, Indonesian Borneo. Orangutan populations are in decline due to habitat destruction and fragmentation. Documenting changes within existing orangutan populations over time is important to understand demographic changes that may indicate pre-extinction processes and imminent collapse. Wild orangutan behavior has been studied at Camp Leakey since 1971. Observations of orangutans over the past five decades have documented a greatly decreased number of encounters with flanged adult males. A supplementary six-month genetic study was hindered by the fact that only two adult males briefly appeared in the study area in 2016 as compared to 40 adult male encounters in the same time period in 1976. The decline which appears most visible in data from 1986 to 1996 continues into 2006 and 2016. Genotypes from 24 wild adult orangutans encountered in 2016 were analyzed to assess the expected genetic parameters of a wild orangutan population. Pairwise relatedness was high among and between adult females and subadult males. The only two flanged males present during the genetic survey shared zero pairwise relatednesses. However, both flanged males had non-zero pairwise relatedness with other members of the Camp Leakey community and thus it is likely they were from different local areas. These data show the genetic consequences of the observed demographic changes. As TPNP forests have become disconnected from neighboring habitats, natural orangutan male dispersal may be disrupted. Disruption of male dispersal would increase the risk of accelerated extirpation for the orangutan population in TPNP as well as other orangutan populations, especially those that are remnant and less protected.