<b>Background and Objective:</b> The <i>Helarctos malayanus</i> is the sole bear species-living in Indonesia (Sumatra and Borneo). The available biological data for sun bears (<i>H. malayanus</i>) in Sumatra is limited, especially for morphological and genetic data. A morphological approach is difficult to do. Therefore, a molecular approach is the most likely choice. Phylogenetic analysis was carried out on <i>H. malayanus</i> in Central Sumatra (Dharmasraya, South Solok and Riau) using the Cytochrome B gene. <b>Materials and Methods:</b> Blood samples from three individuals of <i>H. malayanus</i> were obtained at the Sumatran Tiger Rehabilitation Center, Dharmasraya. Three <i>H. malayanus</i> Central Sumatra sequences and 62 GenBank sequences were used in the analysis. The DNA sequences were analyzed using the DNA Star, AliView, Bioedit, DNA SP, haplotype network, IQ Tree and MEGA software. <b>Results:</b> Forty-one haplotypes were identified in 65 sequences, with 17 haplotypes belonging to <i>H. malayanus</i>. Haplotype network analysis divides <i>H. malayanus</i> into Haplogroup I (Sundaland) and Haplogroup II (Mainland). All individuals of <i>H. malayanus</i> in Central Sumatra have the same haplotype as Peninsular Malaysia sequence. The sun bear (<i>H. malayanus</i>) has a monophyletic relationship with other bear species. The <i>H. malayanus</i> has a higher genetic distance between the two lineages (1.0-2.3%) than the genetic distance within the subpopulations of each lineage. <b>Conclusion:</b> The study results supported sun bear (<i>H. malayanus</i>) divided into two different lineages: Mainland (subcluster 1) and Sundaland (subcluster 2 and 3). The geographic isolation causes the absence of gene flow, which results in high genetic distance between sun bears (<i>H. malayanus</i>) in Sundaland and Mainland lineages.
Cardiomyopathy (CMP) constitutes a diverse group of myocardium diseases affecting the pumping ability of the heart. Genetic predisposition is among the major factors affecting the development of CMP. Globally, there are over 100 genes in autosomal and mitochondrial DNA (mtDNA) that have been reported to be associated with the pathogenesis of CMP. However, most of the genetic studies have been conducted in Western countries, with limited data being available for the Asian population. Therefore, this study aims to investigate the mutation spectrum in the mitochondrial genome of 145 CMP patients in Malaysia. Long-range PCR was employed to amplify the entire mtDNA, and whole mitochondrial genome sequencing was conducted on the MiSeq platform. Raw data was quality checked, mapped, and aligned to the revised Cambridge Reference Sequence (rCRS). Variants were named, annotated, and filtered. The sequencing revealed 1,077 variants, including 18 novel and 17 CMP and/or mitochondrial disease-associated variants after filtering. In-silico predictions suggested that three of the novel variants (m.8573G>C, m.11916T>A and m.11918T>G) in this study are potentially pathogenic. Two confirmed pathogenic variants (m.1555A>G and m.11778G>A) were also found in the CMP patients. The findings of this study shed light on the distribution of mitochondrial mutations in Malaysian CMP patients. Further functional studies are required to elucidate the role of these variants in the development of CMP.
Mitochondrial cardiomyopathy (MCM) is characterized by abnormal heart-muscle structure and function, caused by mutations in the nuclear genome or mitochondrial DNA. The heterogeneity of gene mutations and various clinical presentations in patients with cardiomyopathy make its diagnosis, molecular mechanism, and therapeutics great challenges. This review describes the molecular epidemiology of MCM and its clinical features, reviews the promising diagnostic tests applied for mitochondrial diseases and cardiomyopathies, and details the animal and cellular models used for modeling cardiomyopathy and to investigate disease pathogenesis in a controlled in vitro environment. It also discusses the emerging therapeutics tested in pre-clinical and clinical studies of cardiac regeneration.
