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Saturday 3 March 2012
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Taphonomy of Vertebrate Dirt DNA

Insights from studies of free-ranging animals


DNA molecules originating from animals and plants can be retrieved directly from sediments and have been used for reconstructing both contemporary and past ecosystems. However, studies of the taphonomic processes by which ‘dirt’ DNA accumulate, disperse and degrade in the environment, is needed to explore potential bias in biodiversity estimates using the approach.

This study explores the accuracy and reliability of species detection from soil samples, using Rosche GS-FLX high-throughput sequencing, coupled with 16S mitochondrial DNA (mtDNA) metabarcoding. Study sites at safari parks, zoological gardens and farms were selected due to detailed records of the presence of exotic species. This framework was used to monitor how edaphic and biotic factors influence taphonomic processes of ‘dirt’ DNA originating from free-ranging vertebrate species.

The measured Vertebrate species richness inferred from ‘dirt’ DNA in surface soil, was improved by increasing the sample density and spatial scale, rather than increasing the amount of soil processed from individual soil samples. Intriguingly, the relative proportions of mammal ‘dirt’ DNA haplotypes identified in the soil surface more closely reflects the total biomass of the species on site, rather than the individual populations census size. However, animal behavior was observed to bias biodiversity estimates at the sampled scale, and one species, which had recently been introduced, was not detected.

Additionally, the use of marker DNA molecules in high-throughput sequencing experiments, allows between sample comparisons of relative haplotype frequencies. This approach was used to explore different sediment types for their susceptibility to DNA leaching, and general guidelines are defined as to when leaching is likely to affect diversity estimates from ancient sediments. A better understanding of this process, leading to the incorrect temporal association of results, is important for the analysis of sediment ancient DNA (sedaDNA) obtained from ancient environmental samples.

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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)
  • ZINGER Lucie
    • IBENS
    • Paris (France)
  • 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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