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

Laura Parducci, Irina Matetovici, Sonia L. Fontana, K.D. Bennett, Yoshihisa Suyama, James Haile, Kurt H. Kjær, Nicolaj K. Larsen, Andreas D. Drouzas, Eske Willerslev

Research output: Contribution to journalArticle

53 Citations (Scopus)

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.
LanguageEnglish
Pages3511–3524
Number of pages14
JournalMolecular Ecology
Volume22
Issue number13
DOIs
Publication statusPublished - Jul 2013

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Scandinavian and Nordic Countries
Scandinavia
Lakes
Pollen
lacustrine deposit
pollen
barcoding
lakes
sediments
vegetation
palynology
botanical composition
Biodiversity
biodiversity
taphonomy
lake
amplification
flora
Holocene
fossil

Keywords

  • ancient DNA
  • barcoding
  • environmental DNA
  • palaeoecology
  • pollen

Cite this

Parducci, L., Matetovici, I., Fontana, S. L., Bennett, K. D., Suyama, Y., Haile, J., ... Willerslev, E. (2013). Molecular- and pollen-based vegetation analysis in lake sediments from central Scandinavia. Molecular Ecology, 22(13), 3511–3524. https://doi.org/10.1111/mec.12298
Parducci, Laura ; Matetovici, Irina ; Fontana, Sonia L. ; Bennett, K.D. ; Suyama, Yoshihisa ; Haile, James ; Kjær, Kurt H. ; Larsen, Nicolaj K. ; Drouzas, Andreas D. ; Willerslev, Eske. / Molecular- and pollen-based vegetation analysis in lake sediments from central Scandinavia. In: Molecular Ecology. 2013 ; Vol. 22, No. 13. pp. 3511–3524.
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Parducci, L, Matetovici, I, Fontana, SL, Bennett, KD, Suyama, Y, Haile, J, Kjær, KH, Larsen, NK, Drouzas, AD & Willerslev, E 2013, 'Molecular- and pollen-based vegetation analysis in lake sediments from central Scandinavia', Molecular Ecology, vol. 22, no. 13, pp. 3511–3524. https://doi.org/10.1111/mec.12298

Molecular- and pollen-based vegetation analysis in lake sediments from central Scandinavia. / Parducci, Laura; Matetovici, Irina; Fontana, Sonia L.; Bennett, K.D.; Suyama, Yoshihisa; Haile, James; Kjær, Kurt H.; Larsen, Nicolaj K.; Drouzas, Andreas D.; Willerslev, Eske.

In: Molecular Ecology, Vol. 22, No. 13, 07.2013, p. 3511–3524.

Research output: Contribution to journalArticle

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AU - Suyama, Yoshihisa

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Parducci L, Matetovici I, Fontana SL, Bennett KD, Suyama Y, Haile J et al. Molecular- and pollen-based vegetation analysis in lake sediments from central Scandinavia. Molecular Ecology. 2013 Jul;22(13):3511–3524. https://doi.org/10.1111/mec.12298