Is molecular evolution better explained by selective or neutral processes?

Abstract

As technology enables scientists to study the changes in molecular level, evolution, one of the most fundamental and challenging fields in science, extend its body to molecular level – molecular evolution. At the same time selective theory, which almost perfectly fits to macroevolution, enters this new field smoothly almost without any tests. It is not long, however, until a provocative new theory – neutral theory, come into being. The neutral theory gains more and more evidence and now seems to have equal role with the selective theory. However, there is also much evidence against it. The field of molecular evolution can accommodate two opposite theories? 

Introduction

Historical background

Since his book “The origin of species” was published, Charles Darwin’s theory on evolution, summarized as natural selection has become widespread among most people’s thought, including that in most evolutionary biologists. Because it is so good to explain the evolution on the organisms or higher level, many evolutionists took it for granted that it was also correct in the molecular level before 1960s. At that time, most evolutionary biologists believed that almost all alleles, including those found as polymorphisms within populations, differed in their effects on organisms’ fitness, so that their frequencies were affected chiefly by natural selection(Futuyma, 1997). As Ernst Mayr(Mary, 1963) declared:” it is altogether unlikely that two genes would have identical selective value under all the conditions under which they may coexist in a population.”, “…cases of neutral polymorphism do not exist” and “it appears probably that random fixation is of negligible evolutionary importance.” Mayr’s belief is widely shared by other evolutionists. As Ford(Ford,1964) said in his book “Ecological Genetics” that not only are neutral genes very rare, but also they are unlikely to attain appreciable frequencies, because their neutrality will be upset by changes in the environment and in the genetic outfit of the organism. Fisher (Fisher, 1936), one of the leading evolutionists in the world at that time, states as follows, “Evolution is progressive adaptation and consists of nothing else. The production of differences recognizable by systematists is a secondary by-product, produced incidentally in the process of becoming better adapted.”

 In fact, however, early in 1937 J.B.S Haldane (Dietrich-Michaesl, 1994) found the effect on fitness did not depend on the harmfulness of the mutant: it was strictly a matter of the mutation rate and the dominance of mutant. Also in 1966, Lewontin and Hubby, having shown that a high proportion of enzyme loci are polymorphic in Drosophila populations, argued that natural selection could not actively maintain so much genetic variation and suggested that much of it might be selectively neutral (Futuyma, 1997). Such experiments gave lights to the birth of the neutral theory.

 Only two years later, the neutral theory was introduced by the Japanese geneticist Motoo Kimura. In his paper published in Nature in 1968 (Kimura 1968), he calculated that evolutionary rate of protein and found it is much higher than expected by the result of natural selection. In the last paragraph he declared:”…we must recognize that great importance of random genetic drift due to finite population number in forming the genetic structure of biological populations.” The conclusion is so different from the classical on and so Kimura is regarded as the founder of the neutral theory.

 The neutral theory was soon enhanced by Jack Lester King and Thomas H. Jukes in 1969 in their Science paper (King and Jukes, 1969). The paper, with a provocative title NonDarwinian Evolution, contains cogent data from molecular biology and so it along with Kimura’s Nature paper, gave birth to neutral theory. The authors thus initiated the neutralist-selectionist debate”, which has not yet been resolved.

 The points of the neutral theory

 According to Kimura, the neutral theory holds two points:

1. The main cause of evolutionary change at the molecular level – change in the genetic material itself – is random fixation of selectively neutral or nearly neutral mutations rather than positive Darwinian selection. (Kimura, 1983)
2. Most of the intraspecific variability at the molecular level, such as is manifested by protein polymorphism, is essentially neutral, so the most polymorphic alleles are maintained in the species by mutational input and random extinction. In other words, the neutral theory regards protein and DNA polymorphisms as a transient phase of molecular evolution and rejects the notion that the majority of such polymorphisms are adaptive and maintained in the species by some form of balancing selection. (Kimura, 1983)

But several points should be made clear for better understanding. (Avise, 1993) 1. Neutral theory is concerned with the evolution on the molecular level, not the organism level. 2. Neutral theory doesn’t suggest that most genes are dispensable, but are functionally equivalent. 3. The neutral theory doesn’t assert that natural selection plays no role, but the selection intensity involved in the process is so weak that mutation pressure and random drift prevail in molecular evolution.

 Under the light of neutral theory, the feature of molecular evolution may be summarized as following (Kimura, 1983). These features are often as testing object by later experiments.

1. For each protein, the rate of evolution in terms of amino acid substitutions is approximately constant per year per site for various lines, as long as the function and tertiary structure of the molecule remains essentially unaltered. This is also called rate- constancy hypothesis.

