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Combining DNA and morphological analyses of faecal samples improves insight into trophic interactions: a case study using a generalist predator

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Abstract

The diet of pinnipeds is most commonly inferred from morphologically diagnostic remains of prey in their scats. Although this method can generate quantitative estimates of diet simply, important prey types may not always be detected. DNA-based methods improve detection of prey in scats, but they are not quantitative. While some studies have combined morphological and DNA-based methods, these have only assessed prey that are represented by their hard remains in scats. To overcome this bias, we apply molecular and morphological analyses to the soft and hard portions of faecal samples respectively, to estimate the diet of lactating Antarctic fur seals (Arctocephalus gazella) on Heard Island. The diet of this population is of particular interest because it is expanding rapidly and may rely to some extent on mackerel icefish (Champsocephalus gunnari), which are subject to commercial fisheries. Based on results from morphological analysis and likely important prey types, we tested for DNA remains of C. gunnari, myctophids and squid in faecal samples. The proportion of samples (n = 54) yielding no dietary information was reduced from around 25.9% using either method alone, to 9.3% when combined. Detection of all prey types tested for was notably improved by integrating molecular and morphological data. Data from either method alone would have underestimated the number of animals consuming C. gunnari by around 25.7%. Detection of multiple prey types in samples increased from 9.3% when using morphological analysis only, to 33.3% when using DNA only, to 46.3% when using both methods. Taken in isolation, morphological data inferred that individual seals consume either C. gunnari or myctophids, probably foraging in separate locations characteristic of those prey. Including molecular data demonstrated that while this may be true of some individuals, many other seals consume a mixed diet of at least C. gunnari, myctophids and squid. This new approach of combining DNA-based and morphological analyses of diet samples markedly increased the number of samples yielding dietary information, as well as increasing the amount of information attained from those samples. Our findings illustrate the broad potential of this technique to improve insight into trophic interactions in marine ecosystems.

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Notes

  1. Heard Island Predator–Prey Investigation and Ecosystem Study.

References

  • Acuna HO, Francis JM (1995) Spring and summer prey of the Juan Fernandez fur seal, Arctocephalus philippii. Can J Zool 73:1444–1452

    Article  Google Scholar 

  • Adams NJ, Klages NT (1987) Seasonal variation in the diet of the king penguin (Aptenodytes patagonicus) at sub-Antarctic Marion Island. J Zool 212:303–324

    Article  Google Scholar 

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    Article  CAS  Google Scholar 

  • Anon (2004) Chromo 4 real-time detector operations manual. MJ Research®, Incorporated, USA

  • Arnould JPY, Boyd IL, Speakman JR (1996) The relationship between foraging behaviour and energy expenditure in Antarctic fur seals. J Zool 239:769–782

    Article  Google Scholar 

  • Bonadonna F, Lea MA, Dehorter O, Guinet C (2001) Foraging ground fidelity and route-choice tactics of a marine predator: the Antarctic fur seal Arctocephalus gazella. Mar Ecol Prog Ser 223:287–297

    Article  Google Scholar 

  • Boyd IL (1999) Foraging and provisioning in Antarctic fur seals: interannual variability in time-energy budgets. Behav Ecol 10:198–208

    Article  Google Scholar 

  • Boyd IL, Murray AWA (2001) Monitoring a marine ecosystem using responses of upper trophic level predators. J Animal Ecol 70:747–760

    Article  Google Scholar 

  • Boyd IL, Staniland IJ, Martin AR (2002) Distribution of foraging by female Antarctic fur seals. Mar Ecol Prog Ser 242:285–294

    Article  Google Scholar 

  • Budd GM, Downes MC (1969) Population increase and breeding in the Kerguelen fur seal, Arctocephalus tropicalis gazella, at Heard Island. Mammalia 33:58–67

    Article  Google Scholar 

  • Casper RM, Gales NJ, Hindell MA, Robinson SM (2006) Diet estimation based on an integrated mixed prey feeding experiment using Arctocephalus seals. J Exp Mar Biol Ecol 328:228–239

    Article  Google Scholar 

  • Casper RM, Jarman SN, Deagle BE, Gales NJ, Hindell MA (2007) Detecting prey from DNA in predator scats: a comparison with morphological analysis, using Arctocephalus seals fed a known diet. J Exp Mar Biol Ecol. doi:10.1016/j.jembe.2007.04.002

