Multilocus and multitrait measures of differentiation for gene markers and phenotypic traits

Multilocus measures of differentiation taking into account gametic disequilibrium are developed. Even if coupling and repulsion heterozygotes cannot be separated at the multilocus level, a method is given to calculate a composite measure of differentiation (CFst) at the zygotic level, which accounts for allelic associations combining both gametic and nongametic effects. Mean and maximum differentiations may be relevant when multilocus measures are computed. Maximum differentiation is the highest eigenvalue of the Fst matrix, whereas mean differentiation corresponds to the mean value of all eigenvalues of the Fst matrix. Gametic disequilibrium has a stronger effect on maximum differentiation than on mean differentiation and takes into account the anisotropy that may exist between within- and between-population components of disequilibria. Multilocus mean and maximum differentiation are calculated for a set of 81 Quercus petraea (sessile oak) populations assessed with eight allozyme loci and two phenotypic traits (bud burst and height growth). The results indicate that maximum differentiation increases as more loci (traits) are considered whereas mean differentiation remains constant or decreases. Phenotypic traits exhibit higher population differentiation than allozymes. The applications and uses of mean and maximum differentiations are further discussed.