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

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.

Proxy comparison in ancient peat sediments: pollen, macrofossil and plant DNA

“…There are several reasons why the DNA and the traditional palaeoecological approaches produce different results and these have been recently discussed by Parducci et al [7]. One reason may be that the pollen, macrofossil and DNA originate from different plant tissues with only partial mixing and may even represent different plant communities depending on the study environment that is under investigation (lakes or peat).…”

“…These records have indicated that plants have expanded and contracted their ranges many times during the last glacial-interglacial cycles in both hemispheres. A weakness of the fossil pollen record is, however, that the absence of pollen in a sediment sample does not rule out the possibility of small low-density populations [6,7]. In these cases, plant macrofossils, such as bark, leaves and needles, offer stronger evidence of the local presence of taxa, thus complementing pollen analysis [8][9][10][11].…”

Pollen DNA barcoding: current applications and future prospects

“…A significant amount of pollen is likely present in the samples taken, together with plant fragments and anything else present in the sediment. Parducci et al (2013) showed that sedaDNA metabarcoding is better at detecting plants that produce restricted amounts of pollen, taxa that are difficult to identify with palynology, and rare plants. It is not certain whether the result is from pollen, or DNA from other parts of plants taken from the sediment sample.…”

“…Most ancient DNA barcoding studies have used sedimentary ancient DNA (sedaDNA) to provide complementary data to macrofossil identification and classic palynology (Jørgensen et al 2012a;Parducci et al 2013;Pedersen et al 2013). A significant amount of pollen is likely present in the samples taken, together with plant fragments and anything else present in the sediment.…”

Sedimentary DNA versus morphology in the analysis of diatom-environment relationships

“…Sedimentary DNA can be used to characterise recent and past biodiversity and thus is suitable to reveal information about past environmental change (Jørgensen et al 2012;Parducci et al 2012;Pedersen et al 2013). A metabarcoding approach to environmental DNA and subsequent DNA sequencing is commonly applied to characterise the composition of communities in environmental samples (Taberlet et al 2012a;Pedersen et al 2015).…”