19 Works

Data from: Effects of two grass species on the composition of soil fungal communities

Bello Mouhamadou, Jeremy Puissant, Emanuelle Personeni, Marie Desclos-Theveniau, Eva M. Kastl, Michael Schloter, Lucie Zinger, Julien Roy, Sandra Lavorel & Roberto A. Geremia
Many studies have shown effects of plants species on fungal communities, but these are often confounded with soil effects. Thus, the specific role of plant species in structuring rhizospheric and soil fungal communities is poorly described. Our study used microcosms in which plants were grown under artificial conditions to bridge this gap. Two perennial grasses dominating subalpine grasslands, Festuca paniculata and Dactylis glomerata, were grown at two levels of fertilization on standard soil. Fungal communities...

Data from: Prey preference of snow leopard (Panthera uncia) in South Gobi, Mongolia

Wasim Shehzad, Thomas Michael McCarthy, François Pompanon, Lkhagvajav Purevjav, Eric Coissac, Tiayyba Riaz & Pierre Taberlet
Accurate information about the diet of large carnivores that are elusive and inhabit inaccessible terrain, is required to properly design conservation strategies. Predation on livestock and retaliatory killing of predators have become serious issues throughout the range of the snow leopard. Several feeding ecology studies of snow leopards have been conducted using classical approaches. These techniques have inherent limitations in their ability to properly identify both snow leopard feces and prey taxa. To examine the...

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: DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet

Marta De Barba, Christian Miquel, Frederic Boyer, Céline Mercier, Delphine Rioux, Eric Coissac & Pierre Taberlet
Ecological understanding of the role of consumer-resource interactions in natural food webs is limited by the difficulty of accurately and efficiently determining the complex variety of food types animals have eaten in the field. We developed a method based on DNA metabarcoding multiplexing and next-generation sequencing to uncover different taxonomic groups of organisms from complex diet samples. We validated this approach on 91 faeces of a large omnivorous mammal, the brown bear, using DNA metabarcoding...

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: Genetic diversity in widespread species is not congruent with species richness in alpine plant communities

Pierre Taberlet, Niklaus E. Zimmermann, Thorsten Englisch, Andreas Tribsch, Rolf Holderegger, Nadir Alvarez, Harald Niklfeld, Zbigniew Mirek, Atte Moilanen, Wolfgang Ahlmer, Paolo Ajmone Marsan, Enzo Bona, Maurizio Bovio, Philippe Choler, Elżbieta Cieślak, Gheorghe Coldea, Licia Colli, Vasile Cristea, Jean-Pierre Dalmas, Božo Frajman, Luc Garraud, Myriam Gaudeul, Ludovic Gielly, Walter Gutermann, Nejc Jogan … & Karol Marhold
The Convention on Biological Diversity (CBD) aims at the conservation of all three levels of biodiversity, i.e. ecosystems, species and genes. Genetic diversity represents evolutionary potential and is important for ecosystem functioning. Unfortunately, genetic diversity in natural populations is hardly considered in conservation strategies because it is difficult to measure and has been hypothesized to co-vary with species richness. This means that species richness is taken as a surrogate of genetic diversity in conservation planning,...

Data from: AFLP markers reveal high clonal diversity and extreme longevity in four arctic-alpine key species

Lucienne C. De Witte, Georg F.J. Armbruster, Ludovic Gielly, Pierre Taberlet & Jürg Stöcklin
We investigated the clonal diversity, genet size structure and genet longevity in populations of four arctic-alpine plants (Carex curvula, Dryas octopetala, Salix herbacea and Vaccinium uliginosum) in order to evaluate their persistence under past climatic oscillations and their potential resistance to future climate change. The size and number of genets was determined with molecular markers (AFLP) using a standardized sampling design in several homogenous climax populations across arctic-alpine regions in Europe. Genet age was estimated...

