ARS | Publication request: DNA Barcoding Will Frequently Fail in Complicated Groups: An Example in Wild Potatoes

Submitted to: American Journal of Botany
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 30, 2009
Publication Date: June 1, 2009
Citation: Spooner, D.M. 2009. DNA Barcoding Will Frequently Fail in Complicated Groups: An Example in Wild Potatoes. American Journal of Botany. 96:1177-1189.

Interpretive Summary: Taxonomy is the theory and practice of describing, naming, and classifying organisms. Taxonomists help not only to define what a species is, but to identify them for diverse user groups. These include genebank managers who need stable identifications for their collection, to plant breeders seeking material for their breeding programs, to biodiversity scientists, to officers at ports of entry needing identifications of potential plant and animal pathogens or bioterrorism agents. However, there is a greater need to identify organisms than competent taxonomists available to perform this service, providing what has been labeled the taxonomic impediment. Recently, an idea has been advanced to use short sections of DNA from the same region of major groups or organisms (as some regions from plants and others for animals) to serve as a DNA barcoding region, similar to the use of barcodes to identify grocery items. This study shows that DNA barcoding fails in wild relatives of wild potatoes. It argues that it is bound to fail in many other plant groups, surveys the many reasons why this is likely to be so, and argues that DNA barcoding is a very poor investment of funds to solve the taxonomic impediment.

Technical Abstract: DNA barcoding has been proposed as a rapid and practical molecular tool to identify species using short orthologous DNA sequences from one or a small number of universal regions. It seeks to overcome the “taxonomic impediment” of a greater need to identify organisms than the availability of competent taxonomists to perform them. A number of barcoding regions have been proposed for plants, to include the internal non-transcribed spacer of nuclear ribosomal DNA (ITS), the plastid trnH-psbA intergenic spacer, and other plastid regions, with the first two being the most variable.This study tests the utility of DNA barcoding with these two most variable regions, in a complex plant group (Solanum sect. Petota; wild potatoes), that like many other groups is composed of morphologically similar species, has different ploidy levels, shows introgressive hybridization, and contains stabilized hybrid species and allopolyploids. Barcoding fails in sect. Petota due to a combination of lack of sufficient polymorphism and intraspecific variation. DNA barcoding in plants has been poorly tested with replicate samples, overlooks many common complicating biological phenomena, is a retroactive procedure that relies on well defined species to function, and overlooks considerable and unresolved problems in defining species. The taxonomic impediment will be much more effectively aided by investing into a comprehensive program of taxonomic research and training, not the generation of sequences that in many cases are inappropriate to resolve or address complex taxonomic groups.