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

Predicting the responses of European grassland communities to climate and land cover change

European grasslands are among the most species-rich ecosystems on small spatial scales. However, human-induced activities like land use and climate change pose significant threats to this diversity. To explore how climate and land cover change will affect biodiversity and community composition in grassland ecosystems, we conducted joint species distribution models (SDMs) on the extensive vegetation-plot database sPlotOpen to project distributions of 1178 grassland species across Europe under current conditions and three future scenarios. We further compared model accuracy and computational efficiency between joint SDMs (JSDMs) and stacked SDMs, especially for rare species. Our results show that: (i) grassland communities in the mountain ranges are expected to suffer high rates of species loss, while those in western, northern and eastern Europe will experience substantial turnover; (ii) scaling anomalies were observed in the predicted species richness, reflecting regional differences in the dominant drivers of assembly processes; (iii) JSDMs did not outperform stacked SDMs in predictive power but demonstrated superior efficiency in model fitting and predicting; and (iv) incorporating co-occurrence datasets improved the model performance in predicting the distribution of rare species. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.

Using ancient sedimentary DNA to forecast ecosystem trajectories under climate change

Ecosystem response to climate change is complex. In order to forecast ecosystem dynamics, we need high-quality data on changes in past species abundance that can inform process-based models. Sedimentary ancient DNA (sedaDNA) has revolutionised our ability to document past ecosystems' dynamics. It provides time series of increased taxonomic resolution compared to microfossils (pollen, spores), and can often give species-level information, especially for past vascular plant and mammal abundances. Time series are much richer in information than contemporary spatial distribution information, which have been traditionally used to train models for predicting biodiversity and ecosystem responses to climate change. Here, we outline the potential contribution of sedaDNA to forecast ecosystem changes. We showcase how species-level time series may allow quantification of the effect of biotic interactions in ecosystem dynamics, and be used to estimate dispersal rates when a dense network of sites is available. By combining palaeo-time series, process-based models, and inverse modelling, we can recover the biotic and abiotic processes underlying ecosystem dynamics, which are traditionally very challenging to characterise. Dynamic models informed by sedaDNA can further be used to extrapolate beyond current dynamics and provide robust forecasts of ecosystem responses to future climate change. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.

A novel approach for quantitatively distinguishing between anthropogenic and natural effects on paleovegetation

How to distinguish and quantify past human impacts on vegetation is a significant challenge in paleoecology. Here, we propose a novel method, the error inflection point-discriminant technique. It finds out the inflection points (IPs) of the regression errors of pollen-climate transfer functions using modern pollen spectra from vegetation with different values of the Human Influence Index (HII), which represent the HII threshold values of native/secondary and secondary/artificial vegetation systems. Our results show that the HII value at the native/secondary vegetation IPs is approximately 22 and globally uniform, whereas it varies regionally for the secondary/artificial vegetation IPs. In a case study of the Liangzhu archaeological site in the lower Yangtze River, discriminant functions for pollen spectra from three vegetation types and pollen-climate transfer functions of the native vegetation were established to reconstruct paleovegetation and paleoclimate over the past 6,600 years. Our study demonstrates this method's feasibility for quantitatively distinguishing human impacts on paleovegetation and assessing quantitative paleoclimate reconstructions using pollen data.

Mitochondrial genomes of Pleistocene megafauna retrieved from recent sediment layers of two Siberian lakes

Ancient environmental DNA (aeDNA) from lake sediments has yielded remarkable insights for the reconstruction of past ecosystems, including suggestions of late survival of extinct species. However, translocation and lateral inflow of DNA in sediments can potentially distort the stratigraphic signal of the DNA. Using three different approaches on two short lake sediment cores of the Yamal peninsula, West Siberia, with ages spanning only the past hundreds of years, we detect DNA and identified mitochondrial genomes of multiple mammoth and woolly rhinoceros individuals-both species that have been extinct for thousands of years on the mainland. The occurrence of clearly identifiable aeDNA of extinct Pleistocene megafauna (e.g. >400 K reads in one core) throughout these two short subsurface cores, along with specificities of sedimentology and dating, confirm that processes acting on regional scales, such as extensive permafrost thawing, can influence the aeDNA record and should be accounted for in aeDNA paleoecology.

Late Pleistocene stickleback environmental genomes reveal the chronology of freshwater adaptation

Directly observing the chronology and tempo of adaptation in response to ecological change is rarely possible in natural ecosystems. Sedimentary ancient DNA (sedaDNA) has been shown to be a tractable source of genome-scale data of long-dead organisms1,2,3 and to thereby potentially provide an understanding of the evolutionary histories of past populations.4,5 To date, time series of ecosystem biodiversity have been reconstructed from sedaDNA, typically using DNA metabarcoding or shotgun sequence data generated from less than 1 g of sediment.6,7 Here, we maximize sequence coverage by extracting DNA from ∼50× more sediment per sample than the majority of previous studies1,2,3 to achieve genotype resolution. From a time series of Late Pleistocene sediments spanning from a marine to freshwater ecosystem, we compare adaptive genotypes reconstructed from the environmental genomes of three-spined stickleback at key time points of this transition. We find a staggered temporal dynamic in which freshwater alleles at known loci of large effect in marine-freshwater divergence of three-spined stickleback (e.g., EDA)8 were already established during the brackish phase of the formation of the isolation basin. However, marine alleles were still detected across the majority of marine-freshwater divergence-associated loci, even after the complete isolation of the lake from marine ingression. Our retrospective approach to studying adaptation from environmental genomes of three-spined sticklebacks at the end of the last glacial period complements contemporary experimental approaches9,10,11 and highlights the untapped potential for retrospective "evolve and resequence" natural experiments using sedaDNA.

Transnational conservation to anticipate future plant shifts in Europe

To meet the COP15 biodiversity framework in the European Union (EU), one target is to protect 30% of its land by 2030 through a resilient transnational conservation network. The European Alps are a key hub of this network hosting some of the most extensive natural areas and biodiversity hotspots in Europe. Here we assess the robustness of the current European reserve network to safeguard the European Alps' flora by 2080 using semi-mechanistic simulations. We first highlight that the current network needs strong readjustments as it does not capture biodiversity patterns as well as our conservation simulations. Overall, we predict a strong shift in conservation need through time along latitudes, and from lower to higher elevations as plants migrate upslope and shrink their distribution. While increasing species, trait and evolutionary diversity, migration could also threaten 70% of the resident flora. In the face of global changes, the future European reserve network will need to ensure strong elevation and latitudinal connections to complementarily protect multifaceted biodiversity beyond national borders.

Human-triggered magnification of erosion rates in European Alps since the Bronze Age

A major feature of the Anthropocene is the drastic increase in global soil erosion. Soil erosion is threatening Earth habitability not only as soils are an essential component of the Earth system but also because societies depend on soils. However, proper quantification of the impact of human activities on erosion over thousands of years is still lacking. This is particularly crucial in mountainous areas, where the highest erosion rates are recorded. Here we use the Lake Bourget catchment, one of the largest in the European Alps, to estimate quantitatively the impact of human activities on erosion. Based on a multi-proxy, source-to-sink approach relying on isotopic geochemistry, we discriminate the effects of climate fluctuations from those of human activities on erosion over the last 10,000 years. We demonstrate that until 3800 years ago, climate is the only driver of erosion. From that time on, climate alone cannot explain the measured rates of erosion. Thanks to an unprecedented regional paleoenvironmental reconstruction, we highlight that the development of pastoralism at high altitudes from the Bronze Age onwards and the extension of agriculture starting in the Middle Ages were key factors in the drastic increase in erosion observed in the Alps.