Molecular techniques involving the application of DNA based molecular markers for the conservation and management of endemic and endangered species have assumed significance as
genome sequencing projects have generated an extensive database which can be mined for informative genomic regions. Scientific approaches towards conservation involve several stages, which encompass determination of appropriate genomic regions for characterization, design and testing of specific molecular markers, screening of multiple populations and statistical treatment and
interpretation of data. Population data can be utilized to develop controlled breeding and relocation programs aimed at ensuring that genetic diversity within populations of endangered species is
sustained within the context of an overall conservation program. The information derived as a result of this approach can be applied to establish a scientific and legal framework for the conservation of endemic species. Species specific genomic markers can be applied to enforce the implementation of CITES within the guidelines of a national biodiversity conservation policy.
Year 2020 has brought the greatest global pandemic to hit the world since the end of the First World War. The severe acute respiratory syndrome coronavirus 2 and the resulting disease named coronavirus disease 2019 has brought the world to its knees both financially and medically. The American Society of Primatologists has postponed their annual meetings from the end of May 2020 until the end of September 2020, while the International Primatological Society have postponed their biennial congress from August 2020 to August 2021, which has also resulted in their 2022 meetings in Malaysia being pushed back until 2023. Here, I explore the potential dangers of pursuing any primate fieldwork during this pandemic on our study species, their ecosystems, and local peoples. I believe that the risk of bringing this virus into our study ecosystems is too great and that primatologists should cancel all field research until the pandemic ends or a vaccine/reliable treatment is widely available. This is the year we all must become One Health practitioners!
The endangered Asian tapir (Tapirus indicus) is threatened by large-scale habitat loss, forest fragmentation and increased hunting pressure. Conservation planning for this species, however, is hampered by a severe paucity of information on its ecology and population status. We present the first Asian tapir population density estimate from a camera trapping study targeting tigers in a selectively logged forest within Peninsular Malaysia using a spatially explicit capture-recapture maximum likelihood based framework. With a trap effort of 2496 nights, 17 individuals were identified corresponding to a density (standard error) estimate of 9.49 (2.55) adult tapirs/100 km(2) . Although our results include several caveats, we believe that our density estimate still serves as an important baseline to facilitate the monitoring of tapir population trends in Peninsular Malaysia. Our study also highlights the potential of extracting vital ecological and population information for other cryptic individually identifiable animals from tiger-centric studies, especially with the use of a spatially explicit capture-recapture maximum likelihood based framework.
Mammalian carnivores play a vital role in ecosystem functioning. However, they are prone to extinction because of low population densities and growth rates, and high levels of persecution or exploitation. In tropical biodiversity hotspots such as Peninsular Malaysia, rapid conversion of natural habitats threatens the persistence of this vulnerable group of animals. Here, we carried out the first comprehensive literature review on 31 carnivore species reported to occur in Peninsular Malaysia and updated their probable distribution. We georeferenced 375 observations of 28 species of carnivore from 89 unique geographic locations using records spanning 1948 to 2014. Using the Getis-Ord Gi*statistic and weighted survey records by IUCN Red List status, we identified hotspots of species that were of conservation concern and built regression models to identify environmental and anthropogenic landscape factors associated with Getis-Ord Gi* z scores. Our analyses identified two carnivore hotspots that were spatially concordant with two of the peninsula's largest and most contiguous forest complexes, associated with Taman Negara National Park and Royal Belum State Park. A cold spot overlapped with the southwestern region of the Peninsula, reflecting the disappearance of carnivores with higher conservation rankings from increasingly fragmented natural habitats. Getis-Ord Gi* z scores were negatively associated with elevation, and positively associated with the proportion of natural land cover and distance from the capital city. Malaysia contains some of the world's most diverse carnivore assemblages, but recent rates of forest loss are some of the highest in the world. Reducing poaching and maintaining large, contiguous tracts of lowland forests will be crucial, not only for the persistence of threatened carnivores, but for many mammalian species in general.
