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

{"title":"Characterizing coral reef biodiversity: genetic species delimitation in brachyuran crabs of Palmyra Atoll, Central Pacific.","authors":"Jennifer A Servis,&nbsp;Brendan N Reid,&nbsp;Molly A Timmers,&nbsp;Vasiliki Stergioula,&nbsp;Eugenia Naro-Maciel","doi":"10.1080/24701394.2020.1769087","DOIUrl":"https://doi.org/10.1080/24701394.2020.1769087","url":null,"abstract":"<p><p>Coral reefs are highly threatened ecosystems, yet there are numerous challenges in conducting inventories of their vanishing biodiversity, partly because many taxa remain difficult to detect and describe. Genetic species delimitation methods provide a standardized means for taxonomic classification including of cryptic, rare, or elusive groups, but results can vary by analytical method and genetic marker. In this study, a combination of morphological and genetic identification methods was used to estimate species richness and identify taxonomic units in true crabs (Infraorder Brachyura; n = 200) from coral reefs of Palmyra Atoll, Central Pacific. Genetic identification was based on matches between mitochondrial 16S ribosomal RNA (16S rRNA) and/or cytochrome <i>c</i> oxidase subunit I (COI) sequences to GenBank data, while morphological work relied on the taxonomic literature. Broad agreement in the number of candidate species delimited by genetic distance thresholds and tree-based approaches was found, although the multi-rate Poisson tree process (mPTP) was less appropriate for this dataset. The COI sequence data identified 30-32 provisional species and the 16S data revealed 34-35. The occurrence of 10 families, 20 genera, and 19 species of brachyurans at Palmyra was corroborated by at least two methods. Diversity levels within <i>Chlorodiella laevissima</i> indicated possible undescribed or cryptic species in currently lumped taxa. These results illustrate the efficacy of DNA sequences in identifying organisms and detecting cryptic variation, and underscore the importance of using appropriate genetic markers and multiple species delimitation analyses, with applications for future species descriptions.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 5","pages":"178-189"},"PeriodicalIF":0.0,"publicationDate":"2020-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1769087","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38016186","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":"TaqMan real-time quantitative PCR for identification of antlers in tradition Chinese medicine.","authors":"Jie Pan,&nbsp;Rui Feng,&nbsp;Qing Hu,&nbsp;Hong Chen,&nbsp;Su Zhang,&nbsp;Jian Sun,&nbsp;Shen Ji","doi":"10.1080/24701394.2020.1741560","DOIUrl":"https://doi.org/10.1080/24701394.2020.1741560","url":null,"abstract":"<p><p>In this study, a method was established for discriminating the true <i>Cervus</i> antlers from its counterfeits using TaqMan real-time quantitative PCR. The method combines the use of true <i>Cervus</i> antlers-specific primers, that amplify a 226 bp fragment from true <i>Cervus</i> antlers DNA, and mammalian-specific primers amplifying a 146 bp fragment from mammalian species DNA, which are used as endogenous control. A TaqMan probe that hybridizes in the '<i>Cervus</i> antler' and also in the 'mammalian' DNA fragments is used to monitor the amplification of the target gene. The <i>Cervus</i> antler mitochondrial DNA was used as target gene to design the primers and TaqMan probes. The data revealed that the TaqMan real-time PCR-based assay can be used for identification of the true <i>Cervus</i> antlers from counterfeits in a single step. The limit of detection (LOD) was lower than 1 pg of DNA per reaction.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 5","pages":"173-177"},"PeriodicalIF":0.0,"publicationDate":"2020-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1741560","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37909433","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":"Invalidation of taxa within the silvery wooly monkey (<i>Lagothrix lagothricha poeppigii</i>, Atelidae, Primates).","authors":"Manuel Ruiz-García,&nbsp;Myreya Pinedo-Castro,&nbsp;Aymara Albino,&nbsp;Jessica Yanina Arias-Vásquez,&nbsp;Armando Castellanos,&nbsp;Joseph Mark Shostell","doi":"10.1080/24701394.2020.1757084","DOIUrl":"https://doi.org/10.1080/24701394.2020.1757084","url":null,"abstract":"<p><p>The