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Thursday 18 April 2013
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Comparison of conventional otolith analysis and DNA metabarcoding approach to assess the diet of the Mediterranean Shag from pellets

Jon Bent Kristoffersen (1), Aris Christidis (2), Jakob Fric, (2) Panagiotis Kasapidis (1)

(1) Hellenic Centre for Marine Research, P.O. Box 2214, GR 71003, Heraklion, Greece
(2) Hellenic Ornithological Society, 24 Vas. Herakliou, GR 10682, Athens, Greece

The recent development of next generation sequencing technologies allows the molecular identification of a species’ diet from prey remains by the direct characterization of dozens of samples with several thousand sequences per PCR product, and has the potential to reveal many consumed species simultaneously (DNA metabarcoding). The Mediterranean shag, a seabird, is a subspecies of high conservation concern, with global population of less than 10,000 pairs, 10% of which reproduces on the Greek islands. Within the frame of the EU LIFE project “ConShagAudMIBAGR”, a diet analysis was carried out using both conventional prey identification and next generation sequencing. Regurgitated pellets containing undigested prey remains were collected from different colonies of the species in the Aegean and the Ionian Sea. First, conventional prey analysis was carried out on the pellets, by identifying morphologically the indigestible part remains, mainly fish otoliths. Then, the same pellets were subjected to amplicon sequencing using the 454 GS-FLX platform. By analyzing the same samples both by conventional and molecular techniques, we were able to check whether molecular approaches perform better than conventional ones for prey identification at the species’ level and if they can give reliable semi-quantitative estimations. The molecular analysis produced results that were generally concordant with the otolith analysis. However, there were some discrepancies: a) molecular analysis gave systematically lower or higher relative frequency for certain prey species, b) there were prey species found in the otolith analysis but not in the DNA analysis and vice versa, mainly in low abundance prey items, c) DNA analysis revealed few cases of species that had been misidentified in the otolith analysis and improved the recognition of prey items to the species’ level, when this was not possible with the conventional analysis (e.g. in some Gobidae and Sparidae taxa). The discrepancies between the two methods may be attributed to the following reasons, which remain to be evaluated: a) DNA results are proportional to the prey biomass, while otoliths are proportional to the number of prey individuals, b) PCR biases, so that some species may amplify better than others and be overrepresented in the number of sequences produced, c) misidentification in the otolith analysis or inability to record a species because the otoliths are worn or missing, d) false hit in the GenBank if the sequence of the species under consideration is missing. Nevertheless, this study shows that DNA analysis seems to be reliable for the diet analysis of seabirds and can be routinely used since the recent advances in sequencing technologies (next generation sequencing) render it a cost effective method.

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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)
  • PAWLOWSKI Jan
    • Université de Genève
    • Genève 4 (Switzerland)
  • TABERLET Pierre
    • LECA,
    • Grenoble (France)
  • WILLERSLEV Eske
    • Centre for GeoGenetics
    • Copenhagen (Denmark)
  • ZINGER Lucie
    • IBENS
    • Paris (France)
Editorial
  • 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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