A clear understanding of population structure is essential for assessing conservation status and implementing management strategies. A small, non-migratory population of humpback whales in the Arabian Sea is classified as "Endangered" on the IUCN Red List of Threatened Species, an assessment constrained by a lack of data, including limited understanding of its relationship to other populations. We analysed 11 microsatellite markers and mitochondrial DNA sequences extracted from 67 Arabian Sea humpback whale tissue samples and compared them to equivalent datasets from the Southern Hemisphere and North Pacific. Results show that the Arabian Sea population is highly distinct; estimates of gene flow and divergence times suggest a Southern Indian Ocean origin but indicate that it has been isolated for approximately 70,000 years, remarkable for a species that is typically highly migratory. Genetic diversity values are significantly lower than those obtained for Southern Hemisphere populations and signatures of ancient and recent genetic bottlenecks were identified. Our findings suggest this is the world's most isolated humpback whale population, which, when combined with low population abundance estimates and anthropogenic threats, raises concern for its survival. We recommend an amendment of the status of the population to "Critically Endangered" on the IUCN Red List.
Fisheries bycatch is a widespread and serious issue that leads to declines of many important and threatened marine species. However, documenting the distribution, abundance, population trends and threats to sparse populations of marine species is often beyond the capacity of developing countries because such work is complex, time consuming and often extremely expensive. We have developed a flexible tool to document spatial distribution and population trends for dugongs and other marine species in the form of an interview questionnaire supported by a structured data upload sheet and a comprehensive project manual. Recognising the effort invested in getting interviewers to remote locations, the questionnaire is comprehensive, but low cost. The questionnaire has already been deployed in 18 countries across the Indo-Pacific region. Project teams spent an average of USD 5,000 per country and obtained large data sets on dugong distribution, trends, catch and bycatch, and threat overlaps. Findings indicated that >50% of respondents had never seen dugongs and that 20% had seen a single dugong in their lifetimes despite living and fishing in areas of known or suspected dugong habitat, suggesting that dugongs occurred in low numbers. Only 3% of respondents had seen mother and calf pairs, indicative of low reproductive output. Dugong hunting was still common in several countries. Gillnets and hook and line were the most common fishing gears, with the greatest mortality caused by gillnets. The questionnaire has also been used to study manatees in the Caribbean, coastal cetaceans along the eastern Gulf of Thailand and western Peninsular Malaysia, and river dolphins in Peru. This questionnaire is a powerful tool for studying distribution and relative abundance for marine species and fishery pressures, and determining potential conservation hotspot areas. We provide the questionnaire and supporting documents for open-access use by the scientific and conservation communities.
Genetic variation in mitochondrial genes could underlie metabolic adaptations because mitochondrially encoded proteins are directly involved in a pathway supplying energy to metabolism. Macquarie perch from river basins exposed to different climates differ in size and growth rate, suggesting potential presence of adaptive metabolic differences. We used complete mitochondrial genome sequences to build a phylogeny, estimate lineage divergence times and identify signatures of purifying and positive selection acting on mitochondrial genes for 25 Macquarie perch from three basins: Murray-Darling Basin (MDB), Hawkesbury-Nepean Basin (HNB) and Shoalhaven Basin (SB). Phylogenetic analysis resolved basin-level clades, supporting incipient speciation previously inferred from differentiation in allozymes, microsatellites and mitochondrial control region. The estimated time of lineage divergence suggested an early- to mid-Pleistocene split between SB and the common ancestor of HNB+MDB, followed by mid-to-late Pleistocene splitting between HNB and MDB. These divergence estimates are more recent than previous ones. Our analyses suggested that evolutionary drivers differed between inland MDB and coastal HNB. In the cooler and more climatically variable MDB, mitogenomes evolved under strong purifying selection, whereas in the warmer and more climatically stable HNB, purifying selection was relaxed. Evidence for relaxed selection in the HNB includes elevated transfer RNA and 16S ribosomal RNA polymorphism, presence of potentially mildly deleterious mutations and a codon (ATP6113) displaying signatures of positive selection (ratio of nonsynonymous to synonymous substitution rates (dN/dS) >1, radical change of an amino-acid property and phylogenetic conservation across the Percichthyidae). In addition, the difference could be because of stronger genetic drift in the smaller and historically more subdivided HNB with low per-population effective population sizes.
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.
