MEASURING AND TESTING GENETIC DIFFERENTIATION WITH ORDERED VERSUS UNORDERED ALLELES

Estimates and variances of diversity and differentiation measures in s ubdivided populations are proposed that can be applied to haplotypes p es (ordered alleles such as DNA sequences, which may contain a record of their own histories). Hence, two measures of differentiation can be compared for a single data set: one (G(ST)) that makes use only of th e allelic frequencies and the other (N-ST) for which similarities betw een the haplotypes are taken into account in addition. Tests are propo sed to compare N-ST and G(ST) with zero and with each other. The diffe rence between N-ST and G(ST) can be caused by several factors, includi ng sampling artefacts, unequal effect of mutation rates and phylogeogr aphic structure. The method presented is applied to a published data s et where a nuclear DNA sequence had been determined from individuals o f a grasshopper distributed in 24 regions of Europe. Additional insigh ts into the genetic subdivision of these populations are obtained by p rogressively combining related haplotypes and reanalyzing the data eac h time.