On a practical note, it's not always useful to eliminate allometry
(e.g., by regressing shape variables on centroid size and analyzing the
residuals).
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A few years ago I did a study of the shape differences between two
species of clams, Mercenaria mercenaria and Mercenaria campechiensis,
and their hybrids.  If size and allometry were removed, the clams were
unable to be differentiated based on shape.  However, they had different
"allometric trajectories"; as clams of each species grow in size they
become more and more different in shape.  Clams of the same size but of
different species were able to be differentiated based on shape when
allometry was left in.

In my experience I have found that many studies automatically eliminate 
allometry as a matter of course.  In my case, the differences between
the species were entirely due to allometry, but the differences in shape
were not artifactual.

I think this is an obvious point for morphometricians, but I wanted to
add my two cents.

Matt
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