20 Works

Data from: Long-term dynamics in microbial eukaryotes communities: a paleolimnological view based on sedimentary DNA

Eric Capo, Didier Debroas, Fabien Arnaud, Typhaine Guillemot, Vincent Bichet, Laurent Millet, Emilie Gauthier, Charly Massa, Anne-Lise Develle, Cecile Pignol, Franck Lejzerowicz & Isabelle Domaizon
Assessing the extent to which changes in lacustrine biodiversity are affected by anthropogenic or climatic forces requires extensive palaeolimnological data. We used high-throughput sequencing to generate time-series data encompassing over 2200 years of microbial eukaryotes (protists and Fungi) diversity changes from the sedimentary DNA record of two lakes (Lake Bourget in French Alps and Lake Igaliku in Greenland). From 176 samples, we sequenced a large diversity of microbial eukaryotes, with a total 16 386 operational...

Data from: Parasitic versus nutritional regulation of natural fish populations

Amélie Frantz, Marie-Elodie Perga & Jean Guillard
1. Although parasites are expected to affect their host’s fitness, quantitative proof for impacts of parasitism on wild populations is hampered by confounding environmental factors, including dietary resource. 2. Herein, we evaluate whether the physiological conditions of European perch (Perca fluviatilis) in three large peri-alpine lakes (Geneva, Annecy, and Bourget) depend on (a) the nutritional status of the juvenile fish, as revealed by stable isotope and fatty acid compositions, (b) the prevalence of the tapeworm...

Data from: Energy and physiological tolerance explain multi-trophic soil diversity in temperate mountains

Irene Calderon Sanou, Lucie Zinger, Mickael Hedde, Camille Martinez-Almoyna, Amelie Saillard, Julien Renaud, Ludovic Gielly, Norine Khedim, Clement Lionnet, Marc Ohlmann, Tamara Münkemüller & Wilfried Thuiller
Aim – Although soil biodiversity is extremely rich and spatially variable, both in terms of species and trophic groups, we still know little about its main drivers. Here, we contrast four long-standing hypotheses to explain the spatial variation of soil multi-trophic diversity: energy, physiological tolerance, habitat heterogeneity, and resource heterogeneity. Location – French Alps Methods – We built on a large-scale observatory across the French Alps (Orchamp) made of seventeen elevational gradients (~90 plots) ranging...

Interpreting the mammal deposits of Cloggs Cave (SE Australia), GunaiKurnai Aboriginal Country, through community-led partnership research

Matthew McDowell, Bruno David, Russell Mullett, Joanna Fresløv, Jean-Jacques Delannoy, Jerome Mialanes, Jeremy Ash, Joe Crouch, Fiona Petchey, Jessie Buettel & Lee Arnold
Palaeontological animal bone deposits are rarely investigated through research partnerships where the local First Nations communities have a defining hand in both the research questions asked and the research processes. Here we report research undertaken through such a partnership approach at the iconic archaeological site of Cloggs Cave (GunaiKurnai Country, East Gippsland), in the southern foothills of SE Australia’s Great Dividing Range. A new excavation was combined with detailed chronometric dating, high-resolution 3D mapping, and...

Data from: Environment and evolutionary history shape phylogenetic turnover in European tetrapods

Bianca Saladin, Wilfried Thuiller, Catherine H. Graham, Sébastien Lavergne, Luigi Maiorano, Nicolas Salamin & Niklaus E. Zimmermann
Phylogenetic turnover quantifies the evolutionary distance among species assemblages and is central to understanding the main drivers shaping biodiversity. It is affected both by geographic and environmental distance between sites. Therefore, analyzing phylogenetic turnover in environmental space requires removing the effect of geographic distance. Here, we apply a novel approach by deciphering phylogenetic turnover of European tetrapods in environmental space after removing geographic land distance effects. We demonstrate that phylogenetic turnover is strongly structured in...

Spectra induce polarization data of bacteria in soil

Yalin Song, Xiaoqing Shi, André Revil & Xueyuan Kang
Real-time monitoring of microbial activity in porous media is still facing critical challenges because conventional analytical procedures are intrusive. Induced polarization (IP) has shown promises as a non-intrusive monitoring approach of such process. However, there is still a lack of quantitative analysis of soil column experiments to show how IP-based parameters can be related to the density of bacteria. The evolution of bacteria density and induced polarization is here performed in a soil-packed column experiment...

Environmental and biotic drivers of soil microbial β‐diversity across spatial and phylogenetic scales

Loïc Chalmandrier, Johan Pansu, Lucie Zinger, Frederic Boyer, Eric Coissac, Alexandre Génin, Ludovic Gielly, Sébastien Lavergne, Nicolas Legay, Vincent Schilling, Pierre Taberlet, Tamara Münkemüller & Wilfried Thuiller
Soil microbial communities play a key role in ecosystem functioning but still little is known about the processes that determine their turnover (β-diversity) along ecological gradients. Here, we characterize soil microbial β-diversity at two spatial scales and at multiple phylogenetic grains to ask how archaeal, bacterial and fungal communities are shaped by abiotic processes and biotic interactions with plants. We characterized microbial and plant communities using DNA metabarcoding of soil samples distributed across and within...