systematics of the Humboldt's wooly monkeys (<i>L. lagothricha</i>; Atelidae) is essential to preserve this Neotropical primate species. Traditionally, four morphological subspecies have been described, which recently have been molecularly confirmed. However, no population genetics studies have been carried out throughout the geographical distribution of one of these subspecies, <i>Lagothrix lagothricha poeppigii</i>. For this reason, we analyzed nine mitochondrial genes of <i>L. l. poeppigii</i> mainly collected from the Ecuadorian and Peruvian Amazon in order to better understand the evolutionary history of this taxon. The mitochondrial genetic diversity levels (haplotype and nucleotide diversity) we estimated are likely the highest yet reported for <i>L. lagothricha.</i> Our results did not detect important genetic structure within <i>L. l. poeppigii</i>. Furthermore, our phylogenetic analyses did not detect any relevant molecular cluster in the area where Groves hypothesized the existence of <i>L. poeppigii castelnaui</i>. Therefore, based on these data, <i>castelnaui</i> is not a valid taxon from a molecular perspective. The most differentiated subpopulation within <i>L. l. poeppigii</i> was from Morona-Santiago province (Ecuador) and had a genetic distance of 0.8-1.2% relative to the other subpopulations studied. However, this genetic distance range is within the variability found within a population. We estimated the mitochondrial temporal diversification within <i>L. l. poeppigii</i> to have occurred during the Pleistocene, 1.8-1.2 million years ago. Similarly, all our analyses detected a strong Pleistocene female population expansion for this taxon. Diverse spatial genetic analyses, perhaps with the exception of Monmonier's Algorithm, did not detect differentiated taxa within the area analyzed for <i>L. l. poeppigii</i>. These genetics results could be of importance to conservation efforts to preserve this taxon as one unit.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 4","pages":"147-162"},"PeriodicalIF":0.0,"publicationDate":"2020-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1757084","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37868170","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 Tibetan medicine Dida based on DNA barcoding.","authors":"Ruoshi Li,&nbsp;Shuixian Li,&nbsp;Xiaoquan Yang,&nbsp;Yongqiang Guo,&nbsp;Baozhong Duan,&nbsp;Li Xu,&nbsp;Conglong Xia","doi":"10.1080/24701394.2020.1741563","DOIUrl":"https://doi.org/10.1080/24701394.2020.1741563","url":null,"abstract":"<p><p>The purpose of this study was to test the ability of DNA barcoding to identify the herbal raw trade of Tibetan medicine Dida in China. A reference database for plant-material DNA barcodes was successfully constructed and used to identify 36 commercially samples of Dida collected from Southwest China. The ITS sequence was amplified from these samples and the efficiency of the PCR amplification of ITS was 100%. The DNA sequencing results revealed that 3 samples (8.3%) were authenticated as <i>Swertia chirayita</i>, 2 sequences (5.6%) were authenticated as <i>Swertia mussotii</i>, 3 sequences (8.3%) were authenticated as <i>Swertia ciliata</i>, as recorded in the Tibetan Pharmacopeia. The other samples were authenticated as adulterants and all of them originated from common plants belonging to <i>Saxifraga</i>, <i>Swertia</i> and <i>Halenia</i>. This result indicates Dida pieces that are available in the market have complex origins and may indicate a potential safety issue and DNA barcoding is a convenient tool for market supervision.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 4","pages":"131-138"},"PeriodicalIF":0.0,"publicationDate":"2020-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1741563","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37789510","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":"Retraction: Complete mitochondrial genome of the Swan Goose (<i>Anser cygnoides</i> L.) and its phylogenetic analysis.","authors":"","doi":"10.1080/24701394.2020.1758395","DOIUrl":"https://doi.org/10.1080/24701394.2020.1758395","url":null,"abstract":"","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 