New methods for estimating the numbers of synonymous and nonsynonymous substitutions (original) (raw)
- Anderson S, Bankier AT, Barrell BG, De Bruijn MHL, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, Shreier PH, Smith AJH, Staden R, Young IG (1981) Sequence and organization of the human mitochondrial genome. Nature 290:457–465
Google Scholar - Brown WM, Prager EM, Wang A, Wilson AC (1982) Mitochondrial DNA sequences of primates: tempo and mode of evolution. J Mol Evol 18:225–239
Google Scholar - Easteal S (1985) Generation time and the rate of molecular evolution. Mol Biol Evol 2:450–453
Google Scholar - Easteal S (1990) The pattern of mammalian evolution and the relative rate of molecular evolution. Genetics 124:165–173
Google Scholar - Gojobori T, Ishii K, Nei M (1982a) Estimation of average number of nucleotide substitutions when the rate of substitution varies with nucleotide. J Mol Evol 18:414–423
Google Scholar - Gojobori T, Li W-H, Grant D (1982b) Patterns of nucleotide substitution in pseudogenes and functional genes. J Mol Evol 18:360–369
Google Scholar - Gojobori T, Moriyama EN, Kimura M (1990) Statistical methods for estimating sequence divergence. In: Doolittle RF (ed) Methods in enzymology 183: Molecular evolution: computer analysis of protein and nucleic acid sequences. Academic Press, New York, pp 531–550
Google Scholar - Gojobori T (1983) Codon substitution in evolution and the “saturation” of synonymous changes. Genetics 105:1011–1027
Google Scholar - Hasegawa M, Kishino H, Yano T (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22:160–174
Google Scholar - Hayasaka K, Gojobori T, Horai S (1988) Molecular phylogeny and evolution of primate mitochondrial DNA. Mol Biol Evol 5:626–644
Google Scholar - Horai S, Satta Y, Hayasaka K, Kondo R, Inoue T, Ishida T, Hayashi S, Takahata N (1992) Man's place in hominoidea revealed by mitochondrial DNA genealogy. J Mol Evol 35:32–43
Google Scholar - Hughes AL, Nei M (1988) Pattern of nucleotide substitution at major histocompatibility complex loci reveals overdominant selection. Nature 335:167–170
Google Scholar - Jin L, Nei M (1990) Limitations of the evolutionary parsimony method of phylogenetic analysis. Mol Biol Evol 7:82–102
Google Scholar - Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism. Academic Press, New York, pp 21–132
Google Scholar - Kikuno R, Hayashida H, Miyata T (1985) Rapid rate of rodent evolution. Proc Jpn Acad 61B:153–155
Google Scholar - Kimura M (1968) Evolutionary rate at the molecular level. Nature 217:624–626
Google Scholar - Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120
Google Scholar - Kimura M (1981) Estimation of evolutionary distances between homologous nucleotide sequences. Proc Natl Acad Sci USA 78:454–458
Google Scholar - Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge
Google Scholar - Kondo R, Horai S, Satta Y, Takahata N (1993) Evolution of hominoid mitochondrial DNA with special reference to the silent substitution rate over the genome. J Mol Evol 36:517–531
Google Scholar - Li W-H (1993) Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J Mol Evol 36:96–99
Google Scholar - Li W-H, Tanimura M, Sharp PM (1987) An evaluation of the molecular clock hypothesis using mammalian DNA sequences. J Mol Evol 25:330–342
Google Scholar - Li W-H, Wu C-I, Luo C-C (1984) Nonrandomness of point mutation as reflected in nucleotide substitutions in pseudogenes and its evolutionary implications. J Mol Evol 21:58–71
Google Scholar - Li W-H, Wu C-I, Luo C-C (1985) A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol Biol Evol 2:150–174
Google Scholar - Li W-H, Tanimura M (1987) The molecular clock runs more slowly in man than in apes and monkeys. Nature 326:93–96
Google Scholar - Miyata T, Miyazawa S, Yasunaga T (1979) Two types of amino acid substitutions in protein evolution. J Mol Evol 12:219–236
