Neutral theory of molecular evolution
Encyclopedia
The neutral theory of molecular evolution states that the vast majority of evolution
Evolution
Evolution is any change across successive generations in the heritable characteristics of biological populations. Evolutionary processes give rise to diversity at every level of biological organisation, including species, individual organisms and molecules such as DNA and proteins.Life on Earth...

ary changes at the molecular level
DNA sequence
The sequence or primary structure of a nucleic acid is the composition of atoms that make up the nucleic acid and the chemical bonds that bond those atoms. Because nucleic acids, such as DNA and RNA, are unbranched polymers, this specification is equivalent to specifying the sequence of...

 are caused by random drift
Genetic drift
Genetic drift or allelic drift is the change in the frequency of a gene variant in a population due to random sampling.The alleles in the offspring are a sample of those in the parents, and chance has a role in determining whether a given individual survives and reproduces...

 of selectively
Selection
In the context of evolution, certain traits or alleles of genes segregating within a population may be subject to selection. Under selection, individuals with advantageous or "adaptive" traits tend to be more successful than their peers reproductively—meaning they contribute more offspring to the...

 neutral mutants
Mutation
In molecular biology and genetics, mutations are changes in a genomic sequence: the DNA sequence of a cell's genome or the DNA or RNA sequence of a virus. They can be defined as sudden and spontaneous changes in the cell. Mutations are caused by radiation, viruses, transposons and mutagenic...

 (not affecting fitness). The theory was introduced by Motoo Kimura
Motoo Kimura
was a Japanese biologist best known for introducing the neutral theory of molecular evolution in 1968. He became one of the most influential theoretical population geneticists. He is remembered in genetics for his innovative use of diffusion equations to calculate the probability of fixation of...

 in the late 1960s and early 1970s. Neutral theory is compatible with Darwin's
Charles Darwin
Charles Robert Darwin FRS was an English naturalist. He established that all species of life have descended over time from common ancestry, and proposed the scientific theory that this branching pattern of evolution resulted from a process that he called natural selection.He published his theory...

 theory of evolution by natural selection
Natural selection
Natural selection is the nonrandom process by which biologic traits become either more or less common in a population as a function of differential reproduction of their bearers. It is a key mechanism of evolution....

: adaptive changes are acknowledged as present and important, but hypothesized to be a small minority of all the changes seen fixed
Fixation (population genetics)
In population genetics, fixation is the change in a gene pool from a situation where there exist at least two variants of a particular gene to a situation where only one of the alleles remains...

 in DNA sequences. Since then, this hypothesis has been tested using the McDonald-Kreitman test
McDonald-Kreitman test
The McDonald–Kreitman Test looks for ancient selection over long periods, as opposed to the steady accumulation of mutations that confer no selective advantage predicted by the Neutral theory. It was first devised by John McDonald and Martin Kreitman in 1991, based on an investigation of...

, and has not been supported in all species. Even in those species in which adaptive changes are rare, background selection at linked sites may violate neutral theory's assumptions regarding genetic drift.

Overview

While some scientists, such as Sueoka (1962), had hinted that perhaps neutral mutation
Mutation
In molecular biology and genetics, mutations are changes in a genomic sequence: the DNA sequence of a cell's genome or the DNA or RNA sequence of a virus. They can be defined as sudden and spontaneous changes in the cell. Mutations are caused by radiation, viruses, transposons and mutagenic...

s were widespread, a coherent theory of neutral evolution was first formalized by Motoo Kimura in 1968, followed by a 1969 article by Jack L. King and Thomas H. Jukes
Thomas H. Jukes
Thomas Hughes Jukes was a British-American biologist known for his work in nutrition, molecular evolution, and for his public engagement with controversial scientific issues, including DDT, vitamin C and creationism...

, "Non-Darwinian Evolution
Non-Darwinian Evolution
"Non-Darwinian Evolution" is a 1969 scientific paper co-authored by Jack Lester King and Thomas H. Jukes that is credited, along with Motoo Kimura's 1968 paper "Evolutionary Rate at the Molecular Level", with proposing what became known as the neutral theory of molecular evolution...

