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Genetic similarity of polyploids: a new version of the computer program POPDIST (version 1.2.0) considers intraspecific genetic differentiation

Authors

  • JÜRGEN TOMIUK,

    1. Division of General Human Genetics, Department of Medical Genetics, Institute of Human Genetics, University of Tübingen, Wilhelmstrasse 27, DE-72074 Tübingen, Germany
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  • BERNT GULDBRANDTSEN,

    1. Department of Genetics and Biotechnology, Research Centre Foulum, Faculty of Agricultural Sciences, University of Aarhus, Blichers Allé, Postbox 50, DK-8830 Tjele, Denmark
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  • VOLKER LOESCHCKE

    1. Department of Biological Sciences, University of Aarhus, Ny Munkegade, Building 1540, DK-8000 Aarhus C, Denmark
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Tomiuk, Jürgen, Fax: +0497071295233; E-mail: juergen.tomiuk@uni-tuebingen.de

Abstract

For evolutionary studies of polyploid species estimates of the genetic identity between species with different degrees of ploidy are particularly required because gene counting in samples of polyploid individuals often cannot be done, e.g., in triploids the phenotype AB can be genotypically either ABB or AAB. We recently suggested a genetic distance measure that is based on phenotype counting and made available the computer program POPDIST. The program provides maximum-likelihood estimates of the genetic identities and distances between polyploid populations, but this approach is not informative for populations within species that only differ in their allele frequencies. We now close this gap by applying the frequencies of shared ‘bands’ in both populations to Nei's identity measure. Our simulation study demonstrates the close correlation between the band-sharing identity and the genetic identity calculated on the basis of gene frequencies for any degree of ploidy. The new extended version of POPDIST (version 1.2.0) provides the option of choosing either the maximum-likelihood estimator or the band-sharing measure.

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