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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 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 noncoding 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 processes of mutation and drift, and the identification of molecular changes responsible for various human characteristics especially those pertaining to infection, disease, and cognition.
Principles of molecular evolution 
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 
- 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.
- Recurrent mutation can increase the frequency of a mutant allele.
Molecular 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 
Depending on the relative importance assigned to the various forces of evolution, three perspectives 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. Those 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, led to a fierce debate about the relevance of neodarwinism at the molecular level. The Neutral theory of molecular evolution states that most mutations are deleterious and quickly removed by natural selection, but of the remaining ones, the vast majority are neutral with respect to fitness while the amount of advantageous mutations is vanishingly small. The fate of neutral mutations are governed by genetic drift, and contribute to both nucleotide polymorphism and fixed differences between species.
Mutationists hypotheses emphasize random drift and biases in mutation patterns. Sueoka 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.
History of the science 
The history of molecular evolution starts in the early 20th century with "comparative biochemistry", but the field of molecular evolution came into its own in the 1960s and 1970s, following the rise of molecular biology. The advent of protein sequencing allowed molecular biologists to create phylogenies based on sequence comparison, and to use the differences between homologous sequences as a molecular clock to estimate the time since the last common ancestor. In the late 1960s, the neutral theory of molecular evolution provided a theoretical basis for the molecular clock, though both the clock and the neutral theory were controversial, since most evolutionary biologists held strongly to panselectionism, with natural selection as the only important cause of evolutionary change. After the 1970s, nucleic acid sequencing allowed molecular evolution to reach beyond proteins to highly conserved ribosomal RNA sequences, the foundation of a reconceptualization of the early history of life.
The theoretical frameworks for molecular systematics were laid in the 1960s in the works of Emile Zuckerkandl, Emanuel Margoliash, Linus Pauling and Walter M. Fitch. Applications of molecular systematics were pioneered by Charles G. Sibley (birds), Herbert C. Dessauer (herpetology), and Morris Goodman (primates), followed by Allan C. Wilson, Robert K. Selander, and John C. Avise (who studied various groups). Work with protein electrophoresis began around 1956. Although the results were not quantitative and did not initially improve on morphological classification, they provided tantalizing hints that long-held notions of the classifications of birds, for example, needed substantial revision. In the period of 1974–1986, DNA-DNA hybridization was the dominant technique.
Genome evolution 
Genomic evolution is the process that changes the structure (sequence) or size of a genome over time.
The study of genome evolution involves multiple fields such as structural analysis of the genome, the study of genomic parasites, gene and ancient genome duplications, polyploidy, and comparative genomics.
Origins of new genes 
Some new genes arise from old genes through a process of duplication followed by divergence. Novel genes can also arise from previously non-coding DNA. For instance, Levine and colleagues reported the origin of five new genes in the D. melanogaster genome from noncoding DNA. Subsequently, de novo origin of genes has been also shown in other organisms such as yeast, rice and humans. De novo genes may evolve from transcripts that are already expressed at low levels.
Related fields 
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
- Dan Graur – Neutral models of molecular evolution
- Wen-Hsiung Li – Neutral models of 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.
See also 
- Graur, D. and Li, W.-H. (2000). Fundamentals of molecular evolution. Sinauer. ISBN 0-87893-266-6.
- Gillespie, J. H (1991). The Causes of Molecular Evolution. Oxford University Press, New York. ISBN 0-19-506883-1.
- Kimura, M. (1983). The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge. ISBN 0-521-23109-4.
- Kimura, Motoo (1968). "Evolutionary rate at the molecular level". Nature 217 (5129): 624–626. doi:10.1038/217624a0. PMID 5637732.
- King, J.L. and Jukes, T.H. (1969). "Non-Darwinian Evolution". Science 164 (3881): 788–798. doi:10.1126/science.164.3881.788. PMID 5767777.
- Nachman M. (2006). In C.W. Fox and J.B. Wolf. "Detecting selection at the molecular level" in: Evolutionary Genetics: concepts and case studies. pp. 103–118.
- 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.
- Ohta, T (1992). "The nearly neutral theory of molecular evolution". Annual Review of Ecology and Systematics 23 (1): 263–286. doi:10.1146/annurev.es.23.110192.001403.
- Nei, M. (2005). "Selectionism and Neutralism in Molecular Evolution". Molecular Biology and Evolution 22 (12): 2318–2342. doi:10.1093/molbev/msi242. PMC 1513187. PMID 16120807.
- Sueoka, N. (1964). "On the evolution of informational macromolecules". In In: Bryson, V. and Vogel, H.J. Evolving genes and proteins. Academic Press, New-York. pp. 479–496.
- Suárez-Díaz, Edna and Anaya-Muñoz, Victor H. (2008). "History, objectivity, and the construction of molecular phylogenies". Stud. Hist. Phil. Biol. & Biomed. Sci. 39 (4): 451–468. doi:10.1016/j.shpsc.2008.09.002. PMID 19026976.
- Ahlquist, Jon E. (1999). "Charles G. Sibley: A commentary on 30 years of collaboration". The Auk 116 (3): 856–860. doi:10.2307/4089352.
- Tautz, Diethard and Domazet-Lošo, Tomislav (2011). "The evolutionary origin of orphan genes". Nature Review Genetics 12 (10): 692–702. doi:10.1038/nrg3053.
- Levine MT, Jones CD, Kern AD et al (2006). "Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression". Proc Natl Acad Sci USA 103 (26): 9935–9939. doi:10.1073/pnas.0509809103. PMC 1502557. PMID 16777968.
- Zhou Q, Zhang G, Zhang Y et al (2008). "On the origin of new genes in Drosophila". Genome Res 18 (9): 1446–1455. doi:10.1101/gr.076588.108. PMC 2527705. PMID 18550802.
- Cai J, Zhao R, Jiang H et al (2008). "De novo origination of a new protein-coding gene in Saccharomyces cerevisiae". Genetics 179 (1): 487–496. doi:10.1534/genetics.107.084491. PMC 2390625. PMID 18493065.
- Xiao W, Liu H, Li Y et al (2009). "A rice gene of de novo origin negatively regulates pathogen- induced defense response". In El-Shemy, Hany A. PLoS One 4 (2): e4603. doi:10.1371/journal.pone.0004603. PMC 2643483. PMID 19240804.
- Knowles DG, McLysaght A (2009). "Recent de novo origin of human protein-coding genes". Genome Res 19 (10): 1752–1759. doi:10.1101/gr.095026.109. PMC 2765279. PMID 19726446.
- Wilson, Ben A.; Joanna Masel (2011). "Putatively Noncoding Transcripts Show Extensive Association with Ribosomes". Genome Biology & Evolution 3: 1245–1252. doi:10.1093/gbe/evr099.
Further reading 
- Li, W.-H. (2006). Molecular Evolution. Sinauer. ISBN 0-87893-480-4.
- Lynch, M. (2007). The Origins of Genome Architecture. Sinauer. ISBN 0-87893-484-7.
- A. Meyer (Editor), Y. van de Peer, "Genome Evolution: Gene and Genome Duplications and the Origin of Novel Gene Functions", 2003, ISBN 978-1-4020-1021-7
- T. Ryan Gregory, "The Evolution of the Genome", 2004, YSBN 978-0123014634