".

Kimura posited that when one compares the genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....

s of existing species, the vast majority of molecular differences are selectively "neutral", i.e. the molecular changes represented by these differences do not influence the fitness
Fitness (biology)
Fitness is a central idea in evolutionary theory. It can be defined either with respect to a genotype or to a phenotype in a given environment...

 of the individual organism. As a result, the theory regards these genomic features as neither subject to, nor explicable by, natural selection. This view is based in part on the degenerate genetic code, in which sequences of three nucleotides (codons) may differ and yet encode the same amino acid
Amino acid
Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...

 (GCC and GCA both encode alanine
Alanine
Alanine is an α-amino acid with the chemical formula CH3CHCOOH. The L-isomer is one of the 20 amino acids encoded by the genetic code. Its codons are GCU, GCC, GCA, and GCG. It is classified as a nonpolar amino acid...

, for example). Consequently, many potential single-nucleotide changes are in effect "silent" or "unexpressed" (see synonymous or silent substitution
Synonymous substitution
A synonymous substitution is the evolutionary substitution of one base for another in an exon of a gene coding for a protein, such that the produced amino acid sequence is not modified. Synonymous substitutions and mutations affecting noncoding DNA are collectively known as silent mutations...

). Such changes are presumed to have little or no biological effect. However, it should be noted that the original theory was based on the consistency in rates of amino acid changes, and hypothesized that the majority of those changes were also neutral.

A second hypothesis of the neutral theory is that most evolutionary change is the result of genetic drift
Genetic drift
Genetic drift or allelic drift is the change in the frequency of a gene variant in a population due to random sampling.The alleles in the offspring are a sample of those in the parents, and chance has a role in determining whether a given individual survives and reproduces...

 acting on neutral allele
Allele
An allele is one of two or more forms of a gene or a genetic locus . "Allel" is an abbreviation of allelomorph. Sometimes, different alleles can result in different observable phenotypic traits, such as different pigmentation...

s. A new allele arises typically through the spontaneous mutation
Mutation
In molecular biology and genetics, mutations are changes in a genomic sequence: the DNA sequence of a cell's genome or the DNA or RNA sequence of a virus. They can be defined as sudden and spontaneous changes in the cell. Mutations are caused by radiation, viruses, transposons and mutagenic...

 of a single nucleotide within the sequence of a gene. In single-celled organisms, such an event immediately contributes a new allele to the population, and this allele is subject to drift. In sexually reproducing
Sexual reproduction
Sexual reproduction is the creation of a new organism by combining the genetic material of two organisms. There are two main processes during sexual reproduction; they are: meiosis, involving the halving of the number of chromosomes; and fertilization, involving the fusion of two gametes and the...

 multicellular organisms, the nucleotide substitution must arise within one of the many sex cells
Gamete
A gamete is a cell that fuses with another cell during fertilization in organisms that reproduce sexually...

 that an individual carries. Then only if that sex cell participates in the genesis of an embryo
Embryo
An embryo is a multicellular diploid eukaryote in its earliest stage of development, from the time of first cell division until birth, hatching, or germination...

 does the mutation contribute a new allele to the population. Neutral substitutions create new neutral alleles.

Through drift, these new alleles may become more common within the population. They may subsequently be lost, or in rare cases they may become fixed
Fixation (population genetics)
In population genetics, fixation is the change in a gene pool from a situation where there exist at least two variants of a particular gene to a situation where only one of the alleles remains...

, meaning that the new allele becomes standard in the population.

According to the mathematics of drift, when comparing divergent populations, most of the single-nucleotide differences can be assumed to have accumulated at the same rate as individuals with mutations are born. This latter rate, it has been argued, is predictable from the error rate of the enzyme
Enzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...

s that carry out DNA replication
DNA replication
DNA replication is a biological process that occurs in all living organisms and copies their DNA; it is the basis for biological inheritance. The process starts with one double-stranded DNA molecule and produces two identical copies of the molecule...

