Pub Date : 2017-11-01DOI: 10.1080/24701394.2016.1192615
Jaffarali H Abdul, Soban A Akram, Kaleem M L Arshan
Abstract Ascidians (tunicates) are marine benthic organisms possessing various pharmacological activities, including anti-oxidant, anti-tumour, antimicrobial, etc. They also play a key role as model organisms to study various neurobehavioral disorders. Ascidian diversity is reportedly less in India due to lack of taxonomists as well as the limitations in morphology based taxonomy. Molecular taxonomy, comprising the sequencing of cytochrome c oxidase 1 gene (barcode region) otherwise known as DNA barcoding reduces these bottlenecks. Since several species of the family Didemnidae closely resemble in morphology, the present study was aimed to develop DNA barcodes of a colonial ascidian, Lissoclinum fragile belonging to the family Didemnidae. CO1 gene of L. fragile from Thoothukudi, Mandapam, and Vizhinjam waters were sequenced and submitted in GenBank, NCBI through Barcode submission tool. BLAST results showed maximum identity (97–100%) for L. fragile collected from different stations. The pairwise genetic distances within species and genera were calculated using Kimura two parameter (K2P) and the phylogenetic tree was constructed using Neighbour-Joining Tree.
{"title":"DNA barcoding of a colonial ascidian, Lissoclinum fragile (Van Name, 1902)","authors":"Jaffarali H Abdul, Soban A Akram, Kaleem M L Arshan","doi":"10.1080/24701394.2016.1192615","DOIUrl":"https://doi.org/10.1080/24701394.2016.1192615","url":null,"abstract":"Abstract Ascidians (tunicates) are marine benthic organisms possessing various pharmacological activities, including anti-oxidant, anti-tumour, antimicrobial, etc. They also play a key role as model organisms to study various neurobehavioral disorders. Ascidian diversity is reportedly less in India due to lack of taxonomists as well as the limitations in morphology based taxonomy. Molecular taxonomy, comprising the sequencing of cytochrome c oxidase 1 gene (barcode region) otherwise known as DNA barcoding reduces these bottlenecks. Since several species of the family Didemnidae closely resemble in morphology, the present study was aimed to develop DNA barcodes of a colonial ascidian, Lissoclinum fragile belonging to the family Didemnidae. CO1 gene of L. fragile from Thoothukudi, Mandapam, and Vizhinjam waters were sequenced and submitted in GenBank, NCBI through Barcode submission tool. BLAST results showed maximum identity (97–100%) for L. fragile collected from different stations. The pairwise genetic distances within species and genera were calculated using Kimura two parameter (K2P) and the phylogenetic tree was constructed using Neighbour-Joining Tree.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81098674","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}
Pub Date : 2017-11-01DOI: 10.1080/24701394.2016.1214728
Jedsada Sukantamala, K. Sing, N. Jaturas, R. Polseela, John-James Wilson
Abstract Certain species of Phlebotomine sandflies (Diptera: Psychodidae) are vectors of the protozoa which causes leishmaniasis. Sandflies are found breeding in enclosed places like caves. Thailand is a popular tourist destination, including for ecotourism activities like caving, which increases the risk of contact between tourists and sandflies. Surveillance of sandflies is important for monitoring this risk but identification of species based on morphology is challenged by phenotypic plasticity and cryptic diversity. DNA barcodes have been used for the identification of sandflies in Thailand. We collected sandflies using CDC light trap from four tourist caves in Northern Thailand. Female sandflies were provisionally sorted into 13 morphospecies and 19 unidentified specimens. DNA was extracted from the thorax and legs of sandflies and the DNA barcode region of cytochrome c oxidase I mtDNA amplified and sequenced. The specimens were sorted into 22 molecular operational taxonomic units (MOTU) based on the 145 DNA barcodes, which is significantly more than the morphospecies. Several of the taxa thought to be present in multiple caves, based on morphospecies sorting, split into cave-specific MOTU which likely represent cryptic species. Several MOTU reported in an earlier study from Wihan Cave, Thailand, were also found in these caves. This supports the use of DNA barcodes to investigate species diversity of sandflies and their useful role in surveillance of sandflies in Thailand.
