Secondary predation constrains DNA-based diet reconstruction in two threatened shark species

Mark De Bruyn,Matt K Broadhurst,Matteo Barbato,Joseph D Dibattista

doi:10.1038/s41598-021-96856-w

Abstract

Increasing fishing effort, including bycatch and discard practices, are impacting marine biodiversity, particularly among slow-to-reproduce taxa such as elasmobranchs, and specifically sharks. While some fisheries involving sharks are sustainably managed, collateral mortalities continue, contributing towards > 35% of species being threatened with extinction. To effectively manage shark stocks, life-history information, including resource use and feeding ecologies is pivotal, especially among those species with wide-ranging distributions. Two cosmopolitan sharks bycaught off eastern Australia are the common blacktip shark (Carcharhinus limbatus; globally classified as Near Threatened) and great hammerhead (Sphyrna mokarran; Critically Endangered). We opportunistically sampled the digestive tracts of these two species (and also any whole prey; termed the ‘Russian-doll’ approach), caught in bather-protection gillnets off northern New South Wales, to investigate the capacity for DNA metabarcoding to simultaneously determine predator and prey regional feeding ecologies. While sample sizes were small, S. mokkaran fed predominantly on stingrays and skates (Myliobatiformes and Rajiformes), but also teleosts, while C. limbatus mostly consumed teleosts. Metabarcoding assays showed extensive intermixing of taxa from the digestive tracts of predators and their whole prey, likely via the predator’s stomach chyme, negating the opportunity to distinguish between primary and secondary predation. This Russian-doll effect requires further investigation in DNA metabarcoding studies focussing on dietary preferences and implies that any outcomes will need to be interpreted concomitant with traditional visual approaches.

Highlights

Global biodiversity is under threat, with accelerating losses of species and increasing concern about ecosystem changes[1]
Carcharhinidae and/or Chondrichthyes reads were ubiquitous across all three genetic assays, including the Urolophus sp. and A. rostrata rays removed from the S. mokarran stomachs, and most likely represent the host predator’s DNA
The data collected here represent the first efforts at metabarcoding the stomach contents of S. mokarran and C. limbatus off eastern Australia

Summary

Introduction

Global biodiversity is under threat, with accelerating losses of species and increasing concern about ecosystem changes[1]. Among the total known species of ‘ground sharks’ or the Carcharhiniformes (n = 287), 36% are listed as threatened with extinction by the International Union for Conservation of Nature (IUCN), and a further 18% are classified as ‘Data Deficient’[4] To mitigate this extinction threat, there is a critical need for more information on the ecology of sharks, those that are threatened or endangered. Shark feeding ecology has been quantified mainly by visually identifying stomach contents, biochemical techniques (e.g. stable isotope, lipid and amino acid signatures) or telemetry (e.g. satellite and acoustic tagging) via habitat association[23] Each of these methods has inherent strengths and weaknesses (reviewed in[24,25]). The DNA metabarcoding of digestive-tract contents is commonplace in studies on terrestrial taxa (reviewed in26,29,30) and recently has been applied to marine taxa, mostly teleosts and elasmobranchs (e.g.31–37)

Methods

Results

Conclusion