; these enzymes have been well studied and are highly conserved
Conserved sequence
In biology, conserved sequences are similar or identical sequences that occur within nucleic acid sequences , protein sequences, protein structures or polymeric carbohydrates across species or within different molecules produced by the same organism...

 across all species. Thus the neutral theory provides a rationale for the molecular clock
Molecular clock
The molecular clock is a technique in molecular evolution that uses fossil constraints and rates of molecular change to deduce the time in geologic history when two species or other taxa diverged. It is used to estimate the time of occurrence of events called speciation or radiation...

, although the discovery of a molecular clock predates neutral theory. The observed overdispersion
Overdispersion
In statistics, overdispersion is the presence of greater variability in a data set than would be expected based on a given simple statistical model....

 of the molecular clock is not predicted by or compatible with neutral theory.

Many molecular biologists
Molecular biology
Molecular biology is the branch of biology that deals with the molecular basis of biological activity. This field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry...

 and population geneticists
Population genetics
Population genetics is the study of allele frequency distribution and change under the influence of the four main evolutionary processes: natural selection, genetic drift, mutation and gene flow. It also takes into account the factors of recombination, population subdivision and population...

 also contributed to the development of the neutral theory, which may be viewed as an offshoot of the modern evolutionary synthesis
Modern evolutionary synthesis
The modern evolutionary synthesis is a union of ideas from several biological specialties which provides a widely accepted account of evolution...

.

Neutral theory does not contradict natural selection, nor does it deny that selection occurs. Hughes writes: "Evolutionary biologists typically distinguish two main types of natural selection: purifying selection, which acts to eliminate deleterious mutations; and positive (Darwinian) selection, which favors advantageous mutations. Positive selection can, in turn, be further subdivided into directional selection
Directional selection
In population genetics, directional selection is a mode of natural selection in which a single phenotype is favored, causing the allele frequency to continuously shift in one direction...

, which tends toward fixation of an advantageous allele, and balancing selection
Balancing selection
Balancing selection refers to a number of selective processes by which multiple alleles are actively maintained in the gene pool of a population at frequencies above that of gene mutation. This usually happens when the heterozygotes for the alleles under consideration have a higher adaptive value...

, which maintains a polymorphism
Polymorphism (biology)
Polymorphism in biology occurs when two or more clearly different phenotypes exist in the same population of a species — in other words, the occurrence of more than one form or morph...

. The neutral theory of molecular evolution predicts that purifying selection is ubiquitous, but that both forms of positive selection are rare, whereas not denying the importance of positive selection in the origin of adaptations." In another essay, Hughes writes: "Purifying selection is the norm in the evolution of protein coding genes. Positive selection is a relative rarity — but of great interest, precisely because it represents a departure from the norm."

The "neutralist–selectionist" debate

A heated debate arose when Kimura's theory was published, largely revolving around the relative percentages of alleles that are "neutral" versus "non-neutral" in any given genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....

. Contrary to the perception of many onlookers, the debate was not about whether natural selection does occur. Kimura argued that molecular evolution
Molecular evolution
Molecular evolution is in part a process of evolution at the scale of DNA, RNA, and proteins. Molecular evolution emerged as a scientific field in the 1960s as researchers from molecular biology, evolutionary biology and population genetics sought to understand recent discoveries on the structure...

 is dominated by selectively neutral evolution, but at the phenotypic level changes in characters were probably dominated by natural selection
Natural selection
Natural selection is the nonrandom process by which biologic traits become either more or less common in a population as a function of differential reproduction of their bearers. It is a key mechanism of evolution....

 rather than sampling drift
Genetic drift
Genetic drift or allelic drift is the change in the frequency of a gene variant in a population due to random sampling.The alleles in the offspring are a sample of those in the parents, and chance has a role in determining whether a given individual survives and reproduces...

