Cross Species use of Human Microarray Genotyping Technology for Bornean Orangutan (Pongo pygmaeus) SNP Discovery

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.

Niche Overlap between Pongo pygmaeus wurmbii and Helarctos malayanus Raffles within Small Scale Habitat in Punggualas Area, Sebangau National Park

The Sebangau National Park is a major stronghold for Bornean Orangutan (Pongo pygmaeus wurmbii) ranging from 6000 – 9000 individuals. In comparison with Bornean Orangutans, very little ecological fieldwork has been conducted to investigate sun bear biology, and there have been no thorough surveys of distribution or population densities. Thus, this study aimed to investigate the basic information on niche overlap between these two endangered species, specifically to quantify their relationship within the small-scale habitat in Punggualas area, SNP. Data was collected and measured during 15 – 21 June 2019; using line transects methods. A total of 6580 m was walked along 8 consecutive transects. Bear and aging sign follow Augeri protocols. A total 18 printed mark-claw and 17 Orangutan nests was measured according to the mentioned methodology. The relationships between signs use binary logistic regressions (StatPlus for Mac) and PCA model (using R), while interspecific relationships use Co-Occurrence modeling, ESP for Windows. The results showed that there is no difference between bear sign and orangutan nest (c2: 26.249; df :1, p-value : 0.001); While the results on habitat selection between transects is failed to reject the null hypothesis (c2 = 0.29; df :1, p-value : 0.490). The Mann-Whitney U test, also confirmed no distinctive overlap between the Orangutan and the Sun Bear (Z: 0.84; p-value: 0.40). The co-occurrence simulations also revealed significant results (C-Score = 1.00), by means both target animals co-existed in the habitat. Obviously, the Orangutan and Sun Bear occupy the same habitat. There is no distinctive overlap between them in terms of tree species selection and having a close interrelationship in terms of feeding ground, whereas the fruiting is not available. The only distinctive difference is that the Bear sign was tend hindering waterlogged terrain.

Deforestation projections imply range-wide population decline for critically endangered Bornean orangutan

Assessing where wildlife populations are at risk from future habitat loss is particularly important for land-use planning and avoiding biodiversity declines. Combining projections of future deforestation with species density information provides an improved way to anticipate such declines. Using the endemic and critically endangered Bornean orangutan (Pongo pygmaeus) as a case study we applied a spatio-temporally explicit deforestation model to forest loss data from 2001-2017 and projected future impacts on orangutans to the 2030s. Our projections point to continued deforestation across the island, amounting to a loss of forest habitat for 26,200 (CI: 19,500-34,000) orangutans. Populations currently persisting in forests gazetted for industrial timber and oil palm concessions, or unprotected forests outside of concessions, were projected to experience the worst losses within the next 15 years, amounting to 15,400 (CI: 12,000-20,500) individuals. Lowland forests with high orangutan densities in West and Central Kalimantan were also projected to be at high risk from deforestation, irrespective of land-use. In contrast, most protected areas and logging concessions currently harboring orangutans will continue to face low levels of deforestation. Our business-as-usual projections indicate the importance of protected areas, efforts to prevent the conversion of logged forests for the survival of highly vulnerable wildlife, and protecting orangutan habitat in plantation landscapes. The modeling framework could be expanded to other species with available density or occurrence data. Our findings highlight that species conservation should not only attempt to act on the current situation, but also be adapt to changes in drivers to be effective.

Drivers of Bornean Orangutan Distribution across a Multiple-Use Tropical Landscape

Logging and conversion of tropical forests in Southeast Asia have resulted in the expansion of landscapes containing a mosaic of habitats that may vary in their ability to sustain local biodiversity. However, the complexity of these landscapes makes it difficult to assess abundance and distribution of some species using ground-based surveys alone. Here, we deployed a combination of ground-transects and aerial surveys to determine drivers of the critically endangered Bornean Orangutan (Pongo pygmaeus morio) distribution across a large multiple-use landscape in Sabah, Malaysian Borneo. Ground-transects and aerial surveys using drones were conducted for orangutan nests and hemi-epiphytic strangler fig trees (Ficus spp.) (an important food resource) in 48 survey areas across 76 km2, within a study landscape of 261 km2. Orangutan nest count data were fitted to models accounting for variation in land use, above-ground carbon density (ACD, a surrogate for forest quality), strangler fig density, and elevation (between 117 and 675 m). Orangutan nest counts were significantly higher in all land uses possessing natural forest cover, regardless of degradation status, than in monoculture plantations. Within these natural forests, nest counts increased with higher ACD and strangler fig density, but not with elevation. In logged forest (ACD 14–150 Mg ha−1), strangler fig density had a significant, positive relationship with orangutan nest counts, but this relationship disappeared in a forest with higher carbon content (ACD 150–209 Mg ha−1). Based on an area-to-area comparison, orangutan nest counts from ground transects were higher than from counts derived from aerial surveys, but this did not constitute a statistically significant difference. Although the difference in nest counts was not significantly different, this analysis indicates that both methods under-sample the total number of nests present within a given area. Aerial surveys are, therefore, a useful method for assessing the orangutan habitat use over large areas. However, the under-estimation of nest counts by both methods suggests that a small number of ground surveys should be retained in future surveys using this technique, particularly in areas with dense understory vegetation. This study shows that even highly degraded forests may be a suitable orangutan habitat as long as strangler fig trees remain intact after areas of forest are logged. Enrichment planting of strangler figs may, therefore, be a valuable tool for orangutan conservation in these landscapes.

First Bornean orangutan sighting in Usun Apau National Park, Sarawak

Wildlife surveys were conducted in Usun Apau National Park (UANP), Sarawak from Oct 2017 to Oct 2020. This was the first attempt to document fauna diversity in Usun Apau National Park on the UANP plateau at 1200-1400 m a.s.l. On 17 September 2020, 10 AM, we observed an orangutan individual, Pongo pygmaeus, over a period of one minute at Libut Camp UANP (E: 114039’.546, N: 2052’36.44) at 1,020 m a.s.l. We also recorded four nests and orangutan vocalisation twice. This observation is important for Bornean orangutan conservation as this was the first orangutan sighting in UANP and well outside the species distribution range for in Sarawak.