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: DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous dietMarta 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...
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 discoveryStephane 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: Plant functional traits reveal the relative contribution of habitat and food preferences to the diet of grasshoppersSébastien 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 studyFabrice 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...
Data from: The number of markers and samples needed for detecting bottlenecks under realistic scenarios, with and without recovery: a simulation-based studySean 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...
Joseph Fourier University7
French National Institute for Agricultural Research2
Botany and Modelling of Plant Architecture and Vegetation1
Office National de la Chasse et de la Faune Sauvage1
French National Centre for Scientific Research1
Paul Sabatier University1
Laboratoire d'Écologie Alpine1
University of Ferrara1
University of Houston1
Swiss Federal Institute for Forest, Snow and Landscape Research1