期刊
MOLECULAR BIOLOGY AND EVOLUTION
卷 27, 期 3, 页码 520-536出版社
OXFORD UNIV PRESS
DOI: 10.1093/molbev/msp260
关键词
adaptive evolution; codon models; evolutionary distance; machine classification
资金
- DMS/NIGMS [NSF-0714991]
- National Institutes of Health [AI43638, AI47745, AI57167]
- University of California Universitywide AIDS Research Program [IS02-SD-701]
- University of California, San Diego Center for AIDS Research/NIAID Developmental Award [AI36214]
- Royal Society Wolfson Research Merit Award
- Direct For Mathematical & Physical Scien
- Division Of Mathematical Sciences [0714991] Funding Source: National Science Foundation
To test this hypothesis, we develop a novel model of coding sequence evolution that uses a general bivariate discrete parameterization of the evolutionary rates. We show that this approach provides a better fit to the data using a smaller number of parameters than existing models. Next, we use the model to represent evolutionary fingerprints as probability distributions and present a methodology for comparing these distributions in a way that is robust against variations in data set size and divergence. Finally, using sequences of three rapidly evolving RNA viruses (HIV-1, hepatitis C virus, and influenza A virus), we demonstrate that genes within the same functional group tend to have similar evolutionary fingerprints. Our framework provides a sound statistical foundation for efficient inference and comparison of evolutionary rate patterns in arbitrary collections of gene alignments, clustering homologous and nonhomologous genes, and investigation of biological and functional correlates of evolutionary rates.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据