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

2018 ◽  
Vol 19 (5) ◽  
pp. 1601-1606 ◽  
Author(s):  
BADRUL MUNIR MD-ZAIN ◽  
AQILAH ABDUL-AZIZ ◽  
NUR SYAFIKA MOHD-YUSUF ◽  
ROSLI NORSYAMIMI ◽  
JEFFRINE JAPNING ROVIE-RYAN ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Wildlife Conservation ◽  
Sequence Variation ◽  
Peninsular Malaysia ◽  
Management Program ◽  
Chain Reactions ◽  
Loop Region ◽  
D Loop ◽  
Bos Gaurus ◽  
Common Parent

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.

scholarly journals Genetic variations among selected wild Asian elephant populations in Peninsular Malaysia based on mitochondrial D-loop region DNA sequences

2019 ◽  
Vol 20 (9) ◽  
Author(s):  
KAYAL VIZI KARUPPANNAN ◽  
NOR AIFAT RAHMAN ◽  
KHAIRUL AMIRIN MOHAMED ◽  
NURUL FARAH DIYANA AHMAD TAHIR ◽  
FATIN MARDHIAH NORDIN ◽  
...  
Keyword(s):  
National Parks ◽  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Haplotype Diversity ◽  
Mitochondrial Control Region ◽  
Genetic Variations ◽  
Peninsular Malaysia ◽  
Asian Elephant ◽  
Loop Region ◽  
D Loop

Abstract. Karuppannan KV, Aifat NR, Mohamed KA,  Ahmad-Tahir NFD,  Nordin FM, Yaakop S, Maldonado JE, Md-Zain BM. 2019. Genetic variations among selected wild Asian elephant populations in Peninsular Malaysia based on mitochondrial D-loop region DNA sequences. Biodiversitas 20: 2494-2502. Asian elephant (Elephas maximus) is an important large mammal in Peninsular Malaysia and is completely protected by the Wildlife Conservation Act 2010 (Act 716). The conservation of this species requires strong information-based research, such as genetic evaluations. The aim of this study was to compare mitochondrial control region variation among selected elephants from the Taman Negara National Parks (TNNP) population with other selected populations in Peninsular Malaysia. DNA materials were extracted from fecal samples and amplified using partial mitochondrial D-loop region. Total 13 haplotypes with haplotype diversity (Hd) of 0.7524 were observed. A total of 34 base pair (bp) segregation sites were formed in 547 bp sequences. Both phylogenetic trees showed that a few individual elephants from the TNNP formed a clade together with individuals from other populations. The remaining individual elephants from TNNP formed a monophyletic clade supported by a high bootstrap value. Low genetic distance was detected among the tested populations, which proved that both individuals from the TNNP and other selected populations have similar genetic patterns. High gene flow among tested populations would impact on fitness and long-term resilience of the populations. This highly significant outcome provides strong baseline data for Department of Wildlife and National Parks (DWNP) in monitoring elephant populations in order to reduce number of human-elephant conflicts which indirectly minimize translocating conflict elephants to TNNP.

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

Data in Brief ◽  
2019 ◽  
Vol 24 ◽  
pp. 103532 ◽  
Author(s):  
Badrul Munir Md-Zain ◽  
Aqilah Abdul-Aziz ◽  
Nor Rahman Aifat ◽  
Nur Syafika Mohd-Yusof ◽  
Nadiatur Akmar Zulkifli ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Sequence Variation ◽  
Loop Region ◽  
Variation Data ◽  
D Loop ◽  
Bos Gaurus

scholarly journals Sequence variation and structural conservation in the D-loop region and flanking genes of mitochondrial DNA from Japanese pond frogs.

2000 ◽  
Vol 75 (2) ◽  
pp. 79-92 ◽  
Author(s):  
Masayuki Sumida ◽  
Hideki Kaneda ◽  
Yoji Kato ◽  
Yasushi Kanamori ◽  
Hiromichi Yonekawa ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Sequence Variation ◽  
Loop Region ◽  
D Loop ◽  
Structural Conservation

Study on Tandem Repeat Sequence Variation in Sheep mtDNA D-loop Region

2006 ◽  
Vol 33 (12) ◽  
pp. 1087-1095 ◽  
Author(s):  
LI Xiang-Long ◽  
GONG Yuan-Fang ◽  
LIU Zheng-Zhu ◽  
ZHENG Gui-Ru ◽  
ZHOU Rong-Yan ◽  
...  
Keyword(s):  
Tandem Repeat ◽  
Sequence Variation ◽  
Repeat Sequence ◽  
Tandem Repeat Sequence ◽  
Loop Region ◽  
D Loop

mtDNA D-loop sequence analysis of Kalang, Krayan, and Thale Noi buffaloes (Bubalus bubalis) in Indonesia and Thailand reveal genetic diversity

2021 ◽  
Vol 46 (2) ◽  
pp. 93-105
Author(s):  
S. Suhardi ◽  
P. Summpunn ◽  
S. Wuthisuthimethavee
Keyword(s):  
Genetic Diversity ◽  
Sequence Analysis ◽  
Phylogenetic Tree ◽  
Dna Sequences ◽  
Haplotype Diversity ◽  
Bubalus Bubalis ◽  
Relationship Patterns ◽  
Loop Region ◽  
Loop Sequence ◽  
D Loop

