DNA Barcoding: Promise and Pitfalls

1529 I n this issue of PLoS Biology, Hebert et al. (2004) have set out to test the resolution and performance of " DNA barcoding, " using a single mtDNA gene, cytochrome c oxidase I (COI), for a sample of North American birds. Before turning to details of this study, it is useful as context to consider the following questions: What is DNA barcoding, and what does it promise? What is new about it? Why is it controversial? What are the potential pitfalls? Put simply, the intent of DNA barcoding is to use large-scale screening of one or a few reference genes in order to (i) assign unknown individuals to species, and (ii) enhance discovery of new species (Hebert et al. 2003; Stoeckle 2003). Proponents envisage development of a comprehensive database of sequences, preferably associated with voucher specimens representing described species, against which sequences from sampled individuals can be compared. Given the long history of use of molecular markers (e.g., allozymes, rDNA, and mtDNA) for these purposes (Avise 2004), there is nothing fundamentally new in the DNA barcoding concept, except increased scale and proposed standardization. The former is inevitable. Standardization, i.e., the selection of one or more reference genes, is of proven value in the microbial community and in stimulating large-scale phylogenetic analyses, but whether " one gene fi ts all " is open to debate. Why, then, all the fuss? Initial reactions to the DNA barcoding concept have ranged from unbridled enthusiasm, especially from ecologists (Janzen 2004), to outright condemnation, largely from taxonomists (e.g., see the February 2003 issue of Trends in Ecology and Evolution). The former view refl ects a real need to connect different life history stages and to increase the precision and effi ciency of fi eld studies involving diverse and diffi cult-to-identify taxa. The criticisms are mainly in response to the view that single-gene sequences should be the primary identifi er for species (" DNA taxonomy " ; Tautz et al. 2002; see also Blaxter 2004). At least for the macrobiota, the DNA barcoding community has moved away from this to emphasize the importance of embedding any large-scale sequence database within the existing framework and practice of systematics, including the importance of voucher specimens and of integrating molecular with morphological characters. Another point of contention—that DNA barcodes have limited phylogenetic resolution—arises from confusion about the scope of inference. At best, single-gene assays can hope to …