4","pages":"172"},"PeriodicalIF":0.0,"publicationDate":"2020-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1758395","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37869705","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":"Use of complete mitochondrial genome sequences to identify barcoding markers for groups with low genetic distance.","authors":"Aline Torres de Azevedo Chagas,&nbsp;Sandra Ludwig,&nbsp;Juliana da Silva Martins Pimentel,&nbsp;Nazaré Lúcio de Abreu,&nbsp;Daniela Lidia Nunez-Rodriguez,&nbsp;Hortensia Gomes Leal,&nbsp;Evanguedes Kalapothakis","doi":"10.1080/24701394.2020.1748609","DOIUrl":"https://doi.org/10.1080/24701394.2020.1748609","url":null,"abstract":"<p><p>Complete mitochondrial sequences can be rapidly obtained and are widely available, providing a great source of species information and allowing for the discovery of new specific molecular markers. However, for some taxonomic groups, traditional approaches for species delimitation are impaired by the low genetic distance values. In these cases, other species-level markers are used. For <i>Prochilodus</i>, which includes important neotropical fish species, species-level delimitation usually results in poor phylogenetic resolution when using mitochondrial COI/<i>cytB</i> genes as barcoding markers because of low genetic variability and low species-level resolution. Thus, in this study, we developed an approach to design and validate new barcoding markers with high species-level resolution obtained from the D-loop region, using <i>Prochilodus</i> spp. as a model. For the new barcoding marker validation, the amplicon region was used to infer the phylogenetic relationships of <i>Prochilodus</i> spp. through three distinct methods: Bayesian inference (BI), Neighbor-Joining method (NJ), and Maximum Likelihood method (ML). The phylogenetic relationships of <i>Prochilodus</i> spp. revealed high resolution at species-level, nonoverlapping clades, and high branch support. The genetic distance results allied to two different clustering methods (Bayesian Poisson tree processes and automatic barcode gap discovery) revealed the existence of a barcoding gap, thus, validating the use of the barcoding markers designed in this study. The approach proposed here may, therefore, be expanded to other taxa to access and validate new barcoding markers with higher resolution at the species level.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 4","pages":"139-146"},"PeriodicalIF":0.0,"publicationDate":"2020-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1748609","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37854280","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":"Retraction: Complete mitochondrial genome of Paracobitis variegates and its phylogenetic analysis.","authors":"","doi":"10.1080/24701394.2020.1758393","DOIUrl":"https://doi.org/10.1080/24701394.2020.1758393","url":null,"abstract":"","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 4","pages":"171"},"PeriodicalIF":0.0,"publicationDate":"2020-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1758393","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37869703","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":"Spatial genetic structure of black francolin (<i>Francolinus francolinus asiae</i>) in the North-Western Himalayan region based on mitochondrial control region.","authors":"Anand Kumar,&nbsp;Saurabh Dewan,&nbsp;Rajeev Lochan,&nbsp;Dinesh K Sharma","doi":"10.1080/24701394.2020.1757664","DOIUrl":"https://doi.org/10.1080/24701394.2020.1757664","url":null,"abstract":"<p><p>Due to specific habitat preferences and behavioural limitations, black francolin is not uniformly distributed across the northwestern Himalayan landscape, rather is confined to certain land mosaic. The habitable zones are further reduced due to several manmade threats as logging and forest fire leading to sparse distribution. Overall 54 samples were used for partial sequence analysis of mitochondrial control region. A well evident divergence pattern was observed as individuals collected from low altitude, terrai region significantly distanced from high altitude sampled individuals. Also, the individuals at lower elevation sites exhibited higher genetic diversity in comparison to the samples collected at higher elevations. This indicates that patchy distribution and low dispersal rate have resulted in fine-scale patterns of genetic diversity among the black francolin population. Further, habitat loss and forest fragmentation could lead to more small and isolated populations that could suffer from reduced genetic diversity and may be higher extinction rates.