Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis最新文献

{"title":"Mitochondrial DNA: the common confusions.","authors":"Mikhail Alexeyev","doi":"10.1080/24701394.2020.1734586","DOIUrl":"https://doi.org/10.1080/24701394.2020.1734586","url":null,"abstract":"In theory, scientific discovery follows the path of putting forward a hypothesis, testing it and either accepting it as a theory or discarding it based on the outcome of testing. As it often happens, real life is more complicated than this straightforward scheme; research undergoes unexpected twists and turns, and the total body of experimental evidence often both provides support for and refutes the hypothesis in question. After protracted arguments, the focus of scientific debate eventually shifts, often without solidifying the outcome in a clearly articulated conclusion allowing each side to cling to its own subset of gathered evidence. As a consequence, old misconceptions often persist in the literature, confusing newcomers and slowing the pace of scientific discovery. In this editorial, I identify some of these outdated concepts and confusions as they relate to mtDNA, outline their historical contexts and provide criticisms.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 2","pages":"45-47"},"PeriodicalIF":0.0,"publicationDate":"2020-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1734586","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37717841","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DNA barcoding and phylogenetic analysis of bagrid catfish in China based on mitochondrial COI gene.","authors":"Rui Zou,&nbsp;Cong Liang,&nbsp;Mengmeng Dai,&nbsp;Xiaodong Wang,&nbsp;Xiuyue Zhang,&nbsp;Zhaobin Song","doi":"10.1080/24701394.2020.1735379","DOIUrl":"https://doi.org/10.1080/24701394.2020.1735379","url":null,"abstract":"<p><p>The family Bagridae is a collection of species widely distributed in Africa and Asia with a high diversity of morphology. The species identification and phylogenetic relationship in this family have been confused and controversial. In order to explore the effectiveness of DNA barcoding in species identification of Bagridae, sequences of mitochondrial cytochrome c oxidase I (COI) gene of 20 species in four genera of Bagridae were used to analyse barcoding gap and to reconstruct phylogenetic relationship. Both the barcoding gap and the phylogenetic tree analysis showed that the COI gene-based DNA barcoding is an effective molecular technique for most species recognition of Chinese Bagridae. However, the rapid speciation and incomplete lineage sorting may affect the accuracy of DNA barcoding in species identification in certain species, and adding additional genes, such as nuclear gene, may help to achieve accurate identification of these species. The phylogenetic tree showed that the monophyly of genera <i>Pelteobagrus</i>, <i>Leiocassis</i> and <i>Pseudobagrus</i> did not exist, which supports that the species of genera <i>Pelteobagrus</i>, <i>Pseudobagrus</i> and <i>Leiocassis</i> distributed in China should be revised into one genus.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 2","pages":"73-80"},"PeriodicalIF":0.0,"publicationDate":"2020-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1735379","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37701503","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 identification of Cerithiidae (Mollusca: Gastropod) in Hainan island, China.","authors":"Ke Ran,&nbsp;Qi Li,&nbsp;Lu Qi,&nbsp;Weidong Li,&nbsp;Lingfeng Kong","doi":"10.1080/24701394.2020.1726898","DOIUrl":"https://doi.org/10.1080/24701394.2020.1726898","url":null,"abstract":"<p><p>A number of same species of Cerithiidae are morphologically unlike, whereas most of species in the same genus are morphologically similar and just exhibit subtle differences. It is difficult to identify them by morphological methods alone. DNA barcoding is a modern molecular technique that can be used to identify species accurately, and is particularly helpful when distinguishing morphologically similar species. In order to identify species of Cerithiidae using DNA barcoding technology based on mitochondrial cytochrome oxidase subunit I (COI) and 16S ribosomal RNA (16S rRNA) genes, this study calculated intraspecific and interspecific genetic distance and constructed the phylogenetic trees. A total of 80 COI and 16S rRNA barcode sequences were obtained from 10 species and 3 genera. Some unknown specimens were further identified and a cryptic species may exist in <i>Cerithium traillii</i>, showing that DNA barcoding technology has the potential to discover new species and cryptic species. The phylogenetic trees revealed that all of the cerithiids could converge upon a monophyly with high support values and two genera (<i>Cerithium</i> and <i>Clypeomorus</i>) maybe support the reclassification. It is necessary for traditional morphological methods to combine with the DNA barcoding for classification and identification of Cerithiidae.