Mitochondrial Dna Part a最新文献_第5页

Phylogeography of freshwater fish Puntius sophore in India 印度淡水鱼的系统地理学

4区生物学

Mitochondrial Dna Part a Pub Date : 2018-02-17 DOI: 10.1080/24701394.2016.1275598

R. K. Negi, B. Joshi, J. Johnson, Rahul De, S. Goyal

{"title":"Phylogeography of freshwater fish Puntius sophore in India","authors":"R. K. Negi, B. Joshi, J. Johnson, Rahul De, S. Goyal","doi":"10.1080/24701394.2016.1275598","DOIUrl":"https://doi.org/10.1080/24701394.2016.1275598","url":null,"abstract":"Abstract Phylogeography and evolutionary history of the freshwater species are poorly known. We document the phylogeography of widely distributed Puntius sophore using cytochrome oxidase subunit I (COI) gene of 650 bp. In the present study, we used 61 individual sequences from known geographic locations across India whereas data are lacking from other parts of its distribution range. Total 20 haplotypes with the intra-species sequence divergence ranging from 0.004 to 0.025 were observed and they were split into two major clades (North and Northeastern to Central India). Two distant geographic (North and Northeastern to Central India) regions shared haplotype suggesting ancient river connectivity or introduction of species from Northeast and Central India. Overall nucleotide and haplotype diversities were 0.00971 and 0.915. The Tajima’s D and Fu’s Fs values were found negative but non-significant thus rejecting the population expansion model followed by the multimodal mode of mismatch distribution. Bayesian skyline plots from both the clade showed steady population history over time; and start of decline in recent years in the clade B (∼1000–1500 years). The present finding is in support to the ‘Satpura hypothesis’ proposed to explain species movement patterns from Southeast Asian countries to Indian subcontinent, seconded by P. sophore showing high genetic diversity within Northern India clade (high genetic splits) because of presence of high river network in comparison to other parts of the country.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":"14 1","pages":"256 - 265"},"PeriodicalIF":0.0,"publicationDate":"2018-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90920829","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 8

No homology means there can be no analyses; a comment on Jose & Harikrishnan 没有同源性意味着没有分析;对何塞和哈里克里希南的评论

4区生物学

Mitochondrial Dna Part a Pub Date : 2018-02-17 DOI: 10.1080/24701394.2016.1267159

T. J. Page, D. Steinke

引用次数: 2

Mitogenomics phylogenetic relationships of the current sloth’s genera and species (Bradypodidae and Megalonychidae) 现代树懒属和种(慢足科和巨足科)的有丝分裂基因组学系统发育关系

4区生物学

Mitochondrial Dna Part a Pub Date : 2018-02-17 DOI: 10.1080/24701394.2016.1275602

M. Ruiz‐García, Diego Chacón, T. Pleše, Ingrid Schuler, J. Shostell

{"title":"Mitogenomics phylogenetic relationships of the current sloth’s genera and species (Bradypodidae and Megalonychidae)","authors":"M. Ruiz‐García, Diego Chacón, T. Pleše, Ingrid Schuler, J. Shostell","doi":"10.1080/24701394.2016.1275602","DOIUrl":"https://doi.org/10.1080/24701394.2016.1275602","url":null,"abstract":"Abstract We sequenced the complete mitogenome of 39 sloths (19 Bradypus variegatus, 4 B. tridactylus, 1 B. pygmaeus, 1 B. torquatus, 4 Choloepus didactylus, and 10 C. hoffmanni). A Bayesian tree (BI) indicated a temporal split between Bradypus and Choloepus around 31 million years ago (MYA, Oligocene) and the other major splits within each genera during the Miocene and Pliocene. A haplotype network (MJN) estimated a lower temporal split between the sloth genera (around 23.5 MYA). Both methods detected the ancestor of B. torquatus as the first to diverge within Bradypus (21 for BI and 19 MJN), followed by that of the ancestor of B. tridactylus. The split of B. pygmaeus from the common ancestor with B. variegatus was around 12 MYA (BI) or 4.3 MYA (MJN). The splits among the previous populations of B. variegatus began around 8 MYA (BI) or 3.6 MYA (MJN). The trans-Andean population was the first to diverge from the remaining cis-Andean populations of B. variegatus. The genetic differentiation of the trans-Andean B. variegatus population relative to the cis-Andean B. variegatus is similar to that found for different species of sloths. The mitogenomic analysis resolved the differentiation of C. hoffmanni from the C. didactylus individuals of the Guiana Shield. However, one C. didactylus from the Colombian Amazon specimen was inside the C. hoffmanni clade. This could be the first example of possible natural hybridization in the Amazon of both Choloepus taxa or the existence of un-differentiable phenotypes of these two species in some Amazonian areas.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":"39 2 1","pages":"281 - 299"},"PeriodicalIF":0.0,"publicationDate":"2018-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89481907","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 10