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 4","pages":"163-170"},"PeriodicalIF":0.0,"publicationDate":"2020-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1757664","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37877067","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":"Strong genetic differentiation among populations of <i>Cheirotonus gestroi</i> (Coleoptera: Euchiridae) in its native area sheds lights on species conservation.","authors":"Chen Yang,&nbsp;En-Jiao Zhu,&nbsp;Qiu-Ju He,&nbsp;Chuan-Hui Yi,&nbsp;Xu-Bo Wang,&nbsp;Shao-Ji Hu,&nbsp;Shu-Jun Wei","doi":"10.1080/24701394.2020.1741565","DOIUrl":"https://doi.org/10.1080/24701394.2020.1741565","url":null,"abstract":"<p><p>The long-armed scarab (<i>Cheirotonus gestroi</i>) is an endangered large insect in southwestern China and neighboring countries; however, limited information is available regarding its population genetics, hindering conservation efforts. Therefore, we investigated the population genetic structure and evolutionary history of <i>C. gestroi</i> in southwestern China. Twenty-five haplotypes were obtained from 47 specimens across five populations. The Dawei Mountain (DWS) population differed from other populations by a high genetic distance. Population structure analysis generated three distinct clades, corresponding to Hengduan Mountains (HM), Ailao Mountains (AM), and Dawei Mountains (DM), and high-level genetic diversity was found in two HM populations. Collectively, the strong genetic differentiation among populations might be due to limited gene flow, geographical isolation, and habitat fragmentation. Therefore, while developing a conservation strategy, HM, AM, and DM groups should be defined as separate management units. Additionally, the DWS population should be given priority protection due to its uniqueness and low genetic diversity.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 3","pages":"108-119"},"PeriodicalIF":0.0,"publicationDate":"2020-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1741565","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37763420","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":"Spatial genetic structure of <i>Opsariichthys hainanensis</i> in South China.","authors":"Wen-Jun Zhang,&nbsp;Jun-Jie Wang,&nbsp;Chao Li,&nbsp;Jia-Qi Chen,&nbsp;Wei Li,&nbsp;Shu-Ying Jiang,&nbsp;Kui-Ching Hsu,&nbsp;Meiting Zhao,&nbsp;Hung-Du Lin,&nbsp;Jun Zhao","doi":"10.1080/24701394.2020.1741564","DOIUrl":"https://doi.org/10.1080/24701394.2020.1741564","url":null,"abstract":"<p><p>South China presents an excellent opportunity to build a phylogeographic paradigm for complex geological history, including mountain lifting, climate change, and river capture/reversal events. The phylogeography of cyprinids, particularly <i>Opsariichthys hainanensis</i>, an endemic species restricted to South China, was examined to explore the relationship between the populations in Red River, Hainan Island and its adjacent mainland China. A total of 37 haplotypes were genotyped for the mitochondrial cytochrome <i>b</i> (Cyt <i>b</i>) gene in 115 specimens from 11 river systems. Relatively high levels of haplotype diversity (h = 0.946) and low levels of nucleotide diversity (π = 0.014) were detected in <i>O. hainanensis</i>. Four major phylogenetic haplotype groups revealed a relationship between phylogeny and geography. Our results found that (i) the ancestral populations of <i>O. hainanensis</i> were distributed south of the Wuzhishan and Yinggeling mountains, including the Changhua River on Hainan Island, and then spread to the surrounding areas, (ii) the admixtures within lineages occurred between the Red River in North Vietnam and the Changhua River in western Hainan Island and (iii) indicated that the exposure of straits and shelves under water retreat, provides opportunities for population dispersion during glaciations.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 3","pages":"98-107"},"PeriodicalIF":0.0,"publicationDate":"2020-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1741564","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37749469","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}