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 2","pages":"57-63"},"PeriodicalIF":0.0,"publicationDate":"2020-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1726898","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37641402","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":"Comparative phylogeny of (<i>Schizothorax esocinus</i>) with reference to 12s and 16 sribosomal RNA from River Swat, Pakistan.","authors":"Aqsa Rehman,&nbsp;Muhammad Fiaz Khan,&nbsp;Saira Bibi,&nbsp;Faisal Nouroz","doi":"10.1080/24701394.2020.1741561","DOIUrl":"https://doi.org/10.1080/24701394.2020.1741561","url":null,"abstract":"<p><p><i>Schizothorax esocinus</i> is one of the important cold water delicious fish belonging to family Cyprinidae and found in River Swat which is one of the main river flowing in Khyber Pakhtunkhwa, Pakistan.The complete mitochondrial genomes of the <i>S. esocinus</i> species was found to be 16,591bp. Phylogenetic analysis of <i>S. esocinus</i> based on 12 s ribosomal RNA and 16S rRNA confirmed that, the phylogenetic position of <i>S. esocinus</i> was slightly different, but clustered closed to <i>S. plagiostomus, S. labiatus</i>, <i>S. richardsonii, S. nepalensis,</i> and <i>S. progastus</i> predicting a close homology in genome and hence a monophyletic line of evolution also this specie showed close relationship and homologs to the <i>Aspiorhynchus laticeps, Spinibarbus sinensis, Aspiorhynchus laticeps,</i> and <i>Percocypris</i> respectively. This study provided phylogenetic relationship between Schizothoracinae fishes and with the other fishes of family cyprinidae even at the subfamily level.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 2","pages":"81-85"},"PeriodicalIF":0.0,"publicationDate":"2020-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1741561","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37754306","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":"Genetic differentiation and phylogenetic relationship of 11 Asian Sisorinae genera (Siluriformes: Sisoridae) with new record of <i>Pseudolaguvia foveolata</i>.","authors":"Kavita Kumari,&nbsp;Manas H M,&nbsp;Archana Sinha,&nbsp;Satish Kumar Koushlesh,&nbsp;Soma Das Sarkar,&nbsp;Simanku Borah,&nbsp;Raju BaItha,&nbsp;Bijay Kumar Behera,&nbsp;Basanta Kumar Das","doi":"10.1080/24701394.2020.1714605","DOIUrl":"https://doi.org/10.1080/24701394.2020.1714605","url":null,"abstract":"<p><p>Studies on <i>Sisorinae</i> systematics have been largely restricted to morphological data with few studies on examination of phylogenetic relations. However, no study has been done to evaluate genetic distance of the genera under <i>Sisorinae</i> sub-family and detailed phylogenetic relations within it. We used nuclear recombination activating 2 (<i>rag2</i>) gene and mitochondrial cytochrome c oxidase I (<i>COI</i>) gene from 64 species to examine genetic differentiation and phylogenetic relationships within 11 Asian <i>Sisorinae</i> genera. The range of interspecies K2P distance for <i>rag2</i> was 0-0.061 and <i>COI</i> was 0-0.204. Phylogenetic analysis based on maximum likelihood (ML) and Bayesian (BI) approaches for each locus individually and for the concatenated <i>rag2</i> and <i>COI</i> sequences revealed three major subclades viz. Bagariini, Sisorini and Erethistini under subfamily Sisorinae. The analysis based on <i>COI</i> gene showed ((Sisorini, Bagariini), Erethistini) relationship. <i>Rag</i>2 and combined <i>rag2</i> and <i>COI</i> showed ((Sisorini, Erethistini), Bagariini) relationship. Combined <i>rag</i>2 and <i>COI</i> analyses resulted into better resolved trees with a good bootstrap support. In this study, new record of <i>Pseudolaguvia foveolata</i> (Erethistini) has been documented based on 13 specimens collected from Torsa River, Jaldapara, Alipurduar district, West Bengal, India (26°43'44.66″ N and 89°19'32.34″ E), extending its distribution range in Brahmaputra drainage, India. The genetic distance between the <i>P. foveolata</i> new record and the reported <i>P. foveolata</i> (holotype: UMMZ 244867) was 0.00 at both <i>rag2</i> and <i>COI</i> locus and it was further grouped with <i>P. foveolata</i> Type specimen (holotype: UMMZ 244867) with 100% bootstrap support. This report gives additional information on occurrence of the species <i>P. foveolata</i>, along with discussion on morphometric, meristic and molecular (<i>COI</i> and <i>rag2</i> gene) data.