Geographic variation in the spotted-wing drosophila, Drosophila suzukii (Diptera: Drosophilidae), based on mitochondrial DNA sequences 基于线粒体DNA序列的斑点翼果蝇铃木果蝇(双翅目:果蝇科)的地理变异

4区生物学

Mitochondrial Dna Part a Pub Date : 2018-02-17 DOI: 10.1080/24701394.2016.1278534

Deuk‐Soo Choi, J. Park, Min Jee Kim, Jong Seok Kim, S. Jeong, Jun Seong Jeong, Jinyoung Park, Iksoo Kim

{"title":"Geographic variation in the spotted-wing drosophila, Drosophila suzukii (Diptera: Drosophilidae), based on mitochondrial DNA sequences","authors":"Deuk‐Soo Choi, J. Park, Min Jee Kim, Jong Seok Kim, S. Jeong, Jun Seong Jeong, Jinyoung Park, Iksoo Kim","doi":"10.1080/24701394.2016.1278534","DOIUrl":"https://doi.org/10.1080/24701394.2016.1278534","url":null,"abstract":"Abstract The spotted-wing drosophila (SWD), Drosophila suzukii (Diptera: Drosophilidae), is an economically damaging pest that feeds on most thin-skinned fruits. It was originally native to a few Asian countries, including Korea, but is now found in North America and Europe. In this study, we sequenced portions of the mitochondrial (mt) COI and ND4 genes from a total of 195 individuals collected mainly from Korea. We then combined GenBank-registered COI sequences from all ancestral-range and introduced-range populations with our own COI data to assess the worldwide diversity, divergence, and relatedness of SWD haplotypes. A total of 139 haplotypes were obtained from the concatenated COI and ND4 sequences. Most haplotypes were confined to single localities, but 12 of them were found in more than two localities, and one haplotype (SWDCN61) was found from Korea to Canada. A dataset combining GenBank sequences with our own data identified a total of 94 worldwide COI haplotypes with a maximum sequence divergence (MSD) of 5.433% (32 bp). Although most haplotypes were found in only a single country, a few haplotypes were found commonly in China, Korea, and Japan; these occurred at a higher frequency and were often involved in introductions. A rough estimate of genetic diversity in each country showed higher diversity in ancestral distributional ranges, but the invasion over Asian countries seems to have been substantial because haplotype diversity was only 2.35 to 3.97-fold lower in the U.S.A, Canada, and Italy than that in the populations’ ancestral ranges.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":"31 1","pages":"312 - 322"},"PeriodicalIF":0.0,"publicationDate":"2018-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89642354","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 10

Rapid and robust authentication of deer antler velvet product by fast PCR-RFLP analysis 采用快速PCR-RFLP分析方法对鹿茸产品进行快速、可靠的鉴定

4区生物学

Mitochondrial Dna Part a Pub Date : 2018-02-17 DOI: 10.1080/24701394.2016.1275599

