Eyeing DNA barcoding for species identification of fish larvae

Identification of fish larvae based on morphology is typically limited to higher taxonomic ranks (e.g., family or order) because fish larvae possess few morphological diagnostic characters for precise discrimination to species. When a large number of samples are presented at any one time, the use of morphology to identify such specimens can be laborious and time-consuming. Using a reverse workflow for specimen sorting and identification based on high-throughput DNA sequencing, thousands of fish larvae can be DNA barcoded and sorted into molecular operational taxonomic units (mOTUs) via a single sequencing run with the nanopore sequencing technology (e.g., MinION). This process reduces the time and financial costs of morphology-based sorting, and instead deploys experienced taxonomists for species taxonomic work where they are needed most. In this study, a total of 3,022 fish larval specimens from plankton tows across four sites in Singapore were collected, sorted and eye tissue from individual samples were used for DNA extraction and sequencing. We generated a total of 2,776 barcodes after filtering (89.93% barcoding success), identified 2,067 DNA barcodes (82.38% identification success) and uncovered 256 mOTUs. This approach expedites taxonomic identification and contributes to the expansion and enhancement of reference barcode databases. The accurate taxonomic identification of fish larvae results in more precise sampling to maximise species representation and leads to better understanding of fish connectivity.