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DetSel: An R-Package to Detect Marker Loci Responding to Selection

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Data Production and Analysis in Population Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 888))

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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Acknowledgments

I am grateful to Hélène Fréville and François Pompanon for useful comments on a previous version of this chapter. I also sincerely acknowledge Eric Bazin for providing me some hints and tips during the packaging of DetSel into R. Part of this work was carried out by using the resources of the Computational Biology Service Unit from the Museum national d’Histoire naturelle (MNHN—CNRS UMS 2700). This work was funded by the ANR grants “EMILE” (09-BLAN-0145) and “NUTGENEVOL” (07-BLAN-0064).

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Authors and Affiliations

  1. CNRS, INRA, UMR CBGP (INRA–IRD–CIRAD–Montpellier SupAgro), Montferrier-sur-Lez Cedex, France

    Renaud Vitalis

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  1. Renaud Vitalis
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Correspondence to Renaud Vitalis .

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Editors and Affiliations

  1. , Laboratoire d'Ecologie Alpine, Université Grenoble I, CNRS-UMR5553, rue de la Piscine 2233, Grenoble Cedex 09, 38041, France

    François Pompanon

  2. Laboratoire d'Ecologie Alpine, Université Grenoble 1, Rue de la Piscine 2233, Grenoble, 38041, France

    Aurélie Bonin

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Vitalis, R. (2012). DetSel: An R-Package to Detect Marker Loci Responding to Selection. In: Pompanon, F., Bonin, A. (eds) Data Production and Analysis in Population Genomics. Methods in Molecular Biology, vol 888. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-870-2_16

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  • DOI: https://doi.org/10.1007/978-1-61779-870-2_16

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-61779-869-6

  • Online ISBN: 978-1-61779-870-2

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