Single nucleotide mapping of trait space reveals Pareto fronts that constrain adaptation (original) (raw)

References

  1. Loschiavo, S. R. Effect of oviposition sites on egg production and longevity of Trogoderma parabile (Coleoptera: Dermestidae)1. Can. Entomol. 100, 86–89 (1968).
    Article Google Scholar
  2. Tinkle, D. W. The concept of reproductive effort and its relation to the evolution of life histories of lizards. Am. Nat. 103, 501–516 (1969).
    Article Google Scholar
  3. Reznick, D. A., Bryga, H. & Endler, J. A. Experimentally induced life-history evolution in a natural population. Nature 346, 357–359 (1990).
    Article Google Scholar
  4. Stearns, S. C. The Evolution of Life Histories (Oxford Univ. Press, 1992).
  5. Camargo, A., Sarroca, M. & Maneyro, R. Reproductive effort and the egg number vs. size trade-off in Physalaemus frogs (Anura: Leiuperidae). Acta Oecologica 34, 163–171 (2008).
    Article Google Scholar
  6. Cunningham, J. T. Degenerative mutations. Nature 130, 203–204 (1932).
    Article Google Scholar
  7. Wang, Y. et al. Contribution of both positive selection and relaxation of selective constraints to degeneration of flyability during geese domestication. PLoS ONE 12, e0185328 (2017).
    Article Google Scholar
  8. Darwin, C. The Descent of Man, and Selection in Relation to Sex (introduction by Bonner, J.T. & May, R.M.) (Princeton Univ. Press, 1981).
  9. Shoval, O. et al. Evolutionary trade-offs, Pareto optimality, and the geometry of phenotype space. Science 336, 1157–1160 (2012).
    Article CAS Google Scholar
  10. Tendler, A., Mayo, A. & Alon, U. Evolutionary tradeoffs, Pareto optimality and the morphology of ammonite shells. BMC Syst. Biol. 9, 12 (2015).
    Article Google Scholar
  11. Mooney, K. A., Halitschke, R., Kessler, A. & Agrawal, A. A. Evolutionary trade-offs in plants mediate the strength of trophic cascades. Science 327, 1642–1644 (2010).
    Article CAS Google Scholar
  12. Fraebel, D. T. et al. Environment determines evolutionary trajectory in a constrained phenotypic space. eLife 6, e24669 (2017).
    Article Google Scholar
  13. Nidelet, T. & Kaltz, O. Direct and correlated responses to selection in a host–parasite system: testing for the emergence of genotype specificity. Evol. Int. J. Org. Evol. 61, 1803–1811 (2007).
    Article Google Scholar
  14. Buckling, A., Brockhurst, M. A., Travisano, M. & Rainey, P. B. Experimental adaptation to high and low quality environments under different scales of temporal variation. J. Evol. Biol. 20, 296–300 (2007).
    Article CAS Google Scholar
  15. Bono, L. M., Smith, L. B., Pfennig, D. W. & Burch, C. L. The emergence of performance trade-offs during local adaptation: insights from experimental evolution. Mol. Ecol. 26, 1720–1733 (2017).
    Article Google Scholar
  16. McGee, L. W. et al. Synergistic pleiotropy overrides the costs of complexity in viral adaptation. Genetics 202, 285–295 (2016).
    Article CAS Google Scholar
  17. Jasmin, J.-N. & Kassen, R. On the experimental evolution of specialization and diversity in heterogeneous environments. Ecol. Lett. 10, 272–281 (2007).
    Article Google Scholar
  18. Bennett, A. F. & Lenski, R. E. An experimental test of evolutionary trade-offs during temperature adaptation. Proc. Natl Acad. Sci. USA 104, 8649–8654 (2007).
    Article CAS Google Scholar
  19. Satterwhite, R. S. & Cooper, T. F. Constraints on adaptation of Escherichia coli to mixed-resource environments increase over time. Evolution 69, 2067–2078 (2015).
    Article CAS Google Scholar
  20. Levy, S. F. et al. Quantitative evolutionary dynamics using high-resolution lineage tracking. Nature 519, 181–186 (2015).
    Article CAS Google Scholar
  21. Venkataram, S. et al. Development of a comprehensive genotype-to-fitness map of adaptation-driving mutations in yeast. Cell 166, 1585–1596.e22 (2016).
