【目的】应用线粒体DNA条形码技术对尤犀金龟属(Eupatorus Burmeister,1847)昆虫物种界定进行探索,以解决该属物种形态鉴定困难的问题。【方法】基于尤犀金龟属物种线粒体cox1和cox2基因序列数据集,使用Automatic Barcode Gap Discovery...【目的】应用线粒体DNA条形码技术对尤犀金龟属(Eupatorus Burmeister,1847)昆虫物种界定进行探索,以解决该属物种形态鉴定困难的问题。【方法】基于尤犀金龟属物种线粒体cox1和cox2基因序列数据集,使用Automatic Barcode Gap Discovery(ABGD)和Bayesian Poisson Tree Processes(bPTP)对3个形态种进行分子物种界定,并与形态学鉴定结果进行比较。【结果】使用ABGD方法时,cox1数据集的界定结果与形态学鉴定结果一致,cox2数据集的界定结果与形态学鉴定结果存在差异;使用bPTP方法时,2种数据集的界定结果均远高于形态学鉴定结果,且均存在不同程度的过度划分。【结论】cox1是更适合用于鉴定尤犀金龟属昆虫的DNA条形码,使用ABGD方法时,其数据集界定结果与形态学鉴定结果一致。利用分子界定与形态特征鉴定相结合,可极大地提高鉴定效率和准确性。展开更多
[目的]为了探究3种常用物种界定方法(jMOTU、ABGD、GMYC)的界定效果。[方法]本研究以中国北京周边地区10个采样点483个舟蛾科样品为例,利用线粒体细胞色素C氧化酶Ⅰ亚基基因(Cytochrome c oxidase subunitⅠgene,COⅠ或COX1,约650 bp)...[目的]为了探究3种常用物种界定方法(jMOTU、ABGD、GMYC)的界定效果。[方法]本研究以中国北京周边地区10个采样点483个舟蛾科样品为例,利用线粒体细胞色素C氧化酶Ⅰ亚基基因(Cytochrome c oxidase subunitⅠgene,COⅠ或COX1,约650 bp)的部分序列,进行3种物种界定算法(jMOTU、ABGD、GMYC)的实例比较研究。[结果]3种物种界定方法的鉴定效力存在差异,与形态学结果相比较,ABGD方法划分物种的准确率为100%,基于BEAST的GMYC模型结果与形态学结果一致,产生的置信区间(64~68)覆盖了形态学的结果(67)。然而,基于d8tree/MPLtree的GMYC方法倾向于高估MOTUs,jMOTU方法倾向于低估物种数目。[结论]结果显示,ABGD方法和基于BEAST的GMYC模型方法对于本文研究对象舟蛾科能够较好地划分,可以对基于形态学的物种界定进行有效补充。展开更多
为了探讨DNA条形码技术在蟹蛛科蜘蛛物种鉴定中的可行性,本研究基于线粒体COI基因序列,使用邻接法和贝叶斯法构建系统发育树,ABGD(automatic barcode gap discovery)软件对样本进行划分,对小五台山25种蟹蛛110个样本进行DNA条形码分子鉴...为了探讨DNA条形码技术在蟹蛛科蜘蛛物种鉴定中的可行性,本研究基于线粒体COI基因序列,使用邻接法和贝叶斯法构建系统发育树,ABGD(automatic barcode gap discovery)软件对样本进行划分,对小五台山25种蟹蛛110个样本进行DNA条形码分子鉴定.结果表明:邻接法和贝叶斯法构建的系统发育树聚类结果与ABGD软件划分结果以及形态分类鉴定结果相一致.据此笔者认为DNA条形码作为一种有效的分子鉴定工具可以应用到蟹蛛科蜘蛛物种鉴定中.展开更多
The relatively conserved 18S is often used in the phylogenetic analysis of microalgae. However, whether it can really help in barcoding microalgae needs to be evaluated. In this study the multiple approaches of coales...The relatively conserved 18S is often used in the phylogenetic analysis of microalgae. However, whether it can really help in barcoding microalgae needs to be evaluated. In this study the multiple approaches of coalescent, distance and character-based barcoding are first employed in C hlorella and Scenedesmus to test the efficiency of 18S sequences for barcoding green microalgae. We show that most Chlorella and Scenedesmus species, including the cryptic species, can be distinguished by 18S sequences with all coalescent General Mixed Yule-coalescent(GMYC), poisson tree process(PTP), and P ID, distance(ABGD) and character-based approaches. Both GMYC and PTP analyses produce more genetic groups. The P ID and ABGD analyses only cluster some species. All species(apart from a few of lineages) can be separated in character-based barcoding analysis with more than three character attributes. In comparison with previous barcoding results with r bcL, tufA, ITS and 16 S, 18S produces good resolution in identifying Chlorella and Scenedesmus. Our results reveal that 18S is highly efficient in identifying taxa of green microalgae at species level, based on a combination of multiple barcoding approaches. Combining 18S with other gene markers may be useful in barcoding microalgae.展开更多
