47 Works

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...

Data from: Cold adaptation in the Asian tiger mosquito’s native range precedes its invasion success in temperate regions

Stéphanie Sherpa, Michael G. B. Blum & Laurence Després
Adaptation to environmental conditions within the native range of exotic species can condition the invasion success of these species outside their range. The striking success of the Asian tiger mosquito, Aedes albopictus, to invade temperate regions has been attributed to the winter survival of diapause eggs in cold environments. In this study, we evaluate genetic polymorphisms (SNPs) and wing morphometric variation among three biogeographical regions of the native range of A. albopictus. Reconstructed demographic histories...

Data from: Speciation with gene flow: evidence from a complex of alpine butterflies (Coenonympha, Satyridae)

Thibaut Capblancq, Jesús Mavárez, Delphine Rioux & Laurence Després
Until complete reproductive isolation is achieved, the extent of differentiation between two diverging lineages is the result of a dynamic equilibrium between genetic isolation and mixing. This is especially true for hybrid taxa, for which the degree of isolation in regard to their parental species is decisive in their capacity to rise as a new and stable entity. In this work, we explored the past and current patterns of hybridization and divergence within a complex...

Data from: Conserved G-matrices of morphological and life-history traits among continental and island blue tit populations

Boris Delahaie, Anne Charmantier, Stéphane Chantepie, Dany Garant, Melody Porlier & Céline Teplitsky
The genetic variance–covariance matrix (G-matrix) summarizes the genetic architecture of multiple traits. It has a central role in the understanding of phenotypic divergence and the quantification of the evolutionary potential of populations. Laboratory experiments have shown that G-matrices can vary rapidly under divergent selective pressures. However, because of the demanding nature of G-matrix estimation and comparison in wild populations, the extent of its spatial variability remains largely unknown. In this study, we investigate spatial variation...

Chameleon biogeographic dispersal associated with extreme life history strategies

Sarah-Sophie Weil, Laure Gallien, Sébastien Lavergne, Luca Börger, Hassler Gabriel, Michaël P. J. Nicolaï & William L. Allen
This dataset contains data and code that support the results in Weil, S.-S., Gallien, L., Lavergne, S., Börger, L., Hassler, G., Nicolaï, Michaël P. J., Allen, William L. (2022) Chameleon biogeographic dispersal associated with extreme life history strategies (DOI: 10.1111/ecog.06323). We used species distribution, phylogenetic and life history trait data of 181 chameleons to determine the relationship between three traits (coastal distribution, body size, position on the fast/slow life history continuum) and past dispersal probability...

Data from: Unlocking biodiversity and conservation studies in high‐diversity environments using environmental DNA (eDNA): a test with Guianese freshwater fishes

Kévin Cilleros, Alice Valentini, Luc Allard, Tony Dejean, Roselyne Etienne, Gaël Grenouillet, Amaia Iribar, Pierre Taberlet, Régis Vigouroux & Sébastien Brosse
Determining the species compositions of local assemblages is a prerequisite to understanding how anthropogenic disturbances affect biodiversity. However, biodiversity measurements often remain incomplete due to the limited efficiency of sampling methods. This is particularly true in freshwater tropical environments that host rich fish assemblages, for which assessments are uncertain and often rely on destructive methods. Developing an efficient and non-destructive method to assess biodiversity in tropical freshwaters is highly important. In this study, we tested...

Data from: Loss of connectivity among island-dwelling Peary caribou following sea ice decline

Deborah A. Jenkins, Nicolas Lecomte, James A. Schaefer, Steffen M. Olsen, Didier Swingedouw, Steeve D. Côté, Loïc Pellissier & Glenn Yannic
Global warming threatens to reduce population connectivity for terrestrial wildlife through significant and rapid changes to sea ice. Using genetic fingerprinting, we contrasted extant connectivity in island-dwelling Peary caribou in northern Canada with continental-migratory caribou. We next examined if sea-ice contractions in the last decades modulated population connectivity and explored the possible impact of future climate change on long-term connectivity among island caribou. We found a strong correlation between genetic and geodesic distances for both...

