Advertisement

Polar Biology

, Volume 36, Issue 5, pp 755–759 | Cite as

Faecal DNA amplification in Pacific walruses (Odobenus rosmarus divergens)

  • Ella Bowles
  • Andrew W. Trites
Short Note

Abstract

Dietary information is critical for assessing the population status of seals, sea lions and walruses—and is determined for most species of pinnipeds using non-invasive methods. However, diets of walruses continue to be described from the stomach contents of dead individuals. Our goal was to assess whether DNA could be extracted from the faeces of Pacific walruses (Odobenus rosmarus divergens) collected at haulout sites, and whether potential prey species or taxa could be amplified from that DNA. We extracted DNA from 70 faecal samples collected from ice pans in the Bering Sea during the spring of 2008 and 2009 (with between 4.6 and 308.9 ng/μl of DNA in every sample). We also extracted DNA from 12 potential prey species or taxa collected by bottom-grabs in 2009 to identify positive controls for primers and to test the ability of previously published taxon-specific and species-specific primers to correctly identify the prey using conventional PCR. We tested primers that successfully amplified DNA from the tissue of at least one potential prey species or taxon on all 70 walrus faecal samples. We found that two sets of primers successfully amplified many of the potential prey species or taxa using DNA from their tissue, and that one of these primer sets produced positive amplification in 4 of the 70 faecal samples. The band size that was produced for prey organisms and in the faecal samples was consistent with expectations, although prey identities were not verified with sequencing. Our pilot study demonstrates that DNA can be successfully extracted and amplified from walrus faeces, providing a stepping stone towards describing the diets of walruses from faecal DNA.

Keywords

Pacific walrus PCR Prey identification Faecal DNA 

Notes

Acknowledgments

We thank Jacqueline Grebmeier for providing and identifying bottom-grab samples, Chad Jay and Tony Fischbach for assistance in collecting walrus scats, and Patricia Schulte and Sean Rogers for use of laboratory equipment. We also thank Chad Jay and two reviewers for their constructive comments. DNA analysis was funded by the US Geological Survey, and prey and faecal samples were obtained with the support of the National Science Foundation and the North Pacific Research Board through the Bering Sea Integrated Research Program. This study was part of BEST-BSIERP Bering Sea Project # 81, and is NPRB publication # 396.

Supplementary material

300_2013_1296_MOESM1_ESM.doc (292 kb)
Supplementary material 1 (DOC 292 kb)
300_2013_1296_MOESM2_ESM.doc (998 kb)
Supplementary material 2 (DOC 998 kb)

