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Benefits and challenges to using DNA-based identification methods: An example study of larval fish from nearshore areas of Lake Superior
Citation:
Meredith, C., J. Hoffman, A. Trebitz, Greg Peterson, J. Lietz, C. Hatzenbuhler, E. Pilgrim, S. Okum, AND J. Martinson. Benefits and challenges to using DNA-based identification methods: An example study of larval fish from nearshore areas of Lake Superior. Minnesota Society of the American Fisheries Society, Duluth, MN, February 01 - 03, 2016.
Impact/Purpose:
not applicable
Description:
DNA-based identification methods could increase the ability of aquatic resource managers to track patterns of invasive species, especially for taxa that are difficult to identify morphologically. Nonetheless, use of DNA-based identification methods in aquatic surveys is still uncommon and presents many challenges. In 2012 and 2013, we used a combination of morphological and DNA-based methods (metabarcoding) to identify larval fish collected in the St. Louis River Estuary and other nearshore areas of Lake Superior. We generally found close agreement between species composition using either method. DNA-based identification needed only very low levels of biomass to detect presence of a species, revealed some species not identifiable using morphology (including eggs of non-native species), and also revealed several errors in morphological identification. One of these errors resulted in a non-native species being much more prevalent than suggested by morphology alone.Despite these positive aspects, DNA metabarcoding had some problems, including returning sequence “hits” for several species whose actual presence was biologically implausible based on their distributions. The DNA method also demonstrated substantial inter-species variability and dependency of results on laboratory processing methods. We use our data to illustrate approaches to contrasting morphology-based and DNA-based approaches to taxonomy, especially with respect to detection sensitivity and potential errors. This work represents an advancement in our efforts to evaluate how DNA-based taxonomy can benefit aquatic inventories and early-detection efforts, especially in conjunction with morphological data.