Table 1 Summary of data sets
NameSpeciesEnvironmentMutation typeMutation and genotype numberFitness measureMeasurement errorNoteReferences
A1, A2A.nigerMinimal mediumRandom (phenotypic markers)Two data sets of 5 mutations, 25 genotypesRate of increase in colony radius per unit time, relative to the ancestorWe calculated a single standard error using the two replicate measurementsThe two sets of five mutations are not independentde Visser et al. (1997, 2009)
B1–B10S. cerevisiaeStandard medium (on plates)Random (gene deletions)1711 + 3885 mutations, 5.4 million genotypesIncrease in colony size per unit time relative to the ancestorStandard error reported for each fitness measureAnalysis done on 10 independent subsets of 20 mutations. 1 + 20 + 100 genotypes corresponding to single and double mutantsCostanzo et al. (2010)
C1, C2D. melanogasterLaboratory environment.Random (phenotypic markers)Five mutations, 25 genotypesProductivity (product of fecundity and survival) C1 and mating success C2We roughly estimated standard error for the productivity measure (File S1)Two genotypes with 0 mating success removedWhitlock and Bourguet (2000)
DSingle-stranded DNA bacteriophage ID11E. coli (host)Independently selected (experimental evolution)Nine mutations, nine single mutants, 18 double mutantsLog2 increase in phage population per hourStandard error reported for each fitness measureRokyta et al. (2011)
E1, E2Vesicular stomatitis virusBaby hamster kidney (BHK21) cells (host)Independently selected (E1, found in natural isolates) and random (E2)Six mutations, six single mutants, 15 double mutants (E1)Growth rate relative to ancestorStandard error reported for each fitness measureSanjuán et al. (2004)
28 mutations, 76 double mutants (E2)
FE. coliNew, low-glucose environmentCoselected in experimental evolutionFive mutations, 25 genotypesGrowth rate relative to ancestor95% CIs reportedKhan et al. (2011)
GMethylobacterium extorquensMethanol environmentCoselected in experimental evolutionFour mutations, 24 genotypesGrowth rate relative to ancestorStandard errors not reported, but we estimated them using standard errors reported for another set of genotypes (File S1)Order of fixation of mutations not known; mutations were assumed to fix from the largest-effect mutation to the smallest-effect mutation(Chou et al. 2011)
H1, H2E. coliCefotaxime (β-lactam antibiotic)Independently selected (found in natural isolates); mutations chosen because together increase resistance to cefotaxime 100,000-foldFive mutations, 25 genotypesCefotaxime resistance measured as MICFor H1, we calculated single errors using the three replicate measurements; for H2, standard errors were reportedH2 is the same data set as H1, with MIC remeasured on same genotypes; resistance to piperacillin + clavulanic acid was also measured but not used hereWeinreich et al. (2006); Tan et al. (2011)
H3, H4E. coliCefotaxime (β-lactam antibiotic)Independently selected (found in natural isolates)four mutations, 24 genotypes; two independent data setsCefotaxime resistance measured as IC99.99 (highly correlated with MIC)Standard errors not reported, but we used the average standard error of H2One data set with four mutations of smallest effect H3, one with four mutations of largest effect H4 among 48 mutationsSchenk et al. (2013)
I1, I2, I3Plasmodium falciparum DHFR gene transformed into E. coli I1 and S. cerevisiae I2; Plasmodium vivax DHFR gene transformed into S. cerevisiae (I3)Pyrimethamine (antimalarial drug)Independently selected (found in clinical isolates)four mutations, 24 genotypes; I2 includes the same four mutations as I1 plus two additional mutations affecting another locus Pyrimethamine resistance measured as IC50 in μg/ml (I1) and M (mol/L) (I2); growth rate of the transformed strain at concentration 1 μmol/L (I3)Standard errors for I1 and I2 reportedIn I2 (Brown et al. 2010), one locus has three possible alleles; the third allele was ignored, resulting in 17 fitness valuesLozovsky et al. (2009); Brown et al. (2010); Jiang et al. (2013)