Environmental Biology of Fishes

, Volume 97, Issue 9, pp 999–1012 | Cite as

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

  • Lyndell M. Bade
  • Christopher N. Balakrishnan
  • Erik M. Pilgrim
  • Susan B. McRae
  • Joseph J. Luczkovich
Article

Abstract

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.

Keywords

Elasmobranch Diet Feeding ecology Molecular techniques COI 

References

  1. Ajemian M, Powers S (2011) Habitat-specific feeding by cownose rays (Rhinoptera bonasus) of the northern Gulf of Mexico. Environ Biol Fish 95(1):79–97CrossRefGoogle Scholar
  2. 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, GreenvilleGoogle Scholar
  3. Barnes RD (1974) Invertebrate Zoology 3. Ed. WB Saunders Co, Philadelphia, PennsylvaniaGoogle Scholar
  4. 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):188–192CrossRefGoogle Scholar
  5. Bigelow HB, Schroeder WC (2002) Bigelow and Schroeder’s fishes of the gulf of Maine, 3rd edn. Smithsonian Institution Press, WashingtonGoogle Scholar
  6. Blaylock RA (1989) A massive school of cownose rays, rhinoptera bonasus (rhinopteridae), in lower chesapeake Bay, Virginia. Copeia 1989(3):744–748CrossRefGoogle Scholar
  7. 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 CrossRefGoogle Scholar
  8. 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 CrossRefGoogle Scholar
  9. 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 CrossRefGoogle Scholar
  10. 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 CrossRefGoogle Scholar
  11. Deagle BE, Kirkwood R, Jarman SN (2009) Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces. Mol Ecol 18(9):2022–2038PubMedCrossRefGoogle Scholar
  12. 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 157:923–930CrossRefGoogle Scholar
  13. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32(5):1792–1797PubMedCentralPubMedCrossRefGoogle Scholar
  14. Fisher R (2010) Life History, Trophic Ecology, and Prey Handling by Cownose Ray, Rhinoptera bonasus, from Chesapeake Bay. National Oceanic and Atmospheric AdministrationGoogle Scholar
  15. Fisher R, Garrett C, Grubbs RD (2011) Cownose ray (Rhioptera bonasus) predation relative to bivalve ontogeny. J Shellfish Res 30(1):187–196CrossRefGoogle Scholar
  16. 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):294–299PubMedGoogle Scholar
  17. 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 CrossRefGoogle Scholar
  18. 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 CrossRefGoogle Scholar
  19. King RA, Read DS, Traugott M, Symondson WOC (2008) Molecular analysis of predation: a review of best practice for DNA-based approaches. Mol Ecol 17:947–963PubMedCrossRefGoogle Scholar
  20. 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 CrossRefGoogle Scholar
  21. 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 Google Scholar
  22. 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):1931–1950PubMedCrossRefGoogle Scholar
  23. Rambaut A (1995) Se-Al: Sequence alignment program. Oxford University Press, OxfordGoogle Scholar
  24. Ratnasingham S, Hebert PDN (2007) bold: The Barcode of Life Data System (http://www.barcodinglife.org). Molecular Ecology Notes 7 (3):355–364. doi:10.1111/j.1471-8286.2007.01678.x
  25. 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, ColumbiaGoogle Scholar
  26. 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):195–209PubMedCrossRefGoogle Scholar
  27. Sasko DE, Dean MN, Motta PJ, Hueter RE (2006) Prey capture behavior and kinematics of the Atlantic cownose ray, Rhinoptera bonasus. Zoology 109(3):171–181PubMedCrossRefGoogle Scholar
  28. 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 CrossRefGoogle Scholar
  29. Smith J, Merriner J (1986) Observations on the reproductive biology of the cownose ray, Rhinoptera bonasus, in Chesapeake Bay. Fish Bull 84(4):871–877Google Scholar
  30. 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 CrossRefGoogle Scholar
  31. Yoccoz NG (2012) The future of environmental DNA in ecology. Mol Ecol 21:2031–2038PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Lyndell M. Bade
    • 1
    • 3
  • Christopher N. Balakrishnan
    • 1
  • Erik M. Pilgrim
    • 2
  • Susan B. McRae
    • 1
  • Joseph J. Luczkovich
    • 1
  1. 1.Department of BiologyEast Carolina UniversityGreenvilleUSA
  2. 2.Ecological Exposure Research Division U.S. EPACincinnatiUSA
  3. 3.Departments of Biology and ChemistryBates CollegeLewistonUSA

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