Data from: Evaluating the impact of domestication and captivity on the horse gut microbiome

Jessica L. Metcalf, Se Jin Song, James T. Morton, Sophie Weiss, Andaine Seguin-Orlando, Frédéric Joly, Claudia Feh, Pierre Taberlet, Eric Coissac, Amnon Amir, Eske Willerslev, Rob Knight, Valerie McKenzie & Ludovic Orlando
The mammal gut microbiome, which includes host microbes and their respective genes, is now recognized as an essential second genome that provides critical functions to the host. In humans, studies have revealed that lifestyle strongly influences the composition and diversity of the gastrointestinal microbiome. We hypothesized that these trends in humans may be paralleled in mammals subjected to anthropogenic forces such as domestication and captivity, in which diets and natural life histories are often greatly...

Derivation of the functional response of a foraging herbivore

Etienne Sirot, Pierrick Blanchard, Anne Loison & Olivier Pays
The actual rate of food intake of a consumer depends on the way this animal shares its time between its different activities. Using a mathematical approach, we show how the proportions of time an herbivore spends searching for food, cropping food, and handling food, determine its feeding rate. We also show how this feeding rate is affected by the animal's ability to detect food and to handle it. The equation we finally get corresponds to...

Influence of climate, soil and land cover on plant species distribution in the European Alps

Yohann Chauvier, Wilfried Thuiller, Philipp Brun, Sébastien Lavergne, Patrice Descombes, Dirk Karger, Julien Renaud & Niklaus Zimmermann
Although the importance of edaphic factors and habitat structure for plant growth and survival is known, both are often neglected in favor of climatic drivers when investigating the spatial patterns of plant species and diversity. Yet, especially in mountain ecosystems with complex topography, missing edaphic and habitat components may be detrimental for a sound understanding of biodiversity distribution. Here, we compare the relative importance of climate, soil and land cover variables when predicting the distributions...

Data from : Vacant yet invasible niches in forest community assembly

Pierre Gauzere, Xavier Morin, Cyrille Violle, Ivanna Caspeta, Courtenay Ray & Benjamin Blonder
It is controversial whether communities are saturated with species, or have vacant niches. The prevalence of vacant niches and the processes likely to promote their existence are poorly known. We used a process‐based forest gap‐model to simulate plant community dynamics in 11 sites along a climatic gradient across central Europe. We then used hypervolume analyses to study the existence of vacant niches (seen as empty volumes in the trait space of local species pools and...

Data from: Onset of autumn shapes the timing of birth in Pyrenean chamois more than onset of spring

Charlotte Kourkgy, Mathieu Garel, Joël Appolinaire, Anne Loison & Carole Toïgo
1. In seasonal environments, birth dates are a central component for a species’ life history, with potential long-term fitness consequences. Yet our understanding of selective pressures of environmental changes on birth dates is limited in wild mammals due to the difficulty of data collection. In a context of rapid climate change, the question of a possible mismatch between plant phenology and birth phenology also remains unanswered for most species. 2. We assessed whether and how...

Data from: Last Glacial Maximum environmental conditions at Andøya, northern Norway; evidence for a northern ice-edge ecological “hotspot”

Inger Alsos, Per Sjögren, Antony Brown, Ludovic Gielly, Marie Merkel, Aage Paus, Youri Lammers, Mary Edwards, Torbjørn Alm, Melanie Leng, Tomasz Goslar, Catherine Langdon, Jostein Bakke & Willem Van Der Bilt
Andøya on the NW coast of Norway is a key site for understanding the Last Glacial Maximum (LGM) in northern Europe. Controversy has arisen concerning the local conditions, especially about the timing and extent of local glacial cover, maximum July temperatures and whether pine and/or spruce could have grown there. We reviewed all existing data and add newly analysed ancient sedimentary DNA, pollen, macrofossils, geochemistry and stable isotopes from three lake sediment cores from Øvre...