Data from: Land use in mountain grasslands alters drought response and recovery of carbon allocation and plant-microbial interactions

Stefan Karlowsky, Angela Augusti, Johannes Ingrisch, Roland Hasibeder, Markus Lange, Sandra Lavorel, Michael Bahn & Gerd Gleixner
1. Mountain grasslands have recently been exposed to substantial changes in land-use and climate and in the near future will likely face an increased frequency of extreme droughts. To date is not known how the drought responses of carbon (C) allocation, a key process in the C cycle, are affected by land-use changes in mountain grassland. 2. We performed an experimental summer drought on an abandoned grassland and a traditionally managed hay meadow and traced...

Data from: Evolutionary history and genetic parallelism affect correlated responses to evolution

Mickael Le Gac, Tim F. Cooper, Stéphane Cruveiller, Claudine Médigue & Dominique Schneider
We investigated the relationship between genomic and phenotypic evolution among replicate populations of Escherichia coli evolved for 1000 generations in four different environments. By re-sequencing evolved genomes, we identified parallel changes in genes encoding transcription regulators within and between environments. Depending on both the environment and the altered gene, genetic parallelism at the gene level involved mutations that either repeatedly affected identical codons or domains or were more widely distributed within the relevant genes. Evolved...

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: Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family

Pierre-Jean G. Malé, Léa Bardon, Guillaume Besnard, Eric Coissac, Frédéric Delsuc, Julien Engel, Emeline Lhuillier, Caroline Scotti-Saintagne, Alexandra Tinaut & Jérôme Chave
Whole genome sequencing is helping generate robust phylogenetic hypotheses for a range of taxonomic groups that were previously recalcitrant to classical molecular phylogenetic approaches. As a case study, we performed a shallow shotgun sequencing of eight species in the tropical tree family Chrysobalanaceae to retrieve large fragments of high-copy number DNA regions and test the potential of these regions for phylogeny reconstruction. We were able to assemble the nuclear ribosomal cluster (nrDNA), the complete plastid...

Data from: Plant functional traits reveal the relative contribution of habitat and food preferences to the diet of grasshoppers

Sébastien Ibanez, Olivier Manneville, Christian Miquel, Pierre Taberlet, Alice Valentini, Serge Aubert, Eric Coissac, Marie-Pascale Colace, Quentin Duparc, Sandra Lavorel & Marco Moretti
Food preferences and food availability are two major determinants of the diet of generalist herbivores and of their spatial distribution. How do these factors interact and eventually lead to diet differentiation in co-occurring herbivores? We quantified the diet of four grasshopper species co-occurring in subalpine grasslands using DNA barcoding of the plants contained in the faeces of individuals sampled in the field. The food preferences of each grasshopper species were assessed by a choice (cafeteria)...

Data from: Unveiling the diet of elusive rainforest herbivores in next generation sequencing era? The tapir as a case study

Fabrice Hibert, Pierre Taberlet, Jérôme Chave, Caroline Scotti-Saintagne, Daniel Sabatier & Cécile Richard-Hansen
Characterizing the trophic relationships between large herbivores and the outstanding plant diversity in rainforest is a major challenge because of their elusiveness. This is crucial to understand the role of these herbivores in the functioning of the rainforest ecosystems. We tested a non-invasive approach based on the high-throughput sequencing of environmental samples using small plant plastid sequences (the trnL P6 loop) and ribosomal ITS1 primers, referred to as DNA metabarcoding, to investigate the diet of...

Diet of the brown bear in Himalaya: combining classical and molecular genetic techniques

Muhammad Ali Nawaz, Alice Valentini, Noor Kamal Khan, Christian Miquel, Pierre Taberlet & Jon E. Swenson
The ecological requirements of brown bears are poorly known in the Himalaya region, which complicates conservation efforts. We documented the diet of the Himalayan brown bear ( Ursus arctos isabellinus ) by combining classical scat analysis and a newly developed molecular genetic technique (the trn L approach), in Deosai National Park, Pakistan. Brown bears consumed over 50 plant species, invertebrates, ungulates, and several rodents. Eight plant families; Poaceae, Polygonaceae, Cyperaceae, Apiaceae, Asteraceae, Caryophyllaceae, Lamiaceae, and...

