Shot gun sequencing of sedimentary ancient DNA from an Arctic lake reveals ecosystem changes through climate regime transitions over the last 50,000 years

Sedimentary ancient DNA is a valuable proxy to study ecosystem change during the past. In particular, Arctic lakes provide fantastic archives of well-preserved DNA in lake sediment cores and provide reconstructions of ecosystem change during climate transitions in the past, which help to predict prospective environmental changes under current rapid warming known to be strongest in the Arctic. Our analyses are conducted on a 10 m sediment core from Lake Ilirney, located in Eastern Chukotka, which covers the last 50 ka of major climate transitions from the lake’s development within a warmer period previous to the last glacial towards nowadays. We prepared seventeen single-stranded DNA libraries from different time slices and used shot gun sequencing, an innovative method neglecting target enrichment, to achieve a portray of the past biotic composition. The bioinformatic data analyses included data trimming and merging with Fastp and k-mer based taxonomic classification against the nucleotide database using Kraken2. Preliminary results revealed about 372 bacterial families (about 90.1% of total reads), 651 eukaryotic families (8.7%) and a few Archaea (1.1%). Dominant eukaryotic groups are plants (Saliceae, Poaceae, and Rosaceae), protists (Monodopsidaceae, Oomycota and flagellates), fish (Salmonidae, Cyprinidae), birds (Phasianidae) and mammals (Muridae). Our data confirms compositional changes of plants throughout the last 28 ka known from pollen and metabarcoding analyses of a parallel core. Further, our data revealed most prominent turnover of the eukaryotic key taxa at about 30 and 12 ka which corresponds to the major climatic transitions from glacial-interglacial periods. The detailed investigation of compositional patterns and authenticity of ancient DNA data will improve our understanding of ecosystem change in the Arctic over millennial time scales.