The phylogenetic relationships of genera in the subfamily Apaturinae were examined using mtDNA sequence data from 1,471 bp of cytochrome oxidase subunit Ⅰ （COI）. The mitochondrial COI gene from a total of 16 specie...The phylogenetic relationships of genera in the subfamily Apaturinae were examined using mtDNA sequence data from 1,471 bp of cytochrome oxidase subunit Ⅰ （COI）. The mitochondrial COI gene from a total of 16 species in 11 genera were sequenced to obtain mtDNA data, along with those of 4 species obtained from GenBank, to construct the MP and the NJ trees using Athyma jina, Penthema adelma, Polyura nepenthes, and Charaxes bernardus as outgroups. The transitions at the third codon positions of the COI data set were found saturated, but they were retained for analysis, because they contain the majority of the phylogenetic information. The impacts of equal weight assumptions for all characters in the parsimonious analysis were assessed by potential alternations in clades in response to different transition/transversion weighting schemes. The results indicated four distinct major groups in Apaturinae. Moreover, several well supported and stable clades were found in the Apaturinae. The study also identified undetermined taxon groups whose positions were weakly supported and were subject to changes under different weighting schemes. Within the Apaturinae, the clustering results are approximately identical to the classical morphological classification. The mtDNA data suggest the genus Mimathyma as a monophyletic group. Lelecella limenitoides and Dilipa fenestra have close relationship with very strong support in all phylogenetic trees. It also supports the taxonomic revision of removing several species from Apatura to other genera, namely Mimathyma schrenckii, M. chevana, M. nycteis, Chitoria subcaerulea, C. fasciola, C. pallas, and Helcyra subalba.展开更多
The bombycid moth, Triuncina daii Xing Wang ＆ Zolotuhin, 2015, plays an important role for analyzing the phylogenetic relationships of the family Bombycidae （Lepidoptera： Bombycoidea）. Here we first describe the c...The bombycid moth, Triuncina daii Xing Wang ＆ Zolotuhin, 2015, plays an important role for analyzing the phylogenetic relationships of the family Bombycidae （Lepidoptera： Bombycoidea）. Here we first describe the complete mitochondrial genome （mitogenome） of T. daii, which includes thirteen protein-coding genes （PCGs）, twenty-two transfer RNA genes, two ribosomal RNA genes and an A＋T-rich region, and we find the mitogenome is 15,482 bp in length （GenBank no. KY091643）. The genes order and orientation in the T. daii mitogenome are similar to other sequenced lepidopteran species. Except for cox1, all of the PCGs started with ATN. Twelve PCGs stopped at TAA except for cox1 which stops at a single T. Thirteen PCGs of available species are used to demonstrate the inner phylogenetic relationships of Bombycoidea. The bombycid species form a monophyletic clade with a bootstrap value of 100% and a posterior probability of 1.00.展开更多
Population genetic structure and historical demography of Chinese horseshoe crab (T.tridentatus)along southeast coast of China were inferred from the sequence data of mitochondrial cytochrome c oxidase subunit Ⅰ (COI...Population genetic structure and historical demography of Chinese horseshoe crab (T.tridentatus)along southeast coast of China were inferred from the sequence data of mitochondrial cytochrome c oxidase subunit Ⅰ (COI) fragment.The sequence analysis for 964 bp COI fragment was conducted in 28 individuals collected from five localities:Ninghai in Zhejiang Province,Meizhou and Zhangpu in Fujian Province,Beihai of Guangxi Zhuang Autonomous Region and Danzhou of Hainan Province.Sequence variation was relatively low with a total of seven transitions observed.In all localities,Haplotype H3 was the dominant type observed among eight haplotypes defined