A New Subspecies Identification and Population Study of the Asian Small-Clawed Otter (<i>Aonyx cinereus</i>) in Malay Peninsula and Southern Thailand Based on Fecal DNA Method

Rosli, Mira Khalisa; Syed-Shabthar, S. M. F.; Abdul‐Patah, Pazil; Abdul-Samad, Z.; Abdul, S; Burhanuddin, M. N.; Zulkifli, Nadiatur Akmar; Shukor, M. N.; Budsabong, K.; Changtragoon, Suchitra; Sekiguchi, Toshio; Sasaki, Hiroshi; Md-Zain, Badrul Munir

doi:10.1155/2014/457350

Cited by 11 publications

(7 citation statements)

References 41 publications

(39 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Previous Malaysian mammal studies also conducted haplotype analyses of the mtDNA D-loop region using the DnaSP software. These haplotype analyses were conducted in the Asian elephant of Peninsular Malaysia (Elliza et al 2015) and in a population study of otters in Peninsular Malaysia in which a new subspecies of an otter was identified (Rosli et al 2014). Other loci, such as cytochrome b, have also been used, but these results are considered less effective.…”

Section: Haplotype Analysismentioning

confidence: 99%

Sequence variation of captive Malayan Gaur (Bos gaurus hubbacki) based on mitochondrial D-loop region DNA sequences

et al. 2018

View full text Add to dashboard Cite

Md-Zain BM, Abdul-Aziz A, Aifat NR, Mohd-Yusof NS, Norsyamimi R, Rovie-Ryan JJ, Karuppannan KV, Zulkifli NA, YaakopS. 2018. Sequence variation of captive Malayan Gaur (Bos gaurus hubbacki) based on mitochondrial D-loop region DNA sequences.Biodiversitas 19: 1601-1606. Malayan gaur (Bos gaurus hubbacki) can only be found in Peninsular Malaysia and southern Thailand.The International Union for Conservation of Nature (IUCN) has listed Malayan gaur in the Red List as vulnerable. The main objectiveof this study was to investigate sequence variation in the mitochondrial D-loop region of B. g. hubbacki from two captive centers. Wecollected 30 DNA samples of Malayan gaur from Jenderak Selatan Wildlife Conservation Center in Pahang and the Sungkai WildlifeReserve in Perak. Polymerase chain reactions were performed to amplify all the samples. DNA sequences were analyzed usingNeighbor-Joining (NJ) and Maximum Parsimony (MP) methods. Based on the 652 base pairs obtained, we found only seven variablecharacters with a value of 1% and a genetic distance between the two captive centers of 0.001. Haplotype analyses using DnaSPsoftware detected only four haplotypes between these two captive centers. Both NJ and MP trees portrayed all Malayan gaur individualsin Jenderak Selatan and Sungkai captive centers as belonging to the same clade. Genetic variation of Malayan gaur in these centers isconsidered low due to individuals possibly sharing the same common parent. This sequence variation information is of paramountimportance for the proper breeding and conservation management program of Malayan gaur in the future.

show abstract

Section: Haplotype Analysismentioning

confidence: 99%

Sequence variation of captive Malayan Gaur (Bos gaurus hubbacki) based on mitochondrial D-loop region DNA sequences

et al. 2018

View full text Add to dashboard Cite

show abstract

“…This represents a limitation to a current suite of available species-specific primers (Holmes et al 2009); and the challenge is particularly great in samples of degraded DNA from processed products, such as dried or salted fins. The primers may not be 100% specific, or they may have annealed to the nuclear insertion of mtDNA (numts), which can compromise the identification process (Rosli et al 2014;Abdul-Latiff et al 2017). The DNA barcoding method using the universal primers targeting the COI loci were utilized in this analysis and provided with significantly good stretches of COI sequences of ~750 bp.…”

