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Genetic monitoring plays a crucial role in the conservation management of amphibians due to their vulnerability to habitat changes. Traditional biodiversity monitoring methods, such as trapping and morphological identification, are being complemented by advanced technologies that enhance species identification sensitivity and monitoring capabilities. Genetic resource availability is essential for effective amphibian biodiversity assessment and monitoring. This study aims to evaluate the current state of genetic resources and their comprehensiveness for amphibian biomonitoring and conservation in Malaysia. The study focused on seven targeted mitochondrial DNA loci, and data regarding these loci were obtained from the National Centre for Biotechnology Information (NCBI) database. The results showed that 69.8% of amphibian species in Malaysia had genetic data available for at least one or more of the targeted genes, with the 16S gene being the most widely represented. However, only 12.1% of threatened species and 61.2% of endemic species had accessible genetic information. Biological utilization was identified as the primary threat to amphibian species in Malaysia, accounting for 27.0% of recorded threats. These findings highlight the need for further improvement in achieving comprehensive genetic resource information for amphibians in Malaysia. Advancements in enpromisesntal DNA (eDNA) analysis and Next Generation Sequencing (NGS) technologies hold promise in enhancing efforts to conserve amphibian diversity. It is crucial to continue expanding genetic resources to support ongoing monitoring and preservation initiatives for amphibians in Malaysia, ensuring effective conservation management. [ABSTRACT FROM AUTHOR]

The approach of combining cost‐effective nanopore sequencing and emerging environmental DNA (eDNA) metabarcoding could prove to be a promising tool for biodiversity documentation, especially in Malaysia. Given the substantial funding constraints in recent years, especially in relation to the country's biodiversity, many researchers have been limited to conduct restricted research without extended monitoring periods, potentially hindering comprehensive surveys and could compromise the conservation efforts. Therefore, the present study aimed to evaluate the application of eDNA metabarcoding on freshwater fish using short reads generated through nanopore sequencing. This assessment focused on species detection in three selected rivers within the Endau Rompin Landscape in Malaysia. Additionally, the study compared levels of species detection between eDNA metabarcoding and conventional sampling methods, examined the effectiveness of primer choice, and applied both metabarcoding and shotgun sequencing to the eDNA approach. We successfully identified a total of 22 and 71 species with an identification threshold of >97% and >90%, respectively, through the MinION platform. The eDNA metabarcoding approach detected over 13% more freshwater fish species than when the conventional method was used. Notably, the distinction in freshwater fish detection between eDNA primers for 12S rRNA and cytochrome oxidase I was insignificant. The cost for eDNA metabarcoding proved to be more effective compared to conventional sampling with cost reduction at 33.4%. With favourable cost‐effectiveness and increased species detection, eDNA metabarcoding could complement existing methods, enhance holistic diversity documentation for targeted habitats and facilitate effective conservation planning. [ABSTRACT FROM AUTHOR]

Ayer Hitam Utara State Park Forest (AHUSPF) is an invaluable sanctuary in Johor, the last remaining intact peat swamp forest reserve that hosts many species unique to this distinctive habitat. Some rapid surveys conducted from 2019 to 2022 recorded 40 species of freshwater fish within AHUSPF. Notably, 11 are stenotopic to acid blackwater, and 12 are stenotopic to acid water, most belonging to the family Osphronemidae and Danionidae. The International Union for Conservation of Nature Red List has designated two species, Encheloclarias curtisoma and Betta persephone, as Endangered, while Betta omega is classified as Critically Endangered. The checklist presented herein was first produced from an inventory study in AHUSPF. The preservation of peat swamp forests in the area is under imminent threat due to the alarming rate of land conversion, forest fires, and the recent potential threat from the red-claw crayfish invasion in the aquatic environment. Hence, continuous monitoring is vital for documenting and updating the conservation status of the fish species. These endeavours will facilitate the development of practical conservation approaches to ensure the long-term sustainability of AHUSPF and its associated species. [ABSTRACT FROM AUTHOR]

