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MBE Advance Access published online on February 2, 2009
Molecular Biology and Evolution, doi:10.1093/molbev/msp019
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© The Author 2009. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

Quantification of adaptive evolution of genes expressed in avian brain and the population size effect on the efficacy of selection

Erik Axelsson1,2 and Hans Ellegren1,3

1 Dept of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
2 Present address: Department of Biology, Evolutionary Biology, Copenhagen University, Copenhagen, Denmark

3 Correspondence: Hans.Ellegren{at}ebc.uu.se

Received for publication October 2, 2008. Revision received January 8, 2009. Accepted for publication January 27, 2009.

Whether protein evolution is mainly due to fixation of beneficial alleles by positive selection or to random genetic drift has remained a contentious issue over the years. Here we use two genome-wide polymorphism data sets collected from chicken populations, together with divergence data from >5,000 chicken – zebra finch gene orthologues expressed in brain, to assess the amount of adaptive evolution in protein-coding genes of birds. First, we show that estimates of the fixation index (FI, the ratio of fixed nonsynonymous to synonymous changes over the ratio of the corresponding polymorphisms) are highly dependent on the character of the underlying data sets. Second, by using polymorphism data from high-frequency alleles, to avoid the confounding effect of slightly deleterious mutations segregating at low frequency, we estimate that about 20% of amino acid changes have been brought to fixation through positive selection during avian evolution. This estimate is intermediate to that obtained in humans (lower) and flies as well as bacteria (higher), and is consistent with population genetics theory that stipulates a positive relationship between the efficiency of selection and the effective population size. Further, by comparing the fixation indexes for common and all alleles, we estimate that {approx}20% of nonsynonymous variation segregating in chicken populations represent slightly deleterious mutations, which is less than in Drosophila. Overall, these results highlight the link between the effective population size and positive as well as negative selection.

Key Words: comparative genomics • positive selection • slightly deleterious mutations • chicken • zebra finch


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