The apportionment of dinucleotide repeat diversity in Native Americans and Europeans: a new approach to measuring gene identity reveals asymmetric patterns of divergence

The purpose of this paper is to assess the extent of gene identity anddifferentiation at 33 dinucleotide repeat loci (377 total alleles) withinand among three European and three Native American populations. In order todo this, we show that a maximum-likelihood method proposed for phylogenetictrees (Cavalli-Sforza and Piazza 1975) can be used to estimate geneidentity (Nei 1987) with respect to any hierarchical structure. This methodallows gene differentiation to be evaluated with respect to any internalnode of a hierarchy. It also allows a generalization of F- and G-statisticsto situations with unequal expected levels of differentiation. Ourprincipal finding is that levels of genetic differentiation are unique tospecific populations and levels of nesting. The populations of Europeanorigin show very little internal differentiation; moreover, theircontinental average is close to the total population defined by theaggregate of Europeans and Native Americans. By contrast, the NativeAmerican populations show moderate levels of internal differentiation, anda great distance between their continental average and the total. Theresults of analyses of subsets of loci that were selected to have high genediversities in either Europeans or Native Americans closely parallel thosefrom the total set of loci. This suggests that the principal results areunlikely to be caused by a European ascertainment bias in locus selection.In summary, our findings demonstrate that partitions of gene diversity intowithin- and between-populations components are heavily biased by thepopulations analyzed and the models fitted. Optimistically, however, moreinformation is available to analyze population history and evolution byquantifying, as we have done, the uniqueness of patterns ofdifferentiation.