Adult survival in migratory caribou is negatively associated with MHC functional diversity

Marianne Gagnon, Glenn Yannic, Frédéric Boyer & Steeve Côté
The genes of the major histocompatibility complex (MHC) are involved in acquired, specific immunity in vertebrates. Yet, only a few studies have investigated the fitness consequences of MHC gene diversity in wild populations. Here, we looked at the association between annual survival and body mass and MHC-DRB exon 2 (MHC-DRB) genetic diversity, obtained from high-throughput sequencing, in two declining migratory caribou (Rangifer tarandus) herds. To disentangle the potential direct and general effects of MHC-DRB genetic...

Searching for genetic evidence of demographic decline in an arctic seabird: beware of overlapping generations

Emeline Charbonnel, Claire Daguin, Lucille Caradec, Eléonore Moittié, Olivier Gilg, Maria Gavrilo, Hallvard Strom, Mark L Mallory, Grant Gilchrist, R. I. Guy Morrisson, Raphael Leblois, Camille Roux, Jonathan M Yearsley, Glenn Yannic & Thomas Broquet
Genetic data are useful for detecting sudden population declines in species that are difficult to study in the field. Yet this indirect approach has its own drawbacks, including population structure, mutation patterns, and generation overlap. The ivory gull (Pagophila eburnea), a long-lived Arctic seabird, is currently suffering from rapid alteration of its primary habitat (i.e., sea ice), and dramatic climatic events affecting reproduction and recruitment. However, ivory gulls live in remote areas, and it is...

Full-factorial breeding experiment with lake char (Lake Geneva, winter 2017/2018)

Laura Garaud, David Nusbaumer, Christian De Guttry, Laurie Ançay, Stéphan Jacquet, Emilien Lasne & Claus Wedekind
We sampled 16 wild lake char (Salvelinus umbla) and used their gametes to investigate the genetic consequences of different mating scenarios. A full-factorial breeding was used to separate additive genetic from maternal environmental effects, and embryos were raised singly after sublethal exposures to a pathogen, a common pollutant, or water only. In all treatment groups, embryo development was strongly reduced with increased genetic relatedness between the parents. Contrary to predictions of ‘good genes’ sexual selection,...

Data collected for: The contrasted impacts of grasshoppers on soil microbial activities in function of ecosystem productivity and herbivore diet

Sébastien Ibanez
Herbivory can have contrasted impacts on soil microbes and nutrient cycling, which has stimulated the development of conceptual frameworks exploring the links between below- and aboveground processes. The “productivity model” predicts that herbivores stimulate microbial activities and accelerate nutrient mineralization in productive ecosystems, while they have an opposite effect in less productive ecosystems. In parallel, the “diet model” predicts that herbivores feeding on conservative plants accelerate nutrient cycling while those feeding on exploitative plants decelerate...

Data from: Spatial scale and intraspecific trait variability mediate assembly rules in alpine grasslands

Loïc Chalmandrier, Tamara Münkemüller, Marie-Pascale Colace, Julien Renaud, Serge Aubert, Bradley Z. Carlson, Jean Christophe Clement, Nicolas Legay, Gilles Pellet, Amélie Saillard, Sebastien Lavergne & Wilfried Thuiller
Assembly of grassland communities has long been scrutinized through the lens of functional diversity. Studies generally point to an overwhelming influence of climate on observed patterns of functional diversity, despite experimental evidence demonstrating the importance of biotic interactions. We postulate that this is because most observational studies neglect both scale dependencies of assembly processes and phenotypic variation between individuals. Here, we test for changes in the importance of abiotic filtering and biotic interactions along a...

Data from: Local human pressures influence gene flow in a hybridizing Daphnia species complex

Benjamin Alric, Markus Möst, Isabelle Domaizon, Cecile Pignol, Piet Spaak & Marie-Elodie Perga
Anthropogenic environmental changes are considered critical drivers of the genetic structure of populations and communities through, for example, the facilitation of introgressive hybridization between syntopic species. However, the mechanisms by which environmental perturbations trigger changes in the genetic structure of populations and communities, such as the processes that determine the directionality of hybridization and patterns of mitochondrial introgression over many generations, remain largely unexplored. In this study, the changes in genetic structure of hybridizing members...

Electrical conductivity versus temperature in freezing conditions: a field experiment using a basket geothermal heat exchanger

Andre Revil, A. Coperey & B. Stutz
In-situ experiment. Geothermal setup: Five heat exchangers (HE) are arranged in a line and are buried between 1.1 and 3.5 meters. Just two baskets worked: one (HE.5) for a correct functioning of the heat pump and the other (HE1) to freeze the ground. only, this last exchanger (HE1) has been monitored in temperature and electrical resistivity tomography. The basket HE.5 is too far away to have an influence during this experiment, the heat pump was...

