Skip to main content
SpringerLink
Log in

Population Epigenetics

  • Chapter
  • First Online:
Nuclear Functions in Plant Transcription, Signaling and Development

Abstract

Epigenetics is the study of molecular-level mechanisms resulting in heritable changes in phenotype not due to DNA sequence changes. Epigenetic variation can change in response to environmental conditions, which allows for the examination of within-generation environmental response. This is one reason epigenetics could lend new insight into population-level processes. Population-level studies are currently rare, but because environment can affect phenotype we must show that findings from controlled epigenetic systems matter in natural populations. In this chapter, we emphasize studies in nonmodel organisms and in natural populations examining epigenetic response to ecological conditions. Future studies should incorporate experimental validation of stable versus induced epigenetic changes and modification of current statistical approaches.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Lewontin RC. The genetic basis of evolutionary change. West Sussex: Columbia University Press; 1974.

    Google Scholar 

  2. Pigliucci M. Do we need an extended evolutionary synthesis? Evolution 2007;61:2743–49.

    Article  PubMed  Google Scholar 

  3. Hartl DL, Jones EW. Essential genetics. 2nd ed. Sudbury: Jones and Bartlett; 1999.

    Google Scholar 

  4. Jablonka E, Lamb MJ. The epigenome in evolution: beyond the modern synthesis. VOGis Herald 2008;12:242–54.

    Google Scholar 

  5. Pigliucci M, Müller GB. Evolution – the extended synthesis. Cambridge: MIT Press; 2010.

    Book  Google Scholar 

  6. Jablonka E, Lamb MJ. Evolution in four dimensions: genetic, epigenetic, behavioral, and symbolic. Cambridge: MIT Press; 2005.

    Google Scholar 

  7. Jablonka E, Raz G. Transgenerational epigenetic inheritance: prevalence, mechanisms, and implications for the study of heredity and evolution. Q Rev Biol. 2009;84:131–76.

    Article  PubMed  Google Scholar 

  8. Richards EJ. Inherited epigenetic variation – revisiting soft inheritance. Nat Rev Genet. 2006;7:395–401.

    Article  CAS  PubMed  Google Scholar 

  9. Richards EJ. Population epigenetics. Curr Opin Genet Dev. 2008;18:221–6.

    Article  CAS  PubMed  Google Scholar 

  10. Grandjean V, Yaman R, Cuzin F, Rassoulzadegan M. Inheritance of an epigenetic mark: the CpG DNA methyltransferase 1 is required for de novo establishment of complex patterns of non-CpG methylation. PLoS One. 2007;11:e1136.

    Article  Google Scholar 

  11. Johannes F, Porcher E, Teixeira FK, Saliba-Combani V, Simon M, Agier N, Bulski A, Albuisson J, Heredia F, Audigier P, Bouchez D, Dillman C, Guerche P, Hospital F, Colot V. Assessing the impact of transgenerational epigenetic variation on complex traits. PLoS Genet. 2009;6:e1000530.

    Article  Google Scholar 

  12. Cubas P, Vincent C, Coen E. An epigenetic mutation responsible for natural variation in floral symmetry. Nature. 1999;401:157–61.

    Article  CAS  PubMed  Google Scholar 

  13. Bollati V, Baccarelli A. Environmental epigenetics. Heredity. 2010;105:105–12.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  14. Verhoeven KJF, Jansen JJ, van Dijk PJ, Biere A. Stress-induced DNA methylation changes and their heritability in asexual dandelions. New Phytol. 2010;185:1108–18.

    Article  CAS  PubMed  Google Scholar 

  15. Angers B, Castonguay E, Massicotte R. Environmentally induced phenotypes and DNA methylation: how to deal with unpredictable conditions until the next generation and after. Mol Ecol. 2010;19:1283–95.

