Literature DB >> 29198859

Selecting among three basic fitness landscape models: Additive, multiplicative and stickbreaking.

Craig R Miller1, James T Van Leuven2, Holly A Wichman3, Paul Joyce4.   

Abstract

Fitness landscapes map genotypes to organismal fitness. Their topographies depend on how mutational effects interact - epistasis - andare important for understanding evolutionary processes such as speciation, the rate of adaptation, the advantage of recombination, and the predictability versus stochasticity of evolution. The growing amount of data has made it possible to better test landscape models empirically. We argue that this endeavor will benefit from the development and use of meaningful basic models against which to compare more complex models. Here we develop statistical and computational methods for fitting fitness data from mutation combinatorial networks to three simple models: additive, multiplicative and stickbreaking. We employ a Bayesian framework for doing model selection. Using simulations, we demonstrate that our methods work and we explore their statistical performance: bias, error, and the power to discriminate among models. We then illustrate our approach and its flexibility by analyzing several previously published datasets. An R-package that implements our methods is available in the CRAN repository under the name Stickbreaker.
Copyright © 2017 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  Additive; Epistasis; Fitness landscape; Multiplicative; Stickbreaking

Mesh:

Year:  2017        PMID: 29198859      PMCID: PMC5984659          DOI: 10.1016/j.tpb.2017.10.006

Source DB:  PubMed          Journal:  Theor Popul Biol        ISSN: 0040-5809            Impact factor:   1.570


  67 in total

Review 1.  A general multivariate extension of Fisher's geometrical model and the distribution of mutation fitness effects across species.

Authors:  Guillaume Martin; Thomas Lenormand
Journal:  Evolution       Date:  2006-05       Impact factor: 3.694

2.  The population genetics of adaptation on correlated fitness landscapes: the block model.

Authors:  H Allen Orr
Journal:  Evolution       Date:  2006-06       Impact factor: 3.694

3.  Environment determines epistatic patterns for a ssDNA virus.

Authors:  S Brian Caudle; Craig R Miller; Darin R Rokyta
Journal:  Genetics       Date:  2013-11-08       Impact factor: 4.562

4.  Natural selection and the concept of a protein space.

Authors:  J M Smith
Journal:  Nature       Date:  1970-02-07       Impact factor: 49.962

5.  Quantitative evolutionary dynamics using high-resolution lineage tracking.

Authors:  Sasha F Levy; Jamie R Blundell; Sandeep Venkataram; Dmitri A Petrov; Daniel S Fisher; Gavin Sherlock
Journal:  Nature       Date:  2015-02-25       Impact factor: 49.962

6.  A systematic survey of an intragenic epistatic landscape.

Authors:  Claudia Bank; Ryan T Hietpas; Jeffrey D Jensen; Daniel N A Bolon
Journal:  Mol Biol Evol       Date:  2014-11-03       Impact factor: 16.240

7.  Epistasis among adaptive mutations in deer mouse hemoglobin.

Authors:  Chandrasekhar Natarajan; Noriko Inoguchi; Roy E Weber; Angela Fago; Hideaki Moriyama; Jay F Storz
Journal:  Science       Date:  2013-06-14       Impact factor: 47.728

8.  Microbial evolution. Global epistasis makes adaptation predictable despite sequence-level stochasticity.

Authors:  Sergey Kryazhimskiy; Daniel P Rice; Elizabeth R Jerison; Michael M Desai
Journal:  Science       Date:  2014-06-27       Impact factor: 47.728

9.  The consistency of beneficial fitness effects of mutations across diverse genetic backgrounds.

Authors:  Victoria M Pearson; Craig R Miller; Darin R Rokyta
Journal:  PLoS One       Date:  2012-08-24       Impact factor: 3.240

10.  A bayesian MCMC approach to assess the complete distribution of fitness effects of new mutations: uncovering the potential for adaptive walks in challenging environments.

Authors:  Claudia Bank; Ryan T Hietpas; Alex Wong; Daniel N Bolon; Jeffrey D Jensen
Journal:  Genetics       Date:  2014-01-07       Impact factor: 4.562

View more
  4 in total

1.  Evolution of resistance under alternative models of selective interference.

Authors:  Philip G Madgwick; Ricardo Kanitz
Journal:  J Evol Biol       Date:  2021-09-25       Impact factor: 2.516

2.  Endogenous viral mutations, evolutionary selection, and containment policy design.

Authors:  Patrick Mellacher
Journal:  J Econ Interact Coord       Date:  2022-01-07

3.  Genetic Context Significantly Influences the Maintenance and Evolution of Degenerate Pathways.

Authors:  Eric L Bruger; Lon M Chubiz; José I Rojas Echenique; Caleb J Renshaw; Nora Victoria Espericueta; Jeremy A Draghi; Christopher J Marx
Journal:  Genome Biol Evol       Date:  2021-06-08       Impact factor: 3.416

4.  ΦX174 Attenuation by Whole-Genome Codon Deoptimization.

Authors:  James T Van Leuven; Martina M Ederer; Katelyn Burleigh; LuAnn Scott; Randall A Hughes; Vlad Codrea; Andrew D Ellington; Holly A Wichman; Craig R Miller
Journal:  Genome Biol Evol       Date:  2021-02-03       Impact factor: 3.416

  4 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.