Synonymous and nonsynonymous rate variation in nuclear genes of mammals

Journal of Molecular Evolution

Volumn 46, Issue 4, 1998, Pages 409-418

  Yang, Ziheng ^a,b   Nielsen, Rasmus ^a,c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

^c HARVARD UNIVERSITY   (United States)

Author keywords

Codon substitution; Likelihood; Mammalian genes; Neutral theory; Nonsynonymous rates; Synonymous rates; Transition transversion rate bias

Indexed keywords

AMINO ACID SUBSTITUTION; ANALYTIC METHOD; ARTICLE; ARTIODACTYLA; GENE; GENETIC CODE; INTERMETHOD COMPARISON; MAMMAL; MUTATION RATE; NONHUMAN; PRIMATE; RODENT; STATISTICAL MODEL;

ANIMALS; ARTIODACTYLA; CELL NUCLEUS; EVOLUTION, MOLECULAR; GENES; LIKELIHOOD FUNCTIONS; MAMMALS; MODELS, GENETIC; PHYLOGENY; PRIMATES; RODENTIA; TIME FACTORS; VARIATION (GENETICS);

ARTIODACTYLA; MAMMALIA; PRIMATES; RODENTIA;

EID: 0031960185     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/PL00006320     Document Type: Article

References (26)

1. Cameron JM (1995) A method for estimating the numbers of synonymous and nonsynonymous substitutions per site. J Mol Evol 41: 1152-1159
2. Easteal S, Collet C (1994) Consistent variation in amino-acid substitution rate, despite uniformity of mutation rate: protein evolution in mammals is not neutral. Mol Biol Evol 11:643-647
3. Eyre-Walker A, Gaut BS (1997) Correlated rates of synonymous site evolution across plant genomes. Mol Biol Evol 14:455-460
4. Gillespie JH (1987) Molecular evolution and the neutral allele theory. Oxf Surv Evol Biol 4:10-37
5. Gillespie JH (1989) Lineage effects and the index of dispersion of molecular evolution. Mol Biol Evol 6:636-647
6. Gillespie JH (1991) The causes of molecular evolution. Oxford University Press, Oxford
7. Goldman N (1994) Variance to mean ratio, R(t), for Poisson processes on phylogenetic trees. Mol Phylogenet Evol 3:230-239
8. Goldman N, Yang Z (1994) A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol 11: 725-736
9. Grantham R (1974) Amino acid difference formula to help explain protein evolution. Science 185:862-864
10. Ina Y (1995) Amino acid difference formula to help explain protein evolution. Science 185:862-864
11. Ina Y (1995) New methods for estimating the numbers of synonymous and nonsynonymous substitutions. J Mol Evol 40:190-226
12. Ina Y (1996) Patterns of synonymous and nonsynonymous substitutions: an indicator of mechanisms of molecular evolution. J Genet 75:91-115
13. Kimura M (1968) Evolutionary rate at the molecular level. Nature 217:624-626
14. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111-120
15. Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge
16. Li W-H (1993) Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J Mol Evol 36:96-99
17. Li W-H, Wu C-I, Luo C-C (1985) A new method for estimating synonymous and nonsynonymous rates of nucleotide substitutions considering the relative likelihood of nucleotide and codon changes. Mol Biol Evol 2:150-174
18. McDonald JH, Kreitman M (1991) Adaptive protein evolution at the Adh locus in Drosophila. Nature 351:652-654
19. Miyata T, Yasunaga T (1980) Molecular evolution of mRNA: a method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its applications. J Mol Evol 16:23-36
20. Muse SV, Gaut BS (1994) A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to chloroplast genome. Mol Biol Evol 11:715-724
21. Nei M, Gojobori T (1986) Simple methods for estimating the number of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3:418-426
22. Nielsen R (1997) Robustness of the estimator of the index of dispersion for DNA sequences. Mol Phylogenet Evol 7:346-351
23. Ohta T (1993) A examination of the generation-time effect on molecular evolution. Proc Natl Acad Sci USA 90:10676-10680
24. Ohta T (1995) Synonymous and nonsynonymous substitutions in mammalian genes and the nearly neutral theory. J Mol Evol 40:56-63
25. Pamilo P, Bianchi NO (1993) Evolution of the Zfx and Zfy genes - rates and interdependence between the genes. Mol Biol Evol 10: 271-281
26. Yang Z (1997) Phylogenetic analysis by maximum likelihood (PAML), version 1.3. University of California, Berkeley, California, USA