Kalang (KBuf), Krayan (KrBuf), and Thale Noi buffaloes (TBuf) are swamp buffalo genetic resources in Indonesia and Thailand. The maternally inherited mitochondrial DNA (mtDNA), particularly D-loop region is an important material for phylogenetic inference and analyzing genetic diversity. Therefore, the objectives of the present study were to evaluate genetic diversity and to reconstruct the phylogenetic tree within buffalo breeds in Kalimantan, Indonesia, and Phatthalung, Thailand using mtDNA D-loop sequences. A total of one hundred forty buffaloes (70 males and 70 females) were observed including 40 buffaloes from North (NK), 40 from East (EK), and 40 from South Kalimantan (SK) provinces Indonesia and 20 from Phatthalung (PT) province, Thailand. DNA samples were isolated from buffalo tail hairs. DNA sequences were manually assembled using BioEdit program with consideration of gaps and ambiguous sequences. The phylogenetic tree of buffalo was generated by PHYLIP software. The observed variables included haplotype diversity, genetic distance, and genetic tree. The 956 bp of amplified mtDNA D-loop fragment presented a total of 24 haplotypes with several mutations that included transitions (293), transversions (60), deletions (15), and insertions (20). The neighbor-joining tree using the Kimura 2 parameter model demonstrated two local buffalo clusters among buffalo from Kalimantan and Thailand with four buffalo relationship patterns observed from buffaloes in Kalimantan Island (KBuf and KrBuf), Indonesia. The Results of the present study demonstrated that the buffaloes sequence analysis revealed relatively high diversity and is a good basis to perform selection and modern buffalo breeding development.

scholarly journals Mitochondrial D-loop sequence variation among Hucul horse

2013 ◽  
Vol 58 (No. 10) ◽  
pp. 437-442 ◽  
Author(s):  
V. Czerneková ◽  
T. Kott ◽  
I. Majzlík
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Information ◽  
Sequence Variation ◽  
Dna Typing ◽  
Conservation Strategies ◽  
Base Pairs ◽  
Horse Population ◽  
Loop Region ◽  
Loop Sequence ◽  
D Loop

Genetic variation in the Czech Hucul horse population was analyzed using a sequence analysis of the D-loop region of mitochondrial DNA. One hundred and sixty-five Hucul horses were tested. Sequencing of the 700-base pairs fragment of the mitochondrial DNA D-loop region revealed 38 mutation sites representing 14 haplotypes, which were clustered into six haplogroups. The genetic information obtained from the mitochondrial DNA typing is of utmost importance for the future breed-conservation strategies.  

scholarly journals Phylogenetic Relationships of Turkish Indigenous Donkey Populations Determined by Mitochondrial DNA D-loop Region

Animals ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1970
Author(s):  
Emel Özkan Ünal ◽  
Fulya Özdil ◽  
Selçuk Kaplan ◽  
Eser Kemal Gürcan ◽  
Serdar Genç ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Sequences ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Loop Region ◽  
Geographical Regions ◽  
D Loop ◽  
Significant Comparison ◽  
Loop Regions ◽  
Frequent Haplotype

In this study, to analyze the mtDNA D-loop region and the origin of the maternal lineages of 16 different donkey populations, and to assess the domestication of Turkish indigenous donkeys in seven geographical regions, we investigated the DNA sequences of the D-loop region of 315 indigenous donkeys from Turkey. A total of 54 haplotypes, resulting from 35 polymorphic regions (27 parsimoniously informative and 6 singleton sites), were defined. Twenty-eight of these haplotypes are unique (51.85%), and 26 are shared among different Turkish indigenous donkey populations. The most frequent haplotype was Hap 1 (45.71%), followed by two haplotypes (Hap 4, 15.55% and Hap 7, 5.39%). The breed genetic diversity, evaluated by the haplotype diversity (HD) and nucleotide diversity (πD), for the Turkish donkey populations ranged from 0.533 ± 0.180 (Tekirdağ–Malkara, MAL) to 0.933 ± 0.122 (Aydin, AYD), and from 0.01196 ± 0.0026 (Antalya, ANT) to 0.02101 ± 0.0041 (Aydin, AYD), respectively. We observed moderate-to-high levels of haplotype diversity and moderate nucleotide diversity, indicating plentiful genetic diversity in all of the Turkish indigenous donkey populations. Phylogenetic analysis (NJT) and median-joining network analysis established that all haplotypes were distinctly grouped into two major haplogroups. The results of AMOVA analyses, based on geographic structuring of Turkish native donkey populations, highlighted that the majority of the observed variance is due to differences among samples within populations. The observed differences between groups were found to be statistically significant. Comparison among Turkish indigenous donkey mtDNA D-loop regions and haplotypes, and different countries’ donkey breeds and wild asses, identified two clades and which is named Somali (Clade IV) and Nubian (Clade V) lineages. The results can be used to understand the origin of Turkish donkey populations clearly, and to resolve the phylogenetic relationship among all of the different regions.

scholarly journals Continental Monophyly and Molecular Divergence of Peninsular Malaysia’sMacaca fascicularis fascicularis

2014 ◽  
Vol 2014 ◽  
pp. 1-18 ◽  
Author(s):  
Muhammad Abu Bakar Abdul-Latiff ◽  
Farhani Ruslin ◽  
Hamdan Faiq ◽  
Mohd Salleh Hairul ◽  
Jeffrine Japning Rovie-Ryan ◽  
...  
Keyword(s):  
Macaca Fascicularis ◽  
Peninsular Malaysia ◽  
The Other ◽  
Posterior Probabilities ◽  
Monophyletic Clade ◽  
Loop Region ◽  
Minimum Spanning Network ◽  
D Loop ◽  
Isthmus Of Kra ◽  
Insular Populations

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’sM. f. fascicularisbased 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 (FST, 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’sM. f. fascicularisbelonged to Indochinese populations as opposed to the previously claimed Sundaic populations.M. f. fascicularisgroups 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.

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