The Promise of DNA Barcoding for Taxonomy

DNA barcoding is a novel system designed to provide rapid, accurate, and automatable species identifications by using short, standardized gene regions as internal species tags. As a consequence, it will make the Linnaean taxonomic system more accessible, with benefits to ecologists, conservationists, and the diversity of agencies charged with the control of pests, invasive species, and food safety. More broadly, DNA barcoding allows a day to be envisioned when every curious mind, from professional biologists to schoolchildren, will have easy access to the names and biological attributes of any species on the planet. In addition to assigning specimens to known species, DNA barcoding will accelerate the pace of species discovery by allowing taxonomists to rapidly sort specimens and by highlighting divergent taxa that may represent new species. By augmenting their capabilities in these ways, DNA barcoding offers taxonomists the opportunity to greatly expand, and eventually complete, a global inventory of life's diversity. Despite the potential benefits of DNA barcoding to both the practitioners and users of taxonomy, it has been controversial in some scientific circles (Wheeler, 2004; Will and Rubinoff, 2004; Ebach and Holdredge, 2005; Will et al., 2005). A few have even characterized DNA barcoding as being “anti-taxonomy,” arguing that its implementation will signal the death of a system 250 years in the making. We feel that this opposition stems from misconceptions about the DNA barcoding effort. As such, we welcome this opportunity to clarify both the rationale and potential impacts of DNA barcoding. In responding to this set of questions, we emphasize the multiple positive impacts of this approach for taxonomy and biodiversity science. This question ignores an inescapable reality; there is no prospect of a single $2 billion infusion of support for any biodiversity research program. Such a level of investment may ultimately be achieved—but, if so, it will reflect a staged and geographically dispersed process of positive funding decisions that will depend heavily on both scientific progress and societal demand for species-level identifications. The small amount of funding so far directed to DNA barcoding has yielded a rich harvest of scientific insights. This fact has led new organizations to provide the support needed to explore the scalability of these results across the animal kingdom. The early and positive results from this second wave of investigations have now motivated larger research groups to coalesce. In fact, the first alliances with a global reach have been assembled to lead the development of barcode sequence libraries for all birds and fishes. Segments of much more species-rich groups, such as plants and lepidopterans, are in the earlier stages of this process (www.barcoding.si.edu). These research groups may, in the longer term, form the nuclear units needed for the barcode initiative to move into the “big science” domain where success depends upon the coupling of a clearly enunciated, socially significant research agenda with strong international research alliances. It is also important to note that the quest for large-scale support for DNA barcoding is not being carried out at the expense of taxonomic funding. Indeed, it is clear that any successful campaign to generate this support will result in a substantial infusion of funding for institutions and individuals engaged in taxonomic research. Overall, the costs associated with DNA sequencing will represent a small component of DNA barcoding efforts; the majority of funding will be employed for global collection efforts, for the curation of resultant specimens, and for developing online databases containing detailed information about them. Moreover, it bears pointing out that the funding already acquired has come from large foundations and government agencies and programs with no tradition of supporting taxonomic research, and that in some cases DNA barcoding proposals have competed directly with medical and comparative genomics projects rather than any related to taxonomic research. Viewed from this perspective, any large-scale DNA barcoding effort will represent a substantial boon, both financially and scientifically, to biodiversity and taxonomic research. It will certainly leave a lasting legacy in the form of a comprehensive, widely accessible system for the identification of species. In our view the decline of alpha taxonomy is not a consequence of the growing use of molecular methods, as has sometimes been suggested (Wheeler, 2004). In fact, we expect DNA barcoding to aid the resurgence of taxonomy. DNA barcoding programs will certainly direct new funding into the collection and cataloguing of specimens. They will, as well, aid taxonomic investigations by helping to reveal cryptic species (Hebert et al., 2004a, 2004b), by connecting sexes and life stages (Beskansky et al., 2003), and by clarifying problems of synonymy that now consume much taxonomic effort (Alroy, 2002). The novelty and scientific promise of DNA barcoding will additionally draw public interest to taxonomic and biodiversity issues, encouraging young researchers to enter the discipline and both academic departments and biomanagement agencies to hire them. We are confident that DNA barcoding will play an increasingly important role as a taxonomic screening tool because of its ability to rapidly reveal the genetic discontinuities that ordinarily separate distinct species (e.g., Janzen et al., 2005; Smith et al., 2005). Its application in this fashion will allow an inversion of standard taxonomic approaches that operate in an a priori fashion—seeking the morphological discontinuities that signal reproductive isolation among unsorted assemblages of organisms. By contrast, DNA barcoding allows a more efficient a posteriori approach where predefined, genetically divergent groups are examined for trait variation. In this sense, DNA barcoding will clearly be a powerful enabler of alpha taxonomy. Overlap in the variation of single characters is not problematic for any taxonomic system, be it morphological or molecular, so long as multiple characters are employed for taxon diagnosis. One common misunderstanding of DNA barcoding is that it is based on a single character, namely “one DNA sequence.” In fact, the 648-bp cytochrome c