    Article CAS Google Scholar
  22. Li, Y. et al. Hidden complexity of yeast adaptation under simple evolutionary conditions. Curr. Biol. 28, 515–525.e6 (2018).
    Article CAS Google Scholar
  23. Seedorf, M. & Silver, P. A. Importin/karyopherin protein family members required for mRNA export from the nucleus. Proc. Natl Acad. Sci. USA 94, 8590–8595 (1997).
    Article CAS Google Scholar
  24. Rosenblum, J. S., Pemberton, L. F. & Blobel, G. A nuclear import pathway for a protein involved in tRNA maturation. J. Cell Biol. 139, 1655–1661 (1997).
    Article CAS Google Scholar
  25. Baccarini, L., Martínez-Montañés, F., Rossi, S., Proft, M. & Portela, P. PKA-chromatin association at stress responsive target genes from Saccharomyces cerevisiae. Biochim. Biophys. Acta Gene Regul. Mech. 1849, 1329–1339 (2015).
    Article CAS Google Scholar
  26. Yona, A. H. et al. Chromosomal duplication is a transient evolutionary solution to stress. Proc. Natl Acad. Sci. USA 109, 21010–21015 (2012).
    Article CAS Google Scholar
  27. Natesuntorn, W. et al. Genome-wide construction of a series of designed segmental aneuploids in Saccharomyces cerevisiae. Sci. Rep. 5, 12510 (2015).
    Article CAS Google Scholar
  28. Sunshine, A. B. et al. The fitness consequences of aneuploidy are driven by condition-dependent gene effects. PLoS Biol. 13, e1002155 (2015).
    Article Google Scholar
  29. Garay, E. et al. High-resolution profiling of stationary-phase survival reveals yeast longevity factors and their genetic interactions. PLoS Genet. 10, e1004168 (2014).
    Article Google Scholar
  30. Levins, R. Theory of fitness in a heterogeneous environment. I. The fitness set and adaptive function. Am. Nat. 96, 361–373 (1962).
    Article Google Scholar
  31. Ehrlich, E., Kath, N. J. & Gaedke, U. The shape of a defense-growth trade-off governs seasonal trait dynamics in natural phytoplankton. Preprint at bioRxiv https://doi.org/10.1101/462622 (2018).
  32. Jessup, C. M. & Bohannan, B. J. M. The shape of an ecological trade-off varies with environment. Ecol. Lett. 11, 947–959 (2008).
    Article Google Scholar
  33. Maharjan, R. et al. The form of a trade-off determines the response to competition. Ecol. Lett. 16, 1267–1276 (2013).
    Article Google Scholar
  34. Roff, D. A. & Fairbairn, D. J. The evolution of trade-offs: where are we? J. Evol. Biol. 20, 433–447 (2007).
    Article CAS Google Scholar
  35. Yi, X. & Dean, A. M. Phenotypic plasticity as an adaptation to a functional trade-off. eLife 5, e19307 (2016).
    Article Google Scholar
  36. Sexton, J. P., Montiel, J., Shay, J. E., Stephens, M. R. & Slatyer, R. A. Evolution of ecological niche breadth. Annu. Rev. Ecol. Evol. Syst. 48, 183–206 (2017).
    Article Google Scholar
  37. Zhao, L., Liu, Z., Levy, S. F. & Wu, S. Bartender: a fast and accurate clustering algorithm to count barcode reads. Bioinformatics 34, 739–747 (2018).
    Article CAS Google Scholar
  38. Kryazhimskiy, S., Rice, D. P., Jerison, E. R. & Desai, M. M. Global epistasis makes adaptation predictable despite sequence-level stochasticity. Science 344, 1519–1522 (2014).
    Article CAS Google Scholar
  39. Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. J. 17, 10–12 (2011).
    Article Google Scholar
  40. Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at https://arxiv.org/abs/1303.3997 (2013).
  41. Freed, D. N., Aldana, R., Weber, J. A. & Edwards, J. S. The Sentieon genomics tools – a fast and accurate solution to variant calling from next-generation sequence data. Preprint at bioRxiv https://doi.org/10.1101/115717 (2017).
  42. Cingolani, P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff. Fly (Austin) 6, 80–92 (2012).
    Article CAS Google Scholar

Download references