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

{"title":"Population differentiation and genetic diversity of endangered <i>Brachymystax tsinlingensis</i> Li between Yangtze River and Yellow River in China based on mtDNA.","authors":"Jian Shao,&nbsp;Dongmei Xiong,&nbsp;Zhipeng Chu,&nbsp;Jinming Wu,&nbsp;Hao Du,&nbsp;Feng Wang,&nbsp;Sien Wen,&nbsp;Qiwei Wei","doi":"10.1080/24701394.2019.1572130","DOIUrl":"https://doi.org/10.1080/24701394.2019.1572130","url":null,"abstract":"<p><p><i>Brachymystax tsinlingensis</i> Li, distributed scatteredly in Qinling Mountains of China, is an ideal material for studies of conservation and phylogeography. In the present study, the genetic variations and phylogeographical patterns of <i>B. tsinlingensis</i> collecting from the Yangtze River (<i>n</i> = 30) and the Yellow River (<i>n</i> = 70) were compared based on 1082-1163 bp control region with partial tRNA and 912 bp cyt <i>b</i> partial sequence of mtDNA. Analysis of variance indicated that a high proportion of the total genetic variance (96.03%) was distributed among populations, supporting strong geographic structuring of mtDNA polymorphism. Ten haplotypes were assigned to two clades that were related to geographic regions. No haplotype shared between geographic populations from the Yangtze River and the Yellow River, and two clades related to geographic regions can be clearly found from phylogenetic analysis by Bayesian approach, one from individuals in the Yangtze River and the other from individuals in the Yellow River, which probably indicated artificial carrying not happened historically. The mitochondrial results revealed an obvious differentiation of genetic structure of <i>B. tsinlingensis</i> between populations of Yellow River and Yangtze River, and the estimated diverge time around 0.20 MY. It was suggested that each of the two evolutionarily distinct groups of <i>B. tsinlingensis</i> should be protected and crossing individuals between two river systems should be avoided for conservation purpose.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"30 5","pages":"695-701"},"PeriodicalIF":0.0,"publicationDate":"2019-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2019.1572130","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37405666","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 barcoding of the rodent genus <i>Oligoryzomys</i> (Cricetidae: Sigmodontinae): mitogenomic-anchored database and identification of nuclear mitochondrial translocations (Numts).","authors":"Marcos O R da Cruz,&nbsp;Marcelo Weksler,&nbsp;Cibele R Bonvicino,&nbsp;Alexandra M R Bezerra,&nbsp;Francisco Prosdocimi,&nbsp;Carolina Furtado,&nbsp;Lena Geise,&nbsp;François Catzeflis,&nbsp;Benoit de Thoisy,&nbsp;Luiz F B de Oliveira,&nbsp;Claudia Silva,&nbsp;João Alves de Oliveira","doi":"10.1080/24701394.2019.1622692","DOIUrl":"https://doi.org/10.1080/24701394.2019.1622692","url":null,"abstract":"<p><p>DNA barcoding has become a standard method for species identification in taxonomically complex groups. An important step of the barcoding process is the construction of a library of voucher-based material that was properly identified by independent methods, free of inaccurate identification, and paralogs. We provide here a <i>cytochrome oxidase I</i> (<i>mt-Co1</i>) DNA barcode database for species of the genus <i>Oligoryzomys</i>, based on type material and karyotyped specimens, and anchored on the mitochondrial genome of one species of <i>Oligoryzomys</i>, <i>O. stramineus</i>. To evaluate the taxonomic determination of new COI sequences, we assessed species intra/interspecific genetic distances (barcode gap), performed the General Mixed Yule Coalescent method (GMYC) for lineages' delimitation, and identified diagnostic nucleotides for each species of <i>Oligoryzomys</i>. Phylogenetic analyses of <i>Oligoryzomys</i> were performed on 2 datasets including 14 of the 23 recognized species of this genus: a <i>mt-Co1</i> only matrix, and a concatenated matrix including <i>mt-Co1</i>, <i>cytochrome b</i> (<i>mt-Cytb</i>), and <i>intron 7 of the nuclear fibrinogen beta chain gene</i> (<i>i7Fgb</i>). We recovered nuclear-mitochondrial translocated (Numts) pseudogenes on our samples and identified several published sequences that are cases of Numts. We analyzed the rate of non-synonymous and synonymous substitution, which were higher in Numts in comparison to mtDNA sequences. GMYC delimitations and DNA barcode gap results highlight the need for further work that integrate molecular, karyotypic, and morphological analyses, as well as additional sampling, to tackle persistent problems in the taxonomy of <i>Oligoryzomys</i>.