Kiran S Kumar, Sivakumar K Chandrika, Sanil George
{"title":"Genetic structure and demographic history of <i>Indirana semipalmata</i>, an endemic frog species of the Western Ghats, India.","authors":"Kiran S Kumar, Sivakumar K Chandrika, Sanil George","doi":"10.1080/24701394.2020.1830077","DOIUrl":"https://doi.org/10.1080/24701394.2020.1830077","url":null,"abstract":"<p><p>The evolutionary potential of a species mainly depends on the level of genetic variation in their populations. Maintenance of gene variation enables populations to adapt more quickly to environmental changes. The geographical gaps also influence the distribution and evolutionary history of many mountain frogs in the world. Hence, a sound knowledge in population genetic structure of a species will help understand its population dynamics and develop conservation strategies. In the context of facing threats to the amphibian fauna of Western Ghats due to habitat loss, we used both mitochondrial and nuclear DNA markers to investigate the genetic structure of an endemic frog species of the Western Ghats (<i>Indirana semipalmata</i>) with restricted distribution. The present study showed the importance of mountain gaps in shaping the species' structuring in the Western Ghats. Though a high genetic diversity was observed for the species when considering a single unit in the southern Western Ghats, the restricted gene flow on/between either side of the Shencottah gap with genetic clustering of the sampled populations may warrant a unique management plan for the species. The habitat fragmentation of the Western Ghats through anthropogenic activities may result in severe setbacks to the survival of the species in the future.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 8","pages":"365-378"},"PeriodicalIF":0.0,"publicationDate":"2020-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1830077","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38562218","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abbas Heydari, Mohammad Ali Oshaghi, Alireza Nazari, Mansoureh Shayeghi, Elham Sanatgar
{"title":"Genetic structure of rice striped stem borer, Chilo suppressalis (Lepidoptera:Crambidae) in North of Iran.","authors":"Abbas Heydari, Mohammad Ali Oshaghi, Alireza Nazari, Mansoureh Shayeghi, Elham Sanatgar","doi":"10.1080/24701394.2020.1815718","DOIUrl":"https://doi.org/10.1080/24701394.2020.1815718","url":null,"abstract":"<p><p>Information on the genetic structure of rice striped stem borer, <i>Chilo suppressalis</i> (Walker), is essential for an effective pest management program and can corporate with control program and prompt the modification of current control methods. In this study, the genetic structure of COI gene has been investigated for 18 populations of this pest in north of Iran. <i>Chilo suppressalis</i> specimens were collected from rice fields on rice and weeds in Guilan and Mazanderan provinces, at Caspian Sea coast at both seasonal activity (spring) and overwintering stage from May through October 2018 and identified using morphological characters. Genetic structure of 18 populations of the species was evaluated using polymerase chain reaction (PCR)-direct-sequencing of a fragment (869 bp) of mtDNA-COI gene. Results revealed that almost all specimens from different generations, hosts, and locations belong to a single haplotype very close to a South Korean haplotype. To the best our knowledge, it is the first comprehensive molecular typing of striped stem borer in both Northern provinces of the country and suggests a high gene flow among different populations of this pest in the region.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 8","pages":"327-334"},"PeriodicalIF":0.0,"publicationDate":"2020-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1815718","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38440532","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Riazul Islam Barbhuiya, Arif Uddin, Supriyo Chakraborty
{"title":"Codon usage pattern and its influencing factors for mitochondrial <i>CO</i> genes among different classes of Arthropoda.","authors":"Riazul Islam Barbhuiya, Arif Uddin, Supriyo Chakraborty","doi":"10.1080/24701394.2020.1800661","DOIUrl":"https://doi.org/10.1080/24701394.2020.1800661","url":null,"abstract":"<p><p>Analysis of codon usage bias (CUB) is very much important in perceiving the knowledge of molecular biology, the discovery of a new gene, designing of transgenes and evolution of gene. In this study, we analyzed compositional features and codon usage of <i>MT-CO</i> (<i>COI</i>, <i>COII</i> and <i>COIII</i>) genes among the classes of Arthropoda to explore the pattern of CUB as no research work was reported