Between Two Extremes: Mitochondrial DNA is neither the Panacea nor the Nemesis of Phylogenetic and Taxonomic Inference

Recently, the role of mitochondrial DNA (mtDNA) sequences in taxonomy and phylogenetic inference has become contentious, and two extreme viewpoints have emerged, although, as far as we know, never juxtaposed prior to this article. One position criticizes the use of mtDNA because the marker suggests misleading patterns of variation; specifically, phylogenies 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 “barcode” movement, 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 extreme 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 concert with other independent data sources (e.g., nuclear DNA, cytosystematic, morphological, behavioral). We are against the abolition of the use of mtDNA in phylogenetics but also against its narrow use in barcoding as currently 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.