Primate population assessment relies heavily on ecological techniques such as camera traps, distance sampling, and passive acoustic detection. Although these techniques have proven effective in estimating the number of individuals and primate groups, challenges arise when attempting to scale them up to larger areas such as districts, states, or national levels. This study aims to evaluate the reliability of public responses in determining the primate population at district level. Specifically, an online survey was designed to collect information from the public regarding the primate population within their respective areas of knowledge, focusing on Muar district in Johor, Malaysia. This district comprises of 12 sub-districts ('Mukims'). The survey was conducted over two consecutive months (February to March 2021). A combination of online social media platforms and face-to-face interviews was employed to distribute the survey and successfully gathered responses from 257 respondents. The data collected encompassed species availability, habitat availability, individual primate counts and human-primate conflicts. Chi-squared analysis, point biserial correlation, descriptive statistics and alpha diversity indices were used to analyse the data. The results indicated that Macaca fascicularis reported the highest number of individuals and was predominantly present across all sub-districts. This species also frequently engaged in conflicts with humans, primarily as agricultural pests and residential nuisances. The method described herein proved effective in providing reliable tests for species presence-absence, and collecting human-wildlife conflict data with specific geographical locations. However, further improvements in the design are required to more accurately evaluate the primate populations. Nonetheless, this method serves as a promising pilot approach for estimating wildlife populations at the state level, offering a rapid, cost-effective, and extensive alternative to traditional ecological techniques. [ABSTRACT FROM AUTHOR]

Flying fox (Pteropus hypomelanus) belongs to the frugivorous bats, which play a crucial role in maintaining proper functioning of an ecosystem and conservation of the environment. Bats are well-known carriers of pathogenic viruses, such as BatCov RaTG13 from the coronavirus family that share 90.55% with SARS-CoV-2, the pathogen causing recent global pandemic coronavirus disease 19 (COVID-19). However, bats' possible role as a carrier of pathogenic bacteria is less explored. Here, using metabarcoding analysis through high-throughput sequencing, we explored the gut microbiome composition of different island populations on the east and west coasts of Peninsula Malaysia. The 16S rRNA gene in samples from Redang Island, Langkawi Island, Pangkor Island and Tinggi Island was amplified. Bacterial community composition and structure were analysed with a and ß diversity metrics. A total of 25,658 operational taxonomic units at 97% similarity were assigned to eight phyla, 44 families, 61 genera and 94 species of microbes. The Proteobacteria was the dominant phylum in all populations. Meanwhile, the genera Enterobacter, Pseudomonas and Klebsiella, isolated in this study, were previously found in the rectum of other fruit bats. Our analyses suggest that Redang Island and Langkawi Island have high bacteria diversity. Thus, we found geographic locality is a strong predictor of microbial community composition and observed a positive correlation between ecological features and bacterial richness. [ABSTRACT FROM AUTHOR]

èPhylogenetic 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 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. [ABSTRACT FROM AUTHOR]

Simple Summary: This study investigated plant diet of wild Macaca arctoides in the Malaysia–Thailand border region using a chloroplast tRNL DNA metabarcoding approach. It is a comprehensive molecular technique to assess foods eaten by primates. We have chosen chloroplast tRNL because this region has been widely used for identifying plant species. Chloroplast tRNL DNA was amplified and sequenced using the Illumina MiniSeq platform. Sequences were analyzed using the CLC Genomic Workbench software version 12.0 to check for M. arctoides plant diet. Across these samples, we successfully identified 29 plant orders, 46 families, 124 genera, and 145 species. As the first report in Malaysia, the findings provide an important understanding on diet of wild M. arctoides that only reside in Perlis State Park, Malaysia. Understanding dietary diversity is a fundamental task in the study of stump-tailed macaque, Macaca arctoides in its natural habitat. However, direct feeding observation and morphological identification using fecal samples are not effective and nearly impossible to obtain in natural habitats because this species is sensitive to human presence. As ecological methods are challenging and time-consuming, DNA metabarcoding offers a more powerful assessment of the diet. We used a chloroplast tRNL DNA metabarcoding approach to identify the diversity of plants consumed by free-ranging M. arctoides in the Malaysia–Thailand border region located in Perlis State Park, Peninsular Malaysia. DNA was extracted from three fecal samples, and chloroplast tRNL DNA was amplified and sequenced using the Illumina MiniSeq platform. Sequences were analyzed using the CLC Genomic Workbench software. A total of 145 plant species from 46 families were successfully identified as being consumed by M. arctoides. The most abundant species were yellow saraca, Saraca thaipingensis (11.70%), common fig, Ficus carica (9.33%), aramata, Clathrotropis brachypetala (5.90%), sea fig, Ficus superba (5.44%), and envireira, Malmea dielsiana (1.70%). However, Clathrotropis and Malmea are not considered Malaysian trees because of limited data available from Malaysian plant DNA. Our study is the first to identify plant taxa up to the species level consumed by stump-tailed macaques based on a DNA metabarcoding approach. This result provides an important understanding on diet of wild M. arctoides that only reside in Perlis State Park, Malaysia. [ABSTRACT FROM AUTHOR]

