A comparative study of ancient sedimentary DNA, pollen and macrofossils from permafrost sediments of northern Siberia reveals long‐term vegetational stability

Abstract

Although ancient DNA from sediments (sedaDNA) has been used to investigate past ecosystems, the approach has never been directly compared with the traditional methods of pollen and macrofossil analysis. We conducted a comparative survey of 18 ancient permafrost samples spanning the Late Pleistocene (46-12.5 thousand years ago), from the Taymyr Peninsula in northern Siberia. The results show that pollen, macrofossils and sedaDNA are complementary rather than overlapping and, in combination, reveal more detailed information on plant palaeocommunities than can be achieved by each individual approach. SedaDNA and macrofossils share greater overlap in plant identifications than with pollen, suggesting that sedaDNA is local in origin. These two proxies also permit identification to lower taxonomic levels than pollen, enabling investigation into temporal changes in species composition and the determination of indicator species to describe environmental changes. Combining data from all three proxies reveals an area continually dominated by a mosaic vegetation of tundra-steppe, pioneer and wet-indicator plants. Such vegetational stability is unexpected, given the severe climate changes taking place in the Northern Hemisphere during this time, with changes in average annual temperatures of >22 °C. This may explain the abundance of ice-age mammals such as horse and bison in Taymyr Peninsula during the Pleistocene and why it acted as a refugium for the last mainland woolly mammoth. Our finding reveals the benefits of combining sedaDNA, pollen and macrofossil for palaeovegetational reconstruction and adds to the increasing evidence suggesting large areas of the Northern Hemisphere remained ecologically stable during the Late Pleistocene.

The ecology of environmental DNA and implications for conservation genetics

“…Although the detection of ancient DNA in terrestrial (Willerslev et al 2003;Lydolph et al 2005;Haile et al 2009;Hebsgaard et al 2009;Jørgensen et al 2012) and aquatic (Matisoo-Smith et al 2008;Anderson-Carpenter et al 2011;Pedersen et al 2013;Stager et al 2015) sediments as well as frozen ice cores (Willerslev et al 2007) testifies to the fact that eDNA from diverse taxa can remain in the environment for a very long period of time under certain conditions, DNA possesses limited chemical stability (Lindahl 1993); in most cases, as soon as it is shed from an organism eDNA begins to degrade (Fig. 1d).…”

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

“…What are required for plant aDNA studies are (i) a well-preserved source of aDNA information of local origin, (ii) abundant and well-dated fossil material, and (iii) powerful molecular techniques to extract aDNA information efficiently. Pollen, macrofossils and sedimentary DNA preserved in peat and lake sediments have proven to be an optimal source of plant DNA information in the recent past [1][2][3][4][5].…”

“…Nonetheless, whether macrofossils or other plant tissues like pollen are the primary source of sedDNA is not clear and this can only be tested by performing comparative studies with sedDNA, macrofossils and pollen from the same sediment settings. Jørgensen et al [3] conducted such a comparative survey and used the metabarcoding technique (identification of taxa from environmental samples such as sedDNA against a database/library of reference sequences [13]) on ancient permafrost samples from northern Siberia spanning the Late Pleistocene. Using generic primers specifically designed for plant-degraded DNA recovered from sediments (trnL, [2]), they showed that the three proxies (pollen, macrofossils and sedDNA) are complementary rather than overlapping, but that sedDNA shared a greater overlap with macrofossils, suggesting that it predominantly originates from these remains.…”

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).…”