Extensive parallelism in protein evolution

Georgii A Bazykin¹^,2 , Fyodor A Kondrashov³ , Michael Brudno⁴ , Alexander Poliakov⁵ , Inna Dubchak⁵^,6 and Alexey S Kondrashov⁷

¹Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoi Karetny pereulok 19, Moscow, 127994, Russia

²Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA

³Section on Ecology, Behavior and Evolution, University of California at San Diego, La Jolla, CA 92093, USA

⁴Department of Computer Science and Banting & Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3J4, Canada

⁵Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA

⁶Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA

⁷Life Sciences Institute and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109-2216, USA

author email corresponding author email

Biology Direct 2007, 2:20doi:10.1186/1745-6150-2-20


Published:	16 August 2007

Abstract

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 50–80% 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.

Reviewers

This article was reviewed by John McDonald (nominated by Laura Landweber), Sarah Teichmann and Subhajyoti De, and Chris Adami.