Original Publication: 01/02/2012
Edited for grammar/syntax: 07/24/2019
DNA barcoding is an exciting new genetic method for classifying living animals at the species level. Here, in an article published in the 2011 volume 30(1) edition of the Journal of the North American Benthological Society, the efficacy of DNA barcoding and its potential benefits for routine bioassessment were analyzed. The authors hypothesized that genetic methods, specifically DNA barcoding using the cytochrome oxidase subunit 1 (COI) gene, could improve over traditional, morphologically based taxonomic methods and shed light on previously unknown levels of biodiversity in aquatic macroinvertebrate communities.
In order to test this hypothesis, the two sites along White Clay Creek near Avondale, PA were chosen for their known differences in water quality. One site (Site 11) represents a creek unaffected by human development, whereas the other (Site 12) has suffered degradation due to several different possible sources of human contamination (a golf course, mushroom-growing operation, an orchard, and other farming establishments). All of these rural human-developments pose the possibility of adding many different types of contamination into nearby water sources. At each site, specimens were identified to four different identification levels; amateur, expert genus, expert species, and barcode. These different methods were meant to represent the differences in biodiversity assessments between amateur (hobbyist, college undergrad), expert (college graduate/professional), and barcode “species” determined through a type of phylogenetic analysis.
The authors found that DNA barcoding increased overall taxonomic richness from 26 morpho-species to 150 barcode species at the amateur level (475%) and from 62 to 150 (70%) at the expert species level. They also found that there were more differences between sites (pristine vs. degraded) using the barcode species method than using any of the other morphological methods.
This suggests that there is a large amount of cryptic biodiversity present in macroinvertebrate communities that is missed using traditional taxonomic methods, and that routine bioassessment programs could benefit from using DNA barcoding instead of traditional taxonomic methods. That isn’t to say, however, that traditional taxonomic methods (morphology) are not still needed, because in order for DNA barcoding to work in a routine setting, there must exist a library of already identified barcode species of which new sequences can be easily matched too.
One area that an improvement on this type of study would be that, since barcode species have now been identified, the pollution-tolerance values for those barcode species must be determined. Another important area of future work would be to understand the midge (Chironomidae) diversity better since it is traditionally only taken to the family/tribe level.
One drawback to DNA barcoding, in general, is determining which DNA sequences are legitimate species and which ones may be pseudogenes (closely related genes that are no longer functional) or contamination (unwanted DNA that has been amplified from the environment). However, overall, it would seem that the benefits of DNA barcoding outweigh the potential pitfalls and drawbacks.
Literature Cited Sweeney, B.W., Battle, J.M., Jackson, J.K. and Dapkey, T., 2011. Can DNA barcodes of stream macroinvertebrates improve descriptions of community structure and water quality?. Journal of the North American Benthological Society, 30(1), pp.195-216. doi: https://doi.org/10.1899/10-016.1