A negative association between horn length and survival in a weakly dimorphic ungulate

Mathieu Douhard, Jean-Paul Crampe, Anne Loison & Christophe Bonenfant
While all models of sexual selection assume that the development and expression of enlarged secondary sexual traits are costly, males with larger ornaments or weapons generally show greater survival or longevity. These studies have mostly been performed in species with high sexual size dimorphism, subject to intense sexual selection. Here we examined the relationships between horn growth and several survival metrics in the weakly dimorphic Pyrenean chamois (Rupicapra pyrenaica). In this unhunted population living at...

No evidence of inbreeding depression in fast declining herds of migratory caribou

Marianne Gagnon, Glenn Yannic, Charles Perrier & Steeve D. Côté
Identifying inbreeding depression early in small and declining populations is essential for management and conservation decisions. Correlations between heterozygosity and fitness (HFCs) provide a way to identify inbreeding depression without prior knowledge of kinship among individuals. In Northern Quebec and Labrador, the size of two herds of migratory caribou (Rivière‐George, RG and Rivière‐aux‐Feuilles, RAF) has declined by one to two orders of magnitude in the last three decades. This raises the question of a possible...

Data from: Tetra-EU 1.0: a species-level trophic meta-web of European tetrapods

Luigi Maiorano, Alessandro Montemaggiori, Gentile Francesco Ficetola, Louise O'Connor & Wilfried Thuiller
Motivation Documenting potential interactions between species represents a major step to understand and predict the spatial and temporal structure of multi-trophic communities and their functioning. The metaweb concept summarises the potential trophic (and non-trophic) interactions in a given species-pool. As such, it generalises the regional species-pool of community ecology by incorporating the potential relationships between species from different trophic levels along with their functional characteristics. However, while this concept is theoretically very attractive, it has...

Resistance-recovery tradeoff of soil microbial communities under altered rain regimes: An experimental test across European agroecosystems

Gabin Piton, Arnaud Foulquier, Laura B. Martinez-García, Nicolas Legay, Lijbert Brussaard, Katarina Hedlund, Pedro Martins Da Silva, Eduardo Nascimento, Filipa Reis, José Paulo Sousa, Jean Christophe Clement & Gerlinde De Deyn
With the increased occurrence of climate extremes, there is an urgent need to better understand how management strategies affect the capacity of the soil microbial community to maintain its ecosystem functions (e.g. nutrient cycling). To address this issue, intact monoliths were extracted from conventional and ecological managed grasslands in three countries across Europe and exposed under common air condition (temperature and moisture) to one of three altered rain regimes (dry, wet and intermittent wet/dry) as...

On this side of the fence: Functional responses to linear landscape features shape the home range of large herbivores

Juliette Seigle-Ferrand, Pascal Marchand, Mark Hewison, Jean-Michel Gaillard, Nicolas Morellet, Sonia Said, Yannick Chaval, Hugo Santacreu, Anne Loison, Glenn Yannic & Mathieu Garel
1. Understanding the consequences of global change for animal movement is a major issue for conservation and management. In particular, habitat fragmentation generates increased densities of linear landscape features that can impede movements. 2. While the influence of these features on animal movements has been intensively investigated, they may also play a key role at broader spatial scales (e.g. the home range scale) as resources, cover from predators/humans, corridors/barriers, or landmarks. How space use respond...

Metabarcoding data reveal vertical multitaxa variation in topsoil communities during the colonization of deglaciated forelands

Alessia Guerrieri, Alexis Carteron, Aurélie Bonin, Silvio Marta, Roberto Ambrosini, Marco Caccianiga, Isabel Cantera, Chiara Compostella, Guglielmina Diolaiuti, Diego Fontaneto, Ludovic Gielly, Fabrizio Gili, Mauro Gobbi, Jerome Poulenard, Pierre Taberlet, Andrea Zerboni, Wilfried Thuiller & Gentile Francesco Ficetola
Ice-free areas are increasing worldwide due to the dramatic glacier shrinkage and are undergoing rapid colonization by multiple lifeforms, thus representing key environments to study ecosystem development. Soils have a complex vertical structure. However, we know little about how microbial and animal communities differ across soil depths and development stages during the colonization of deglaciated terrains, how these differences evolve through time, and whether patterns are consistent among different taxonomic groups. Here, we used environmental...

Registration Year

  • 2023
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  • Dataset


  • University of Savoy
  • Grenoble Alpes University
  • Université Savoie Mont Blanc
  • University of Lausanne
  • French National Institute for Agricultural Research
  • French National Centre for Scientific Research
  • Laboratoire d'Écologie Alpine
  • National Research Institute for Agriculture, Food and Environment
  • University of Milan
  • Sapienza University of Rome