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DNA metabarcoding of fish larvae for detection of non-native fishes
Hoffman, J., C. Meredith, A. Trebitz, Greg Peterson, J. Lietz, C. Hatzenbuhler, E. Pilgrim, S. Okum, AND J. Martinson. DNA metabarcoding of fish larvae for detection of non-native fishes. Ichthyologists and Herpetologists Meeting, Austin, TX, July 12 - 16, 2017.
Impact Statement: Under the Great Lakes Water Quality Agreement, Annex 6 calls for the establishment of a bi-national invasive species early detection program. To do so, state and federal agencies need surveillance designs and sensitive methods for detecting introduced species before they have the opportunity to spread widely. Here, we demonstrate that DNA metabarcoding is more accurate and more sensitive than traditional morphology-based taxonomy for non-native species detection.
Our objective was to evaluate the use of fish larvae for early detection of non-native fishes, comparing traditional and molecular taxonomy approaches to investigate potential efficiencies. Fish larvae present an interesting opportunity for non-native fish early detection because they are abundant and can be readily transported in ballast water. Our approach was to intensively sample a Great Lakes non-native species introduction hotspot and then compare the success and efficiency of fish larvae taxonomic characterization between traditional taxonomy and community-level DNA metabarcoding. We intensively sampled the Duluth-Superior harbor, the Great Lakes largest freshwater port, using a spatially balanced design to equally allocate catch effort across the harbor. To maximize the number of species encountered, we sampled at different time periods throughout the spring spawning period and used multiple types of sampling equipment. Overall, there was strong agreement between the two approaches at the port- and taxonomic family-level, but less so at the sample level. The DNA-based identification required low levels of biomass to detect a species presence, detected taxa not identifiable using morphology (including eggs and non-native species), and revealed limitations in morphological identification. However, DNA-based identification could not fully resolve all the species present and did result in some potential false positives. We conclude with a few notable reservations that DNA metabarcoding presents an important advance for measuring the species richness of larval fish assemblages.