81 Works

Data from: Species Selection Regime and Phylogenetic Tree Shape

George Verboom, Florian Boucher, David Ackerly, Lara Wootton & William Freyman
Species selection, the effect of heritable traits in generating between-lineage diversification rate differences, provides a valuable conceptual framework for understanding the relationship between traits, diversification and phylogenetic tree shape. An important challenge, however, is that the nature of real diversification landscapes – curves or surfaces which describe the propensity of species-level lineages to diversify as a function of one or more traits – remains poorly understood. Here we present a novel, time-stratified extension of the...

Grounding line of Denman Glacier, East Antarctica from satellite radar interferometry

Virginia Brancato, Eric Rignot, Pietro Milillo, Mathieu Morlighem, Jeremie Mouginot, Lu An, Bernd Scheuchl, Seong Su Jeong, Paola Rizzoli, Jose Luiz Bueso Bello & Pau Prats-Iraola
Grounding line, elevation changes, and melt rates maps of Denman Glacier, East Antarctica. Using satellite radar interferometry from the COSMO-SkyMed mission we map the grounding line of Denman Glacier, East Antarctica. We complement these data with some historical interferometric radar acquisition from the European satellite ERS-1/2. We present new maps of elevation changes on the grounded and floating portions of Denman Glacier obtained by temporally differencing TanDEM-X Digital Elevation Models.

Continued adaptation of C4 photosynthesis after an initial burst of changes in the Andropogoneae grasses

Matheus Bianconi, Jan Hackel, Maria Vorontsova, Adriana Alberti, Watchara Arthan, Sean Burke, Melvin Duvall, Elizabeth Kellogg, Sébastien Lavergne, Michael McKain, Alexandre Meunier, Colin Osborne, Paweena Traiperm, Pascal-Antoine Christin & Guillaume Besnard
C4 photosynthesis is a complex trait that sustains fast growth and high productivity in tropical and subtropical conditions and evolved repeatedly in flowering plants. One of the major C4 lineages is Andropogoneae, a group of ~ 1,200 grass species that includes some of the world's most important crops and species dominating tropical and some temperate grasslands. Previous efforts to understand C4 evolution in the group have compared a few model C4 plants to distantly related...

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...

Bird abundance data for the period 2002-2014 from the French Breeding Bird Survey (STOC)

Vicente García-Navas & Wilfried Thuiller
Abundance data on breeding birds from the French Breeding Bird Survey (Suivi Temporel des Oiseaux Communs, STOC), for the period 2002-2014. The dataset comprises 7,115 bird communities. Only 107 common species were included in the study.

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: On-demand sildenafil as a treatment for Raynaud phenomenon: a series of n-of-1 trials

Matthieu Roustit, Joris Giai, Olivier Gaget, Charles Khouri, Myriam Mouhib, Adrien Lotito, Sophie Blaise, Christophe Seinturier, Fabien Subtil, Adeline Paris, Claire Cracowski, Bernard Imbert, Patrick Carpentier, Sunita Vohra & Jean-Luc Cracowski
Background: Treatment of Raynaud phenomenon (RP) with phosphodiesterase-5 inhibitors has shown moderate efficacy. Adverse effects decrease the risk–benefit profile of these drugs, and patients may not be willing to receive long-term treatment. On-demand single doses before or during exposure to cold may be a good alternative. Objective: To assess the efficacy and safety of on-demand sildenafil in RP. Design: Series of randomized, double-blind, n-of-1 trials. (ClinicalTrials.gov: NCT02050360). Setting: Outpatients at a French university hospital. Participants:...

Data from: pcadapt: an R package to perform genome scans for selection based on principal component analysis

Keurcien Luu, Eric Bazin & Michael G. B. Blum
The R package pcadapt performs genome scans to detect genes under selection based on population genomic data. It assumes that candidate markers are outliers with respect to how they are related to population structure. Because population structure is ascertained with principal component analysis, the package is fast and works with large-scale data. It can handle missing data and pooled sequencing data. By contrast to population-based approaches, the package handle admixed individuals and does not require...

Simulation of sheared granular layers activated by fluid pressurization

Nho Gia Hien Nguyen, Luc Scholtès, Yves Guglielmi, Frédéric Victor Donzé, Zady Ouraga & Mountaka Souley
Fluid pressurization of critically stressed sheared zones can trigger slip mechanisms at play in many geological rupture processes, including earthquakes or landslides. The increasing fluid pressure reduces the effective stress, giving possibility to the shear zone to reactivate. Nonetheless, the mechanisms that dictate the mode of slip, from aseismic steady creep to seismic dynamic rupture, remain poorly understood. By using discrete element modeling, we simulate pore-pressure-step creep test experiments on a sheared granular layer under...

