Kuala Lumpur, Malaysia
Kuala Lumpur, Malaysia

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Berry N.J.,University of Leeds | Berry N.J.,Ecometrica | Phillips O.L.,University of Leeds | Lewis S.L.,University of Leeds | And 8 more authors.
Biodiversity and Conservation | Year: 2010

The carbon storage and conservation value of old-growth tropical forests is clear, but the value of logged forest is less certain. Here we analyse >100,000 observations of individuals from 11 taxonomic groups and >2,500 species, covering up to 19 years of post-logging regeneration, and quantify the impacts of logging on carbon storage and biodiversity within lowland dipterocarp forests of Sabah, Borneo. We estimate that forests lost ca. 53% of above-ground biomass as a result of logging but despite this high level of degradation, logged forest retained considerable conservation value: floral species richness was higher in logged forest than in primary forest and whilst faunal species richness was typically lower in logged forest, in most cases the difference between habitats was no greater than ca. 10%. Moreover, in most studies >90% of species recorded in primary forest were also present in logged forest, including species of conservation concern. During recovery, logged forest accumulated carbon at five times the rate of natural forest (1.4 and 0.28 Mg C ha-1 year-1, respectively). We conclude that allowing the continued regeneration of extensive areas of Borneo's forest that have already been logged, and are at risk of conversion to other land uses, would provide a significant carbon store that is likely to increase over time. Protecting intact forest is critical for biodiversity conservation and climate change mitigation, but the contribution of logged forest to these twin goals should not be overlooked. © Springer Science+Business Media B.V. 2010.


Liedigk R.,Leibniz Institute for Primate Research | Kolleck J.,Leibniz Institute for Primate Research | Boker K.O.,Leibniz Institute for Primate Research | Meijaard E.,Borneo Futures Project | And 11 more authors.
BMC Genomics | Year: 2015

Background: Long-tailed macaques (Macaca fascicularis) are an important model species in biomedical research and reliable knowledge about their evolutionary history is essential for biomedical inferences. Ten subspecies have been recognized, of which most are restricted to small islands of Southeast Asia. In contrast, the common long-tailed macaque (M. f. fascicularis) is distributed over large parts of the Southeast Asian mainland and the Sundaland region. To shed more light on the phylogeny of M. f. fascicularis, we sequenced complete mitochondrial (mtDNA) genomes of 40 individuals from all over the taxon's range, either by classical PCR-amplification and Sanger sequencing or by DNA-capture and high-throughput sequencing. Results: Both laboratory approaches yielded complete mtDNA genomes from M. f. fascicularis with high accuracy and/or coverage. According to our phylogenetic reconstructions, M. f. fascicularis initially diverged into two clades 1.70 million years ago (Ma), with one including haplotypes from mainland Southeast Asia, the Malay Peninsula and North Sumatra (Clade A) and the other, haplotypes from the islands of Bangka, Java, Borneo, Timor, and the Philippines (Clade B). The three geographical populations of Clade A appear as paraphyletic groups, while local populations of Clade B form monophyletic clades with the exception of a Philippine individual which is nested within the Borneo clade. Further, in Clade B the branching pattern among main clades/lineages remains largely unresolved, most likely due to their relatively rapid diversification 0.93-0.84 Ma. Conclusions: Both laboratory methods have proven to be powerful to generate complete mtDNA genome data with similarly high accuracy, with the DNA-capture and high-throughput sequencing approach as the most promising and only practical option to obtain such data from highly degraded DNA, in time and with relatively low costs. The application of complete mtDNA genomes yields new insights into the evolutionary history of M. f. fascicularis by providing a more robust phylogeny and more reliable divergence age estimations than earlier studies. © Liedigk et al.; licensee BioMed Central.


