Malayan box turtle (Cuora amboinensis) has been a wildlife-protected vulnerable turtle species in Malaysia since 2005. However, because of its purported usage in traditional medicine, tonic foods and feeds, clandestine black market trade is rampant. Several polymerase chain reaction (PCR) assays for the taxonomic detection and classification of turtle species have been proposed. These assays are based on long-length target amplicons which are assumed to break down under compromised states and, hence, might not be suitable for the forensic tracing and tracking of turtle trafficking. For the first time this paper develops a very short-amplicon-length PCR assay (120 bp) for the detection of Malayan box turtle meat in raw, processed and mixed matrices, and experimental evidence is produced that such an assay is not only more stable and reliable but also more sensitive than those previously published. We checked the assay specificity against 20 different species and no cross-species detection was observed. The possibility of any false-negative detection was eliminated by a universal endogenous control for eukaryotes. The assay detection limit was 0.0001 ng of box turtle DNA from pure meat and 0.01% turtle meat in binary and ternary admixtures and commercial meatballs. Superior target stability and sensitivity under extreme treatments of boiling, autoclaving and microwave cooking suggested that this newly developed assay would be suitable for any forensic and/or archaeological identification of Malayan box turtle species, even in severely degraded specimens. Further, in silico studies indicated that the assay has the potential to be used as a universal probe for the detection of nine Cuora species, all of which are critically endangered.
Confiscated slow lorises (Nycticebus spp.) at Bangpra Water-Bird Breeding Center (BWBC) in Thailand provided an opportunity to demonstrate the application of noninvasive genetic approaches for species identification when morphology of the animals was ambiguous. The slow lorises at BWBC had been assigned to either N. bengalensis or N. pygmaeus, based on body size. However, the morphology of N. bengalensis is highly variable and overlaps with that of N. coucang (sensu stricto). Phylogenetic analysis of cytochrome b and d-loop mitochondrial regions placed all confiscated N. pygmaeus with the published sequences of N. pygmaeus and distinguished them from other Nycticebus. All other confiscated individuals formed a monophyletic clade, most individuals grouping with published N. bengalensis sequences from wild populations in Vietnam and distinct from Peninsular Malaysian and Sumatran N. coucang, Javan N. javanicus and Bornean N. menagensis. Six individuals within the N. bengalensis clade formed a separate subgroup that did not group with any reference material as indicated by phylogenetic and haplotype network analyses. Whether these trafficked individuals are undiscovered wild populations will require further investigation. Additional genetic studies of wild slow loris populations in different regions are therefore urgently required for reference to aid the protection and conservation of these threatened species.
A molecular sexing method by polymerase chain reaction (PCR) amplification of a portion of the sex-determining region Y (SRY) and the zinc finger (ZF) gene, as well as six equine Y-chromosome-specific microsatellite markers, were tested in the Malayan tapir (Tapirus indicus). While the microsatellite markers did not yield any male-specific amplicons for sex-typing, the SRY/ZF marker system produced reliable molecular sexing results by accurately sex-typing 31 reference Malayan tapirs, using whole blood, dried blood spot (DBS), or tissue samples as materials for DNA extraction. The marker system was also tested on 16 faecal samples, and the results were in general consistent with the pre-determined sexes of the animals, despite some amplification failures. A preliminary estimation of wild Malayan tapir population sex ratio was estimated from the Wildlife Genomic Resource Bank (WGRB) database of the Malaysian Department of Wildlife and National Parks (PERHILITAN), zoos, and the Sungai Dusun Wildlife Conservation Centre (WCC), as well as from the results of molecular sexing 12 samples of unknown sex. The overall sex ratio favoured females, but the deviation from parity was statistically not significant when tested using the binomial test (p > 0.05), which may be due to reduced statistical power caused by small sample sizes.
