Sensitivity of the relative-rate test to taxonomic sampling

Molecular Biology and Evolution

Volumn 15, Issue 9, 1998, Pages 1091-1098

  Robinson, Marc ^a,b   Gouy, Manolo ^a   Gautier, Christian ^a   Mouchiroud, Dominique ^a  

^a UNIVERSITÉ LYON 1   (France)

^b TEL AVIV UNIVERSITY   (Israel)

Author keywords

APRT; LCAT; Molecular clock; Murid; Phylogeny; Relative rate test; Sampling; Substitution rate; Topology; Weighting

Indexed keywords

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; DNA SEQUENCE; EXON; GENETIC MODEL; INTRON; MAMMAL; MOLECULAR EVOLUTION; PHYLOGENY; SAMPLING; SPECIES DIFFERENTIATION; TAXONOMY;

MAMMALIA; MURIDAE;

EID: 0031875195     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a026016     Document Type: Article

References (25)

1. BULMER, M. 1991. Use of the method of generalized least squares in reconstructing phylogenies from sequence data. Mol. Biol. Evol. 8:868-883.
2. CUMMINGS, M. P., S. P. OTTO, and J. WAKELEY. 1995. Sampling properties of DNA sequence data in phylogenetic analysis. Mol. Biol. Evol. 12:814-822.
3. FELSENSTEIN, J. 1984. Distance methods for inferring phylogenies: a justification. Evolution 38:16-24.
4. _. 1988. Phylogenies from molecular sequences: inference and reliability. Annu. Rev. Genet. 22:521-565.
5. FIELDHOUSE, D., F. YAZDANI, and G. B. GOLDING. 1997. Substitution rate variation in closely related rodent species. Heredity 78:21-31.
6. GOLDMAN, N. 1993. Statistical tests of models of DNA substitution. J. Mol. Evol. 36:182-198.
7. GRAUR, D., L. DURET, and M. GOUY. 1996. Phylogenetic position of the ordre Lagomorpha (rabbits, hares and allies). Nature 379:333-335.
8. GRAUR, D., A. H. HIDE, and W. H. LI. 1991. Is the guinea-pig a rodent? Nature 351:649-652.
9. GU, X., and W. H. LI. 1992. Higher rates of amino acid substitution in rodents than in humans. Mol. Phylogenet. Evol. 1:211-214.
10. HARVEY, P. H., and A. PUVIS. 1991. Comparative methods for explaining adaptations. Nature 351:619-624.
11. JUKES, T. H., and C. R. CANTOR. 1969. Evolution of protein molecules. Pp. 21-132 in H. N. MUNRO, ed. Mammalian protein metabolism. Academic Press, New York.
12. LECOINTRE, G., H. PHILIPPE, H. L. VAN LE, and H. LE GUYADER. 1993. Species sampling has a major impact on phylogenetic inference. Mol. Phylogenet. Evol. 2:205-224.
13. LI, P., and J. BOUSQUET. 1992. Relative-rate test for nucleotide substitutions between two lineages. Mol. Biol. Evol. 9: 1185-1189.
14. LI, W. H. 1993. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36: 96-99.
15. LI, W. H., D. L. ELLSWORTH, J. KRUSHKAL, B. H. J. CHANG, and D. HEWETT-EMETT. 1996. Rates of nucleotide substitution in Primates and Rodents and the generation-time hypothesis. Mol. Phylogenet. Evol. 5:182-187.
16. LUCKETT, W. P., and J. L. HARTENBERGER. 1993. Monophyly or polyphyly of the order Rodentia: possible conflict between morphological and molecular interpretations. J. Mamm. Evol. 1:127-147.
17. MUSE, S. V., and B. S. WEIR. 1992. Testing for equality of evolutionary rates. Genetics 132:269-276.
18. MUSE, S. V., and B. S. GAUT. 1994. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol. Biol. Evol. 11:715-724.
19. PAMILO, P., and N. O. BIANCHI. 1993. Evolution of the Zfx and Zfy genes: rates and interdependence between the genes. Mol. Biol. Evol. 10:271-281.
20. ROBINSON, M., F. M. CATZEFLIS, J. BRIOLAY, and D. MOUCHIROUD. 1997. Molecular phylogeny of rodents, with special emphasis on murids: evidence from nuclear gene LCAT. Mol. Phylogenet. Evol. 8:423-434.
21. SARICH, V. M., and A. C. WILSON. 1973. Generation time and genomic evolution in primates. Science 179:1144-1147.
22. TAJIMA, F. 1993. Simple methods for testing the molecular evolutionary clock hypothesis. Genetics 135:599-607.
23. TAKEZAKI, N., A. RZHETSKY, and M. NEI. 1995. Phylogenetic test of the molecular clock and linearized trees. Mol. Biol. Evol. 12:823-833.
24. UYENOYAMA, M. K. 1995. A generalized least-squares estimate for the origin of sporophytic self-incompatibility. Genetics 139:975-992.
25. WU, C. I., and W. H. LI. 1985. Evidence for higher rates of nucleotide substitution in rodents than in man. Proc. Natl. Acad. Sci. USA 82:1741-1745.