Nei M 2005 Selectionism and neutralism in molecular evolution. Mol Biol Evol 22:2318-2342. Charles Darwin proposed that evolution occurs primarily by natural selection this view has been controversial from the beginning this controversy is…

Itoh T, Martin W & Nei M 2002 Acceleration of genomic evolution caused by enhanced mutation rate in endocellular symbionts. PNAS 99:12944-12948. we are not considering the strict neutrality of alleles which would never exist in nature we a…

Nei M & Kumar S 2000 Molecular evolution and phylogenetics. Oxford UP. ISBN:9780195135855 the problem is the fate of slightly deleterious mutations the continuous accumulation of slightly deleterious mutations in a protein will eventually …

Takahata N 2007 Molecular clock: an anti-neo-Darwinian legacy. Genetics 176:1-6. the high evolutionary rate estimated from hemoglobin and other proteins was a key to development of the neutral theory by Motoo Kimura rather than, as sometim…

Takahata N 1996 Neutral theory of molecular evolution. Curr Opin Genet Dev 6:767-772. Kimura was once sympathetic to the 'slightly deleterious' hypothesis of Ohta when criticisms against the neutral theory were most intense he himself prop…

Ohta T 2002 Near-neutrality in evolution of genes and gene regulation. PNAS 99:16134-16137. the nearly neutral mutations are defined such that their fate in the population depends on both selection and drift (12) stabilizing selection on e…

Ohta T & Gillespie JH 1996 Development of neutral and nearly neutral theories. Theor Popul Biol 49:128-142. emphasis is placed on the nearly neutral theory as this version of the neutral theory has explained the widest range of phenomena h…

Gillespie JH 1995 On Ohta's hypothesis: most amino acid substitutions are deleterious. J Mol Evol 40:64-69. Ohta's hypothesis that most amino acid substitutions are deleterious grew out of a class of population-genetics models called shift…

Ohta T 1995 Synonymous and nonsynonymous substitutions in mammalian genes and the nearly neutral theory. J Mol Evol 40:56-63. the slightly deleterious mutation theory predicted a negative correlation between amino acid substitutions and th…

Ohta T 1992 The nearly neutral theory of molecular evolution. Annu Rev Ecol Syst 23:263-286. in view of the importance of negative selection caused by constraints, it is likely that many nearly neutral mutants are very slightly deleterious…

Tachida H 1991 A study on a nearly neutral mutation model in finite populations. Genetics 128:183-192. as a nearly neutral mutation model, the house-of-cards model is studied in finite populations if 4Nσ is large compared to one, a few adv…

Ohta T & Tachida H 1990 Theoretical study of near neutrality. I. Heterozygosity and rate of mutant substitution. Genetics 126:219-229. the definition of near neutrality is that the product of effective population size (N) and selection coe…

Ohta T 1974 Mutational pressure as the main cause of molecular evolution and polymorphism. Nature 252:351-354. it becomes increasingly necessary to re-examine evolutionary theories in particular the orthodox neo-Darwinian view that the rat…

Ohta T 1973 Slightly deleterious mutant substitutions in evolution. Nature 252:351-354. the concept of neutral mutant substitution in the population by random genetic drift can be extended to include random fixation of very slightly delete…

Ohta T 1972 Population size and rate of evolution. J Mol Evol 1:305-314. there is much substitution of nearly neutral mutations, for which the selection intensity varies from time to time or from region to region the hypothesis presented h…

Ohta T 1972 Evolutionary rate of cistrons and DNA divergence. J Mol Evol 1:150-157. the majority of the amino acid substitutions in evolution are the result of random fixation of nearly neutral mutations for which selection intensity fluct…

Ohta T & Kimura M 1971 On the constancy of the evolutionary rate of cistrons. J Mol Evol 1:18-25. remarkable constancy of the rate of amino acid substitution in each protein over a vast period of geologic time constitutes so far the strong…

Gillespie JH 2004 Why k = 4Nus is silly. Pages 178-192 in Singh RS & Uyenoyama MK, eds. The evolution of population biology. Cambridge UP. ISBN:9780521814375 k = 4Nus ... (9.1) Wright (1949) appears to be the first to have used this formul…

Sella G 2009 An exact steady state solution of Fisher's geometric model and other models. Theor Popul Biol 75:30-34.

Sella G & Hirsh AE 2005 The application of statistical physics to evolutionary biology. PNAS 102:9541-9546. we concentrate on the family of models that depict the evolutionary process as a succession of mutant fixations, each of which occu…

Kimura M 1969 The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations. Genetics 61:893-903. the probability of a particular site being heterozygous for a selectively neutral mutant is 4…

Povolotskaya IS & Kondrashov FA 2010 Sequence space and the ongoing expansion of the protein universe. Nature 465:922-926. ancient proteins are still diverging from each other indicating an ongoing expansion of the protein sequence univers…

Kondrashov AS, Povolotskaya IS, Ivankov DN & Kondrashov FA 2010 Rate of sequence divergence under constant selection. Biol Direct 5:5. we assume that Neμi, j ≪ 1 for all i, j, so that most of the time one of the alleles is fixed in the pop…

Crow JF 1987 Twenty-five years ago in Genetics: Motoo Kimura and molecular evolution. Genetics 116:183-184. Fisher (1930) had called attention to the considerable chance of stochastic loss of an new mutant even a favorable one yet, in any …

Kopp M & Hermisson J 2009 The genetic basis of phenotypic adaptation II: the distribution of adaptive substitutions in the moving optimum model. Genetics 183:1453-1476. a new mutation reaches fixation if and only if it survives stochastic …

Kryazhimskiy S, Tkačik G & Plotkin JB 2009 The dynamics of adaptation on correlated fitness landscapes. PNAS 106:18638-18643. we assume that the mutation rate is sufficiently small that, at most, one mutant segregates in the populat…

Harrigan RJ, Mazza ME & Sorenson MD 2008 Computation vs. cloning: evaluation of two methods for haplotype determination. Mol Ecol Res 8:1239-1248. the computational method may actually outperform cloning, at least when the latter is based …

Bulmer M 1991 The selection-mutation-drift theory of synonymous codon usage. Genetics 129:897-907. Kimura (1981, 1983) considered a model of stabilizing selection on codon usage there is an optimal state of highest fitness when the relativ…

Campbell RB 1984 The manifestation of phenotypic selection at constituent loci. I. Stabilizing selection. Evolution 38:1033-1038. perhaps Kimura overstated the importance of selection when the population mean deviates from the optimum rath…

Kimura M 1981 Possibility of extensive neutral evolution under stabilizing selection with special reference to non-random usage of synonymous codons. PNAS 78:5773-5777. if the deviation of the mean from the optimum is much larger than the …