Predation on Multiple Prey Types Across a Disturbance Gradient in Tropical Montane Forests of Peninsular Malaysia

Predation plays a critical role in animal and plant survivorship, and can be highly sensitive to habitat loss and disturbance. Tropical montane forests in Southeast Asia are being modified rapidly by land-use change, and the consequences of this on predation likelihood are poorly understood. In Peninsular Malaysia, we conducted predation experiments at eight tropical montane forest sites along a disturbance gradient. We investigated whether (1) predation pressure in primary forests differs between different mountains; (2) predation probability is linked to habitat degradation; and (3) vegetation variables explain predation occurrence. At each forest site, we placed artificial nests with real and model quail eggs, dishes with real and artificial seeds of the cempedak (Artocarpus champeden), models resembling four-lined tree frogs (Polypedetes leucomystax) and models of the late instar caterpillar of the common Mormon (Papilio polytes) at points 100 m apart for three nights. Using Bayesian binomial simulations, we showed that predation likelihood in primary forests from different mountains can vary (e.g., probability of the difference in predation rate of artificial caterpillars between two primary forests was estimated at 82–100%). We also found that higher predation was not linked to habitat degradation for all artificial prey and seeds (e.g., comparing forests of varying degrees of disturbance from the same mountain, the probability that predation of an artificial caterpillar is lower at the primary forest was estimated at 2–20% only). Model selection and hierarchical partitioning showed that vegetation variables can explain predation occurrence, suggesting microhabitat characteristics may be influential. Conducting predation experiments by using artificial prey and seeds is useful for comparing predation likelihood at different sites, making ecological comparisons, and for informing conservation decisions. This novel approach of using multiple prey items also showed that predation for each can vary and thus caution against deploying a single prey type to draw broad inferences of predation in degraded systems

Mitogenomic phylogeny of the common long-tailed macaque (Macaca fascicularis fascicularis)

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

Phylogenetic relationships of Malaysia’s long-tailed macaques, Macaca fascicularis, based on cytochrome b sequences

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

Is Malaysia’s banded langur, Presbytis femoralis femoralis, actually Presbytis neglectus neglectus? Taxonomic revision with new insights on the radiation history of the Presbytis species group in Southeast Asia

The disjunct distribution of Presbytis femoralis subspecies across Sumatra (P. f. percura), southern (P. f. femoralis) and northern (P. f. robinsoni) Peninsular Malaysia marks the unique vicariance events in the Sunda Shelf. However, the taxonomic positions and evolutionary history of P. f. femoralis are unresolved after decades of research. To elucidate this evolutionary history, we analyzed 501 base pairs of the mitochondrial HVSI gene from 25 individuals representing Malaysia’s banded langur, with the addition of 29 sequences of Asian Presbytis from Genbank. Our results revealed closer affinity of P. f. femoralis to P. m. mitrata and P. m. sumatrana while maintaining the monophyletic state of P. f. femoralis as compared to P. f. robinsoni. Two central theses were inferred from the results; (1) P. f. femoralis does not belong in the same species classification as P. f. robinsoni, and (2) P. f. femoralis is the basal lineage of the Presbytis in Peninsular Malaysia. Proving the first hypothesis through genetic analysis, we reassigned P. f. femoralis of Malaysia to Presbytis neglectus (Schlegel’s banded langur) (Schlegel in Revue Methodique, Museum d’Histoire Naturelle des Pays-Bas 7:1, 1876) following the International Code of Zoological Nomenclature (article 23.3). The ancestors of P. neglectus are hypothesized to have reached southern Peninsular Malaysia during the Pleistocene and survived in refugium along the western coast. Consequently, they radiated upward, forming P. f. robinsoni and P. siamensis resulting in the highly allopatric distribution in Peninsular Malaysia. This study has successfully resolved the taxonomic position of P. neglectus in Peninsular Malaysia while providing an alternative biogeographic theory for the Asian Presbytis

Predation on Multiple Prey Types Across a Disturbance Gradient in Tropical Montane Forests of Peninsular Malaysia

