High resolution ancient sedimentary DNA shows that alpine plant diversity is associated with human land use and climate change

Abstract

The European Alps are highly rich in species, but their future may be threatened by ongoing changes in human land use and climate. Here, we reconstructed vegetation, temperature, human impact and livestock over the past ~12,000 years from Lake Sulsseewli, based on sedimentary ancient plant and mammal DNA, pollen, spores, chironomids, and microcharcoal. We assembled a highly-complete local DNA reference library (PhyloAlps, 3923 plant taxa), and used this to obtain an exceptionally rich sedaDNA record of 366 plant taxa. Vegetation mainly responded to climate during the early Holocene, while human activity had an additional influence on vegetation from 6 ka onwards. Land-use shifted from episodic grazing during the Neolithic and Bronze Age to agropastoralism in the Middle Ages. Associated human deforestation allowed the coexistence of plant species typically found at different elevational belts, leading to levels of plant richness that characterise the current high diversity of this region. Our findings indicate a positive association between low intensity agropastoral activities and precipitation with the maintenance of the unique subalpine and alpine plant diversity of the European Alps.

Environmental DNA of aquatic macrophytes: the potential for reconstructing past and present vegetation and environments

“…Beyond ecological and environmental reconstructions, the sed aDNA signal from macrophytes could in the future be leveraged to address evolutionary questions. High-resolution time series can be combined with other proxies in order to allow statistical analyses and inference of causal relationships among drivers of ecosystem changes, such as human land use and climate change (Garcés-Pastor et al, 2022). With the rapid ongoing methodological improvements, distinguishing closely related species and even haplotypes could support the fine-scale mapping of genetic diversity and its variation in time and space (Epp et al, 2018), and help retrace postglacial colonisation routes to solve the origin of modern boreal and arctic vegetation.…”

Towards exhaustive community ecology via DNA metabarcoding

“…Furthermore, to maximize the utility, taxonomic identification should use data across the genome. Unfortunately, so far genomic information outside the barcode regions is mostly limited to vertebrates, some plants (Alsos et al, 2020; Garcés‐Pastor et al, 2022), and commercially important species. As a consequence, evidences of the advantage of shotgun sequencing over PCR‐based metabarcoding for broadscale community analyses remain mixed, so far (Bell et al, 2021; Murchie et al, 2020; Parducci et al, 2019; Paula et al, 2022).…”

“…Nevertheless, one could imagine enrichment in taxonomically informative DNA molecules by designing probes based on highly conserved regions of ribosomal RNAs, and analysing the more variable flanking regions to retrieve taxonomic information. Of course, as with the shotgun sequencing approach, reference databases constructed from genome skimming are required for both the definition of probes and for identification (Coissac et al, 2016; Garcés‐Pastor et al, 2022).…”

“…New, more complete reference databases can be generated using high‐throughput sequencing approaches (e.g., genome skimming; Coissac et al, 2016). Genome skimming would allow covering broad sections of the genome (i.e., organelle(s) and nuclear ribosomal DNA), can be useful for all the above‐described approaches, and might even serve as starting point for the identification of new markers (Coissac et al, 2016; Garcés‐Pastor et al, 2022). An additional issue is related to the completeness of databases, which is highly variable across taxa and geographic areas (Weigand et al, 2019).…”

Radiocarbon sampling efforts for high-precision lake sediment chronologies

“…Indeed, recently published sedimentary studies usually include records based on a similar number of radiocarbon ages as earlier studies, resulting in records with intermediate chronological precision (e.g. Duprat-Oualid et al, 2017; Garcés-Pastor et al, 2022; Gassner et al, 2020; Rösch et al, 2021). These chronologies generally have relatively wide 95% (2σ) probabilities of many decades to several hundred calibrated years in some cases, resulting in large chronological uncertainties (e.g.…”