{"title":"Unexpected diversity of sandflies (Diptera: Psychodidae) in tourist caves in Northern Thailand","authors":"Jedsada Sukantamala, K. Sing, N. Jaturas, R. Polseela, John-James Wilson","doi":"10.1080/24701394.2016.1214728","DOIUrl":"https://doi.org/10.1080/24701394.2016.1214728","url":null,"abstract":"Abstract Certain species of Phlebotomine sandflies (Diptera: Psychodidae) are vectors of the protozoa which causes leishmaniasis. Sandflies are found breeding in enclosed places like caves. Thailand is a popular tourist destination, including for ecotourism activities like caving, which increases the risk of contact between tourists and sandflies. Surveillance of sandflies is important for monitoring this risk but identification of species based on morphology is challenged by phenotypic plasticity and cryptic diversity. DNA barcodes have been used for the identification of sandflies in Thailand. We collected sandflies using CDC light trap from four tourist caves in Northern Thailand. Female sandflies were provisionally sorted into 13 morphospecies and 19 unidentified specimens. DNA was extracted from the thorax and legs of sandflies and the DNA barcode region of cytochrome c oxidase I mtDNA amplified and sequenced. The specimens were sorted into 22 molecular operational taxonomic units (MOTU) based on the 145 DNA barcodes, which is significantly more than the morphospecies. Several of the taxa thought to be present in multiple caves, based on morphospecies sorting, split into cave-specific MOTU which likely represent cryptic species. Several MOTU reported in an earlier study from Wihan Cave, Thailand, were also found in these caves. This supports the use of DNA barcodes to investigate species diversity of sandflies and their useful role in surveillance of sandflies in Thailand.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84265566","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}
Pub Date : 2017-11-01DOI: 10.1080/24701394.2016.1197218
S. De Fanti, D. Vianello, C. Giuliani, Andrea Quagliariello, Anna Cherubini, F. Sevini, Nicoletta Iaquilano, C. Franceschi, M. Sazzini, D. Luiselli
Abstract Investigation of human mitochondrial DNA variation patterns and phylogeny has been extensively used in Anthropological and Population Genetics studies and sequencing the whole mitochondrial genome is progressively becoming the gold standard. Among the currently available massive parallel sequencing technologies, Ion Torrent™ semiconductor sequencing represents a promising approach for such studies. Nevertheless, an experimental protocol conceived to enable the achievement of both as high as possible yield and of the most homogeneous sequence coverage through the whole mitochondrial genome is still not available. The present work was thus aimed at improving the overall performance of whole mitochondrial genomes Ion Torrent™ sequencing, with special focus on the capability to obtain robust coverage and highly reliable variants calling. For this purpose, a series of cost-effective modifications in standard laboratory workflows was fine-tuned to optimize them for medium- and large-scale population studies. A total of 54 human samples were thus subjected to sequencing of the whole mitochondrial genome with the Ion Personal Genome Machine™ System in four distinct experiments and using Ion 314 chips. Seven of the selected samples were also characterized by means of conventional Sanger sequencing for the sake of comparison. Obtained results demonstrated that the implemented optimizations had definitely improved sequencing outputs in terms of both variants calling efficiency and coverage uniformity, enabling to setup an effective and accurate protocol for whole mitochondrial genome sequencing and a considerable reduction in experimental time consumption and sequencing costs.
