¹Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK

Correspondence: DJ Obbard, Current address: Institute of Evolutionary Biology, University of Edinburgh, Ashworth Labs, Kings Buildings, West Mains Road, Edinburgh, Midlothian EH9 3JT, UK. E-mail: darren.obbard@ed.ac.uk

Received 30 November 2005; Accepted 5 June 2006; Published online 5 July 2006.

Abstract

The analysis of genetic diversity within and between populations is a routine task in the study of diploid organisms. However, population genetic studies of polyploid organisms have been hampered by difficulties associated with scoring and interpreting molecular data. This occurs because the presence of multiple alleles at each locus often precludes the measurement of genotype or allele frequencies. In allopolyploids, the problem is compounded because genetically distinct isoloci frequently share alleles. As a result, analysis of genetic diversity patterns in allopolyploids has tended to rely on the interpretation of phenotype frequencies, which loses information available from allele composition. Here, we propose the use of a simple allelic-phenotype diversity statistic (H') that measures diversity as the average number of alleles by which pairs of individuals differ. This statistic can be extended to a population differentiation measure (F'_ST), which is analogous to F_ST. We illustrate the behaviour of these statistics using coalescent computer simulations that show that F'_ST behaves in a qualitatively similar way to F_ST, thus providing a useful way to quantify population differentiation in allopolyploid species.