DNA barcoding of animal species—response to DeSalle

In issue number 29.12 of this journal, DeSalle recently commented on the review by Waugh, which outlined the conceptual basis and progress on the worldwide effort to DNA barcode animal species. DeSalle’s paper is a useful clarification of a number of the issues relating to the analytical approach to DNA barcoding data and to the role that DNA barcodingmight play inmodern biology.He criticised theuseof distance-basedapproaches toDNAbarcodingandpointedout that thesemethodshaveanumber of drawbacks.Moreover, he also pointed out that such distance-based approaches are not typically used by taxonomists in the process of describing new species. Instead, DeSalle argued for the use of characterbased or diagnostic approaches to both species discoveryand species identification. He suggested that this approach was preferable because first, diagnostic DNA sequence characters can be easily extracted from COI sequences without assuming any particular model of nucleotide substitution (sic evolution). Second, character-based methods do not require arbitrary cutoffs, as do distance-basedmethods. Third a DNA diagnostic can be determined without reference to other organisms. Fourth, it avoids the confounding effects of distance-based methods that occur as a result of anagenetic changes. Finally, DeSalle suggested that diagnostic-based techniques aremore adaptable to the possible development of handheld DNA-based identification devices at some time in the future. Conceptually, there is much to recommend DeSalle’s approach. Species represent a major component of the diversity that is inherent in nature. Of course, there is also diversity at the individual and population levels, for example. Although there has been over the centuries much debate about species definitions, there has been little disagreement about the reality of species and their importance to the diversity of life. DNA barcoding is not directed at species definition but to the problem of their identification. DeSalle points out that his approach is consistent with the methods of taxonomy and we would point out that it is also consistent with the biological reality of species and with their existence, independent of other species. Notwithstanding DeSalle’s comments, a distance-based approach to DNA barcoding appears generally successful. Specifically, the Kimura 2 parameter model of nucleotide substitution, when applied to the measurement of intraand interspecific variation in mitochondrial cytochrome c oxidase I (COI) gene sequences, has been widely used. The COI gene (58–705 from the 50 end) works well as an identifier of a large number of animal species. It is hard to gainsay the evidence ofmore than 300,000 successful identifications from over 30,000 formally described species, using the distancebased approach to the analysis of DNA barcodes. Nonetheless, if, as Desalle remarks, a character-based approach can easily be applied to DNA barcoding, it could have potential advantages and should certainly be explored. In an earlier paper, DeSalle et al. successfully applied this approach using various DNA sequences from a number of taxa. Similarly, we have compared COI barcode sequences from 11 species of the extinct New Zealand moa, which we had previously investigated using distance-based analyses of DNA barcodes. In this case, we used a character-based or diagnostic approach to identify any unique nucleotides at specific sites within the COI region. These would then enable species identification. Results showed that unique nucleotides within the barcode region of moa species correctly identified 10 of the 11 putative species (Fig. 1). However, all species can be identified using a combination of the COI characters from the dataset available. By comparison, a K2P distance analysis of the same data also correctly identified all 11 species. Hence, in this case, as in many others, both character and distance-based approaches to the analysis of DNA-barcoding data are successful. However, it is not difficult to imagine a situation inwhich some species can be identified basedonone or a small number of nucleotide characters. In this situation, it is unlikely that a distance-based approach would be successful. Thus, diagnostic or character-based approaches may generally be more successful than distance based measures. At the more general level, DeSalle also suggested that taxonomy should be regarded as species discovery, while DNA barcoding should be about species identification. This distinction between these two concepts is useful and DeSalle is correct that we should be mindful of blurring the distinction between them. However, just as taxonomymust be about both species discovery and identification, so too DNA barcoding can contribute to both. If it becomes possible to rapidly identify known species using DNA barcoding, unknown species can then be more easily identified. We also agree with DeSalle on the importanceof thedistinction betweenofDNA taxonomy, and species discovery and identification. The former represents the concept that information in DNA sequences is sufficient to identify and discover species. However, few authors have proposed DNA taxonomy as an alternative to existing approaches and Waugh did not either. No authors that we know of have suggested that DNA barcoding is without merit. Some authors have criticized the costs which, they argue, drain resources from other areas of biodiversity sciencewhilemanyothers suchasDeSalle have argued that DNA barcoding will not and should not replace taxonomy per se. DeSalle’s central point is about the analysis of DNA-barcoding data and about the importance of