oxidase subunit I (cox1 or COI) gene region used as the DNA barcode standard for members of the animal kingdom represents a complex composite character involving hundreds of independently varying components. Some of these component characters are invariant and therefore not all 648 bp are informative within a given taxonomic assemblage, but most are variable. For example, we have found variation at 512 of the 648 sites in a large set of lepidopteran barcodes (9715 sequences from 2215 species and 1047 genera). This means that even within a single insect order, DNA barcodes integrate the patterning of similarities and differences among hundreds of characters. In a certain sense, it is like the patterning generated by the scales on a moth's wing—each scale is of almost no significance, but the composite character of wing coloration pattern is highly informative. DNA barcoding using a single gene region does not assure complete taxonomic resolution, but it does promise proximity. Based on past results for varied animal groups, DNA barcoding will deliver species-level resolution in 95% to 97% of cases (Hebert et al., 2004b; Janzen et al., 2005; Ward et al., 2005). When it fails, it will narrow the options to a small number of congeneric taxa (which, in many cases, could be resolved fully with additional genetic or other data). This impressive performance reflects two important, and perhaps unexpected, observations: the rarity of mitochondrial sequence sharing among species and the dearth of deep barcode divergences within species. Constrained intraspecific variation in diverse animal groups is a key early finding of the DNA barcode effort; one that merits deeper scientific investigation. Certainly, cox1 shows far less variation within species than some early critics had projected would be the case (e.g., Mallet and Willmott, 2003), and this may reflect the impact of selective sweeps related to the coevolution of nuclear and mitochondrial genomes. Importantly, for the use of barcodes as species-level identifiers, barcode differences appear to accumulate quickly, making it possible to distinguish all but the youngest of sister species. We recognize both the general utility of genetic data in taxonomic studies and the strong concordance in taxonomic signals from different genes. However, we emphasize that there is no such thing as “informal DNA barcoding.” A DNA barcode is not just any DNA sequence—it is a rigorously standardized sequence of a minimum length and quality from an agreed-upon gene, deposited in a major sequence database, and attached to a voucher specimen whose origins and current status are recorded. In fact, it has already been established that only those cox1 sequences that meet these strict criteria will be designated as DNA barcodes by the National Center for Biotechnology Information's GenBank (NCBI, GenBank; www.ncbi.nlm.nih.gov/Genbank), the European Molecular Biology Laboratory (EMBL; www.embl.org), and the DNA Data Bank of Japan (DDBJ; www.ddbj.nig.ac.jp). There is an important distinction between “describing” and “delimiting” species, but a conflation of the two has created uneasiness about the use of DNA barcodes as the foundation of future taxonomic descriptions. We emphasize that DNA barcoding seeks merely to aid in delimiting species—to highlight genetically distinct groups exhibiting levels of sequence divergence suggestive of species status. By contrast, DNA barcodes—by themselves—are never sufficient to describe new species. At some stage, clearly divergent DNA barcodes, in combination with other information, will be used as the basis for providing a new Linnaean name (Smith et al., 2005) and, as with any taxonomic hypothesis, this would be subject to ongoing reevaluation. For example, in a recent survey of North American birds, the threshold for delineating probable new species was arbitrarily set at 10 × the average within-species variation of the entire barcode data set. This led to the revelation of four presumptive new species (Hebert et al., 2004b), but decisions regarding the formal recognition of these taxa are left, appropriately, to the ornithological community (notably, existing morphological and behavioral information supports these new hypotheses). The synergy between DNA barcoding and studies of morphological/ecological diversity is further illustrated by the case of the skipper butterfly, Astraptes fulgerator, in which a combined morphological, natural history and barcoding approach revealed a complex of 10 species in one small area of Costa Importantly, of these species a small barcode but a coupling of this information with on plants and the diversity of the complex (Hebert et al., We emphasize that DNA barcodes not to to known species and to aid the discovery of new Despite this fact, some have that DNA barcoding as a taxonomic approach because it does not species (e.g., Will and Rubinoff, 2004). 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We that species identifications are a for many and biodiversity as as for taxonomic research, and that DNA barcoding will therefore both a on taxonomists and a current with important benefits to both taxonomy and biodiversity science. In a taxonomists will their role in the and of about the character variation that species and this for level taxonomy. As their on new assemblages of life may be by using barcode results to an a posteriori approach to species will, of also to other molecular and morphological approaches to explore deeper taxonomic It has been suggested that sequencing is or for taxonomists to out (e.g., Mallet and Willmott, et al., However, taxonomists are no more to their sequencing than to their has already to the stage, with of of specimens being at in barcoding (e.g., at the of and the The direct on taxonomic the by providing small from specimens to be As the one expect the development of not that integrate all stages from DNA of the barcode sequence to an identification to the in the with we expect such to standard for both taxonomic research and for the community of organizations and individuals that access to species this certainly does not that barcoding will taxonomists into molecular We the by DNA barcoding will to the and of taxonomic has been using discontinuities in to species an approach that has generated a of taxonomic 250 DNA barcoding allows these to be using an DNA data there has been between species morphological approaches with based on barcodes, there are These cases be as will both taxonomic and for barcode and may lead to new regarding and of these benefits have been in early barcoding A major and rationale DNA barcoding in its for species in and programs (Smith et al., 2005). 