On measuring selection in experimental evolution

Distributions of mutation fitness effects from evolution experiments are available in an increasing number of species, opening the way for a vast array of applications in evolutionary biology. However, comparison of estimated distributions among studies is hampered by inconsistencies in the definitions of fitness effects and selection coefficients. In particular, the use of ratios of Malthusian growth rates as ‘relative fitnesses’ leads to wrong inference of the strength of selection. Scaling Malthusian fitness by the generation time may help overcome this shortcoming, and allow accurate comparison of selection coefficients across species. For species reproducing by binary fission (neglecting cellular death), ln2 can be used as a correction factor, but in general, the growth rate and generation time of the wild-type should be provided in studies reporting distribution of mutation fitness effects. I also discuss how density and frequency dependence of population growth affect selection and its measurement in evolution experiments.

[1]  R. Kassen,et al.  Distribution of fitness effects among beneficial mutations before selection in experimental populations of bacteria , 2006, Nature Genetics.

[2]  R. Lenski,et al.  Long-Term Experimental Evolution in Escherichia coli. I. Adaptation and Divergence During 2,000 Generations , 1991, The American Naturalist.

[3]  Thomas Lenormand,et al.  Distributions of epistasis in microbes fit predictions from a fitness landscape model , 2007, Nature Genetics.

[4]  R. Lenski,et al.  Long-term experimental evolution in Escherichia coli. XI. Rejection of non-transitive interactions as cause of declining rate of adaptation , 2002, BMC Evolutionary Biology.

[5]  H. A. Orr,et al.  ADAPTATION AND THE COST OF COMPLEXITY , 2000, Evolution; international journal of organic evolution.

[6]  B. Charlesworth,et al.  Evolution in Age-Structured Populations. , 1995 .

[7]  T. Lenormand,et al.  A GENERAL MULTIVARIATE EXTENSION OF FISHER'S GEOMETRICAL MODEL AND THE DISTRIBUTION OF MUTATION FITNESS EFFECTS ACROSS SPECIES , 2006, Evolution; international journal of organic evolution.

[8]  M. Kimura,et al.  An introduction to population genetics theory , 1971 .

[9]  H. A. Orr,et al.  The genetic theory of adaptation: a brief history , 2005, Nature Reviews Genetics.

[10]  T Kibota,et al.  Estimate of the genomic mutation rate deleterious to overall fitness in E. coli , 1996 .

[11]  Isabel Gordo,et al.  Adaptive Mutations in Bacteria: High Rate and Small Effects , 2007, Science.

[12]  Toby Johnson,et al.  The Fixation Probability of a Beneficial Allele in a Population Dividing by Binary Fission , 2002, Genetica.

[13]  C. Knight,et al.  Adaptive Divergence in Experimental Populations of Pseudomonas fluorescens. III. Mutational Origins of Wrinkly Spreader Diversity , 2007, Genetics.

[14]  Jeffrey E. Barrick,et al.  Genome evolution and adaptation in a long-term experiment with Escherichia coli , 2009, Nature.

[15]  Rafael Sanjuán,et al.  The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[16]  R. Korona,et al.  Low Frequency of Mutations with Strongly Deleterious but Nonlethal Fitness Effects , 2009, Evolution; international journal of organic evolution.

[17]  Hilla Peretz,et al.  Ju n 20 03 Schrödinger ’ s Cat : The rules of engagement , 2003 .

[18]  Mandy J. Haldane,et al.  A Mathematical Theory of Natural and Artificial Selection, Part V: Selection and Mutation , 1927, Mathematical Proceedings of the Cambridge Philosophical Society.

[19]  J. Crow,et al.  Mutation rate and dominance of genes affecting viability in Drosophila melanogaster. , 1972, Genetics.

[20]  B. Charlesworth,et al.  Estimates of the Genomic Mutation Rate for Detrimental Alleles in Drosophila melanogaster Dedicated to the memory of Terami Mukai, whose pioneering paper on mutation accumulation appeared in Genetics 40 years ago. , 2004, Genetics.

[21]  R. Punnett,et al.  The Genetical Theory of Natural Selection , 1930, Nature.

[22]  Brian Charlesworth,et al.  Selection in Density‐Regulated Populations , 1971 .

[23]  T. Prout.  Some Relationships between Density-Independent Selection and Density-Dependent Population Growth , 1980 .

[24]  Olivier Tenaillon,et al.  The Evolution of Epistasis and Its Links With Genetic Robustness, Complexity and Drift in a Phenotypic Model of Adaptation , 2009, Genetics.

[25]  M. Lynch,et al.  MUTATION LOAD AND THE SURVIVAL OF SMALL POPULATIONS , 1990, Evolution; international journal of organic evolution.

[26]  L. Wahl,et al.  Fixation Probability Favors Increased Fecundity Over Reduced Generation Time , 2004, Genetics.

[27]  R H Borts,et al.  Direct estimate of the mutation rate and the distribution of fitness effects in the yeast Saccharomyces cerevisiae. , 2001, Genetics.

[28]  R. Lenski,et al.  Long-term experimental evolution in Escherichia coli , 1991 .

[29]  W. Ewens.  Selection and Mutation , 1968 .

[30]  R. Lande,et al.  THE EVOLUTION OF SELF‐FERTILIZATION AND INBREEDING DEPRESSION IN PLANTS. I. GENETIC MODELS , 1985, Evolution; international journal of organic evolution.

[31]  P. Keightley,et al.  A Comparison of Models to Infer the Distribution of Fitness Effects of New Mutations , 2013, Genetics.

[32]  Nigel F. Delaney,et al.  Darwinian Evolution Can Follow Only Very Few Mutational Paths to Fitter Proteins , 2006, Science.

[33]  H. Caswell.  Matrix population models : construction, analysis, and interpretation , 2001 .

[34]  Rafael Sanjuán,et al.  Mutational fitness effects in RNA and single-stranded DNA viruses: common patterns revealed by site-directed mutagenesis studies , 2010, Philosophical Transactions of the Royal Society B: Biological Sciences.

[35]  M Imhof,et al.  Fitness effects of advantageous mutations in evolving Escherichia coli populations. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[36]  S. Otto,et al.  Evolution of sex: Resolving the paradox of sex and recombination , 2002, Nature Reviews Genetics.

[37]  Richard E. Lenski,et al.  Distribution of fitness effects caused by random insertion mutations in Escherichia coli , 2004, Genetica.