Indigenous Peoples' lands cover over one-quarter of Earth's surface, a significant proportion of which is still free from industrial-level human impacts. As a result, Indigenous Peoples and their lands are crucial for the long-term persistence of Earth's biodiversity and ecosystem services. Yet, information on species composition on these lands globally remains largely unknown. We conducted the first comprehensive analysis of terrestrial mammal composition across mapped Indigenous lands based on data on area of habitat (AOH) for 4460 mammal species assessed by the International Union for Conservation of Nature. We overlaid each species' AOH on a current map of Indigenous lands and found that 2695 species (60% of assessed mammals) had ≥10% of their ranges on Indigenous Peoples' lands and 1009 species (23%) had >50% of their ranges on these lands. For threatened species, 473 (47%) occurred on Indigenous lands with 26% having >50% of their habitat on these lands. We also found that 935 mammal species (131 categorized as threatened) had ≥ 10% of their range on Indigenous Peoples' lands that had low human pressure. Our results show how important Indigenous Peoples' lands are to the successful implementation of conservation and sustainable development agendas worldwide.
Six extant species of non-human great apes are currently recognized: Sumatran and Bornean orangutans, eastern and western gorillas, and chimpanzees and bonobos [1]. However, large gaps remain in our knowledge of fine-scale variation in hominoid morphology, behavior, and genetics, and aspects of great ape taxonomy remain in flux. This is particularly true for orangutans (genus: Pongo), the only Asian great apes and phylogenetically our most distant relatives among extant hominids [1]. Designation of Bornean and Sumatran orangutans, P. pygmaeus (Linnaeus 1760) and P. abelii (Lesson 1827), as distinct species occurred in 2001 [1, 2]. Here, we show that an isolated population from Batang Toru, at the southernmost range limit of extant Sumatran orangutans south of Lake Toba, is distinct from other northern Sumatran and Bornean populations. By comparing cranio-mandibular and dental characters of an orangutan killed in a human-animal conflict to those of 33 adult male orangutans of a similar developmental stage, we found consistent differences between the Batang Toru individual and other extant Ponginae. Our analyses of 37 orangutan genomes provided a second line of evidence. Model-based approaches revealed that the deepest split in the evolutionary history of extant orangutans occurred ∼3.38 mya between the Batang Toru population and those to the north of Lake Toba, whereas both currently recognized species separated much later, about 674 kya. Our combined analyses support a new classification of orangutans into three extant species. The new species, Pongo tapanuliensis, encompasses the Batang Toru population, of which fewer than 800 individuals survive. VIDEO ABSTRACT.
Plants play a crucial role in foodstuff, medicine, industry, and environmental protection. The skill of recognising plants is very important in some applications, including conservation of endangered species and rehabilitation of lands after mining activities. However, it is a difficult task to identify plant species because it requires specialized knowledge. Developing an automated classification system for plant species is necessary and valuable since it can help specialists as well as the public in identifying plant species easily. Shape descriptors were applied on the myDAUN dataset that contains 45 tropical shrub species collected from the University of Malaya (UM), Malaysia. Based on literature review, this is the first study in the development of tropical shrub species image dataset and classification using a hybrid of leaf shape and machine learning approach. Four types of shape descriptors were used in this study namely morphological shape descriptors (MSD), Histogram of Oriented Gradients (HOG), Hu invariant moments (Hu) and Zernike moments (ZM). Single descriptor, as well as the combination of hybrid descriptors were tested and compared. The tropical shrub species are classified using six different classifiers, which are artificial neural network (ANN), random forest (RF), support vector machine (SVM), k-nearest neighbour (k-NN), linear discriminant analysis (LDA) and directed acyclic graph multiclass least squares twin support vector machine (DAG MLSTSVM). In addition, three types of feature selection methods were tested in the myDAUN dataset, Relief, Correlation-based feature selection (CFS) and Pearson's coefficient correlation (PCC). The well-known Flavia dataset and Swedish Leaf dataset were used as the validation dataset on the proposed methods. The results showed that the hybrid of all descriptors of ANN outperformed the other classifiers with an average classification accuracy of 98.23% for the myDAUN dataset, 95.25% for the Flavia dataset and 99.89% for the Swedish Leaf dataset. In addition, the Relief feature selection method achieved the highest classification accuracy of 98.13% after 80 (or 60%) of the original features were reduced, from 133 to 53 descriptors in the myDAUN dataset with the reduction in computational time. Subsequently, the hybridisation of four descriptors gave the best results compared to others. It is proven that the combination MSD and HOG were good enough for tropical shrubs species classification. Hu and ZM descriptors also improved the accuracy in tropical shrubs species classification in terms of invariant to translation, rotation and scale. ANN outperformed the others for tropical shrub species classification in this study. Feature selection methods can be used in the classification of tropical shrub species, as the comparable results could be obtained with the reduced descriptors and reduced in computational time and cost.
