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.

scholarly journals 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

2014 ◽  
Vol 2014 ◽  
pp. 1-11 ◽  
Author(s):  
M. K. A. Rosli ◽  
S. M. F. Syed-Shabthar ◽  
P. Abdul-Patah ◽  
Z. Abdul-Samad ◽  
S. N. Abdul ◽  
...  
Keyword(s):  
The Other ◽  
Malay Peninsula ◽  
New Subspecies ◽  
Distance Analysis ◽  
Loop Region ◽  
Southern Thailand ◽  
Northern Regions ◽  
Minimum Spanning Network ◽  
D Loop

Three species of otter can be found throughout Malay Peninsula: Aonyx cinereus, Lutra sumatrana, and Lutrogale perspicillata. In this study, we focused on the A. cinereus population that ranges from the southern and the east coast to the northern regions of Malay Peninsula up to southern Thailand to review the relationships between the populations based on the mitochondrial D-loop region. Forty-eight samples from six populations were recognized as Johor, Perak, Terengganu, Kelantan, Ranong, and Thale Noi. Among the 48 samples, 33 were identified as A. cinereus, seven as L. sumatrana, and eight as L. perspicillata. Phylogenetically, two subclades formed for A. cinereus. The first subclade grouped all Malay Peninsula samples except for samples from Kelantan, and the second subclade grouped Kelantan samples with Thai sample. Genetic distance analysis supported the close relationships between Thai and Kelantan samples compared to the samples from Terengganu and the other Malaysian states. A minimum-spanning network showed that Kelantan and Thailand formed a haplogroup distinct from the other populations. Our results show that Thai subspecies A. cinereus may have migrated to Kelantan from Thai mainland. We also suggest the classification of a new subspecies from Malay Peninsula, the small-clawed otter named A. cinereus kecilensis.

scholarly journals Age, growth and genetic status of the white shark (Carcharodon carcharias) from Kashima-nada, Japan

2011 ◽  
Vol 62 (6) ◽  
pp. 548 ◽  
Author(s):  
S. Tanaka ◽  
T. Kitamura ◽  
T. Mochizuki ◽  
K. Kofuji
Keyword(s):  
South Africa ◽  
Life History ◽  
Life History Traits ◽  
Growth Parameters ◽  
White Shark ◽  
Von Bertalanffy ◽  
Top Predator ◽  
Monophyletic Clade ◽  
Loop Region ◽  
D Loop

The white shark, a top predator inhabiting the world’s oceans, is an endangered species. However, knowledge of its life-history traits and population structure is still limited. We hypothesised that life-history traits would vary among populations because the species’ various habitats are diverse and change through time. Age was estimated by counting growth bands in the centra of white sharks caught in Japan. The von Bertalanffy growth parameters were estimated at L∞ = 455 cm TL, k = 0.196 year–1 and t0 = –1.92 years for males and L∞ = 607 cm TL, k = 0.159 year–1 and t0 = –1.80 years for females. The growth rate to maturity was higher than that known for individuals from California and South Africa. Male sharks matured at 310 cm TL at 4 years of age and females began to mature at ~450 cm TL and 7 years. The D-loop-region sequences of mitochondrial DNA extracted from Japanese white sharks and GenBank datasets from sharks of California, Australia, New Zealand and South Africa indicate that Japanese white sharks form a monophyletic clade separate from the populations of other regions. The results suggest that unique life-history traits of Japanese white sharks may be caused by genetic differences.

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 Mitochondrial DNA Methylation and Human Diseases

2021 ◽  
Vol 22 (9) ◽  
pp. 4594
Author(s):  
Andrea Stoccoro ◽  
Fabio Coppedè
Keyword(s):  
Dna Methylation ◽  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Nuclear Dna ◽  
Epigenetic Modification ◽  
Nuclear Genome ◽  
Epigenetic Modifications ◽  
Human Diseases ◽  
Loop Region ◽  
D Loop

Epigenetic modifications of the nuclear genome, including DNA methylation, histone modifications and non-coding RNA post-transcriptional regulation, are increasingly being involved in the pathogenesis of several human diseases. Recent evidence suggests that also epigenetic modifications of the mitochondrial genome could contribute to the etiology of human diseases. In particular, altered methylation and hydroxymethylation levels of mitochondrial DNA (mtDNA) have been found in animal models and in human tissues from patients affected by cancer, obesity, diabetes and cardiovascular and neurodegenerative diseases. Moreover, environmental factors, as well as nuclear DNA genetic variants, have been found to impair mtDNA methylation patterns. Some authors failed to find DNA methylation marks in the mitochondrial genome, suggesting that it is unlikely that this epigenetic modification plays any role in the control of the mitochondrial function. On the other hand, several other studies successfully identified the presence of mtDNA methylation, particularly in the mitochondrial displacement loop (D-loop) region, relating it to changes in both mtDNA gene transcription and mitochondrial replication. Overall, investigations performed until now suggest that methylation and hydroxymethylation marks are present in the mtDNA genome, albeit at lower levels compared to those detectable in nuclear DNA, potentially contributing to the mitochondria impairment underlying several human diseases.

scholarly journals Genetic Diversity of Maternal Lineage in the Endangered Kiso Horse Based on Polymorphism of the Mitochondrial DNA D-Loop Region

2014 ◽  
Vol 76 (11) ◽  
pp. 1451-1456 ◽  
Author(s):  
Masaki TAKASU ◽  
Namiko ISHIHARA ◽  
Teruaki TOZAKI ◽  
Hironaga KAKOI ◽  
Masami MAEDA ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Maternal Lineage ◽  
Loop Region ◽  
D Loop
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