previously,and was at the center of radiation in Median-Joining network.The prolonged star-like network suggests a signature of population expansions.The level of diversity was low in total,with haplotype diversity ( Hd) being equal to 0.765 and nucleotide diversity (π) being equal to 0.00118,respectively.The genetic structure analysis revealed the significant genetic difference between Ninghai and Danzhou populations.Both mismatch distribution analysis and Fu's Fs test provided consistent inference of historic population expansion.The low genetic diversity of horseshoe crab observed along China coast indicated that urgent measures should be taken to protect this rare marine animal.展开更多
The phylogenetic relationships of the subfamily Nymphalinae （sensu Chou 1994） were analyzed based on 1 488 bp of mtDNA cytochrome oxidase subunit I （COI） gene sequence data obtained from 24 individuals, along with...The phylogenetic relationships of the subfamily Nymphalinae （sensu Chou 1994） were analyzed based on 1 488 bp of mtDNA cytochrome oxidase subunit I （COI） gene sequence data obtained from 24 individuals, along with those of eight species obtained from GenBank. The base compositions of this COI fragment varied among the individuals as follows： T 39.9%, C 14.6%, A 32.2%, and G 13.4%, with a strong AT bias （72.1%）, as usually found in insect mitochondrial genomes. The A ＋T contents of the third, second, and first codon positions of the COI fragments in this study was 92.4, 62.2, and 61.4%, respectively. The phylogenetic trees were reconstructed by neighbor-joining （NJ）, maximum likelihood （ML）, and Bayesian methods by using Byblia anvatara as outgroup. Phylogenetic analyses based on the COI gene sequence data created very similar topologies, which were producing trees with two main clades A and B, and five subclades. The data indicated that the tribes Nymphalini and Hypolimni （sensu Chou 1994） are not monophyletic groups, and the genus Junonia should be removed from Nymphalini to Hypolimni （=Junoniini）. On the basis of the data, the Symbrenthia and Araschnia had a relative distant relationship with the rest of Nymphalini. The relationships of species in the Nymphalini were confirmed via the NJ, ML, and Bayesian methods, namely （（（（Nymphalis ＋ Kaniska） ＋ Polygonia） ＋Aglais） ＋ Vanessa） ＋ （Symbrenthia ＋Araschnia）. This investigation provides a little novel information for Chinese researches of butterflies.展开更多
The aim of this study was to evaluate the genetic variability in bees Apis mellifera from Benin by using mitochondrial DNA （mtDNA） as a molecular marker in their cytochrome c oxidase subunit I and II （COI-COI1） in...The aim of this study was to evaluate the genetic variability in bees Apis mellifera from Benin by using mitochondrial DNA （mtDNA） as a molecular marker in their cytochrome c oxidase subunit I and II （COI-COI1） intergenic region. A total of 304 bee colonies were sampled in 27 municipalities of the cashew growing area of Benin. These samples were analyzed by the cleaved amplified polymorphisms technique for determining the haplotypes of subspecies present in the sampled population. Eight PCR-RFLP profiles of African lineage A were then identified in the 304 samples of bees investigated. Forty-nine percent （49%） of the samples showed the profile of haplotype A1 （subspecies adansonii of Zambia）, 40% of haplotype A4 （subspecies scutellata of South Africa） and 3% of haplotype A 19 （subspecies adansonii of Guinea）. Five other haplotypes of the African branch （A） that had been described in a previous study were also identified： new 1 （2%）, new 2 （2%）, new 3 （1%）, new 4 （2%） and new 5 （1%）. This study showed that A. rnellifera from Benin belonged only to lineage A with the predominance of haplotypes AI and A4. This study will contribute to the development of coherent policies for conservation of local bees in Benin.展开更多
