Epigenomic plasticity within populations: Its evolutionary significance and potential

Heredity

Volumn 105, Issue 1, 2010, Pages 113-121

  Johnson, L J ^a   Tricker, P J ^a  

^a UNIVERSITY OF READING   (United Kingdom)

Author keywords

Canalisation; Capacitance; Epigenetics; Population genomics

Indexed keywords

CANALIZATION (BIOLOGY); EVOLUTIONARY BIOLOGY; GENOMICS; MOLECULAR ANALYSIS; PHENOTYPIC PLASTICITY; POPULATION GENETICS;

GENETIC EPIGENESIS; GENETIC VARIABILITY; HUMAN; MOLECULAR EVOLUTION; PHENOTYPE; POPULATION GENETICS; REVIEW;

EPIGENESIS, GENETIC; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENETICS, POPULATION; HUMANS; PHENOTYPE;

EID: 77953809085     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/hdy.2010.25     Document Type: Review

References (98)

1. Agrawal AF, Hadany L, Otto SP (2005). The evolution of plastic recombination. Genetics 171: 803-812.
2. Albert R (2007). Network inference, analysis, and modeling in systems biology. Plant Cell 19: 3327-3338.
3. Arnold SJ, Pfrender E, Jones AG (2001). The adaptive landscape as a conceptual bridge between micro and macroevolution. Genetica 112-113: 9-32.
4. Baldwin JM (1896). A new factor in evolution. Am Nat 30: 441-451.
5. Barton NH, Otto SP (2005). Evolution of recombination due to random drift. Genetics 169: 2353-2370.
6. Baurle I, Smith L, Baulcombe DC, Dean C (2007). Widespread role for the flowering-time regulators FCA and FPA in RNAmediated chromatin silencing. Science 318: 109-112.
7. Berger SL, Kouzarides T, Shiekhattar R, Shilatifard A (2009). An operational definition of epigenetics. Genes Dev 23: 781-783.
8. Bininda-Emonds ORP, Cardillo M, Jones KE, MacPhee RDE, Beck RMD, Grenyer R et al. (2007). The delayed rise of present-day mammals. Nature 446: 507-511.
9. Bird AP (1995). Gene number, noise reduction and biological complexity. Trends Genet 11: 94-100.
10. Bird AP (2002). DNA methylation patterns and epigenetic memory. Genes Dev 16: 6-21.
11. Bock C,Walter J, Paulsen M, Lengauer T (2008). Inter-individual variation of DNA methylation and its implications for largescale epigenome mapping. Nuc Acids Res 35: e55.
12. Brandl R, Mann W, Sprinzl M (1992). Estimation of the monocot-dicot age through tRNA sequences from the chloroplast. Proc R Soc Lond Ser B-Biol Sci 249: 13-17.
13. Brink RA (1956). A genetic change associated with the R locus in maize which is directed and potentially reversible. Genetics 41: 872-890.
14. Brookfield JFY (2005). The ecology of the genome: mobile DNA elements and their hosts. Nat Rev Genet 6: 128-136.
15. Buggs RJA, Doust AN, Tate JA, Koh J, Soltis K, Feltus FA et al. (2009). Gene loss and silencing in Tragopogon miscellus (Asteraceae): comparison of natural and synthetic allotetraploids. Heredity 103: 73-81.
16. Burt A (2000). Perspective: sex, recombination, and the efficacy of selection-was Weismann right? Evolution 54: 337-351.
17. Burt A, Trivers R (2006). Genes in Conflict. Harvard University Press: London.
18. Celniker SE, Dillon LAL, Gerstein MB, Gunsalus KC, Henikoff S, Karpen GH et al. (2009). Unlocking the secrets of the genome. Nature 459: 927-930.
19. Chandler V, Alleman M (2008). Paramutation: epigenetic instructions passed across generations. Genetics 178: 1839-1844.
20. Choi J, Hyun Y, Kang M-J, In Yun H, Yun J-Y, Lister C et al. (2009). Resetting and regulation of FLOWERING LOCUS C expression during Arabidopsis reproductive development. Plant J 57: 918-931.
21. Choi JK, Kim SC (2007). Environmental effects on gene expression phenotype have regional biases in the human genome. Genetics 175: 1607-1613.
22. Comfort NC (1995). Two genes, no enzyme: a second look at Barbara McClintock and the 1951 Cold Spring Harbor Symposium. Genetics 140: 1161-1166.