PubMed | Borneo Futures Project, Km 10, National University of Malaysia, Kent State University and 3 more.
Type: | Journal: BMC genomics | Year: 2015

Long-tailed macaques (Macaca fascicularis) are an important model species in biomedical research and reliable knowledge about their evolutionary history is essential for biomedical inferences. Ten subspecies have been recognized, of which most are restricted to small islands of Southeast Asia. In contrast, the common long-tailed macaque (M. f. fascicularis) is distributed over large parts of the Southeast Asian mainland and the Sundaland region. To shed more light on the phylogeny of M. f. fascicularis, we sequenced complete mitochondrial (mtDNA) genomes of 40 individuals from all over the taxons range, either by classical PCR-amplification and Sanger sequencing or by DNA-capture and high-throughput sequencing.Both laboratory approaches yielded complete mtDNA genomes from M. f. fascicularis with high accuracy and/or coverage. According to our phylogenetic reconstructions, M. f. fascicularis initially diverged into two clades 1.70 million years ago (Ma), with one including haplotypes from mainland Southeast Asia, the Malay Peninsula and North Sumatra (Clade A) and the other, haplotypes from the islands of Bangka, Java, Borneo, Timor, and the Philippines (Clade B). The three geographical populations of Clade A appear as paraphyletic groups, while local populations of Clade B form monophyletic clades with the exception of a Philippine individual which is nested within the Borneo clade. Further, in Clade B the branching pattern among main clades/lineages remains largely unresolved, most likely due to their relatively rapid diversification 0.93-0.84Ma.Both laboratory methods have proven to be powerful to generate complete mtDNA genome data with similarly high accuracy, with the DNA-capture and high-throughput sequencing approach as the most promising and only practical option to obtain such data from highly degraded DNA, in time and with relatively low costs. The application of complete mtDNA genomes yields new insights into the evolutionary history of M. f. fascicularis by providing a more robust phylogeny and more reliable divergence age estimations than earlier studies.


Bakar Abdul-Latiff M.A.,National University of Malaysia | Ruslin F.,National University of Malaysia | Faiq H.,National University of Malaysia | Hairul M.S.,Km 10 | And 4 more authors.
BioMed Research International | Year: 2014

The phylogenetic relationships of long-tailed macaque (Macaca fascicularis fascicularis) populations distributed in Peninsular Malaysia in relation to other regions remain unknown. The aim of this study was to reveal the phylogeography and population genetics of Peninsular Malaysia's M. f. fascicularis based on the D-loop region of mitochondrial DNA. Sixty-five haplotypes were detected in all populations, with only Vietnamand Cambodia sharing four haplotypes. The minimum-spanning network projected a distant relationship between Peninsular Malaysian and insular populations. Genetic differentiation (FST, Nst) results suggested that the gene flow among Peninsular Malaysian and the other populations is very low. Phylogenetic tree reconstructions indicated a monophyletic clade of Malaysia's population with continental populations (NJ = 97%, MP = 76%, and Bayesian = 1.00 posterior probabilities).The results demonstrate that PeninsularMalaysia's M. f. fascicularis belonged to Indochinese populations as opposed to the previously claimed Sundaic populations. M. f. fascicularis groups are estimated to have colonized PeninsularMalaysia 0.47 million years ago (MYA) directly fromIndochina through seaways, by means of natural sea rafting, or through terrestrial radiation during continental shelf emersion. Here, the Isthmus of Kra played a central part as biogeographical barriers that then separated it from the remaining continental populations. Copyright © 2014 Muhammad Abu Bakar Abdul-Latiff et al.


