non-conservative changes in amino acid sequences

John Clement clement at
Thu Oct 2 13:09:44 EST 1997

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


and so forth.  Is this a legitimate approach?

John Clement
Botany Department
University of Texas
Austin, TX  78713
clement at

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