Estimating selection pressures from limited comparative data.

We recently introduced a novel method for estimating selection pressures on proteins, termed "volatility," which requires only a single genome sequence. Some criticisms that have been levied against this approach are valid, but many others are based on misconceptions of volatility, or they apply equally to comparative methods of estimating selection. Here, we introduce a simple regression technique for estimating selection pressures on all proteins in a genome, on the basis of limited comparative data. The regression technique does not depend on an underlying population-genetic mechanism. This new approach to estimating selection across a genome should be more powerful and more widely applicable than volatility itself.

[1]  M. Archetti.  Genetic robustness and selection at the protein level for synonymous codons , 2006, Journal of evolutionary biology.

[2]  L. Hurst,et al.  Hearing silence: non-neutral evolution at synonymous sites in mammals , 2006, Nature Reviews Genetics.

[3]  Andreas Prlic,et al.  Ensembl 2006 , 2005, Nucleic Acids Res..

[4]  Joshua B. Plotkin,et al.  Codon Usage and Selection on Proteins , 2006, Journal of Molecular Evolution.

[5]  J. Hermisson,et al.  A dissection of volatility in yeast. , 2005, Molecular biology and evolution.

[6]  P. Sharp,et al.  Gene "volatility" is most unlikely to reveal adaptation. , 2005, Molecular biology and evolution.

[7]  A. Hughes,et al.  Codon volatility as an indicator of positive selection: data from eukaryotic genome comparisons. , 2005, Molecular biology and evolution.

[8]  Dan Graur,et al.  The comparative method rules! Codon volatility cannot detect positive Darwinian selection using a single genome sequence. , 2005, Molecular biology and evolution.

[9]  J. J. Emerson,et al.  Evolutionary genomics: Codon volatility does not detect selection , 2005, Nature.

[10]  Hunter B. Fraser,et al.  Evolutionary genomics: Codon volatility does not detect selection (reply) , 2005, Nature.

[11]  Andrew D. Kern,et al.  Evolutionary genomics: Codon bias and selection on single genomes , 2005, Nature.

[12]  Jianzhi Zhang,et al.  On the Evolution of Codon Volatility , 2005, Genetics.

[13]  A. E. Hirsh,et al.  Adjusting for selection on synonymous sites in estimates of evolutionary distance. , 2005, Molecular biology and evolution.

[14]  G. B. Golding,et al.  Expected frequencies of codon use as a function of mutation rates and codon fitnesses , 2005, Journal of Molecular Evolution.

[15]  Joshua B. Plotkin,et al.  Detecting selection using a single genome sequence of M. tuberculosis and P. falciparum , 2004, Nature.

[16]  R. Nichols,et al.  Application of DNA microarrays to study the evolutionary genomics of Yersinia pestis and Yersinia pseudotuberculosis. , 2003, Genome research.

[17]  D. P. Wall,et al.  Detecting putative orthologs , 2003, Bioinform..

[18]  B. Birren,et al.  Sequencing and comparison of yeast species to identify genes and regulatory elements , 2003, Nature.

[19]  Jonathan Dushoff,et al.  Codon bias and frequency-dependent selection on the hemagglutinin epitopes of influenza A virus , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[20]  Z. Yang,et al.  Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. , 2000, Molecular biology and evolution.

[21]  H. Akashi,et al.  Translational selection and molecular evolution. , 1998, Current opinion in genetics & development.

[22]  Ziheng Yang,et al.  PAML: a program package for phylogenetic analysis by maximum likelihood , 1997, Comput. Appl. Biosci..

[23]  E. Fikrig,et al.  Borrelia burgdorferi P35 and P37 proteins, expressed in vivo, elicit protective immunity. , 1997, Immunity.

[24]  N. Goldman,et al.  A codon-based model of nucleotide substitution for protein-coding DNA sequences. , 1994, Molecular biology and evolution.

[25]  Wen-Hsiung Li,et al.  The rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias. , 1987, Molecular biology and evolution.

[26]  J. J. Emerson,et al.  Codon bias and selection on single genomes , 2022 .