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 1","pages":"35-41"},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1714605","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37562368","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":"Response to the critique of Sameer Padhye and Neelesh Dahanukar (2019).","authors":"Shil Abhyankar,&nbsp;Kshama Khobragade,&nbsp;Ganesh Khanwelkar,&nbsp;Anita Tiknaik,&nbsp;Gulab Khedkar","doi":"10.1080/24701394.2019.1703964","DOIUrl":"https://doi.org/10.1080/24701394.2019.1703964","url":null,"abstract":"We are pleased that Sameer Padhye and Neelesh Dahanukar (hereafter referred to as PN) agree that there is a significant need for DNA barcode data on this important group of organisms, and that a major goal of the paper (Abhyankar et al. 2019) was to initiate an effort to fill this gap. PN, do however, make other comments questioning other points made in the paper, and here we will attempt to address each of them","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 1","pages":"42-43"},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2019.1703964","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37475451","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":"An enigmatic population of <i>Alsodes</i> (Anura, Alsodidae) from the Andes of central Chile with three species-level mitochondrial lineages.","authors":"Claudio Correa,&nbsp;Jesús Morales,&nbsp;Constantino Schussler,&nbsp;Juan C Ortiz","doi":"10.1080/24701394.2019.1704744","DOIUrl":"https://doi.org/10.1080/24701394.2019.1704744","url":null,"abstract":"<p><p>The genus <i>Alsodes</i> is the most diverse amphibian taxon of southern Andes, where a series of endemic species occur from north to south (∼33° to 48°30'S), mainly on the western slopes (Chile), with little overlap of geographic ranges. In this study, we describe a new population of <i>Alsodes</i> from the western slopes of the Andes (Fundo El Rosario, 36°52'S), located in a section of this mountain range where it is not clear which congeneric species inhabit. Phylogenetic analyses show that this population presents a mix of mitochondrial DNA related to three nominal species, <i>A. hugoi</i>, <i>A. igneus</i> and <i>A. pehuenche</i>, although the last is mainly present. However, the population presents external characteristics attributable to <i>A. hugoi</i> and <i>A. igneus</i>, differing notably from <i>A. pehuenche</i>. The population inhabits a stream surrounded by temperate deciduous forests at 1130 m elevation, an environment similar to that of <i>A. hugoi</i> and <i>A. igneus</i>, but very different from that of <i>A. pehuenche</i> (high Andean steppe environments between 2000 and 2500 m). This finding represents an enigma from the evolutionary and biogeographical point of view, because it might involve hybridization and/or introgression phenomena between more than two species. As the taxonomic status of this population cannot be determined with the available genetic and morphological evidence, we speculate about its probable origin, taking into account the scarce knowledge of the geographic distributions of the species of <i>Alsodes</i> in the area.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 1","pages":"25-34"},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2019.1704744","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37514181","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":"<i>Pristimantis</i> in the Eastern Brazilian Amazon: DNA barcoding reveals underestimated diversity in a megadiverse genus.","authors":"Elciomar Araújo De Oliveira,&nbsp;Marcos Penhacek,&nbsp;Karen Larissa Auzier Guimarães,&nbsp;Gessica Amorim do Nascimento,&nbsp;Luís Reginaldo Ribeiro Rodrigues,&nbsp;Emil José Hernández-Ruz","doi":"10.1080/24701394.2019.1634696","DOIUrl":"https://doi.org/10.1080/24701394.2019.1634696","url":null,"abstract":"<p><p>The genus <i>Pristimantis</i> has the highest species diversity among all terrestrial vertebrates, with most species observed in the Andean region and the Guiana Shield. Even with the recent description of a new species, only <i>P. latro</i>, <i>P. dundeei</i> and <i>P. zimmermanae</i> occur in the south of the Amazon River. The lack of taxonomists specialized in the field leads to the propagation of dubious terminologies (e.g. <i>Pristimantis</i> sp1, <i>Pristimantis</i> sp2, <i>P.</i> aff. <i>Fenestratus</i> and <i>P.</i> gr. c<i>onspicillatus</i>) or even misidentification of species, resulting in erroneous species distributions. In this study, we applied the Automatic Barcode Gap Discovery (ABGD) algorithm for the delimitation of candidate species and values of genetic distances using the mitochondrial marker Cytochrome Oxidase Subunit I (COI), proposed in the barcode methodology, where values greater than 10% are considered as indicative of different species. We found large genetic distances between <i>P. latro</i> and <i>Pristimantis</i> sp1 Unconfirmed Candidate Species - UCS1 (21%), and between <i>P. altamazonicus</i> and <i>Pristimantis</i> sp2 UCS2 (14%). The ABGD method recognized UCS1 and UCS2 as distinct species. <i>Pristimantis</i> sp. UCS1 and UCS2 in the east of the Brazilian Amazon are indicated as candidate species. We suggest greater sampling of <i>Pristimantis</i> sp. UCS1 and UCS2, integrating morphology and bioacoustics to solve the taxonomic status in the east of the Brazilian Amazon.