Charline Giguet-Covex

Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data

Environmental DNA (eDNA) metabarcoding is increasingly used to study the present and past biodiversity. eDNA analyses often rely on amplification of very small quantities or degraded DNA. To avoid missing detection of taxa that are actually present (false negatives), multiple extractions and amplifications of the same samples are often performed. However, the level of replication needed for reliable estimates of the presence/absence patterns remains an unaddressed topic. Furthermore, degraded DNA and PCR/sequencing errors might produce false positives. We used simulations and empirical data to evaluate the level of replication required for accurate detection of targeted taxa in different contexts and to assess the performance of methods used to reduce the risk of false detections. Furthermore, we evaluated whether statistical approaches developed to estimate occupancy in the presence of observational errors can successfully estimate true prevalence, detection probability and false‐positive rates. Replications reduced the rate of false negatives; the optimal level of replication was strongly dependent on the detection probability of taxa. Occupancy models successfully estimated true prevalence, detection probability and false‐positive rates, but their performance increased with the number of replicates. At least eight PCR replicates should be performed if detection probability is not high, such as in ancient DNA studies. Multiple DNA extractions from the same sample yielded consistent results; in some cases, collecting multiple samples from the same locality allowed detecting more species. The optimal level of replication for accurate species detection strongly varies among studies and could be explicitly estimated to improve the reliability of results.

Long livestock farming history and human landscape shaping revealed by lake sediment DNA

The reconstruction of human-driven, Earth-shaping dynamics is important for understanding past human/environment interactions and for helping human societies that currently face global changes. However, it is often challenging to distinguish the effects of the climate from human activities on environmental changes. Here we evaluate an approach based on DNA metabarcoding used on lake sediments to provide the first high-resolution reconstruction of plant cover and livestock farming history since the Neolithic Period. By comparing these data with a previous reconstruction of erosive event frequency, we show that the most intense erosion period was caused by deforestation and overgrazing by sheep and cowherds during the Late Iron Age and Roman Period. Tracking plants and domestic mammals using lake sediment DNA (lake sedDNA) is a new, promising method for tracing past human practices, and it provides a new outlook of the effects of anthropogenic factors on landscape-scale changes.

Changes in erosion patterns during the Holocene in a currently treeless subalpine catchment inferred from lake sediment geochemistry (Lake Anterne, 2063 m a.s.l., NW French Alps): The role of climate and human activities

A high-resolution sedimentological and geochemical study was performed on a 20 m long core from the alpine Lake Anterne (2063 m a.s.l., NW French Alps) spanning the last 10 ka. Sedimentation is mainly of minerogenic origin. The organic matter quantity (TOC%) as well as its quality (hydrogen (HI) and oxygen (OI) indices) both indicate the progressive onset and subsequent stabilization of vegetation cover in the catchment from 9950 to 5550 cal. BP. During this phase, the pedogenic process of carbonate dissolution is marked by a decrease in the calcium content in the sediment record. Between 7850 and 5550 cal. BP, very low manganese concentrations suggest anoxic conditions in the bottom-water of Lake Anterne. These are caused by a relatively high organic matter (terrestrial and lacustrine) content, a low flood frequency and longer summer stratification triggered by warmer conditions. From 5550 cal. BP, a decrease in TOC, stabilization of HI and higher sedimentation rates together reflect increased erosion rates of leptosols and developed soils, probably due to a colder and wetter climate. Then, three periods of important soil destabilization are marked by an increased frequency and thickness of flood deposits during the Bronze Age and by increases in topsoil erosion relative to leptosols (HI increases) during the late Iron Age/Roman period and the Medieval periods. These periods are also characterized by higher sedimentation rates. According to palynological data, human impact (deforestation and/or pasturing activity) probably triggered these periods of increased soil erosion.

Reconstructing long-term human impacts on plant communities : an ecological approach based on lake sediment DNA