Google Scholar - 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 application. J Mol Evol 16:23–36
Google Scholar - Miyata T, Hayashida H, Kuma K, Yasunaga T (1987a) Male-driven molecular evolution demonstrated by different rates of silent substitutions between autosome- and sex chromosome-linked genes. Proc Jpn Acad 6313:327–331
Google Scholar - Miyata T, Hayashida H, Kuma K, Mitsuyasu K, Yasunaga T (1987b) Male-driven molecular evolution: a model and nucleotide sequence analysis. Cold Spring Harbor Symp Quanti Biol 52:863–867
Google Scholar - Miyata T, Kuma K, Iwabe N, Hayashida H, Yasunaga T (1990) Different rates of evolution of autosome-, X chromosome- and Y chromosome-linked genes: hypothesis of male-driven molecular evolution. In: Takahata N, Crow JF (eds) Population biology of genes and molecules. Baifukan Press, Tokyo, pp 341–357
Google Scholar - Moriyama EN (1987) Higher rates of nucleotide substitution in Drosophila than in mammals. Jpn J Genet 62:139–147
Google Scholar - Moriyama EN, Gojobori T (1992) Rates of synonymous substitution and base composition of nuclear genes in Drosophila. Genetics 130:855–864
Google Scholar - Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York
Google Scholar - Nei M, Gcjobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3:418–426
Google Scholar - Ohta T (1992) The nearly neutral theory of molecular evolution. Annu Rev Ecol Syst 23:263–286
Google Scholar - Ohta T (1993) An examination of generation-time effect on molecular evolution. Proc Natl Acad Sci USA 90:10676–10680
Google Scholar - Pamilo P, Bianchi NO (1993) Evolution of the Zfx and Zfy genes: rates and interdependence between the genes. Mol Biol Evol 10:271–281
Google Scholar - Saitou N (1987) Patterns of nucleotide substitutions in influenza A virus genes. Jpn J Genet 62:439–443
Google Scholar - Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Google Scholar - Schöniger M, von Haeseler A (1993) A simple method to improve the reliability of tree reconstructions. Mol Biol Evol 10:471–483
Google Scholar - Sharp PM, Li W-H (1989) On the rate of DNA sequence evolution in Drosophila. J Mol Evol 28:398–402
Google Scholar - Shields DC, Sharp PM, Higgins DG, Wright F (1988) “Silent” sites in Drosophila genes are not neutral: evidence of selection among synonymous codons. Mol Biol Evol 5:704–716
Google Scholar - Sneath PHA, Sokal RR (1973) Numerical taxonomy. Freeman, San Francisco
Google Scholar - Tajima F (1993) Unbiased estimation of evolutionary distance between nucleotide sequences. Mol Biol Evol 10:677–688
Google Scholar - Tajima F, Nei M (1984) Estimation of evolutionary distance between nucleotide sequences. Mol Biol Evol 1:269–285
Google Scholar - Tajima F, Takezaki N (1994) Estimation of evolutionary distance for reconstructing molecular phylogenetic tree. Mol Biol Evol 11:278–286
Google Scholar - Takahata N, Kimura M (1981) A model of evolutionary base substitutions and its application with special reference to rapid change of pseudogenes. Genetics 98:641–657
Google Scholar - Tamura K (1992) Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G + C-content biases. Mol Biol Evol 9:678–687
Google Scholar - Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512–526
Google Scholar - Tanaka T, Nei M (1989) Positive Darwinian selection observed at the variable-region genes of immunoglobulins. Mol Biol Evol 6:447–459
Google Scholar - Wolfe KH, Sharp PM, Li W-H (1989) Mutation rates differ among regions of the mammalian genome. Nature 337:283–285
Google Scholar - Wolfe KH, Sharp PM (1993) Mammalian gene evolution: nucleotide sequence divergence between mouse and rat. J Mol Evol 37:441–456
Google Scholar - Wu C-I, Li W-H (1985) Evidence for higher rates of nucleotide substitution in rodents than in man. Proc Natl Acad Sci USA 82:1741–1745
Google Scholar