    Article  CAS  PubMed  Google Scholar 

  16. Pál C. Plasticity, memory, and the adaptive landscape of the genotype. Proc R Soc Lond Biol. 1998;265:1319–23.

    Article  Google Scholar 

  17. Pál C, Miklós I. Epigenetic inheritance, genetic assimilation, and speciation. J Theor Biol. 1999;200:19–37.

    Article  PubMed  Google Scholar 

  18. Bonduriansky R, Day T. Non-genetic inheritance and its evolutionary implications. Annu Rev Ecol Evol Syst. 2009;40:103–25.

    Article  Google Scholar 

  19. Klironomos FD, Berg J, Collins S. How epigenetic mutations can affect genetic evolution: model and mechanism. BioEssays. 2013;35:571–8.

    Article  PubMed  Google Scholar 

  20. Geoghegan JL, Spencer HG. Population-epigenetic models of selection. Theor Pop Biol. 2012;81:232–42.

    Article  Google Scholar 

  21. Waddington CH. Canalization of development and the inheritance of acquired characters. Nature. 1942;150:563–65.

    Article  Google Scholar 

  22. Waddington CH. Genetic assimilation of an acquired character. Evolution. 1953;7:118–26.

    Article  Google Scholar 

  23. Jablonka E, Lamb MJ. The changing concept of epigenetics. Ann NY Acad Sci. 2002;981:82–96.

    Article  PubMed  Google Scholar 

  24. Holliday R. Epigenetics: a historical review. Epigenetics. 2006;1:76–80.

    Article  PubMed  Google Scholar 

  25. Holliday R. Epigenetics: an overview. Dev Genet. 1994;15:453–7.

    Article  CAS  PubMed  Google Scholar 

  26. Bird A. Perceptions of epigenetics. Nature. 2007;447:396–8.

    Article  CAS  PubMed  Google Scholar 

  27. Bossdorf O, Richards CL, Pigliucci M. Epigenetics for ecologists. Ecol Lett. 2008;11:106–15.

    PubMed  Google Scholar 

  28. Hallgrímsson B, Hall BK, editors. Epigenetics: linking genotype and phenotype in development and evolution. Berkeley: University of California Press; 2011.

    Google Scholar 

  29. Ho DH, Burggren WW. Epigenetics and transgenerational transfer: a physiological perspective. J Exp Biol. 2010;213:3–16.

    Article  CAS  PubMed  Google Scholar 

  30. Kovalchuk I. Transgenerational epigenetic inheritance in animals. Front Genet. 2012;3:1–2.

    Article  Google Scholar 

  31. Ledón-Rettig CC, Richards CL, Martin LB. Epigenetics for behavioral ecologists. Behav Ecol. 2013;24:311–24.

    Article  Google Scholar 

  32. Kilvitis H, Alvarez M, Foust CM, Robertson M, Schrey AW, Richards CL. Ecological epigenetics. In Landry C, Aubin-Horth N, editors. Ecological and evolutionary genomics. Dordrecht: Springer; 2014.

    Google Scholar 

  33. Schrey AW, Alvarez M, Foust CM, Kilvitis HJ, Lee JD, Liebl AL, Martin LB, Richards CL, Robertson M. Ecological epigenetics: beyond MS-AFLP. Integr Comp Biol. 2013;53:340–50.

    Article  PubMed  Google Scholar 

  34. Rapp RA, Wendel JF. Epigenetics and plant evolution. New Phytol. 2005;168:81–91.

    Article  CAS  PubMed  Google Scholar 

  35. Jaenisch R, Bird A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet. 2003;33:245–54.

    Article  CAS  PubMed  Google Scholar 

  36. Jablonka E, Lamb MJ. The evolution of information in the major transitions. J Theor Biol. 2006;239:236–46.

    Article  CAS  PubMed  Google Scholar 

  37. Herrera CM, Pozo MI, Bazaga P. Jack of all nectars, master of most: DNA methylation and the epigenetic basis of niche width in a flower-living yeast. Mol Ecol. 2012;21:2602–16.

    Article  CAS  PubMed  Google Scholar 

  38. Herrera CM, Medrano M, Bazaga P. Epigenetic differentiation persists after male gametogenesis in natural populations of the perennial herb Helleborus foetidus (Ranunculaceae). PLoS One. 2013;7:e70730.

