Can mtDNA Barcodes Be Used to Delimit Species? A Response to Pons et al. (2006)
Can mtDNA Barcodes Be Used to Delimit Species? A Response to Pons et al. (2006)
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DOI：
10.1093/sysbio/syp039
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发表时间：
2009-08-01
影响因子：
6.5
通讯作者：
Lohse, Konrad
中科院分区：
文献类型：
--
作者：
Lohse, Konrad
DNA条形码如何能够和应该在分类中使用的问题已经争论了一段时间（Lipscomb et al. 2003; Tautz et al. 2003; Blaxter 2004; Vogler and Monaghan 2007; Wiens 2007）。虽然很少有人怀疑条形码是一种有价值的分子工具，可以将未识别的标本与已描述的分类群相匹配，但这与条形码是否可以用于划分物种的问题几乎没有关系。这场争论中最激进的转变是对基于dna的分类法的请求（Tautz et al. 2003; Blaxter 2004; Pons et al. 2006; Vogler and Monaghan 2007）。它的支持者认为，“自然界中绝大多数的序列变异被划分为明确定义的集群”（Vogler和Monaghan 2007， p. 4），其中“[…]]大致反映了物种类别”（Papadopoulou et al. 2008, p. 1），因此可以作为基本的分类单位。采用这种“条形码间隙”的最初尝试依赖于先验地定义序列发散的截止值（例如，Blaxter 2004）。考虑到物种内部遗传多样性的数量可以以数量级变化，很明显，这种方法充其量是武断的。Pons等人（2006）最近提出了一种可能性方法，通过测试超测量树的聚类来规避这个问题。他们认为，“这些新的定量方法可以直接从分支率的转变中推断出难以捉摸的物种边界，并构成了从序列变化定义物种的令人兴奋的可能性……（Vogler and Monaghan 2007，第6页）。鉴于这种说法，这种方法越来越受欢迎也就不足为奇了，它已被应用于许多线粒体DNA （mtDNA）数据集（例如，Pons等人，2006年；Ahrens等人，2007年；Fontaneto等人，2007年；Papadopoulou等人，2008年）。
The question of how DNA barcodes can and should be used in taxonomy has been debated for some time (Lipscomb et al. 2003; Tautz et al. 2003; Blaxter 2004; Vogler and Monaghan 2007; Wiens 2007). Although few doubt that they are a valuable molecular tool for matching unidentified specimens to described taxa, this has little to do with the question of whether barcodes can be used to delimit species in the first place. The most radical turn in this debate has been the plea for a DNA-based taxonomy (Tautz et al. 2003; Blaxter 2004; Pons et al. 2006; Vogler and Monaghan 2007). Its proponents argue that “the vast majority of sequence variation in nature is partitioned into clearly defined clusters”(Vogler and Monaghan 2007, p. 4), which “[...] broadly mirror the species category”(Papadopoulou et al. 2008, p. 1) and could thus serve as basic taxonomic units. Initial attempts to employ this “barcoding gap” have relied on defining cutoff values of sequence divergence a priori (eg, Blaxter 2004). Considering that the amount of genetic diversity within species can vary by orders of magnitude, it is clear that such an approach is arbitrary at best. Pons et al.(2006) have recently proposed a likelihood method that circumvents this problem by testing for clustering in ultrametric trees. They argue that “these new quantitative approaches can infer the elusive species boundary directly from the transition in branching rate and constitute an exciting possibility to define species from sequence variation [...]”(Vogler and Monaghan 2007, p. 6). Given such claims, it is not surprising that this method enjoys increasing popularity, having been applied to a number of mitochondrial DNA (mtDNA) data sets (eg, Pons et al. 2006; Ahrens et al. 2007; Fontaneto et al. 2007; Papadopoulou et al. 2008).