Data for: Environmental and anthropogenic constraints on animal space use drive extinction risk worldwide

Myriam R. Hirt, Andrew D. Barnes, Alessandro Gentile, Laura J. Pollock, Benjamin Rosenbaum, Wilfried Thuiller, Marlee A. Tucker & Ulrich Brose
Animals require a certain amount of habitat to persist and thrive, and habitat loss is one of the most critical drivers of global biodiversity decline. While habitat requirements have been predicted by relationships between species traits and home range size, little is known about constraints imposed by environmental conditions and human impacts on a global scale. Our meta-analysis of 395 vertebrate species shows that global climate gradients in temperature and precipitation exert indirect effects via...

Biotic homogenisation in bird communities leads to large-scale changes in species associations

Stanislas Rigal, Vincent Devictor, Pierre Gaüzère, Sonia Kéfi, Jukka Forsman, Mira Kajanus, Mikko Mönkkönen & Vasilis Dakos
This is the dataset used for the manuscript Biotic homogenisation in bird communities leads to large-scale changes in species associations Aim: The impact of global change on biodiversity is commonly assessed in terms of changes in species distributions, community richness and community composition. Whether and how much associations between species, i.e. the degree of correlation in their spatial co-occurrence, are also changing is much less documented and mostly limited to local studies of ecological networks....

Using proxies of microbial community‐weighted means traits to explain the cascading effect of management intensity, soil and plant traits on ecosystem resilience in mountain grasslands

Gabin Piton, Nicolas Legay, Cindy Arnoldi, Sandra Lavorel, Jean-Christophe Clément, Arnaud Foulquier & Jean Christophe Clément
1. Trait-based approaches provide a framework to understand the role of functional biodiversity on ecosystem functioning under global change. While plant traits have been reported as potential drivers of soil microbial community composition and resilience, studies directly assessing microbial traits are scarce, limiting our mechanistic understanding of ecosystem functioning. 2. We used microbial biomass and enzyme stoichiometry, and mass-specific enzymes activity as proxies of microbial community-weighted mean (CWM) traits, to infer trade-offs in microbial strategies...

Data from: Contrasting microbial biogeographical patterns between anthropogenic subalpine grasslands and natural alpine grasslands

Roberto A. Geremia, Mihai Pușcaș, Lucie Zinger, Jean-Marc Bonneville, Philippe Choler & Jean-Marc Bonneville
The effect of plant species composition on soil microbial communities was studied at the multiregional level. We compared the soil microbial communities of alpine natural grasslands dominated by Carex curvula and anthropogenic subalpine pastures dominated by Nardus stricta. We conducted paired sampling across the Carpathians and the Alps and used Illumina sequencing to reveal the molecular diversity of soil microbes. We found that bacterial and fungal communities exhibited contrasting regional distributions and that the distribution...

Data from: High-throughput microsatellite genotyping in ecology: improved accuracy, efficiency, standardization and success with low-quantity and degraded DNA

Marta De Barba, Christian Miquel, Stephane Lobreaux, Pierre Yves Quenette, Jon E. Swenson & Pierre Taberlet
Microsatellite markers have played a major role in ecological, evolutionary and conservation research during the past 20 years. However, technical constrains related to the use of capillary electrophoresis and a recent technological revolution that has impacted other marker types have brought to question the continued use of microsatellites for certain applications. We present a study for improving microsatellite genotyping in ecology using high-throughput sequencing (HTS). This approach entails selection of short markers suitable for HTS,...

Data from: Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA

Sanne Boessenkool, Laura S. Epp, James Haile, Eva Bellemain, Mary Edwards, Eric Coissac, Eske Willerslev & Christian Brochmann
Analyses of degraded DNA are typically hampered by contamination, especially when employing universal primers such as commonly used in environmental DNA studies. In addition to false-positive results, the amplification of contaminant DNA may cause false-negative results due to competition, or bias, during the PCR. In this study, we test the utility of human-specific blocking primers in mammal diversity analyses of ancient permafrost samples from Siberia. Using quantitative PCR (qPCR) on human and mammoth DNA we...

