There are various levels of interacting networks, within a protein or nucleic acid molecule, among proteins and nucleic acids, and genetic regulatory networks. At all these levels, interacting systems are dynamically evolving and repeated appearance of modular structures is noted. These modular structures repeatedly appear at different levels from proteins to genetic regulatory networks. Evolution of primary structure of proteins and nucleic acids depends on all these systems. For the evolution of such interacting systems, both drift and selection play important roles. Therefore, the near neutrality holds. The nearly neutral theory argues that slightly deleterious mutant substitutions disturb such systems mildly and occur by drift. Compensatory mutant substitutions are expected to follow. Drift and selection often become inseparable, such that formation and maintenance of networks depends on the interaction of drift and selection. By considering the effects of drift and selection on evolution of genetic regulatory elements that determine gene expression, the nearly neutral theory may be extended to morphological evolution, because organismal development is mainly controlled by regulation of gene expression.
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Ohta, T. (2007). Drift and Selection in Evolving Interacting Systems. In: Bastolla, U., Porto, M., Roman, H.E., Vendruscolo, M. (eds) Structural Approaches to Sequence Evolution. Biological and Medical Physics, Biomedical Engineering. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-35306-5_13
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