.

After flirting (in 1973) with the idea that slightly deleterious mutations may be common, Tomoko Ohta
Tomoko Ohta
is a Japanese scientist working on molecular evolution. In 1956, she graduated from the University of Tokyo. After working on the neutral theory of evolution with her mentor, Motoo Kimura, she became convinced of the importance of the mutations that were nearly neutral. She developed the slightly...

, a student of Kimura, made an important generalisation of the neutral theory by including the concept of "near-neutrality", that is, genes that are affected mostly by drift or mostly by selection depending on the effective size of a breeding population. The neutralist-selectionist debate has since cooled, yet the question of the relative percentages of neutral and non-neutral alleles remains. Graur & Li (2000), go as far as to say;
"There are only two predictions we are willing to make about the future of molecular evolution. The first concerns old controversies. Issues such as the neutralist-selectionist controversy or the antiquity of introns, will continue to be debated with varying degrees of ferocity, and roars of "The Neutral Theory Is Dead" and "Long Live the Neutral Theory" will continue to reverberate, sometimes in the title of a single article."


As of the early 2000s, the neutral theory is widely used as a "null model" for so-called null hypothesis
Null hypothesis
The practice of science involves formulating and testing hypotheses, assertions that are capable of being proven false using a test of observed data. The null hypothesis typically corresponds to a general or default position...

 testing. However, serious doubt has been cast on the neutral theory by the application of the McDonald-Kreitman test
McDonald-Kreitman test
The McDonald–Kreitman Test looks for ancient selection over long periods, as opposed to the steady accumulation of mutations that confer no selective advantage predicted by the Neutral theory. It was first devised by John McDonald and Martin Kreitman in 1991, based on an investigation of...

 to show that a substantial proportion of amino acid changes may be due to selection. The reliance of neutral theory on genetic drift also fails to explain the "paradox of variation", where genetic diversity has not been found to depend strongly on the size of different populations: while this can be addressed by nearly neutral theory
Nearly neutral theory of molecular evolution
The nearly neutral theory of molecular evolution is a modification of the neutral theory of molecular evolution that accounts for slightly advantageous or deleterious mutations at the molecular level...

, it requires the increase in the diversity of neutral alleles with increasing population size to exactly cancel out the decrease in the proportion of alleles that are neutral with increasing population size. Neither neutral theory nor nearly neutral theory predicts the observation that genetic diversity depends on the recombination rate in that part of the genome. These observations do not contradict the possibility that many or most substitutions are neutral, however these observations are better explained if selection at linked sites
Genetic hitchhiking
Genetic hitchhiking is the process by which an allele may increase in frequency by virtue of being linked to a gene that is positively selected. Proximity on a chromosome may allow genes to be dragged along with a selective sweep experienced by an advantageous gene nearby...

 rather than genetic drift
Genetic drift
Genetic drift or allelic drift is the change in the frequency of a gene variant in a population due to random sampling.The alleles in the offspring are a sample of those in the parents, and chance has a role in determining whether a given individual survives and reproduces...

 is driving changes in the frequencies of neutral alleles.

Implications for evolvability in asexual populations

In a series of recent papers, Swiss researcher Andreas Wagner proposed a reconciliation between selectionism and neutralism. His proposal demonstrates how evolutionary change involving several independent stepwise mutations might take place. In pure selectionism, such change would be impossible, because each step must occur independently. Each step must be favored by positive selection to become established in the genome, in order for the next step to occur. In Wagner's model, "innovation occurs via cycles of exploration of nearly neutral spaces," which he refers to as a neutralist regime. During a neutralist regime, neutral mutations accumulate, and so genetic diversity increases. When a new phenotype with higher fitness occurs, its genotype sweeps through the population to fixation, and genetic diversity is reduced during a selectionist regime.

Wagner's model uses RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....

 sequences as genotype
Genotype
The genotype is the genetic makeup of a cell, an organism, or an individual usually with reference to a specific character under consideration...

