Genetics Diversity of Captive and Semi-Wild Orangutan in Malaysia

Orangutan is known to be genetically diverse than any other primates in the world. There are three species of Orangutan namely Pongo abelii, Pongo tapanuliensis and Pongo pygmaeus. The Bornean Orangutan, P. pygmaeus were further diverged into three subspecies, namely P. p. pygmaeus, P. p. wurmbii and P. p. morio. The wild populations are highly endangered due to habitat loss and hunting. As a result, all the species and subspecies of Orangutan were declared as critically endangered. Orangutans are also being kept in numerous captive and semi-wild centres around the world. However, not much data is available in term of genetic diversity of these Orangutan in captive and semi-wild facilities in Malaysia which is important for its management. This is because, each species as well as subspecies of Orangutan are geographically isolated in the wild. Further, studies have shown significant genetic differences among them. Therefore, it is critical to genetically assess all Orangutan in captive to maintain their species/subspecies genetic integrity. We used non-invasive samples from five captive and two semi-wild centres in Malaysia. The genetic diversity of Orangutan was determined using both mitochondrial protein coding (NADH Dehydrogenase Subunit 5) and non-coding (Hypervariable Region 1) DNA. Results revealed high genetic diversity among all the Orangutan in captive and semi-wild centres in Malaysia. Several misclassifications of Orangutan species and subspecies were also detected. However, all those misclassifications were resolved through our phylogenetic data with high confidence. Moreover, we have provided reliable species and subspecies information for all the Orangutans involved in this study

Genetic diversity of the cave roosting dusky fruit bat, Penthetor lucasi from Sarawak

Previous studies have revealed a high genetic divergence in Penthetor lucasi population in Sarawak, indicating it may consist of multiple genetic lineages. However, these studies are not accompanied by morphological data from the studied population suggesting this may be an effect of isolation by distance, especially with small sampling coverage. Here, we provide information based on D-loop sequence analysis from 32 individuals of Penthetor lucasi collected from four different regions in Sarawak. Our results revealed a high haplotype diversity and low nucleotide diversity, suggesting that these populations are possibly recovering from a recent geological and climatic event. However, neutrality test and mismatch distributions showed longterm population stability with no population subdivision observed among the studied populations. The moderate to high level of gene flow found in this study indicates that Penthetor lucasi population is likely panmictic. Meanwhile, the low level of genetic divergence value among and within populations could account for the absence of species complexity in this study. Our result highlighted the importance of sampling coverage in proper assessment of species diversity especially in species with wide distribution

Genetic Diversity of Captive and Semi-Wild Orangutan (Pongo spp.) in Malaysia

There are two major components in this study, i) taxonomic status and genetic diversity of captive Orangutan in Malaysia and ii) pedigree information of Orangutan in captive and rehabilitation centres in Sarawak. Orangutan is the only great ape that has wild populations outside of Africa, which is in Northern Sumatra and Borneo. Currently there are three species of Orangutan recognized, which are the Sumatran Orangutan (Pongo abelii), Tapanuli Orangutan (Pongo tapanuliensis) and Bornean Orangutan (Pongo pygmaeus). The Bornean Orangutan were further classified into three subspecies which are P. p. pygmaeus, P. p. wurmbii and P. p. morio. Orangutans were listed as critically endangered in wild due to their rapid population decline caused by habitat destructions and hunting. Meanwhile many captive facilities around the world are keeping Orangutans for conservation and tourism purposes. More than 100 Orangutans are kept in various captive and rehabilitation centres in Malaysia. However, its taxonomic status is poorly known by the management. As all the species and subspecies within the genus Pongo are geographically isolated in wild, there must be notable genetic differences among them. These genetic variations should be maintained even in captive facilities. Moreover, taxonomic information of Orangutan could eventually aid in determining its original wild population for its reintroduction. Thus, noninvasive samplings were conducted at various captive and rehabilitation centres in Malaysia to perform a genetic profiling of captive Orangutans. The mitochondrial protein-coding (ND5) and non-coding (Dloop-HVR1) genes used in the phylogenetic analysis has provided substantial taxonomic information of all the captive Orangutans included in this study. There were several species misidentifications recorded in this study along with the noteworthy finding of Pongo tapanuliensis in A’famosa Resort, Malacca where it was previously misidentified as P. abelii. This is the first report of Tapanuli Orangutan in captivity. Besides that, it is also crucial to have the pedigree information of captive Orangutans. This is because unknown pedigree information could lead to inbreeding depression where the loss of unique alleles could be severe. Moreover, parentage misclassifications were reported to be common among captive Orangutans in Sarawak. Therefore, microsatellite genotyping was done using the non-invasive samples of Orangutans from Matang Wildlife Centre and Semenggoh Orangutan Rehabilitation Centre. The results have resolved parentage misclassifications and provided reliable pedigree information as well as accessing their genetic diversity that can help in the proper management of these critically endangered species. This study has highlighted the importance of genetic profiling of captive animals where species identification and pedigree assessment could be accurate

Genetic diversity of the cave roosting dusky fruit bat, Penthetor lucasi from Sarawak

Previous studies have revealed a high genetic divergence in Penthetor lucasi population in Sarawak, indicating it may consist of multiple genetic lineages. However, these studies are not accompanied by morphological data from the studied population suggesting this may be an effect of isolation by distance, especially with small sampling coverage. Here, we provide information based on D-loop sequence analysis from 32 individuals of Penthetor lucasi collected from four different regions in Sarawak. Our results revealed a high haplotype diversity and low nucleotide diversity, suggesting that these populations are possibly recovering from a recent geological and climatic event. However, neutrality test and mismatch distributions showed longterm population stability with no population subdivision observed among the studied populations. The moderate to high level of gene flow found in this study indicates that Penthetor lucasi population is likely panmictic. Meanwhile, the low level of genetic divergence value among and within populations could account for the absence of species complexity in this study. Our result highlighted the importance of sampling coverage in proper assessment of species diversity especially in species with wide distribution