[R] Mantel - like analysis

[serrouya]

Hello,

I've used mantel tests a fair bit for standard genetic/geographic/landscape
analyses.  I realize it involves permutations of rows and columns in the
matrix to obtain correlation coefficients.

However, for a certain question, I am interested in populations that are
nearest neighbours to each other, and identifying factors that affect
genetic distance between them.  So because of autocorrelation problems, I
can't use standard regression or correlation, because some populations
appear several times depending upon their spatial arrangement.  In essence I
am cherry picking a typical matrix, but only for populations that are
closest.

Is there code or a test that can handle this problem? It seems very similar
to a mantel, but only for a subset of possible pairs, not all possible
pairwise comparisons as a mantel would handle.  What about a bootstrapping
algorithm than handles populations as the sample unit instead of individual
data points?
I bet mixed models could handle this problem somehow, but I'd like to stick
to the theme of a mantel test.

The data look like this

pop1 pop2  genetic_distance(dependent)  (independent1)
popa popb    data    data
popb popd    data    data
popc pope    data    data
popf popg    data    data
popg  poph  data   data

So for example, popb appears twice, as does popg.  Clearly each row is not
independent.

Thanks for any insight

Rob.

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