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.
This is a preview of subscription content, access via your institution.
Buy single article
Instant access to the full article PDF.
Tax calculation will be finalised during checkout.
Subscribe to journal
Immediate online access to all issues from 2019. Subscription will auto renew annually.
Tax calculation will be finalised during checkout.
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.
Ajemian M, Powers S (2011) Habitat-specific feeding by cownose rays (Rhinoptera bonasus) of the northern Gulf of Mexico. Environ Biol Fish 95(1):79–97
Bade LM (2013) Use of genetic techniques to identify the diet of cownose rays, Rhinoptera bonasus, in North Carolina and Virginia: an analysis of shellfish prey items. East Carolina University, Greenville
Barnes RD (1974) Invertebrate Zoology 3. Ed. WB Saunders Co, Philadelphia, Pennsylvania
Barnett A, Redd KS, Frusher SD, Stevens JD, Semmens JM (2010) Non-lethal method to obtain stomach samples from a large marine predator and the use of DNA analysis to improve dietary information. J Exp Mar Biol Ecol 393(1):188–192
Bigelow HB, Schroeder WC (2002) Bigelow and Schroeder’s fishes of the gulf of Maine, 3rd edn. Smithsonian Institution Press, Washington
Blaylock RA (1989) A massive school of cownose rays, rhinoptera bonasus (rhinopteridae), in lower chesapeake Bay, Virginia. Copeia 1989(3):744–748
Blaylock R (1993) Distribution and abundance of the cownose ray, Rhinoptera bonasus, in lower Chesapeake Bay. Estuar Coasts 16(2):255–263. doi:10.2307/1352498
Collins AB, Heupel MR, Hueter RE, Motta PJ (2007) Hard prey specialists or opportunistic generalists? An examination of the diet of the cownose ray, Rhinoptera bonasus. Mar Freshw Res 58(1):135–144. doi:10.1071/MF05227
Collins A, Heupel M, Simpfendorfer C (2008) Spatial distribution and long-term movement patterns of cownose rays Rhinoptera bonasus within an estuarine river. Estuar Coasts 31(6):1174–1183. doi:10.1007/s12237-008-9100-5
Craig JK, Gillikin PC, Magelnicki MA, May LN (2010) Habitat use of cownose rays (Rhinoptera bonasus) in a highly productive, hypoxic continental shelf ecosystem. Fish Oceanogr 19(4):301–317. doi:10.1111/j.1365-2419.2010.00545.x
Deagle BE, Kirkwood R, Jarman SN (2009) Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces. Mol Ecol 18(9):2022–2038
Dunn MR, Szabo A, McVeagh MS, Smith PJ (2010) The diet of deepwater sharks and the benefits of using DNA identification of prey. Deep-Sea Res I 157:923–930
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32(5):1792–1797
Fisher R (2010) Life History, Trophic Ecology, and Prey Handling by Cownose Ray, Rhinoptera bonasus, from Chesapeake Bay. National Oceanic and Atmospheric Administration
Fisher R, Garrett C, Grubbs RD (2011) Cownose ray (Rhioptera bonasus) predation relative to bivalve ontogeny. J Shellfish Res 30(1):187–196
Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol 3(5):294–299
Goodman M, Conn P, Fitzpatrick E (2010) Seasonal occurrence of cownose rays (rhinoptera bonasus) in north Carolina’s estuarine and coastal waters. Estuar Coasts 34(3):640–651. doi:10.1007/s12237-010-9355-5
Hebert PDN, Cywinska A, Ball SL, deWaard JR (2003) Biological identifications through DNA barcodes. Proc R Soc Lond Ser B Biol Sci 270(1512):313–321. doi:10.1098/rspb.2002.2218
King RA, Read DS, Traugott M, Symondson WOC (2008) Molecular analysis of predation: a review of best practice for DNA-based approaches. Mol Ecol 17:947–963
Orth RJ (1975) Destruction of eelgrass, Zostera marina, by the cownose ray, Rhinoptera bonasus, in the Chesapeake Bay. Chesap Sci 16(3):205–208. doi:10.2307/1350896
Peterson C, Fodrie J, Summerson H, Powers S (2001) Site-specific and density-dependent extinction of prey by schooling rays: generation of a population sink in top-quality habitat for bay scallops. Oecologia 129(3):349–356. doi:10.1007/s004420100742
Pompanon F, Deagle BE, Symondson WOC, Brown DS, Jarman SN, Taberlet P (2011) Who is eating what: diet assessment using next generation sequencing. Mol Ecol 21(8):1931–1950
Rambaut A (1995) Se-Al: Sequence alignment program. Oxford University Press, Oxford
Ruppert EE, Fox RS (1988) Seashore animals of the Southeast: A guide to common shallow-water invertebrates of the southeastern Atlantic coast. Univ of South Carolina Press, Columbia
Saccone C, De Giorgi C, Gissi C, Pesole G, Reyes A (1999) Evolutionary genomics in Metazoa: the mitochondrial DNA as a model system. Gene 238(1):195–209
Sasko DE, Dean MN, Motta PJ, Hueter RE (2006) Prey capture behavior and kinematics of the Atlantic cownose ray, Rhinoptera bonasus. Zoology 109(3):171–181
Smith J, Merriner J (1985) Food habits and feeding behavior of the cownose ray, Rhinoptera bonasus, in lower Chesapeake Bay. Estuar Coasts 8(3):305–310. doi:10.2307/1351491
Smith J, Merriner J (1986) Observations on the reproductive biology of the cownose ray, Rhinoptera bonasus, in Chesapeake Bay. Fish Bull 84(4):871–877
Smith J, Merriner J (1987) Age and growth, movements and distribution of the cownose ray, Rhinoptera bonasus, in Chesapeake Bay. Estuar Coasts 10(2):153–164. doi:10.2307/1352180
Yoccoz NG (2012) The future of environmental DNA in ecology. Mol Ecol 21:2031–2038
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.
About this article
Cite this article
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
- Feeding ecology
- Molecular techniques