Recent advances in DNA taxonomy

Large-scale DNA sequencing of living species holds great promise in taxonomy, but has been controversial. In this article, we review the recent advances that follow the dramatic increase in data generation. We distinguish DNA taxonomy from DNA barcoding, where the former directly concerns the circumscription and delineation of species using evolutionary species concepts and the latter is a means of identifying a priori entities by sequence similarity. A key finding from recent studies in animals is that variation in mitochondrial DNA (mtDNA) is partitioned as tight clusters of closely related genotypes, which group specimens largely according to traditionally recognized species limits, and which are congruent with nuclear markers. This finding provides confidence to use sequence variation as the primary information for species delimitation in poorly known groups. A number of recent, large-scale studies support the power of mtDNA in species recognition, and previous application of molecular techniques to taxonomically complicated cases has likely led to an overestimate of the proportion of species with polyphyletic mtDNA haplotypes. The continued development of DNA taxonomy will lead to more refined sampling strategies and data analyses than those that are presently used. Sophisticated statistical methods of grouping have already been developed based on sequence similarity; yet, the units defined in this way have largely unknown evolutionary relevance. In future, a standard DNA taxonomic analysis will include broad sampling of the target taxa across their geographic range, followed by large-scale sequencing of representative samples for a DNA profile of the group, and algorithmic procedures for delineating species limits. The taxonomic system will be derived from the data rather than expert opinion, and hypothesized species entities can be tested against morphology, biogeography and other data, providing an evolutionary justification of the procedures used for species delimitation. Discrepancies between DNA and other data are used to refine species delimitations via a feedback loop that incorporates new data. We argue, however, that the use of DNA methodology in taxonomy (including DNA barcoding) will remain controversial until it is better founded in existing theory of evolutionary biology and phylogenetics.