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Codon Usage Patterns in Cytochrome Oxidase I Across Multiple Insect Orders

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Abstract

Synonymous codon usage bias is determined by a combination of mutational biases, selection at the level of translation, and genetic drift. In a study of mtDNA in insects, we analyzed patterns of codon usage across a phylogeny of 88 insect species spanning 12 orders. We employed a likelihood-based method for estimating levels of codon bias and determining major codon preference that removes the possible effects of genome nucleotide composition bias. Three questions are addressed: (1) How variable are codon bias levels across the phylogeny? (2) How variable are major codon preferences? and (3) Are there phylogenetic constraints on codon bias or preference? There is high variation in the level of codon bias values among the 88 taxa, but few readily apparent phylogenetic patterns. Bias level shifts within the lepidopteran genus Papilio are most likely a result of population size effects. Shifts in major codon preference occur across the tree in all of the amino acids in which there was bias of some level. The vast majority of changes involves double-preference models, however, and shifts between single preferred codons within orders occur only 11 times. These shifts among codons in double-preference models are phylogenetically conservative.

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Acknowledgements

We thank George Roderick, Montgomery Slatkin, Felix Sperling, and Dennis Wall for discussions and assistance. J.H. supported by NSF PEET Grant 9521835 to J. Powell and F. Sperling. J.N. was supported in part by NIH Grant GM40282 to M. Slatkin. We greatly appreciate the helpful comments of Martin Kreitman and two anonymous reviewers.

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Authors and Affiliations

  1. Division of Insect Biology, University of California, Berkeley, Berkeley, CA 94720, USA

    Joshua T. Herbeck

  2. Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA

    John Novembre

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  1. Joshua T. Herbeck
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Correspondence to Joshua T. Herbeck.

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Herbeck, J.T., Novembre, J. Codon Usage Patterns in Cytochrome Oxidase I Across Multiple Insect Orders. J Mol Evol 56, 691–701 (2003). https://doi.org/10.1007/s00239-002-2437-7

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  • DOI: https://doi.org/10.1007/s00239-002-2437-7

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