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"30 5","pages":"702-712"},"PeriodicalIF":0.0,"publicationDate":"2019-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2019.1622692","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37077069","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":"Forensic analysis reveals fraud in fillets from the \"Gurijuba\" <i>Sciades parkeri</i> (Ariidae - Siluriformes): a vulnerable fish in Brazilian Coastal Amazon.","authors":"Grazielle Gomes,&nbsp;Rafael Correa,&nbsp;Ivana Veneza,&nbsp;Raimundo da Silva,&nbsp;Danillo da Silva,&nbsp;Josy Miranda,&nbsp;Iracilda Sampaio","doi":"10.1080/24701394.2019.1622694","DOIUrl":"https://doi.org/10.1080/24701394.2019.1622694","url":null,"abstract":"<p><p>The utilization of molecular tools for the certification of fishery products has been increasing over the last years. In general, economically important species are replaced by less valuable species, characterizing a commercial fraud. We evaluated the authenticity of 107 frozen fillets tagged as Gurijuba (<i>Sciades parkeri</i>) and Uritinga (<i>Sciades proops</i>) from local markets in northern amazon coast by sequencing two mitochondrial genes: Cytochrome oxidase subunit I and cytochrome b (Cyt b). About 16% of fillets putatively related to <i>S. parkeri</i> were replaced by <i>S. proops</i>. The Gurijuba faces high fishing pressure, being currently listed by the International Union for Conservation of Nature as vulnerable. Forensic analysis with DNA markers, proved to be highly efficient in the discrimination of the processed seafood products, providing unequivocal identification of species, revealing commercial fraud in the fillets of the Gurijuba, and revealing the utility of Cytb sequences as barcode in fishes.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"30 5","pages":"721-729"},"PeriodicalIF":0.0,"publicationDate":"2019-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2019.1622694","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37319584","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 <i>Andricus</i> species (Hymenoptera: Cynipidae) inducing various oak galls in Central Zagros of Iran.","authors":"Majid Tavakoli,&nbsp;Samad Khaghaninia,&nbsp;George Melika,&nbsp;Graham N Stone,&nbsp;Asadollah Hosseini-Chegeni","doi":"10.1080/24701394.2019.1622693","DOIUrl":"https://doi.org/10.1080/24701394.2019.1622693","url":null,"abstract":"<p><p>This study uses an integrated approach to address the taxonomic status of six different and problematic oak galls and their inducing wasps sampled from two sites in the Central Zagros Mountains (Lorestan province) in western Iran. Our aim was to establish whether morphologically similar but different galls are induced by the same or distinct gall-inducers. The gall wasp specimens were identified morphologically to species level, and their genomic DNA was extracted. We used PCR and Sanger sequencing to amplify three fragments comprising cytochrome oxidase subunit I (<i>COI</i>), cytochrome b (<i>cytB</i>), and a multi-gene fragment of ribosomal DNA (rDNA) including partial 5.8S, complete internal transcribed spacer 2 (<i>ITS2</i>), and partial 28S rRNA. We found that a pair of structurally similar but differently coloured galls are induced by the sexual generation of <i>Andricus grossulariae,</i> while another similar pair are induced by the asexual generation of <i>A. sternlichti.</i> In contrast, we found that two similar galls that differ in some structural details and in developmental phenology are induced by two closely related but different gall wasps; one is the sexual generation of <i>A. cecconii</i>, while the second is a new but closely related sexual generation <i>Andricus</i> sp.