Demand for pangolin scales in East Asia has increased dramatically in the past two decades, raising concern to the pangolin survival and bringing them to the brink of local extinction. Enumerating the number of individuals from the seized pangolin scales primarily goes undocumented, mostly due to the unavailability of the appropriate methods. In this study, we developed a Pangolin Indexing System, a multi-locus STR panel of eight dinucleotide microsatellites that showed promising results in individualization and assignment of scales into Chinese and Indian pangolins. The combined power of exclusion was 0.83 and 0.99 for Chinese and Indian pangolin. The select panel of eight polymorphic STRs exhibited the cumulative probability of identity 3.7 × 10-9 for Indian pangolin and 3.6 × 10-7 for Chinese pangolin and identified 51 unique genotypes from the 74 scales selected from the four pangolin seizures. The study demonstrated the first report of cross-species validation of STRs developed from Malayan pangolin to Indian pangolin and showed the potential application of Pangolin Indexing System in screening of large seizures through DNA profiling from the scales of Indian and Chinese pangolin.
The proboscis monkey, Nasalis larvatus, is an endemic species to the island of Borneo. It is listed in the IUCN Red List as Endangered with a decreasing population trend. Nevertheless, biological information, especially on the genetic diversity of the species, is still incomplete. Its fragmented distribution poses difficulties in gathering genetic samples along with its widespread distribution across Borneo. This study aims to determine the genetic variation and structure of N. larvatus with an emphasis on Malaysian Borneo populations to elucidate its gene flow. The genetic variation and structure of N. larvatus were examined using 50 sequences of the 1,434-bp cytochrome oxidase subunit I (COI) gene region of mitochondrial DNA. The COI sequences revealed low genetic variation among N. larvatus populations in Malaysian Borneo. This low genetic variability could be the result of inbreeding pressure that may have occurred due to the absence of population expansion in this species over the last 30,000 years. This is supported in our analysis of molecular variance, which showed that groups of N. larvatus are significantly differentiated possibly due to natural geographic barriers. This study provides baseline information on the genetic diversity among proboscis monkey populations in Borneo for the future genetic assessment of the species.
Across the tropics, large-bodied mammals have been affected by selective logging in ways that vary with levels of timber extraction, collateral damage, species-specific traits and secondary effects of hunting, as facilitated by improved access through logging roads. In Peninsular Malaysia, 3.0 million hectares or 61 percent of its Permanent Reserved Forests is officially assigned for commercial selective logging. Understanding how wildlife adapts and uses logged forest is critical for its management and, for threatened species, their conservation. In this study, we quantify the population status of four tropical ungulate species in a large selectively logged forest reserve and an adjacent primary forest protected area. We then conduct finer scale analyses to identify the species-specific factors that determine their occurrence. A combined indirect sign-camera trapping approach with a large sampling effort (2,665 km and 27,780 trap nights surveyed) covering a wide area (560 km2) generated species-specific detection probabilities and site occupancies. Populations of wild boar were widespread across both logged and primary forests, whereas sambar and muntjac occupancy was lower in logged forest (48.4% and 19.2% respectively), with gaur showing no significant difference. Subsequent modelling revealed the importance of conserving lower elevation habitat in both habitat types, particularly <1,000 m asl, for which occupancies of sambar, muntjac and gaur were typically higher. This finding is important because 75 percent (~13,400 km2) of Peninsular Malaysia's Main Range Forest (Banjaran Titiwangsa) is under 1,000 m asl and therefore at risk of being converted to industrial timber plantations, which calls for renewed thinking around forest management planning.
We describe unique reproductive features of two threatened Galliformes species, the Malaysian peacock-pheasant (Polyplectron malacense) and Bornean peacock-pheasant (P. schleiermacheri). These features pose challenges to successful captive breeding to build up sustainable populations for conservation purposes. Single egg clutches in both species mean that reproductive rates are low and population increase is slow. The very rounded eggs of Bornean Peacock-pheasant cause difficulties for egg orientation in incubators. Single chicks with special requirements are poorly suited to rearing by broody bantams and successful husbandry requires increased human time, commitment, and skills.
