Identification and characterization of nuclear and mitochondrial markers to assess genetic variation in Sun Bears (Helacrctos Malayanus)

Lai, Wai Ling (2020) Identification and characterization of nuclear and mitochondrial markers to assess genetic variation in Sun Bears (Helacrctos Malayanus). Masters thesis, Sunway University.

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The only ursid in Malaysia, Helarctos malayanus (sun bear), is listed as “Vulnerable” by the IUCN due to decreasing populations threatened by habitat destructions and illegal harvest. Two subspecies of sun bear are recognised: H. m. malayanus occurs in Peninsular (West) Malaysia and Sumatra whereas H. m. euryspilus is only found in East Malaysia and Borneo. Scientific information on sun bears, including population size and trends, genetic diversity, inbreeding and gene flow among populations, is scarce and needed for conservation planning. My objectives were to develop a panel of mitochondrial and microsatellite genetic markers to resolve genetic divergence between sun bears in East and West Malaysia and as a tool for future studies of population size and population connectivity. Using next generation sequencing (NGS), the first complete mitochondrial genome of the Malaysian sun bear was sequenced and included in a phylogenetic analysis using 25 published complete mitochondrial genomes from the Ursidae. Three pairs of novel mitochondrial markers were developed to target the hypervariable control region (CR). 21 nuclear microsatellites, consisting of 16 trinucleotide and 5 tetranucleotide loci, were optimized into six multiplex polymerase chain reactions. Both mitochondrial and microsatellite markers were used to genotype 64 sun bears from East and West Malaysia. The complete sun bear mitochondrial genome consists of 16,770 base pairs, including 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a non-coding AT-rich region. The revised Ursidae phylogeny based on the complete mitochondrial genome confirmed a close genetic relationship between sun bears and the two sister species, Ursus thibetanus and Ursus americanus. Mitochondrial CR markers resolved 48 bears of known origin into two clades, corresponding to peninsular and East Malaysia. Microsatellite loci showed relatively low polymorphism, resolving 64 bears to 30 genotypes. Eight of the twenty-one microsatellite loci were diallelic and the remaining were monoallelic. However, 20 genotypes were found uniquely in Bornean bears, suggesting potential use of these microsatellite markers for analyzing gene flow between the two subspecies of sun bears. Phylogenies using whole mitochondrial genomes showed strong consistency, robust nodal support, including the ability to detect intraspecific divergence among geographically separated populations. The mitochondrial phylogenetic analysis supports the historic differentiation of East and West Malaysian sun bears. The markers may be used to elucidate patterns of sun bear radiation, identify evolutionarily significant units, and differentiate among sun bear populations from different parts of their geographic range within Southeast Asia.

Item Type: Thesis (Masters)
Uncontrolled Keywords: Sun Bears; Helacrctos Malayanus; genetic markers; microsatellites (genetics); mitochondrial markers; nuclear markers.
Subjects: Q Science > QH Natural history > QH426 Genetics
Q Science > QL Zoology
Divisions: Sunway University > School of Engineering and Technology [formerly School of Science and Technology until 2020] > Dept. Biological Sciences moved to SMLS wef 2021
Depositing User: Ms Yong Yee Chan
Date Deposited: 04 Oct 2023 00:35
Last Modified: 04 Oct 2023 03:07

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