23. Corpet A, Almouzni G (2009). Making copies of chromatin: the challenge of nucleosomal organization and epigenetic information. Trends Cell Biol 19: 29-41.
24. Crispo E (2007). The Baldwin effect and genetic assimilation: revisiting two mechanisms of evolutionary change mediated by phenotypic plasticity. Evolution 61: 2469-2479.
25. Cummings WJ, Bednarski DW, Maizels N (2007). Genetic variation stimulated by epigenetic modification. PLoS One 3: e4075.
26. Draghi J, Wagner GP (2009). The evolutionary dynamics of evolvability in a gene network model. J Evol Biol 22: 599-611.
27. Drinnenberg IA, Weinberg DE, Xie KT, Mower JP, Wolfe KH, Fink GR et al. (2009). RNAi in budding yeast. Science 326: 544-550.
28. ENCODE Project Consortium (2004). The ENCODE (ENCyclopedia of DNA elements) project. Science 306: 636-640.
29. Evans GA (2000). Designer science and the 'omics' revolution. Nat Biotechnol 18: 127.
30. Eyre-Walker A (2006). The genomic rate of adaptive evolution. Trends Ecol Evol 21: 569-575.
31. Fabre E, Muller H, Therizols P, Lafontaine I, Dujon B, Fairhead C (2005). Comparative genomics in hemiascomycete yeasts: evolution of sex, silencing, and subtelomeres. Mol Biol Evol 22: 856-873.
32. Fraga MF, Ballestar E, Paz MF, Ropero S, Setien F, Ballestar ML et al. (2005). Epigenetic differences arise during the lifetime of monozygotic twins. Proc Natl Acad Sci USA 102: 10604-10609.
33. Galagan JA, Calvo SE, Borkovich KA, Selker EU, Read ND, Jaffe D et al. (2003). The genome sequence of the filamentous fungus Neurospora crassa. Nature 422: 859-868.
34. Galloway LF, Etterson JR (2007). Transgenerational plasticity is adaptive in the wild. Science 318: 1134-1136.
35. Gartner K (1990). A third component causing random variability beside environment and genotype. A reason for the limited success of a 30 year long effort to standardize laboratory animals? Lab Anim 24: 71-77.
36. Gehring M, Bubb KL, Henikoff S (2009). Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 324: 1447-1451.
37. Goldschmidt R (1951). Chromosomes and genes Cold Spring Harb Symp Quant 16: 1-11.
38. Gordon AJE, Halliday JA, Blankschien MD, Burns PA, Yatagai F, Herman C (2009). Transcriptional infidelity promotes heritable phenotypic change in a bistable gene network. PLoS Biol 7: e1000044.
39. Gould SJ, Eldredge N (1977). Punctuated equilibria: the tempo and mode of evolution reconsidered. Paleobiology 3: 115-151.
40. Grewal SIS, Moazed D (2003). Heterochromatin and epigenetic control of gene expression. Science 301: 798-802.
41. Hager R, Cheverud JM, Wolf JB (2009). Change in maternal environment induced by cross-fostering alters genetic and epigenetic effects on complex traits in mice. Proc R Soc Lond Ser B-Biol Sci 276: 2949-2954.
42. Hansen TF (2006). The evolution of genetic architecture. Annu Rev Ecol Evol Systemat 37: 123-157.
43. Hauenschild A, Ringrose L, Altmutter C, Paro R, Rehmsmeier M (2008). Evolutionary plasticity of polycomb/trithorax response elements in drosophila species. PLoS Biol 6: e261.
44. Hegarty MJ, Barker GL, Brennan AC, Edwards KJ, Abbott RJ, Hiscock SJ (2008). Changes to gene expression associated with hybrid speciation in plants: further insights from transcriptomic studies in Senecio. Phil Trans R Soc Lond B 363: 3055-3069.
45. Hemberger M, Dean W, Reik W (2009). Epigenetic dynamics of stem cells and cell lineage commitment: digging Waddington's canal. Nat Rev Mol Cell Biol 10: 526.
46. Husband BC, Sabara HA (2004). Reproductive isolation between autotetraploids and their diploid progenitors in fireweed, Chamerion angustifolium (Onagraceae). New Phytologist 161: 703-713.
47. Johannes F, Porcher E, Teixeira FK, Saliba-Colombani V, Simon M, Agier N et al. (2009). Assessing the impact of transgenerational epigenetic variation on complex traits. PLoS Gen 5: e1000530.