    Article  Google Scholar 

  • CCAMLR (2003) Schedule of conservation measures in force 2003/2004. CCAMLR, Hobart

  • Cherel Y, Guinet C, Tremblay Y (1997) Fish prey of Antarctic fur seals Arctocephalus gazella at Ile de Croy, Kerguelen. Polar Biol 17:87–90

    Article  Google Scholar 

  • Cherel Y, Weimerskirch H (1999) Spawning cycle of onychoteuthid squids in the southern Indian Ocean: new information from seabird predators. Mar Ecol Prog Ser 188:93–104

    Article  Google Scholar 

  • Cottrell PE, Trites AW, Miller EH (1996) Assessing the use of hard parts in faeces to identify harbour seal prey: Results of captive-feeding trials. Can J Zool 74:875–880

    Article  Google Scholar 

  • Davies CR, Lamb T, Constable A, Williams R (2004) Preliminary assessment of mackerel icefish, Champsocephalus gunnari, for the Heard Island plateau region (Division 58.5.2) based on a survey in May 2004, WG-FSA-04/77, Hobart

  • Deagle BE, Tollit DJ (2007) Quantitative analysis of prey DNA in pinniped faeces: potential to estimate diet composition? Cons Gen 8:743–747

    Article  CAS  Google Scholar 

  • Deagle BE, Bax NJ, Hewitt CL, Patil JG (2003) Development and evaluation of a PCR-based test for detection of Asterias (Echinodermata : Asteroidea) larvae in Australian plankton samples from ballast water. Mar Fresh Res 54:709–719

    Article  CAS  Google Scholar 

  • Deagle BE, Tollit DJ, Jarman SN, Hindell M, Trites AW, Gales N (2005) Molecular scatology as a tool to study diet: analysis of prey DNA in scats from captive Stellar sea lions. Mol Ecol 14:1831–1842

    Article  CAS  Google Scholar 

  • Doidge DW, Croxall JP (1985) Diet and energy budget of the Antarctic fur seal, Arctocephalus gazella, at South Georgia. In: Siegfried WR, Condy PR, Laws RM (eds) Antarctic nutrient cycles and food webs. Springer, Heidelberg, pp 543–550

    Chapter  Google Scholar 

  • Doidge DW, McCann TS, Croxall JP (1986) Attendance behaviour of Antarctic fur seals. In: Gentry RL, Kooyman GL (eds) Fur seals: maternal strategies on land and at sea. Princeton University Press, Princeton, pp 102–114

    Google Scholar 

  • Duhamel G (1991) The biological and demographic peculiarities of the icefish Champsocephalus gunnari Lonnberg, 1905 from the Kerguelen Plateau. In: di Prisco G, Maresca B, Tota B (eds) Biology of Antarctic fish. Springer, Berlin, pp 40–53

    Chapter  Google Scholar 

  • Duhamel G (1995) New data on spawning, hatching and growth of Champsocephalus gunnari on the shelf of the Kerguelen Islands. CCAMLR Sci 2:21–34

    Google Scholar 

  • Everson I, Parkes G, Kock KH, Boyd IL (1999) Variation in standing stock of the mackerel icefish Champsocephalus gunnari at South Georgia. J Appl Ecol 36:591–603

    Article  Google Scholar 

  • Fea NI, Harcourt R, Lalas C (1999) Seasonal variation in the diet of New Zealand fur seals (Arctocephalus forsteri) at Otago peninsula, New Zealand. Wild Res 26:147–160

    Article  Google Scholar 

  • Gales N, Mattlin RH (1998) Fast, safe, field portable gas anesthesia for otariids. Mar Mamm Sci 14:355–361

    Article  Google Scholar 

  • Gales N, Constable A, Williams R (2005) A new era in conservation science: ecosystem scale experiments at Heard Island. In: Green K, Woehler EJ (eds) Heard Island: Southern Ocean Sentinel. Surrey Beatty & Sons, Chipping Norton, pp 254–256

    Google Scholar 

  • Green K (1997) Diving behaviour of Antarctic fur seals Arctocephalus gazella Peters around Heard Island. In: Hindell M, Kemper C (eds) Marine mammal research in the Southern Hemisphere. Status ecology and medicine, vol 1. Surrey Beatty & Sons, Chipping Norton, pp 97–104