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"30 5","pages":"713-720"},"PeriodicalIF":0.0,"publicationDate":"2019-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2019.1622693","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37345621","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 discrimination of <i>Ancistrus</i> lineages (Siluriformes: Loricariidae) using barcode DNA tool.","authors":"Rafael Splendore de Borba,&nbsp;Sandra Mariotto,&nbsp;Liano Centofante,&nbsp;Claudio Henrique Zawadzki,&nbsp;Patricia Pasquali Parise-Maltempi","doi":"10.1080/24701394.2019.1597071","DOIUrl":"https://doi.org/10.1080/24701394.2019.1597071","url":null,"abstract":"<p><p>Although several species of <i>Ancistrus</i> have been described from the Amazon and Paraguay river basins in the states of Amazonas and Mato Grosso, Brazil, the taxonomic status of most specimens from these regions remains doubtful. In the present work, cytogenetic and molecular data were used to discriminate and isolate unexpected <i>Ancistrus</i> lineages from the Amazon and Paraguay basins. For that, it was used DNA barcoding based on mitochondrial Cytochrome Oxidase Subunit I (COI) gene and cytogenic data to perform such molecular discrimination. The analyzed sequences had 669 bp, of which 171 bp were conserved and 491 bp were variable. The Neighbor-joining and Bayesian analysis revealed 21 distinct groups in topology. The genetic distances within each group was 0.4%, 21 times smaller than the mean distance observed among groups, which was 8.4%. These values showed seven distinct lineages of <i>Ancistrus</i> from the studied points of the Amazon basin and eight lineages from the Paraguay basin points. Our results illustrate the efficiency of this technique for the discrimination of the <i>Ancistrus</i> lineages once it indicates the occurrence of cryptic species in these regions, which cannot yet be identified either with just chromosomal or morphological analyzes.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"30 4","pages":"602-608"},"PeriodicalIF":0.0,"publicationDate":"2019-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2019.1597071","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37151040","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 diversity and population structure of goliath frogs (<i>Conraua goliath</i>) from Cameroon.","authors":"Daniel Nguete Nguiffo,&nbsp;Mbida Mpoame,&nbsp;Charles S Wondji","doi":"10.1080/24701394.2019.1615060","DOIUrl":"https://doi.org/10.1080/24701394.2019.1615060","url":null,"abstract":"<p><p>The goliath frog (<i>Conraua goliath</i>) is an Endangered species exclusively found in Cameroon and Equatorial Guinea. Climate change, deforestation and overhunting are principal causes driving this species to extinction. Therefore, a better understanding of the genetic diversity and population structure of this species is necessary to improve conservation efforts. Here we used two mitochondrial genes (Cytochrome Oxidase subunit 1 (COI) and 16S) extracted from 54 <i>C. goliath</i> individuals from six localities in Cameroon to examine their genetic diversity. The result shows a low DNA substitution between the sequences. There were four 16S and two COI haplotypes in total. Overall, genetic diversity was very low for all the genes with nucleotide diversity of 0.00106 and 0.00007 for 16S and COI respectively. The Tajima D and Fu Fs statistics were negative. The TCS haplotype network revealed a predominant and ancestral haplotype (H1) for these genes which is distributed in the 6 populations. Pairwise genetic differentiation (<i>F_ST</i>) generated between these populations using 16S revealed very high differentiation between populations from Nkam and Mungo Administrative Divisions in Cameroon. In contrast, we observed low differentiation among the geographically clustered Mungo and Nkam populations. Overall, human activities and perhaps climate change can appear to have depleted genetic diversity in the scattered populations that remain of this amphibian. To sustain the Goliath frog, we suggest to the Cameroonian government to implement more effective strategies to conserve and manage remnant populations of this iconic species through more effort against poaching which contribute to reduce the genetic diversity.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"30 4","pages":"657-663"},"PeriodicalIF":0.0,"publicationDate":"2019-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2019.1615060","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37419088","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":"Intra-species variation and geographic differentiation among the populations of the quarantine agricultural pest <i>leucinoides orbonalis</i> (lepidoptera: Crambidae) in the global assemblage - a prospective of DNA barcoding.","authors":"Pushparaj Karthika,&nbsp;Chithravel Vadivalagan,&nbsp;Durairaj Thirumurugan,&nbsp;Kadarkarai Murugan","doi":"10.1080/24701394.2019.1622691","DOIUrl":"https://doi.org/10.1080/24701394.2019.1622691","url":null,"abstract":"<p><p><i>Leucinodes