User:PhDP/Draft of 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 1960's 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.

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 recongnizing the important 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 relevence 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 relevent to their dynamics.

Mutationits 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 postive selection, but a consequence of the GC mutational pressure.

Nucleotide substitution
Main article: Models of Nucleotide Substitution

While population genetics aims to understand the dynamics of alleles in populations, molecular evolution aims to understand the effect of evolution on the molecular machinery of living organisms. The direct method of observation sometime used in population genetics is impossible for most studies of molecular evolution because the patterns created by molecular evolution are generally too slow.

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Molecular clock
Main article: Molecular clock

Duplication
Main article: Gene duplication

Molecular phylogenetics
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.

Genome evolution
Main article: Genome evolution

History of molecular evolution
Main article: History of molecular evolution

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.

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.