Data from: Functional biogeography of dietary strategies in birds

Jean-Yves Barnagaud, Nathan Mazet, François Munoz, Matthias Grenié, Pierre Denelle, Mar Sobral, W. Daniel Kissling, Çağan H. Sekercioglu & Cyrille Violle
Aim: Diet is key to understanding species’ resource use, relationships with their environment and biotic interactions. We aimed to identify the major strategies that shape birds’ diet space, and to investigate their spatial distributions in association with biogeographic, bioclimatic and anthropogenic drivers. Location: Global Time period: Current Major taxa studied: Birds Methods: We analysed score-based assessments of eight diet categories for 8937 out of 10964 extant bird species. We constructed a multivariate diet space by...

Data from: The number of markers and samples needed for detecting bottlenecks under realistic scenarios, with and without recovery: a simulation-based study

Sean M. Hoban, Oscar E. Gaggiotti & Giorgio Bertorelle
Detecting bottlenecks is a common task in molecular ecology. While several bottleneck detection methods exist, evaluations of their power have focused only on severe bottlenecks (e.g. to Ne ~10). As a component of a recent review, Peery et al. () analysed the power of two approaches, the M-ratio and heterozygote excess tests, to detect moderate bottlenecks (e.g. to Ne ~100), which is realistic for many conservation situations. In this Comment, we address three important points...

Data from: Assessment of the food habits of the Moroccan dorcas gazelle in M’Sabih Talaa, West central Morocco, using the trnL approach

Moulay Abdeljalil Ait Baamrane, Wasim Shehzad, Ahmed Ouhammou, Abdelaziz Abbad, Mohamed Naimi, Eric Coissac, Pierre Taberlet & Mohamed Znari
Food habits of the Moroccan dorcas gazelle, Gazella dorcas massaesyla, previously investigated in the 1980s using microhistological fecal analysis, in the M’Sabih Talaa reserve west central Morocco, were re-evaluated over three seasons (spring, summer and autumn 2009) using the trnL approach to determine the diet composition and its seasonal variation from fecal samples. Taxonomic identification was carried out using the identification originating from the database built from EMBL and the list of plant species within...

Data from: Geographic isolation and larval dispersal shape seascape genetic patterns differently according to spatial scale

Alicia Dalongeville, Marco Andrello, David Mouillot, Stephane Lobreaux, Marie-Josée Fortin, Frida Lasram, Jonathan Belmaker, Delphine Rocklin & Stéphanie Manel
Genetic variation, as a basis of evolutionary change, allows species to adapt and persist in different climates and environments. Yet, a comprehensive assessment of the drivers of genetic variation at different spatial scales is still missing in marine ecosystems. Here, we investigated the influence of environment, geographic isolation, and larval dispersal on the variation in allele frequencies, using an extensive spatial sampling (47 locations) of the striped red mullet (Mullus surmuletus) in the Mediterranean Sea....

Data from: AFLP markers reveal high clonal diversity and extreme longevity in four arctic-alpine key species

Lucienne C. De Witte, Georg F.J. Armbruster, Ludovic Gielly, Pierre Taberlet & Jürg Stöcklin
We investigated the clonal diversity, genet size structure and genet longevity in populations of four arctic-alpine plants (Carex curvula, Dryas octopetala, Salix herbacea and Vaccinium uliginosum) in order to evaluate their persistence under past climatic oscillations and their potential resistance to future climate change. The size and number of genets was determined with molecular markers (AFLP) using a standardized sampling design in several homogenous climax populations across arctic-alpine regions in Europe. Genet age was estimated...

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Affiliations

  • Joseph Fourier University
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  • Laboratoire d'Écologie Alpine
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