A noninvasive molecular approach: exploiting species-locus-specific PCR primers in defeating numts and DNA cross-contamination of cercopithecidae

The lack of a standardized, noninvasive molecular approach to studying genetic aspects of primates has made it hard for primatologists to decode the evolutionary history of these species. Researchers must optimize their own techniques to fully exploit the available samples. Lack of species-locus-specific primers also contributes to difficulties in using noninvasive genetic samples. Thus, the objectives of this study were to develop a standardized technique to collecting samples noninvasively, propose newly designed species-locus-specific primers, and optimize conditions for polymerase chain reaction (PCR) for Macaca fascicularis, M. nemestrina, Trachypithecus cristatus, and T. obscurus. Nine new species-locus-specific primers for three different loci of mitochondrial DNA, namely D-loop, cytochrome oxidase subunit I (COI), and cytochrome b, were successfully designed. These primers proved to be efficient in amplifying larger datasets (up to ~1,000 bp) of the targeted species in the optimized PCR conditions. The species-locus-specific primers are able to anneal to host DNA alone in highly contaminated feces of highlighted species. They can also offer alternatives measures in avoiding contamination related to nuclear insertion of mitochondrial pseudogenes (numts)

Agonistic behavior of captive saltwater crocodile, crocodylus porosus in Kota Tinggi, Johor

Agonistic behavior in Crocodylus porosus is well known in the wild, but the available data regarding this behavior among the captive individuals especially in a farm setting is rather limited. Studying the aggressive behavior of C. porosus in captivity is important because the data obtained may contribute for conservation and the safety for handlers and visitors. Thus, this study focuses on C. porosus in captivity to describe systematically the agonistic behaviour of C. porosus in relation to feeding time, daytime or night and density per pool. This study was carried out for 35 days in two different ponds. The data was analysed using Pearson’s chi-square analysis to see the relationship between categorical factors. The study shows that C. porosus was more aggressive during daylight, feeding time and non-feeding time in breeding enclosure (Pond C, stock density =0.0369 crocodiles/m2) as compared to non-breeding pond (Pond B, stock density =0.3317 crocodiles/m2) where it is only aggressive during the nighttime. Pond C shows the higher domination in the value of aggression in feeding and non-feeding time where it is related to its function as breeding ground. Chi-square analysis shows that there is no significant difference between ponds (p=0.47, χ2= 2.541, df= 3), thus, there is no relationship between categorical factors. The aggressive behaviour of C. porosus is important for the farm management to evaluate the risk in future for the translocation process and conservation of C. porosus generally

Isolation of a pigment-producing bacterium chryseobacterium sp. from the tentacle of holothuria (lessonothuria) pardalis (Selenka 1867) from Pulau Tinggi, Johor

Chryseobacterium sp, a bacteria producing pigment was isolated from the tentacles of Holothuria (Lessonothuria) pardalis (Selenka 1867) from Pulau Tinggi, Johor. This study aimed to observe and genetically identified the presence of bacteria focusing on pigmentproducing bacteria. Thus, the partial 16S ribosomal RNA gene sequence of bacteria obtained and the shape, number of bacteria and gram staining observed using a digital compound microscope. Six gene sequence successfully obtained and the Basic Local Alignment Search Tool (BLAST) analysis suggested three species of bacteria identified from genus Pseudomonas, Chryseobacterium and Klebsiella. Besides, the neighbourhood-joining and Maximum Likelihood method had been used in the phylogenetic analysis to support the identification of bacteria species. The visible spectra of Chryseobacterium sp. were recorded between 400nm to 600nm which is a visible spectrum for carotenoid; orange pigment. However, further analysis is needed to confirm the characterisation and the potential of this pigment in industria

Molecular systematic position of the Sarawak Malay badger, Mydaus javanensis

The presence of the Malay badger, Mydaus javanensis, has been recorded for nearly 100 years in Sarawak, Malaysia, but it has rarely been seen. In addition, this animal is among the least studied carnivores in Borneo. The Malay badger is not protected under the Sarawak Wildlife Protection Ordinance. To initiate conservation efforts, we conducted a phylogenetic analysis to characterize the Malay badger’s genetic attributes. In August 2013, a Malay badger was trapped at Mentung Berawan, Serian, and sent to the Matang Wildlife Centre. We managed to collect its genetic materials and sequenced 356 bp of 12S rRNA and 405 bp of cytochrome b (Cyt b) genes. We portrayed its phylogenetic relationships with other Mephitidae family members and calculated its molecular divergence. Our results indicated that the Malay badger could be distinguished from its sister taxon, M. marchei. The teledu clade diverged 2.71 million years ago, after the divergences of Mephitis mephitis and Spilogale putorius

