References
Bailey, S. F., and R. Kassen. 2012. Spatial structure of ecological
opportunity drives adaptation in a bacterium. Am Nat. 180: 270–283.
Baird , L., B. L. Steinsiek, S. Raina, and C.
Georgopoulos. 1991. Identification of the Escherichia coli sohB gene, a
multicopy suppressor of the HtrA (DegP) null phenotype. J Bacteriol.
173: 5763-70.
Bennett, A. F., and R. E. Lenski. 2007. An experimental test of
evolutionary trade-offs during temperature adaptation. Proc Natl Acad
Sci USA. 104: S8649–8654.
Blank, D., L. Wolf, M. Ackermann and O. K. Silander. 2014. The
predictability of molecular evolution during functional innovation. Proc
Natl Acad Sci USA. 111: 3044–3049.
Björkman, J., D. Hughes and D. I. Andersson. 1998. Virulence of
antibiotic-resistant Salmonella typhimurium . Proc Natl Acad Sci
USA. 95: 3949–3953.
Björkman, J., I. Nagaev, O. G. Berg, D. Hughes and D. I. Andersson.
2000. Effects of environment on compensatory mutations to ameliorate
costs of antibiotic resistance. Science. 287: 1479–1482.
Blount, Z. D., C. Z. Borland and R. E. Lenski. 2008. Historical
contingency and the evolution of a key innovation in an experimental
population of Escherichia coli . Proc Natl Acad Sci USA. 105:
7899–7906.
Blount, Z. D., J. E. Barrick, C. J. Davidson, and R. E. Lenski. 2012.
Genomic analysis of a key innovation in an experimentalEscherichia coli population. Nature. 489: 513–518.
Bono, L. M., L. B. Smith, D. W. Pfennig, and C. L. Burch. 2017. The
emergence of performance trade‐offs during local adaptation: insights
from experimental evolution. Molecular Ecology. 26: 1720–1733.
Brandis, G., M. Wrande, L. Liljas and D. Hughes. 2012.
Fitness‐compensatory mutations in rifampicin‐resistant RNA polymerase.
Mol Micro. 85: 142–151.
Buckling, A., R. Kassen, G. Bell, and P. B. Rainey. 2000. Disturbance
and diversity in experimental microcosms. Nature. 408: 961–964.
Buckling, A., M. A. Brockhurst, M. Travisano and P. B. Rainey. 2007.
Experimental adaptation to high and low quality environments under
different scales of temporal variation. J Evol Biol. 20: 296–300.
Choi, K.-H., J. B. Gaynor, K. G. White, C. Lopez, C. M. Bosio, R. R.
Karkhoff-Schweizer and H. P. Schweizer. 2005. A Tn7 -based
broad-range bacterial cloning and expression system. Nature Meth. 2:
443–448.
Cooper, T. F. and R. E. Lenski. 2010. Experimental evolution withE. coli in diverse resource environments. I. Fluctuating
environments promote divergence of replicate populations. BMC Evol Biol.
10: 11–10.
Cooper, T. F., D. E. Rozen and R. E. Lenski. 2003. Parallel changes in
gene expression after 20,000 generations of evolution inEscherichia coli . Proc Natl Acad Sci USA. 100: 1072–1077.
Covert A. W., R. E. Lenski, C. O. Wilke and C. Ofria. 2013. Experiments
on the role of deleterious mutations as stepping stones in adaptive
evolution. Proc Natl Acad Sci USA. 110: E3171-E3178
Daber, R. and M. Lewis. 2009. A novel molecular switch. J Mol Biol. 391:
661–670.
Dekel, E. U. Alon. 2005. Optimality and evolutionary tuning of the
expression level of a protein. Nature. 436: 588–592.
Eames, M., T. Kortemme. 2012. Cost-benefit tradeoffs in engineeredlac operons. Science. 336: 911–915.
Ferenci, T. 1996. Adaptation to life at micromolar nutrient levels: the
regulation of Escherichia coli glucose transport by endoinduction and
cAMP. FEMS Microbiol Rev. 18: 301–317.
Ferrières, L., G. Hémery, T. Nham, A.-M. Guérout, D. Mazel, C. Beloin,
and J. M. Ghigo. 2010. Silent mischief: bacteriophage Mu insertions
contaminate products of Escherichia coli random mutagenesis performed
using suicidal transposon delivery plasmids mobilized by
broad-host-range RP4 conjugative machinery. J Bacteriol. 192:
6418–6427.
