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

Abstract

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.

Hybridization capture of larch (LarixMill) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forests

“…Slon et al (2017), assigned more than 10% of their shotgun reads that derived from cave sediments and Ahmed et al (2018) reported 16% of assigned sequences from ancient lake sediments and 70% of hits over multiple taxa. On the other hand, Pedersen et al (2016) assigned 0.3% of the quality filtered reads obtained from ancient lake sediments, and Parducci et al (2019) reported a read assignment of 3.4% of sedaDNA shotgun sequencing. Different sample material, wet lab processing and sequence databases used for assignment make it difficult to properly compare the assignment rate.…”

“…Sequencing of the entire DNA extracted from ancient sediments, termed metagenomic shotgun sequencing, has been shown to provide information on the entire taxonomic composition of the sample (e.g., fungi, bacteria, archaea; Ahmed et al 2018;Parducci et al 2019). By sequencing complete DNA molecules, it is possible to authenticate ancient sequences versus modern contaminants by their specific postmortem DNA damage patterns towards the ends of the molecules (Ginolhac, Rasmussen, Gilbert, Willerslev, & Orlando, 2011).…”

An open-sourced bioinformatic pipeline for the processing of Next-Generation Sequencing derived nucleotide reads: Identification and authentication of ancient metagenomic DNA

“…Currently, there are few pipelines available for the analysis of ancient metagenomic DNA (aDNA) [1][2][3][4] The limited number of bioinformatic pipelines for aDNA metagenomics can be attributed to a low yield of DNA compared to that achieved in modern metagenomic DNA extraction. This results in the use of high-cost DNA capture techniques to improve aDNA yields to levels suitable for bioinformatic assessment [3][4][5][6][7] .…”

“…Those metagenomic studies performed using DNA capture techniques, necessary for existing bioinformatic pipelines, allow for the implementation of "quick" bioinformatic comparisons using RefSeq or Blastn megablast options due to higher yields of DNA [5][6][7] . Due to higher yields, however, these pipelines, by their nature, often compromise between read conservation and processing time, thus losing sequences throughout individual computational steps.…”

“…The damage pattern of aDNA serves as a useful tool in the distinction between ancient and modern DNA sequences 10,11 . Characteristically, ancient sequences should consist of heavily fragmented DNA strands 6,12,13 , depurination, depyrimidination and deamination events 14,15 and miscoding lesions 16,17 . These characteristics therefore form the central damage pattern for aDNA authentication in the development of this bioinformatic pipeline.…”