Rosli M.K.A.,National University of Malaysia | Syed-Shabthar S.M.F.,National University of Malaysia | Abdul-Patah P.,Km 10 | Abdul-Samad Z.,National University of Malaysia | And 9 more authors.
The Scientific World Journal | Year: 2014

Three species of otter can be found throughout Malay Peninsula: Aonyx cinereus, Lutra sumatrana, and Lutrogale perspicillata. In this study, we focused on the A. cinereus population that ranges from the southern and the east coast to the northern regions of Malay Peninsula up to southern Thailand to review the relationships between the populations based on the mitochondrial D-loop region. Forty-eight samples from six populations were recognized as Johor, Perak, Terengganu, Kelantan, Ranong, and Thale Noi. Among the 48 samples, 33 were identified as A. cinereus, seven as L. sumatrana, and eight as L. perspicillata. Phylogenetically, two subclades formed for A. cinereus. The first subclade grouped all Malay Peninsula samples except for samples from Kelantan, and the second subclade grouped Kelantan samples with Thai sample. Genetic distance analysis supported the close relationships between Thai and Kelantan samples compared to the samples from Terengganu and the other Malaysian states. A minimum-spanning network showed that Kelantan and Thailand formed a haplogroup distinct from the other populations. Our results show that Thai subspecies A. cinereus may have migrated to Kelantan from Thai mainland. We also suggest the classification of a new subspecies from Malay Peninsula, the small-clawed otter named A. cinereus kecilensis. © 2014 M. K. A. Rosli et al.


Abdul-Latiff M.A.B.,National University of Malaysia | Ruslin F.,National University of Malaysia | Fui V.V.,National University of Malaysia | Fui V.V.,UCSI University | And 7 more authors.
ZooKeys | Year: 2014

Phylogenetic relationships among Malaysia's long-tailed macaques have yet to be established, despite abundant genetic studies of the species worldwide. The aims of this study are to examine the phylogenetic relationships of Macaca fascicularis in Malaysia and to test its classification as a morphological subspecies. A total of 25 genetic samples of M. fascicularis yielding 383 bp of Cytochrome b (Cyt b) sequences were used in phylogenetic analysis along with one sample each of M. nemestrina and M. arctoides used as outgroups. Sequence character analysis reveals that Cyt b locus is a highly conserved region with only 23% parsimony informative character detected among ingroups. Further analysis indicates a clear separation between populations originating from different regions; the Malay Peninsula versus Borneo Insular, the East Coast versus West Coast of the Malay Peninsula, and the island versus mainland Malay Peninsula populations. Phylogenetic trees (NJ, MP and Bayesian) portray a consistent clustering paradigm as Borneo's population was distinguished from Peninsula's population (99% and 100% bootstrap value in NJ and MP respectively and 1.00 posterior probability in Bayesian trees). The East coast population was separated from other Peninsula populations (64% in NJ, 66% in MP and 0.53 posterior probability in Bayesian). West coast populations were divided into 2 clades: the North-South (47%/54% in NJ, 26/26% in MP and 1.00/0.80 posterior probability in Bayesian) and Island-Mainland (93% in NJ, 90% in MP and 1.00 posterior probability in Bayesian). The results confirm the previous morphological assignment of 2 subspecies, M. f. fascicularis and M. f. argentimembris, in the Malay Peninsula. These populations should be treated as separate genetic entities in order to conserve the genetic diversity of Malaysia's M. fascicularis. These findings are crucial in aiding the conservation management and translocation process of M. fascicularis populations in Malaysia. © M.A.B. Abdul-Latiff et al.


Takaoka H.,University of Malaya | Sofian-Azirun M.,University of Malaya | Hashim R.,University of Malaya | Otsuka Y.,Oita University | And 3 more authors.
Raffles Bulletin of Zoology | Year: 2012

Two species of black flies, Simulium (Simulium) jasmoni Takaoka, Sofian-Azirun & Belabut, 2012 and S. (S.) tiomanense Takaoka, Sofian-Azirun & Belabut, 2012, described from Tioman Island, Pahang, Malaysia, are placed in two different lineages of the tuberosum species-group in the subgenus Simulium (Simulium) Latreille, and have close similarities to S. (S.) tani Takaoka & Davies, 1995 and S. (S.) brevipar Takaoka & Davies, 1995, respectively, which were the only members of the same species-group in the nearest mainland of Peninsular Malaysia. It is suggested that S. (S.) jasmoni and S. (S.) tani in one lineage, as well as S. (S.) tiomanense and S. (S.) brevipar in another, had a common vicariant origin and were isolated after sea levels rose. Comparisons of character states of several pupal morphological features among four species in one lineage and five species in another lineage show that both S. (S.) jasmoni and S. (S.) tiomanense on Tioman Island retain more putative ancestral characters than S. (S.) tani and S. (S.) brevipar and other species in the same lineages on the continent and its adjacent large islands. Keys to 10 Malaysian members of the tuberosum species-group are provided for females, males, pupae, and mature larvae. © National University of Singapore.


