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Matters Arising 630 Nature Vol. 295 18 February 1982 rate per nucleotide position than the neu­ substitution is much lower than that in Positive selection 1 2 tral substitutions in functionally less fibrinopeptides • • The neutralist's causes purifying selection important genes or parts of genes. For the explanation for this is that these proteins short time span that an adaptive mutation have strong functional constraints, which IN their support of the neutral mutation is being fixed in a lineage by the positive cause many new mutations to be elim­ hypothesis of molecular evolution, Li et darwinian form of natural selection, there inated from the population, and only al. 1 oversimplify the views of selectionists could follow a very long time span during those mutations (amino acid sequences) which the fixed mutation was maintained that are functionally equivalent are and use a specious logic that should not go 2 unchallenged. They assert after Clark2 by the stabilizing form of natural selec­ incorporated into the genome • In the and Milkman3 that "selectionists believe tion. Thus over the total time span of neutral theory, therefore, the entire set of that most nucleotide substitutions are many millions of years, the average substitution data from pseudogenes to caused by positive darwinian selection" evolutionary rate for such adaptive muta­ highly conserved proteins such as histone 4 5 tions could be relatively small. Neverthe­ can be explained by the simple and realis­ and then using King and Jukes ' as their 1 authorities argue "in which case the rate less, the findings of Li et al. on pseudo­ tic assumption that the mutation rate is the of nucleotide substitution in functionally genes do not exclude the possibility that same for all segments of DNA (genes or unimportant genes or parts of genes is for certain important categories of base parts of genes) but the proportion of fresh expected to be relatively lower because substitutions, for example, those that mutations eliminated varies with DNA the mutations in these regions of DNA change amino acids, a relatively large segment and the higher this proportion, would not produce any significant selec­ proportion were fixed by selection rather the slower the rate of gene substitution. tive advantages". than random drift. Available data support this view, that is, I believe that the assertion of Li et al. 1 is fresh mutations are known to occur almost an oversimplication. There are molecular MORRIS GOODMAN at random in the entire coding region of evolutionists who are selectionists Department of Anatomy, haemoglobin DNA5, and any amino acid because they consider natural selection to Wayne State University substitutions generally occur between two School of Medicine, amino acids having similar biochemical be a driving force steering protein evolu­ 6 7 tion6-8; however, such proponents of Detroit, Michigan 48201, USA properties · • However, if natural selec­ darwinian evolution of proteins are quite tion is the driving force for protein evolu­ willing to have neutral substitutions occur tion, it would be difficult to explain at a high rate in pseudogenes, in the third I. Li, W-H, Gojobori, T. & Nei. M. Nature 292, 237-239 the inverse relationship between the (1981). functional importance of genes and position of the codons when the base 2. Clark, B. Science 168, 1009-1011 (1970). 8 Note that changes do not cause amino acid changes , 3. Milkman, R. Trends Bioc/r,m. Sci. 1, N152-N154 (1976). the rate of gene substitution·4. 4. King, J. L. & Jukes, T. H. Science 164, 788-798 (1969). the rate of gene substitution due to dar­ and in general in functionally less 5. Jukes, T. H. & King, J. L. Nature 231, 114-115 (1971). important regions of DNA. 6. Goodman, M .. Moore, G. W. & Matsuda, G. Nature 253, winian selection depends not only on the 1 is specious 603-608 (1975). mutation rate but also on the selection The argument of Li et al. 7. Goodman, M. & Czelusniak, J. Protein Biol. Fluids 28, 8 because it ignores two factors: (1) the time 57-60 (1980). coefficient and population size • In any span for molecular evolution above the 8. Goodman, M. Prog. Biophys. molec. Biol. 38, 105-164 theory based on selection these three (1981). species level is in millions of years, not factors must be considered. hundreds; and (2) the selection, which is Goodman's statement that we have positive darwinian selection when it ignored the two factors mentioned by him increases the frequency of an allele in an is unfounded. Our conclusion is based on a evolving lineage, becomes stabilizing study of evolutionary change of genes for (=purifying or negative) selection after LI ET AL.REPLY-Goodman accepts our 80 Myr and on a due consideration of the the allele replaces all others in that view that random fixation of neutral effects of mutation, selection and random lineage. When these two factors are alleles occurs at a high rate in such unim­ genetic drift. Note also that neutralists considered it follows that the nucleotide portant genes as pseudogenes or in believe that adaptive evolution occurs by substitutions in functionally important general in functionally less important positive darwinian selection but a small regions of DNA, but believes that natural proportion of gene substitutions is parts of genes, as measured in distant 9 pairwise comparisons such as those of Li et selection is a driving force steering protein sufficient for this • 1 al. , could be primarily adaptive substitu­ evolution. He suggests that a large pro­ tions and still yield a slower evolutionary portion of amino acid substitutions in proteins are caused by natural selection. It WEN-HSIUNG LI is known, however, that the rate of amino TAKASHI GOJOBORI acid substitution is also higher in MASATOSH I NEI functionally less important proteins or parts of proteins, as in the case of nucleo­ 1 2 Center for Demographic and Matters Arising tide substitution in DNA • • For example, Population Genetics, fibrinopeptides A and B, which University of Texas at Houston, Matters Arising is meant as a vehicle apparently do not have any biological for comment and discussion about Houston, Texas 77030, function except for holding other poly­ USA papers that appear in Nature. The peptides that later form a protein, show a originator of a Matters Arising rate of nucleotide (amino acid) substitu­ contribution should initially send his 3 4 tion as high as that of pseudogenes • • The manuscript to the author of the ori­ fact that amino acid sequence apparently l. King, J. L. & Jukes, T. H. Science 164, 788- 798 (1969). ginal paper and both parties should, 2. Kimura, M. & Ohta, T. Proc. nam. Acad. Sci. U.S.A. 71, does not affect appreciably fibrinopeptide 2848-2852 (1974). wherever possible, agree on what is to function, and the mutation rate per 3. Kafatos, F. C. et al. Proc. natn. Acad. Sci. U.S.A. 74, be submitted. Neither contribution nucleotide site is presumably the same for 5618-5622 (1977). is necessary) should 4. Li, W.-H .. Gojobori, T. & Nei, M. Nature 292, 237-239 nor reply (if one these peptides and pseudogenes, strongly (1981). be longer than 300 words and the suggests that the amino acid substitutions 5. Vogel, F. J. molec. Evol. l, 334-367 (1972). briefest of replies, to the effect that a 6. Jukes, T. H. & King, J. L. Nature 231, 114-115 (1971). in fibrinopeptides are mainly due to 7. Grantham, R. Science 185, 862-864 (1974). point i• t~ken, should be considered. random fixation of neutral alleles. 8. Kimura, M. & Ohta, T. Theoretical Aspects of Population Genetics (Princeton University Press, Princeton, 1971). In functionally important proteins or 9. Nei, M. Molecular Population Genetics and Evolution parts of proteins, the rate of amino acid (North Holland, Amsterdam, 1975). 0028-0836/82/07063~1$01.00 © 1982 Macmillan Journals Ltd .
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