Literature DB >> 15778707

An empirical test of the mutational landscape model of adaptation using a single-stranded DNA virus.

Darin R Rokyta1, Paul Joyce, S Brian Caudle, Holly A Wichman.   

Abstract

The primary impediment to formulating a general theory for adaptive evolution has been the unknown distribution of fitness effects for new beneficial mutations. By applying extreme value theory, Gillespie circumvented this issue in his mutational landscape model for the adaptation of DNA sequences, and Orr recently extended Gillespie's model, generating testable predictions regarding the course of adaptive evolution. Here we provide the first empirical examination of this model, using a single-stranded DNA bacteriophage related to phiX174, and find that our data are consistent with Orr's predictions, provided that the model is adjusted to incorporate mutation bias. Orr's work suggests that there may be generalities in adaptive molecular evolution that transcend the biological details of a system, but we show that for the model to be useful as a predictive or inferential tool, some adjustments for the biology of the system will be necessary.

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Year:  2005        PMID: 15778707     DOI: 10.1038/ng1535

Source DB:  PubMed          Journal:  Nat Genet        ISSN: 1061-4036            Impact factor:   38.330


  82 in total

1.  Real time forecasting of near-future evolution.

Authors:  Philip J Gerrish; Paul D Sniegowski
Journal:  J R Soc Interface       Date:  2012-04-18       Impact factor: 4.118

Review 2.  Molecular spandrels: tests of adaptation at the genetic level.

Authors:  Rowan D H Barrett; Hopi E Hoekstra
Journal:  Nat Rev Genet       Date:  2011-10-18       Impact factor: 53.242

3.  The distribution of fitness effects of new beneficial mutations in Pseudomonas fluorescens.

Authors:  Michael J McDonald; Tim F Cooper; Hubertus J E Beaumont; Paul B Rainey
Journal:  Biol Lett       Date:  2010-07-21       Impact factor: 3.703

Review 4.  Mutational fitness effects in RNA and single-stranded DNA viruses: common patterns revealed by site-directed mutagenesis studies.

Authors:  Rafael Sanjuán
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2010-06-27       Impact factor: 6.237

Review 5.  The population genetics of beneficial mutations.

Authors:  H Allen Orr
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2010-04-27       Impact factor: 6.237

6.  Mutational effects and population dynamics during viral adaptation challenge current models.

Authors:  Craig R Miller; Paul Joyce; Holly A Wichman
Journal:  Genetics       Date:  2010-11-01       Impact factor: 4.562

7.  Lack of evidence for sign epistasis between beneficial mutations in an RNA bacteriophage.

Authors:  Andrea J Betancourt
Journal:  J Mol Evol       Date:  2010-10-12       Impact factor: 2.395

8.  Mutation-biased adaptation in Andean house wrens.

Authors:  Arlin Stoltzfus; David M McCandlish
Journal:  Proc Natl Acad Sci U S A       Date:  2015-10-21       Impact factor: 11.205

9.  Synergistic Pleiotropy Overrides the Costs of Complexity in Viral Adaptation.

Authors:  Lindsey W McGee; Andrew M Sackman; Anneliese J Morrison; Jessica Pierce; Jeremy Anisman; Darin R Rokyta
Journal:  Genetics       Date:  2015-11-12       Impact factor: 4.562

10.  Inference for one-step beneficial mutations using next generation sequencing.

Authors:  Andrzej J Wojtowicz; Craig R Miller; Paul Joyce
Journal:  Stat Appl Genet Mol Biol       Date:  2015-02
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