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.
Pangolins are scale-covered mammals, containing eight endangered species. Maintaining pangolins in captivity is a significant challenge, in part because little is known about their genetics. Here we provide the first large-scale sequencing of the critically endangered Manis javanica transcriptomes from eight different organs using Illumina HiSeq technology, yielding ~75 Giga bases and 89,754 unigenes. We found some unigenes involved in the insect hormone biosynthesis pathway and also 747 lipids metabolism-related unigenes that may be insightful to understand the lipid metabolism system in pangolins. Comparative analysis between M. javanica and other mammals revealed many pangolin-specific genes significantly over-represented in stress-related processes, cell proliferation and external stimulus, probably reflecting the traits and adaptations of the analyzed pregnant female M. javanica. Our study provides an invaluable resource for future functional works that may be highly relevant for the conservation of pangolins.
Indo-Pacific humpback dolphins (Sousa chinensis) are documented from various locations along Borneo's coast, including three sites in Sarawak, Malaysia, three sites in Sabah, Malaysia, three locations in Kalimantan, Indonesia and the limited coastal waters of the Sultanate of Brunei. Observations in all these areas indicate a similar external morphology, which seems to fall somewhere between that documented for Chinese populations known as S. chinensis, and that of Sousa sahulensis in Australia and Papua New Guinea. Sightings occur in shallow nearshore waters, often near estuaries and river mouths, and associations with Irrawaddy dolphins (Orcaella brevirostris) are frequently documented. Population estimates exist for only two locations and sightings information throughout Borneo indicates that frequency of occurrence is rare and group size is usually small. Threats from fisheries by-catch and coastal development are present in many locations and there are concerns over the ability of these small and fragmented populations to survive. The conservation and taxonomic status of humpback dolphins in Borneo remain unclear, and there are intriguing questions as to where these populations fit in our evolving understanding of the taxonomy of the genus.
Orangutan survival is threatened by habitat loss and illegal killing. Most wild populations will disappear over the next few decades unless threats are abated. Saving orangutans is ultimately in the hands of the governments and people of Indonesia and Malaysia, which need to ensure that habitats of viable orangutan populations are protected from deforestation and well managed to ensure no hunting takes place. Companies working in orangutan habitat also have to play a much bigger role in habitat management. Although the major problems and the direct actions required to solve them-reducing forest loss and hunting-have been known for decades, orangutan populations continue to decline. Orangutan populations in Sumatra and Borneo have declined by between 2,280 and 5,250 orangutans annually over the past 25 years. As the total current population for the two species is some 60,000 animals in an area of about 90,000 km(2) , there is not much time left to make conservation efforts truly effective. Our review discusses what has and has not worked in conservation to guide future conservation efforts.
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.
We report here the complete mitochondrial (mt) genomes of six individuals of Cheilinus undulatus (Napoleon Wrasse), an endangered marine fish species. The six mt DNA sequences had an average size of 17,000 kb and encoded 22 tRNA, two sRNA, 13 highly conserved protein coding genes and a control region. The polymorphic variation (control region) in these six individuals suggests their potential use as a specific marker for phylogeographic conservation. Moreover, the sequence polymorphism within the control region (D-loop) suggests that this locus can be applied for phylogenetic studies.