人类线粒体DNA变异模式和系统发育的研究已广泛应用于人类学和群体遗传学研究，全线粒体基因组测序正逐渐成为金标准。在目前可用的大规模并行测序技术中，Ion Torrent™半导体测序代表了这类研究的一种有前途的方法。然而，一种旨在实现尽可能高的产量和通过整个线粒体基因组实现最均匀序列覆盖的实验方案仍然不可用。因此，目前的工作旨在提高全线粒体基因组Ion Torrent™测序的整体性能，特别关注获得强大覆盖和高度可靠的变体调用的能力。为此，对标准实验室工作流程进行了一系列具有成本效益的修改，以优化它们，以适应中型和大规模的人口研究。因此，共有54份人类样本在四个不同的实验中使用Ion Personal genome Machine™System对整个线粒体基因组进行测序，并使用Ion 314芯片。为了便于比较，所选样本中的7个也通过常规桑格测序进行了表征。得到的结果表明，所实施的优化在效率和覆盖均匀性两方面都明显提高了测序输出，能够建立有效和准确的全线粒体基因组测序方案，并大大降低了实验耗时和测序成本。
{"title":"Massive parallel sequencing of human whole mitochondrial genomes with Ion Torrent technology: an optimized workflow for Anthropological and Population Genetics studies","authors":"S. De Fanti, D. Vianello, C. Giuliani, Andrea Quagliariello, Anna Cherubini, F. Sevini, Nicoletta Iaquilano, C. Franceschi, M. Sazzini, D. Luiselli","doi":"10.1080/24701394.2016.1197218","DOIUrl":"https://doi.org/10.1080/24701394.2016.1197218","url":null,"abstract":"Abstract Investigation of human mitochondrial DNA variation patterns and phylogeny has been extensively used in Anthropological and Population Genetics studies and sequencing the whole mitochondrial genome is progressively becoming the gold standard. Among the currently available massive parallel sequencing technologies, Ion Torrent™ semiconductor sequencing represents a promising approach for such studies. Nevertheless, an experimental protocol conceived to enable the achievement of both as high as possible yield and of the most homogeneous sequence coverage through the whole mitochondrial genome is still not available. The present work was thus aimed at improving the overall performance of whole mitochondrial genomes Ion Torrent™ sequencing, with special focus on the capability to obtain robust coverage and highly reliable variants calling. For this purpose, a series of cost-effective modifications in standard laboratory workflows was fine-tuned to optimize them for medium- and large-scale population studies. A total of 54 human samples were thus subjected to sequencing of the whole mitochondrial genome with the Ion Personal Genome Machine™ System in four distinct experiments and using Ion 314 chips. Seven of the selected samples were also characterized by means of conventional Sanger sequencing for the sake of comparison. Obtained results demonstrated that the implemented optimizations had definitely improved sequencing outputs in terms of both variants calling efficiency and coverage uniformity, enabling to setup an effective and accurate protocol for whole mitochondrial genome sequencing and a considerable reduction in experimental time consumption and sequencing costs.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90018222","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}
Pub Date : 2017-11-01DOI: 10.1080/24701394.2016.1197220
H. Yacoub, M. A. Sadek
Abstract This study was conducted to find out the fraud in chicken-processed meat ingredients to protect consumers from commercial adulteration and authentication through a reliable way: direct amplification of conserved segment of cytochrome b gene of mitochondrial DNA, in addition, using species-specific primer assay for a certain cytochrome b. The results reported that chicken-processed meats were identified as a chicken meat based on amplification of conserved cytochrome b gene of mtDNA, while different fragments sizes were produced after the application of species-specific primer as follows: 227, 157, 274, 331, 389 and 439 bp for raw meat of chicken, goat, cattle, sheep, pig and horse, respectively. The results revealed that all chicken meat products are produced with 227 bp in size. While, an adulteration with pork stuffs was observed in some of the chicken meat products using a species-specific primer of cytochrome b gene, namely, chicken luncheon and chicken burger. This study represents a reliable technique that could be used to provide a promising solution for identifying the commercial adulteration and substitutions in processed meat in retail markets.
{"title":"Identification of fraud (with pig stuffs) in chicken-processed meat through information of mitochondrial cytochrome b","authors":"H. Yacoub, M. A. Sadek","doi":"10.1080/24701394.2016.1197220","DOIUrl":"https://doi.org/10.1080/24701394.2016.1197220","url":null,"abstract":"Abstract This study was conducted to find out the fraud in chicken-processed meat ingredients to protect consumers from commercial adulteration and authentication through a reliable way: direct amplification of conserved segment of cytochrome b gene of mitochondrial DNA, in addition, using species-specific primer assay for a certain cytochrome b. The results reported that chicken-processed meats were identified as a chicken meat based on amplification of conserved cytochrome b gene of mtDNA, while different fragments sizes were produced after the application of species-specific primer as follows: 227, 157, 274, 331, 389 and 439 bp for raw meat of chicken, goat, cattle, sheep, pig and horse, respectively. The results revealed that all chicken meat products are produced with 227 bp in size. While, an adulteration with pork stuffs was observed in some of the chicken meat products using a species-specific primer of cytochrome b gene, namely, chicken luncheon and chicken burger. This study represents a reliable technique that could be used to provide a promising solution for identifying the commercial adulteration and substitutions in processed meat in retail markets.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83520416","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}
Pub Date : 2017-11-01DOI: 10.1080/24701394.2016.1197219
Xiao-hong He, Xiaofei Chen, Wenbin Zhang, Y. Pu, Shen Song, Jianlin Han, K. Dong, Qianjun Zhao, W. Guan, Yuehui Ma, Lin Jiang
Abstract Heteroplasmy is the presence of more than one mitochondrial DNA (mtDNA) variant within a cell, tissue, or individual. In this study, sequence variation was investigated in the control region (CR) of mitochondrial DNA (mtDNA) from 135 individuals belonging to five primary domestic Bactrian camel breeds in China and Mongolia. Due to variation of the repeat unit G(T/C)(AC)n, length heteroplasmy was detected within each camel by direct sequencing and fragment analysis. A high occurrence of mtDNA heteroplasmy, up to 100 percentages was observed in five camel populations. Our study provides the first evidence of extensive length heteroplasmy in Bactrian camels.