The mitochondrial cytochrome oxidase II (Co II) from four different apterygotens Cryptopygus nanjiensis (Collembola), Neanura latior (Collembola), Gracilentulus maijiawensis (Protura) and Lepidocampa weberi (Diplura) ...The mitochondrial cytochrome oxidase II (Co II) from four different apterygotens Cryptopygus nanjiensis (Collembola), Neanura latior (Collembola), Gracilentulus maijiawensis (Protura) and Lepidocampa weberi (Diplura) were sequenced. Their A+T content, number of nucleotide substitutions, TV/TV ratio, and Tamura-Nei’s distance were calculated. A series of phylogenetic trees were constructed by parsimony and distance methods using a crustacean Artemia franciscana as outgroup. Finally the evolutionary trend A+T content of CO II genetic divergence and phylogenetic relationship of apterygotan groups were discussed.展开更多
条形码数据库是开展基于DNA的生物监测关键先决条件。为在珠江流域有效开展基于DNA的生物监测,迫切需要了解物种DNA条形码的覆盖或空缺状况。整理了珠江流域常见鱼类和大型底栖动物的物种清单,从National Center and Biotechnology Info...条形码数据库是开展基于DNA的生物监测关键先决条件。为在珠江流域有效开展基于DNA的生物监测,迫切需要了解物种DNA条形码的覆盖或空缺状况。整理了珠江流域常见鱼类和大型底栖动物的物种清单,从National Center and Biotechnology Information (NCBI)数据库中检索了物种清单的DNA条形码序列,分析了常见鱼类(包括线粒体组和12s rRNA基因)和大型底栖动物(包括线粒体组、COI和18s rRNA基因)的DNA条形码覆盖范围和空缺程度。数据分析表明:(1)珠江流域共记录了常见鱼类221种,隶属于2纲18目51科和137属;常见大型底栖动物105种/属,隶属于6纲14目53科。(2)共检索到常见鱼类线粒体组序列913条和12s rRNA基因序列962条,分别占总物种的81.45%和57.92%;有12.67%的物种没有线粒体组和12s rRNA基因序列,若将条形码阈值设置为至少包含5个参考序列,则空缺度上升至52.94%;(3)共检索到常见大型底栖动物线粒体组65条序列、COI基因26,988条序列和18s rRNA基因175条序列,分别占总种/属数的29.52%、68.57%和37.14%;有25.71%的种/属在线粒体组、COI和18s rRNA基因区域皆无序列收录,若将条形码阈值设置为至少包含5个参考序列,则空缺度上升至41.90%。总之,本研究将为珠江流域开展基于DNA的鱼类和大型底栖动物监测提供基础数据支撑,为完善珠江本土DNA条形码数据库提供参考建议。展开更多
【目的】基于mtDNA CO Ⅰ基因探究竹笋夜蛾的亲缘关系,以确定其分类地位,为系统进化轨迹提供分子理论基础。【方法】以分布于浙江杭州周边竹子产区的4种竹笋夜蛾为研究对象,使用通用引物分别克隆4种竹笋夜蛾线粒体细胞色素C氧化酶亚基Ⅰ...【目的】基于mtDNA CO Ⅰ基因探究竹笋夜蛾的亲缘关系,以确定其分类地位,为系统进化轨迹提供分子理论基础。【方法】以分布于浙江杭州周边竹子产区的4种竹笋夜蛾为研究对象,使用通用引物分别克隆4种竹笋夜蛾线粒体细胞色素C氧化酶亚基Ⅰ(mtDNA CO Ⅰ)基因5'端709 bp片段序列,通过构建系统进化树,分析4种竹笋夜蛾亲缘关系。【结果】1)4种竹笋夜蛾遗传距离较小;2)与比对昆虫相比,4种竹笋夜蛾同属一个进化群,分支支持率达到100%。【结论】4种竹笋夜蛾亲缘关系接近,除萨夜蛾外,建议将其他3种竹笋夜蛾归为一个属。4种竹笋夜蛾形态差异较小,生态习性相似,分布区域基本一致,可作为理想的同域物种进化研究素材。本研究可为4种竹笋夜蛾分类地位的确定提供初步分子基础,同时可为竹笋夜蛾DNA条形码鉴定提供理论基础。展开更多
基金This work was supported by National Natural Science Foundation of China (No. 30570247)the Natural Science Foundation of Shanxi Province (No. 2003-1087)
文摘The phylogenetic relationships of genera in the subfamily Apaturinae were examined using mtDNA sequence data from 1,471 bp of cytochrome oxidase subunit Ⅰ （COI）. The mitochondrial COI gene from a total of 16 species in 11 genera were sequenced to obtain mtDNA data, along with those of 4 species obtained from GenBank, to construct the MP and the NJ trees using Athyma jina, Penthema adelma, Polyura nepenthes, and Charaxes bernardus as outgroups. The transitions at the third codon positions of the COI data set were found saturated, but they were retained for analysis, because they contain the majority of the phylogenetic information. The impacts of equal weight assumptions for all characters in the parsimonious analysis were assessed by potential alternations in clades in response to different transition/transversion weighting schemes. The results indicated four distinct major groups in Apaturinae. Moreover, several well supported and stable clades were found in the Apaturinae. The study also identified undetermined taxon groups whose positions were weakly supported and were subject to changes under different weighting schemes. Within the Apaturinae, the clustering results are approximately identical to the classical morphological classification. The mtDNA data suggest the genus Mimathyma as a monophyletic group. Lelecella limenitoides and Dilipa fenestra have close relationship with very strong support in all phylogenetic trees. It also supports the taxonomic revision of removing several species from Apatura to other genera, namely Mimathyma schrenckii, M. chevana, M. nycteis, Chitoria subcaerulea, C. fasciola, C. pallas, and Helcyra subalba.