  • Green K (2005) The marine mammals of Heard Island. In: Green K, Woehler EJ (eds) Heard Island: Southern Ocean Sentinel. Surrey Beatty & Sons, Chipping Norton, pp 166–183

    Google Scholar 

  • Green K, Burton HR, Williams R (1989) The diet of Antarctic fur seals Arctocephalus gazella (Peters) during the breeding season at Heard Island. Antarct Sci 1:317–324

    Article  Google Scholar 

  • Green K, Williams R, Burton HR (1991) The diet of Antarctic fur seals during the late autumn and early winter around Heard Island. Antarct Sci 3:359–361

    Article  Google Scholar 

  • Green K, Williams R, Burton HR (1997) Foraging ecology of Antarctic fur seals Arctocephalus gazella Peters around Heard Island. In: Hindell M, Kemper C (eds) Marine mammal research in the Southern Hemisphere. Status ecology and medicine, vol 1. Surrey Beatty & Sons, Chipping Norton, pp 105–113

  • Hecht T (1987) A guide to the otoliths of Southern Ocean fishes. S Afr J Antarct Res 17:1–87

    Google Scholar 

  • Hulley PA (1990) Myctophidae. In: Gon O, Heemstra PC (eds) Fishes of the Southern Ocean. J.L.B. Smith Institute of Ichthyology, Grahamstown, pp 146–178

    Google Scholar 

  • Jackson GD, McKinnon JF, Lalas C, Ardern R, Buxton NG (1998) Food spectrum of the deepwater squid Moroteuthis ingens (Cephalopoda : Onychoteuthidae) in New Zealand waters. Polar Biol 20:56–65

    Article  Google Scholar 

  • 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 11:2679–2690

    Article  CAS  Google Scholar 

  • Jarman SN, Deagle BE, Gales NJ (2004) Group-specific polymerase chain reaction for DNA-based analysis of species diversity and identity in dietary samples. Mol Ecol 13:1313–1322

    Article  CAS  Google Scholar 

  • Kock KH (2005a) Antarctic icefishes (Channichthyidae): a unique family of fishes. A review, Part I. Polar Biol 28:862–895

    Article  Google Scholar 

  • Kock KH (2005b) Antarctic icefishes (Channichthyidae): a unique family of fishes. A review, Part II. Polar Biol 28:897–909

    Article  Google Scholar 

  • Kock KH, Everson I (2003) Shedding new light on the life cycle of mackerel icefish in the Southern Ocean. J Fish Biol 63:1–21

    Article  Google Scholar 

  • Kvitrud M, Riemer S, Brown R, Bellinger M, Banks M (2005) Pacific harbor seals (Phoca vitulina) and salmon: genetics presents hard numbers for elucidating predator-prey dynamics. Mar Biol 147:1459–1466

    Article  Google Scholar 

  • Lake S (1997) Analysis of the diet of New Zealand fur seals Arctocephalus forsteri in Tasmania. In: Hindell M, Kemper C (eds) Marine mammal research in the Southern Hemisphere, volume 1: status, ecology and medicine. Surrey Beatty & Sons, pp 125–129

  • Lea MA, Cherel Y, Guinet C, Nichols PD (2002a) Antarctic fur seals foraging in the Polar Frontal Zone: inter- annual shifts in diet as shown from fecal and fatty acid analyses. Mar Ecol Prog Ser 245:281–297

    Article  Google Scholar 

  • Lea MA, Nichols PD, Wilson G (2002b) Fatty acid composition of lipid-rich myctophids and mackerel icefish (Champsocephalus gunnari)—Southern ocean food-web implications. Polar Biol 25:843–854

    Google Scholar 

  • Linkowski TB (1985) Population biology of the myctophid fish Gymnoscopelus nicholsi (Gillbert, 1911) from the Western South-Atlantic. J Fish Biol 27:683–698

    Article  Google Scholar 

  • Mårtensson PE, Nordøy ES, Messelt EB, Blix AS (1998) Gut length, food transit time and diving habit in phocid seals. Polar Biol 20:213–217

    Article  Google Scholar 

  • McArthur T, Butler ECV, Jackson GD (2003) Mercury in the marine food chain in the Southern Ocean at Macquarie Island: an analysis of a top predator, Patagonian toothfish (Dissostichus eleginoides) and a mid-trophic species, the warty squid (Moroteuthis ingens). Polar Biol 27:1–5