Section: Discussionmentioning

confidence: 99%

Molecular identification of shark fins in Malaysian Borneo’s local markets

Md-Zain¹,

Abid-Kamal²,

Aifat³

et al. 2018

Biodiversitas

View full text Add to dashboard Cite

Abstract. Md-Zain BM, Abid-Kamal SNA, Aifat NR, Abdul-Latiff MAB, Mohd-Hashim A, Ampeng A, Yaakop S, Samat A. 2018.Molecular identification of shark fins in Malaysian Borneo’s local markets. Biodiversitas 19: 1035-1043. A molecular study was carriedout to investigate the potential of the cytochrome c oxidase subunit I (COI) gene as a molecular marker for the genetic identification ofshark fin samples that have gone through various preservation processes. A total number of 17 shark fin samples were collected fromlocal markets in Sabah and Sarawak (Malaysian Borneo). The DNA sequences of the 17 samples were amplified by using polymerasechain reaction. The results from the analysis showed that, in the 17 sequences, there were 16 haplotypes present, with 244 sites from 688bp of the sequences. For phylogeny analysis, tree topologies were reconstructed using the neighbor-joining (NJ) and maximumparsimony (MP) methods. DNA barcoding technique successfully identifies shark fins collected in local markets in Malaysian Borneo atspecies level employed during this study. Phylogenetic analysis showed that there were four clades that distinguish the four differentorders present in the sample species. These clades had bootstrap values higher than 80. In addition, results indicated that 88.2% of theindividuals are listed as endangered (Lamiopsis tephrodes, Sphyrna mokarran, and Sphyrna lewini), vulnerable (Alopias pelagicus andRhynchobatus australiae), and near threatened (Carcharhinus limbatus, Chiloscyllium griseum, Carcharhinus sorrah, and Carcharhinusbrevipinna), in the International Union for Conservation of Nature (IUCN) Red Data List.

show abstract

“…We used two methods of analysis in PAUP: first, neighbor joining with the Kimura 2-parameter model [7] to reconstruct a neighbor joining phylogram ( Fig. 3 ) and calculate the genetic distance ( Table 5 ), second, a maximum parsimony analysis with stepwise additions (1000 replicates) in a heuristic search [8] and 50% majority rule consensus ( Fig. 4 ).…”

Section: Experimental Design Materials and Methodsmentioning

confidence: 99%

Sequence variation data of the mitochondrial DNA D-loop region of the captive Malayan Gaur (Bos gaurus hubbacki)

et al. 2019

View full text Add to dashboard Cite

This article contains data of the sequence variation in the mitochondrial DNA D-loop region of the Malayan gaur ( Bos gaurus hubbacki ), locally known as the seladang, from two captive centers. Thirty fecal samples of Malayan gaur were collected from Jenderak Selatan Wildlife Conservation Center (Pahang) and the Sungkai Wildlife Reserve (Perak) for DNA extraction and amplification with polymerase chain reactions. DNA sequences were then analyzed using neighbor joining (NJ) and maximum parsimony (MP) methods. Based on the 652 base pairs obtained, we found seven variable characters with a value of 1%. The genetic distance between the two captive centers was 0.001. Haplotype analyses detected only four haplotypes between these two captive centers. Both NJ and MP trees demonstrate that all individuals in the Jenderak and Sungkai captive centers are in the same clade. Genetic variation of the Malayan gaur in these centers is considered low, possibly because individuals share the same common parent. This sequence variation data are of paramount importance for designing a proper breeding and management program of the Malayan gaur in the future.

show abstract

A New Subspecies Identification and Population Study of the Asian Small-Clawed Otter (Aonyx cinereus) in Malay Peninsula and Southern Thailand Based on Fecal DNA Method

Cited by 11 publications

References 41 publications

Sequence variation of captive Malayan Gaur (Bos gaurus hubbacki) based on mitochondrial D-loop region DNA sequences

Sequence variation of captive Malayan Gaur (Bos gaurus hubbacki) based on mitochondrial D-loop region DNA sequences

Molecular identification of shark fins in Malaysian Borneo’s local markets

Sequence variation data of the mitochondrial DNA D-loop region of the captive Malayan Gaur (Bos gaurus hubbacki)

Contact Info

Product

Resources

About