基金supported by the National Natural Science Foundation of China(31100482,31411140034)the Scientific Research Fund of Hunan Provincial Education Department(16B119)
文摘The bombycid moth, Triuncina daii Xing Wang ＆ Zolotuhin, 2015, plays an important role for analyzing the phylogenetic relationships of the family Bombycidae （Lepidoptera： Bombycoidea）. Here we first describe the complete mitochondrial genome （mitogenome） of T. daii, which includes thirteen protein-coding genes （PCGs）, twenty-two transfer RNA genes, two ribosomal RNA genes and an A＋T-rich region, and we find the mitogenome is 15,482 bp in length （GenBank no. KY091643）. The genes order and orientation in the T. daii mitogenome are similar to other sequenced lepidopteran species. Except for cox1, all of the PCGs started with ATN. Twelve PCGs stopped at TAA except for cox1 which stops at a single T. Thirteen PCGs of available species are used to demonstrate the inner phylogenetic relationships of Bombycoidea. The bombycid species form a monophyletic clade with a bootstrap value of 100% and a posterior probability of 1.00.
基金F5 Subject from Science and Technology Department of Fujian Province under contract No. 2008F5038the Open Foundation from Ocean Fishery Science and Technology in the Most Important Subjects of Zhejiang under contract No.20100210
文摘Population genetic structure and historical demography of Chinese horseshoe crab (T.tridentatus)along southeast coast of China were inferred from the sequence data of mitochondrial cytochrome c oxidase subunit Ⅰ (COI) fragment.The sequence analysis for 964 bp COI fragment was conducted in 28 individuals collected from five localities:Ninghai in Zhejiang Province,Meizhou and Zhangpu in Fujian Province,Beihai of Guangxi Zhuang Autonomous Region and Danzhou of Hainan Province.Sequence variation was relatively low with a total of seven transitions observed.In all localities,Haplotype H3 was the dominant type observed among eight haplotypes defined previously,and was at the center of radiation in Median-Joining network.The prolonged star-like network suggests a signature of population expansions.The level of diversity was low in total,with haplotype diversity ( Hd) being equal to 0.765 and nucleotide diversity (π) being equal to 0.00118,respectively.The genetic structure analysis revealed the significant genetic difference between Ninghai and Danzhou populations.Both mismatch distribution analysis and Fu's Fs test provided consistent inference of historic population expansion.The low genetic diversity of horseshoe crab observed along China coast indicated that urgent measures should be taken to protect this rare marine animal.
基金funded by the National Natural Science Foundation of China(30570247 and 30670361)the Natural Science Foundation of Shanxi Province,China(2006011075).
文摘The phylogenetic relationships of the subfamily Nymphalinae （sensu Chou 1994） were analyzed based on 1 488 bp of mtDNA cytochrome oxidase subunit I （COI） gene sequence data obtained from 24 individuals, along with those of eight species obtained from GenBank. The base compositions of this COI fragment varied among the individuals as follows： T 39.9%, C 14.6%, A 32.2%, and G 13.4%, with a strong AT bias （72.1%）, as usually found in insect mitochondrial genomes. The A ＋T contents of the third, second, and first codon positions of the COI fragments in this study was 92.4, 62.2, and 61.4%, respectively. The phylogenetic trees were reconstructed by neighbor-joining （NJ）, maximum likelihood （ML）, and Bayesian methods by using Byblia anvatara as outgroup. Phylogenetic analyses based on the COI gene sequence data created very similar topologies, which were producing trees with two main clades A and B, and five subclades. The data indicated that the tribes Nymphalini and Hypolimni （sensu Chou 1994） are not monophyletic groups, and the genus Junonia should be removed from Nymphalini to Hypolimni （=Junoniini）. On the basis of the data, the Symbrenthia and Araschnia had a relative distant relationship with the rest of Nymphalini. The relationships of species in the Nymphalini were confirmed via the NJ, ML, and Bayesian methods, namely （（（（Nymphalis ＋ Kaniska） ＋ Polygonia） ＋Aglais） ＋ Vanessa） ＋ （Symbrenthia ＋Araschnia）. This investigation provides a little novel information for Chinese researches of butterflies.