The continuing development of improved capture-recapture (CR) modeling techniques used to study apex predators has also limited robust temporal and cross-site analyses due to different methods employed. We develop an approach to standardize older non-spatial CR and newer spatial CR density estimates and examine trends for critically endangered Sumatran tigers (Panthera tigris sumatrae) using a meta-regression of 17 existing densities and new estimates from our own fieldwork. We find that tiger densities were 47% higher in primary versus degraded forests and, unexpectedly, increased 4.9% per yr from 1996 to 2014, likely indicating a recovery from earlier poaching. However, while tiger numbers may have temporarily risen, the total potential island-wide population declined by 16.6% from 2000 to 2012 due to forest loss and degradation and subpopulations are significantly more fragmented. Thus, despite increasing densities in smaller parks, we conclude that there are only two robust populations left with >30 breeding females, indicating Sumatran tigers still face a high risk of extinction unless deforestation can be controlled.
Unsustainable exploitation of natural resources is increasingly affecting the highly biodiverse tropics [1, 2]. Although rapid developments in remote sensing technology have permitted more precise estimates of land-cover change over large spatial scales [3-5], our knowledge about the effects of these changes on wildlife is much more sparse [6, 7]. Here we use field survey data, predictive density distribution modeling, and remote sensing to investigate the impact of resource use and land-use changes on the density distribution of Bornean orangutans (Pongo pygmaeus). Our models indicate that between 1999 and 2015, half of the orangutan population was affected by logging, deforestation, or industrialized plantations. Although land clearance caused the most dramatic rates of decline, it accounted for only a small proportion of the total loss. A much larger number of orangutans were lost in selectively logged and primary forests, where rates of decline were less precipitous, but where far more orangutans are found. This suggests that further drivers, independent of land-use change, contribute to orangutan loss. This finding is consistent with studies reporting hunting as a major cause in orangutan decline [8-10]. Our predictions of orangutan abundance loss across Borneo suggest that the population decreased by more than 100,000 individuals, corroborating recent estimates of decline [11]. Practical solutions to prevent future orangutan decline can only be realized by addressing its complex causes in a holistic manner across political and societal sectors, such as in land-use planning, resource exploitation, infrastructure development, and education, and by increasing long-term sustainability [12]. VIDEO ABSTRACT.
Human-induced habitat alterations globally threaten animal populations, often evoking complex behavioural responses in wildlife. This may be particularly dramatic when negatively affecting social behaviour, which fundamentally determines individual fitness and offspring survival in group-living animals. Here, we provide first evidence for significant behavioural modifications in sociality of southern pig-tailed macaques visiting Malaysian oil palm plantations in search of food despite elevated predation risk. Specifically, we found critical reductions of key positive social interactions but higher rates of aggression in the plantation interior compared to the plantation edge (i.e. plantation areas bordering the forest) and the forest. At the plantation edge, affiliation even increased compared to the forest, while central positions in the macaques' social network structure shifted from high-ranking adult females and immatures to low-ranking individuals. Further, plantations also affected mother-infant relationships, with macaque mothers being more protective in the open plantation environment. We suggest that although primates can temporarily persist in human-altered habitats, their ability to permanently adapt requires the presence of close-by forest and comes with a trade-off in sociality, potentially hampering individual fitness and infant survival. Studies like ours remain critical for understanding species' adaptability to anthropogenic landscapes, which may ultimately contribute to facilitating their coexistence with humans and preserving biodiversity.
The Sumatran orangutan is currently listed by the IUCN as critically endangered and the Bornean species as endangered. Unless effective conservation measures are enacted quickly, most orangutan populations without adequate protection face a dire future. Two main strategies are being pursued to conserve orangutans: (i) rehabilitation and reintroduction of ex-captive or displaced individuals; and (ii) protection of their forest habitat to abate threats like deforestation and hunting. These strategies are often mirrored in similar programs to save other valued and endangered mega-fauna. Through GIS analysis, collating data from across the literature, and combining this information within a modelling and decision analysis framework, we analysed which strategy or combination of strategies is the most cost-effective at maintaining wild orangutan populations, and under what conditions. We discovered that neither strategy was optimal under all circumstances but was dependent on the relative cost per orangutan, the timescale of management concern, and the rate of deforestation. Reintroduction, which costs twelve times as much per animal as compared to protection of forest, was only a cost-effective strategy at very short timescales. For time scales longer than 10-20 years, forest protection is the more cost-efficient strategy for maintaining wild orangutan populations. Our analyses showed that a third, rarely utilised strategy is intermediate: introducing sustainable logging practices and protection from hunting in timber production forest. Maximum long-term cost-efficiency is achieved by working in conservation forest. However, habitat protection involves addressing complex conservation issues and conflicting needs at the landscape level. We find a potential resolution in that well-managed production forests could achieve intermediate conservation outcomes. This has broad implications for sustaining biodiversity more generally within an economically productive landscape. Insights from this analysis should provide a better framework to prioritize financial investments, and facilitate improved integration between the organizations that implement these strategies.