文摘【目的】应用线粒体DNA条形码技术对尤犀金龟属(Eupatorus Burmeister,1847)昆虫物种界定进行探索,以解决该属物种形态鉴定困难的问题。【方法】基于尤犀金龟属物种线粒体cox1和cox2基因序列数据集,使用Automatic Barcode Gap Discovery(ABGD)和Bayesian Poisson Tree Processes(bPTP)对3个形态种进行分子物种界定,并与形态学鉴定结果进行比较。【结果】使用ABGD方法时,cox1数据集的界定结果与形态学鉴定结果一致,cox2数据集的界定结果与形态学鉴定结果存在差异;使用bPTP方法时,2种数据集的界定结果均远高于形态学鉴定结果,且均存在不同程度的过度划分。【结论】cox1是更适合用于鉴定尤犀金龟属昆虫的DNA条形码,使用ABGD方法时,其数据集界定结果与形态学鉴定结果一致。利用分子界定与形态特征鉴定相结合,可极大地提高鉴定效率和准确性。
文摘[目的]为了探究3种常用物种界定方法(jMOTU、ABGD、GMYC)的界定效果。[方法]本研究以中国北京周边地区10个采样点483个舟蛾科样品为例,利用线粒体细胞色素C氧化酶Ⅰ亚基基因(Cytochrome c oxidase subunitⅠgene,COⅠ或COX1,约650 bp)的部分序列,进行3种物种界定算法(jMOTU、ABGD、GMYC)的实例比较研究。[结果]3种物种界定方法的鉴定效力存在差异,与形态学结果相比较,ABGD方法划分物种的准确率为100%,基于BEAST的GMYC模型结果与形态学结果一致,产生的置信区间(64~68)覆盖了形态学的结果(67)。然而,基于d8tree/MPLtree的GMYC方法倾向于高估MOTUs,jMOTU方法倾向于低估物种数目。[结论]结果显示,ABGD方法和基于BEAST的GMYC模型方法对于本文研究对象舟蛾科能够较好地划分,可以对基于形态学的物种界定进行有效补充。
文摘为了探讨DNA条形码技术在蟹蛛科蜘蛛物种鉴定中的可行性,本研究基于线粒体COI基因序列,使用邻接法和贝叶斯法构建系统发育树,ABGD(automatic barcode gap discovery)软件对样本进行划分,对小五台山25种蟹蛛110个样本进行DNA条形码分子鉴定.结果表明:邻接法和贝叶斯法构建的系统发育树聚类结果与ABGD软件划分结果以及形态分类鉴定结果相一致.据此笔者认为DNA条形码作为一种有效的分子鉴定工具可以应用到蟹蛛科蜘蛛物种鉴定中.
基金Supported by the China Post-doctoral Science Foundation(Nos.2014M561661,2015T80558)the Natural Science Foundation of Jiangsu Province(No.BK20150680)+1 种基金the National Natural Science Foundation of China(No.31600294)the Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization and Fundamental Research Funds for the Central Universities of Ministry of Education of China(No.Y0201600141)
文摘The relatively conserved 18S is often used in the phylogenetic analysis of microalgae. However, whether it can really help in barcoding microalgae needs to be evaluated. In this study the multiple approaches of coalescent, distance and character-based barcoding are first employed in C hlorella and Scenedesmus to test the efficiency of 18S sequences for barcoding green microalgae. We show that most Chlorella and Scenedesmus species, including the cryptic species, can be distinguished by 18S sequences with all coalescent General Mixed Yule-coalescent(GMYC), poisson tree process(PTP), and P ID, distance(ABGD) and character-based approaches. Both GMYC and PTP analyses produce more genetic groups. The P ID and ABGD analyses only cluster some species. All species(apart from a few of lineages) can be separated in character-based barcoding analysis with more than three character attributes. In comparison with previous barcoding results with r bcL, tufA, ITS and 16 S, 18S produces good resolution in identifying Chlorella and Scenedesmus. Our results reveal that 18S is highly efficient in identifying taxa of green microalgae at species level, based on a combination of multiple barcoding approaches. Combining 18S with other gene markers may be useful in barcoding microalgae.