References

  1. Bowles E, Schulte PM, Tollit DJ, Deagle BE, Trites AW (2011) Proportion of prey consumed can be determined from faecal DNA using real time PCR. Mol Ecol Res 11:530–540CrossRefGoogle Scholar
  2. Budge SM, Springer AM, Iverson SJ, Sheffield G (2007) Fatty acid biomarkers reveal niche separation in an Arctic benthic food web. Mar Ecol Prog Ser 336:305–309CrossRefGoogle Scholar
  3. Deagle BE, Tollit DJ (2007) Quantitative analysis of prey DNA in pinniped faeces: potential to estimate diet composition? Conserv Genet 8:743–747CrossRefGoogle Scholar
  4. Deagle BE, Tollit DJ, Jarman SN, Hindell MA, Trites AW, Gales NJ (2005a) Molecular scatology as a tool to study diet: analysis of prey DNA in scats from captive Steller sea lions. Mol Ecol 14:1831–1842PubMedCrossRefGoogle Scholar
  5. Deagle BE, Jarman SN, Pemberton D, Gales NJ (2005b) Genetic screening for prey in the gut contents from a giant squid (Architeuthis sp.). J Hered 96:417–423PubMedCrossRefGoogle Scholar
  6. Deagle BE, Kirkwood R, Jarman SN (2009) Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces. Mol Ecol 18:2022–2038PubMedCrossRefGoogle Scholar
  7. Deagle BE, Chiaradia A, McInnes J, Jarman SN (2010) Pyrosequencing faecal DNA to determine diet of little penguins: is what goes in what comes out? Conserv Genet 11:2039–2048CrossRefGoogle Scholar
  8. Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit 1 from diverse metazoan invertebrates. Mol Mar Biol Biochem 3:294–299Google Scholar
  9. Frost K, Lowry L (1980) Feeding of ribbon seals (Phoca fasciata) in the Bering Sea in spring. Can J Zool 58:1601–1607CrossRefGoogle Scholar
  10. Hobson KA, Sease JL, Merrick RL, Piatt JF (1997) Investigating trophic relationships of pinnipeds in Alaska and Washington using stable isotope ratios of nitrogen and carbon. Mar Mamm Sci 13:114–132CrossRefGoogle Scholar
  11. Iverson SJ, Frost KJ, Lowry LF (1997) Fatty acid signatures reveal fine scale structure of foraging distribution of harbor seals and their prey in Prince William Sound, Alaska. Mar Ecol Prog Ser 151:255–271CrossRefGoogle Scholar
  12. Iverson SJ, Field C, Bowen WD, Blanchard W (2004) Quantitative fatty acid signature analysis: a new method of estimating predator diets. Ecol Monogr 74:211–235CrossRefGoogle Scholar
  13. Jarman SN, Gales NJ, Tierney M, Gill PC, Elliott NG (2002) A DNA-based method for identification of krill species and its application to analysing the diet of marine vertebrate predators. Mol Ecol 11:2679–2690PubMedCrossRefGoogle Scholar
  14. 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
  15. Lovvorn JR, Wilson JJ, McKay D, Bump JK, Cooper LW, Grebmeier JM (2010) Walruses attack spectacled eiders wintering in pack ice of the Bering Sea. Arctic 63:53–56Google Scholar
  16. Lowry L, Fay F (1984) Seal eating by walruses in the Bering and Chukchi Seas. Polar Biol 3:11–18CrossRefGoogle Scholar
  17. Mallory ML, Woo K, Gaston AJ, Davies WE, Mineau P (2004) Walrus (Odobenus rosmarus) predation on adult thick-billed murres (Uria lomvia) at Coats Island, Nunavut, Canada. Polar Res 23:111–114CrossRefGoogle Scholar
  18. Merrick RL, Loughlin TR (1997) Foraging behavior of adult female and young-of-year Steller sea lions in Alaskan waters. Can J Zool 75:776–786CrossRefGoogle Scholar
  19. Newsome SD, Tinker MT, Monson DH, Oftedal OT, Ralls K, Staedler MM, Fogel ML, Estes JA (2009) Using stable isotopes to investigate individual diet specialization in California sea otters (Enhydra lutris nereis). Ecology 90:961–974PubMedCrossRefGoogle Scholar
  20. Nordstrom CA, Wilson LJ, Iverson SJ, Tollit DJ (2008) Evaluating quantitative fatty acid signature analysis (QFASA) using harbour seals Phoca vitulina richardsi in captive feeding studies. Mar Ecol Prog Ser 360:245–263CrossRefGoogle Scholar
  21. Phillips DL (2012) Converting isotope values to diet composition: the use of mixing models. J Mammal 93:342–352CrossRefGoogle Scholar
  22. Pimm SL (2002) Food webs. University of Chicago Press, ChicagoGoogle Scholar
  23. Prime JH, Hammond PS (1987) Quantitative assessment of gray seal diet from fecal analysis. In: Huntley AC, Costa DP, Worthy GAJ, Castellini MA (eds) Approaches to marine mammal energetics. Allen Press, Lawrence, pp 165–181Google Scholar
  24. Rosen DAS, Tollit DJ (2012) Effects of phylogeny and prey type on fatty acid calibration coefficients in three pinniped species: implications for the QFASA dietary quantification technique. Mar Ecol Prog Ser 467:263–276CrossRefGoogle Scholar
  25. Scheffer TH (1928) Precarious status of the seal and sea-lion on our northwest coast. J Mammal 9:10–16CrossRefGoogle Scholar
  26. Sheffield G, Grebmeier JM (2009) Pacific walrus (Odobenus rosmarus divergens): differential prey digestion and diet. Mar Mamm Sci 25:761–777CrossRefGoogle Scholar
  27. Sheffield G, Fay FH, Feder H, Kelly BP (2001) Laboratory digestion of prey and interpretation of walrus stomach contents. Mar Mamm Sci 17:310–330CrossRefGoogle Scholar
  28. Sinclair EH, Zeppelin TK (2002) Seasonal and spatial differences in diet in the western stock of Steller sea lions (Eumetopias jubatus). J Mammal 83:973–990CrossRefGoogle Scholar
  29. Tollit DJ, Heaslip SG, Deagle BE, Iverson SJ, Joy R, Rosen DAS, Trites AW (2006) Estimating diet composition in sea lions: which technique to choose? In: Trites AW, Atkinson SK, DeMaster DP, Frtiz LW, Gelatt TS, Rea LD, Wynne KM (eds) Sea lions of the world. Alaska Sea Grant, Fairbanks, pp 293–308CrossRefGoogle Scholar
  30. Tollit DJ, Heaslip SG, Barrick RL, Trites AW (2007) Impact of diet-index selection and the digestion of prey hard remains on determining the diet of the Steller sea lion (Eumetopias jubatus). Can J Zool 85:1–15CrossRefGoogle Scholar
  31. Tollit DJ, Schulze AD, Trites AW, Olesiuk PF, Crockford SJ, Gelatt TS, Ream RR, Miller KM (2009) Development and application of DNA techniques for validating and improving pinniped diet estimates. Ecol Appl 19:889–905PubMedCrossRefGoogle Scholar
  32. Trites AW (2003) Food webs in the ocean: who eats whom and how much? In: Sinclair M, Valdimarsson G (eds) Responsible fisheries in the marine ecosystem. Rome and CABI Publishing, Wallingford, pp 125–141CrossRefGoogle Scholar
  33. Waits LP, Paetkau D (2005) Noninvasive genetic sampling tools for wildlife biologists: a review of applications and recommendations for accurate data collection. J Wildl Manage 69:1419–1433CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  1. 1.Department of Biological SciencesUniversity of CalgaryCalgaryCanada
  2. 2.Marine Mammal Research Unit, Fisheries CentreUniversity of British ColumbiaVancouverCanada

Personalised recommendations