yet. Nucleotide composition analysis in <i>CO</i> genes suggested that the genes were AT-rich in all the four classes of Arthropoda. CUB was low in all the classes of Arthropoda for <i>MT-CO</i> genes as revealed from a high effective number of codons (ENC). We also found that the evolutionary forces namely mutation pressure and natural selection were the key influencing factors in CUB among <i>MT-CO</i> genes as revealed by correlation analysis between overall nucleotide composition and nucleotide composition at the 3rd codon position. Correspondence analysis suggested that the pattern of CUB was different among the classes of Arthropoda. Further, it was revealed from the neutrality plot that natural selection had a dominant role while mutation pressure exhibited a minor role in structuring the pattern of codon usage in all the classes of Arthropoda across <i>COI</i>, <i>COII</i> and <i>COIII</i> genes.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 8","pages":"313-326"},"PeriodicalIF":0.0,"publicationDate":"2020-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1800661","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38239561","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Exploring new records of <i>Eutyphoeus</i> sp. (haplotaxida: Octochaetidae) from garo hills, Meghalaya, North Eastern state of India with use of DNA barcodes.","authors":"Samrendra Singh Thakur, Azhar Rashid Lone, Nalini Tiwari, Shweta Yadav","doi":"10.1080/24701394.2020.1781834","DOIUrl":"https://doi.org/10.1080/24701394.2020.1781834","url":null,"abstract":"<p><p>The work was aimed to investigate earthworms species particularly <i>Eutyphoeus</i> endemic to India with the use of DNA barcodes and usual morpho-anatomical standards of earthworm taxonomy from protected areas of Garo Hills, Meghalaya, the north-east region (NER) of India. The study revealed two new records <i>Eutyphoeus kempi</i> Stephenson, <i>E. nepalensis</i> Michaelsen and confirms availability of three known sp. namely <i>E. callosus</i> Gates, <i>E. gammiei</i> Beddard and <i>E. turaensis</i> Stephenson. The neighbor-joining tree was constructed using the K2P substitution model and the genomic signature of each species using <i>COI-1</i> gene was generated for the first time and were used to reconfirm the identification of species.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 7","pages":"265-272"},"PeriodicalIF":0.0,"publicationDate":"2020-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1781834","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38368476","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Molecular systematics and phylogeography of the genus <i>Alburnus</i> Rafinesque, 1820 (Teleostei, Leuciscidae) in Turkey.","authors":"Yusuf Bektas, Ismail Aksu, Cüneyt Kaya, Esra Bayçelebi, Fahrettin Küçük, Davut Turan","doi":"10.1080/24701394.2020.1791840","DOIUrl":"https://doi.org/10.1080/24701394.2020.1791840","url":null,"abstract":"<p><p>In this study, the phylogeny of <i>Alburnus</i> genus distributed in Turkish freshwaters was performed by analyzing mitochondrial cyt <i>b</i> gene (1141 bp) and COI gene (1551 bp) sequences from 1172 samples representing 112 populations of 24 species through their geographical distribution. According to our findings, 20 valid species are distributed in Turkey of which 18 have already been known. While six <i>Alburnus</i> species (<i>A. battalgilae, A. istanbulensis, A. carinatus, A. schischkovi, A. nasreddini ve A. adanensis</i>) have been synonomized, two new species (<i>Alburnus</i> sp.1 and <i>Alburnus</i> sp.2) from Dicle River and Çapraz Stream/Susurluk River have been identified. Extinct species such as <i>A</i>. <i>akili</i> and <i>A. nicaeensis</i> have not been observed <i>in situ</i>. Phylogenetic tree topologies and haplotype network of the 119 cyt <i>b</i> and 80 COI haplotypes detected in <i>Alburnus</i> species have indicated a consensus tree topology containing twenty lineages, each of corresponding to one species, and three <i>Alburnus</i> haplogroups corresponding to the geographical origins: Eastern Anatolia (I), Mediterranean (2) and Western & Northern Anatolia (3). The results indicate that the divergence between those haplogroups may have occurred during the Middle Miocene-Middle Pleistocene periods (from 14.9 to 5.29 million years).