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Single nucleotide polymorphisms derived from ancestral populations show no evidence for biased diversity estimates in Drosophila melanogaster

Authors

  • Christian Schlötterer,

    Corresponding author
    1. Institut für Tierzucht und Genetik, Veterinärmedizinische Universität Wien, Austria
      C. Schlötterer. Fax: + 43 25077 5693; E-mail: christian.schloetterer@vu-wien.ac.at
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  • Bettina Harr

    1. Institut für Tierzucht und Genetik, Veterinärmedizinische Universität Wien, Austria
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  • Bettina Harr and Christian Schlötterer are interested in the use of molecular markers in natural populations, with special emphasis on the identification and characterization of mutations conferring a selective advantage in a novel environment.

C. Schlötterer. Fax: + 43 25077 5693; E-mail: christian.schloetterer@vu-wien.ac.at

Abstract

Single nucleotide polymorphisms (SNPs) are about to become one of the most popular genetic markers for genetic model organisms. To test the usefulness of SNPs for estimating genetic diversity, we surveyed three genomic regions in two Drosophila melanogaster populations, one from Africa and one European, collected in Austria. Diversity estimates based on the full SNP set indicated higher levels of variability in the African than in the European flies. When the analysis was based on the European SNP set, European and African flies had similar levels of variability. Interestingly, this bias was not observed for diversity estimates using SNPs derived from the ancestral African population. This result suggests that diversity estimates based on SNPs from ancestral populations could provide a general strategy to avoid biased SNP diversity estimates. Finally, the potential of SNPs for nonmodel organisms is discussed.

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