期刊
MOLECULAR BIOLOGY AND EVOLUTION
卷 24, 期 1, 页码 228-235出版社
OXFORD UNIV PRESS
DOI: 10.1093/molbev/msl146
关键词
codon usage bias; codon usage; maximum likelihood; codon-based models; selection
资金
- NIGMS NIH HHS [GM36431, R01 GM036431] Funding Source: Medline
- PHS HHS [0201037] Funding Source: Medline
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R01GM036431] Funding Source: NIH RePORTER
We present a likelihood method for estimating codon usage bias parameters along the lineages of a phylogeny. The method is an extension of the classical codon-based models used for estimating d(N)/d(S) ratios along the lineages of a phylogeny. However, we add one extra parameter for each lineage: the selection coefficient for optimal codon usage (S), allowing joint maximum likelihood estimation of S and the d(N)/d(S) ratio. We apply the method to previously published data from Drosophila melanogaster, Drosophila simulans, and Drosophila yakuba and show, in accordance with previous results, that the D. melanogaster lineage has experienced a reduction in the selection for optimal codon usage. However, the D. melanogaster lineage has also experienced a change in the biological mutation rates relative to D. simulans, in particular, a relative reduction in the mutation rate from A to G and an increase in the mutation rate from C to T. However, neither a reduction in the strength of selection nor a change in the mutational pattern can alone explain all of the data observed in the D. melanogaster lineage. For example, we also confirm previous results showing that the Notch locus has experienced positive selection for previously classified unpreferred mutations.
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