A total of 1951 species of freshwater and marine fishes belonging to 704 genera and 186 families are recorded in Malaysia. Almost half (48%) are currently threatened to some degree, while nearly one third (27%) mostly from the marine and coral habitats require urgent scientific studies to evaluate their status. Freshwater habitats encompass the highest percentage of threatened fish species (87%) followed by estuarine habitats (66%). Of the 32 species of highly threatened (HT) species, 16 are freshwater and 16 are largely marine-euryhaline species. Fish extinctions in Malaysia are confined to two freshwater species, but both freshwater and marine species are being increasingly threatened by largely habitat loss or modification (76%), overfishing (27%) and by-catch (23%). The most important threat to freshwater fishes is habitat modification and overfishing, while 35 species are threatened due to their endemism. Brackish-water, euryhaline and marine fishes are threatened mainly by overfishing, by-catch and habitat modification. Sedimentation (pollution) additionally threatens coral-reef fishes. The study provides recommendations to governments, fish managers, scientists and stakeholders to address the increasing and unabated extinction risks faced by the Malaysian fish fauna.
The Klang Gates Quartz Ridge (KGQR) is proposed for protection as National Heritage and as a UNESCO World Heritage Site because of its spectacular size, exceptional beauty and significant biodiversity. The checklist of vascular plants documents 314 species that comprise a unique combination that grows on lowland quartz and that is distinct from the surrounding lowland equatorial rain forest by the absence of orchids, palms, gingers and tree canopy families. The Rubiaceae, Gramineae, Moraceae, Apocynaceae, Melastomataceae and Polypodiaceae are the most speciose families. The summit vegetation at 200-400 m elevation is dominated by Baeckea frutescens (Myrtaceae) and Rhodoleia championii (Hamamelidaceae) and shows similarities to the plant community on rocky mountain peaks above 1500 m. About 11% of its species are endemic in Peninsular Malaysia and four are endemic to KGQR: Aleisanthia rupestris (Rubiaceae), Codonoboea primulina (Gesneriaceae), Spermacoce pilulifera (Rubiaceae), and Ilex praetermissa (Aquifoliaceae). All four are provisionally assessed as Critically Endangered. Two, Eulalia milsumi (Gramineae) and Sonerila prostrata (Melastomataceae), are endemic to KGQR and a few neighbouring smaller quartz dykes. They are assessed as Endangered. The KGQR is a fragile habitat and conservation management is urgently required to halt the spread of the aggressive alien grass, Pennisetum polystachion and to prevent further habitat degradation from visitors. Based on KGQR being a threatened habitat, its biodiverse flora, and endangered species, it qualifies as an Important Plant Area.
It is important to provide a baseline of fungal composition in the captive wildlife environment to better understand their role in overall wildlife health. The objectives were to identify species of fungi existing within wildlife animal enclosures and their environment at the National Wildlife Rescue Centre (NWRC) and the National Zoo, Malaysia and to describe their medical and veterinary importance. Samples of air, wall or floor swab, enrichment swab and soil were taken from the animal enclosures, exercise yard and enrichments at NWRC and National Zoo respectively. All samples including those pre-treated samples were plated onto Sabouraud's Dextrose Agar (SDA). Numerous fungi were grown on all sampling SDA plates regardless by either single or multiple growth. Samples of air in both NWRC and National Zoo had the highest growth of Penicillium spp. with a prevalence of 31.2% and 83.7% respectively. Samples of swab from the wall, floor and enrichments were predominantly by Candida spp. (42.6%) in NWRC and Penicillium spp. (41.6%) in the National Zoo. Prevalence of multiple fungi isolated from the soil samples in NWRC were 57.9% and yeast species was the most common in National Zoo with a prevalence of 88.9%. Overall, 29 and 8 isolates were found in both samples from the NWRC and National Zoo with a predominant species of potential zoonotic fungi have been identified in both premises. The expected fungus Aspergillus spp. was not isolated in all samples in NWRC. Prevalent fungal species found in this study are known to cause disease in animals and humans as primary pathogen and also as opportunistic pathogens that may also cause infection. Thus, health safety precautions should be considered particularly in dealing with conservation of endangered wildlife species, along with personnel and public involvements.