异质性是指在细胞、组织或个体中存在一种以上的线粒体DNA (mtDNA)变异。本研究对中国和蒙古5个主要家养双峰驼品种135个个体的线粒体DNA控制区(mtDNA control region, CR)序列变异进行了研究。由于重复单位G(T/C)(AC)n的变化，通过直接测序和片段分析在每只骆驼中检测到长度异质性。在5个骆驼种群中观察到mtDNA异质性的高发生率，高达100%。我们的研究提供了双峰驼广泛长度异质性的第一个证据。
{"title":"High occurrence of length heteroplasmy in domestic Bactrian camel (Camelus bactrianus)","authors":"Xiao-hong He, Xiaofei Chen, Wenbin Zhang, Y. Pu, Shen Song, Jianlin Han, K. Dong, Qianjun Zhao, W. Guan, Yuehui Ma, Lin Jiang","doi":"10.1080/24701394.2016.1197219","DOIUrl":"https://doi.org/10.1080/24701394.2016.1197219","url":null,"abstract":"Abstract Heteroplasmy is the presence of more than one mitochondrial DNA (mtDNA) variant within a cell, tissue, or individual. In this study, sequence variation was investigated in the control region (CR) of mitochondrial DNA (mtDNA) from 135 individuals belonging to five primary domestic Bactrian camel breeds in China and Mongolia. Due to variation of the repeat unit G(T/C)(AC)n, length heteroplasmy was detected within each camel by direct sequencing and fragment analysis. A high occurrence of mtDNA heteroplasmy, up to 100 percentages was observed in five camel populations. Our study provides the first evidence of extensive length heteroplasmy in Bactrian camels.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75914718","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}
Pub Date : 2017-11-01DOI: 10.1080/24701394.2016.1192614
L. Niu, Xiaoyong Chen, Ping Xiao, Qianjun Zhao, Jingxuan Zhou, Jiangtao Hu, Hongxin Sun, Jiazhong Guo, Li Li, Linjie Wang, Hongping Zhang, T. Zhong
Abstract Tibetan sheep, a Chinese indigenous breed, are mainly distributed in plateau and mountain-valley areas at a terrestrial elevation between 2260 and 4100 m. The herd is genetically distinct from the other domestic sheep and undergoes acclimatization to adapt to the hypoxic environment. To date, whether the mitochondrial DNA modification of Tibetan sheep shares the same feature as the other domestic breed remains unknown. In this study, we compared the whole mitogenome sequences from 32 Tibetan sheep, 22 domestic sheep and 24 commercial sheep to identify the selection signatures of hypoxic-tolerant in Tibetan sheep. Nucleotide diversity analysis using the sliding window method showed that the highest level of nucleotide diversity was observed in the control region with a peak value of π = 0.05215, while the lowest π value was detected in the tRNAs region. qPCR results showed that the relative mtDNA copy number in Tibetan sheep was significantly lower than that in Suffolk sheep. None of the mutations in 12S rRNA were fixed in Tibetan sheep, which indicated that there has been less artificial selection in this herd than the other domestic and commercial breeds. Although one site (1277G) might undergo the purifying selection, it was not identified as the breed-specific allele in Tibetan sheep. We proposed that nature selection was the main drive during the domestication of Tibetan sheep and single mutation (or locus) could not reveal the signature of selection as for the high diversity in the mitogenome of Tibetan sheep.
