Mitochondrial cox1 sequence data reliably uncover patterns of insect diversity but suffer from high lineage-idiosyncratic error rates.
Mitochondrial cox1 sequence data reliably uncover patterns of insect diversity but suffer from high lineage-idiosyncratic error rates.
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DOI：
10.1371/journal.pone.0014448
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发表时间：
2010-12-28
期刊：
影响因子：
3.7
通讯作者：
Balke M
中科院分区：
文献类型：
--
作者：
Hendrich L;Pons J;Ribera I;Balke M
对生物多样性科学数据的需求日益增加，但分类学专门知识往往有限或不存在。DNA测序是克服这一分类障碍的潜在补救措施。线粒体DNA最常用，例如，用于物种识别（“DNA条形码”）。在这里，我们提出了第一个研究节肢动物的基础上，从整个澳大利亚地区的一个家庭级类群的一个近乎完整的物种采样。我们的目的是评估如何可靠的mtDNA数据可以捕捉物种多样性时，许多姐妹物种对包括在内。然后，我们对比系统发育亚抽样与迄今为止更常用的地理亚抽样，姐妹物种不一定被捕获。我们对1,439个个体进行了800 bp的cox 1测序，其中包括260个澳大利亚物种（78%的物种覆盖率）。我们使用聚类阈值为1至10%和一般的混合Yule聚结（GMYC）分析的物种丰富度的估计。所使用的性能指标是分类准确性和形态和分子物种丰富度估计之间的协议。聚类（在3%的水平）和GMYC可靠地估计单一或多个地理区域的物种多样性，与低于10%的误差较大的分支，从而优于parataxonomy。然而，一些个别属的错误率较高，值高达45%时，最近的物种形成非单系集群。分类学的准确性总是较低，错误率超过20%，在属的水平上有较大的变化（0至70%）。Sørensen相似性指数计算的形态种，3%的集群和GMYC实体不同对地点之间的方法是一致的，并显示出预期的减少距离。 Cox 1序列数据是大尺度物种丰富度估算的有力工具，在生态学和β多样性研究以及确定保护优先级方面具有巨大潜力。然而，在个别谱系中错误率可能很高。
The demand for scientific biodiversity data is increasing, but taxonomic expertise is often limited or not available. DNA sequencing is a potential remedy to overcome this taxonomic impediment. Mitochondrial DNA is most commonly used, e.g., for species identification (“DNA barcoding”). Here, we present the first study in arthropods based on a near-complete species sampling of a family-level taxon from the entire Australian region. We aimed to assess how reliably mtDNA data can capture species diversity when many sister species pairs are included. Then, we contrasted phylogenetic subsampling with the hitherto more commonly applied geographical subsampling, where sister species are not necessarily captured. We sequenced 800 bp cox1 for 1,439 individuals including 260 Australian species (78% species coverage). We used clustering with thresholds of 1 to 10% and general mixed Yule Coalescent (GMYC) analysis for the estimation of species richness. The performance metrics used were taxonomic accuracy and agreement between the morphological and molecular species richness estimation. Clustering (at the 3% level) and GMYC reliably estimated species diversity for single or multiple geographic regions, with an error for larger clades of lower than 10%, thus outperforming parataxonomy. However, the rates of error were higher for some individual genera, with values of up to 45% when very recent species formed nonmonophyletic clusters. Taxonomic accuracy was always lower, with error rates above 20% and a larger variation at the genus level (0 to 70%). Sørensen similarity indices calculated for morphospecies, 3% clusters and GMYC entities for different pairs of localities was consistent among methods and showed expected decrease over distance. Cox1 sequence data are a powerful tool for large-scale species richness estimation, with a great potential for use in ecology and β-diversity studies and for setting conservation priorities. However, error rates can be high in individual lineages.
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DOI：
10.1098/rsbl.2003.0025
发表时间：
2003-08-07
影响因子：
4.7
作者：
Hebert, PDN;Ratnasingham, S;deWaard, JR
通讯作者：
deWaard, JR
影响因子：
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作者：
Hebert PD;Stoeckle MY;Zemlak TS;Francis CM
通讯作者：
Francis CM
影响因子：
4.9
作者：
Clement, M;Posada, D;Crandall, KA
通讯作者：
Crandall, KA
影响因子：
9.8
作者：
Fontaneto, Diego;Herniou, Elisabeth A;Boschetti, Chiara;Caprioli, Manuela;Melone, Giulio;Ricci, Claudia;Barraclough, Timothy G
通讯作者：
Barraclough, Timothy G
DOI：
10.1098/rspb.2008.0679
发表时间：
2009-01-07
影响因子：
4.7
作者：
Jousselin, Emmanuelle;Desdevises, Yves;Coeur d'Acier, Armelle
通讯作者：
Coeur d'Acier, Armelle