Agonistic Behavior of Captive Saltwater Crocodile, Crocodylus Porosus in Kota Tinggi, Johor

Agonistic behavior in Crocodylus porosus is well known in the wild, but the available data regarding this behavior among the captive individuals especially in a farm setting is rather limited. Studying the aggressive behavior of C. porosus in captivity is important because the data obtained may contribute for conservation and the safety for handlers and visitors. Thus, this study focuses on C. porosus in captivity to describe systematically the agonistic behaviour of C. porosus in relation to feeding time, daytime or night and density per pool. This study was carried out for 35 days in two different ponds. The data was analysed using Pearson’s chi-square analysis to see the relationship between categorical factors. The study shows that C. porosus was more aggressive during daylight, feeding time and non-feeding time in breeding enclosure (Pond C, stock density =0.0369 crocodiles/m2) as compared to non-breeding pond (Pond B, stock density =0.3317 crocodiles/m2) where it is only aggressive during the nighttime. Pond C shows the higher domination in the value of aggression in feeding and non-feeding time where it is related to its function as breeding ground. Chi-square analysis shows that there is no significant difference between ponds (p=0.47, χ2= 2.541, df= 3), thus, there is no relationship between categorical factors. The aggressive behaviour of C. porosus is important for the farm management to evaluate the risk in future for the translocation process and conservation of C. porosus generally.&nbsp

Feeding Regime and Management of Captive Saltwater Crocodile, Crocodylus Porosus in Kota Tinggi, Johor

Crocodylus porosus is the largest species of crocodile and can be found in estuarine and riverine area in Malaysia. Crocodile in captivity can be found in Malaysia for various purposes such as tourism, conservation and leather industry. However, the management practice in established crocodile farm varies across park for example in terms of feeding regime. Thus, this study focusses on the feeding regime of C. porosus in captivity and evaluation of management of crocodile of Teluk Sengat Crocodile Farm. This study was carried out for 35 days in two different ponds of Teluk Sengat Crocodile Farm, Kota Tinggi, Johor. The results show majority of the food given to crocodile were chicken (64%), followed by fish (28%) and prawn (8%). Prawn was only given to juvenile crocodile every day, while fish and whole chicken were given to adult crocodile once a week. The feeding frequency are adequate for the juvenile crocodile however, the feeding quantity for adult pond are worrying. Future research should be conducted on other captive population of C. porosus in other areas in Malaysia as well to better understand the overall management practices in Malaysia

Molecular phylogenetic inference of White-Spotted Guitarfish (Rhynchobatus australiae) collected from local Malaysian fish markets

The white-spotted guitarfish (Rhynchobatus australiae) is in high demand at local Malaysian fish markets because its fins are a valuable food source. To date, few molecular studies have characterized their genetic identity. We have conducted a molecular study to infer the phylogenetic relationships of white-spotted guitarfish, which portray a similar morphology to sharks and rays. The main objective of this study was to determine the phylogenetic position of R. australiae using cytochrome oxidase I (COI) sequences of mitochondrial DNA based on fish samples collected from local Malaysian fish markets. This study included nine genetic samples of R. australiae and fourteen samples from other members of the shark and ray families, including Sphyrna lewini (Sphyrnidae), Rhizoprionodon oligolinx and Carcharhinus sorrah (Carcharhinidae), Dasyatis zugei, Himantura walga, Himantura gerradi, Himantura jenkinsii and Neotrygon kuhlii (Dasyatidae). Chimaera fulva, a member of the Chimaera family, was used as the outgroup. Sequences in size of ~701 base pairs were successfully obtained from all fish samples. The phylogenetic tree topology was reconstructed using distance-based (neighbor-joining) and character-based (maximum parsimony) methods using MEGA and PAUP software. Results indicated that R. australiae formed monophyletic clade and is closely related to sharks (Sphyrnidae and Carcharhinidae). This conclusion was also supported by genetic distance analysis which indicated that Rhynchobatidae and sharks (Carcharhinidae and Sphyrnidae) were closer to each other than to rays (Dasyatidae). This study has proven the efficiency of the COI mitochondrial locus in revealing the phylogenetic position of R. australiae. Research findings from this study have increased our understanding of the phylogenetic relationships among guitarfish, sharks, and rays, and their respective taxonomic positions are given their shared morphological characters. This will benefit us in identifying these fish species before consumption from local fish markets

