title: Evolutionary genomics: codon bias and selection on single genomes.
abstract: The idea that natural selection on genes might be detected using only a single genome has been put forward by Plotkin and colleagues, who present a method that they claim can detect selection without the need for comparative data and which, if correct, would confer greater power of analysis with less information. Here we argue that their method depends on assumptions that confound their conclusions and that, even if these assumptions were valid, the authors' inferences about adaptive natural selection are unjustified.
authors.affiliation: Center for Population Biology and Section of Evolution and Ecology, University of California, Davis, California 95616, USA. mwhahn@ucdavis.edu
authors.forename: Matthew W
authors.initials: MW
authors.lastname: Hahn
authors.forename: Jason G
authors.initials: JG
authors.lastname: Mezey
authors.forename: David J
authors.initials: DJ
authors.lastname: Begun
authors.forename: John H
authors.initials: JH
authors.lastname: Gillespie
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Kern
authors.forename: Charles H
authors.initials: CH
authors.lastname: Langley
authors.forename: Leonie C
authors.initials: LC
authors.lastname: Moyle
mesh_terms: D015982:Bias; D005075:Biological Evolution; D003062:Codon / Q000235:genetics*; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods*; D008957:Models, Genetic; D020125:Mutation, Missense / Q000235:genetics; D009169:Mycobacterium tuberculosis / Q000235:genetics; D015203:Reproducibility of Results; D012641:Selection, Genetic
chemical_list: D003062:Codon