Past, present and future of chamois science

Luca Corlatti, Laura Iacolina, Toni Safner, Marco Apollonio, Elena Buzan, Francesco Ferretti, Sabine Hammer, Juan Herrero, Luca Rossi, Emmanuel Serrano, Mari Cruz Arnal, Francesca Brivio, Roberta Chirichella, Antonella Cotza, Barbara Crestanello, Johan Espunyes, Daniel Fernández De Luco, Saskia Friedrich, Dragan Gačić, Laura Grassi, Stefano Grignolio, Heidi Hauffe, Kresmir Kavčić, Andreas Kinser, Francesca Lioce … & Nikica Šprem
The chamois Rupicapra spp. is the most abundant mountain ungulate of Europe and the Near East, where it occurs as two species, the Northern chamois R. rupicapra and the Southern chamois R. pyrenaica. Here, we provide a state-of-the-art overview of research trends and the most challenging issues in chamois research and conservation, focusing on taxonomy and systematics, genetics, life history, ecology and behavior, physiology and disease, management, and conservation. Research on Rupicapra has a longstanding...

Data from: Integrating correlation between traits improves spatial predictions of plant functional composition

Rafael O. Wüest, Tamara Muenkenmuller, Sebastien Lavergne, Laura Pollock & Wilfried Thuiller
Functional trait composition is increasingly recognized as key to better understand and predict community responses to environmental gradients. Predictive approaches traditionally model the weighted mean trait values of communities (CWMs) as a function of environmental gradients. However, most approaches treat traits as independent regardless of known trade-offs between them, which could lead to spurious predictions. To address this issue, we suggest jointly modeling a suit of functional traits along environmental gradients while accounting for relationships...

Data from: Is there any evidence for rapid, genetically-based, climatic niche expansion in the invasive common ragweed?

Laure Gallien, Wilfried Thuiller, Noémie Fort, Marti Boleda, Florian J. Alberto, Delphine Rioux, Juliette Lainé & Sébastien Lavergne
Climatic niche shifts have been documented in a number of invasive species by comparing the native and adventive climatic ranges in which they occur. However, these shifts likely represent changes in the realized climatic niches of invasive species, and may not necessarily be driven by genetic changes in climatic affinities. Until now the role of rapid niche evolution in the spread of invasive species remains a challenging issue with conflicting results. Here, we document a...

Glacier catchments/basins for the Greenland Ice Sheet

Jeremie Mouginot & Eric Rignot
We divide Greenland, including its peripheral glaciers and ice caps, into 260 basins grouped in seven regions: southwest (SW), central west (CW), (iii) northwest (NW), north (NO), northeast (NE), central east (CE), and southeast (SE). These regions are selected based on ice flow regimes, climate, and the need to partition the ice sheet into zones comparable in size (200,000 km2 to 400,000 km2) and ice production (50 Gt/y to 100 Gt/y, or billion tons per...

Data from: A quantitative proteomic analysis of cofilin phosphorylation in myeloid cells and its modulation using the LIM kinase inhibitor Pyr1

Renaud Prudent, Nathalie Demoncheaux, Hélène Diemer, Véronique Collin-Faure, Reuben Kapur, Fabrice Paublant, Laurence Lafanechère, Sarah Cianférani & Thierry Rabilloud
LIM kinases are located at a strategic crossroad, downstream of several signaling pathways and upstream of effectors such as microtubules and the actin cytoskeleton. Cofilin is the only LIM kinases substrate that is well described to date, and its phosphorylation on serine 3 by LIM kinases controls cofilin actin-severing activity. Consequently, LIM kinases inhibition leads to actin cytoskeleton disorganization and blockade of cell motility, which makes this strategy attractive in anticancer treatments. LIMK has also...

Data from: Decomposing changes in phylogenetic and functional diversity over space and time

Loïc Chalmandrier, Tamara Münkemüller, Vincent Devictor, Sébastien Lavergne & Wilfried Thuiller
1. The α, β, γ diversity decomposition methodology is commonly used to investigate changes in diversity over space or time but rarely conjointly. However, with the ever-increasing availability of large-scale biodiversity monitoring data, there is a need for a sound methodology capable of simultaneously accounting for spatial and temporal changes in diversity. 2. Using the properties of Chao's index, we adapted Rao's framework of diversity decomposition between orthogonal dimensions to a multiplicative α, β, γ...

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...

Data from: Mapping the imprint of biotic interactions on β-diversity

Marc Ohlmann, Florent Mazel, Loïc Chalmandrier, Stéphane Bec, Eric Coissac, Ludovic Gielly, Johan Pansu, Vincent Schilling, Pierre Taberlet, Lucie Zinger, Jerome Chave & Wilfried Thuiller
Investigating how trophic interactions influence the β-diversity of meta-communities is of paramount importance to understanding the processes shaping biodiversity distribution. Here, we apply a statistical method for inferring the strength of spatial dependencies between pairs of species groups. Using simulated community data generated from a multi-trophic model, we showed that this method can approximate biotic interactions in multi-trophic communities based on β-diversity patterns across groups. When applied to soil multi-trophic communities along an elevational gradient...

