6 Works

Data from: pcadapt: an R package to perform genome scans for selection based on principal component analysis

Keurcien Luu, Eric Bazin & Michael G. B. Blum
The R package pcadapt performs genome scans to detect genes under selection based on population genomic data. It assumes that candidate markers are outliers with respect to how they are related to population structure. Because population structure is ascertained with principal component analysis, the package is fast and works with large-scale data. It can handle missing data and pooled sequencing data. By contrast to population-based approaches, the package handle admixed individuals and does not require...

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: Is there any evidence for rapid, genetically-based, climatic niche expansion in the invasive common ragweed?

Laure Gallien, Wilfried Thuiller, Noémie Fort, Marti Boleda, Florian J. Alberto, Delphine Rioux, Juliette Lainé & Sébastien Lavergne
Climatic niche shifts have been documented in a number of invasive species by comparing the native and adventive climatic ranges in which they occur. However, these shifts likely represent changes in the realized climatic niches of invasive species, and may not necessarily be driven by genetic changes in climatic affinities. Until now the role of rapid niche evolution in the spread of invasive species remains a challenging issue with conflicting results. Here, we document a...

Data from: Extracellular DNA extraction is a fast, cheap and reliable alternative for multi-taxa surveys based on soil DNA

Lucie Zinger, Jérôme Chave, Eric Coissac, Amaia Iribar, Eliane Louisanna, Sophie Manzi, Vincent Schilling, Heidy Schimann, Guilhem Sommeria-Klein & Pierre Taberlet
DNA metabarcoding on soil samples is increasingly used for large-scale and multi-taxa biodiversity studies. However, DNA extraction may be a major bottleneck for such wide uses. It should be cost/time effective and allow dealing with large sample volumes so as to maximise the representativeness of both micro- and macro-organisms diversity. Here, we compared the performances of a fast and cheap extracellular DNA extraction protocol with a total DNA extraction method in retrieving bacterial, eukaryotic and...

Data from: Detecting genomic signatures of natural selection with principal component analysis: application to the 1000 Genomes data

Nicolas Duforet-Frebourg, Guillaume Laval, Eric Bazin, Michael G.B. Blum & Keurcien Luu
To characterize natural selection, various analytical methods for detecting candidate genomic regions have been developed. We propose to perform genome-wide scans of natural selection using principal component analysis (PCA). We show that the common FST index of genetic differentiation between populations can be viewed as the proportion of variance explained by the principal components. Considering the correlations between genetic variants and each principal component provides a conceptual framework to detect genetic variants involved in local...

Data from: Tempo and mode of genome evolution in a 50,000-generation experiment

Olivier Tenaillon, Jeffrey E. Barrick, Noah Ribeck, Daniel E. Deatherage, Jeffrey L. Blanchard, Aurko Dasgupta, Gabriel C. Wu, Sébastien Wielgoss, Stéphane Cruveiller, Claudine Médigue, Dominique Schneider & Richard E. Lenski
Adaptation by natural selection depends on the rates, effects and interactions of many mutations, making it difficult to determine what proportion of mutations in an evolving lineage are beneficial. Here we analysed 264 complete genomes from 12 Escherichia coli populations to characterize their dynamics over 50,000 generations. The populations that retained the ancestral mutation rate support a model in which most fixed mutations are beneficial, the fraction of beneficial mutations declines as fitness rises, and...

Registration Year

  • 2016
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Resource Types

  • Dataset
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Affiliations

  • Grenoble Alpes University
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  • French National Centre for Scientific Research
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  • Centre national de la recherche scientifique
    1
  • University of Massachusetts Amherst
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  • The University of Texas at Austin
    1
  • French National Institute for Agricultural Research
    1
  • Inserm
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  • Laboratoire d'Écologie Alpine
    1
  • Norwegian University of Life Sciences
    1
  • Norwegian Institute for Nature Research
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