McCandlish, D. M., Rajon, E., Shah, P., Ding, Y., Plotkin, J. B. (May 2013) The role of epistasis in protein evolution. Nature, 497 (7451). E1-2; discussion E2. ISSN 1476-4687 (Electronic)0028-0836 (Linking)
Abstract
An important question in molecular evolution is whether an amino acid that occurs at a given site makes an independent contribution to fitness, or whether its contribution depends on the state of other sites in the organism’s genome, a phenomenon known as epistasis1, 2, 3, 4, 5. Breen and colleagues recently argued6 that epistasis must be “pervasive throughout protein evolution” because the observed ratio between the per-site rates of non-synonymous and synonymous substitutions (dN/dS)7 is much lower than would be expected in the absence of epistasis. However, when calculating the expected dN/dS ratio in the absence of epistasis, Breen et al.6 assumed that all amino acids observed at a given position in a protein alignment have equal fitness. Here, we relax this unrealistic assumption and show that any dN/dS value can in principle be achieved at a site, without epistasis; furthermore, for all nuclear and chloroplast genes in the Breen et al. data set, we show that the observed dN/dS values and the observed patterns of amino-acid diversity at each site are jointly consistent with a non-epistatic model of protein evolution.
| Item Type: | Paper |
|---|---|
| Uncontrolled Keywords: | Animals Epistasis, Genetic/*genetics *Evolution, Molecular |
| Subjects: | bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification evolution |
| CSHL Authors: | |
| Communities: | CSHL labs > McCandlish lab |
| Depositing User: | Matt Covey |
| Date: | 30 May 2013 |
| Date Deposited: | 18 Jan 2017 20:29 |
| Last Modified: | 18 Jan 2017 20:29 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/34042 |
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