{"title":"Detecting signatures of selection within the Tibetan sheep mitochondrial genome","authors":"L. Niu, Xiaoyong Chen, Ping Xiao, Qianjun Zhao, Jingxuan Zhou, Jiangtao Hu, Hongxin Sun, Jiazhong Guo, Li Li, Linjie Wang, Hongping Zhang, T. Zhong","doi":"10.1080/24701394.2016.1192614","DOIUrl":"https://doi.org/10.1080/24701394.2016.1192614","url":null,"abstract":"Abstract Tibetan sheep, a Chinese indigenous breed, are mainly distributed in plateau and mountain-valley areas at a terrestrial elevation between 2260 and 4100 m. The herd is genetically distinct from the other domestic sheep and undergoes acclimatization to adapt to the hypoxic environment. To date, whether the mitochondrial DNA modification of Tibetan sheep shares the same feature as the other domestic breed remains unknown. In this study, we compared the whole mitogenome sequences from 32 Tibetan sheep, 22 domestic sheep and 24 commercial sheep to identify the selection signatures of hypoxic-tolerant in Tibetan sheep. Nucleotide diversity analysis using the sliding window method showed that the highest level of nucleotide diversity was observed in the control region with a peak value of π = 0.05215, while the lowest π value was detected in the tRNAs region. qPCR results showed that the relative mtDNA copy number in Tibetan sheep was significantly lower than that in Suffolk sheep. None of the mutations in 12S rRNA were fixed in Tibetan sheep, which indicated that there has been less artificial selection in this herd than the other domestic and commercial breeds. Although one site (1277G) might undergo the purifying selection, it was not identified as the breed-specific allele in Tibetan sheep. We proposed that nature selection was the main drive during the domestication of Tibetan sheep and single mutation (or locus) could not reveal the signature of selection as for the high diversity in the mitogenome of Tibetan sheep.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91205651","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}
Pub Date : 2017-11-01DOI: 10.1080/24701394.2016.1202943
Ankita Rajpoot, V. Kumar, A. Bahuguna, Dhyanendra Kumar
Abstract Monitor lizards are Varanus species widely distributed, endangered reptile in the IUCN red data list. In India, based on the morphological and ecological characteristic, it is divided into four species viz. Bengal monitor lizard, Yellow monitor lizard, Desert monitor lizard and Water monitor lizard. These four species listed as Schedule I species in Indian Wildlife (Protection) Act 1972. This paper first attempt to present Forensically Informative Nucleotide Sequencing (FINS) for the Indian Varanus based on three mitochondrial genes. The molecular framework will be useful for the identification of Indian Varanus species and trade products derived from monitors and as such, have important applications for wildlife management and conservation. Here, we used known 14 individual skin pieces of four species of monitor lizards; the partial fragment of three mitochondrial genes (Cyt b, 12S rRNA, and 16S rRNA) were amplified for genetic study. In Cyt b, 12S rRNA and 16s rRNA, we observed, 5, 5 and 4 Haplotypes; 71, 69, and 43 Variables sites; 90, 89, and 50 Parsimony Informative sites within four species of Indian monitor lizards, respectively. Despite it, the nucleotide composition was T 26.4, C 32.8, A 29.2 and G11.6; T 18.8, C 29.7, A 34.0 and G 17.5; T 21.7, C 27.3, A 32.5 and G 18.5 in Cyt b, 12S rRNA and 16S rRNA, respectively. The neighbor joining phylogenetic tree and maximum parsimony tree of three mitochondrial genes, showed similar results and reveal that, there are two major clades are present in Indian monitor lizards.
