MBE Advance Access published online on November 25, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn272
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Research Article |
Estimating translational selection in Eukaryotic genomes
a School of Crystallography, Birkbeck College, Malet Street, London, WC1E 7HX, UK
b Mathematical Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK
c MRC Biostatistics Unit, Institute of Public Health, Forvie Site, Robinson Way, Cambridge, CB2 0SR, UK
* mdosrei{at}nimr.mrc.ac.uk, +44 (0)20 8816 2300, Fax: + 44 (0)20 8816 2460
Received for publication October 24, 2008. Accepted for publication November 17, 2008.
Natural selection on codon usage is a pervasive force that acts on a large variety of prokaryotic and eukaryotic genomes. Despite this, obtaining reliable estimates of selection on codon usage has proved complicated, perhaps due to the fact that the selection coefficients involved are very small. In this work, a population genetics model is used to measure the strength of selected codon usage bias, S, in ten eukaryotic genomes. It is shown that the strength of selection is closely linked to expression, and that reliable estimates of selection coefficients can only be obtained for genes with very similar expression levels. We compare the strength of selected codon usage for orthologous genes across all ten genomes classified according to expression categories. Fungi genomes present the largest S values (2.24-2.56), while multicellular invertebrate and plant genomes present more moderate values (0.61-1.91). The large mammalian genomes (human and mouse) show low S values (0.22-0.51) for the most highly expressed genes. This might not be evidence for selection in these organisms as the technique used here to estimate S does not properly account for nucleotide composition heterogeneity along such genomes. The relationship between estimated S values and empirical estimates of population size is presented here for the first time. It is shown, as theoretically expected, that population size has an important role in the operativity of translational selection.
Key Words: Translational selection • tAI • tRNA • codon usage bias • population size • eukaryotes
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