Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden

Laura Parducci1, Inger Greve Alsos2, Per Unneberg3, Mikkel W. Pedersen4, Lu Han1, 5, Youri Lammers2, J. Sakari Salonen6, Minna M. Väliranta7, Tanja Slotte8, 9, Barbara Wohlfarth10

1Department of Ecology and Genetics, The Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
2Tromsø Museum, University of Tromsø – The Arctic University of Norway, Tromsø, Norway
3Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
4Department of Zoology, University of Cambridge, Cambridge, United Kingdom
5Ancient DNA Laboratory, College of Life Sciences, Jilin University, Changchun, China
6Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland
7Environmental Change Research Unit (ECRU), Ecosystems and Environment Research Programme, University of Helsinki, Helsinki, Finland
8Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
9Science for Life Laboratory, Solna, Sweden
10Department of Geological Sciences and Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden

The lake sediments of Hässeldala Port in south-east Sweden provide an archive of local and regional environmental conditions ~14.5–9.5 ka BP (thousand years before present) and allow testing DNA sequencing techniques to reconstruct past vegetation changes. We combined shotgun sequencing with plant micro- and macrofossil analyses to investigate sediments dating to the Allerød (14.1–12.7 ka BP), Younger Dryas (12.7–11.7 ka BP), and Preboreal (<11.7 ka BP). Number of reads and taxa were not associated with sample age or organic content. This suggests that, beyond the initial rapid degradation, DNA is still present. The proportion of recovered plant DNA was low, but allowed identifying an important number of plant taxa, thus adding valid information on the composition of the local vegetation. Importantly, DNA provides a stronger signal of plant community changes than plant micro- and plant macrofossil analyses alone, since a larger number of new taxa were recorded in Younger Dryas samples. A comparison between the three proxies highlights differences and similarities and supports earlier findings that plants growing close to or within a lake are recorded by DNA. Plant macrofossil remains moreover show that tree birch was present close to the ancient lake since the Allerød; together with the DNA results, this indicates that boreal to subarctic climatic conditions also prevailed during the cold Younger Dryas interval. Increasing DNA reference libraries and enrichment strategies prior to sequencing are necessary to improve the potential and accuracy of plant identification using the shotgun metagenomic approach.

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