Molecular Biology and Evolution, Vol 15, 1091-1098, Copyright © 1998 by Society for Molecular Biology and Evolution
M Robinson, M Gouy, C Gautier and D Mouchiroud
Relative-rate tests may be used to compare substitution rates between more
than two sequences, which yields two main questions: What influence does
the number of sequences have on relative-rate tests and what is the
influence of the sampling strategy as characterized by the phylogenetic
relationships between sequences? Using both simulations and analysis of
real data from murids (APRT and LCAT nuclear genes), we show that comparing
large numbers of species significantly improves the power of the test. This
effect is stronger if species are more distantly related. On the other
hand, it appears to be less rewarding to increase outgroup sampling than to
use the single nearest outgroup sequence. Rates may be compared between
paraphyletic ingroups and using paraphyletic outgroups, but unbalanced
taxonomic sampling can bias the test. We present a simple phylogenetic
weighting scheme which takes taxonomic sampling into account and
significantly improves the relative- rate test in cases of unbalanced
sampling. The answers are thus: (1) large taxonomic sampling of compared
groups improves relative-rate tests, (2) sampling many outgroups does not
bring significant improvement, (3) the only constraint on sampling strategy
is that the outgroup be valid, and (4) results are more accurate when
phylogenetic relationships between the investigated sequences are taken
into account. Given current limitations of the maximum-likelihood and
nonparametric approaches, the relative-rate test generalized to any number
of species with phylogenetic weighting appears to be the most general test
available to compare rates between lineages.
ORIGINAL ARTICLE
Sensitivity of the relative-rate test to taxonomic sampling
UMR CNRS 5558-Biometrie, Genetique et Biologie des Populations, Universite Claude Bernard, Lyon, France. marc@kimura.tau.ac.il
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