    Article  Google Scholar 

  39. Herrera CM, Bazaga P. Epigenetic correlates of plant phenotypic plasticity: DNA methylation differs between prickly and nonprickly leaves in heterophyllous Ilex aquifolium (Aquifoliaceae) trees. Bot J Linean Soc. 2013;171:441–52.

    Article  Google Scholar 

  40. Richards CL, Schrey AW, Pigliucci M. Invasion of diverse habitats by few Japanese knotweed genotypes is correlated with epigenetic differentiation. Ecol Lett. 2012;15:1016–25.

    Article  PubMed  Google Scholar 

  41. Herrera CM, Bazaga P. Epigenetic differentiation and relationship to adaptive genetic divergence in discrete populations of the violet Viola cazorlensis. New Phytol. 2010;187:867–76.

    Article  CAS  PubMed  Google Scholar 

  42. Massicotte R, Whitelaw E, Angers B. DNA methylation: a source of random variation in natural populations. Epigenetics. 2011;6:421–7.

    Article  CAS  PubMed  Google Scholar 

  43. Schrey AW, Coon CAC, Grispo MT, Awad M, Imboma T, McCoy ED, Mushinsky HR, Richards CL, Martin LB. Epigenetic variation may compensate for decreased genetic variation with introductions: a case study using house sparrows (Passer domesticus) on two continents. Genet Res Int. 2012;2012:1–7.

    Google Scholar 

  44. Becker C, Hagmann J, Müller J, Koenig D, Stegle O, Borgwardt K, Weigel D. Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature. 2011;480:245–9.

    Article  CAS  PubMed  Google Scholar 

  45. Schmitz RJ, Schultz MD, Urich MA, Nery JR, Pelizzola M, Libiger O, Alix A, McCosh RB, Chen H, Schork NJ, Ecker JR. Patterns of population epigenomic diversity. Nature. 2013;495:193–8.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  46. Bossdorf O, Richards CL, Pigliucci M. Experimental alteration of DNA methylation affects the phenotypic plasticity of ecologically relevant traits in Arabidopsis thaliana. Evol Ecol. 2010;24:541–53.

    Article  Google Scholar 

  47. Supnick M. On the function of leaf spines in Ilex opaca. Bull Torrey Bot Club. 1983;110:228–30.

    Article  Google Scholar 

  48. Potter DA, Kimmerer TW. Do holly leaf spines really deter herbivory? Oecologia 1988;75:216–21.

    Article  Google Scholar 

  49. Obeso JR. The induction of spinescence in European holly leaves by browsing ungulates. Plant Ecol 1997;129:149–56.

    Article  Google Scholar 

  50. Lira-Medeiros, CF, Parisod C, Fernandes RA, Mata CS, Cardoso MA, Ferreira PCG. Epigenetic variation in mangrove plants occurring in contrasting natural environment. PLoS One. 2010;5:e10326.

    Article  PubMed Central  PubMed  Google Scholar 

  51. Vergreer P, Wagemaker NCAM, Ouborg NJ. Evidence for an epigenetic role in inbreeding depression. Biol Lett. 2012;8:798–801.

    Article  Google Scholar 

  52. Anderson TR. Biology of the ubiquitous house sparrow: from genes to populations. New York: Oxford University Press; 2006.

    Book  Google Scholar 

  53. Schrey AW, Grispo M, Awad M, Cook MB, McCoy ED, Mushinsky HR, Albayrak T, Bensch S, Burke T, Butler LK, Dor R, Fokidis HB, Jensen H, Imboma T, Kessler-Rios MM, Marzal A, Stewart IRK, Westerdahl H, Westneat DF, Zehtindjiev P, Martin LB. Broad-scale latitudinal patterns of genetic diversity among native European and introduced house sparrow (Passer domesticus) populations. Mol Ecol. 2011;20:1133–43.

