Bazykin, Georgii A; Kondrashov, FyodorISTA ; Brudno, Michael; Poliakov, Alexander V; Dubchak, Inna L; Kondrashov, Alexey S
Background: Independently evolving lineages mostly accumulate different changes, which leads to their gradual divergence. However, parallel accumulation of identical changes is also common, especially in traits with only a small number of possible states. Results: We characterize parallelism in evolution of coding sequences in three four-species sets of genomes of mammals, Drosophila, and yeasts. Each such set contains two independent evolutionary paths, which we call paths I and II. An amino acid replacement which occurred along path I also occurs along path II with the probability 50-8211;80% of that expected under selective neutrality. Thus, the per site rate of parallel evolution of proteins is several times higher than their average rate of evolution, but still lower than the rate of evolution of neutral sequences. This deficit may be caused by changes in the fitness landscape, leading to a replacement being possible along path I but not along path II. However, constant, weak selection assumed by the nearly neutral model of evolution appears to be a more likely explanation. Then, the average coefficient of selection associated with an amino acid replacement, in the units of the effective population size, must exceed ∼0.4, and the fraction of effectively neutral replacements must be below ∼30%. At a majority of evolvable amino acid sites, only a relatively small number of different amino acids is permitted. Conclusion: High, but below-neutral, rates of parallel amino acid replacements suggest that a majority of amino acid replacements that occur in evolution are subject to weak, but non-trivial, selection, as predicted by Ohta's nearly-neutral theory.
G.A.B. gratefully acknowledges fellowships from the Pew Charitable Trusts award 2000-002558 and the Burroughs Wellcome Fund award 1001782, both to Princeton University. F.A.K. is a National Science Foundation Graduate Fellow. M.B.'s work is partially supported by the NSERC Discovery grant. I.D. and A.P. were partially supported by grant HL066681 (L.A.P., I.D. and S.M.), Berkeley-PGA, under the Programs for Genomic Applications, funded by National Heart, Lung, & Blood Institute and Department of Energy Contract DE-AC02-05CH11231, University of California. This work was partially supported through the Molecular and Cellular Biology Program of the Russian Academy of Sciences.
Bazykin G, Kondrashov F, Brudno M, Poliakov A, Dubchak I, Kondrashov A. Extensive parallelism in protein evolution. Biology Direct. 2007;2. doi:10.1186/1745-6150-2-20
Bazykin, G., Kondrashov, F., Brudno, M., Poliakov, A., Dubchak, I., & Kondrashov, A. (2007). Extensive parallelism in protein evolution. Biology Direct. BioMed Central. https://doi.org/10.1186/1745-6150-2-20
Bazykin, Georgii, Fyodor Kondrashov, Michael Brudno, Alexander Poliakov, Inna Dubchak, and Alexey Kondrashov. “Extensive Parallelism in Protein Evolution.” Biology Direct. BioMed Central, 2007. https://doi.org/10.1186/1745-6150-2-20.
G. Bazykin, F. Kondrashov, M. Brudno, A. Poliakov, I. Dubchak, and A. Kondrashov, “Extensive parallelism in protein evolution,” Biology Direct, vol. 2. BioMed Central, 2007.
Bazykin G, Kondrashov F, Brudno M, Poliakov A, Dubchak I, Kondrashov A. 2007. Extensive parallelism in protein evolution. Biology Direct. 2.
Bazykin, Georgii, et al. “Extensive Parallelism in Protein Evolution.” Biology Direct, vol. 2, BioMed Central, 2007, doi:10.1186/1745-6150-2-20.