Polyalthia bullata is an endangered medicinal plant species. Hence, establishment of P. bullata callus culture is hoped to assist in mass production of secondary metabolites. Leaf and midrib were explants for callus induction. Both of them were cultured on Murashige and Skoog (MS) and Woody Plant Medium (WPM) containing different types and concentrations of auxins (2,4-dichlorophenoxyacetic acid (2,4-D), α-naphthaleneacetic acid (NAA), picloram, and dicamba). The callus produced was further multiplied on MS and WPM supplemented with different concentrations of 2,4-D, NAA, picloram, dicamba, indole-3-acetic acid (IAA), and indole-3-butyric acid (IBA) media. The quantification of total phenolic content (TPC), total flavonoid content (TFC) and antioxidant capacity was further carried out on P. bullata callus, and the results were subjected to correlation analysis. Among the media, the WPM + 16.56 µM picloram (53.33 ± 22.06%) was the best for callus induction while MS + 30 µM dicamba was the best for callus multiplication. The TPC, TFC, and EC50 of DPPH scavenging activity were determined at 0.657 ± 0.07 mg GAE/g FW, 0.491 ± 0.03 mg QE/g, and 85.59 ± 6.09 µg/mL in P. bullata callus, respectively. The positive correlation between DPPH scavenging activity with TPC was determined at r = 0.869, and that of TFC was at r = 0.904. Hence, the P. bullata callus has an ability to accumulate antioxidants. It therefore can be a medium for secondary metabolites production.
We collected data on the trade of seven turtle and tortoise species endemic to Indonesia and Malaysia (Amyda cartilaginea, Batagur borneoensis, Cuora amboinensis, Carettochelys insculpta, Heosemys annandalii, Heosemys grandis, and Heosemys spinosa). The data on those species included: operations costs of three breeding farms and one export facility; species life-history traits; and species international legal trade and confiscation data. We collected data for the facilities (one in Malaysia and three in Indonesia) using site visits and a semi-structured questionnaire. We conducted a literature review to compile relevant information on species' life-history traits to estimate breeding viability. We downloaded species-specific data on international trade from the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) Trade Database for the exporting countries (Malaysia and Indonesia) for 2000-2015. We compared legal trade with confiscation data obtained from CITES. The data in this article can provide insights into the operations of turtle breeding farms in Southeast Asia. These data can be used as a reference for the inspection of breeding farms and for legislative bodies to determine whether captive breeding for select turtle species is feasible.
As wild population threats for the endangered false gharial (Tomistoma schlegelii) persist, conservation breeding programs, including developing semen collection techniques for subsequent artificial insemination, are becoming important species conservation measures. Developing reproductive biology understanding of a species is important to developing best practices and hopefully maximizing reproductive successes. However, information on crocodylians functional copulatory anatomy in general is lacking. To that end, zoological facilities and conservation centres have the exceptional opportunity to contribute new understandings that may not otherwise be attainable regarding crocodylian reproductive anatomy, particularly during routine physical examinations or post-mortem necropsies. Therefore, to better understand T. schlegelii reproductive biology, to contribute knowledge in support of zoo breeding conservation efforts and to contribute to what is known overall about crocodylian reproduction, we investigated phallic anatomy of adult male Tomistoma from two zoological populations, the St. Louis Zoo, USA and Sungai Dusun Wildlife Reserve, Peninsular Malaysia. Here, we present the gross anatomical features and histological analysis of underlying tissue-level details in pursuit of a better understanding of copulatory function and associated gamete transfer mechanisms. While much of the overall Tomistoma phallic morphology and inferred function corresponds to that of other crocodylian species and speaks to conserved aspects of functional anatomy across taxa, species-specific aspects of glans and glans tip morphology are also identified. These novelties are discussed in a general function and overall broader evolutionary contexts.