48. Johnson LJ (2007). The genome strikes back: the evolutionary importance of defence against mobile elements. Evol Biol 34: 121-129.
49. Kadota M, Yang HH, Hu N, Wang C, Hu Y, Taylor PR et al. (2007). Allele-specific chromatin immunoprecipitation studies show genetic influence on chromatin state in human genome. PLoS Gen 3: e81.
50. Ledford H (2008). Population genomics for fruitflies. Nature 453: 1154-1155.
51. Leitch AR, Leitch IJ (2008). Genomic plasticity and the diversity of polyploid plants. Science 320: 481-483.
52. Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J et al. (2009). Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462: 315-322.
53. Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA et al. (2009). Population genomics of domestic and wild yeasts. Nature 458: 337-341.
54. Liu Z, Adams KL (2007). Expression partitioning between genes duplicated by polyploidy under abiotic stress and during organ development. Curr Biol 17: 1669-1674.
55. Madlung A, Comai L (2004). The effect of stress on genome regulation and structure. Ann Bot 94: 481-495.
56. Makarevitch I, Stupar RM, Iniguez AL, Haun WJ, Barbazuk WB, Kaeppler SM et al. (2007). Natural variation for alleles under epigenetic control by the maize chromomethylase Zmet2. Genetics 177: 749-760.
57. Marhold J, Rothe N, Mund C, Kuehle K, Brueckner B, Lyko F (2004). Conservation of DNA methylation in dipteran insects. Insect Mol Biol 13: 117-123.
58. Martin A, Troadec C, Boualem A, Rajab M, Fernandez R, Morin H et al. (2009). A transposon-induced epigenetic change leads to sex determination in melon. Nature 461: 1135-1139.
59. Masel J, Bergman A (2003). The evolution of the evolvability properties of the yeast prion [PSI+]. Evolution 57: 1498-1512.
60. McClintock B (1951). Chromosome organization and genic expression. Cold spring harbor symp. Quant Biol 16: 13-47.
61. Meyerowitz EM (2002). Plants compared to animals: the broadest comparative study of development. Science 295: 1482-1485.
62. Michalak P (2008). Epigenetic, transposon and small RNA determinants of hybrid dysfunctions. Heredity 102: 45-50.
63. Mitchell A, Romano GH, Groisman B, Yona A, Dekel E, Kupiec M et al. (2009). Adaptive prediction of environmental changes by microorganisms. Nature 460: 220-224.
64. Modrich P (1989). Methyl-directed DNA mismatch correction. J Biol Chem 264: 6597-6600.
65. Molinier J, Ries G, Zipfel C, Hohn B (2006). Transgeneration memory of stress in plants. Nature 442: 1046-1049.
66. Ni Z, Kim E-D, Ha M, Lackey E, Liu J, Zhang Y et al. (2009). Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids. Nature 457: 327-331.
67. Pagel M, Venditti C, Meade A (2006). Large punctuational contribution of speciation to evolutionary divergence at the molecular level. Science 314: 119-121.
68. Pal C (1998). Plasticity, memory and the adaptive landscape of the genotype. Proc R Soc Lond Ser B-Biol Sci 265: 1319-1323.
69. Parkinson SE, Gross SM, Hollick JB (2007). Maize sex determination and abaxial leaf fates are canalized by a factor that maintains repressed epigenetic states. Dev Biol 308: 462-473.
70. Partridge L, Barton NH (2000). Evolving evolvability. Nature 407: 457-458.
71. Pennington PD, Costa LM, Gutierrez-Marcos JF, Greenland AJ, Dickinson HG (2008). When genomes collide: aberrant seed development following maize interploidy crosses. Ann Bot 101: 833-843.
72. Pigliucci M, Murren CJ, Schlichtling CD (2006). Phenotypic plasticity and evolution by genetic assimilation. J Exp Biol 209: 2362-2367.
73. Price TD, Qvarnstrom A, Irwin DE (2003). The role of phenotypic plasticity in driving genetic evolution. Proc R Soc Lond Ser B-Biol Sci 270: 1433-1440.