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"30 6","pages":"731-738"},"PeriodicalIF":0.0,"publicationDate":"2019-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2019.1634696","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37386837","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":"Prey, populations, and the pleistocene: evidence for low COI variation in a widespread North American leech.","authors":"Joseph Mack,&nbsp;Danielle de Carle,&nbsp;Sebastian Kvist","doi":"10.1080/24701394.2019.1634698","DOIUrl":"https://doi.org/10.1080/24701394.2019.1634698","url":null,"abstract":"<p><p><i>Placobdella rugosa</i> has long presented challenges to leech biologists. Its extreme morphological variability and similarity to some congeneric species has confounded classification for over a century. Recent molecular analyses revealed a surprising lack of genetic variation among morphologically disparate, geographically widespread specimens of <i>P. rugosa</i>. Given the lack of any obvious mechanism by which this species could disperse between distant habitats, it was expected that widespread populations would be genetically isolated from each other. In the present study, we investigate the relationship between geographic distance and genetic diversity in <i>P. rugosa</i> using COI sequences from specimens collected across Canada and the United States. Although we find preliminary evidence for a barrier to gene flow between eastern and western collecting localities, our vastly expanded dataset largely corroborates prior studies, showing minimal phylogeographic signal among the sequences and negligible levels of genetic isolation by distance. A recent range expansion following the last ice age and/or host-mediated dispersal are discussed as potential explanations for this unexpected phylogeographic pattern.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"30 6","pages":"749-763"},"PeriodicalIF":0.0,"publicationDate":"2019-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2019.1634698","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37391845","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":"Identification of leopard frogs (Anura: Ranidae: <i>Lithobates</i>) distributed in some localities of the Southern Mexican Plateau using mitochondrial DNA sequences.","authors":"Daniel Ochoa-Vázquez,&nbsp;Rogelio Rosas-Valdez,&nbsp;Elizabeth A Martínez-Salazar,&nbsp;Oscar Flores-Villela","doi":"10.1080/24701394.2019.1634697","DOIUrl":"https://doi.org/10.1080/24701394.2019.1634697","url":null,"abstract":"<p><p>Species of the genus <i>Lithobates</i> are difficult to identify, especially on the <i>'Rana pipiens'</i> complex, because the morphological differences among the species are often subtle. In this study, we used 12S ribosomal RNA gene partial sequences to identify specimens of leopard frogs from some new localities (not sampled on previous studies) of the Southern Mexican Plateau, to carry out a phylogenetic analysis, and also a morphometric analysis of some morphological features were analyzed to evaluate their morphological variation. A phylogenetic analysis using partial sequences of 12S rDNA mitochondrial gene for 31 samples was carried out using Bayesian Inference, Maximum Parsimony, and Maximum Likelihood. In addition, 20 morphological lineal measurements from 97 specimens were analyzed by principal component analysis (PCA) to evaluate if the frogs studied are conspecific. Partial sequences of the 12S rDNA obtained from frogs distributed in the Southern Mexican Plateau show two haplotypes with a divergence of 0.4%. Phylogenetic hypothesis shows an exclusive group with a previous sequence of <i>Lithobates montezumae</i>. The PCA indicates that variables are not linearly correlated and specimens belong to a single group. Evidence found, let us consider that specimens studied belong to one species of the <i>Lithobates montezumae</i> subgroup, distributed principally in the Southern Mexican Plateau.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"30 6","pages":"739-748"},"PeriodicalIF":0.0,"publicationDate":"2019-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2019.1634697","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37115472","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}