Exceptionally rich sedaDNA record from a subalpine lake in the Central Alps reveals plant responses to climate change and human land use

The increase in plant species richness in the Alps over the last century has been described as a direct response to climate warming. Alpine ecosystems are expected to have an upward displacement of vegetation, resulting in shifts of species ranges, high replacement rates, and species loss. To apply proper management measures, it is necessary to understand how drivers of change affect species and ecosystem tipping points. Palaeoecological studies allow us to understand how species responded to similar situations in the past. However, such studies are often challenged by proxy preservation and taxonomic resolution. Metabarcoding approaches based on sedimentary ancient DNA (sedaDNA) can overcome these caveats. 

Here we use plant sedaDNA and the new PhyloAlps taxonomic reference database, which covers 4500 plant taxa from the Alps, to explore alpine floral diversity of Sulseewlii, a subalpine lake in the Central Alps (Switzerland). We present a 12,000 year record of vegetational composition and structural changes in a subalpine ecosystem. To disentangle the relationship between climate and vegetation, we used a novel local temperature reconstruction inferred from chironomids of the same lake. We also used coprophilous fungal spores and charcoal, together with pastoral and arable indicators, to infer human pressure. 

With 377 identified taxa, including 140 at species level, Sulseewlii has yielded the richest dataset of plant sedaDNA to date and emphasizes the Alps as an important biodiversity hotspot in Europe. Out of the identified taxa, 91 are indicators that allowed us to reconstruct the vegetation stages and altitudinal shifts of the main vegetation groups. Total taxonomic richness increases from the onset of the Holocene and has a similar pattern to subalpine-montane DNA taxa, with three marked drops at 8200, 3200, and ~500 cal yr BP. Plant sedaDNA registered a marked transition from alpine to subalpine communities at the onset of the Holocene. The highest proportions of montane taxa occurred during the Holocene climatic optimum (9,000-6,000 cal yr BP). Finally, a shift back to subalpine-montane species with some lowland influence occurs as we approach the present.