Type 2 Diabetes Mellitus is a major chronic metabolic disorder in public health. Due to mitochondria's indispensable role in the body, its dysfunction has been implicated in the development and progression of multiple diseases, including Type 2 Diabetes mellitus. Thus, factors that can regulate mitochondrial function, like mtDNA methylation, are of significant interest in managing T2DM. In this paper, the overview of epigenetics and the mechanism of nuclear and mitochondrial DNA methylation were briefly discussed, followed by other mitochondrial epigenetics. Subsequently, the association between mtDNA methylation with T2DM and the challenges of mtDNA methylation studies were also reviewed. This review will aid in understanding the impact of mtDNA methylation on T2DM and future advancements in T2DM treatment.
The Eurasian lynx (Lynx lynx) exhibits geographic variability and phylogenetic intraspecific relationships. Previous morphological studies have suggested the existence of multiple lynx subspecies, but recent genetic research has questioned this classification, particularly in Central Asia. In this study, we aimed to analyse the geographic and genetic variation in Central Asian lynx populations, particularly the Turkestan lynx and Altai lynx populations, using morphometric data and mtDNA sequences to contribute to their taxonomic classification. The comparative analysis of morphometric data revealed limited clinal variability between lynx samples from the Altai and Tien Shan regions. By examining mtDNA fragments (control region and cytochrome b) obtained from Kazakhstani lynx populations, two subspecies were identified: L. l. isabellinus (represented by a unique haplotype of the South clade, H46) and L. l. wrangeli (represented by haplotypes H36, H45, and H47 of the East clade). L. l. isabellinus was recognized only in Tien Shan Mountain, while Altai lynx was likely identical to L. l. wrangeli and found in northern Kazakhstan, Altai Mountain, Saur and Tarbagatai Mountains, and Tien Shan Mountain. The morphological and mtDNA evidence presented in this study, although limited in sample size and number of genetic markers, renders the differentiation of the two subspecies challenging. Further sampling and compilation of whole-genome sequencing data are necessary to confirm whether the proposed subspecies warrant taxonomic standing.
Anabas testudineus (Anabantidae) is an important food fish in Southeast Asia. We analyzed the mitochondrial DNA control region sequence data to evaluate the genetic variability and population structure of this species. Sixty specimens were collected from four populations in Sumatra and two populations in Peninsular Malaysia. We found a very low level of genetic variability, with five of the six populations exhibiting total absence of genetic variation. Based on analysis of molecular variance, 84.72% of the total variation was among populations and 15.28% within populations. A geographical division based on FST values indicated highly significant genetic differentiation among populations from the four drainage systems: Aceh, Sumatra Utara, Pulau Pinang, and Terengganu (FST ranging from 0.633 to 1.000). No phylogeographic relationships among populations were detected, despite the generation of four distinct clades in a neighbor-joining phylogenetic tree.
We report the fact that D. albomicans invaded into Shanghai suddenly in the autumn of 1991. Using 9 restriction enzymes, we analyse the RFLPs of mitochondrial DNA of 29 isofemale lines belonging to 4 populations of Shanghai, Jiading, Qinpu and Nanhui. We find that all 29 haplotypes are different from each other. Comparing with the populations of Canton, Kunming, Sanhutan (Taiwan), Sumoto (Japan), and Kuala Lumper (Malaysia), we come to the conclusion that D. albomicans caught in Shanghai and areas nearby is from a few of places in the south of China-mainland. This conclusion agrees with the viewpoint that this species is on the speciation stage of migration towards north. We also discuss the mtDNA polymorphism within the species.
Aim: Mitochondrial DNA (mtDNA) alterations play an important role in the multistep processes of cancer development. Gliomas are among the most diagnosed brain cancer. The relationship between mtDNA alterations and different grades of gliomas are still elusive. This study aimed to elucidate the profile of somatic mtDNA mutations in different grades of gliomas and correlate it with clinical phenotype. Materials & methods: Forty histopathologically confirmed glioma tissue samples and their matched blood were collected and subjected for mtDNA sequencing. Results & conclusion: About 75% of the gliomas harbored at least one somatic mutation in the mtDNA gene, and 45% of these mutations were pathogenic. Mutations were scattered across the mtDNA genome, and the commonest nonsynonymous mutations were located at complex I and IV of the mitochondrial respiratory chain. These findings may have implication for future research to determine the mitochondrial energetics and its downstream metabolomics on gliomas.
