Comparison of larval fish detections using morphology-based taxonomy versus high-throughput sequencing for invasive species early detection

Abstract

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.