鳈属(Sarcocheilichthys)鱼类是东亚地区常见小型淡水鱼类,并具有一定的养殖开发潜力。深入了解鳈属鱼类的遗传结构及其地域变异,对科学制定保护计划和可持续利用野生资源具有重要意义。试验采用鳈属鱼类包括小鳈(S.parvus,XQ)20尾,江西...鳈属(Sarcocheilichthys)鱼类是东亚地区常见小型淡水鱼类,并具有一定的养殖开发潜力。深入了解鳈属鱼类的遗传结构及其地域变异,对科学制定保护计划和可持续利用野生资源具有重要意义。试验采用鳈属鱼类包括小鳈(S.parvus,XQ)20尾,江西鳈(S.kiangsiensis,JXQ)20尾,黑鳍鳈(S.nigripinnis,HQQ)20尾,东北鳈(S.lacustris,DBQ)24尾,华鳈(S.sinensis)淮河群体(HQ_(HH))20尾、闽江群体(HQ_(MJ))17尾、江西群体(HQ_(JX))15尾和建德群体(HQ_(JD))17尾,并对每个群体的线粒体细胞色素C氧化酶亚基Ⅰ(cytochrome C oxidase subunitⅠ,COI)序列片段进行了测序和分析。试验结果表明,在获得的153个样本序列(668 bp)中,保守位点507个,变异位点154个,简约信息位点150个,碱基缺失或插入位点27个,平均转换与颠换比值为5.2。HQQ群体的单倍型多样性(Hd)最低(0.442),HQHH群体的Hd略高于HQQ群体(0.574),DBQ群体的Hd则稍高于HQHH群体(0.707),而XQ群体的Hd最高(0.963),HQMJ和HQJX群体的Hd则略低于XQ群体(0.860、0.848)。核苷酸多样变化趋势则与Hd结果类似。153尾个体定义了56种单倍型,各群体的单倍型网络中均存在各自群体的主要单倍型,如Hap_2、Hap_33和Hap_37等。基于遗传距离构建的UPGMA分子系统发育树、层次聚类树和NeighborNet分子系统发育网络表明,XQ、HQQ、JXQ和其他鳈属鱼类间遗传关系较远,而DBQ与HQHH群体间遗传关系较近。该研究利用COI序列片段评估了4个华鳈地理群体及其他4种鳈属鱼类的遗传多样性。研究结果将有助于了解华鳈不同地理群体及其他4种鳈属鱼类野生资源的遗传多样性现状,为今后华鳈以及其他4种鳈属鱼类种质资源保护及利用提供参考。展开更多
Objective:To address the phylogenetic and phylogeographic relationship between different lineages of Anopheles(An.)subpictus species complex in most parts of the Asian continent by maximum utilization of Internal Tran...Objective:To address the phylogenetic and phylogeographic relationship between different lineages of Anopheles(An.)subpictus species complex in most parts of the Asian continent by maximum utilization of Internal Transcriber Spacer 2(ITS2)and cytochrome C oxidase I(COI)sequences deposited at the GenBank.Methods:Seventy-five ITS2,210 COI and 26 concatenated sequences available in the NCBI database were used.Phylogenetic analysis was performed using Bayesian likelihood trees,whereas median-joining haplotype networks and time-scale divergence trees were generated for phylogeographic analysis.Genetic diversity indices and genetic differentiation were also calculated.Results:Two genetically divergent molecular forms of An.subpictus species complex corresponding to sibling species A and B are established.Species A evolved around 37-82 million years ago in Sri Lanka,India,and the Netherlands,and species B evolved around 22-79 million years ago in Sri Lanka,India,and Myanmar.Vietnam,Thailand,and Cambodia have two molecular forms:one is phylogenetically similar to species B.Other forms differ from species A and B and evolved recently in the above mentioned countries,Indonesia and the Philippines.Genetic subdivision among Sri Lanka,India,and the Netherlands is almost absent.A substantial genetic differentiation was obtained for some populations due to isolation by large geographical distances.Genetic diversity indices reveal the presence of a long-established stable mosquito population,at mutation-drift equilibrium,regardless of population fluctuations.Conclusions:An.subpictus species complex consists of more than two genetically divergent molecular forms.Species A is highly divergent from the rest.Sri Lanka and India contain only species A and B.展开更多
