Proc. Nati. Acad. Sci. USA Vol. 88, pp. 5%9-5973, July 1991 Evolution Recent development of the neutral theory viewed from the Wrightian tradition of theoretical population genetics* (molecular evolution/population genetics/macroevolution) MOToo KIMURA National Institute of Genetics, Mishima, 411 Japan Contributed by Motoo Kimura, April 1, 1991 ABSTRACT In contrast to the Darwinian theory of evo- continued mutation pressure (for details, see ref. 8). This lution by natural selection, the neutral theory emphasizes the view is in sharp contrast to the traditional neo-Darwinian great importance of random genetic drift (due to rinite popu- (i.e., the synthetic) theory ofevolution, which claims that the lation size) and mutation pressure as the main causes of spreading of mutants within the species in the course of molecular evolution. In this paper, after a brief review of the evolution can occur only with the help of positive natural neutral theory, recent data strongly supporting the neutral selection. theory are presented. Also discussed are such topics as com- The neutral theory also asserts that most intraspecific pensatory neutral evolution and an approach to a unified variability at the molecular level (including protein and DNA understanding of molecular and phenotypic evolution. It is polymorphisms) is selectively neutral, and it is maintained in concluded that random genetic drift acting on selectively the species by the balance between mutational input and neutral mutants must have played some very important role in random extinction. In other words, the neutral theory regards organic evolution, including the origin of life and macroevo- protein and DNA polymorphisms as a transient phase of lution. molecular evolution (9) and rejects the notion that the ma- jority of such polymorphisms are adaptive and actively The late Professor Sewall Wright was my idol when I was maintained in the species by some form of balancing selec- young. Soon after graduating from Kyoto University, I read tion. Wright's 1931 classic "Evolution in Mendelian populations" The neutral theory differs from traditional theories of (1) and his subsequent papers on random genetic drift and the evolution in that it is quantitative-namely, we can derive distribution of gene frequencies [such as refs. 2-5; see also simple formulae for such quantities as the rate of evolution Provine (6) for additional references]. These papers im- and the amount of intraspecific variability-and in that we pressed me deeply and, in fact, inspired me to become a can check the validity of the formulae by comparing theo- theoretical population geneticist. Without this foundation I retical predictions with actual data. would never have been able to propose the neutral theory or First, let us consider the cumulative process in which to incorporate new knowledge from molecular genetics into neutral mutants are substituted sequentially at a given locus the framework of population genetics. or site through random genetic drift under continued input of When the neutral theory was proposed (7), the only avail- new mutants. Then we have for the rate of evolution per able data consisted ofamino acid sequences ofa few proteins generation the formula in related organisms, such as hemoglobin molecules in some vertebrate species. Also, genetic variability at the molecular kg= Vo, [1] level could be inferred only from electrophoretic data on where kg represents the long-term average per generation of enzyme polymorphisms for a few species such as fruit flies the number of mutants that spread through the population and humans. Resolution ofthe ensuing controversy regarding and vo is the rate of production of neutral mutants per locus the pros and cons ofthe neutral theory ofmolecular evolution (or site) per generation. This formula is based on the well- was much limited by nonavailability of DNA data. The known property (7, 10) that, for neutral mutations, the situation has changed dramatically with the emergence of long-term rate of mutant substitution is equal to the mutation DNA sequence data, which resulted from the development of rate. rapid DNA sequencing techniques. I am glad to note that, If we denote by VT the total mutation rate, and iffo is the following this development, strong evidence for the neutral fraction of neutral mutations at the time of occurrence, so theory has accumulated steadily with the passage of time, that = VO/VT, then Eq. 1 may be rewritten as particularly during the past decade. fo In this paper I shall review recent developments of mo- kg = VTfO. [2] lecular evolutionary studies from the standpoint of the neu- tral theory. I shall also discuss some neutralist views on Advantageous mutations may occur, but the neutral theory evolution in general. assumes that they are so rare that they may be neglected in our quantitative consideration. Thus, (1 - fo) represents the Neutral Theory of Molecular Evolution fraction of definitely