Sensitivity of the relative-rate test to taxonomic sampling.

Details

Serval ID
serval:BIB_1EAF3F71ADE9
Type
Article: article from journal or magazin.
Collection
Publications
Title
Sensitivity of the relative-rate test to taxonomic sampling.
Journal
Molecular Biology and Evolution
Author(s)
Robinson M., Gouy M., Gautier C., Mouchiroud D.
ISSN
0737-4038 (Print)
ISSN-L
0737-4038
Publication state
Published
Issued date
1998
Volume
15
Number
9
Pages
1091-1098
Language
english
Abstract
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.
Keywords
Adenine Phosphoribosyltransferase/genetics, Animals, Humans, Phosphatidylcholine-Sterol O-Acyltransferase/genetics, Phylogeny
Pubmed
Web of science
Create date
24/01/2008 17:47
Last modification date
20/08/2019 12:54
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