Accurate species identification is a key component of biodiversity research.DNA barcoding is an effective molecular method used for fish species identification.We aimed to study the DNA barcoding of fish in Zhoushan c...Accurate species identification is a key component of biodiversity research.DNA barcoding is an effective molecular method used for fish species identification.We aimed to study the DNA barcoding of fish in Zhoushan coastal waters,explore the differences and applicability of two gene fragments(12S rRNA and COI)of DNA barcoding in fish species identification,and established a comprehensive fish barcoding reference database.Two hundred and eighty-seven captured fish samples from Zhoushan coastal waters were identified using morphological characteristics and DNA barcoding.A total of 26412S rRNA sequences(belonging to eight orders,31 families,55 genera,and 66 species)and 188 COI sequences(belonging to seven orders,30 families,48 genera,and 58 species)were obtained.The lengths of the 12S rRNA sequences ranged from 165 to 178 bp,and the guanine-cytosine(GC)content was 45.37%.The average 12S rRNA interspecific and intraspecific genetic distances(K2P)were 0.10%and 26.66%,respectively.The length of the COI sequence ranged 574–655 bp,and the content of GC was 45.97%.The average 12S rRNA interspecific and intraspecific genetic distances(K2P)were 0.16%and 27.45%,respectively.The minimum interspecific genetic distances of 12S rRNA and COI(1.23%and 1.86%)were both greater than their maximum intraspecific genetic distances(2.42%and 8.66%).Three molecular analyses(NJ tree,ABGD,and GMYC)were performed to accurately identify and delineate species.Clustering errors occurred when the 12S rRNA sequences were delimited using the NJ tree method,and the delimitation results of ABGD and GMYC are consistent with the final species identification results.Our results demonstrate that DNA barcoding based on 12S rRNA and COI can be used as an effective tool for fish species identification,and 12S rRNA has good application prospects in the environmental DNA(eDNA)metabarcoding of marine fish.展开更多
文摘鳈属(Sarcocheilichthys)鱼类是东亚地区常见小型淡水鱼类,并具有一定的养殖开发潜力。深入了解鳈属鱼类的遗传结构及其地域变异,对科学制定保护计划和可持续利用野生资源具有重要意义。试验采用鳈属鱼类包括小鳈(S.parvus,XQ)20尾,江西鳈(S.kiangsiensis,JXQ)20尾,黑鳍鳈(S.nigripinnis,HQQ)20尾,东北鳈(S.lacustris,DBQ)24尾,华鳈(S.sinensis)淮河群体(HQ_(HH))20尾、闽江群体(HQ_(MJ))17尾、江西群体(HQ_(JX))15尾和建德群体(HQ_(JD))17尾,并对每个群体的线粒体细胞色素C氧化酶亚基Ⅰ(cytochrome C oxidase subunitⅠ,COI)序列片段进行了测序和分析。试验结果表明,在获得的153个样本序列(668 bp)中,保守位点507个,变异位点154个,简约信息位点150个,碱基缺失或插入位点27个,平均转换与颠换比值为5.2。HQQ群体的单倍型多样性(Hd)最低(0.442),HQHH群体的Hd略高于HQQ群体(0.574),DBQ群体的Hd则稍高于HQHH群体(0.707),而XQ群体的Hd最高(0.963),HQMJ和HQJX群体的Hd则略低于XQ群体(0.860、0.848)。核苷酸多样变化趋势则与Hd结果类似。153尾个体定义了56种单倍型,各群体的单倍型网络中均存在各自群体的主要单倍型,如Hap_2、Hap_33和Hap_37等。基于遗传距离构建的UPGMA分子系统发育树、层次聚类树和NeighborNet分子系统发育网络表明,XQ、HQQ、JXQ和其他鳈属鱼类间遗传关系较远,而DBQ与HQHH群体间遗传关系较近。该研究利用COI序列片段评估了4个华鳈地理群体及其他4种鳈属鱼类的遗传多样性。研究结果将有助于了解华鳈不同地理群体及其他4种鳈属鱼类野生资源的遗传多样性现状,为今后华鳈以及其他4种鳈属鱼类种质资源保护及利用提供参考。
文摘Objective:To address the phylogenetic and phylogeographic relationship between different lineages of Anopheles(An.)subpictus species complex in most parts of the Asian continent by maximum utilization of Internal Transcriber Spacer 2(ITS2)and cytochrome C oxidase I(COI)sequences deposited at the GenBank.Methods:Seventy-five ITS2,210 COI and 26 concatenated sequences available in the NCBI database were used.Phylogenetic analysis was performed using Bayesian likelihood trees,whereas median-joining haplotype networks