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Incorporation of DNA barcoding into a large-scale biomonitoring program: opportunities and pitfalls
Citation:
PILGRIM, E., S. A. JACKSON, S. Swenson, I. Turcsanyi, E. Friedman, L. Weigt, AND M. BAGLEY. Incorporation of DNA barcoding into a large-scale biomonitoring program: opportunities and pitfalls. JOURNAL OF THE NORTH AMERICAN BENTHOLOGICAL SOCIETY. North American Benthological Society, Lawrence, KS, 30(1):217-231, (2011).
Impact/Purpose:
A completely developed indicator of genetic diversity will bring significant new data to the assessment of the biological integrity of aquatic resources and the sustainability of fish, invertebrate, and plant communities. These new data will be used to help characterize (1) appropriate ecological units (including cryptic species and biological populations) for assessment of fish and macroinvertebrate communities; (2) the inherent vulnerability of aquatic species to further exposure to stressors; (3) the relationship between genetic diversity and environmental condition; (4) temporal trends in the condition of fish and invertebrate populations; and (5) linkages between landscape-level stressors and population-level outcomes for aquatic organisms. By identifying the spatial scale at which individuals migrate and breed, measures of genetic diversity define biological populations, which are the most meaningful units for assessing species and communities. A significant loss of genetic diversity is detrimental to populations and affects their sustainability into the future. In the short term, reduced genetic diversity can contribute to inbreeding depression, lowering population fitness. In the long term, it reduces the population’s resilience because the population's genetic pool of potential responses to stress is restricted. The population’s lack of selectively propitious genes may lead to further population declines and eventual extirpation when faced with novel stressors or changes in stressor intensity. In addition, since past and present environments have shaped current levels of genetic diversity, molecular genetic markers are natural indicators of cumulative population exposure. Habitat degradation (chemical, physical, or biological), hybridization with introduced taxa, and habitat fragmentation have predictable effects on genetic diversity. Coupling of these molecular genetic data with quantitative environmental data and landscape data gathered through EMAP and other initiatives will allow powerful inferences to ecological condition and population responses to environmental stressors.
Description:
Taxonomic identification of benthic macroinvertebrates is critical to protocols used to assess the biological integrity of aquatic ecosystems. The time, expense, and inherent error rate of species-level morphological identifications has necessitated use of genus- or family-level identifications in most large, statewide bioassessment programs. Use of coarse-scale taxonomy can obscure signal about biological condition, particularly if the range of species tolerances is large within genera or families. We hypothesized that integration of deoxyribonucleic acid (DNA) barcodes (partial cytochrome c oxidase subunit I sequences) into bioassessment protocols would provide greater discriminatory ability than genus-level identifications and that this increased specificity could lead to more sensitive assessments of water quality and habitat. Analysis of DNA barcodes from larval specimens of Ephemeroptra, Plecoptera, and Trichoptera (EPT) taxa collected as part of Maryland's Biological Stream Survey (MBSS) revealed ~2 to 3x as many DNA-barcode groups or molecular operational taxonomic units (mOTUs) as morphologically identified genera. As expected, geographic distributions for several mOTUs were tighter than for the parent genus, but few mOTUs showed closer associations with water-quality variables or physical-habitat features than did the genus in which they belonged. The need for improved protocols for the consistent generation of DNA barcodes is discussed.