Molecular evolution is the process of the genetic material in populations of organisms changing over time. The genetic material consists of DNA, long sequences of nucleotides in each individual organism. Because most heritable changes in visible traits are a result of changes in the DNA, molecular evolution must be seen as part of general evolution. The boundary between molecular and other aspects of evolution is not clearly defined. One inequivalence is that molecular evolution takes place also in DNA with no known function (so-called "junk DNA"). Therefore the DNA of a population may "evolve molecularly", while the phenotype of descendants remains constant.
Genomic imprinting (which is "epigenetic") constitutes heritability that is not coded in DNA. Evolution is prevalent also in viruses, although these are not considered to be organisms. The genetic material in viruses may consist of DNA or RNA.
Main article: Mutation
Mutations are permanent, transmissible changes to the genetic material (usually DNA or RNA) of a cell. Mutations can be caused by copying errors in the genetic material during cell division and by exposure to radiation, chemicals, or viruses, or can occur deliberately under cellular control during the processes such as meiosis or hypermutation. Mutations are considered the driving force of evolution, where less favorable (or deleterious) mutations are removed from the gene pool by natural selection, while more favorable (or beneficial) ones tend to accumulate. Neutral mutations do not affect the organism's chances of survival in its natural environment and can accumulate over time, which might result in what is known as punctuated equilibrium; the modern interpretation of classic evolutionary theory.
Main article: Population genetics
The production and redistribution of variation is produced by three of the four agents of evolution: mutation, genetic drift, and gene flow. Natural selection, in turn, acts on the variation produced by these agents.
Molecular systematics is a product of the traditional field of systematics and molecular genetics. It is the process of using data on the molecular constitution of biological organisms' DNA, RNA, or both, in order to resolve questions in systematics, i.e. about their correct scientific classification or taxonomy from the point of view of evolutionary biology.
Molecular systematics has been made possible by the availability of techniques for gene sequencing, which allow the determination of the exact sequence of nucleotides or bases in either DNA or RNA. At present it is still a long and expensive process to sequence the entire genome of an organism, and this has been done for only a few species. However it is quite feasible to determine the sequence of a defined area of a particular chromosome. Typical molecular systematic analyses require the sequencing of around 1000 base pairs.
Main article: Neutral theory of molecular evolution
One of the questions concerning molecular evolution is what proportion of mutations are neutral with respect to natural selection, meaning mutations that do not convey a selective advantage or disadvantage to the individual that inherits them. Answering such questions is an aim of population genetics.
Rare spontaneous errors in DNA replication cause the mutations that drive molecular evolution. The molecular clock technique, which researchers use to date when two species diverged by comparing their DNA, deduces elapsed time from the number of differences. The technique was inspired by the once common assumption that the DNA error rate is constant--not just over time, but across all species and every part of a genome that you might want to compare. Because the enzymes that replicate DNA differ only very slightly between species, the assumption seemed reasonable a priori. But as molecular evidence has accumulated, the constant-rate assumption has proven false--or at least overly general. Molecular clock users are developing workaround solutions.
The Japanese geneticist Motoo Kimura and American geneticist James Crow (1964) introduced the infinite alleles model, an attempt to determine for a finite population what proportion of loci would be homozygous. This was, in part, motivated by assertions by other geneticists that more than 50 percent of Drosophila loci were heterozygous, a claim they initially doubted. In order to answer this question they assumed first, that there were a large enough number of alleles so that any mutation would lead to a different allele (that is the probability of back mutation to the original allele would be low enough to be negligible); and second, that the mutations would result in a number of different outcomes from neutral to deleterious.
They determined that in the neutral case, the probability that an individual would be homozygous, F, was:
where u is the mutation rate, and Ne is the effective population size. From this it is possible to determine an upper limit to the number of possible alleles in a population, n as the inverse of the homozygosity:
If the effective population is large, then a large number of alleles can be maintained. However, this result only holds for the neutral case, and is not necessarily true for the case when some alleles are more or less fit than others, for example when the fittest genotype is a heterozygote (a situation often referred to as overdominance or heterosis).
In the case of overdominance, because Mendel's second law (the law of segregation) necessarily results in the production of homozygotes (which are by definition in this case, less fit), this means that population will always harbor a number of less fit individuals, which leads to a decrease in the average fitness of the population. This is sometimes referred to as genetic load, in this case it is a special kind of load known as segregational load. Crow and Kimura showed that at equilibrium conditions, for a given strength of selection (s), that there would be an upper limit to the number of fitter alleles (polymorphisms) that a population could harbor for a particular locus. Beyond this number of alleles, the selective advantage of presence of those alleles in heterozygous genotypes would be cancelled out by continual generation of less fit homozygous genotypes.
These results became important in the formation of the neutral theory, because neutral (or nearly neutral) alleles create no such segregational load, and allow for the accumulation of a great deal of polymorphism. When Richard Lewontin and J. Hubby published their groundbreaking results in 1966 which showed high levels of genetic variation in Drosophila via protein electrophoresis, the theoretical results from the infinite alleles model were used by Kimura and others to support the idea that this variation would have to be neutral (or result in excess segregational load).