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DETSEL: an R-package to detect marker loci responding to selection.

Abstract

In the new era of population genomics, surveys of genetic polymorphism ("genome scans") offer the opportunity to distinguish locus-specific from genome-wide effects at many loci. Identifying presumably neutral regions of the genome that are assumed to be influenced by genome-wide effects only, and excluding presumably selected regions, is therefore critical to infer population demography and phylogenetic history reliably. Conversely, detecting locus-specific effects may help identify those genes that have been, or still are, targeted by natural selection. The software package DETSEL has been developed to identify markers that show deviation from neutral expectation in pairwise comparisons of diverging populations. Recently, two major improvements have been made: the analysis of dominant markers is now supported, and the estimation of empirical P-values has been implemented. These features, which are described below, have been incorporated into an R package, which replaces the stand-alone DETSEL software package.

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    MeSH

    Amplified Fragment Length Polymorphism Analysis
    Animals
    Anura
    Drosophila
    Fishes
    Genetic Loci
    Genetic Markers
    Genetics, Population
    Genome
    Humans
    Models, Genetic
    Phylogeny
    Plants
    Polymorphism, Genetic
    Selection, Genetic
    Software

    Pub Type(s)

    Journal Article
    Research Support, Non-U.S. Gov't

    Language

    eng

    PubMed ID

    22665287