Standardizing for microsatellite length in comparisons of genetic diversity

Authors

  • RÉMY J. PETIT,

    Corresponding author
    1. UMR Biodiversity, Genes & Ecosystems, Institut National de la Recherche Agronomique, 69 route d Arcachon, F-33612 Cestas cedex, France,
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  • MARIE-FRANCE DEGUILLOUX,

    1. UMR Biodiversity, Genes & Ecosystems, Institut National de la Recherche Agronomique, 69 route d Arcachon, F-33612 Cestas cedex, France,
    2. Laboratory of Past Population Anthropology, University of Bordeaux I, avenue des Facultés, 33405 Talence, France,
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  • JOËLLE CHAT,

    1. UMR ECOBIOP, Institut National de la Recherche Agronomique, B.P. 3, F-64310 Saint-Pée sur Nivelle, France,
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  • DELPHINE GRIVET,

    1. UMR Biodiversity, Genes & Ecosystems, Institut National de la Recherche Agronomique, 69 route d Arcachon, F-33612 Cestas cedex, France,
    2. University of California Los Angeles, Department of OBEE, Warren Hall, 900 Veteran Avenue, Los Angeles, CA 90024, USA,
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  • PAULINE GARNIER-GÉRÉ,

    1. UMR Biodiversity, Genes & Ecosystems, Institut National de la Recherche Agronomique, 69 route d Arcachon, F-33612 Cestas cedex, France,
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  • GIOVANNI G. VENDRAMIN

    1. Plant Genetics Institute, Florence Division, National Research Council, Via Madonna del Piano, 50019 Sesto Fiorentino, Firenze, Italy
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Rémy J. Petit, Fax: +33(0)557122881; E-mail: petit@pierroton.inra.fr

Abstract

Mutation rates at microsatellites tend to increase with the number of repeats of the motif, leading to higher levels of polymorphism at long microsatellites. To standardize levels of diversity when microsatellites differ in size, we investigate the relationship between tract length and variation and provide a formula to adjust allelic richness to a fixed mean number of repeats in the specific case of chloroplast microsatellites. A comparison between 39 loci from eight species of conifers (where chloroplast DNA is paternally inherited) and 64 loci from 12 species of angiosperms (where chloroplast DNA is generally predominantly maternally inherited) indicates that the greater allelic richness found in conifers remains significant after controlling for number of repeats. The approach stresses the advantage of reporting variation in number of repeats instead of relative fragment sizes.

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