Home > Events > 1 Metabarcoding spring school in French Alps (5-9 March 2012) > Presentations > Diet analysis of the Mediterranean shag (Phalacrocorax aristotelis (...)

Wednesday 29 February 2012

Diet analysis of the Mediterranean shag (Phalacrocorax aristotelis desmarestii) using conventional techniques and next generation sequencing

KASAPIDIS Panagiotis

The Mediterranean shag is an avian subspecies endemic of the Mediterranean. Its global population is estimated to be less than 10,000 pairs, with 1,000-2,000 in the Greek islands of the Aegean and Ionian Sea. It is classified as “Nearly Threatened” in the Red Data Book of Endangered Animals of Greece. The EU LIFE project “ConShagAudMIBAGR” aims to improve the knowledge on the species’ distribution and ecology, giving special attention to the designation of Marine Important Bird Areas in Greece. Within the frame of this project, a diet analysis is carried out using both conventional prey identification methods and next generation sequencing. Regurgitates (undigested prey remains) and faeces have been collected from a large colony of the species in the N. Aegean Sea. A conventional prey analysis has been carried out by identifying indigestible part remains, mainly fish otoliths, from regurgitates. The latter, as well as faecal samples will be subjected to amplicon sequencing using the 454 GS-FLX platform, following the protocol of Deagle et al. (2009). By analyzing the same samples (i.e. regurgitates) both by conventional and molecular techniques, we will be able to check whether molecular approaches perform better for prey identification at the species’ level and if they can give reliable quantitative estimations. Moreover, the analysis of faecal samples will show whether there are prey items that are not detected in the regurgitates. Finally, we will estimate which approach is more cost effective for determining the diet of the Mediterranean shag.

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Editorial board
  • BRANDNER Melissa
    • University of Nordland
    • Bodø (Norway)
  • BROCHMANN Christian
    • National Centre for Biosystematics
    • Oslo (Norway)
  • CHARITON Anthony
    • CSIRO Land and Water
    • Lucas Heights NA (Australia)
  • DEAGLE Bruce
    • University of Victoria
    • Victoria (Canada)
  • Eric Coissac
    • LECA
    • Grenoble (France)
  • KASAPIDIS Panagiotis
    • Hellenic Center for Marine Research
    • Irakleion, Crete (Greece)
    • Université de Genève
    • Genève 4 (Switzerland)
  • TABERLET Pierre
    • LECA,
    • Grenoble (France)
    • Centre for GeoGenetics
    • Copenhagen (Denmark)
  • Vodka, Bison and Metabarcoding

    31 July 2015, by BRANDNER Melissa

    The start of last month saw the occurrence of the Fifth Metabarcoding Spring School held in Białowieża National Park , Poland. A variety of scientists attended from all over the globe to learn, share and inspire with unique stories of metabarcoding.
    The scientists at the Mammal Research Institute PAS in Białowieża National Park hosted this year’s workshop. And our hats go off to them for the organizational skills, warmth and hospitality. During the week, experienced metabarcoders gave lectures on their trials and tribulations in the field of metabarcoding, sparking conversations between the attendees. The end of the first day saw flash talks from all participants of the event, creating an icebreaker and showing the wide variety of applications for metabarcoding, including, dietary studies, environmental health, fundamental ecology and exploration of rare and ancient habitats.
    Pierre Taberlet (who is rumoured to run 8000 PCR a day!) taught technical aspects such as DNA extraction in (...)

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