</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 7","pages":"273-284"},"PeriodicalIF":0.0,"publicationDate":"2020-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1791840","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38150180","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"DNA bar coding of Aplousobranchiata and Phlebobranchiata Ascidians (Phylum:Chordata) inferred from mitochondrial cytochrome oxidase subunit I (COI) gene sequence approach in Andaman and Nicobar Islands, India: a first report.","authors":"Rajaram Murugan, Gnanakkan Ananthan, Anandakumar Arunkumar","doi":"10.1080/24701394.2020.1798417","DOIUrl":"https://doi.org/10.1080/24701394.2020.1798417","url":null,"abstract":"<p><p>Ascidians (Phylum: Chordata) are sessile and filter-feeding marine animal, species identification of ascidians is possible by observing various morphological and anatomical features in various stages of life span. However, this method is labor intensive, time-consuming and very difficult for non-specialists particularly when dealing with field collections. Suborder Aplousobranchiata and Phlebobranchiata is the largest group of tunicates within, morphological and molecular data suggest that Didemnidae and Ascidiidae are monophyletic, but the monophyly of each genus and their phylogenetic relationships are still poorly understood. Therefore, this study was aimed to develop DNA barcodes of ascidians belonging to the orders of Aplousobranchiata and Phlebobranchiata species namely <i>Diplosoma listerianum</i>, <i>Lissoclinum fragile</i>, <i>Didemnum psammatode</i>, <i>Phallusia fumigata</i> and <i>Phallusia ingeria</i> collected from Andaman and Nicobar Islands were sequenced and submitted in Gen Bank. Colony structure, Scanning Electron Microscope (SEM) for spicules of colonial ascidians, larval type and zooids formation were found to be the most useful morphological characters for discriminating the species. Our BLAST results proved <i>D. Listerianum</i> KP842724 (98%) <i>L. fragile</i> KP842726 (100%) <i>D. psammatode</i> KP779902 (99%), <i>P. fumigata</i> KP779904 (99%) and <i>P. ingeria</i> KP842727 (100%) similarity and this is the first report of mitochondrial COI gene of these ascidians from Andaman and Nicobar Islands. We explored the usefulness of CO1 gene sequences for molecular level identification and mtDNA data in assessing a phylogenetic relationship of ascidian species.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 7","pages":"285-297"},"PeriodicalIF":0.0,"publicationDate":"2020-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1798417","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38207921","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Correction.","authors":"","doi":"10.1080/24701394.2020.1798057","DOIUrl":"https://doi.org/10.1080/24701394.2020.1798057","url":null,"abstract":"","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 7","pages":"311"},"PeriodicalIF":0.0,"publicationDate":"2020-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1798057","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38183410","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Noorul-Azliana Jamaludin, Wahidah Mohd-Arshaad, Noor Adelyna Mohd Akib, Danial-Hariz Zainal Abidin, Nguyen Viet Nghia, Siti-Azizah Mohd Nor
{"title":"Phylogeography of the Japanese scad, <i>Decapterus maruadsi</i> (Teleostei; Carangidae) across the Central Indo-West Pacific: evidence of strong regional structure and cryptic diversity.","authors":"Noorul-Azliana Jamaludin, Wahidah Mohd-Arshaad, Noor Adelyna Mohd Akib, Danial-Hariz Zainal Abidin, Nguyen Viet Nghia, Siti-Azizah Mohd Nor","doi":"10.1080/24701394.2020.1799996","DOIUrl":"https://doi.org/10.1080/24701394.2020.1799996","url":null,"abstract":"<p><p>The Japanese scad <i>Decapterus maruadsi</i> (Carangidae) is an economically important marine species in Asia but its exploitation shows signs of overfishing. To document its stock structure, a population genetic and phylogeographic study of several populations of this species from the central part of the Indo-West Pacific region was conducted using the mitochondrial cytochrome <i>b</i> gene. Genetic homogeneity within the Sundaland region's population, including Rosario (the Philippines) and Ranong (Andaman Sea) populations was revealed with low nucleotide diversity (<i>π</i> = 0.001-0.003) but high haplotype diversity (<i>h</i> = 0.503-0.822). In contrast, a clear genetic structure was observed between this group and the northern Vietnam populations as revealed by <i>F</i><sub>ST</sub>, AMOVA and SAMOVA, while the central Vietnam population of Khanh Hoa is an admixed group between the two differentiated regional populations. The neutrality and mismatch distribution analyses supported a demographic expansion of <i>D. maruadsi</i> in between last Pleistocene to early Holocene period which influenced present day distribution pattern. Contemporary factors such as oceanic currents and different life history traits are also believed to play significant roles in the observed population structure and biogeographical pattern. Based on these results, recommendations on how stocks of the Japanese scad should be managed are offered.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 7","pages":"298-310"},"PeriodicalIF":0.0,"publicationDate":"2020-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1799996","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38229309","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Andrew Vanlallawma, Zothan Zami, Jeremy L Pautu, Zothankima Bawihtlung, Lalfakzuala Khenglawt, Doris Lallawmzuali, Lalchhandama Chhakchhuak, Nachimuthu Senthil Kumar