Filteau, M., V. Hamel, M.-C. Pouliot, I. Gagnon-Arsenault, A. K. Dube
and C. R. Landry. 2015. Evolutionary rescue by compensatory mutations is
constrained by genomic and environmental backgrounds. Mol Sys Biol. 11:
832–832.
Gerrish P. and R. E. Lenski. 1998. The fate of competing beneficial
mutations in an asexual population. Genetica 102-103:127–144.
Gong, L. I., M. A. Suchard and J. D. Bloom. 2013. Stability-mediated
epistasis constrains the evolution of an influenza protein. eLife, 2:
e00631.
Gram, C. D. and R. J. Brooker. 1992. An analysis of the side chain
requirement at position 177 within the lactose permease which confers
the ability to recognize maltose. J Biol Chem. 267: 3841–3846.
Harrison, E., D. Guymer, A. J. Spiers, S. Paterson and M. A. Brockhurst.
2015. Parallel compensatory evolution stabilizes plasmids across the
parasitism-mutualism continuum. Curr Biol. 25: 2034–2039.
Jahreis, K., E. F. Pimentel-Schmitt, R. Brueckner and F. Titgemeyer.
2008. Ins and outs of glucose transport systems in eubacteria. FEMS
Microbiol Rev. 32: 891–907.
Jarvik, J. and D. Botstein. 1975. Conditional lethal mutations that
suppress genetic defects in morphogenesis by altering structural
proteins. Proc Natl Acad Sci USA. 72: 2738–2742.
Jasmin, J.-N. and R. Kassen. 2007. Evolution of a single niche
specialist in variable environments. Proc R Soc Lond B. 274: 2761–2767.
Kacar, B., X. Ge, S. Sanyal and E. A. Gaucher. 2017. Experimental
evolution of Escherichia coli harboring an ancient translation
protein. J Mol Evol. 84: 69–84.
Kassen, R. G. Bell. 1998. Experimental evolution inChlamydomonas . IV. Selection in environments that vary through
time at different scales. Heredity. 80: 732–741.
King, S. C. and T. H. Wilson. 1990. Identification of valine 177 as a
mutation altering specificity for transport of sugars by theEscherichia coli lactose carrier. Enhanced specificity for
sucrose and maltose. J Biol Chem. 265: 9638–9644.
Knöppel, A., J. Nasvall and D. I. Andersson. 2016. Compensating the
fitness costs of synonymous mutations. Mol Biol Evol. 33: 1461–1477.
Kurlandzka, A., R. F. Rosenzweig and J. Adams. 1991. Identification of
adaptive changes in an evolving population of Escherichia coli :
the role of changes with regulatory and highly pleiotropic effects. Mol
Biol Evol. 8: 261–281.
Lee, M.-C. and C. J. Marx. 2012. Repeated, selection-driven genome
reduction of accessory genes in experimental populations. PLoS Genetics.
8: e1002651.
Lehming, N., J. Sartorius, M. Niemöller, G. Genenger, B. von
Wilcken-Bergmannand B. Müller-Hill. 1987. The interaction of the
recognition helix of lac repressor with lac operator. EMBO
J. 6: 3145–3153.
Lehming, N., J. Sartorius, B. Kisters-Woike, B. von Wilcken-Bergmann and
B. Müller-Hill. 1990. Mutant lac repressors with new
specificities hint at rules for protein–DNA recognition. EMBO J. 9:
615–621.
Lenski, R. E. 1988. Experimental studies of pleiotropy and epistasis inEscherichia coli . II. Compensation for maldaptive effects
associated with resistance to virus T4. Evolution. 42: 433–440.
Lenski, R. E., M. R. Rose, S. C. Simpson and S. C. Tadler. 1991.
Long-term experimental evolution in Escherichia coli . I.
Adaptation and divergence during 2,000 generations. Am Nat. 138:
1315–1341.
Levin, B. R., V. Perrot and N. Walker. 2000. Compensatory mutations,
antibiotic resistance and the population genetics of adaptive evolution
in bacteria. Genetics. 154: 985–997.
Lunzer, M., G. B. Golding and A. M. Dean. 2010. Pervasive cryptic
epistasis in molecular evolution. PLoS Genetics. 6: e1001162.
