A comparison of morphological and DNA metabarcoding analysis of diets in exploited marine fishes

Ecosystem-based management (EBM) is a cutting-edge framework for managing marine resources. EBM strategies can be evaluated in silico with ecosystem models that represent functional components of ecosystems, including... [ view full abstract ]

Ecosystem-based management (EBM) is a cutting-edge framework for managing marine resources. EBM strategies can be evaluated in silico with ecosystem models that represent functional components of ecosystems, including anthropogenic factors. Foodwebs are at the core of ecosystem models, but because dietary data can be difficult to obtain, they are often only coarsely characterised in models. High-throughput DNA sequencing (HTS) of dietary items is a relatively rapid way to more accurately parameterise foodwebs at enhanced taxonomic resolution, and in doing so, to potentially optimise functioning of ecosystem models and best-practice EBM. Here, we evaluate the relative merits of conventional microscopic analysis and HTS analysis of the diets of eight fish species harvested in Australia’s most intensively fished fishery; the south east trawl fishery. We compare the taxonomic resolution and phylogenetic breadth of diets yielded by these methods, and include a comparison of three alternative DNA barcoding markers (mtDNA COX1, mtDNA 16S, nDNA 18S). Using paired individual gut samples (n = 151), we demonstrate that HTS typically identified similar taxon richness but with significantly higher taxonomic resolution than microscopic assessment. However, DNA barcode selection had a large effect on both the resolution and phylogenetic breadth of estimated diets. Both COX1 and 16S markers provided significantly higher taxonomic resolution than morphological analysis, but the resolution varied between taxonomic groups primarily due to current availabilities of reference data. However, neither COX1 nor 16S recovered the full dietary spectrum revealed by the 18S barcode. HTS also revealed the presence of dietary items not previously recorded for target species, as well as a diverse assemblage of parasites. We conclude that the enhanced breadth and depth of dietary analysis yielded by HTS has the potential to improve and optimise both structure and function of ecosystem models and consequently, best-practice ecosystem based management.