Cited by 116

The DOI matches its Crossref record.

Pervasive joint influence of epistasis and plasticity on mutational effects in Escherichia coli

Remold, Susanna K, Lenski, Richard E·2004·Nature Genetics

Abstract

The effects of mutations on phenotype and fitness may depend on the environment (phenotypic plasticity), other mutations (genetic epistasis) or both. Here we examine the fitness effects of 18 random insertion mutations in E. coli in two resource environments and five genetic backgrounds. We tested each mutation for plasticity and epistasis by comparing its fitness effects across these ecological and genetic contexts. Some mutations had no measurable effect in any of these contexts. None of the mutations had effects on phenotypic plasticity that were independent of genetic background. However, half the mutations had epistatic interactions such that their effects differed among genetic backgrounds, usually in an environment-dependent manner. Also, the pattern of mutational effects across backgrounds indicated that epistasis had been shaped primarily by unique events in the evolutionary history of a population rather than by repeatable events associated with shared environmental history.

Overview

Integrity signals

Registry

Crossref · 10.1038/ng1324

Cites

Statistics

Recomputing p-values needs the paper’s full text.

Verification

Claims the paper makes

This paper’s full text isn’t openly available, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Citations

Cites

No references could be resolved yet.

Research works printed but not linked: 29

  1. Wade, M.J. Epistasis as a genetic constraint within populations and an accelerant of adaptive divergence among them. in Epistasis and the Evolutionary Process (eds. Wolf, J.B., Brodie, E.D.I. & Wade, M.J.) 213–231 (Oxford Univ. Press, Oxford, UK, 2000).
  2. Wade, M.J. & Goodnight, C.J. The theories of Fisher and Wright in the context of metapopulations: when nature does many small experiments. Evolution 52, 1537–1553 (1998). · DOI
  3. Otto, S.P. & Feldman, M.W. Deleterious mutations, variable epistatic interactions, and the evolution of recombination. Theor. Pop. Biol. 51, 134–147 (1997). · DOI
  4. Hansen, T.F. & Wagner, G.P. Epistasis and the mutation load: a measurement theoretical approach. Genetics 158, 477–485 (2001). · DOI
  5. Kondrashov, F.A. & Kondrashov, A.S. Multidimensional epistasis and the disadvantage of sex. Proc. Natl. Acad. Sci. USA 98, 12089–12092 (2001). · DOI
  6. Whitlock, M.C., Phillips, P.C., Moore, F.B.-G. & Tonsor, S.J. Multiple fitness peaks and epistasis. Annu. Rev. Ecol. Syst. 26, 601–629 (1995). · DOI
  7. Dean, A.M. A molecular investigation of genotype by environment interactions. Genetics 139, 19–33 (1995). · DOI
  8. Fedorowicz, G.M., Fry, J.D., Anholt, R.R. & Mackay, T.F.C. Epistatic interactions between smell-impaired loci in Drosophila melanogaster. Genetics 148, 1885–1891 (1998). · DOI
  9. Dykhuizen, D.E. & Hartl, D.L. Functional effects of PGI allozymes in Escherichia coli. Genetics 105, 1–18 (1983). · DOI
  10. Lenski, R.E. et al. Epistatic effects of promoter and repressor functions of the Tn10 tetracycline-resistance operon on the fitness of Escherichia coli. Mol. Ecol. 3, 127–135 (1994). · DOI
  11. De Visser, J.A.G.M., Hoekstra, R.F. & van den Ende, H. Test of interaction between genetic markers that affect fitness in Aspergillus niger. Evolution 51, 1499–1505 (1996). · DOI
  12. Elena, S.F. & Lenski, R.E. Test of synergistic interactions among deleterious mutations in bacteria. Nature 390, 395–398 (1997). · DOI
  13. Elena, S.F., Ekunwe, L., Hajela, N., Oden, S.A. & Lenski, R.E. Distribution of fitness effects caused by random insertion mutations in Escherichia coli. Genetica 102/103, 349–358 (1998). · DOI
  14. Elena, S.F. & Lenski, R.E. Epistasis between new mutations and genetic background, and a test of genetic canalization. Evolution 55, 1746–1752 (2001). · DOI
  15. Remold, S.K. & Lenski, R.E. Contribution of individual random mutations to genotype-by-environment interactions in Escherichia coli. Proc. Natl. Acad. Sci. USA 98, 11388–11393 (2001). · DOI
  16. Kishony, R. & Leibler, S. Environmental stresses can alleviate the average deleterious effect of mutations. J. Biol. 2, 14 (2003). · DOI
  17. Miller, J.H. A Short Course in Bacterial Genetics (Cold Spring Harbor Laboratory Press, Plainview, New York, USA, 1992).
  18. Kleckner, N., Bender, J. & Gottesman, S. Uses of transposons with emphasis on Tn10. Meth. Enzymol. 204, 139–180 (1991). · DOI
  19. Lenski, R.E., Rose, M.R., Simpson, S.C. & Tadler, S.C. Long-term experimental evolution in Escherichia coli. I. Adaptation and divergence during 2,000 generations. Am. Nat. 138, 1315–1341 (1991). · DOI
  20. Travisano, M. & Lenski, R.E. Long-term experimental evolution in Escherichia coli. IV. Targets of selection and the specificity of adaptation. Genetics 143, 15–26 (1996). · DOI
  21. Travisano, M. Long-term experimental evolution in Escherichia coli. VI. Environmental constraints on adaptation and divergence. Genetics 146, 471–479 (1997). · DOI
  22. Schmalhausen, I.I. Factors of Evolution: The Theory of Stabilizing Selection (Blakiston, Philadelphia, USA, 1949).
  23. Podlich, D.W. & Cooper, M. Modelling plant breeding programs as search strategies on a complex response surface. in Simulated Evolution and Learning (eds. McKay, B., Yao, X., Newton, C.S., Kim, J.-H. & Furuhashi, T.) 171–178 (Springer, Canberra, Australia, 1998).
  24. Lenski, R.E. & Travisano, M. Dynamics of adaptation and diversification: a 10,000-generation experiment with bacterial populations. Proc. Natl. Acad. Sci. USA 91, 6808–6814 (1994). · DOI
  25. Lenski, R.E., Winkworth, C.L. & Riley, M.A. Rates of DNA sequence evolution in experimental populations of Escherichia coli during 20,000 generations. J. Mol. Evol. 56, 498–508 (2003). · DOI
  26. Lenski, R.E. Phenotypic and genomic evolution during a 20,000-generation experiment with the bacterium, Escherichia coli. Plant Breed. Rev. 24, 225–265 (2004).
  27. Levin, B.R., Stewart, F.M. & Chao, L. Resource-limited growth, competition and predation: a model and experimental studies with bacteria and bacteriophage. Am. Nat. 111, 3–24 (1977). · DOI
  28. Littell, R.C., Milliken, G.A., Stroup, W.W. & Wolfinger, R.D. SAS System for Mixed Models (SAS Institute, Cary, North Carolina, USA, 1996).
  29. Sokal, R.R. & Rohlf, F.J. Biometry (Freeman, New York, USA, 1995).

Cited by

Sorted by citations

Metadata

Authors
Remold, S. K., & Lenski, R. E.
Venue
Nature Genetics
Published
2004-03-14
Volume
36
Issue
4
Pages
423-426
ISSN
  • 1061-4036
  • 1546-1718
Cited by
116
References
0
Language
en

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review