Can functional genomic diversity provide novel insights into mechanisms of community assembly? A pilot-study from an invaded alpine streambed

Hannah Marx, Marta Carboni, Rolland Douzet, Christophe Perrier, Franck Delbart, Wilfried Thuiller, Sebastien Lavergne & David Tank
An important focus of community ecology, including invasion biology, is to investigate functional trait diversity patterns to disentangle the effects of environmental and biotic interactions. However, a notable limitation is that studies usually rely on a small and easy to measure set of functional traits, which might not immediately reflect ongoing ecological responses to changing abiotic or biotic conditions, including those that occur at a molecular or physiological level. We explored the potential of using...

Data from: Strong links between plant traits and microbial activities but different abiotic drivers in mountain grasslands

Sarah-Sophie Weil, Camille Martinez-Almoyna, Gabin Piton, Julien Renaud, Louise Boulangeat, Arnaud Foulquier, Amélie Saillard, Philippe Choler, Jérôme Poulenard, Tamara Münkemüller & Wilfried Thuiller
This dataset contains data and code that support the results in Weil, S.-S., Martinez-Almoyna, C., Piton, G., Renaud, J., Boulangeat, L., Foulquier, A., ... & Thuiller, W. (2021) Strong links between plant traits and microbial activities but different abiotic drivers in mountain grasslands (accepted in Journal of Biogeography). We used an extensive plant-soil dataset that covers 14 elevational gradients (between 1500 and 2800 m of elevation) distributed over the whole French Alps to analyse the...

Data from: Development of an Arabis alpina genomic contig sequence dataset and application to single nucleotide polymorphisms discovery

Stephane Lobreaux, Stéphanie Manel, Christelle Melo De Lima & Christelle Melodelima
The alpine plant Arabis alpina is an emerging model in the ecological genomic field which is well-suited to identifying the genes involved in local adaptation in contrasted environmental conditions, a subject which remains poorly understood at molecular level. This paper presents the assembly of a pool of A. alpina genomic fragments using Next Generation Sequencing technologies. These contigs cover 172 Mb of the A. alpina genome (i.e. 50% of the genome) and were shown to...

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

Johan Pansu, Charline Giguet-Covex, Gentile Francesco Ficetola, Ludovic Gielly, Frédéric Boyer, Lucie Zinger, Fabien Arnaud, Jérôme Poulenard, Pierre Taberlet, Philipe Choler & Philippe Choler
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...

Data from: Extreme climate events counteract the effects of climate and land-use changes in Alpine treelines

Ceres Barros, Maya Guéguen, Rolland Douzet, Marta Carboni, Isabelle Boulangeat, Niklaus E. Zimmermann, Tamara Münkemüller & Wilfried Thuiller
Climate change and extreme events, such as drought, threaten ecosystems world-wide and in particular mountain ecosystems, where species often live at their environmental tolerance limits. In the European Alps, plant communities are also influenced by land-use abandonment leading to woody encroachment of subalpine and alpine grasslands. In this study, we explored how the forest–grassland ecotone of Alpine tree lines will respond to gradual climate warming, drought events and land-use change in terms of forest expansion...

Data from: Paying for conservation: a bioeconomic analysis of the effects of land management options on the viability of an endangered species, Eryngium alpinum

Marco Andrello, Caroline Devaux, Fabien Quétier & Irène Till-Bottraud
1. Land management is critical for biodiversity conservation in mountain grasslands. It should be both ecologically effective and economically efficient. We provide an economic analysis of different options (spring and autumn grazing, mowing and abandonment) and their effects on population viability of a rare plant species, Eryngium alpinum (Apiaceae), in two French mountain grassland sites (Fournel and Pralognan). 2. Using data collected in a ten-year, individual-based demographic study, we estimated the effects of land management...

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  • Laboratoire d'Écologie Alpine
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