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11 avril 2018

Estimating intraspecific genetic diversity from community DNA metabarcoding data [PeerJ]

Keywords : biogeography, bioinformatics, molecular biology, freshwater biology

DNA metabarcoding is used to generate species composition data for entire communities. However, sequencing errors in high-throughput sequencing instruments are fairly common, usually requiring reads to be clustered into operational taxonomic units (OTUs), losing information on intraspecific diversity in the process. While Cytochrome c oxidase subunit I (COI) haplotype information is limited in resolving intraspecific diversity it is nevertheless often useful e.g. in a phylogeographic context, helping to formulate hypotheses on taxon distribution and dispersal.(...)

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11 avril 2018

Revealing hidden insect–fungus interactions ; moderately specialized, modular and anti-nested detritivore networks [Proceedings of the Royal Society B - Biological Sciences]

Keywords : weighted networks, nestedness, spore dispersal, dead wood, plant pathogenic fungi, symbiont fungi

Ecological networks are composed of interacting communities that influence ecosystem structure and function. Fungi are the driving force for ecosystem processes such as decomposition and carbon sequestration in terrestrial habitats, and are strongly influenced by interactions with invertebrates. Yet, interactions in detritivore communities have rarely been considered from a network perspective. In the present study, we analyse the interaction networks between three functional guilds of fungi and insects sampled from dead wood. Using DNA metabarcoding to identify fungi, we reveal a diversity of interactions differing in specificity in the detritivore networks, involving three guilds of fungi.(...)

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6 avril 2018

Plastic response of four maritime pine (Pinus pinaster Aiton) families to controlled soil water deficit [Annals of Forest Science]

Sara Marin

Separating the internal (ontogenetic) and external (environmental) components of maritime pine development during controlled soil water deficit helps to highlight the plastic response. The adjusted measurements reveal significant differences between families for their plastic response for several physiology and growth traits.(...)

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6 avril 2018

The evolutionary history of vertebrate RNA viruses [Nature]

Keywords : molecular evolution, viral evolution

Our understanding of the diversity and evolution of vertebrate RNA viruses is largely limited to those found in mammalian and avian hosts and associated with overt disease. Here, using a large-scale meta-transcriptomic approach, we discover 214 vertebrate-associated viruses in reptiles, amphibians, lungfish, ray-finned fish, cartilaginous fish and jawless fish. The newly discovered viruses appear in every family or genus of RNA virus associated with vertebrate infection, including those containing human pathogens such as influenza virus, the Arenaviridae and Filoviridae families, and have branching orders that broadly reflected the phylogenetic history of their hosts.(...)

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6 avril 2018

The Missing Response to Selection in the Wild [Trends in Ecology & Evolution]

Benoit Pujol, Simon Blanchet, Etienne Danchin, Pascal Marrot, Caroline E. Thomson, Isabel Winney

Recent discoveries at the intersection of quantitative genetics and evolutionary ecology are challenging our views on the potential of wild populations to respond to selection.
Multiple biological mechanisms can disconnect genetic variation from the response to selection in the wild. We highlight areas for future research.
We provide an integrative framework that can be used to qualitatively assess the combined influence of these mechanisms on the response to selection.
Although there are many examples of contemporary directional selection, evidence for responses to selection that match predictions are often missing in quantitative genetic studies of wild populations. This is despite the presence of genetic variation and selection pressures – theoretical prerequisites for the response to selection. This conundrum can be explained by statistical issues with accurate parameter estimation, and by biological mechanisms that interfere with the response to selection. These biological mechanisms can accelerate or constrain this response. These mechanisms are generally studied independently but might act simultaneously. We therefore integrated these mechanisms to explore their potential combined effect. This has implications for explaining the apparent evolutionary stasis of wild populations and the conservation of wildlife.

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