orbonalis</i> Guenée is serious quarantine pest occurring globally, studies are needed to enlighten the genetic complexities associated with the species. India is considered to be the origin of the <i>L. orbonalis</i>, therefore availability of species records from this region enable to analyse the genetic differences and dispersal of the lineages. The results of the study reported 47 haplotypes in four clusters pertaining to their ancestral lineage. The transition/transversion bias (R) was observed to be higher with 1.238 and 1.312 in the first and third codon positions respectively. The overall intraspecies divergence was found to be 0.302. AMOVA revealed that the total variations were then as reported 67.15 among the south-east countries but our studies reported the total variation to be 77.25% (Germany, India, South east and Australia). <i>F_ST</i> and Mantel's test indicated that there was no correlation between the genetic variation and geographical distance. The overall haplotype diversity was 0.852, where the nucleotide diversity of H31 (0.00593) was highest and H1 (0.00087) was lowest. The genetic diversity indices Tajima D and Fu's Fs static for H1, H13 and H31 had negative values which possibly inferred for the bottle neck effect. The ML tree was constituted the branch length of 5.0157 with one out-group. The tree was formed with ten distinctive clades with the haplotypes congregated together based on similar genetic composition.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"30 4","pages":"682-693"},"PeriodicalIF":0.0,"publicationDate":"2019-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2019.1622691","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37040878","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":"Refutation of media reports on introduction of the red bellied piranha and potential impacts on aquatic biodiversity in India.","authors":"Anita Tiknaik,&nbsp;Amol Kalyankar,&nbsp;Mahesh Shingare,&nbsp;Rahul Suryawanshi,&nbsp;Bharathi Prakash,&nbsp;Tejswini A Sontakke,&nbsp;Dinesh Nalage,&nbsp;Raveendranathanpillai Sanil,&nbsp;Gulab Khedkar","doi":"10.1080/24701394.2019.1611798","DOIUrl":"https://doi.org/10.1080/24701394.2019.1611798","url":null,"abstract":"<p><p>The presence of a new, potentially deadly exotic fish resembling the Red Bellied Piranha, <i>Pygocentrus nattereri</i> was reported in India by print media from various aquatic resources. These reports raised dramatic concerns over public health issues and threats to the aquatic biodiversity of India. Considering the potential severity of the issue and concerns raised by the media, we undertook a study to evaluate the reliability of identification reports of the suspected fish, any relationships to other species of piranha and to address any possible threats to the aquatic biodiversity of India. For this study, samples were collected from most of the major river systems and lakes in India and evaluated for taxonomic identifications of the suspect fish and phylogenetic relationships to other fish species. Our results clearly show that the suspect fish is in fact <i>Piaractus brachypomus</i>, a species commonly referred as \"Pacu\", and not the red bellied piranha, <i>P. nattereri</i>. Comparisons of both fish do show striking similarities that may account for the misreporting in the media. Furthermore, <i>P. brachypomus</i>as is still an exotic fish, and as such may still have potentially harmful impacts on the native aquatic fauna of India. Quick attention to this issue and the imposition of control measures, including market bans, should be considered to prevent further loss of biodiversity.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"30 4","pages":"643-650"},"PeriodicalIF":0.0,"publicationDate":"2019-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2019.1611798","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37233155","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":"Mutation pressure and natural selection on codon usage in chloroplast genes of two species in <i>Pisum</i> L. (Fabaceae: Faboideae).","authors":"Debjyoti Bhattacharyya,&nbsp;Arif Uddin,&nbsp;Sudipa Das,&nbsp;Supriyo Chakraborty","doi":"10.1080/24701394.2019.1616701","DOIUrl":"https://doi.org/10.1080/24701394.2019.1616701","url":null,"abstract":"<p><p>This study was attempted to focus on the pattern of codon usage bias (CUB) of chloroplast genes in two species