Isolation of bacteria associated with the tentacles of holothuria (lessonothuria) pardalis (selenka 1867) from Pulau Tinggi, Johor including pigment-producing chryseobacterium sp.

Pigment-producing microorganisms have become a main focus due to the search of food-grade microbial pigments for natural food colourant industry. Therefore, this study aimed to isolate and genetically identify bacteria including pigmentproducing bacterial strains associated with the tentacles of Holothuria (Lessonothuria) pardalis (Selenka 1867) from Pulau Tinggi, Johor. Morphological characteristics of bacteria based on Gram staining were observed using a digital compound microscope. Partial 16S ribosomal RNA (rRNA) gene sequencing was also incorporated to support the morphological approach. A number of six partial gene sequences of non-protein coding 16S rRNA were obtained and the Basic Local Alignment Search Tool (BLAST) analysis suggested the presence of three known bacteria species from the genera of Pseudomonas, Chryseobacterium and Klebsiella. The neighbourhood-joining method and Maximum Likelihood method used in the phylogenetic analysis supported the identification and classification of the bacteria species. Among the bacterial isolates, only strain B14 identified as Chryseobacterium sp. produced pigment i.e. orange pigment. The highest point of cell density of Chryseobacterium sp. was recorded at 16 hours. However, further analysis is needed to confirm the pigment characterisation and the potential of this pigment to be exploited as natural colourant in the food industry

Population census and age category character of Stump tailed macaque, Macaca arctoides, in Northern Peninsular Malaysia

Macaca arctoides is reported to be distributed only in the northern part of Malay Peninsula. Intensive scientific observations have never been carried out before on this neglected macaque in the northern range. Thus, in this article, an estimation of population data on the Malaysian stump-tailed macaques that were found in Wang Kelian forest areas in Perlis State Park, Malaysia is presented. Intensive field observations were conducted from Sept 2018 to January 2019 with scanning sampling. The study revealed a total of 171-176 stump-tailed macaques, consisting of 44 (25%) adult males, 28 (16%) adult females, 19-22 (11%) sub-adult males, 16-19 (10%) sub-adult females, 43 (25%) juveniles, and 21-23 (13%) infants. Two main groups were observed, which were the Nomad and the Batat groups. Their ranging areas appear to sometimes overlap each other, while some Nomad members were observed in the Batat group. The age structure can be differentiated through body size and pelage coloration. The stump-tailed macaque populations in Wang Kelian are sensitive to human presence, while their habitat area is threatened by human illegal poaching activities. More conservation efforts are needed to conserve this neglected macaque from local extinction

Mixed-species association among malaysian primates during the covid-19 outbreak in Genting Highlands, Peninsular Malaysia

This is the first report to elucidate primate mixed-species association during Covid-19 outbreak in Malaysia. The observations were carried out at Genting Highlands between 14-24th April 2020 using ad libitum sampling. Five Genting Highlands primate species were observed at approximately 66 observation hours which include Symphalangus syndactylus (siamang), Trachypithecus obscurus obscurus (dusky langur), Presbytis siamensis siamensis (Malayan pale-thighed surili), Macaca nemestrina (southern pig-tailed macaque), and Macaca fascicularis (long-tailed macaque). Primates in Genting Highlands were seen interacting among themselves during the third phase of the MCO. Siamangs, dusky langurs, and long-tailed macaques were observed sharing space and interacting in an old section of Genting View Resorts that is currently under renovation. Malayan pale- thighed langurs were also observed approaching this area. During the third phase of the MCO, siamangs, dusky langurs, long-tailed macaques, and pig-tailed macaques consumed fruits of the fig tree (Ficus benjamina), which last for only one week. Strict controls on public movement are believed to have created environmental conditions that enabled Genting Highlands primates to move and interact freely among themselves