A genetic technique to identify the diet of cownose rays, Rhinoptera bonasus: analysis of shellfish prey items from North Carolina and Virginia


Cownose rays are implicated in the consumption of commercially important shellfish on the U.S. East Coast. We tested this assumption by developing a molecular technique for species identification from cownose ray gut contents. Digestive tracts sampled from 33 rays in Pamlico Sound, NC and Chesapeake Bay, VA contained pieces of partially-digested tissue, well-digested tissue, fluid, and minute shell fragments which made visual identification to the species level nearly impossible. We sequenced the cytochrome oxidase subunit I (COI) for seven locally acquired bivalve species, chosen for their commercial and ecological importance in NC and VA. Sequences were used to design species-specific primers for each bivalve species to amplify polymerase chain reaction (PCR) products. We designed primers such that PCR products were sufficiently different in size to be distinguishable from one another when resolved on an agarose gel, and multiplexing of several species in one reaction was possible. Digestive tract sample testing revealed that cownose rays in Chesapeake Bay ate stout tagelus and soft shell clams. There was no evidence of the rays in the study consuming commercially important oysters, hard clams, and bay scallops. Further sampling over an extended period of time and additional locations is required to confirm these results. Our diagnostic tests could easily be expanded to elucidate the impact of cownose ray predation on prey populations.

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  1. 1.

    Baltic macoma primers were found to have amplified digestive tract samples that also tested positive with stout tagelus clam primers. The cross-amplification rate of the Baltic macoma primers with stout tagelus positives was 86 %, making those positives uncertain, and require further testing. To test for species identification of those uncertain samples, we sequenced a subsample (n = 8) of the uncertains and all samples were a match for stout tagelus sequence. BLAST searches of the Baltic macoma primers revealed significant matching to stout tagelus DNA sequences, so this cross-amplification is not unexpected.


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The authors wish to acknowledge the Institute for Coastal Science and Policy and the Department of Biology at East Carolina University for logistics and financial support. Animal collection and handling procedures were approved by the East Carolina University Animal Use and Care Committee, Animal Use Protocol #D268. The American Elasmobranch Society, Save Our Seas Foundation, and the ECU-American Fisheries Society subunit contributed symposium, publication, travel, and student funding support. We are grateful for the help of Robert Fisher, Joseph Smith, R. Dean Grubbs, John Morrissey, Denise Mayer, Captain George Beckwith, Jason Rock, NCDMF, Lena Keller, Shona Paterson, and for the generosity of numerous friends and colleagues who helped with shellfish collection and cownose ray sampling. The authors wish to thank Matthew Ajemian and Julie A. Neer, symposium organizers and special issue editors, for their contributions and guidance. The views expressed in this article are those of the authors and do not necessarily represent the views or policies of the U.S. Environmental Agency.

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Correspondence to Lyndell M. Bade.

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Bade, L.M., Balakrishnan, C.N., Pilgrim, E.M. et al. A genetic technique to identify the diet of cownose rays, Rhinoptera bonasus: analysis of shellfish prey items from North Carolina and Virginia. Environ Biol Fish 97, 999–1012 (2014). https://doi.org/10.1007/s10641-014-0290-3

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  • Elasmobranch
  • Diet
  • Feeding ecology
  • Molecular techniques
  • COI