Phylogenetic relationships of Malaysian monkeys, Cercopithecidae, based on mitochondrial cytochrome c sequences

Mitochondrial DNA cytochrome c oxidase II (COII) gene sequences of Malaysian Cercopithecidae were examined to ascertain their phylogenetic relationships. Colobinae were represented by the genera Presbytis, Trachypithecus and Nasalis, while the genus Macaca represented Cercopithecinae. DNA amplification and sequencing of the COII gene was performed on 16 samples. Symphalangus syndactylus (Hylobatidae) was used as the outgroup. Data were analyzed using both character (maximum parsimony) and distance (neighbor-joining) methods. Tree topologies indicated that Colobinae and Cercopithecinae have their own distinct monophyletic clade. This result was well supported by bootstrap values and genetic distances derived from the Kimura-2-parameter algorithm. Separation of Macaca nemestrina from M. fascicularis was also well supported by bootstrap values. In addition, tree topologies indicate a good resolution of the Colobinae phylogenetic relationships at the intergeneric level, but with low bootstrap support. The position of Nasalis remained problematic in both trees. Overall, COII is a good gene candidate for portraying the phylogenetic relationships of Malaysian primates at the inter- and intra-subfamily levels

Phylogenetic relationships of Malayan gaur with other species of the genus Bos based on cytochrome b gene DNA sequences

The Malayan gaur (Bos gaurus hubbacki) is one of the three subspecies of gaurs that can be found in Malaysia. We examined the phylogenetic relationships of this subspecies with other species of the genus Bos (B. javanicus, B. indicus, B. taurus, and B. grunniens). The sequence of a key gene, cytochrome b, was compared among 20 Bos species and the bongo antelope, used as an outgroup. Phylogenetic reconstruction was employed using neighbor joining and maximum parsimony in PAUP and Bayesian inference in MrBayes 3.1. All tree topologies indicated that the Malayan gaur is in its own monophyletic clade, distinct from other species of the genus Bos. We also found significant branching differences in the tree topologies between wild and domestic cattle

Haplotype distribution among endangered asian elephants (Elephas maximus) in Peninsular Malaysia

Asian elephants are classified as an endangered species on the IUCN red list, warranting more research and conservation efforts to protect them. A study of the distribution of haplotypes among Asian elephants in Peninsular Malaysia was performed using a partial DNA sequencing of a D-loop region. In this study, 10 haplotypes (Hap01–Hap10) were detected in Peninsular Malaysian populations with a high haplotype diversity (Hˆ ) of 83%. Hap01 was shared by Kelantan (n = 1), Johor (n = 2), Pahang (n = 2), and Perak (n = 2). The other shared haplotype was Hap06, which was evident in the Pahang (n = 1) and Johor (n = 1) samples. DnaSP analysis demonstrated that low genetic diversity (π) was observed in Peninsular Malaysian elephants (0.55%). Conversely, the gene flow was high (Nm = 9.65 migrants per generation). In a test of population subdivision, all pairwise comparisons for Peninsular Malaysia were low (0.00 to 0.13) except for Kelantan–Pahang (0.57). Our results demonstrated that the genetic diversity was low within the different populations of Peninsular Malaysia. The level of genetic differentiation was also low, but the gene flow was high regardless of the geographic distance of the Asian elephant populations in Peninsular Malaysia

Low genetic variability in the recovering urban banded leaf monkey population of Singapore

Raffles Bulletin of Zoology602589-59

Phylogenetic relationships of the Orang Asli and Iban of Malaysia based on maternal markers

Malaysia remains as a crossroad of different cultures and peoples, and it has long been recognized that studying its population history can provide crucial insight into the prehistory of Southeast Asia as a whole. The earliest inhabitants were the Orang Asli in Peninsular Malaysia and the indigenous groups in Sabah and Sarawak. Although they were the earliest migrants in this region, these tribes are divided geographically by the South China Sea. We analyzed DNA sequences of 18 Orang Asli using mitochondrial DNA extracted from blood samples, each representing one sub-tribe, and from five Sarawakian Iban. Mitochondrial DNA was extracted from hair samples in order to examine relationships with the main ethnic groups in Malaysia. The D-loop region and cytochrome b genes were used as the candidate loci. Phylogenetic relationships were investigated using maximum parsimony and neighbor joining algorithms, and each tree was subjected to bootstrap analysis with 1000 replicates. Analyses of the HVS I region showed that the Iban are not a distinct group from the Orang Asli; they form a sub-clade within the Orang Asli. Based on the cytochrome b gene, the Iban clustered with the Orang Asli in the same clade. We found evidence for considerable gene flow between Orang Asli and Iban. We concluded that the Orang Asli, Iban and the main ethnic groups of Malaysia are probably derived from a common ancestor. This is in agreement with a single-route migration theory, but it does not dismiss a two-route migration theory