deleterious mutants that are eliminated from the population without contributing to either evolution According to the neutral theory, the great majority of evo- or polymorphism, even though the selective disadvantages lutionary mutant substitutions at the molecular level are involved may be very small in the ordinary sense. The above caused by random fixation, through sampling drift, of selec- formulation has a remarkable simplicity in that the evolu- tively neutral (i.e., selectively equivalent) mutants under tionary rate (on the long-term basis) is independent of pop- ulation size and environmental conditions of each organism. The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" *This paper is an extended version of my talk presented at the Sewall in accordance with 18 U.S.C. §1734 solely to indicate this fact. Wright Centennial Symposium, Madison, WI, June 8-9, 1990. 5969 Downloaded by guest on September 25, 2021 5970 Evolution: Kimura Proc. Natl. Acad. Sci. USA 88 (1991) In molecular evolutionary studies, it is customary to mea- than in rodents (16, 17). According to my estimate (18), the sure the evolutionary rate in terms of years (i.e., taking one mouse line evolves faster than the human line with respect to year as the unit length of time) rather than in generations. amino acid replacements per year in hemoglobin a and X3 Therefore, it is convenient to modify Eq. 2 so that it gives the chains by a factor of 34.5/14.6, or approximately 2.4. Note evolutionary rate per year. that, from the standpoint ofthe neutral theory, the difference of the evolutionary rates in these lines is caused by the k, = (vT/g)fO. [31 difference in their neutral mutation rates per year. Thus, In this formula, g stands for the generation span (in years), assuming an average generation span of 20 years for the and VT/g is the total mutation rate per year. human lineage, the total mutation rate per generation is Next, let us consider intraspecific variability, assuming neutral mutations. For the average heterozygosity per nucle- VT = (3 X 109) x (5 X 10 9) X 20 2.4, otide site we have the following formula: or VT = 125.0, which means that the total number of new mutations per generation due to base substitutions amounts H = 4NeVonuc), [4] to 125 per gamete, and twice as many per zygote. where Ne is the effective population size and VO(nuc) is the In the above calculation, we assumed that the mouse line neutral mutation rate per nucleotide site. I first derived this evolved 2.4 times faster than the human line. It is possible, formula by using the "infinite site model" (11). and also likely, however, that this is an underestimate. In fact, Li and Tanimura (19) obtained a result that the rate of Some Recent Data Supporting the Neutral Theory of synonymous substitutions in rodents is about 7 times higher Molecular Evolution than that in higher primates. If we adopt this estimate, we obtain VT 43, which is about 1/3 of the above estimate. Still, The first definitive evidence supporting the neutral theory this is a very high value when compared with the traditional was the discovery that synonymous base substitutions, estimates of the genomic mutation rate. From the consider- which do not cause amino acid changes, almost always occur ation ofgenetic load (cf. ref. 20), the mutational load becomes at much higher rate than nonsynonymous-that is, amino- intolerably high unless the great majority (say, 99.5%) of acid-altering-substitutions. It was also found that evolution- them are selectively neutral (i.e., nondeleterious). ary base substitutions at other "silent" sites, such as introns, An equally interesting example suggesting neutral evolu- occur at comparably high rates. These observations suggest tion is the recent observation that the evolutionary rate of the that molecular changes that are less likely to be subjected to eye lens protein aA-crystallin has been much enhanced in the natural selection occur more frequently in evolution and blind mole rat, Spalax ehrenbergi (21). This animal is com- therefore show higher evolutionary rates. This is easy to pletely blind and is adapted to a burrowing subterranean way understand from the neutral theory, because such changes of life (and possibly has been for the last 25 million years, are more likely to turn out to be nondeleterious (i.e., selec- according to fossil evidence). Although this animal is com- tively neutral) and therefore fo in Eq. 2 is larger for them. pletely blind, the crystallins are still expressed in the atro- More than a decade and a half ago, in collaboration with phied lens cells. Generally speaking, aA-crystallin is a slowly Ohta, I enumerated (12) five principles that govern molecular evolving protein, with an average replacement rate of about evolution, one ofwhich states that functionally less important 0.3 x 10-9 per amino acid site per year in rodents and other molecules or parts of a molecule evolve (in terms of mutant vertebrates.