The Bering Land Bridge connecting North America and Eurasia was periodically exposed and inundated by oscillating sea levels during the Pleistocene glacial cycles. This land connection allowed the intermittent dispersal of animals, including humans, between Western Beringia (far northeast Asia) and Eastern Beringia (northwest North America), changing the faunal community composition of both continents. The Pleistocene glacial cycles also had profound impacts on temperature, precipitation and vegetation, impacting faunal community structure and demography. While these palaeoenvironmental impacts have been studied in many large herbivores from Beringia (e.g., bison, mammoths, horses), the Pleistocene population dynamics of the diverse guild of carnivorans present in the region are less well understood, due to their lower abundances. In this study, we analyse mitochondrial genome data from ancient brown bears (Ursus arctos; n = 103) and lions (Panthera spp.; n = 39), two megafaunal carnivorans that dispersed into North America during the Pleistocene. Our results reveal striking synchronicity in the population dynamics of Beringian lions and brown bears, with multiple waves of dispersal across the Bering Land Bridge coinciding with glacial periods of low sea levels, as well as synchronous local extinctions in Eastern Beringia during Marine Isotope Stage 3. The evolutionary histories of these two taxa underline the crucial biogeographical role of the Bering Land Bridge in the distribution, turnover and maintenance of megafaunal populations in North America.
Mitochondrial replacement technology (MRT) is an emerging and complex bioethical issue. This treatment aims to eliminate maternal inherited mitochondrial DNA (mtDNA) disorders. For Muslims, its introduction affects every aspect of human life, especially the five essential interests of human beings-namely, religion, life, lineage, intellect, and property. Thus, this technology must be assessed using a comprehensive and holistic approach addressing these human essential interests. Consequently, this article analyses and assesses tri-parent baby technology from the perspective of Maqasidic bioethics-that is, Islamic bioethics based on the framework of Maqasid al-Shariah. Using this analysis, this article suggests that tri-parent baby technology should not be permitted for Muslims due to the existence of third-party cell gametes which lead to lineage mixing and due to the uncertain safety of the therapy itself and because the major aim of the technology is to fulfil the affected couples interest to conceive their own genetically healthy child, not to treat and cure mtDNA disorders sufferers.
The variability in the stenotopic miniature rasborine Boraras maculatus (Cypriniformes: Danionidae: Rasborinae) across acidic-water habitats of Peninsular Malaysia (PM) was investigated using two molecular markers (the mitochondrial cytochrome c oxidase subunit I [COI] gene and the nuclear rhodopsin gene), as well as morphological evidence. Molecular phylogenetic analyses revealed differentiation among populations of B. maculatus in PM with the distinction of four allopatric lineages. Each of them was recognized as a putative species by automatic species delimitation methods. These lineages diverged from each other between 7.4 and 1.9 million years ago. A principal component analysis (PCA) was conducted to examine the multivariate variation in 11 morphometric measurements among three of these lineages. PCA results showed a significant overlap in morphological characteristics among these lineages. Additionally, a photograph-based machine learning approach failed to fully differentiate these lineages, suggesting limited morphological differentiation. B. maculatus represents a case of morphological stasis in a stenotopic miniature species. Strong habitat preference, coupled with long-term habitat fragmentation, may explain why each lineage of B. maculatus has a restricted distribution and did not disperse to other regions within and outside of PM, despite ample possibilities when the Sunda shelf was emerged and drained by large paleodrainages for most of the past 7 million years. The conservation status of B. maculatus and its peat swamp habitats are discussed, and it is concluded that peat swamps comprise several evolutionary units. Each of these units is considered a conservation unit and deserves appropriate protection.