The impact of a range of different threats has resulted in the listing of six out of seven sea turtle species on the IUCN Red List of endangered species. Disease risk analysis (DRA) tools are designed to provide objective, repeatable and documented assessment of the disease risks for a population and measures to reduce these risks through management options. To the best of our knowledge, DRAs have not previously been published for sea turtles, although disease is reported to contribute to sea turtle population decline. Here, a comprehensive list of health hazards is provided for all seven species of sea turtles. The possible risk these hazards pose to the health of sea turtles were assessed and "One Health" aspects of interacting with sea turtles were also investigated. The risk assessment was undertaken in collaboration with more than 30 experts in the field including veterinarians, microbiologists, social scientists, epidemiologists and stakeholders, in the form of two international workshops and one local workshop. The general finding of the DRA was the distinct lack of knowledge regarding a link between the presence of pathogens and diseases manifestation in sea turtles. A higher rate of disease in immunocompromised individuals was repeatedly reported and a possible link between immunosuppression and environmental contaminants as a result of anthropogenic influences was suggested. Society based conservation initiatives and as a result the cultural and social aspect of interacting with sea turtles appeared to need more attention and research. A risk management workshop was carried out to acquire the insights of local policy makers about management options for the risks relevant to Queensland and the options were evaluated considering their feasibility and effectiveness. The sea turtle DRA presented here, is a structured guide for future risk assessments to be used in specific scenarios such as translocation and head-starting programs.
BACKGROUND: Asian slow lorises (Nycticebus spp.) are one of few known venomous mammals, yet until now only one published case report has documented the impact of their venomous bite on humans. We describe the reaction of a patient to the bite of a subadult Nycticebus kayan, which occurred in the Mulu District of Sarawak in 2012.
FINDINGS: Within minutes of the bite, the patient experienced paraesthesia in the right side of the jaw, ear and right foot. By 40 minutes, swelling of the face was pronounced. The patient was admitted to Mulu National Park Health Clinic/Klinik Kesihatan Taman Mulu Tarikh, at which time he was experiencing: swollen mouth, chest pain, mild abdominal pain, nausea, numbness of the lips and mouth, shortness of breath, weakness, agitation and the sensation of pressure in the ears due to swelling. The blood pressure was 110/76, the heart ratio was 116 and oxygen saturation was 96%. The patient was treated intramuscularly with adrenaline (0.5 mL), followed by intravenous injection of hydrocortisone (400 mg) and then intravenous fluid therapy of normal saline (500 mg). By 8 h10 the next day, the patient's condition had significantly improved with no nausea, and with blood pressure and pulse rate stable.
CONCLUSIONS: A handful of anecdotes further support the real danger that slow loris bites pose to humans. As the illegal pet trade is a major factor in the decline of these threatened species, we hope that by reporting on the danger of handling these animals it may help to reduce their desirability as a pet.
A century ago, tigers (Panthera tigris Linnaeus, 1758) were so common in parts of Southeast Asia as to be considered pests, and governments sponsored their killing. Habitat loss and fragmentation, market-driven poaching and loss of prey have since led to the disappearance of Indochinese tigers from most their former range. Despite 15 years of dedicated tiger conservation funding, national estimates of Indochinese tiger subpopulations can at best only be roughly approximated. The future for the subspecies appears grim unless very focused efforts can be applied to stabilize and recover subpopulations. On a regional scale, the 2 proposed subspecies Panthera tigris corbetti and P. tigris jacksoni are effectively managed as separate conservation units. Evaluating where to place conservation efforts should consider the vulnerability (likelihood of extinction) and irreplaceability (likelihood that an area contributes uniquely to regional conservation) of tiger subpopulations. Only 1 site in Thailand supporting <200 individuals (Huai Kha Khaeng-Thung Yai) is considered low vulnerability, and is irreplaceable. Five sites in Lao, Thailand and Peninsular Malaysia are medium vulnerability and irreplaceable. Priorities at these 6 sites are to double tiger numbers within 10 years through protection and monitoring. Seven sites in Lao, Thailand and Myanmar are high vulnerability and irreplaceable, and might be recovered if government commitment to tigers, staff capacity and legal frameworks for tiger protection are established. Tigers are extremely vulnerable or even extinct in Cambodia's Eastern Plains and the site is irreplaceable for tigers because it represents the only large (>10,000 km(2) ) block of dry forest habitat available in the region. A reintroduction program is the only option to recover tigers there.