I was wondering if there are methods available for determining if there
are branches on an evolutionary tree where amino acid sequences have
undergone signficant amounts of non-conservative change in their
side-chain chemistry.
I would also like to know if my own naive method is valid. PROTDIST in
PHYLIP allows distance estimation based on Felsenstein's CATEGORIES
model. This model allows you to set a parameter such that changes among
chemical classes of amino acids are either highly unlikely (as the value
approaches zero) or are not treated differently from conservative
changes (when the value = 1.0). It seems to me that if you estimated
the distances for a set of sequences using both extremes of this
parameter, and fit those distances to a tree, branches on which a
considerable amount of non-conservative change had occurred would have a
much higher length under, say, value=0.1 than under value=1.0, relative
to other branches of the tree.
In other words, if you have three branches of a tree, a, b, and c,
estimate the distances using both values, and fit them to the tree. If
l(a,0.1)/l(a,1.0) is much greater than l(b,0.1)/l(b,1.0) and
l(c,0.1)/l(c,1.0), then that is evidence for a greater amount of
non-conservative change on a than on b and c. Or perhaps one could
weight the branch lengths by the proportion of change each represent in
the tree. I. e., instead of l(a,0.1), use
l(a,0.1)/(l(a,0.1)+l(b,0.1)+l(c,0.1))
and so forth. Is this a legitimate approach?
John Clement
Botany Department
University of Texas
Austin, TX 78713
clement at mail.utexas.edu