    Article  CAS  PubMed  Google Scholar 

  54. Liebl AL, Schrey AW, Richards CL, Martin LB. Patterns of DNA methylation throughout a range expansion of an introduced songbird. Integr Comp Biol. 2013;53:351–8.

    Article  CAS  PubMed  Google Scholar 

  55. Genereux DP, Miner BE, Bergstrom CT, Laird CD. A population-epigenetic model to infer site-specific methylation rates from double-stranded DNA methylation patterns. Proc Natl Acad Sci. 2005;16:5802–07.

    Article  Google Scholar 

  56. Reinders J, Wulff BH, Mirouze M, Marí-Ordóñez A, Dapp M, Rozhon W, Bucher E, Theiler G, Paszkowski J. Compromised stability of DNA methylation and transposon immobilization in mosaic Arabidopsis epigenomes. Genes Dev. 2009;23:939–50.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  57. Cortijo S, Wardenaar R, Tatché MC, Gilly A, Etcheverny M, Labaclie K, Caillieux E, Hospital F, Aury JM, Wincker P, Roudier F, Jansen RC, Colot V, Johannes F. Mapping the transgenerational epigenetic basis for complex traits. Science. 2014;343:1045–1048.

    Google Scholar 

  58. Brachi B, Faure N, Horton M, Flahauw E, Vazquez A, Nordborg M, Bergelson J, Cuguen J, Roux F. Linkage and association mapping of Arabidopsis thaliana flowering time in nature. PLoS Genet. 2010;6:e1000940.

    Article  PubMed Central  PubMed  Google Scholar 

  59. Atwel, S, Huang YS, Vilhja´lmsson BJ, Willems G, Horton M, Li Y, Meng D, Platt A, Tarone AM, Hu TT, Jiang R, Muliyati NW, Zhang X, Amer MA, Baxter I, Brachi B, Chory J, Dean C, Debieu M, de Meaux J, Ecker JR, Faure N, Kniskern JM, Jones JDG, Michael T, Nemri A, Roux F, Salt DE, Tang C, Todesco M, Traw MB, Weigel D, Marjoram P, Borevitz JO, Bergelson J, Nordborg M. Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature. 2010;465:627–31.

    Article  Google Scholar 

  60. Fenster CB, Armbruster WS, Wilson P, Dudash MR, Thomson JD. Pollination syndromes and floral specialization. Annu Rev Ecol Evol Syst. 2004;35:375–403.

    Article  Google Scholar 

  61. Day T, Bonduriansky R. A unified approach to the evolutionary consequences of genetic and non-genetic inheritance. Am Nat. 2011;178:E18–36.

    Article  PubMed  Google Scholar 

  62. West-Eberhard MJ. Developmental plasticity and the origin of species differences. Proc Natl Acad Sci. 2005;102:6543–9.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  63. Duckworth RA. Epigenetic inheritance systems act as a bridge between ecological and evolutionary timescales. Behav Ecol. 2013;24:327–8.

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Integrative Biology, University of South Florida, 4202 E Fowler Avenue, 33620, Tampa, FL, USA

    Christy M. Foust & Christina L. Richards

  2. Department of Biology, Armstrong State University, 11935 Abercorn Street, Savannah, GA, 31419, USA

    Aaron W. Schrey

Authors
  1. Christy M. Foust
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Aaron W. Schrey
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Christina L. Richards
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Christy M. Foust .

Editor information

Editors and Affiliations

  1. Shanghai Center for Plant Stress Biology (PSC), Shanghai, China

    Olga Pontes

  2. Plant Pathology and Microbiology, University of California, Riverside, California, USA

    Hailing Jin

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer Science+Business Media New York

About this chapter

Cite this chapter

Foust, C., Schrey, A., Richards, C. (2015). Population Epigenetics. In: Pontes, O., Jin, H. (eds) Nuclear Functions in Plant Transcription, Signaling and Development. Springer, New York, NY. https://doi.org/10.1007/978-1-4939-2386-1_9

Download citation

Publish with us

Policies and ethics

Search

Navigation