DNA forensic case study: species identification from suspected crocodile penis

Department of Wildlife and National Parks (PERHILITAN) began developing the capacity on wildlife DNA forensic since 2009 to assist in law enforcement activities. Most of the forensic cases require DNA species identification of animal parts where key morphological characters are missing. Among the cases frequently confiscated are from traditional Chinese medicine (TCM), which often claim to use animal parts such as reproductive organs. Dried crocodile penises, in particular, are believed to have medicinal benefits and are highly demanded in TCM industries since millennials ago. In this case study, we analysed four enforcement cases comprising of 44 exhibits which resemble crocodile penis using the partial cytochrome b gene of the mitochondrial DNA. Sequence similarity searches were conducted using both the BLAST search engines of GenBank and also PERHILITAN’s MyWILDNA database to identify the species. Out of 44 exhibits, 22 items produced DNA sequences in which three were found to be derived from Crocodylus porosus while the remaining was identified as Bos taurus, Bos javanicus, and Bos indicus. This case study showed that most of TCM which claimed to be derived from crocodile penis turned out to be counterfeit products

Carnivore hotspots in Peninsular Malaysia and their landscape attributes

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

Climatic influences on aedes mosquito larvae population

The impact of climate on Aedes larval population was studied.Monitoring of population was done using ovitraps. Ovitrap pr ovides a simple and convenient monitoring method for Aedes surveillance as the number of eggs laid in a standard trap within a specific time period give a relative measurement of the number of mosquito in the same area.Ovitraps were set outdoors in selec ted dengue prone areas in Desa Pandan, Kuala Lumpur for 66 weeks.Weather stations, consisting of a temperature and relative humidity data logger and an automated rain gauge were installed at key locations in the study site.Week-to-week variations of larval densities were correlated against variations in the individual climatic parameters.Results of the study showed that there was a close relationship between the heavy rainfall and the increased mosquito population in the study sites.The study showed that previous week rainfall plays a significant role in increasing the mosquito population

Phylogeography of the Sunda pangolin, Manis javanica: Implications for taxonomy, conservation management and wildlife forensics

The Sunda pangolin (Manis javanica) is the most widely distributed Asian pangolin species, occurring across much of Southeast Asia and in southern China. It is classified as Critically Endangered and is one of the most trafficked mammals in the world, which not only negatively impacts wild Sunda pangolin populations but also poses a potential disease risk to other species, including humans and livestock. Here, we aimed to investigate the species' phylogeography across its distribution to improve our understanding of the species' evolutionary history, elucidate any taxonomic uncertainties and enhance the species' conservation genetic management and potential wildlife forensics applications. We sequenced mtDNA genomes from 23 wild Sunda pangolins of known provenance originating from Malaysia to fill sampling gaps in previous studies, particularly in Borneo. To conduct phylogenetic and population genetic analyses of Sunda pangolins across their range, we integrated these newly generated mitochondrial genomes with previously generated mtDNA and nuclear DNA data sets (RAD‐seq SNP data). We identified an evolutionarily distinct mtDNA lineage in north Borneo, estimated to be ~1.6 million years divergent from lineages in west/south Borneo and the mainland, comparable to the divergence time from the Palawan pangolin. There appeared to be mitonuclear discordance, with no apparent genetic structure across Borneo based on analysis of nuclear SNPs. These findings are consistent with the ‘out of Borneo hypothesis’, whereby Sunda pangolins diversified in Borneo before subsequently migrating throughout Sundaland, and/or a secondary contact scenario between mainland and Borneo. We have elucidated possible taxonomic issues in the Sunda/Palawan pangolin complex and highlight the critical need for additional georeferenced samples to accurately apportion its range‐wide genetic variation into appropriate taxonomic and conservation units. Additionally, these data have improved forensic identification testing involving these species and permit the implementation of geographic provenance testing in some scenarios

Complete mitochondrial genome of Red Junglefowl (<i>Gallus gallus spadiceus</i>) from Peninsular Malaysia

Complete mitochondrial genome sequences have significant relevance in the study of phylogenetic relationships, evolution, and population genetics. In this paper, we present the complete mitochondrial genome of the red junglefowl (Gallus gallus spadiceus) from Peninsular Malaysia, inferred using next-generation sequencing (NGS). The mitogenome is 16,785 bp in length with the structural organization of an avian mitochondrial arrangement compromising 13 protein-coding regions, 22 tRNAs, 2 rRNAs, and 1 control region. No internal stop codon was found in the protein-coding genes. Overall base composition is A: 30.3%, C: 32.5%, G: 13.5%, and T: 23.7%, indicating a high A + T content of 54.0%. Phylogenetic tree analysis revealed that red junglefowl from Peninsular Malaysia is grouped together with other members of Gallus gallus specifically from Southeast Asia, with 89% bootstrap value support. These research findings might be beneficial for red junglefowl genetic identification, molecular systematic studies, and conservation management interest in the future.</p

Carnivores of Malaysia with 2015 IUCN conservation status, and Peninsular Malaysia conservation status in 2007 and 2009 based on percent change in area of occupancy and expert opinion [28].

<p>Although 31 species are listed, three species may not be indigenous or extant. The highest threat status, based on IUCN Red List criteria A–E [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194217#pone.0194217.ref029" target="_blank">29</a>] is reported for each species. EX = extinct, CE = critically endangered, EN = endangered, VU = vulnerable, NT = near threatened, LC = least concern.</p

Distribution of surveys (<i>n</i> = 133) of carnivores among different states in Peninsular Malaysia with records collected during 1948–2014.

<p>Data were based on 60 published papers and reports that used conventional trapping, direct observation, signs, remote cameras, or road kills. Some publications compiled data from several surveys and some geographic locations were surveyed more than once. Boundary layer: U.S. State Department, Humanitarian Information Unit (modified from Global Large Scale International Boundary Polygons). Inset map: U.S. Central Intelligence Agency (The World Factbook).</p

Locations of mammalian carnivore surveys and kernel density surface of Getis-Ord Gi* <i>z</i> scores of weighted ranking of IUCN red list categories for recorded species locations in Peninsular Malaysia, 1948–2014.

<p>Hillshade layer derived from Shuttle Radar Topography Mission (STRM) 90-m Digital Elevation Data from Consultative Group on International Agricultural Research (CGIAR) and reprinted under a CC BY license, with permission from International Center for Tropical Agriculture (CIAT), original copyright 2004. Protected areas mentioned in the text are labeled; reprinted from World Database on Protected Areas (http://<a href="http://www.protectedplanet.net/" target="_blank">www.protectedplanet.net</a>) under a CC BY license, with permission from the United Nations Environmental Programme-World Conservation Monitoring Centre, original copyright 2010.</p

Procedure for the selection of studies of mammalian carnivores in Peninsular Malaysia with records collected during 1948–2014.

<p>Procedure for the selection of studies of mammalian carnivores in Peninsular Malaysia with records collected during 1948–2014.</p

Number of records of Carnivora species in Peninsular Malaysia.

<p>Data were obtained from surveys that used conventional trapping, direct observation, sign, remote cameras, or road kills collected during 1991–2014. Species are grouped by family and ranked by number of records.</p