巨蜥是世界自然保护联盟红色数据名录中分布广泛的濒危爬行动物。在印度，根据形态和生态特征，将其分为孟加拉巨蜥、黄巨蜥、沙漠巨蜥和水巨蜥四种。这四种物种被列为1972年印度野生动物(保护)法案的附表I物种。本文首次尝试提出基于三个线粒体基因的印度瓦纳努斯的法医信息核苷酸测序(FINS)。该分子框架将有助于鉴定印度瓦拉努斯物种和监测所得的贸易产品，因此对野生动物管理和保护具有重要应用。在这里，我们使用了四种巨蜥的14块已知的皮肤碎片;扩增三个线粒体基因(Cyt b、12S rRNA和16S rRNA)的部分片段进行遗传研究。在Cyt b、12S rRNA和16s rRNA中，我们分别观察到5、5和4个单倍型;71、69和43个可变站点;在四种印度巨蜥中分别有90、89和50个简约性信息位点。尽管如此，核苷酸组成分别为T 26.4、C 32.8、A 29.2和G11.6;T 18.8, C 29.7, A 34.0, G 17.5;在Cyt b、12S rRNA和16S rRNA中，T为21.7,C为27.3,A为32.5,G为18.5。邻近连接系统发育树和三个线粒体基因的最大简约树显示了相似的结果，表明印度巨蜥存在两个主要分支。
{"title":"Forensically informative nucleotide sequencing (FINS) for the first time authentication of Indian Varanus species: implication in wildlife forensics and conservation","authors":"Ankita Rajpoot, V. Kumar, A. Bahuguna, Dhyanendra Kumar","doi":"10.1080/24701394.2016.1202943","DOIUrl":"https://doi.org/10.1080/24701394.2016.1202943","url":null,"abstract":"Abstract Monitor lizards are Varanus species widely distributed, endangered reptile in the IUCN red data list. In India, based on the morphological and ecological characteristic, it is divided into four species viz. Bengal monitor lizard, Yellow monitor lizard, Desert monitor lizard and Water monitor lizard. These four species listed as Schedule I species in Indian Wildlife (Protection) Act 1972. This paper first attempt to present Forensically Informative Nucleotide Sequencing (FINS) for the Indian Varanus based on three mitochondrial genes. The molecular framework will be useful for the identification of Indian Varanus species and trade products derived from monitors and as such, have important applications for wildlife management and conservation. Here, we used known 14 individual skin pieces of four species of monitor lizards; the partial fragment of three mitochondrial genes (Cyt b, 12S rRNA, and 16S rRNA) were amplified for genetic study. In Cyt b, 12S rRNA and 16s rRNA, we observed, 5, 5 and 4 Haplotypes; 71, 69, and 43 Variables sites; 90, 89, and 50 Parsimony Informative sites within four species of Indian monitor lizards, respectively. Despite it, the nucleotide composition was T 26.4, C 32.8, A 29.2 and G11.6; T 18.8, C 29.7, A 34.0 and G 17.5; T 21.7, C 27.3, A 32.5 and G 18.5 in Cyt b, 12S rRNA and 16S rRNA, respectively. The neighbor joining phylogenetic tree and maximum parsimony tree of three mitochondrial genes, showed similar results and reveal that, there are two major clades are present in Indian monitor lizards.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83095141","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}
Pub Date : 2017-11-01DOI: 10.1080/24701394.2016.1202942
Meirong Ye, Wei Liu, Qing-yun Xue, B. Hou, Jing Luo, Xiaoyu Ding
Abstract The aim of the current study was to elucidate the phylogeographic history of Dendrobium moniliforme, an endangered orchid species, based on two chloroplast DNA (cpDNA) markers (trnC-petN and trnE-trnT). One hundred and thirty-five samples were collected from 18 natural populations of D. moniliforme covering the entire range of the Sino-Japanese Floristic Region (SJFR) of East Asia. A total of 35 distinct cpDNA haplotypes were identified in these populations, of which 23 haplotypes were each present in only one sample and thus restricted to a single population. The significantly larger NST value (0.586) than GST (0.328) (p < 0.05) demonstrated the presence of strong phylogeographic structure. Phylogenetic analyses indicated that all haplotypes were clustered into two lineages. The genetic diversity of D. moniliforme was high at the species level, reflected in its haplotype diversity (Hd=0.8862), nucleotide diversity (Pi=0.00361), total genetic diversity (HT=0.9011), and significant differentiation (ΦST=0.5482). Based on mismatch distribution analysis and neutrality tests, population expansion was evident in all sampled populations and also in all populations sampled in mainland China. Three refuge areas were identified, one each in southwestern China, central-southeastern China, and the CKJ (Taiwan, Japan and Korea) Islands. The results supported the hypothesis that glacial refugia were maintained on different spatial-temporal scales in the SJFR during the last glacial maximum or earlier cold periods, suggesting that Quaternary refugial isolation promoted allopatric speciation of D. moniliforme in East Asia.
