Ichthyoplankton metabarcoding: an efficient tool for early detection of invasive species establishment

In this study, we used DNA metabarcoding of bulk samples of early life-stage fishes to analyze species composition and monitor invasive fishes in four major rivers in southern Ontario, Canada. Samples were collected using two different gear types, and we analyzed each sample by amplifying and sequencing two different barcode fragments, COI and 12S, allowing comparison of how differences in methodology affect our results. We compared invasive species detections, species richness, and community composition among the four rivers sampled. We also evaluate invasive species detections and species richness in relation to the number of individuals sequenced, gear type, primer set, depth of sequencing, and reference database completeness. Based on the results of this study, we evaluated the most effective methods for detecting invasive species early in establishment using DNA metabarcoding.