Epigenetic inheritance and its role in evolutionary biology: Re-evaluation and new perspectives

Biology

Volumn 5, Issue 2, 2016, Pages

  Burggren, Warren ^a  

^a UNIVERSITY OF NORTH TEXAS   (United States)

Author keywords

Climate change; Dynamics; Ecology; Epigenetics; Evolution; Inheritance; Natural selection

Indexed keywords

EID: 84974577007     PISSN: None     EISSN: 20797737     Source Type: Journal    
DOI: 10.3390/biology5020024     Document Type: Article

References (156)

1. Waddington, C.H. The epigenotype. Endeavour 1942, 1, 18-20. [CrossRef] [PubMed]
2. Burggren, W.W, Crews, D. Epigenetics in comparative biology: Why we should pay attention. Integr. Comp. Biol. 2014, 54, 7-20. [CrossRef] [PubMed]
3. Nilsson, E.E, Skinner, M.K. Environmentally induced epigenetic transgenerational inheritance of reproductive disease. Biol. Reprod. 2015, 93. [CrossRef] [PubMed]
4. Skinner, M.K, Guerrero-Bosagna, C, Haque, M.M. Environmentally induced epigenetic transgenerational inheritance of sperm epimutations promote genetic mutations. Epigenetics 2015, 10, 762-771. [CrossRef] [PubMed]
5. Skinner, M.K. Role of epigenetics in developmental biology and transgenerational inheritance. Birth. Defects. Res. C. Embryo Today 2011, 93, 51-55. [CrossRef] [PubMed]
6. Skinner, M.K. Environmental Epigenetics and a Unified Theory of the Molecular Aspects of Evolution: A Neo-Lamarckian Concept that Facilitates Neo-Darwinian Evolution. Genome Biol. Evol. 2015, 7, 1296-1302. [CrossRef] [PubMed]
7. Ho, D.H, Burggren, W.W. Epigenetics and transgenerational transfer: A physiological perspective. J. Exp. Biol. 2010, 213, 3-16. [CrossRef] [PubMed]
8. Crews, D, Gillette, R, Miller-Crews, I, Gore, A.C, Skinner, M.K. Nature, nurture and epigenetics. Mol. Cell. Endocrinol. 2014, 398, 42-52. [CrossRef] [PubMed]
9. Relton, L.R, Smith, G.D. Is epidemiology ready for epigenetics? Int. J. Epidemiol. 2012, 41, 5-9. [CrossRef] [PubMed]
10. Gonzalez-Recio, O, Toro, M.A, Bach, A. Past, present, and future of epigenetics applied to livestock breeding. Front. Genet. 2015, 6. [CrossRef] [PubMed]
11. Deans, C, Maggert, K.A. What do you mean, "epigenetic"? Genetics 2015, 199, 887-896. [CrossRef] [PubMed]
12. Mann, J.R. Epigenetics and memigenetics. Cell Mol. Life Sci. 2014, 71, 1117-1122. [CrossRef] [PubMed]
13. Tammen, S.A, Friso, S, Choi, S.W. Epigenetics: The link between nature and nurture. Mol. Aspects Med. 2013, 34, 753-764. [CrossRef] [PubMed]
14. Dupont, C, Armant, D.R, Brenner, C.A. