Molecular- and pollen-based vegetation analysis in lake sediments from central Scandinavia

Authors

  • Laura Parducci,

    Corresponding author
    1. Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
    2. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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  • Irina Matetovici,

    1. Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
    2. Molecular Biology Centre, Interdisciplinary Research Institute on Bio-Nano-Sciences, Babes-Bolyai-University ClujNapoca, Cluj-Napoca, Romania
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  • Sonia L. Fontana,

    1. Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
    Current affiliation:
    1. Department of Palynology and Climate Dynamics, University of Göttingen, Göttingen, Germany
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  • K. D. Bennett,

    1. School of Geography, Archaeology & Palaeoecology, Queen's University Belfast, Belfast, UK
    2. Department of Earth Sciences, Uppsala University, Uppsala, Sweden
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  • Yoshihisa Suyama,

    1. Graduate School of Agricultural Science, Tohoku University, Osaki, Miyagi, Japan
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  • James Haile,

    1. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
    Current affiliation:
    1. Murdoch University Ancient DNA Laboratory, Murdoch University, Perth, Australia
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  • Kurt H. Kjær,

    1. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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  • Nicolaj K. Larsen,

    1. Department of Geoscience, Aarhus University, Aarhus, Denmark
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  • Andreas D. Drouzas,

    1. School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
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  • Eske Willerslev

    1. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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Errata

This article is corrected by:

  1. Errata: Molecular- and pollen-based vegetation analysis in lake sediments from central Scandinavia Volume 23, Issue 4, 986, Article first published online: 29 January 2014

Abstract

Plant and animal biodiversity can be studied by obtaining DNA directly from the environment. This new approach in combination with the use of generic barcoding primers (metabarcoding) has been suggested as complementary or alternative to traditional biodiversity monitoring in ancient soil sediments. However, the extent to which metabarcoding truly reflects plant composition remains unclear, as does its power to identify species with no pollen or macrofossil evidence. Here, we compared pollen-based and metabarcoding approaches to explore the Holocene plant composition around two lakes in central Scandinavia. At one site, we also compared barcoding results with those obtained in earlier studies with species-specific primers. The pollen analyses revealed a larger number of taxa (46), of which the majority (78%) was not identified by metabarcoding. The metabarcoding identified 14 taxa (MTUs), but allowed identification to a lower taxonomical level. The combined analyses identified 52 taxa. The barcoding primers may favour amplification of certain taxa, as they did not detect taxa previously identified with species-specific primers. Taphonomy and selectiveness of the primers are likely the major factors influencing these results. We conclude that metabarcoding from lake sediments provides a complementary, but not an alternative, tool to pollen analysis for investigating past flora. In the absence of other fossil evidence, metabarcoding gives a local and important signal from the vegetation, but the resulting assemblages show limited capacity to detect all taxa, regardless of their abundance around the lake. We suggest that metabarcoding is followed by pollen analysis and the use of species-specific primers to provide the most comprehensive signal from the environment.

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