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. The nearly neutral theory was proposed by Tomoko Ohta in 1973 (including only deleterious mutations) and expanded in the early 1990s to include both advantageous and deleterious nearly neutral mutations. Unlike in Motoo Kimura's original neutral theory—which dealt only with mutations unaffected by natural selection—the nearly neutral theory predicts a relationship between population size and the rate of molecular evolution: in larger populations, genetic drift, which can bring even slightly deleterious mutations to fixation, is a weaker force, so evolution happens more slowly than in smaller populations.
Origins of the nearly neutral theory
In the early 1970s, evolutionary biologists found that rates of protein evolution (the "molecular clock") are fairly independent of generation time, while rates of noncoding DNA divergence are inversely proportional to generation time. Noting that population size is generally inversely proportional to generation time, Tomoko Ohta proposed that most amino acid substitutions are slightly deleterious while noncoding DNA substitutions are more neutral. In this case, the faster rate of neutral evolution in proteins expected in small populations (due to genetic drift) is offset by longer generation times (and vice versa), but in large populations with short generation times, noncoding DNA evolves faster while protein evolution is retarded by selection (which is more significant than drift for large populations).
In 1973, Ohta published a short letter in Nature suggesting that a wide variety of molecular evidence supported the theory that most mutation events at the molecular level are slightly deleterious rather than strictly neutral. Between then and the early 1990s, many studies of molecular evolution used a "shift model" in which the negative effect on the fitness of a population due to deleterious mutations shifts back to an original value when a mutation reaches fixation. In the early 1990s, Ohta developed a "fixed model" that included both beneficial and deleterious mutations, so that no artificial "shift" of overall population fitness was necessary.
The nearly neutral theory has been validated in a recent study on the origin of complexity in protein networks. Through a comparison of homologous proteins across distant species, a study by Ariel Fernandez and Michael Lynch published in Nature  revealed the role of inefficient selection in species with small population as a mechanism to promote interactome complexity. A structural degradation of proteins resulting from slightly deleterious mutations is shown to be widespread in species with low population, and this degradation fosters protein-protein interactions as a means to maintain structural integrity and functional competence. More specifically, the slightly deleterious mutations enrich the protein in a type of structural defect known as dehydron that is sticky and hence promotes protein associations. The evidence from this study downplays Darwinian selection and favors random genetic drift as a promoter of complexity.
- Ohta, Tomoko (1973-11-09). "Slightly Deleterious Mutant Substitutions in Evolution". Nature 246 (5428): 96–98. doi:10.1038/246096a0. PMID 4585855.
- Ohta, Tomoko; John H. Gillespie (1996-04). "Development of Neutral and Nearly Neutral Theories". Theoretical Population Biology 49 (2): 128–42. doi:10.1006/tpbi.1996.0007. PMID 8813019. , pp 130-131
- Ohta and Gillespie, "Development of Neutral and Nearly Neutral Theories", pp. 135-136
- Philip Ball. "Review in Nature News of the paper by Ariel Fernandez and Michael Lynch published in Nature 474, 502-505, 2011". Nature, McMillan.
- Ariel Fernandez and Michael Lynch. "Ariel Fernandez & Michael Lynch (2011) Nonadaptive origins of interactome complexity. Nature 474, 502-505". Nature, McMillan.
- "Survey on dehydron concept".
- The Nearly Neutral Theory of Molecular Evolution - Perspectives on Molecular Evolution