Predation plays a critical role in animal and plant survivorship, and can be highly sensitive to habitat loss and disturbance. Tropical montane forests in Southeast Asia are being modified rapidly by land-use change, and the consequences of this on predation likelihood are poorly understood. In Peninsular Malaysia, we conducted predation experiments at eight tropical montane forest sites along a disturbance gradient. We investigated whether (1) predation pressure in primary forests differs between different mountains; (2) predation probability is linked to habitat degradation; and (3) vegetation variables explain predation occurrence. At each forest site, we placed artificial nests with real and model quail eggs, dishes with real and artificial seeds of the cempedak (Artocarpus champeden), models resembling four-lined tree frogs (Polypedetes leucomystax) and models of the late instar caterpillar of the common Mormon (Papilio polytes) at points 100 m apart for three nights. Using Bayesian binomial simulations, we showed that predation likelihood in primary forests from different mountains can vary (e.g., probability of the difference in predation rate of artificial caterpillars between two primary forests was estimated at 82–100%). We also found that higher predation was not linked to habitat degradation for all artificial prey and seeds (e.g., comparing forests of varying degrees of disturbance from the same mountain, the probability that predation of an artificial caterpillar is lower at the primary forest was estimated at 2–20% only). Model selection and hierarchical partitioning showed that vegetation variables can explain predation occurrence, suggesting microhabitat characteristics may be influential. Conducting predation experiments by using artificial prey and seeds is useful for comparing predation likelihood at different sites, making ecological comparisons, and for informing conservation decisions. This novel approach of using multiple prey items also showed that predation for each can vary and thus caution against deploying a single prey type to draw broad inferences of predation in degraded systems

Predation of multiple prey types across a disturbance gradient in tropical montane forests of Peninsular Malaysia

Predation plays a critical role in animal and plant survivorship, and can be highly sensitive to habitat loss and disturbance. Tropical montane forests in Southeast Asia are being modified rapidly by land-use change, and the consequences of this on predation likelihood are poorly understood. In Peninsular Malaysia, we conducted predation experiments at eight tropical montane forest sites along a disturbance gradient. We investigated whether (1) predation pressure in primary forests differs between different mountains; (2) predation probability is linked to habitat degradation; and (3) vegetation variables explain predation occurrence. At each forest site, we placed artificial nests with real and model quail eggs, dishes with real and artificial seeds of the cempedak (Artocarpus champeden), models resembling four-lined tree frogs (Polypedetes leucomystax) and models of the late instar caterpillar of the common Mormon (Papilio polytes) at points 100 m apart for three nights. Using Bayesian binomial simulations, we showed that predation likelihood in primary forests from different mountains can vary (e.g., probability of the difference in predation rate of artificial caterpillars between two primary forests was estimated at 82–100%). We also found that higher predation was not linked to habitat degradation for all artificial prey and seeds (e.g., comparing forests of varying degrees of disturbance from the same mountain, the probability that predation of an artificial caterpillar is lower at the primary forest was estimated at 2–20% only). Model selection and hierarchical partitioning showed that vegetation variables can explain predation occurrence, suggesting microhabitat characteristics may be influential. Conducting predation experiments by using artificial prey and seeds is useful for comparing predation likelihood at different sites, making ecological comparisons, and for informing conservation decisions. This novel approach of using multiple prey items also showed that predation for each can vary and thus caution against deploying a single prey type to draw broad inferences of predation in degraded systems

Continental Monophyly and Molecular Divergence of Peninsular Malaysia’s Macaca fascicularis fascicularis

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 Vietnam and 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 Peninsular Malaysia’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 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

Mitogenomic phylogeny of the common long-tailed macaque (Macaca fascicularis fascicularis)

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

WILDLIFE EX-SITU CONSERVATION : FORENSICS, BIOBANKING, ZOONOTIC DISEASES AND CAPTIVE BREEDING

Wildlife ex-situ conservation is a complete process of securing populations outside natural habitats. Tools like captive breeding, population genetics, artificial insemination and many others are key elements in this conservation practice. This book compiles all the advancements in ex-situ conservation via the application of forensics, captive breeding, molecular genetics, disease control and husbandry management by the Department of Wildlife and National Parks (PERHILITAN) Peninsular Malaysia. A very precise and comprehensive explanation of each component is presented in this book. Those components include An Overview of ExSitu Conservation; Wildlife Forensics for Combating Wildlife Crime; Wildlife Biobanking; Wildlife Disease Surveillance; Wildlife Conservation; Wildlife Rescue, Rehabilitation and Release; Wildlife Husbandry Management and Way Forward of PERHILITAN’s ultimate goal in ex-situ conservation. All the information generated in this book will be valuable guidance for wildlife conservationists, policymakers, stakeholders and scholars. The authors of this book comprise a team with extensive experience and a wide range of skills, which make them highly qualified to publish the first-ever book on Ex-Situ Conservation in Peninsular Malaysia