Y. Van De Peer, Molecular evolution and the incorporation of site-to-site rate variation in distance tree construction methods, BELG J ZOOL, 129(1), 1999, pp. 5-15
The construction of evolutionary trees based on sequence data is not self-e
vident Apart from the plethora of methods and software tools to choose from
if one wants to infer phylogenetic tree topologies, one has also to be cau
tious about the sequence data themselves. In this paper, we discuss how sys
tematic errors can be introduced by one of the phenomena that often charact
erize sequence data, i.e. differences in substitution rates among the diffe
rent sites of the molecule. Regarding painwise distance methods, these syst
ematic errors can often be avoided if an appropriate substitution model is
applied to the construction of phylogenetic trees. This is demonstrated for
a phylogeny based on animal small subunit ribosomal RNA sequences.