utan Lipur Jeram Linang in Kelantan was carried out within 0.1 ha plot. All vascular plants (except lianas and epiphytes) were enumerated and identified. A total of 255 taxa representing 121 species belonging to 87 genera in 47 families were identified. Among these were 24 species endemic to Peninsular Malaysia and 47 species with medicinal values. Plants were categorized according to growth forms as follows: 67% trees, 17% shrubs, 7% palms, 6% herbs, and 3% ferns. Based on Important value index (IVI), Elateriospermum tapos, Goniothalamus umbrosus, and Monocarpia marginalis were the most dominant species whilst Rubiaceae, Arecaceae and Fabaceae were the three most diverse families. Species diversity was high based on the Shannon-Weiner index with the value of 4.38. In this study, two species from Dipterocarpaceae, which were Dipterocarpus grandiflorus and Shorea collina, were listed as Endangered (E) and Critically Endangered (CE) species respectively according to IUCN Red List. Information gained from this study showed that the forest harbored high plant diversity and endemism, so proper management is needed to protect and conserve this forest for sustainability and development.
Data on nutrient contents of freshwater crabs are important for ecological studies and species conservation assessments, especially when the species concerned is threatened among others by habitat destruction and uncontrolled resources utilisation. Indeed comprehensive biological information is required to reconcile the needs between sustainable resources utilisation and conservation of the species. This study documents the nutrient contents of a freshwater crab, Isolapotamon bauense which is listed as 'Vulnerable' in the IUCN Red List of Threatened Species and also being harvested by local community for dietary supplement. Results show that muscles of the freshwater crab contain a substantial amount of nutrients in particular water content (male = 79.31 ± 2.30 %, female = 77.63 ± 0.56 %), protein (male = 77.47 ± 6.11 %, female = 63.28 ± 3.62 %), magnesium (male = 51.48 ± 16.10 mg/g, female = 39.73 ± 6.99 mg/g) and calcium (male = 25.50 ± 6.98 mg/g, female = 39.73 ± 6.99 mg/g). Means of nutrient contents between male and female crabs are not significantly different. It is estimated that an individual of I. bauense with weight range of 56-139 g contained on average of 0.35 ± 0.15 g of protein. Our estimation also shows that the number of individuals of the freshwater crab required to meet the recommended daily protein intakes of the community concerned is in the range 35-96 individuals for children, 130-188 individuals for adolescents, 171-179 individuals for men and 149-159 individuals for women. The results imply that harvesting of wild I. bauense as a source of protein supplement naturally may not be practical because of its relatively low population abundance, and conservation of the species for its ecological roles may thus be preferred.
Geographically isolated populations of endemic orchids have evolved and adapted to an existence within specifi c ecological niches. These populations are highly susceptible to anthropogenic
infl uences on their microhabitats. The primary objective of conservation programs is the restoration of endangered populations to their ecologically sustainable levels, and the fi rst stage in the process of conservation involves estimation of molecular diversity at the level of the population. The approach described in this article involves the application of RAPD, Microsatellites and Chloroplast DNA markers for the characterization of the genetic structure of Paphiopedilum rothschildianum and Phalaenopsis gigantea, two endangered and endemic orchids of Sabah. This study has isolated a total of 96 microsatellite loci in P. rothschildianum and P. gigantea, 42 specifi c primer pairs have been designed for amplifi cation of microsatellite loci and are currently being applied to screen the breeding pools. The Chloroplast DNA regions amplifi ed by the primer pairs trnH-psbA and trnL-trnF exhibit distinct polymorphisms and can be used to establish phylogenetic
relationships. The ability of microsatellite loci to cross-amplify selected varieties of orchids has been determined. The molecular markers developed will be applied to estimate population diversity
levels and to formulate long-term management strategies for the conservation of endangered species of orchids of Sabah.