MacLean, R. C., G. Bell and P. B. Rainey. 2004. The evolution of a
pleiotropic fitness tradeoff in Pseudomonas fluorescens . Proc
Natl Acad Sci USA. 101: 8072–8077.
Maisnier-Patin, S., O. G. Berg, L. Liljas and D. I. Andersson. 2002.
Compensatory adaptation to the deleterious effect of antibiotic
resistance in Salmonella typhimurium . Mol Microbiol. 46:
355–366.
Manson, M. D. 2000. Allele-specific suppression as a tool to study
protein–protein interactions in bacteria. Methods. 20: 18–34.
Markiewicz, P., L. G. Kleina, C. Cruz, S. Ehret, and J. H. Miller. 1994.
Genetic studies of the lac repressor. XIV. Analysis of 4000
altered Escherichia coli lac repressors reveals essential and
non-essential residues, as well as “spacers” which do not require a
specific sequence. J Mol Biol. 240: 421–433.
Martin, G., and T. Lenormand. 2015. The fitness effect of mutations
across environments: Fisher’s geometrical model with multiple optima.
Evolution. 69: 1433–1447.
Melnyk, A. H., N. McCloskey, A. J. Hinz, J. Dettman and R. Kassen. 2017.
Evolution of cost-free resistance under fluctuating drug selection inPseudomonas aeruginosa . mSphere, 2: e00158–17.
McGee, L. W., A. M. Sackman, A. J. Morrison, J. Pierce, J. Anisman and
D. R. Rokyta. 2015. Synergistic pleiotropy overrides the costs of
complexity in viral adaptation. Genetics. 202: 285–295.
Moore, F., D. E. Rozen and R. E. Lenski. 2000. Pervasive compensatory
adaptation in Escherichia coli . Proc R Soc Lond B. 267: 515–522.
Moura de Sousa, J., R. Balbontín, P. Durão and I. Gordo. 2017.
Multidrug-resistant bacteria compensate for the epistasis between
resistances. PLoS Biology. 15: e2001741
Nagaev, I., J. Björkman, D. I. Andersson and D. Hughes. 2001. Biological
cost and compensatory evolution in fusidic acid‐resistantStaphylococcus aureus . Mol Microbiol. 40: 433–439.
Nilsson, A. I., O. G. Berg, O. Aspevall, G. Kahlmeter and D. I.
Andersson. 2003. Biological costs and mechanisms of fosfomycin
resistance in Escherichia coli . Antimicrobial Agents and
Chemotherapy. 47: 2850–2858.
Philippe, N., J. -P. Alcaraz, E. Coursange, J. Geiselmann and D.
Schneider. 2004. Improvement of pCVD442, a suicide plasmid for gene
allele exchange in bacteria. Plasmid. 51: 246–255.
Phillips, K. N., G. Castillo, A. Wünsche and T. F. Cooper. 2016.
Adaptation of Escherichia coli to glucose promotes evolvability
in lactose. Evolution. 70: 465–470.
Platt, T., J. G. Files and K. Weber. 1973. Lac repressor: specific
proteolytic destruction of the NH2-terminal region and
loss of the deoxyribonucleic acid-binding activity. J Biol Chem. 248:
110–121.
Ponmani, T. and M. H. Munavar. 2014. G673 could be a novel mutational
hot spot for intragenic suppressors of pheS5 lesion in Escherichia
coli . Microbiology. 3: 369–382.
Poon, A. and L. Chao. 2005a. The rate of compensatory mutation in the
DNA bacteriophage ØX174. Genetics. 170: 989–999.
Poon, A., B. H. Davis and L. Chao. 2005b. The coupon collector and the
suppressor mutation: estimating the number of compensatory mutations by
maximum likelihood. Genetics. 170: 1323–1332.
Poon, A. and L. Chao. 2006. Functional origins of fitness effect-sizes
of compensatory mutations in the DNA bacteriophage ØX174. Evolution. 60:
2032–2043.
Postma, P. W., J. W. Lengeler and G. R. Jacobson. 1993.
Phosphoenolpyruvate:carbohydrate phosphotransferase systems of bacteria.
Microbiol Rev. 57: 543–594.
Quan, S., J. C. J. Ray, Z. Kwota, T. Duong, G. Balazsi, T. F. Cooper and
R. D. Monds. 2012. Adaptive evolution of the lactose utilization network
in experimentally evolved populations of Escherichia coli . PLoS
Genetics. 8: e1002444.