    Article  Google Scholar 

  • Morrison TB, Weis JJ, Wittwer CT (1998) Quantification of low-copy transcripts by continuous SYBR Green I monitoring during amplification. BioTechniques 24:954–962

    CAS  PubMed  Google Scholar 

  • Orr AJ, Harvey JT (2001) Quantifying errors associated with using fecal samples to determine the diet of the California sea lion (Zalophus californianus). Can J Zool 79:1080–1087

    Article  Google Scholar 

  • Orr AJ, Banks AS, Mellman S, Huber HR, DeLong RL, Brown RF (2004) Examination of the foraging habits of Pacific harbor seal (Phoca vitulina richardsi) to describe their use of the Umpqua River, Oregon, and their predation on salmonids. Fish Bull 102:108–117

    Google Scholar 

  • Osman LP, Hucke-Gaete R, Moreno CA, Torres D (2004) Feeding ecology of Antarctic fur seals at Cape Shirreff, South Shetlands, Antarctica. Polar Biol 27:92–98

    Article  Google Scholar 

  • Parsons KM, Piertney SB, Middlemas SJ, Hammond PS, Armstrong JD (2005) DNA-based identification of salmonid prey species in seal faeces. J Zool 266:275–281

    Article  Google Scholar 

  • Peccoud J, Jacob C (1996) Theoretical uncertainty of measurements using quantitative polymerase chain reaction. Biophys J 71:101–108

    Article  CAS  Google Scholar 

  • Phillips KL, Jackson GD, Nichols PD (2001) Predation of myctophids by the squid Moroteuthis ingens around Macquarie and Heard Islands: stomach contents and fatty acid analyses. Mar Ecol Prog Ser 215:179–189

    Article  CAS  Google Scholar 

  • Phillips KL, Nichols PD, Jackson GD (2003) Dietary variation of the squid Moroteuthis ingens at four sites in the Southern Ocean: stomach contents, lipid and fatty acid profiles. J Mar Biol Assoc UK 83:523–534

    Article  Google Scholar 

  • Pierce GJ, Boyle PR (1991) A review of methods for diet analysis in piscivorous marine mammals. Ocean Mar Biol 29:409–486

    Google Scholar 

  • Purcell M, Mackey G, LaHood E (2004) Molecular methods for the genetic identification of salmonid prey from the Pacific harbor seal (Phoca vitulina richardsi) scat. Fish Bull 102:213–220

    Google Scholar 

  • Reid K (1995) The diet of Antarctic fur seals (Arctocephalus gazella Peters 1875) during winter at South Georgia. Antarct Sci 7:241–249

    Article  Google Scholar 

  • Reid K (1996) A guide to the use of otoliths in the study of predators at South Georgia. British Antarctic Survey

  • Reid K, Arnould JPY (1996) The diet of Antarctic fur seals Arctocephalus gazella during the breeding season at South Georgia. Polar Biol 16:105–114

    Article  Google Scholar 

  • Reid K, Hill SL, Diniz TCD, Collins MA (2005) Mackerel icefish Champsocephalus gunnari in the diet of upper trophic level predators at South Georgia: implications for fisheries management. Mar Ecol Prog Ser 305:153–161

    Article  Google Scholar 

  • Reid K, Davis D, Staniland IJ (2006) Spatial and temporal variability in the fish diet of Antarctic fur seal (Arctocephalus gazella) in the Atlantic sector of the Southern Ocean. Can J Zool 84:1025–1037

    Article  Google Scholar 

  • Rodhouse PG, Arnbom TR, Fedak MA, Yeatman J, Murray AWA (1992) Cephalopod prey of the southern elephant seal Mirounga leonina L. Can J Zool 70:1007–1015

    Article  Google Scholar 

  • Rodhouse PG, Prince PA, Trathan PN, Hatfield EMC, Watkins JL, Bone DG, Murphy EJ, White MG (1996) Cephalopods and mesoscale oceanography at the Antarctic Polar Front: satellite tracked predators locate pelagic trophic interactions. Mar Ecol Prog Ser 136:37–50

    Article  Google Scholar 

  • Roux KH (1995) Optimization and troubleshooting in PCR. PCR Methods Appl 4:S185–S194

