Divergence thresholds and divergent biodiversity estimates: can metabarcoding reliably describe zooplankton communities?
Divergence thresholds and divergent biodiversity estimates: can metabarcoding reliably describe zooplankton communities?
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DOI：
10.1002/ece3.1485
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发表时间：
2015-06
影响因子：
2.6
通讯作者：
Cristescu, Melania E.
中科院分区：
文献类型：
--
作者：
Brown, Emily A.;Chain, Frederic J. J.;Crease, Teresa J.;MacIsaac, Hugh J.;Cristescu, Melania E.
DNA元编码是描述群落和估计生物多样性的一种很有前途的方法。这种方法使用目标标记的高通量测序来识别复杂样本中的物种。按照惯例，序列以预定义的序列分歧阈值(通常为3%)聚类成可操作的分类单元(OTU)，作为物种的代理。然而，不同分类群体的种间标记差异水平不同，使得将系统发育不同的数据集的序列以统一的阈值聚类到OTUS是有问题的。在这项研究中，我们使用模拟浮游动物群落来评估物种丰富度估计的准确性，当遵循传统的方案将小亚单位核糖体RNA基因(18S)的V4区的高变量序列聚类到OTUS中时。通过在我们的群落中包括单独标记的单个标本和不同物种的“种群”，我们检查了种内和种间多样性对OTU聚集性的影响。在3%的分化阈值下，每种单一个体组成的群落在OTU数量和物种丰富度之间的一致性为59-84%。然而，当每个物种包含多个个体时，OTU数量与物种丰富度之间的对应关系下降到31-63%。我们的结果表明，该标记的种内变异通常超过3%，因此单个物种并不总是对应于一个OTU。我们主张在分析复杂和分类多样化的群落时，需要应用特定于群体的分歧阈值，但也鼓励开发额外的过滤步骤，以识别可能产生虚假OTU的人工rRNA基因序列或假基因。
DNA metabarcoding is a promising method for describing communities and estimating biodiversity. This approach uses high-throughput sequencing of targeted markers to identify species in a complex sample. By convention, sequences are clustered at a predefined sequence divergence threshold (often 3%) into operational taxonomic units (OTUs) that serve as a proxy for species. However, variable levels of interspecific marker variation across taxonomic groups make clustering sequences from a phylogenetically diverse dataset into OTUs at a uniform threshold problematic. In this study, we use mock zooplankton communities to evaluate the accuracy of species richness estimates when following conventional protocols to cluster hypervariable sequences of the V4 region of the small subunit ribosomal RNA gene (18S) into OTUs. By including individually tagged single specimens and “populations” of various species in our communities, we examine the impact of intra- and interspecific diversity on OTU clustering. Communities consisting of single individuals per species generated a correspondence of 59–84% between OTU number and species richness at a 3% divergence threshold. However, when multiple individuals per species were included, the correspondence between OTU number and species richness dropped to 31–63%. Our results suggest that intraspecific variation in this marker can often exceed 3%, such that a single species does not always correspond to one OTU. We advocate the need to apply group-specific divergence thresholds when analyzing complex and taxonomically diverse communities, but also encourage the development of additional filtering steps that allow identification of artifactual rRNA gene sequences or pseudogenes that may generate spurious OTUs.
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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：
16.6
作者：
Fonseca, Vera G.;Carvalho, Gary R.;Sung, Way;Johnson, Harriet F.;Power, Deborah M.;Neill, Simon P.;Packer, Margaret;Blaxter, Mark L.;Lambshead, P. John D.;Thomas, W. Kelley;Creer, Simon
通讯作者：
Creer, Simon
影响因子：
12.3
作者：
Huse SM;Huber JA;Morrison HG;Sogin ML;Welch DM
通讯作者：
Welch DM
影响因子：
3.7
作者：
Egge E;Bittner L;Andersen T;Audic S;de Vargas C;Edvardsen B
通讯作者：
Edvardsen B
影响因子：
3.7
作者：
Diaz PI;Dupuy AK;Abusleme L;Reese B;Obergfell C;Choquette L;Dongari-Bagtzoglou A;Peterson DE;Terzi E;Strausbaugh LD
通讯作者：
Strausbaugh LD