74. Rando OJ, Verstrepen KJ (2007). Timescales of genetic and epigenetic inheritance. Cell 128: 655-668.
75. Rangwala SH, Elumalai R, Vanier C, Ozkan H, Galbraith D, Richards EJ (2006). meiotically stable natural epialleles of sadhu, a novel Arabidopsis retroposon. PLoS Gen 2: e36.
76. Rangwala SH, Richards EJ (2007). Differential epigenetic regulation within an Arabidopsis retroposon family. Genetics 176: 151-160.
77. Reinders J, Wulff BBH, Mirouze M, Marí-Ordóñez A, Dapp Ml, Rozhon W et al. (2009). Compromised stability of DNA methylation and transposon immobilization in mosaic Arabidopsis epigenomes. Genes Dev 23: 939-950.
78. Richards EJ (2008). Population epigenetics. Curr Opinion Gen Develop 18: 221-226.
79. Richards EJ (2009). Quantitative epigenetics: DNA sequence variation need not apply. Genes Dev 23: 1601-1605.
80. Riddle N, Richards EJ (2002). The control of natural variation in cytosine methylation in Arabidopsis. Genetics 162: 355-363.
81. Rutherford SL, Lindquist S (1998). Hsp90 as a capacitor for morphological evolution. Nature 396: 336-342.
82. Selker EU (1990). Premeiotic instability of repeated sequences in Neurospora crassa. Annu Rev Genet 24: 579-613.
83. Sniegowski PD, Gerrish PJ, Johnson T, Shaver A (2000). The evolution of mutation rates: separating causes from consequences. Bioessays 22: 1057-1066.
84. Sollars V, Lu X, Xiao L, Wang X, Garfinkel MD, Ruden DM (2003). Evidence for an epigenetic mechanism by which Hsp90 acts as a capacitor for morphological evolution. Nat Genet 33: 70-74.
85. Specchia V, Piacentini L, Tritto P, Fanti L, D'Alessandro R, Palumbo G et al. (2010). Hsp90 prevents phenotypic variation by suppressing the mutagenic activity of transposons. Nature 463: 662-665.
86. Suzuki S, Ono R, Narita T, Pask AJ, Shaw G, Wang C et al. (2007). Retrotransposon silencing by DNA methylation can drive mammalian genomic imprinting. PLoS Genet 3: e55.
87. Tsai IJ, Bensasson D, Burt A, Koufopanou V (2008). Population genomics of the wild yeast Saccharomyces paradoxus: quantifying the life cycle. Proc Natl Acad Sci USA 105: 4957-4962.
88. Vaughn MW, Tanurd Ic M, Lippman Z, Jiang H, Carrasquillo R, Rabinowicz PD et al. (2007). Epigenetic natural variation in Arabidopsis thaliana. PLoS Biol 5: e174.
89. Vieira C, Fablet M, Lerat E (2009). Infra- and transspecific clues to understanding the dynamics of transposable elements. Genome Dynamics Stability 4: 21-430.
90. Wade CM, Kulbokas EJ, Kirby AW, Zody MC, Mullikin JC, Lander ES et al. (2002). The mosaic structure of variation in the laboratory mouse genome. Nature 420: 574-578.
91. Walbot V (2009). 10 reasons to be tantalized by the B73 maize genome. PLoS Genet 5: e1000723.
92. Wang R-L, Stec A, Hey J, Lukens L, Doebley J (1999). The limits of selection during maize domestication. Nature 398: 236-239.
93. Whitlock MC (1996). The red queen beats the jack-of-all-trades: the limitations on the evolution of phenotypic plasticity and niche breadth. Am Nat 148: S65-S77.
94. Wolf JB, Frankino WA, Agrawal AF, Brodie III ED, Moore AJ (2009). Developmental interactions and the constituents of quantitative variation. Evolution 55: 232-245.
95. Zeh DW, Zeh JA, Ishida Y (2009). Transposable elements and an epigenetic basis for punctuated equilibria. Bioessays 31: 715-726.
96. Zhai J, Liu J, Liu B, Li P, Meyers BC, Chen X et al. (2008). Small RNA-directed epigenetic natural variation in Arabidopsis thaliana. PLoS Genet 4: e1000056.
97. Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW, Chen H et al. (2006). Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 1126: 1189-1201.
98. Zingg J-M, Jones PA (1997). Genetic and epigenetic aspects of DNA methylation on genome expression, evolution, mutation and carcinogenesis. Carcinogenesis 18: 869-882.