Conservation Genetics

, Volume 11, Issue 5, pp 2039–2048 | Cite as

Pyrosequencing faecal DNA to determine diet of little penguins: is what goes in what comes out?

  • Bruce E. DeagleEmail author
  • André Chiaradia
  • Julie McInnes
  • Simon N. Jarman
Research Article


DNA barcoding of faeces or stomach contents is an emerging approach for dietary analysis. We pyrosequenced mtDNA 16S markers amplified from faeces of captive little penguins (Eudyptula minor) to examine if recovered sequences reflect the proportions of species consumed. We also analysed wild little penguin faeces collected from 100 nests in southeast Australia. In the captive study, pilchards were the primary fish fed to the penguins and DNA sequences from pilchard were the most common sequences recovered. Sequences of three other fish fed in constant mass proportions (45:35:20) were all detected, but proportions of sequences (60:6:34) were considerably different than mass proportions in the diet. Correction factors based on relative mtDNA density in the fish did not improve diet estimates. Consistency between replicate samples suggests that the observed bias resulted from differences in prey digestibility. Detection of DNA from fish consumed before the penguins were brought into captivity indicates that a DNA signal in faeces can persist for at least 4 days after ingestion. In the wild-collected faeces, 24 distinct fish and 1 squid were identified; anchovy, barracouta and pilchard accounted for over 80% of these sequences. Our results highlight that DNA sequences recovered in dietary barcoding studies can provide semi-quantitative information on diet composition, but these data should be given wide confidence intervals.


Eudyptula minor DNA barcoding Seabird diet GS-FLX 454 Sequencing Non-invasive 



We thank M. Healy and T. Murray for help keeping the temporarily captive penguins happy, and L. Renwick, E. Alamo and P. Wasiak for collecting samples in the field. We are grateful for funding from Phillip Island Nature Park and support from the Australian Antarctic Division. BED was supported by an NSERC Postdoctoral Fellowship during the later stages of this study. The project was approved by the Phillip Island Nature Park Animal Experimentation Ethics Committee and by the Department of Sustainability and Environment of Victoria, Australia.


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Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Bruce E. Deagle
    • 1
    Email author
  • André Chiaradia
    • 2
  • Julie McInnes
    • 2
  • Simon N. Jarman
    • 3
  1. 1.Department of BiologyUniversity of VictoriaVictoriaCanada
  2. 2.Research DepartmentPhillip Island Nature ParksCowesAustralia
  3. 3.Australian Marine Mammal Centre, Australian Antarctic DivisionKingstonAustralia

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