{"title":"Pediatric leukemia could be driven predominantly by non-synonymous variants in mitochondrial complex V in Mizo population from Northeast India.","authors":"Andrew Vanlallawma, Zothan Zami, Jeremy L Pautu, Zothankima Bawihtlung, Lalfakzuala Khenglawt, Doris Lallawmzuali, Lalchhandama Chhakchhuak, Nachimuthu Senthil Kumar","doi":"10.1080/24701394.2020.1786545","DOIUrl":"https://doi.org/10.1080/24701394.2020.1786545","url":null,"abstract":"<p><p>Leukemia is the most common childhood malignancy and studies had been carried out with promising revelations in its diagnosis and prognosis. However, majority of the studies are focused on nuclear alterations, while mitochondrial mutations are not well studied. Although there are studies of mitochondrial mutations in the adult leukemias, it does not represent the same for childhood malignancy. This is the first scientific report on the mtDNA mutational pattern of pediatric leukemic cases from a endogamous tribal population in Northeast India. <i>ATP6</i> involved in the Complex V was found to be more altered with respect to the Non-synonymous variants. mtDNA variations in the non-coding region (D-Loop - g.152 T>C) and in the coding region (MT-ND2, g.4824 A>G, p.T119A) showed a maternal inheritance which could reveal a genetic predisposition with lower penetrance. D-Loop variant (g.152 T>C) could be a diagnostic marker in accordance with previous report but is in contrast to pertaining only in AML - M3 subtype rather was found across in myeloid malignancies.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 6","pages":"245-249"},"PeriodicalIF":0.0,"publicationDate":"2020-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1786545","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38107055","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Christian M Hagen, Joanna L Elson, Paula L Hedley, Frederik H Aidt, Ole Havndrup, Morten K Jensen, Jørgen K Kanters, John J Atherton, Julie McGaughran, Henning Bundgaard, Michael Christiansen
{"title":"Evolutionary dissection of mtDNA hg H: a susceptibility factor for hypertrophic cardiomyopathy.","authors":"Christian M Hagen, Joanna L Elson, Paula L Hedley, Frederik H Aidt, Ole Havndrup, Morten K Jensen, Jørgen K Kanters, John J Atherton, Julie McGaughran, Henning Bundgaard, Michael Christiansen","doi":"10.1080/24701394.2020.1782897","DOIUrl":"https://doi.org/10.1080/24701394.2020.1782897","url":null,"abstract":"<p><p>Mitochondrial DNA (mtDNA) haplogroup (hg) H has been reported as a susceptibility factor for hypertrophic cardiomyopathy (HCM). This was established in genetic association studies, however, the SNP or SNP's that are associated with the increased risk have not been identified. Hg H is the most frequent European mtDNA hg with greater than 80 subhaplogroups (subhgs) each defined by specific SNPs. We tested the hypothesis that the distribution of H subhgs might differ between HCM patients and controls. The subhg H distribution in 55 HCM index cases was compared to that of two Danish mtDNA hg H control groups (<i>n</i> = 170 and <i>n</i> = 908, respectively). In the HCM group, H and 12 different H subhgs were found. All these, except subhgs H73, were also found in both control groups. The HCM group was also characterized by a higher proportion of H3 compared to H2. In the HCM group the H3/H2 proportion was 1.7, whereas it was 0.45 and 0.54 in the control groups. This tendency was replicated in an independent group of Hg H HCM index cases (<i>n</i> = 39) from Queensland, Australia, where the H3/H2 ratio was 1.5. In conclusion, the H subhgs distribution differs between HCM cases and controls, but the difference is subtle, and the understanding of the pathogenic significance is hampered by the lack of functional studies on the subhgs of H.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 6","pages":"238-244"},"PeriodicalIF":0.0,"publicationDate":"2020-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1782897","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38105679","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}