Paleoenvironmental studies are essential to understand biodiversity changes over long timescales and to assess the relative importance of anthropogenic and environmental factors. Sedimentary ancient DNA (sedaDNA) is an emerging tool in the field of paleoecology and has proven to be a complementary approach to the use of pollen and macroremains for investigating past community changes. SedaDNA‐based reconstructions of ancient environments often rely on indicator taxa or expert knowledge, but quantitative ecological analyses might provide more objective information. Here, we analysed sedaDNA to investigate plant community trajectories in the catchment of a high‐elevation lake in the Alps over the last 6400 years. We combined data on past and present plant species assemblages along with sedimentological and geochemical records to assess the relative impact of human activities through pastoralism, and abiotic factors (temperature and soil evolution). Over the last 6400 years, we identified significant variation in plant communities, mostly related to soil evolution and pastoral activities. An abrupt vegetational change corresponding to the establishment of an agropastoral landscape was detected during the Late Holocene, approximately 4500 years ago, with the replacement of mountain forests and tall‐herb communities by heathlands and grazed lands. Our results highlight the importance of anthropogenic activities in mountain areas for the long‐term evolution of local plant assemblages. SedaDNA data, associated with other paleoenvironmental proxies and present plant assemblages, appear to be a relevant tool for reconstruction of plant cover history. Their integration, in conjunction with classical tools, offers interesting perspectives for a better understanding of long‐term ecosystem dynamics under the influence of human‐induced and environmental drivers.

High-resolution paleolimnology opens new management perspectives for lakes adaptation to climate warming

Varved lake sediments provide opportunities for high-resolution paleolimnological investigations that may extend monitoring surveys in order to target priority management actions under climate warming. This paper provides the synthesis of an international research program relying on >150 years-long, varved records for three managed perialpine lakes in Europe (Lakes Geneva, Annecy and Bourget). The dynamics of the dominant, local human pressures, as well as the ecological responses in the pelagic, benthic and littoral habitats were reconstructed using classical and newly developed paleo-proxies. Statistical modelling achieved the hierarchization of the drivers of their ecological trajectories. All three lakes underwent different levels of eutrophication in the first half of the XXth century, followed by re-oligotrophication. Climate warming came along with a 2°C increase in air temperature over the last century, to which lakes were unequally thermally vulnerable. Unsurprisingly, phosphorous concentration has been the dominant ecological driver over the last century. Yet, other human-influenced, local environmental drivers (fisheries management practices, river regulations) have also significantly inflected ecological trajectories. Climate change has been impacting all habitats at rates that, in some cases, exceeded those of local factors. The amplitude and ecological responses to similar climate change varied between lakes, but, at least for pelagic habitats, rather depended on the intensity of local human pressures than on the thermal effect of climate change. Deep habitats yet showed higher sensitivity to climate change but substantial influence of river flows. As a consequence, adapted local management strategies, fully integrating nutrient inputs, fisheries management and hydrological regulations, may enable mitigating the deleterious consequences of ongoing climate change on these ecosystems.

Soil community assembly varies across body sizes in a tropical forest

The relative influence of deterministic niche-based (i.e. abiotic conditions, biotic interactions) and stochastic-distance dependent neutral processes (i.e. demography, dispersal) in shaping communities has been extensively studied for various organisms, but is far less explored jointly across the tree of life, in particular in soil environments. Here, using a thorough DNA-based census of the whole soil biota in a large tropical forest plot, we show that soil aluminium, topography, and plant species identity are all important drivers of soil richness and community composition. Body size emerges as an important feature of the comparative ecology of the different taxa at the studied spatial scale, with microorganisms being more importantly controlled by environmental factors, while soil mesofauna rather display random spatial distribution. We infer that niche-based processes contribute differently to community assembly across trophic levels due to spatial scaling. Body size could hence help better quantifying important properties of multitrophic assemblages.

Coupling indicators and lumped-parameter modeling to assess suspended matter and soluble phosphorus losses

For ecological and economic issues, evaluating the environmental fate of dissolved and suspended matter in catchments and river ecosystems still remains a challenge for the preservation and management of natural resources. Models are useful tools and may help to cope with this challenge, and especially to define the relationships between the state of natural systems and land and river management/uses. As it is difficult - even impossible - to carry out experiments on natural systems such as catchments, models are also useful to test hypotheses about the underlying processes acting on dissolved and suspended losses. We propose an innovative approach to achieve these objectives. By coupling environmental indicators and lumped modeling, this study aims to develop a conceptual and general framework to evaluate and test the functions that drive particulate and dissolved matter flows at the catchment and landscape scales, while respecting the constraint of parsimony for the number of model parameters. Calculated suspended matter (SM) and soluble reactive phosphorus (SRP) losses agreed well with field data. 210Pbex (excess Pb) activities in core sediments were also compared to those of 210Pbex calculated from the filling of the reservoir. Our models are parsimonious and this does not impair their accuracy in reproducing recorded outflows or evaluating the sedimentation processes associated to particulate outflows. Considering the adequacy of our models, we validate the hypothesis that river bank erosion and water table behavior are the driving processes that govern losses of particulate and solute forms of P, in the studied extensive agriculture conditions.