GC content and phylogeny reconstruction

sxk228 at ANU.EDU.AU sxk228 at ANU.EDU.AU
Fri Nov 29 01:53:56 EST 1996


The question which Jonathan Wendel raised is really quite important 
because it has far-reacing implications on tree building.  Indeed, 
while the problem is commonly referred to as a lack of stationarity, 
it is rarely dealt with.

A set of sequence are said to evolve under stationarity if they have 
not experience a change in their composition of chatacters.  This is 
not easy to determine because we rarely have the ancestral sequence 
available.  Therefore, if the sequences in question have the same 
composition, it is common to assume that the sequences evolved under 
stationary conditions.

Lack of stationarity can occur at both the DNA and protein level (see 
PG Foster et al., Journal of Molecular Evolution, in press) and thus 
affects phylogenetic analyses of both DNA and protein data.

All the best,

lars jermiin
lars.jermiin at anu.edu.au

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