To perform a partial mantel regression on three different distance matrices:

> library(vegan)
> mantel.partial (xdis, ydis, zdis,
+ method = "pearson", permutations = 1000)
Example.
Matrix 1: Genetic distance, Nei's D.
Matrix 2: Geographic distance
Matrix 3: Regional correspondance (i.e. binary matrix, 1 if two populations belon to the same region, zero otherwise)
This will allow to test if a correlation between geographic distance and genetic differentiation exists, when regional correspondance is taken into account.

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