Molecular Biology and Evolution 19:1390-1394 (2002)
© 2002 Society for Molecular Biology and Evolution
Accounting for Background Nucleotide Composition When Measuring Codon Usage Bias
Department of Integrative Biology, University of California—Berkeley
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The phenomenon of codon usage bias has been important in the study of evolution because it provides examples of weak selection working at the molecular level. During the last two decades, evidence has accumulated that some examples of codon usage bias are driven by selection, particularly for species of fungi (e.g., Bennetzen and Hall 1982
; Ikemura 1985
), bacteria (e.g., Ikemura 1981
; Sharp and Li 1987
), and insects (e.g., Akashi 1997
; Moriyama and Powell 1997
). This connection between codon usage bias and selection has been important in stimulating the development of alternatives to strictly neutral theories of molecular evolution (Ohta and Gillespie 1996
; Kreitman and Antezana 2000
). Uncertainty persists, however, regarding the phylogenetic distribution of codon usage bias (such as whether selection-based codon usage bias is present in mammals; e.g., Karlin and Mrazek 1996
; Iida and Akashi 2000
; Sueoka and Kawanishi
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