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In past cases, such have The is that large-scale discovery at a pace and of that could never have been In this sense, many of the at DNA barcoding are to those given a regarding the DNA barcoding has already been successful in substantial funding from varied agencies and organizations that have not been of taxonomy, but this has not been by the DNA barcoding initiative the of a accessible inventory of life's diversity. It is only by the benefits to and by interest among the public that support for a global biodiversity initiative will be that does not that taxonomy is set to a for other as some have suggested (e.g., et al., 2004; Will and Rubinoff, 2004). A major of DNA barcoding is to the majority of access taxonomic information directly allowing professional taxonomists to on more such to inventory diversity morphological have much The of two taxonomic the past 250 years is an impressive that has a of biological but many DNA barcoding is to aid the inventory of life by species by current taxonomic and by making species identifications more These will not be at the expense of taxonomic or funding. DNA barcoding does not to studies in of a narrow and molecular identification and Rubinoff, it to alliances between molecular and morphological taxonomists (Hebert and 2005). It as well, to the Linnaean by which species are and DNA barcoding species names for and it is these names that are when barcoding is used for It is that the of biodiversity is 2002). It is not easy to this to the of as biodiversity is important and much public However, this area of research does from a of than the biodiversity community has a tradition of and DNA barcoding is no to has been as and as a 2004; Will et al., 2005). 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This performance into a barcode which examined more than species of generated success in their et al., 2005). across in of mitochondrial revealed success in species identification from insect groups with both the and of et al., 2005; Smith et al., 2005). in of the mitochondrial to impact the resolution of DNA as by success in groups, such as birds, with and such as with (Hebert et al., 2004b; and 2005). these past studies are of the general performance of barcodes across the animal a system will deliver taxonomic resolution in of when from a one only of the in as a for barcode data from a single species. that there are 10 animal species, the barcode for this kingdom could be by just of these The global which of about species, will only one of these for the of the will will all 10 have been with barcode the of any new barcode sequence will provide to the out of In fact, based on data for North American birds, the barcode sequence will provide resolution by to an species on the single in of In the cases, the barcode will sequences in two or In a barcode will the in species from any one of 10 species to a single species in most cases, and to a small of species in other A of a that would barcode data on species (e.g., all known One such would barcode for 10 species. In addition to providing a species such a system would as a to all other information on a given species by into other biological is now in to that that the DNA barcode for will by at the providing for some species. this will be far from a complete of species, it will allow DNA barcodes to as an identification tool for those taxonomic groups with barcode For example, as barcode for birds, and approaches this will provide access to the identification of these species of life or As this of species is by barcodes from other a global identification system for this kingdom of life will we that the of barcoding has now been for the animal there a to both and barcode for the other of The of barcode and of sequence are to these but the of gene regions and of their in progress early results on plants et al., 2005) and provide for from its success in known species, DNA barcoding will be a powerful aid in other taxonomic species have been even in groups such as North American birds (Hebert et al., 2004b), (Hebert et al., and et al., 2005). Its role in life stages (Beskansky et al., and et al., and in clarifying will also be of in many other taxonomic The of any major not just a strong scientific but a of societal DNA barcoding such by providing new access to identifications in varied to life are by the for an identification system, and we that this only be by DNA barcoding also Smith et al., 2005). The ability of barcodes to of life has from the resolution of cases of species in the et al., to the of food for example, screening animal for More the ability of DNA barcoding to deliver identifications and has the potential to with biological diversity 2004). DNA barcoding on a large it will generate important for the scientific DNA the barcode of specimens will be allowing future to of sequence diversity in other gene and the collection programs by DNA barcoding will the specimens for morphological The barcode initiative will also a system not just but also providing a to biological information for all species in the DNA barcoding will not the of it will generate its and of of both positive scientific results and its societal there is growing for a large-scale DNA barcoding at for 2003), and more have The most which was by the in more than researchers 2005). The barcode also has a the for the of by the in which was in More than organizations from many have already The first global barcode have been its to barcode all species of birds and all by to to major projects such as and barcode are to specimen and to The first of the of which in to barcode at animal species the We view these of growing synergy among the of the biodiversity community as to their history may view the DNA barcoding as one that not only access to taxonomic information, but also alliances among all those with in the and of prospect We and Janzen for to earlier of this We are also to the and and for their support of DNA barcoding research at the of

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