We classified diversity in eight new complete mitochondrial genome sequences and 41 partial sequences from living Aboriginal Australians into five haplogroups. Haplogroup AuB belongs to global lineage M, and AuA, AuC, AuD, and AuE to N. Within N, we recognize subdivisions, assigning AuA to haplogroup S, AuD to haplogroup O, AuC to P4, and AuE to P8. On available evidence, (S)AuA and (M)AuB are widespread in Australia. (P4)AuC is found in the Riverine region of western New South Wales, and was identified by others in northern Australia. (O)AuD and (P8)AuE were clearly identified only from central Australia. Our eight Australian full mt genome sequences, combined with 20 others (Ingman and Gyllensten 2003 Genome Res. 13:1600-1606) and compared with full mt genome sequences from regions to the north that include Papua New Guinea, Malaya, and Andaman and Nicobar Islands, show that ancestral connections between regions are deep and limited to clustering at the level of the N and M macrohaplogroups. The Australian-specific distribution of the five haplogroups identified indicates genetic isolation over a long period. Ancestral connections within Australia are deeper than those reflected by known linguistic or culturally based affinities. Applying a coalescence analysis to a gene tree for the coding regions of the eight genomic sequences, we made estimates of time depth that support a continuity of presence for the descendants of a founding population already established by 40,000 years ago.
The mitochondrial genome sequence of the ghost crab, Ocypode ceratophthalmus, is documented (GenBank accession number: LN611669) in this article. This is the first mitogenome for the family Ocypodidae and the second for the order Ocypodoidea. Ocypode ceratophthalmus has a mitogenome of 15,564 base pairs consisting of 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of the O. ceratophthalmus mitogenome is 35.78% for T, 19.36% for C, 33.73% for A and 11.13% for G, with an AT bias of 69.51% and the gene order is the typical arrangement for brachyuran crabs.
The mosquito Aedes albopictus is indigenous to Southeast Asian and is a vector for arbovirus diseases. Studies examining the population genetics structure of A. albopictus have been conducted worldwide; however, there are no documented reports on the population genetic structure of A. albopictus in Malaysia, particularly in Penang. We examined the population genetics of A. albopictus based on a 445-base pair segment of the mitochondrial DNA cytochrome oxidase 1 gene among 77 individuals from 9 localities representing 4 regions (Seberang Perai Utara, Seberang Perai Tengah, Northeast, and Southwest) of Penang. A total of 37 haplotypes were detected, including 28 unique haplotypes. The other 9 haplotypes were shared among various populations. These shared haplotypes reflect the weak population genetic structure of A. albopictus. The phylogenetic tree showed a low bootstrap value with no genetic structure, which was supported by minimum spanning network analysis. Analysis of mismatch distribution showed poor fit of equilibrium distribution. The genetic distance showed low genetic variation, while pairwise FST values showed no significant difference between all regions in Penang except for some localities. High haplotype diversity and low nucleotide diversity was observed for cytochrome oxidase 1 mtDNA. We conclude that there is no population genetic structure of A. albopictus mosquitoes in the Penang area.
For centuries, morphology-based fish identification has been applied without molecular evaluation. Many studies showed that specimens with a similar morphology are frequently found to be quite genetically distinct. One of the fish species that still remains taxonomically problematic is a commercial snapper species, Lutjanus johnii. Because of morphological ambiguities among local fish taxonomists in Malaysia, we examined the ability of the cytochrome oxidase I (COI) gene to genetically examine the taxonomic status of L. johnii. A 626-base pair COI region was successfully amplified and aligned with conspecific sequences that were retrieved from GenBank. The phylogenetic tree obtained showed two major clusters; the first cluster consists of L. johnii from Straits of Malacca, Thailand, Australia, and China while the second cluster comprises L. johnii from China and India. The latter group showed sequence divergence greater than 3.5%. After observing this, we suspected that there might be a cryptic species between the South China Sea and Indian Ocean. This is the first molecular report concerning the commercial species of snapper, L. johnii, in Malaysia, which had only gained provisional recognition from morphological examination.
The complete mitochondrial genome of the commercially important snout otter clam Lutraria rhynchaena was obtained from low-coverage shotgun sequencing data on the MiSeq platform. The L. rhynchaena mitogenome has 16,927 base pairs (69% A + T content) and made up of 12 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 953 bp non-coding AT-rich region. This is the first mitogenome to be sequenced from the genus Lutraria, and the seventh to be reported for the family Mactridae.