Chao Jiang, Yan Jin, Xin Zhao, Yuan Yuan, Yuyang Zhao, Lu‐qi Huang

{"title":"Rapid and robust authentication of deer antler velvet product by fast PCR-RFLP analysis","authors":"Chao Jiang, Yan Jin, Xin Zhao, Yuan Yuan, Yuyang Zhao, Lu‐qi Huang","doi":"10.1080/24701394.2016.1275599","DOIUrl":"https://doi.org/10.1080/24701394.2016.1275599","url":null,"abstract":"Abstract Deer antler velvet is widely used as a vitalizing, tonifying, haemopoietic and strengthening agent for debilitated persons in East Asia. To develop a rapid and sensitive method for the identification of the biological source or origin in antler velvet products, a molecular approach was applied using PCR-restriction fragment length polymorphism analysis. The cytochrome b gene sequences of nine cervidae species were analyzed, and a Dde I restriction endonuclease recognition site was found only in sika deer and red deer, the official origin of deer velvet in Chinese pharmacopoeia. A specific primer was designed, and rapid PCR amplified products were subjected to restriction digestion using a fast RFLP procedure. Sika deer and red deer showed two bands of 161 and 102 bp, in contrast to the undigested state of 263 from other antlers. The established PCR-RFLP method was applied in commercial velvet products, and a high frequency of substitution (50%) was revealed in collected commercial samples. The method was successful in detecting contaminated and adulterated antler products in Chinese patent drugs, and the whole detection process was accomplished within 1–1.5 h.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":"34 1","pages":"266 - 272"},"PeriodicalIF":0.0,"publicationDate":"2018-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90070220","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 11

Genetic structure and historical demography of the blue swimming crab (Portunus pelagicus) from southeastern sea of China based on mitochondrial COI gene 基于线粒体COI基因的中国东南海域蓝蟹遗传结构及历史人口学分析

4区生物学

Mitochondrial Dna Part a Pub Date : 2018-02-17 DOI: 10.1080/24701394.2016.1261855

Guijing Ren, G. Miao, Chun-yan Ma, Jianxue Lu, Xiaolong Yang, Hongyu Ma

{"title":"Genetic structure and historical demography of the blue swimming crab (Portunus pelagicus) from southeastern sea of China based on mitochondrial COI gene","authors":"Guijing Ren, G. Miao, Chun-yan Ma, Jianxue Lu, Xiaolong Yang, Hongyu Ma","doi":"10.1080/24701394.2016.1261855","DOIUrl":"https://doi.org/10.1080/24701394.2016.1261855","url":null,"abstract":"Abstract In this study, the population genetic structure and historical demography of the blue swimming crab, Portunus pelagicus, from southeastern sea of China were investigated using cytochrome c oxidase subunit I (COI) gene of mitochondrion. A total of 889 bp segment of COI gene was sequenced, which showed a high haplotype diversity (0.6833–0.8142) and low nucleotide diversity (0.0021–0.0034). Among 30 haplotypes defined in this study, one (H1) was the most dominant (47.7%) and shared by each locality, while the majority (23) were rare and only existed in one individual. The AMOVA analysis revealed a limited population genetic structure, which suggested a high level of gene flow along the distribution areas of China. This conclusion was supported by the pairwise FST comparison values. The topology of the neighbour-joining tree constructed using 30 haplotypes from four localities presented two distinct clades (clade A and clade B). Meanwhile, three sequences of P. pelagicus downloaded from NCBI database showed a high-level divergence with the individuals collected in our study, which might form a new cryptical species. The individuals of clade B were cryptically embedded in the whole population, with a low frequency (7.7–24.2%), while clade A accounted for 75.8–92.3%. Neutrality tests and mismatch analyses suggested a late Pleistocene population expansion for both clade A (47,000–66,000 years ago) and clade B (74,000–100,000 years ago). This study should provide insight into phylogeny, population genetic structure, conservation genetics, and sustainable management of P. pelagicus.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":"7 1","pages":"192 - 198"},"PeriodicalIF":0.0,"publicationDate":"2018-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79804929","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 12

Molecular phylogenetic study on few morphotypes of a patellogastropod Cellana karachiensis from northern Arabian Sea reveals unexpected genetic diversity 阿拉伯海北部扇形足类Cellana karachiensis几种形态的分子系统发育研究揭示了意想不到的遗传多样性

4区生物学

Mitochondrial Dna Part a Pub Date : 2018-02-17 DOI: 10.1080/24701394.2016.1261854

S. Joseph, Bhavik Vakani, R. Kundu

引用次数: 3

Genetic identification of prey species from teeth in faeces from the Endangered leopard cat Prionailurus bengalensis using mitochondrial cytochrome b gene sequence 利用线粒体细胞色素b基因序列对濒危豹猫(Prionailurus bengalensis)粪便牙齿猎物进行遗传鉴定

4区生物学

Mitochondrial Dna Part a Pub Date : 2018-02-17 DOI: 10.1080/24701394.2016.1261852

