Automated DNA sequencing procedures could   greatly accelerate identification of known species (“DNA barcoding”; Hebert et al., 2003)   and provide a framework for the taxonomy of poorly known groups (Tautz et al., 2003).   However, sequencing-based approaches in taxonomy are useful only if an   individual's DNA sequence can unambiguously associate that individual with a   larger group of organisms (a species or higher taxon). Establishing this   association is complicated due to intraspecific variation and the possible   incongruence of gene and species histories that might prevent the easy recognition   of these groups, in particular where only a single fragment of mtDNA is used   (Lipscomb et al., 2003;   Mallet and Willmott, 2003; Will and Rubinoff, 2004). In current   taxonomic DNA sequencing, species-level entities have been accepted to be   known a priori, and their DNA signature is based on genotypes from a   representative sample of well-identified individuals (Hajibabaei et al.,   2006; Hebert et al., 2003; Meyer and Paulay, 2005).

自动化的DNA测序程序可以大大加速已知物种的鉴定（“DNA条形码”；Hebert et al., 2003），并为不知名类群的分类提供参考（Tautz et al., 2003）。然而，只有当个体的DNA序列明确地与一个更大的生物群（一个物种或更高的分类群）联系在一起时，基于序列的分类方法才有用。建立这种联系是复杂的，因为种内变异、基因和物种历史不一致，可能会妨碍这些群体的方便识别，特别是在仅使用线粒体DNA的单个片段的情况下（Lipscomb et al., 2003; Mallet and Willmott, 2003; Will and   Rubinoff, 2004）。在目前的分类DNA测序中，物种水平的实体被认为是先验的，它们的DNA标记是基于一个从具有代表性的已确认个体样本中获得的基因型（Hajibabaei et al., 2006; Hebert et al., 2003; Meyer and Paulay,   2005）。