Genetics, Vol. 178, 2429-2432, April 2008, Copyright © 2008
doi:10.1534/genetics.107.086405

Nearly Neutrality and the Evolution of Codon Usage Bias in Eukaryotic Genomes

Sankar Subramanian1

Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University, Auckland, 0632, New Zealand

1 Address for correspondence: Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University, Private Bag 102 904, North Shore Mail Centre, Auckland, 0632, New Zealand.
E-mail: s.sankarasubramanian{at}massey.ac.nz

Here I show that the mean codon usage bias of a genome, and of the lowly expressed genes in a genome, is largely similar across eukaryotes ranging from unicellular protists to vertebrates. Conversely, this bias in housekeeping genes and in highly expressed genes has a remarkable inverse relationship with species generation time that varies by more than four orders of magnitude. The relevance of these results to the nearly neutral theory of molecular evolution is discussed.