title: New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: the trnL approach.
abstract: The development of DNA barcoding (species identification using a standardized DNA sequence), and the availability of recent DNA sequencing techniques offer new possibilities in diet analysis. DNA fragments shorter than 100-150 bp remain in a much higher proportion in degraded DNA samples and can be recovered from faeces. As a consequence, by using universal primers that amplify a very short but informative DNA fragment, it is possible to reliably identify the plant taxon that has been eaten. According to our experience and using this identification system, about 50% of the taxa can be identified to species using the trnL approach, that is, using the P6 loop of the chloroplast trnL (UAA) intron. We demonstrated that this new method is fast, simple to implement, and very robust. It can be applied for diet analyses of a wide range of phytophagous species at large scales. We also demonstrated that our approach is efficient for mammals, birds, insects and molluscs. This method opens new perspectives in ecology, not only by allowing large-scale studies on diet, but also by enhancing studies on resource partitioning among competing species, and describing food webs in ecosystems.
authors.affiliation: Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, BP 53, F-38041 Grenoble cedex 9, France.
authors.forename: Alice
authors.initials: A
authors.lastname: Valentini
authors.forename: Christian
authors.initials: C
authors.lastname: Miquel
authors.forename: Muhammad Ali
authors.initials: MA
authors.lastname: Nawaz
authors.forename: Eva
authors.initials: E
authors.lastname: Bellemain
authors.forename: Eric
authors.initials: E
authors.lastname: Coissac
authors.forename: François
authors.initials: F
authors.lastname: Pompanon
authors.forename: Ludovic
authors.initials: L
authors.lastname: Gielly
authors.forename: Corinne
authors.initials: C
authors.lastname: Cruaud
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Nascetti
authors.forename: Patrick
authors.initials: P
authors.lastname: Wincker
authors.forename: Jon E
authors.initials: JE
authors.lastname: Swenson
authors.forename: Pierre
authors.initials: P
authors.lastname: Taberlet