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Wednesday 29 February 2012
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Assigning and interpreting on aDNA data from a past Greenland ecosystem

SCHMIDT Astrid

Ancient DNA from basal ice of a Greenland ice core was amplified on a high-throughput sequencing platform and evaluated by a combination of denoising and assignment methods to avoid false positive results. Downstream palaeo-ecological interpretations was based on the reduced and denoised data set.

Ancient DNA has previously been detected in the basal ice from the Dye 3 deep ice core from southern Greenland and used to reconstruct a rich boreal ecosystem based on a limited number of cloned DNA sequences from plants and insects. Here we present an extended study of deep sequenced ancient DNA amplified from basal ice in the Camp Century ice core from northwestern Greenland. With the increased amount of data generated by high throughput sequencing technology there is a need to remove false sequence diversity due to error in order to compensate for possible amplification, sequencing and damage errors that could inflate the biodiversity present in samples used for meta-barcoding studies. By denoising high-throughput sequence data, we removed a large part of the sequences that were produced by error as well as damage. Three different denoising approaches were applied and they differ in how they remove sequences. Each of them was combined with one of three assignment methods that consisted of two phylogeny-based ones (SAP and one in-prep method, OGA) and one similarity-based (EcoTag). Results were only accepted if confirmed by two of three pipelines. The data that was approved according to these criteria was used for down stream interpretations in an ecological context.
The results from the assignment studies were used to deduce ancient biodiversity from the Greenland site that is today covered by a thick ice sheet in northwestern Greenland. Ancient DNA from the Camp Century ice core provided results of flora and fauna from a once diverse boreal ecosystem. Camp Century was drilled on the margin of the supposedly reduced Greenland Ice Sheet during the last interglacial period and the results show that the area remained covered by ice during the previous interglacial, the Eemian, 130-116KY.

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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
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    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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