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New insights on diet variability revealed by DNA barcoding and high-throughput pyrosequencing: chamois diet in autumn as a case study

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Ecological Research

Abstract

Characterizing the diet of large herbivores and the determinants of its variation remains a difficult task in wild species. DNA-based techniques have the potential to complement traditional time-consuming methods based on the microhistology of plant cuticle fragments in fecal or rumen samples. Recently, it has been shown that a short chloroplast DNA fragment, the P6 loop of the trnL (UAA) intron, can act as a minimalist barcode. Here, we used the trnL approach with high-throughput pyrosequencing to study diet from feces in a wild herbivore, the alpine chamois (Rupicapra rupicapra) and showed that the fine resolution in plant determination obtained with this method allows exploring subtle temporal shifts and inter-individual variability in diet composition. First, we built a DNA barcoding database of 475 plants species. Seventy-two percent of plant species can be unambiguously identified to species level, 79% to genus level and 100% to family level using the P6 loop. Second, we analysed 74 feces collected from October to November. Based on 47,896 P6 loop sequences, we identified a total of 110 taxa, 96 in October and 76 in November, with a clear diet shift between October and November. We recognized four and two clusters of feces composition in October and November, respectively, revealing different diet categories among individuals within each month. DNA-based diet analysis is faster and more taxonomically precise than studies based on microhistology, and opens new possibilities for analysing plant-herbivore interactions in the wild.

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Acknowledgments

We thank Nicolas Valy and Bruno Gravelat for their contribution for plant sampling and determination. We also thank Delphine Rioux, Ludovic Gielly and Alice Valentini for their technical help in the laboratory, and David Christianson and Jessica Rocha for correcting the English.

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Authors and Affiliations

  1. Laboratoire d′Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, Grenoble, France

    Gilles Rayé, Christian Miquel, Eric Coissac, Claire Redjadj & Pierre Taberlet

  2. Laboratoire d′Ecologie Alpine, CNRS UMR 5553, Université de Savoie, Le Bourget du Lac, France

    Claire Redjadj & Anne Loison

Authors
  1. Gilles Rayé
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  2. Christian Miquel
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  3. Eric Coissac
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  4. Claire Redjadj
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  5. Anne Loison
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  6. Pierre Taberlet
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Corresponding author

Correspondence to Gilles Rayé.

Additional information

G. Rayé and C. Miquel contributed equally to this work.

Appendices

Appendix 1

See Table 3.

Table 3 Groups of species (“Group”) representing the lowest taxonomic level that can be obtained based on the P6-loop of the trnL (UAA) and their associated family
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Appendix 2

See Table 4.

Table 4 List of the lowest taxonomic levels in the chamois diet with their frequencies of sequences (F S), their frequencies of occurrences (F O) and their presence in October and November
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Rayé, G., Miquel, C., Coissac, E. et al. New insights on diet variability revealed by DNA barcoding and high-throughput pyrosequencing: chamois diet in autumn as a case study. Ecol Res 26, 265–276 (2011). https://doi.org/10.1007/s11284-010-0780-5

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  • DOI: https://doi.org/10.1007/s11284-010-0780-5

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