Da Silva M.-A.O.,Center for Zoo and Wild Animal Health | Da Silva M.-A.O.,Copenhagen University | Kortegaard H.E.,Copenhagen University | Choong S.S.,KM 10 | And 2 more authors.
Journal of Zoo and Wildlife Medicine | Year: 2011

Facial abscessation and osteomyelitis due to dental disease is commonly seen in the Malayan tapir (Tapirus indicus), but little is known about the prevalence or etiology of these lesions. To determine the prevalence of dental ailments, 56 skulls and mandibles of deceased Malayan tapirs were visually and radiographically evaluated. Dental lesions were scored according to severity, and individuals were classified according to their age (juvenile/young adult/adult) and origin (captive/free ranging). All of the lesions identified were of a resorptive nature, seemingly originating at the cementoenamel junction and burrowing towards the center of the tooth. Overall, 27% of the investigated skulls presented radiolucent dental lesions. The prevalence among captive animals was 52% (13/25), while only 6% (2/31) of the free-ranging tapirs had dental lesions. The second, third, and fourth premolars and first molar were the teeth most commonly affected, and the mandibular teeth were more often involved than the maxillary dentition. This study demonstrates a high prevalence of resorptive dental lesions in captive Malayan tapirs and provides a strong indication that age and captivity are significant risk factors in the development of these lesions. © 2011 American Association of Zoo Veterinarians.


PubMed | Chester Zoo, University of Nottingham, University of Nottingham Malaysia Campus and Km. 10
Type: Journal Article | Journal: Conservation physiology | Year: 2017

The use of faecal glucocorticoid metabolites (fGCMs) has facilitated the development of non-invasive methods to study physiological conditions of endangered wildlife populations. One limitation is that fGCM concentrations are known to change over time and to vary according to different environmental conditions. The aim of this study was to perform a controlled dung decay experiment to understand the impact of time (since defecation) and two common environmental variables (exposure to water and direct sunlight) on fGCM concentrations of Asian elephants (


PubMed | University of Kuala Lumpur, National University of Malaysia and Km 10
Type: | Journal: BioMed research international | Year: 2014

The phylogenetic relationships of long-tailed macaque (Macaca fascicularis fascicularis) populations distributed in Peninsular Malaysia in relation to other regions remain unknown. The aim of this study was to reveal the phylogeography and population genetics of Peninsular Malaysias M. f. fascicularis based on the D-loop region of mitochondrial DNA. Sixty-five haplotypes were detected in all populations, with only Vietnam and Cambodia sharing four haplotypes. The minimum-spanning network projected a distant relationship between Peninsular Malaysian and insular populations. Genetic differentiation (F(ST), Nst) results suggested that the gene flow among Peninsular Malaysian and the other populations is very low. Phylogenetic tree reconstructions indicated a monophyletic clade of Malaysias population with continental populations (NJ = 97%, MP = 76%, and Bayesian = 1.00 posterior probabilities). The results demonstrate that Peninsular Malaysias M. f. fascicularis belonged to Indochinese populations as opposed to the previously claimed Sundaic populations. M. f. fascicularis groups are estimated to have colonized Peninsular Malaysia ~0.47 million years ago (MYA) directly from Indochina through seaways, by means of natural sea rafting, or through terrestrial radiation during continental shelf emersion. Here, the Isthmus of Kra played a central part as biogeographical barriers that then separated it from the remaining continental populations.

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