The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.

The effects of climate change on species richness are debated but can be informed by the past. Here, we generated a sedimentary ancient DNA dataset covering 10 lakes and applied novel methods for data harmonization. We assessed the impact of Holocene climate changes and nutrients on terrestrial plant richness in northern Fennoscandia. We find that richness increased steeply during the rapidly warming Early Holocene. In contrast to findings from most pollen studies, we show that richness continued to increase thereafter, although the climate was stable, with richness and the regional species pool only stabilizing during the past three millennia. Furthermore, overall increases in richness were greater in catchments with higher soil nutrient availability. We suggest that richness will increase with ongoing warming, especially at localities with high nutrient availability and assuming that human activity remains low in the region, although lags of millennia may be expected.

SummaryIt is crucial to understand how climate warming and other environmental factors affect biodiversity, especially in the rapidly changing northern latitudes.We use sedimentary ancient DNA (sedaDNA) metabarcoding to estimate taxonomic richness, and local and regional species pools of terrestrial plants for 10 lakes in northern Fennoscandia over the Holocene.In total, 288 taxa were found in the 316 samples analysed, with local species pools of 89-200 and mean taxonomic richness of 21-65 per catchment. Quality control showed that sedaDNA is a reliable estimate of richness. Local and regional species pools showed a steep increase in the Early Holocene, when the highest rate of warming took place, and continued to increase through the Middle and into the Late Holocene, although temperature decreased over these periods. Only the regional species pool levels off during the last two millennia. Richness and local species pools were always higher in catchments with higher bedrock nutrient availability.We find sedaDNA to be a good proxy for diversity, opening avenues to detect patterns hereto unknown, and we provide a robust methodological approach to its application. Our findings suggest we can expect time lags and environmental factors to affect species richness also of the following global warming.