2. Functionally less important molecules or parts of molecules evolve (in terms of mutant substitutions) faster than more important ones.

3. Those mutant substitutions that are less disruptive to the existing structure and function of a molecule (conservative substitutions) occur more frequently in evolution than more disruptive ones.

4. Gene duplication must always precede the emergence of a gene having a new function.

5. Selective elimination of definitely deleterious mutants and random fixation of selectively neutral or very slightly deleterious mutants occur far more frequently in evolution than positive Darwinian selection of definitely advantageous mutants.

Evidence for both sides

Neutral theory has gained more and more attention since it was brought forward and many experiments have been conducted to test the following predictions it suggests. As a result, some experiments enhance it while others disprove it.

1. Synonymous substitution predominates over nonsynonymous substitution.

2. Functionally less important molecules evolve faster.

3. Regions of the genome that evolve at high rates well also exhibit high level of polymorphism.

4. After a gene duplication where both genes are retained, original and duplicate genes diverge at clock-like rates.

5. Molecular polymorphisms are maintained by mutational input and random extinction.

1.Synonymous substitution predominates over nonsynonymous substitution?

As neutral theory declares, the vast majority changes in molecular level are selectively neutral or nearly neutral. So it predicts that synonymous substitution, which causes no amino acid change, is more likely to be selectively neutral than nonsynonymous substitutions and thus the former should predominate over the latter.

Gojobori et al. examined the synonymous and nonsynonymous substitution rate of retroviral oncogene, human immunodeficiency viruses (HIV), hepatitis B viruses (HBV), and influenza A viruses (Gojobori et al., 1990). The result shows that synonymous substitutions always much predominate over nonsynonymous substitutions, even though the substitution rate varies considerably among the viruses. For retroviral oncogenes, the average synonymous and nonsynonymous substitutions are 1.40*10^-3 and 0.52*10^-3, respectively. See Table 1.

On the other hand, Zhang, et al., after examining the evolution of eosinophil cationic protein (ECP) gene, found that he rate of nonsynonymous nucleotide substitution was significantly higher than that of synonymous substitution. Thus the result strongly suggests that positive Darwinian selection operated in the early stage of evolution of the ECP gene. (Zhang et al., 1998) The contrary results from the two experiments suggest different molecule may change in different ways.

 2.Functionlly less important molecules evolve faster?

 According to the neutral theory, the probability of mutation not being harmful and therefore selectively neutral is larger if the mutation occurs in a functionally less important molecule or a part of a molecule, and thus has a higher chance of being fixed in the population by random genetic drift. So a less functionally important molecule evolves faster than important ones.

 As interesting example is that the evolutionary rate of the eye lens protein Alpha-A-crystalline has been much enhanced in the blind mole rat, Spalax ehrenbergi. This animal is completely blind and is adapted to a burrowing subterranean way of life. However, the crystalline are still expressed in the atrophied lens cells. Generally speaking, Alpha-A-crystalline is a slowly evolving protein and the rate is about 0.3*10^-9 per amino acid site per year in rodents and other vertebrates. Comparisons of the blind mole rate alpha-A-crystalline sequence with alpha-A sequences from other rodents reveal a considerable acceleration of the substitution rate at nonsynonymous positions in the mole rate lineage, which reflects a relaxation of selective constraints. (Hendriks, et al. 1987)

 Another example is the glutamine synthetase genes. Thirty DNA sequences of various organisms spanning from prokaryotes to eukaryotes where collected and from the DNA data banks and translated first, they were aligned next, then evolutionary distances were computed. The results reveal that functionally important regions of glutamine synthetase have been evolutionarily more conserved than the remaining regions. Besides, the evolutionary distances show that the rate of synonymous substitutions is higher than that of nonsynonoymous substitutions. (Tateno, 1994)

 3.Region of the genome that evolve at high rates will also exhibit high level of polymorphism?

 The oxytocin-like hormone gene and vasopressin-like hormone gene were derived from the duplication of and ancestral gene that may have been present in agnothans. But interestingly, there is a striking evolutionary stability in bony vertebrates since virtually all species belonging to a given class are endowed with the same peptides, while in cartilaginous fished, for example, in ratfish, the oxytochin-like hormone displays a great diversity, Thus, as the author conclude, ‘ the molecular evolution of neurohypopysial hormones was driven by selection in bony vertebrates, structural invariability in each class or group of classed being explained by a tight fitting of the hormones to specific receptors. In contrast, in cartilaginous fished the oxytocin-like hormones wee subjected to a random genetic drift, according to the neutral theory of molecular evolution. (Acher, 1996)

 The above example is interesting in the sense that two molecular, having a common ancestor, evolve under quite different mechanisms as the author suggests. And so, maybe different molecules have different evolutionary mechanisms.