文摘The aim of this study was to evaluate the genetic variability in bees Apis mellifera from Benin by using mitochondrial DNA （mtDNA） as a molecular marker in their cytochrome c oxidase subunit I and II （COI-COI1） intergenic region. A total of 304 bee colonies were sampled in 27 municipalities of the cashew growing area of Benin. These samples were analyzed by the cleaved amplified polymorphisms technique for determining the haplotypes of subspecies present in the sampled population. Eight PCR-RFLP profiles of African lineage A were then identified in the 304 samples of bees investigated. Forty-nine percent （49%） of the samples showed the profile of haplotype A1 （subspecies adansonii of Zambia）, 40% of haplotype A4 （subspecies scutellata of South Africa） and 3% of haplotype A 19 （subspecies adansonii of Guinea）. Five other haplotypes of the African branch （A） that had been described in a previous study were also identified： new 1 （2%）, new 2 （2%）, new 3 （1%）, new 4 （2%） and new 5 （1%）. This study showed that A. rnellifera from Benin belonged only to lineage A with the predominance of haplotypes AI and A4. This study will contribute to the development of coherent policies for conservation of local bees in Benin.
文摘The mitochondrial cytochrome oxidase II (Co II) from four different apterygotens Cryptopygus nanjiensis (Collembola), Neanura latior (Collembola), Gracilentulus maijiawensis (Protura) and Lepidocampa weberi (Diplura) were sequenced. Their A+T content, number of nucleotide substitutions, TV/TV ratio, and Tamura-Nei’s distance were calculated. A series of phylogenetic trees were constructed by parsimony and distance methods using a crustacean Artemia franciscana as outgroup. Finally the evolutionary trend A+T content of CO II genetic divergence and phylogenetic relationship of apterygotan groups were discussed.
文摘条形码数据库是开展基于DNA的生物监测关键先决条件。为在珠江流域有效开展基于DNA的生物监测,迫切需要了解物种DNA条形码的覆盖或空缺状况。整理了珠江流域常见鱼类和大型底栖动物的物种清单,从National Center and Biotechnology Information (NCBI)数据库中检索了物种清单的DNA条形码序列,分析了常见鱼类(包括线粒体组和12s rRNA基因)和大型底栖动物(包括线粒体组、COI和18s rRNA基因)的DNA条形码覆盖范围和空缺程度。数据分析表明:(1)珠江流域共记录了常见鱼类221种,隶属于2纲18目51科和137属;常见大型底栖动物105种/属,隶属于6纲14目53科。(2)共检索到常见鱼类线粒体组序列913条和12s rRNA基因序列962条,分别占总物种的81.45%和57.92%;有12.67%的物种没有线粒体组和12s rRNA基因序列,若将条形码阈值设置为至少包含5个参考序列,则空缺度上升至52.94%;(3)共检索到常见大型底栖动物线粒体组65条序列、COI基因26,988条序列和18s rRNA基因175条序列,分别占总种/属数的29.52%、68.57%和37.14%;有25.71%的种/属在线粒体组、COI和18s rRNA基因区域皆无序列收录,若将条形码阈值设置为至少包含5个参考序列,则空缺度上升至41.90%。总之,本研究将为珠江流域开展基于DNA的鱼类和大型底栖动物监测提供基础数据支撑,为完善珠江本土DNA条形码数据库提供参考建议。
文摘【目的】基于mtDNA CO Ⅰ基因探究竹笋夜蛾的亲缘关系,以确定其分类地位,为系统进化轨迹提供分子理论基础。【方法】以分布于浙江杭州周边竹子产区的4种竹笋夜蛾为研究对象,使用通用引物分别克隆4种竹笋夜蛾线粒体细胞色素C氧化酶亚基Ⅰ(mtDNA CO Ⅰ)基因5'端709 bp片段序列,通过构建系统进化树,分析4种竹笋夜蛾亲缘关系。【结果】1)4种竹笋夜蛾遗传距离较小;2)与比对昆虫相比,4种竹笋夜蛾同属一个进化群,分支支持率达到100%。【结论】4种竹笋夜蛾亲缘关系接近,除萨夜蛾外,建议将其他3种竹笋夜蛾归为一个属。4种竹笋夜蛾形态差异较小,生态习性相似,分布区域基本一致,可作为理想的同域物种进化研究素材。本研究可为4种竹笋夜蛾分类地位的确定提供初步分子基础,同时可为竹笋夜蛾DNA条形码鉴定提供理论基础。