Tae-wook Kim, H. Lee, Yoo-Kyung Kim, Hong-Shik Oh, Sang-Hyun Han

{"title":"Genetic identification of prey species from teeth in faeces from the Endangered leopard cat Prionailurus bengalensis using mitochondrial cytochrome b gene sequence","authors":"Tae-wook Kim, H. Lee, Yoo-Kyung Kim, Hong-Shik Oh, Sang-Hyun Han","doi":"10.1080/24701394.2016.1261852","DOIUrl":"https://doi.org/10.1080/24701394.2016.1261852","url":null,"abstract":"Abstract To understand the dietary ecology of the leopard cat (Prionailurus bengalensis), DNA analysis was performed to identify prey species using DNA isolated from teeth harvested from the faeces of this feline species. From 70 DNA samples, a total of 52 mitochondrial DNA (mtDNA) cytochrome b (cytb) gene sequences of mammals were identified. The results of a sequence identity test indicated that those sequences were derived from four rodent species (Apodemus agrarius, Apodemus peninsulae, Eothenomys regulus and Tamias sibiricus) and two shrew species (Crocidura lasiura and Crocidura shantungensis). The sequences contained nine unique cytb sequences from site 1 and 13 from site 2. These results indicate that the leopard cat hunts rodents and shrews, and at least nine animals at site 1 and 13 animals at site 2 were eaten. These findings suggest that the animal molecular signatures that remain undigested in the faeces may provide useful ecological information about food items and may contribute to a better understanding of the leopard cat’s feeding ecology.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":"33 1","pages":"170 - 174"},"PeriodicalIF":0.0,"publicationDate":"2018-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86290026","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

Association of low race performance with mtDNA haplogroup L3b of Australian thoroughbred horses 澳大利亚纯种马mtDNA单倍群L3b与低比赛表现的关系

4区生物学

Mitochondrial Dna Part a Pub Date : 2018-02-17 DOI: 10.1080/24701394.2016.1278535

Xiang-rong Lin, Hong-Xiang Zheng, A. Davie, Shi Zhou, L. Wen, Jun Meng, Yong Zhang, QI · Aladaer, B. Liu, Wujun Liu, Xinkui Yao

{"title":"Association of low race performance with mtDNA haplogroup L3b of Australian thoroughbred horses","authors":"Xiang-rong Lin, Hong-Xiang Zheng, A. Davie, Shi Zhou, L. Wen, Jun Meng, Yong Zhang, QI · Aladaer, B. Liu, Wujun Liu, Xinkui Yao","doi":"10.1080/24701394.2016.1278535","DOIUrl":"https://doi.org/10.1080/24701394.2016.1278535","url":null,"abstract":"Abstract Mitochondrial DNA (mtDNA) encodes the genes for respiratory chain sub-units that determine the efficiency of oxidative phosphorylation in mitochondria. The aim of this study was to determine if there were any haplogroups and variants in mtDNA that could be associated with athletic performance of Thoroughbred horses. The whole mitochondrial genomes of 53 maternally unrelated Australian Thoroughbred horses were sequenced and an association study was performed with the competition histories of 1123 horses within their maternal lineages. A horse mtDNA phylogenetic tree was constructed based on a total of 195 sequences (including 142 from previous reports). The association analysis showed that the sample groups with poor racing performance history were enriched in haplogroup L3b (p = .0003) and its sub-haplogroup L3b1a (p = .0007), while those that had elite performance appeared to be not significantly associated with haplogroups G2 and L3a1a1a (p > .05). Haplogroup L3b and L3b1a bear two and five specific variants of which variant T1458C (site 345 in 16s rRNA) is the only potential functional variant. Furthermore, secondary reconstruction of 16s RNA showed considerable differences between two types of 16s RNA molecules (with and without T1458C), indicating a potential functional effect. The results suggested that haplogroup L3b, could have a negative association with elite performance. The T1458C mutation harboured in haplogroup L3b could have a functional effect that is related to poor athletic performance.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":"39 1","pages":"323 - 330"},"PeriodicalIF":0.0,"publicationDate":"2018-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81205319","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

DNA barcodes for dragonflies and damselflies (Odonata) of Mindanao, Philippines 菲律宾棉兰老岛蜻蜓和豆娘的DNA条形码

4区生物学

Mitochondrial Dna Part a Pub Date : 2018-02-17 DOI: 10.1080/24701394.2016.1267157

P. A. Casas, K. Sing, Ping-Shin Lee, O. Nuñeza, R. Villanueva, John-James Wilson

引用次数: 8