This study examines the population genetic structure of Tor tambroides, an important freshwater fish species in Malaysia, using fifteen polymorphic microsatellite loci and sequencing of 464 base pairs of the mitochondrial cytochrome c oxidase I (COI) gene. A total of 152 mahseer samples were collected from eight populations throughout the Malaysia river system. Microsatellites results found high levels of intrapopulation variations, but mitochondrial COI results found high levels of interpopulations differentiation. The possible reasons for their discrepancies might be the varying influence of genetic drift on each marker or the small sample sizes used in most of the populations. The Kelantan population showed very low levels of genetic variations using both mitochondrial and microsatellite analyses. Phylogenetic analysis of the COI gene found a unique haplotype (ER8∗), possibly representing a cryptic lineage of T. douronensis, from the Endau-Rompin population. Nevertheless, the inclusion of nuclear microsatellite analyses could not fully resolve the genetic identity of haplotype ER8∗ in the present study. Overall, the findings showed a serious need for more comprehensive and larger scale samplings, especially in remote river systems, in combination with molecular analyses using multiple markers, in order to discover more cryptic lineages or undescribed "genetic species" of mahseer.
Bactrocera dorsalis s.s. is a pestiferous tephritid fruit fly distributed from Pakistan to the Pacific, with the Thai/Malay peninsula its southern limit. Sister pest taxa, B. papayae and B. philippinensis, occur in the southeast Asian archipelago and the Philippines, respectively. The relationship among these species is unclear due to their high molecular and morphological similarity. This study analysed population structure of these three species within a southeast Asian biogeographical context to assess potential dispersal patterns and the validity of their current taxonomic status.
Amphiboloidea is a small but widespread group of snails found exclusively, and often abundantly, in mudflat and associated salt marsh or mangrove habitat. This study uses molecular data from three loci (COI, 16S and 28S) to infer phylogenetic relationships in Amphiboloidea and examine its position in Euthyneura. All but two of the named extant species of Amphiboloidea and additional undescribed taxa from across Southeast Asia and the Arabian Gulf were sampled. In contrast to the current morphology-based classification dividing Amphiboloidea into three families, analysis of molecular data supports revision of the classification to comprise two families. Maningrididae is a monotypic family basal to Amphibolidae, which is revised to comprise three subfamilies: Amphibolinae, Phallomedusinae and Salinatorinae. Sequence divergence between Asian populations of Naranjia is relatively large and possibly indicative of species complexes divergent across the Strait of Malacca. Salinatorrosacea and Salinator burmana do not cluster with other Salinator species, and require generic reassignment. In addition, sequences were obtained from an undescribed species of Lactiforis from the Malay Peninsula. Reconstruction of ancestral distributions indicates a plesiomorphic distribution and centre of origin in Australasia, with two genera subsequently diversifying throughout Asia. Increasing the sampling density of amphiboloid taxa in a phylogenetic analysis of Euthyneura did not resolve the identity of the sister taxon to Amphibolidae, but confirmed its inclusion in Pulmonata/Panpulmonata.
Little is known about the classification and phylogenetic relationships of the leaf monkeys (Presbytis). We analyzed mitochondrial DNA sequences of cytochrome b (Cyt b) and 12S rRNA to determine the phylogenetic relationships of the genus Presbytis. Gene fragments of 388 and 371 bp of Cyt b and 12S rRNA, respectively, were sequenced from samples of Presbytis melalophos (subspecies femoralis, siamensis, robinsoni, and chrysomelas), P. rubicunda and P. hosei. The genus Trachypithecus (Cercopithecidae) was used as an outgroup. The Cyt b NJ and MP phylogeny trees showed P. m. chrysomelas to be the most primitive, followed by P. hosei, whereas 12S rRNA tree topology only indicated that these two species have close relationships with the other members of the genus. In our analysis, chrysomelas, previously classified as a subspecies of P. melalophos, was not included in either the P. m. femoralis clade or the P. m. siamensis clade. Whether or not there should be a separation at the species level remains to be clarified. The tree topologies also showed that P. m. siamensis is paraphyletic with P. m. robinsoni, and P. m. femoralis with P. rubicunda, in two different clades. Cyt b and 12S rRNA are good gene candidates for the study of phylogenetic relationships at the species level. However, the systematic relationships of some subspecies in this genus remain unclear.