期刊
MOLECULAR BIOLOGY AND EVOLUTION
卷 22, 期 12, 页码 2375-2385出版社
OXFORD UNIV PRESS
DOI: 10.1093/molbev/msi232
关键词
synonymous substitution rate; positive selection; molecular evolution; codon model; model selection
资金
- NIAID NIH HHS [AI47745, AI43638, AI36214, AI57167] Funding Source: Medline
We develop a new model for studying the molecular evolution of protein-coding DNA sequences. In contrast to existing models, we incorporate the potential for site-to-site heterogeneity of both synonymous and nonsynonymous substitution rates. We demonstrate that within-gene heterogeneity of synonymous substitution rates appears to be common. Using the new family of models, we investigate the utility of a variety of new statistical inference procedures, and we pay particular attention to issues surrounding the detection of sites undergoing positive selection. We discuss how failure to model synonymous rate variation in the model can lead to misidentification of sites as positively selected.
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