A bayesian MCMC approach to assess the complete distribution of fitness effects of new mutations: uncovering the potential for adaptive walks in challenging environments
Student AuthorsRyan T. Hietpas
UMass Chan AffiliationsDepartment of Biochemistry and Molecular Pharmacology
Document TypeJournal Article
Keywords*Adaptation, Physiological; Bayes Theorem; Evolution, Molecular; *Genetic Fitness; HSP90 Heat-Shock Proteins; High-Throughput Nucleotide Sequencing; Markov Chains; Models, Genetic; Monte Carlo Method; *Mutation; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins
Fisher’s geometric model (FGM)
distribution of fitness effects
Ecology and Evolutionary Biology
Genetics and Genomics
MetadataShow full item record
AbstractThe role of adaptation in the evolutionary process has been contentious for decades. At the heart of the century-old debate between neutralists and selectionists lies the distribution of fitness effects (DFE)--that is, the selective effect of all mutations. Attempts to describe the DFE have been varied, occupying theoreticians and experimentalists alike. New high-throughput techniques stand to make important contributions to empirical efforts to characterize the DFE, but the usefulness of such approaches depends on the availability of robust statistical methods for their interpretation. We here present and discuss a Bayesian MCMC approach to estimate fitness from deep sequencing data and use it to assess the DFE for the same 560 point mutations in a coding region of Hsp90 in Saccharomyces cerevisiae across six different environmental conditions. Using these estimates, we compare the differences in the DFEs resulting from mutations covering one-, two-, and three-nucleotide steps from the wild type--showing that multiple-step mutations harbor more potential for adaptation in challenging environments, but also tend to be more deleterious in the standard environment. All observations are discussed in the light of expectations arising from Fisher's geometric model.
SourceGenetics. 2014 Mar;196(3):841-52. doi: 10.1534/genetics.113.156190. Epub 2014 Jan 7. Link to article on publisher's site
Permanent Link to this Itemhttp://hdl.handle.net/20.500.14038/33371
Related ResourcesLink to Article in PubMed
RightsCopyright © 2014 by the Genetics Society of America. Available freely online through the author-supported open access option.