{"title":"Phylogeography of the endangered orchid Dendrobium moniliforme in East Asia inferred from chloroplast DNA sequences","authors":"Meirong Ye, Wei Liu, Qing-yun Xue, B. Hou, Jing Luo, Xiaoyu Ding","doi":"10.1080/24701394.2016.1202942","DOIUrl":"https://doi.org/10.1080/24701394.2016.1202942","url":null,"abstract":"Abstract The aim of the current study was to elucidate the phylogeographic history of Dendrobium moniliforme, an endangered orchid species, based on two chloroplast DNA (cpDNA) markers (trnC-petN and trnE-trnT). One hundred and thirty-five samples were collected from 18 natural populations of D. moniliforme covering the entire range of the Sino-Japanese Floristic Region (SJFR) of East Asia. A total of 35 distinct cpDNA haplotypes were identified in these populations, of which 23 haplotypes were each present in only one sample and thus restricted to a single population. The significantly larger NST value (0.586) than GST (0.328) (p < 0.05) demonstrated the presence of strong phylogeographic structure. Phylogenetic analyses indicated that all haplotypes were clustered into two lineages. The genetic diversity of D. moniliforme was high at the species level, reflected in its haplotype diversity (Hd=0.8862), nucleotide diversity (Pi=0.00361), total genetic diversity (HT=0.9011), and significant differentiation (ΦST=0.5482). Based on mismatch distribution analysis and neutrality tests, population expansion was evident in all sampled populations and also in all populations sampled in mainland China. Three refuge areas were identified, one each in southwestern China, central-southeastern China, and the CKJ (Taiwan, Japan and Korea) Islands. The results supported the hypothesis that glacial refugia were maintained on different spatial-temporal scales in the SJFR during the last glacial maximum or earlier cold periods, suggesting that Quaternary refugial isolation promoted allopatric speciation of D. moniliforme in East Asia.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74191420","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}
Pub Date : 2017-11-01DOI: 10.1080/24701394.2016.1225732
V. Kumar, A. Shrivastwa, P. Nigam, Dhyanendra Kumar, S. Goyal
Abstract Swamp deer (Rucervus duvaucelii) is an endemic, Scheduled I species under the Wildlife (Protection) Act 1972, India. According to variations in antler size, it has been classified into three subspecies, namely Western (R. duvaucelii duvaucelii), Central (R. duvaucelii branderi), and Eastern (R. duvaucelii ranjitsinhii). For planning effective ex situ and in situ conservation of a wide-ranging species in different bioclimatic regions and in wildlife forensic, the use of genetic characterization in defining morpho/ecotypes has been suggested because of the geographic clines and reproductive isolation. In spite of these morphotypes, very little is known about the genetic characteristics of the three subspecies, hence no strict subspecies-based breeding plan for retaining the evolutionary characteristics in captive populations for subsequent re-introduction is available except for a few studies. We describe the genetic characteristics of these three subspecies using cytochrome b of the mtDNA genome (400 bp). The DNA sequence data indicated 11 variable sites within the three subspecies. Two paraphyletic clades, namely the Central India and Western-Eastern populations were found, whereas the Western and Eastern populations are monophyletic with a bootstrap value of 69% within the clade. We suggest the need of sorting these three subspecies using different molecular mtDNA markers in zoos for captive breeding purposes so as to retain the genetic diversity of the separate geographic clines and to use a subspecies-specific fixed-state nucleotide to assess the extent of poaching to avoid any population demography stochastically in India.
{"title":"Genetic characterization of wild swamp deer populations: ex situ conservation and forensics implications","authors":"V. Kumar, A. Shrivastwa, P. Nigam, Dhyanendra Kumar, S. Goyal","doi":"10.1080/24701394.2016.1225732","DOIUrl":"https://doi.org/10.1080/24701394.2016.1225732","url":null,"abstract":"Abstract Swamp deer (Rucervus duvaucelii) is an endemic, Scheduled I species under the Wildlife (Protection) Act 1972, India. According to variations in antler size, it has been classified into three subspecies, namely Western (R. duvaucelii duvaucelii), Central (R. duvaucelii branderi), and Eastern (R. duvaucelii ranjitsinhii). For planning effective ex situ and in situ conservation of a wide-ranging species in different bioclimatic regions and in wildlife forensic, the use of genetic characterization in defining morpho/ecotypes has been suggested because of the geographic clines and reproductive isolation. In spite of these morphotypes, very little is known about the genetic characteristics of the three subspecies, hence no strict subspecies-based breeding plan for retaining the evolutionary characteristics in captive populations for subsequent re-introduction is available except for a few studies. We describe the genetic characteristics of these three subspecies using cytochrome b of the mtDNA genome (400 bp). The DNA sequence data indicated 11 variable sites within the three subspecies. Two paraphyletic clades, namely the Central India and Western-Eastern populations were found, whereas the Western and Eastern populations are monophyletic with a bootstrap value of 69% within the clade. We suggest the need of sorting these three subspecies using different molecular mtDNA markers in zoos for captive breeding purposes so as to retain the genetic diversity of the separate geographic clines and to use a subspecies-specific fixed-state nucleotide to assess the extent of poaching to avoid any population demography stochastically in India.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85442965","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}
