Molecular Biology and Evolution, Vol 13, 1255-1265, Copyright © 1996 by Society for Molecular Biology and Evolution
A Rzhetsky and T Sitnikova
The choice of an "optimal" mathematical model for computing evolutionary
distances from real sequences is not currently supported by easy-to-use
software applicable to large data sets, and an investigator frequently
selects one of the simplest models available. Here we study properties of
the observed proportion of differences (p- distance) between sequences as
an estimator of evolutionary distance for tree-making. We show that
p-distances allow for consistent tree- making with any of the popular
methods working with evolutionary distances if evolution of sequences obeys
a "molecular clock" (more precisely, if it follows a stationary
time-reversible Markov model of nucleotide substitution). Next, we show
that p-distances seem to be efficient in recovering the correct tree
topology under a "molecular clock," but produce "statistically supported"
wrong trees when substitutions rates vary among evolutionary lineages.
Finally, we outline a practical approach for selecting an "optimal" model
of nucleotide substitution in a real data analysis, and obtain a crude
estimate of a "prior" distribution of the expected tree branch lengths
under the Jukes-Cantor model. We conclude that the use of a model that is
obviously oversimplified is inadvisable unless it is justified by a
preliminary analysis of the real sequences.
ORIGINAL ARTICLE
When is it safe to use an oversimplified substitution model in tree- making?
Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park 16802, USA.
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