R Core Team (2018). R: A language and environment for statistical
computing. R Foundation for Statistical Computing, Vienna, Austria. URL
https://www.R-project.org/.
Roemhild, R., C. Barbosa, R. E. Beardmore, G. Jansen and H. Schulenburg.
2015. Temporal variation in antibiotic environments slows down
resistance evolution in pathogenic Pseudomonas aeruginosa . Evol
App. 8: 945–955.
Rosenzweig, R. F., R. R. Sharp, D. S. Treves and J. Adams. 1994.
Microbial evolution in a simple unstructured environment: genetic
differentiation in Escherichia coli . Genetics. 137: 903–917.
Rozen, D. E., L. McGee, B. R. Levin and K. P. Klugman. 2007. Fitness
costs of fluoroquinolone resistance in Streptococcus pneumoniae .
Antimicrobial Agents and Chemo. 51: 412–416.
Sahin-Tóth, M., M. C. Lawrence, T. Nishio and H. R. Kaback. 2001. The
C-4 hydroxyl group of galactopyranosides is the major determinant for
ligand recognition by the lactose permease of Escherichia coli .
Biochemistry. 40: 13015–13019.
Salinas, R. K., G. E. Folkers, A. M. J. J. Bonvin, D. Das, R. Boelens
and R. Kaptein. 2005. Altered specificity in DNA binding by thelac repressor: a mutant lac headpiece that mimics thegal repressor. Chembiochem. 6: 1628–1637.
Satterwhite, R. S. and T. F. Cooper. 2015. Constraints on adaptation ofEscherichia coli to mixed-resource environments increase over
time. Evolution. 69: 2067–2078.
Schick, A., S. F. Bailey and R. Kassen. 2015. Evolution of fitness
trade-offs in locally adapted populations of Pseudomonas
fluorescens . Am Nat. 186: S48–S59.
Shah, P., D. M. McCandlish and J. B. Plotkin. 2015. Contingency and
entrenchment in protein evolution under purifying selection. Proc Natl
Acad Sci USA. 112: E3226–E3235.
Stoebel D. M., A. M. Dean and D. E. Dykhuizen. 2008. The cost of
expression of Escherichia coli lac operon proteins is in
the process, not in the products. Genetics 178:1653–1660.
Szamecz, B., G. Boross, D. Kalapis, K. Kovács, G. Fekete, Z. Farkas, et
al. 2014. The genomic landscape of compensatory evolution. PLoS Biol.
12: e1001935.
Tenaillon, O., J. E. Barrick, N. Ribeck, D. E. Deatherage, J. L.
Blanchard, A. Dasgupta, et al. 2016. Tempo and mode of genome evolution
in a 50,000-generation experiment. Nature. 536: 165–170.
Turner, P. E. and S. F. Elena. 2000. Cost of Host Radiation in an RNA
Virus. Genetics. 156: 1465–1470.
van Leeuwen, J., C. Pons, J. C. Mellor, T. N. Yamaguchi, H. Friesen, J.
Koschwanez, et al. 2016. Exploring genetic suppression interactions on a
global scale. Science. 354: aag0839–1 – aag0839–11.
Weickert, M. J. and S. Adhya. 1992. A family of bacterial regulators
homologous to Gal and Lac repressors. J Biol Chem. 267: 15869–15874.
Wielgoss, S., T. Bergmiller, A. M. Bischofberger and A. R. Hall. 2016.
Adaptation to parasites and costs of parasite resistance in mutator and
nonmutator bacteria. Mol Biol Evol. 33: 770–782.
Wood, M. P., A. L. Cole, P. Ruchala, A. J. Waring, L. C. Rohan, P. Marx,
et al. 2013. A compensatory mutation provides resistance to disparate
HIV fusion inhibitor peptides and enhances membrane fusion. PloS One. 8:
e55478.
Woods, R., D. Schneider, C. L. Winkworth, M. A. Riley and R. E. Lenski.
2006. Tests of parallel molecular evolution in a long-term experiment
with Escherichia coli . Proc Natl Acad Sci USA. 103: 9107–9112.
Zee, P. C., H. Mendes-Soares, Y.-T. N. Yu, S. A. Kraemer, H. Keller, S.
Ossowski, et al. 2014. A shift from magnitude to sign epistasis during
adaptive evolution of a bacterial social trait. Evolution. 68:
2701–2708.