and time-scale divergence trees were generated for phylogeographic analysis.Genetic diversity indices and genetic differentiation were also calculated.Results:Two genetically divergent molecular forms of An.subpictus species complex corresponding to sibling species A and B are established.Species A evolved around 37-82 million years ago in Sri Lanka,India,and the Netherlands,and species B evolved around 22-79 million years ago in Sri Lanka,India,and Myanmar.Vietnam,Thailand,and Cambodia have two molecular forms:one is phylogenetically similar to species B.Other forms differ from species A and B and evolved recently in the above mentioned countries,Indonesia and the Philippines.Genetic subdivision among Sri Lanka,India,and the Netherlands is almost absent.A substantial genetic differentiation was obtained for some populations due to isolation by large geographical distances.Genetic diversity indices reveal the presence of a long-established stable mosquito population,at mutation-drift equilibrium,regardless of population fluctuations.Conclusions:An.subpictus species complex consists of more than two genetically divergent molecular forms.Species A is highly divergent from the rest.Sri Lanka and India contain only species A and B.
基金Supported by the Zhejiang Provincial Key Research and Development Program (No.2021C02047)。
文摘Accurate species identification is a key component of biodiversity research.DNA barcoding is an effective molecular method used for fish species identification.We aimed to study the DNA barcoding of fish in Zhoushan coastal waters,explore the differences and applicability of two gene fragments(12S rRNA and COI)of DNA barcoding in fish species identification,and established a comprehensive fish barcoding reference database.Two hundred and eighty-seven captured fish samples from Zhoushan coastal waters were identified using morphological characteristics and DNA barcoding.A total of 26412S rRNA sequences(belonging to eight orders,31 families,55 genera,and 66 species)and 188 COI sequences(belonging to seven orders,30 families,48 genera,and 58 species)were obtained.The lengths of the 12S rRNA sequences ranged from 165 to 178 bp,and the guanine-cytosine(GC)content was 45.37%.The average 12S rRNA interspecific and intraspecific genetic distances(K2P)were 0.10%and 26.66%,respectively.The length of the COI sequence ranged 574–655 bp,and the content of GC was 45.97%.The average 12S rRNA interspecific and intraspecific genetic distances(K2P)were 0.16%and 27.45%,respectively.The minimum interspecific genetic distances of 12S rRNA and COI(1.23%and 1.86%)were both greater than their maximum intraspecific genetic distances(2.42%and 8.66%).Three molecular analyses(NJ tree,ABGD,and GMYC)were performed to accurately identify and delineate species.Clustering errors occurred when the 12S rRNA sequences were delimited using the NJ tree method,and the delimitation results of ABGD and GMYC are consistent with the final species identification results.Our results demonstrate that DNA barcoding based on 12S rRNA and COI can be used as an effective tool for fish species identification,and 12S rRNA has good application prospects in the environmental DNA(eDNA)metabarcoding of marine fish.