    Article  CAS  Google Scholar 

  • Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biological programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: Methods in molecular biology. Humana Press, Totowa, NJ, pp 365–386

  • Sheppard SK, Harwood JD (2005) Advances in molecular ecology: tracking trophic links through predator-prey food-webs. Funct Ecol 19:751–762

    Article  Google Scholar 

  • Staniland IJ (2002) Investigating the biases in the use of hard prey remains to identify diet composition using Antarctic fur seals (Arctocephalus gazella) in captive feeding trials. Mar Mamm Sci 18:223–243

    Article  Google Scholar 

  • Staniland IJ, Boyd IL (2003) Variation in the foraging location of Antarctic fur seals (Arctocephalus gazella) and the effects on diving behavior. Mar Mamm Sci 19:331–343

    Article  Google Scholar 

  • Staniland IJ, Taylor RI, Boyd IL (2003) An enema method for obtaining fecal material from known individual seals on land. Mar Mamm Sci 19:363–370

    Article  Google Scholar 

  • Staniland IJ, Reid K, Boyd IL (2004) Comparing individual and spatial influences on foraging behaviour in Antarctic fur seals Arctocephalus gazella. Mar Ecol Prog Ser 275:263–274

    Article  Google Scholar 

  • Symondson WOC (2002) Molecular identification of prey in predator diets. Mol Ecol 11:627–641

    Article  CAS  Google Scholar 

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882

    Article  CAS  Google Scholar 

  • Tierney M, Hindell M, Goldsworthy S (2002) Energy content of mesopelagic fish from Macquarie Island. Antarct Sci 14:225–230

    Article  Google Scholar 

  • Tollit DJ, Wong M, Winship AJ, Rosen DAS, Trites AW (2003) Quantifying errors associated with using prey skeletal structures from fecal samples to determine the diet of Steller’s sea lion (Eumetopias jubatus). Mar Mamm Sci 19:724–744

    Article  Google Scholar 

  • Williams R, McEldowney A (1990) A guide to the fish otoliths from waters off the Australian Antarctic Territory, Heard and Macquarie Islands. Australian Antarctic Division

  • Williams R, de la Mare WK (1995) Fish distribution and biomass in the Heard Island zone (Division 58.5.2). CCAMLR Sci 2:1–20

    Google Scholar 

  • Williams R, van Wijk E, Constable A, Lamb T (2001) The fishery for Champsocephalus gunnari and its biology at Heard Island (Division 58.5.2), WAMI-01/4, Hobart

  • Wittwer CT, Herrmann MG, Moss AA, Rasmussen RP (1997) Continuous fluorescence monitoring of rapid cycle DNA amplification. BioTechniques 22:130–138

    Article  CAS  Google Scholar 

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Acknowledgments

We thank I. Staniland and S. Goldsworthy for their expert field support, I. Staniland for performing the enemas, R. Williams for comments and providing access to unpublished HIPPIES data, and S. Robinson for fish energy density data. We also thank the three referees for their thoughtful and constructive comments. We gratefully acknowledge the support of all members of the 2003/2004 Heard Island expedition. This research was funded by the Australian Antarctic Division and R. M. Casper was a recipient of a University of Tasmania Postgraduate Scholarship. All procedures complied with the current laws of Australia and were carried out under Antarctic Science Advisory Committee Permit 2388 and University of Tasmania Animal Ethics Permit A7503.

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  1. Southern Ocean Ecosystems, Australian Antarctic Division, 203 Channel Highway, Kingston, TAS, 7050, Australia

    Ruth M. Casper, Simon N. Jarman & Nicholas J. Gales

  2. Antarctic Wildlife Research Unit, School of Zoology, University of Tasmania, GPO Box 252-05, Hobart, TAS, 7001, Australia

    Ruth M. Casper & Mark A. Hindell

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  1. Ruth M. Casper
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  2. Simon N. Jarman
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  3. Nicholas J. Gales
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  4. Mark A. Hindell
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Correspondence to Ruth M. Casper.

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Communicated by S. D. Connell.

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Casper, R.M., Jarman, S.N., Gales, N.J. et al. Combining DNA and morphological analyses of faecal samples improves insight into trophic interactions: a case study using a generalist predator. Mar Biol 152, 815–825 (2007). https://doi.org/10.1007/s00227-007-0732-y

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