Molecular evolution

Molecular evolution is the 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 and function of nucleic acids and protein. Some of the key topics that spurred development of the field have been the evolution of enzyme function, the use of nucleic acid divergence as a "molecular clock" to study species divergence, and the origin of non-functional or junk DNA. Recent advances in genomics, including whole-genome sequencing, high-throughput protein characterization, and bioinformatics have led to a dramatic increase in studies on the topic. In the 2000s, some of the active topics have been the role of gene duplication in the emergence of novel gene function, the extent of adaptive molecular evolution versus neutral drift, and the identification of molecular changes responsible for various human characteristics especially those pertaining to infection, disease, and cognition.

Mutations
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.

Causes of change in allele frequency
Main article: Population genetics

There are four known processes that affect the survival of a characteristic; or, more specifically, the frequency of an allele (variant of a gene):


 * Mutation detailed above.
 * Genetic drift describes changes in gene frequency that cannot be ascribed to selective pressures, but are due instead to events that are unrelated to inherited traits. This is especially important in small mating populations, which simply cannot have enough offspring to maintain the same gene distribution as the parental generation.
 * Gene flow or Migration: or gene admixture is the only one of the agents that makes populations closer genetically while building larger gene pools.
 * Selection, in particular natural selection produced by differential mortality and fertility. Differential mortality is the survival rate of individuals before their reproductive age. If they survive, they are then selected further by differential fertility – that is, their total genetic contribution to the next generation. In this way, the alleles that these surviving individuals contribute to the gene pool will increase the frequency of those alleles. Sexual selection, the attraction between mates that results from two genes, one for a feature and the other determining a preference for that feature, is also very important.

Molecular study of phylogeny
Main articles: Molecular systematics, Phylogenetics

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 DNA 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.

The driving forces of evolution
Main articles: Neutral theory of molecular evolution, Modern evolutionary synthesis, Mutationism

Depending on the relative importance assigned to the various forces of evolution, three perpsectives provide evolutionary explanations for molecular evolution.

While recognizing the importance of random drift for silent mutations, selectionists hypotheses argue that balancing and positive selection are the driving forces of molecular evolution. Thoses hypotheses are often based on the broader view called panselectionism, the idea that selection is the only force strong enough to explain evolution, relaying random drift and mutations to minor roles.

Neutralists hypotheses emphasize the importance of mutation, purifying selection and random genetic drift. The introduction of the neutral theory by Kimura, quickly followed by King and Jukes' own findings, lead to a fierce debate about the relevance of neodarwinism at the molecular level. The nearly neutral theory expanded the neutralist perspective, suggesting that several mutations are nearly neutral, which means both random drift and natural selection is relevant to their dynamics.

Mutationists hypotheses emphasize random drift and biases in mutation patterns. Suedoka was the first to propose a modern mutationist view. He proposed that the variation in GC content was not the result of positive selection, but a consequence of the GC mutational pressure.

Related fields
An important area within the study of molecular evolution is the use of molecular data to determine the correct scientific classification of organisms. This is called molecular systematics or molecular phylogenetics.

Tools and concepts developed in the study of molecular evolution are now commonly used for comparative genomics and molecular genetics, while the influx of new data from these fields has been spurring advancement in molecular evolution.

Key researchers in molecular evolution
Some researchers who have made key contributions to the development of the field:
 * Motoo Kimura — Neutral theory
 * Masatoshi Nei — Adaptive evolution
 * Walter M. Fitch — Phylogenetic reconstruction
 * Walter Gilbert — RNA world
 * Joe Felsenstein — Phylogenetic methods
 * Susumu Ohno — Gene duplication
 * John H. Gillespie — Mathematics of adaptation

Journals and societies
Journals dedicated to molecular evolution include Molecular Biology and Evolution, Journal of Molecular Evolution, and Molecular Phylogenetics and Evolution. Research in molecular evolution is also published in journals of genetics, molecular biology, genomics, systematics, or evolutionary biology. The Society for Molecular Biology and Evolution publishes the journal "Molecular Biology and Evolution" and holds an annual international meeting.