The use of mitochondrial DNA for the identification of fish in the early stages of development from the eastern shores of Lake Huron, Ontario, Canada

Abstract

Ichthyoplankton specimens are notoriously difficult to identify using morphology. DNA barcoding and real-time PCR utilize DNA to identify specimens, rather than morphology. However, no study has yet compared morphological identifications with DNA-based identification for Canadian freshwater fishes. Here, we both compare DNA barcoding with morphological identification of ichthyoplankton and design a multiplex TaqMan real-time PCR assay for the rapid and cost-effective identification of 3 important species in Lake Huron, lake whitefish (Coregonus clupeaformis), deepwater sculpin (Myoxocephalus thompsonii) and round whitefish (Prosopium cylindraceum). Unlike morphological identification, DNA barcoding was able to resolve specimens from the Catostomus genus and Cyprinidae family to the species. Contrarily, DNA barcoding was unable to differentiate some members of the Coregonus genus, whereas morphology identified these specimens to the species. Real-time PCR was able to accurately identify the target species 100% of the time and was the most cost-effective method.