Using DNA barcoding to identify the early life history stages of demersal coastal fishes in shallow nearshore and estuarine benthic habitats of Algoa Bay

Abstract

The accurate identification of early life history stages of fishes, including larval and transformation stages to species level, is critical in spatial and temporal studies of coastal fish assemblages. This enables a better understanding of species-specific settlement patterns, nursery habitat use, and ontogenetic habitat shifts during fish development. In this study determining the relative roles of two permanently open estuaries (the Swartkops and Sundays estuaries) and adjacent nearshore marine areas of Algoa Bay, South Africa, as settlement and nursery habitats for demersal fishes, DNA barcoding was used to identify species that were morphologically similar and difficult to distinguish in the field, particularly during the postflexion and transformation stages. One hundred specimens were collected for DNA barcoding. Measurements and photographs of large individuals were taken in the field, while a dissecting microscope was used to take photographs and measurements of smaller individuals at the larval and transformation stages. Most of the specimens were at transformation stage (n = 31), followed by postflexion stage (n = 28) and young-of-the-year juveniles (n = 27). Eighty-six specimens were positively identified to species level using cytochrome c oxidase subunit I (COI) mitochondrial gene sequences. While traditional fish identification using morphology led to misidentification of early life stages of demersal marine fish, particularly the cryptic species, DNA barcoding used in this study positively and successfully identified these fish to species level. Moreover, detailed images of the morphology and pigmentation patterns of several larval-and transformation-stage demersal marine fish species, which were previously unavailable, have now been recorded.