55 Works

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: Deep-sea, deep-sequencing: metabarcoding extracellular DNA from sediments of marine canyons

Magdalena Guardiola, María Jesús Uriz, Pierre Taberlet, Eric Coissac, Owen Simon Wangensteen & Xavier Turon
Marine sediments are home to one of the richest species pools on Earth, but logistics and a dearth of taxonomic work-force hinders the knowledge of their biodiversity. We characterized α- and β-diversity of deep-sea assemblages from submarine canyons in the western Mediterranean using an environmental DNA metabarcoding. We used a new primer set targeting a short eukaryotic 18S sequence (ca. 110 bp). We applied a protocol designed to obtain extractions enriched in extracellular DNA from...

Data from: Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms

Martial Marbouty, Axel Cournac, Jean-Francois Flot, Herve Marie-Nelly, Julien Mozziconacci & Romain Koszul
Genomic analyses of microbial populations in their natural environment remain limited by the difficulty to assemble full genomes of individual species. Consequently, the chromosome organization of microorganisms has been investigated in a few model species, but the extent to which the features described can be generalized to other taxa remains unknown. Using controlled mixes of bacterial and yeast species, we developed meta3C, a metagenomic chromosome conformation capture approach that allows characterizing individual genomes and their...

Resurrection ecology in Viola arvensis

Pierre-Olivier Cheptou
Premise of the study: As part of global change, climate warming and pollinator decline are expected to affect plant phenology and plant-pollinator interactions. This paper aims at characterizing rapid evolution of life history traits and floral traits over two decades in the wild pansy (Viola arvensis), a common weed in agrosystems. Methods: We used a resurrection ecology approach with genotypes sampled in 1991 and 2012 from a population in Burgundy (France). The species has a...

Urbanization shapes the relation between density and melanin-based colouration in bird communities

Neyla Turak, Alice Monnier-Corbel, Mélanie Gouret & Adrien Frantz
Growing urbanization increasingly influences ecosystems worldwide. While the effects of urban conditions within species (through either plastic or evolutionary responses) have been widely studied, their potential influences among species (through environmental filter), especially concerning their colouration, remain poorly known. Here, we investigated whether avian communities breeding inside and outside a major European city (Paris) differ with regards to melanin-based plumage colouration. Melanins are heritable pigments present in many taxa and have a series of unique...

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