DNA barcoding for the identification of soft remains of prey in the stomach contents of grey seals (Halichoerus grypus) and harbour porpoises (Phocoena phocoena)

Abstract

In recent decades, grey seals (Halichoerus grypus) and harbour porpoises (Phocoena phocoena) have become more numerous along the coasts of Brittany in northwestern France. Their interactions with fisheries are of increasing concern and diet analyses are becoming a requirement to determine the actual overlap between species targeted by fisheries and marine mammal prey. However, as only a few stranded or by-caught animals are available to investigate the diet of these top predators, it is necessary to optimize the results obtained from each animal sampled by increasing the rate of prey species determination in stomach contents. We used a combined analysis of stomach contents, based on prey hard remains and, in parallel, a simple DNA barcoding approach to identify the soft remains. Seven grey seal stomachs and three harbour porpoise stomachs have been analysed. The combined approach, making use of visual observation as well as DNA analysis, increased the identification of prey items by around 32% for grey seal and by 21% for harbour porpoise. Fish species identified include Mediterranean and Atlantic horse mackerel (Trachurus mediterraneus and Trachurus trachurus), Atlantic mackerel (Scomber scombrus), ballan and cuckoo wrasse (Labrus bergylta and Labrus mixtus), European seabass (Dicentrarchus labrax), Atlantic pollock (Pollachius pollachius), European conger (Conger conger) and garfish (Belone belone). One fish species (L. bergylta) was identified only with DNA methods. An area-specific diet for the grey seal in the Iroise Sea, proposed by others in a previous study, seems to be supported.

Key words:

• Diet
• DNA barcoding
• Halichoerus grypus
• marine mammals
• Phocoena phocoena

Acknowledgements

We are grateful to all members of the French Stranding Network (coordinated by PELAGIS, UMS 3462, CNRS-Université de La Rochelle) for their help in collecting data and samples. Thanks are extended to all the members of the Océanopolis marine mammal team. We are also indebted to Sandrine Quemener who participated in laboratory experiments, and to Sandra Fuchs who drew the map for Figure 1. Special thanks go to Chantal Hily-Maze. This manuscript benefited from useful comments during the reviewing and editing process.

Supplementary material

Supplementary material for this article is available via the Supplemental tab of the article's online page at http://dx.doi.org/10.1080/17451000.2014.943240

Editorial responsibility: Gavin Gouws

Additional information

Funding

Eric Alfonsi was supported by a ‘Cifre’ grant of the ANRT (Association Nationale de la Recherche et de la Technologie, http://www.anrt.asso.fr). This work is part of a collaboration with the ‘Parc Naturel Marin d'Iroise’, and was supported by the Conseil Régional de Bretagne in the frame of the project ‘INPECMAM’.