 4.After a gene duplication where both genes are retained, original and duplicate genes diverge at clock-like rates?

 As neutral theory predicts, if both sequence and expression pattern diverge at clock-like rates, a correlation between divergence in sequence and divergence in expression patterns is expected. Duplicate gene pair with more highly diverged sequences should also show more highly diverged expression patterns. This prediction is tested for a large sample of duplicated genes in the yeast Saccaromyces cereisae. However, only a weak correlation is observed, suggesting that coding sequence and mRNA expression patterns of duplicate gene pairs evolve independently and at vastly different rates. (Wagner, 1999)

 5. Molecular polymorphism are maintained by mutational input and random extinction?

 Another test was from ecological aspect, conducted by Nevo, et al. in 1988. The authors tested protein polymorphism in 13 unrelated genera of plants, invertebrates and vertebrates, involving 21 species, 142 populations and 5474 individuals. Each was tested, on average, for 27 enzymatic gene loci. The species share a geographically short and ecologically stressful gradient of increasing aridity in Israel. They found that average heterozygosity and gene diversity were positively and overall significantly correlated with rainfall variation. And thus the results are inconsistent with the neutral theory and suggest that natural selection appears to be and important differentiating evolutionary force hat the protein level. (Nevo and Beiles, 1988)

 Conclusion

 The neutral theory and the selective theory both have much supporting evidence as well as opposite facts and so either of them is far from perfect. However, there is a notable thing. Nearly every paper concerning such a topic has the same mode like “ The hypothesis that a prediction of the neutral theory is correct is tested, and the result shows it is rejected or accepted.” It is, however, unfair to the neutral theory. For a test should be conducted in bi-directional ways. That is, there should be tests aiming at selective theory such as “ a hypothesis of a prediction of selective theory is tested, and it is rejected or accepted.” For, I think, the rejection of a prediction of neutral theory doesn’t automatically mean that such a rejection is a proof for selective theory.

Reference:

Acher-Roger. 1996. Molecular evolution of fish neurohyophysial hormones: neutral and selective evolutionary mechanisms. General and Comparative Endocrinology. 102(2) 157-172

 Avise, J.C.1993. Molecular Marker, Natural history and evolution.Chapman&Hall, New Yourk, NY.28

 Dietrich-Michael R. 1994. The origins of the neutral theory of molecular evolution. Journal of the history of biology. 27(1) 21-59

 Fisher, R.A.1936. The measurement of selective intensity. Proc. Roy. Soc. London, Ser.B.121, 58-62

 Ford, E.B.1964.Ecological Genetics, 1^st edition, London

 Futuyma, D.J.1997. Evolutionary biology,  3^rd edition. Sinauer Asoicateds, Inc.,Sunderland, Massachusetts, 320

 Gojobori,T.et al 1990. Molecular clock of viral evolution, and the neutral theory, Proc. Natl.Acad. Sci. USA 87,10015-10018

 Hendrikes, W. et al. 1987 The lens protein alpha-A-crystalline of the blind mole rat, Spalax ehrenbergi: Evolutionary change and functional constraints Proc. Natl. Acad. Sci. USA. 84. 5320-5324

 Kimura, M. 1968. Evlutionary rate at the molecular level. Nature 217, 624-626

 Kimura, M. 1991. Recent developments of the neutral theory viewed from the Weighitian tradion of theoretical population genetics. Proc. Natl. Acad. Sci. USA 88,5969-5973

 Kimura, M. 1983. The neutral Theory of Molecular Evolution. Cambridge Univ Press, Cambridge.

 King,J.L. and T.H.Jukes. 1969. Non-Darwinian evolution: random fixation of selectively neutral mutations. Science 164, 788-798

 Mayr, E. 1963. Animal Species and Evolution. Harvard University Press, Cambridge, MA. 162, 211

 Nevo E. et al. 1988 Genetic parallelism of protein polymorphism in nature: Ecological test of the neutral theory of molecular evolution. Biological Journal of the linnean society 35(3), 229-246

 Tateno, Y. 1994. Evolution of glutamin synthetase genes is in accordance with the neutral theory of molecular evolution. Japanese Jouranl of Genetics. 69, 489-502

  Wagner, A.1999. Decoupled evolution of coding region and mRNA expression patterns after gene duplication: Implications for the neutralist-selectionist debate. Proc. Natl. Acad. Sci. USA 97, 6579-6584

 Zhang,J. et al. 1998. Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proc. Natl. Acad.Sci. USA 96, 3708-3713

 Table 1. Rates of synonymous and nonsynonymous substitution of RNA viral genes.

MMSV and MMLV, Moloney murine sarcoma and leukemia virus