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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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5 avril 2018

The spatial and temporal domains of modern ecology [Nature Ecology & Evolution]

Keywords : ecology

To understand ecological phenomena, it is necessary to observe their behaviour across multiple spatial and temporal scales. Since this need was first highlighted in the 1980s, technology has opened previously inaccessible scales to observation. To help to determine whether there have been corresponding changes in the scales observed by modern ecologists, we analysed the resolution, extent, interval and duration of observations (excluding experiments) in 348 studies that have been published between 2004 and 2014. We found that observational scales were generally narrow, because ecologists still primarily use conventional field techniques.(...)

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5 avril 2018

Scales of data [Nature Ecology & Evolution - News & Views]

Keywords : biogeography, ecology, macroecology

An audit of recent research on the scales of data collection in ecology highlights the field’s data limitations, which may hinder progress in linking processes across scales.

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5 avril 2018

Gene transfers can date the tree of life [Nature Ecology & Evolution]

Keywords : molecular evolution, palaeontology, phylogenetics

Biodiversity has always been predominantly microbial, and the scarcity of fossils from bacteria, archaea and microbial eukaryotes has prevented a comprehensive dating of the tree of life. Here, we show that patterns of lateral gene transfer deduced from an analysis of modern genomes encode a novel and abundant source of information about the temporal coexistence of lineages throughout the history of life. We use state-of-the-art species tree-aware phylogenetic methods to reconstruct the history of thousands of gene families and demonstrate that dates implied by gene transfers are consistent with estimates from relaxed molecular clocks in Bacteria, Archaea and Eukarya. We present the order of speciations according to lateral gene transfer data calibrated to geological time for three datasets comprising 40 genomes for Cyanobacteria, 60 genomes for Archaea and 60 genomes for Fungi. An inspection of discrepancies between transfers and clocks and a comparison with mammalian fossils show that gene transfer in microbes is potentially as informative for dating the tree of life as the geological record in macroorganisms.

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