, and the final folded structure of RNA as the phenotype
Phenotype
A phenotype is an organism's observable characteristics or traits: such as its morphology, development, biochemical or physiological properties, behavior, and products of behavior...

. The work is made possible by the existence of a computationally efficient algorithm which predicts RNA structure from an RNA sequence. The work shows that RNA phenotype is robust enough to permit considerable variation in the underlying genotypes. This phenotype robustness promotes structure evolvability. The likelihood that a mutation is deleterious is smaller in populations with more robust phenotypes. As genetic diversity increases under such a neutralist regime, opportunities for an advantageous mutation increase. Wagner writes: "Populations evolving on large neutral networks can access greater amounts of variation." He explains the limitations of his work:
"This work leaves three important open questions. First, how robust and evolvable are biologically important phenotypes, such as RNA structures? To answer this question is currently impossible... no reliable and tractable method to do this is currently available. Second, how general is the positive association between phenotypic robustness and evolvability?... Does it occur in many other biological systems? Third, this work does not ask about the evolutionary forces that might cause high evolvability, of which there may be many".

See also

  • Adaptive Evolution in the Human Genome
    Adaptive evolution in the human genome
    Adaptive evolution results from the propagation of advantageous mutations through positive selection. This is the modern synthesis of the process which Darwin and Wallace originally identified as the mechanism of evolution...

  • Coalescent theory
    Coalescent theory
    In genetics, coalescent theory is a retrospective model of population genetics. It attempts to trace all alleles of a gene shared by all members of a population to a single ancestral copy, known as the most recent common ancestor...

  • Evolution
    Evolution
    Evolution is any change across successive generations in the heritable characteristics of biological populations. Evolutionary processes give rise to diversity at every level of biological organisation, including species, individual organisms and molecules such as DNA and proteins.Life on Earth...

  • Ewens's sampling formula
    Ewens's sampling formula
    In population genetics, Ewens' sampling formula, describes the probabilities associated with counts of how many different alleles are observed a given number of times in the sample.-Definition:...

  • John H. Gillespie
    John H. Gillespie
    John H. Gillespie is an evolutionary biologist interested in theoretical population genetics and molecular evolution. In molecular evolution, he emphasized the importance of advantageous mutations and balancing selection. For that reason, Gillespie is well known for his selectionist stance in the...

  • Molecular evolution
    Molecular evolution
    Molecular evolution is in part a process of evolution at the scale of DNA, RNA, and proteins. Molecular evolution emerged as a scientific field in the 1960s as researchers from molecular biology, evolutionary biology and population genetics sought to understand recent discoveries on the structure...

  • Nearly neutral theory of molecular evolution
    Nearly neutral theory of molecular evolution
    The nearly neutral theory of molecular evolution is a modification of the neutral theory of molecular evolution that accounts for slightly advantageous or deleterious mutations at the molecular level...

  • Peter Donnelly
    Peter Donnelly
    Peter Donnelly, FRS is an Australian mathematician and Professor of Statistical Science at the University of Oxford. He is a specialist in applied probability and has made contributions to coalescent theory...

  • Tomoko Ohta
    Tomoko Ohta
    is a Japanese scientist working on molecular evolution. In 1956, she graduated from the University of Tokyo. After working on the neutral theory of evolution with her mentor, Motoo Kimura, she became convinced of the importance of the mutations that were nearly neutral. She developed the slightly...

  • Unified neutral theory of biodiversity
    Unified neutral theory of biodiversity
    The unified neutral theory of biodiversity and biogeography is a hypothesis and the title of a monograph by ecologist Stephen Hubbell...

  • Warren Ewens
    Warren Ewens
    Warren Ewens FRS, FAA is an Australian-born professor of biology at the University of Pennsylvania. He concentrates his research on the mathematical, statistical and theoretical aspects of population genetics. Ewens has worked in human population genetics, computational biology, and evolutionary...

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