Annual Ice Velocity of the Greenland Ice Sheet (1972-1990)

Jeremie Mouginot, Eric Rignot, Romain Millan, Michael Wood & Bernd Scheuchl
We derive surface ice velocity using data from 16 satellite sensors deployed by 6 different space agencies. The list of sensors and the year that they were used are listed in the following (Table S1). The SAR data are processed from raw to single look complex using the GAMMA processor (www.gamma-rs.ch). All measurements rely on consecutive images where the ice displacement is estimated from tracking or interferometry (Joughin et al. 1998, Michel and Rignot 1999,...

Annual Ice Velocity of the Greenland Ice Sheet (2001-2010)

Jeremie Mouginot, Eric Rignot, Bernd Scheuchl, Michael Wood & Romain Millan
We derive surface ice velocity using data from 16 satellite sensors deployed by 6 different space agencies. The list of sensors and the year that they were used are listed in the following (Table S1). The SAR data are processed from raw to single look complex using the GAMMA processor (www.gamma-rs.ch). All measurements rely on consecutive images where the ice displacement is estimated from tracking or interferometry (Joughin et al. 1998, Michel and Rignot 1999,...

Annual Ice Velocity of the Greenland Ice Sheet (2010-2017)

Jeremie Mouginot, Eric Rignot, Bernd Scheuchl, Michael Wood & Romain Millan
We derive surface ice velocity using data from 16 satellite sensors deployed by 6 different space agencies. The list of sensors is given in the Table S1. The SAR data are processed from raw to single look complex using the GAMMA processor (www.gamma-rs.ch). All measurements rely on consecutive images where the ice displacement is estimated from tracking or interferometry (Joughin et al. 1998, Michel and Rignot 1999, Mouginot et al. 2012). Surface ice motion is...

Narwhals react to ship noise and airgun pulses embedded in background noise

Outi Tervo, Susanna Blackwell, Susanne Ditlevsen, Alexander Conrad, Adeline Samson, Eva Garde, Rikke Hansen & Mads Peter Heide-Jørgensen
Anthropogenic activities are increasing in the Arctic posing a threat to species with high seasonal site-fidelity, such as the narwhal Monodon monoceros. In this controlled sound exposure study, six narwhals were live-captured and instrumented with animal-borne tags providing movement and behavioural data, and exposed to concurrent ship noise and airgun pulses. All narwhals reacted to sound exposure by reduced buzzing rates, where the response was dependent on the magnitude of exposure defined as 1/distance to...

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...

Do ecological specialization and functional traits explain the abundance–frequency relationship? Arable weeds as a case study

Guillaume Fried, Laura Armengot, Jonathan Storkey, Bérenger Bourgeois, Sabrina Gaba, Cyrille Violle & François Munoz
Aim: The abundance-frequency relationship (AFR) is among the most-investigated pattern in biogeography, yet the relative contributions of niche-based processes related to ecological strategies, and of neutral processes related to spatial colonization-extinction dynamics, remains uncertain. Here, we tested the influences of ecological specialization and functional traits on local abundance and regional frequency, to determine the contribution of niche-based processes. Location: France and the UK. Taxon: Vascular plants. Methods: We used two arable weed surveys covering 1544...

IS-mediated mutations both promote and constrain evolvability during a long-term experiment with bacteria

Jessika Consuegra, Joël Gaffé, Richard E. Lenski, Thomas Hindre, Jeffrey E. Barrick, Olivier Tenaillon & Dominique Schneider
The long-term dynamics of IS elements and their effects on bacteria are poorly understood, including whether they are primarily genomic parasites or important drivers of adaptation by natural selection. Here, we investigate the dynamics of IS elements and their contribution to genomic evolution and fitness during a long-term experiment with Escherichia coli. This data set includes the Rmd file to analyze the genomic and metagenomic data (Tenaillon et al. 2016 and Good et al. 2017)...

Data from: Plant DNA metabarcoding of lake sediments: how does it represent the contemporary vegetation

Inger Greve Alsos, Youri Lammers, Nigel Giles Yoccoz, Tina Jørgensen, Per Sjögren, Ludovic Gielly & Mary E. Edwards
Metabarcoding of lake sediments have been shown to reveal current and past biodiversity, but little is known about the degree to which taxa growing in the vegetation are represented in environmental DNA (eDNA) records. We analysed composition of lake and catchment vegetation and vascular plant eDNA at 11 lakes in northern Norway. Out of 489 records of taxa growing within 2 m from the lake shore, 17-49% (mean 31%) of the identifiable taxa recorded were...

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