Pub Date : 2017-09-01DOI: 10.1080/24701394.2016.1186665
Gang Wang, Chun-Xiao Li, Wei Zheng, F. Song, Xiao-xia Guo, Zhonghua Wu, Peng Luo, Yongyao Yang, Lei He, T. Zhao
Abstract We assessed the practicality and effectiveness of using variation in the mitochondrial COI and COII genes to discriminate species and reconstruct the phylogeny of anophelene mosquitoes. Phylogenetic relationships among the subfamily Anophelinae were inferred from portions of the mitochondrial COI (92 species) and COII genes (108 species). Phylogenetic trees were reconstructed on the basis of parsimony, maximum likelihood and Bayesian methods. The suitability of COI and COII gene variation for identifying cryptic species was compared by comparing the sequence divergence within species groups and complexes. The results show that the COI gene was more useful for identifying sibling and cryptic species, but that phylogenetic relationships reconstructed using the COII gene were more similar to those based on morphological data. We conclude that: (1) there is a significant molecular divergence among An. sinensis; (2) the COI and COII are valid genetic markers for resolving taxonomic relationships among anopheline mosquitoes and the resultant phylogeny raises some questions about the taxonomic status of anopheline species groups and complexes; (3) the genus Anopheles is not demonstrably monophyletic with regard to the genus Bironella; (4) the subgenera Kerteszia and Nyssorhynchus are monophyletic; (5) below the group-level, COI data support the existence of monophyletic taxa within the Anopheles funestus, Anopheles maculipennis and Anopheles strode and Anopheles barbirostris subgroups, and within the Anopheles nuneztovari complex, whereas COII data support the monophyletic taxa within the Anopheles minimus and Anopheles oswaldoi subgroups, and Anopheles hyrcanus group. The monophyletic taxa within the Anopheles gambiae and Anopheles albitarsis complexes are supported by both COI and COII data.
{"title":"An evaluation of the suitability of COI and COII gene variation for reconstructing the phylogeny of, and identifying cryptic species in, anopheline mosquitoes (Diptera Culicidae)","authors":"Gang Wang, Chun-Xiao Li, Wei Zheng, F. Song, Xiao-xia Guo, Zhonghua Wu, Peng Luo, Yongyao Yang, Lei He, T. Zhao","doi":"10.1080/24701394.2016.1186665","DOIUrl":"https://doi.org/10.1080/24701394.2016.1186665","url":null,"abstract":"Abstract We assessed the practicality and effectiveness of using variation in the mitochondrial COI and COII genes to discriminate species and reconstruct the phylogeny of anophelene mosquitoes. Phylogenetic relationships among the subfamily Anophelinae were inferred from portions of the mitochondrial COI (92 species) and COII genes (108 species). Phylogenetic trees were reconstructed on the basis of parsimony, maximum likelihood and Bayesian methods. The suitability of COI and COII gene variation for identifying cryptic species was compared by comparing the sequence divergence within species groups and complexes. The results show that the COI gene was more useful for identifying sibling and cryptic species, but that phylogenetic relationships reconstructed using the COII gene were more similar to those based on morphological data. We conclude that: (1) there is a significant molecular divergence among An. sinensis; (2) the COI and COII are valid genetic markers for resolving taxonomic relationships among anopheline mosquitoes and the resultant phylogeny raises some questions about the taxonomic status of anopheline species groups and complexes; (3) the genus Anopheles is not demonstrably monophyletic with regard to the genus Bironella; (4) the subgenera Kerteszia and Nyssorhynchus are monophyletic; (5) below the group-level, COI data support the existence of monophyletic taxa within the Anopheles funestus, Anopheles maculipennis and Anopheles strode and Anopheles barbirostris subgroups, and within the Anopheles nuneztovari complex, whereas COII data support the monophyletic taxa within the Anopheles minimus and Anopheles oswaldoi subgroups, and Anopheles hyrcanus group. The monophyletic taxa within the Anopheles gambiae and Anopheles albitarsis complexes are supported by both COI and COII data.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85154573","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}
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