of <i>Pisum viz</i>. <i>P. fulvum</i> and <i>P. sativum</i> and to identify the factors which influence CUB. Bioinformatic tools were used to understand codon usage pattern in the protein-coding sequences of <i>Pisum</i> chloroplast genomes. It was found that GC content was lower than AT content in the genes. Low synonymous codon usage order (SCUO) values of genes indicated low CUB in chloroplast genes of <i>Pisum</i> species. Heatmaps showed positive correlations of GC3 with all the GC and AT ending codons. Neutrality plot analysis revealed that natural selection might have played a prominent role over mutation pressure in sculpturing the CUB of chloroplast genes in these two taxa. Positive correlation between SCUO and mRNA free energy (mFE) suggested that higher energy release by entire mRNA was related to high degree of CUB. Further, highly significant (<i>p</i> < .01) negative correlation was found between parameters in pair i.e. mFE-GC, mFE-GC1, mFE-GC2 and mFE for entire mRNA-GC3. This pointed out that higher GC content might have influenced lesser energy release by mRNA molecules of chloroplast genes.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"30 4","pages":"664-673"},"PeriodicalIF":0.0,"publicationDate":"2019-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2019.1616701","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37266059","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 barcodes and their characteristic diagnostic sites analysis of Schizothoracinae fishes in Qinghai province.","authors":"Ting Wang,&nbsp;Desheng Qi,&nbsp;Shihao Sun,&nbsp;Zhonghao Liu,&nbsp;Yurong Du,&nbsp;Songchang Guo,&nbsp;Jianbin Ma","doi":"10.1080/24701394.2019.1580273","DOIUrl":"https://doi.org/10.1080/24701394.2019.1580273","url":null,"abstract":"<p><p>The Qinghai-Tibetan Plateau (QTP), the source and upper reaches of many Asian rivers, are crisscrossed by rivers and dotted with lakes. Schizothoracinae fishes, species native to the QTP, are distributed widely through these rivers and lakes. Over the past decades, ecological protection has become increasingly intense. The rapid acquisition of the genetic information and accurate gene sequence database are assumed to play an important role in the conservation of species diversity and biodiversity. In this study, 153 <i>COI</i> sequences (648bp in length) covering 13 species in 8 genera of Schizothoracinae fishes in Qinghai Province were used to determine whether barcode could identify Schizothoracinae species accurately. The average Kimura two parameter (K2P) genetic distances within and among species were 0.35% and 8.83%, respectively. The maximum K2P distance within species was observed in <i>Gymnocypris eckloni</i> (1.36%) while minimum K2P distance among species was observed between <i>Chuanchia labiosa</i> and <i>Schizopygopsis pylzovi</i> (0.23%). Overlaps existed in K2P distance intra- and inter- species based on both the genes. Eleven groups with 9 single-species groups and 2 multi-species groups were identified through Automatic Barcode Gap Discovery System, which were consistent with the overlaps of K2P distance. 96.7% as the accurate ratio for <i>COI</i> barcode was calculated and high solution was observed in the phylogenetic trees based on <i>COI</i> gene and <i>Cyt b</i> gene. Except for the similar results based on two genes above, <i>COI</i> barcode was more economical than <i>Cyt b</i> gene. The SOM model successfully predicted characteristic-diagnostic sites at species level: 36 characteristic-diagnostic sites from eight species, in which 12 from <i>Gmnodiptychus pachycgeilus</i>, 2 from <i>Platypharodon extremus</i>, 7 from <i>Ptychobarbus kaznakovi</i>, 2 from <i>Schizopygopsis anteroventris</i>, 2 from <i>Schizopygopsis malacanthus</i>, 3 from <i>Schizopygopsis malacanthus chengi</i>, 3 from <i>Schizothorax dolichonema</i> and 5 from <i>Schizothorax lantsangensis</i>. Our results show that Schizothoracinae fishes can be identified validly by using <i>COI</i> DNA barcode. Thirty-six characteristic-diagnostic sites were proposed to be applied into works of species identification for the Schizothoracinae fishes in Qinghai Province.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"30 4","pages":"592-601"},"PeriodicalIF":0.0,"publicationDate":"2019-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2019.1580273","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37124207","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}