Partitioning the variation in mammalian substitution rates

Molecular Biology and Evolution

Volumn 20, Issue 1, 2003, Pages 10-17

  Smith, Nick G C ^b   Eyre Walker, Adam ^a  

^a UNIVERSITY OF SUSSEX   (United Kingdom)

^b NONE

Author keywords

ANOVA; Molecular clock; Overdispersion; Substitution rate

Indexed keywords

AMINO ACID SUBSTITUTION; ANALYSIS OF VARIANCE; ANALYTIC METHOD; ARTICLE; GENETIC ANALYSIS; MAMMAL; MOLECULAR INTERACTION; NONHUMAN; PARTITION COEFFICIENT;

MAMMALIA;

EID: 0037227363     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a004231     Document Type: Article

References (30)

1. Araki, H., and H. Tachida. 1997. Bottleneck effect on evolutionary rate in the nearly neutral mutation model. Genetics 147:907-914.
2. Bulmer, M. 1986. Neighbouring base effects on substitution rates in pseudogenes. Mol. Biol. Evol. 3:322-329.
3. -. 1989. Estimating the variability of substitution rates. Genetics 123:615-619.
4. Cutler, D. 2000. Understanding the overdispersed molecular clock. Genetics 154:1403-1417.
5. Duret, L., D. Mouchiroud, and M. Gouy. 1994. HOVERGEN, a database of homologous vertebrate genes. Nucleic Acids Res. 22:2360-2365.
6. Gillespie, J. H. 1986. Variability of evolutionary rates of DNA. Genetics 113:1077-1091.
7. -. 1989. Lineage effects and the index of dispersion of molecular evolution. Mol. Biol. Evol. 6:636-647.
8. -. 1991. The causes of molecular evolution. Oxford University Press, Oxford.
9. -. 1993. Substitution processes in molecular evolution. I. Uniform and clustered substitutions in a haploid model. Genetics 134:971-981.
10. Gouy, M., F. Milleret, C. Mugnier, M. Jacobzone, and C. Gautier. 1984. ACNUC: a nucleic acid sequence data base and analysis system. Nucleic Acids Res. 12:121-127.
11. Iwasa, Y. 1993. Overdispersed molecular evolution in constant environments. J. Theor. Biol. 164:373-393.
12. Lanave, C., S. Liuni, E Licciulli, and M. Attimonelli. 2000. Update of AMmtDB: a database of multi-aligned Metazoa mitochondrial DNA sequences status. Nucleic Acids Res. 28:153-154.
13. Lercher, M. J., E. J. B. Williams, and L. D. Hurst. 2001. Local similarity in evolutionary rates extends over whole chromosomes in human-rodent and mouse-rat comparisons: implications for understanding the mechanistic basis of the male mutation bias. Mol. Biol. Evol. 18:2032-2039.
14. Li, W.-H. 1997. Molecular evolution. Sinauer Associates, Sunderland, Mass.
15. Madsen, O., M. Scally, C. J. Douady, D. J. Kao, R. W. DeBry, R. Adkins, H. M. Amrine, M. J. Stanhope, W. W. de Jong, and M. S. Springer. 2001. Parallel adaptive radiations in two major clades of placental mammals. Nature 409:610-614.
16. Matassi, G., P. M. Sharp, and C. Gautier. 1999. Chromosomal location effects on gene sequence evolution in mammals. Curr. Biol. 9:786-791.
17. Messier, W., and C.-B. Stewart. 1997. Episodic adaptive evolution of primate lysozymes. Nature 385:151-154.
18. Mouchiroud, D., C. Gautier, and G. Bernardi. 1995. Frequencies of synonymous substitutions are gene-specific and correlated with frequencies of non-synonymous substitutions. J. Mol. Evol. 40:107-113.
19. Murphy, W. J., E. Elzirik, W. E. Johnson, Y. P. Zhing, O. A. Ryder, and S. J. O'Brien. 2001. Molecular phylogenetics and the origins of placental mammals. Nature 409:614-618.
20. Nielsen, R. 1997. Robustness of the estimator of the index of overdispersion for DNA sequences. Mol. Phylogenet. Evol. 7:346-351.
21. Ohta, T. 1995. Synonymous and nonsynonymous substitutions in mammalian genes and the nearly neutral theory. J. Mol. Evol. 40:56-63.
22. Pesole, G., C. Gissi, A. De Chirico, and C. Saccone. 1999. Nucleotide substitution rate of mammalian mitochondrial genomes. J. Mol. Evol. 48:427-434.
23. Shimodaira, H., and M. Hasegawa. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16:1114-1116.
24. Sved, J., and A. P. Bird. 1990. The expected equilibrium of the CpG dinucleotide in vertebrate genomes under a mutation model. Proc. Natl. Acad. Sci. USA 87:4692-4696.
25. Takahata, N. 1987. On the overdispersed molecular clock. Genetics 116:169-179.
26. -. 1988. More on the episodic clock. Genetics 118:387-388.
27. Thompson, J. D., D. G. Higgins, and T J. Gibson. 1994. ClustalW-improving the sensitivity of progressive multiple alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
28. Wallis, M. 1994. Variable evolutionary rates in the molecular evolution of mammalian growth hormones. J. Mol. Evol. 38:619-627.
29. Yang, Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13:555-556.
30. -. 1998. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol. Biol. Evol. 15:568-573.