Background: The gut microbiota plays an important role in primates, which may be associated with their habitat. In Malaysia, pig-tailed macaques (Macaca nemestrina) live in different habitat environments and have traditionally been used for coconut plucking for more than a century. There is currently no information regarding the gut microbiota of this macaque in Malaysia. To address this oversight, this study employed a fecal metabarcoding approach to determine the gut microbiota composition of pig-tailed macaques and establish how these microbial communities correspond with the macaque external environments of residential area, forest edge, and fragmented forest., Methods: To determine this connection, 300 paired-end sequences of 16S rRNA were amplified and sequenced using the MiSeq platform., Results: In the pig-tailed macaque fecal samples, we identified 17 phyla, 40 orders, 52 families, 101 genera, and 139 species of bacteria. The most prevalent bacterial families in the gut of pig-tailed macaques were Firmicutes (6.31%) and Proteobacteria (0.69%). Our analysis did not identify a significant difference between the type of environmental habitat and the gut microbiota composition of these macaques., Conclusions: There was great variation in the population richness and bacterial community structure. The abundance of Firmicutes and Proteobacteria helps this macaque digest food more easily while maintaining a healthy gut microbiota diversity. Exploring the gut microbiota provides an initial effort to support pig-tailed macaque conservation in the future., (© 2024 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)

Background: The gut morphology of Symphalangus syndactylus exhibits an intermediate structure that aligns with its consumption of fruit and ability to supplement its diet with leaves. The Siamang relies on its gut microbiome for energy extraction, immune system development, and the synthesis of micronutrients. Gut microbiome composition may be structured based on several factors such as age, sex, and habitat. No study has yet been carried out on the gut microbiota of the Hylobatidae members in Malaysia especially S. syndactylus., Methods: This study aims to resolve the gut microbiome composition of S. syndactylus by using a fecal sample as DNA source, adapting high-throughput sequencing, and 16S rRNA as the targeted region., Results: A total of 1 272 903 operational taxonomic units (OTUs) reads were assigned to 22 phyla, 139 families, and 210 genera of microbes. The {Unknown Phylum} Bacteria-2 is the dominant phyla found across all samples. Meanwhile, {Unknown Phylum} Bacteria-2 and Firmicutes are genera that have the highest relative abundance found in the Siamang gut., Conclusions: This study yields nonsignificance relationship between Siamang gut microbiome composition with these three factors: group, sex, and age., (© 2024 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)

The banded langur (Presbytis femoralis) is a critically endangered primate, which within Malaysia has not been known to extend significantly outside the state of Johor. Traditionally, distribution studies on this highly threatened primate have relied on conventional methods such as DNA identification, live counting, and camera trapping. However, ethnoprimatology offers an alternative approach to data collection, involving the active participation of indigenous and local communities possessing valuable knowledge and experience with local primate species. This study employed an integrated approach incorporating ethnoprimatology by utilizing pooled local expert opinion, local surveys, interviews, and fecal DNA analysis, resulting in a novel distribution range for the banded langur. The combination of expert opinions revealed this species' most optimistic distribution scenario across Johor and Pahang, inhabiting various ecosystems, including lowland forests, peat swamps, and human-modified landscapes. Further interviews and surveys conducted within the Orang Asli community in Tasik Chini and Tasek Bera have provided additional support for the revised distribution, documenting occurrences of banded langur utilization in indigenous practices, such as food consumption, cultural beliefs, medicinal applications, and craftsmanship. Phylogenetic analysis demonstrated genetic differentiation between populations in Johor and Pahang, with the populations in the southern part of Peninsular Malaysia likely serving as ancestral sources for other populations. Consequently, this study not only elucidated the updated distribution of banded langur through DNA records and direct observations but also established the efficacy of ethnoprimatology as a precursory tool for uncovering the present distribution patterns of other primate species in Malaysia., (© 2024 Wiley Periodicals LLC.)

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.

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 (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 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.