Recently, the role of mitochondrial DNA (mtDNA) se quences in taxonomy and phylogenetic inference has become contentious, and two extreme viewpoints have emerged, although, as far as we know, never juxta posed prior to this article. One position criticizes the use of mtDNA because the marker suggests mislead ing patterns of variation; specifically, phytogenies that are inconsistent with those derived from nuclear gene sequences in the context of species relationships among closely related taxa (Ballard and Whitlock, 2004; Shaw, 2002). The other extreme, the DNA "barcode77 move ment, espouses the sole use of small fragments of a single mtDNA gene, cytochrome c oxidase I (COI), to identify most of life (Hebert et al., 2003a). The intention of this article is to present the disadvantages of these two ex treme viewpoints and to argue for an integrated role for mtDNA, one that takes advantage of mtDNA's strengths but also accounts for its shortcomings by using it in con cert with other independent data sources (e.g., nuclear DNA, cytosystematic, morphological, behavioral). We are against the abolition of the use of mtDNA in phyloge netics but also against its narrow use in barcoding as cur rently defined. We demonstrate why neither viewpoint is particularly productive and emphasize how analysis of mtDNA can be an important tool in the context of both taxonomic and phylogenetic studies. The use of mtDNA in phylogenetics has been con tentious since it became clear that individual gene and species phylogenetic trees are not always congruent (Avise, 2004; Avise et al., 1983; Avise and Saunders, 1984), and discrepancies between nuclear and mtDNA inheri tance patterns have been well documented (see Funk and Omland, 2003). Recently, there has been a striking dis cord on the suitability of mtDNA in phylogenetics and taxonomy. Some (Hebert et al., 2003b) have argued that mtDNA barcodes, or approximately 600-bp segments of a small and discrete part of the genome, can be used to identify all of life, though the issue is actively debated (Hebert et al, 2003, 2004; Lipscomb et al, 2003; Moritz and Cicero, 2004; Pennisi, 2003; Scotland et al., 2003; Seberg et al., 2003; Will and Rubinoff, 2004). In sharp con trast to advocates of the use of mtDNA barcode segments alone for the identification of all biodiversity, others cau tio against use of certain mtDNA genes in some taxa (Lin and Danforth, 2004; Thalmann et al, 2004), whereas Ballard and Whitlock (2004), referencing studies such as that of Shaw (2002), question the utility of mtDNA for any study of systematics or phylogenetics. They ad vocate elimination of mtDNA from phylogenetic stud ies, sugg sting that it is "risky to infer general patterns from an idiosyncratic small fraction of the genome" (page 731). The implication is that mtDNA can be inaccurate or diverges from the true phylogeny We argue that most phylogenetic studies, other than the handful employ ing a large-scale, multigenomic approach (Rokas et al., 2003), may suffer drawbacks from using only a small fraction of the total genome. But it strikes us as mislead ing t str ngly criticize use of a character source that has yielded over 25 years of phylogenetic data, the majority of which have proven useful, with dozens of published oligonucleotide primer sets and approximately 250,000 entries available in GenBank, DDBJ, and EMBL, includ ing complete mtDNA genomes for more than 800 species (http://www.mitomap.org/euk_mitos.html). The opti mal role for mtDNA is somewhere between these ex

中文翻译：

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在两个极端之间：线粒体 DNA 既不是万能药，也不是系统发育和分类学推断的克星

最近，线粒体 DNA (mtDNA) 序列在分类学和系统发育推断中的作用引起了争议，并且出现了两种极端的观点，尽管据我们所知，在本文之前从未并列过。一个立场批评使用 mtDNA，因为该标记表明变异模式具有误导性；具体而言，在密切相关的分类群之间的物种关系背景下，与源自核基因序列的植物发育不一致的植物发育（Ballard 和 Whitlock，2004 年；Shaw，2002 年）。另一个极端，DNA“barcode77 运动”支持仅使用单个 mtDNA 基因的小片段细胞色素 c 氧化酶 I (COI) 来识别大部分生命（Hebert 等，2003a）。这篇文章的目的是展示这两种极端观点的缺点，并论证 mtDNA 的综合作用，一种利用 mtDNA 的优势但也通过与其他独立数据源协同使用来解释其缺点的（例如，核 DNA、细胞系统、形态、行为）。我们反对在系统发育学中废除 mtDNA 的使用，但也反对其在当前定义的条形码中的狭义使用。我们证明了为什么这两种观点都不是特别有效，并强调了 mtDNA 分析如何成为分类学和系统发育研究背景下的重要工具。mtDNA 在系统发育中的应用一直存在争议，因为很明显单个基因和物种的系统发育树并不总是一致的（Avise，2004 年；Avise 等人，1983年；Avise 和 Saunders，1984），并且核和 mtDNA 遗传模式之间的差异已被充分记录（参见 Funk 和 Omland，2003）。最近，mtDNA 在系统发育学和分类学中的适用性出现了惊人的分歧。一些人（Hebert et al., 2003b）认为，mtDNA 条形码，或基因组的一个小的离散部分的大约 600 bp 片段，可以用来识别所有的生命，尽管这个问题正在积极辩论（Hebert et al., 2003b） , 2003, 2004；Lipscomb 等人，2003 年；Moritz 和 Cicero，2004 年；Pennisi，2003 年；Scotland 等人，2003 年；Seberg 等人，2003 年；Will 和 Rubinoff，2004 年）。与单独使用 mtDNA 条形码片段来识别所有生物多样性的倡导者形成鲜明对比，其他人则反对在某些分类群中使用某些 mtDNA 基因（Lin 和 Danforth，2004 年；Thalmann 等人，2004 年），而 Ballard 和 Whitlock (2004) 参考了诸如 Shaw (2002) 的研究，质疑 mtDNA 在任何系统学或系统发育学研究中的效用。他们主张从系统发育研究中消除 mtDNA，并指出“从基因组的一小部分特异质部分推断一般模式是有风险的”（第 731 页）。这意味着 mtDNA 可能不准确或偏离真正的系统发育我们认为，除了少数采用大规模、多基因组方法的少数系统发育研究（Rokas 等，2003）外，大多数系统发育研究可能会因仅使用总基因组的一小部分。但它让我们感到误导，强烈批评使用已经产生超过 25 年系统发育数据的字符来源，其中大部分已被证明是有用的，拥有数十个已发表的寡核苷酸引物组以及 GenBank、DDBJ 和 EMBL 中的大约 250,000 个条目，包括 800 多个物种的完整 mtDNA 基因组 (http://www.mitomap.org/euk_mitos.html)。mtDNA 的最佳作用介于这些之间