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Comparison of larval fish detections using morphology-based taxonomy versus high-throughput sequencing for invasive species early detection
Citation:
Hoffman, J., C. Meredith, E. Pilgrim, A. Trebitz, C. Hatzenbuhler, J. Kelly, G. Peterson, J. Lietz, S. Okum, AND J. Martinson. Comparison of larval fish detections using morphology-based taxonomy versus high-throughput sequencing for invasive species early detection. CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES. NRC Research Press, Ottawa, Canada, 78(6):752-764, (2021). https://doi.org/10.1139/cjfas-2020-0224
Impact/Purpose:
DNA-based taxonomic identification of species based on high-throughput sequencing (HTS) has the potential to rapidly detect aquatic invasive species with fewer errors than morphology-based taxonomy. However, few studies have been conducted to estimate errors associated with HTS based taxonomy. We conducted a benchmarking study to estimate false negative and false positive errors for species identifications by comparing side-by-side taxonomic data sets based on morphology or HTS taxonomy. We found that both approaches yield false negative and false positives, but that HTS is generally much more accurate than morphology-based taxonomy. Nevertheless, we conclude that conduct benchmarking studies in tandem is recommended to account for errors associated with either approach.
Description:
When first introduced, invasive species typically evade detection; DNA barcoding coupled with high-throughput sequencing (HTS) may be more sensitive and accurate than morphology-based taxonomy and thereby improve invasive (or rare) species detection. We quantified the relative error of species detection between morphology-based and HTS-based taxonomic identification of ichthyoplankton collections from the Port of Duluth, Minnesota, an aquatic non-native species introduction “hot-spot” in the Laurentian Great Lakes. We found HTS-based taxonomy identified 28 species and morphology-based taxonomy identified 30 species, of which 27 were common to both. Among samples, 76% of family-level taxonomic assignments agreed; however, only 42% of species assignments agreed. Most errors were attributed to morphology-based taxonomy, whereas HTS-based taxonomy error was low. For this study system, for most non-native fishes, the detection probability by randomized survey for larvae was similar to that by a survey that is optimized for non-native species early detection of juveniles and adults. We conclude that classifying taxonomic errors by comparing HTS results against morphology-based taxonomy is an important step toward incorporating HTS-based taxonomy into biodiversity surveys.
URLs/Downloads:
DOI: Comparison of larval fish detections using morphology-based taxonomy versus high-throughput sequencing for invasive species early detection
https://cdnsciencepub.com/doi/10.1139/cjfas-2020-0224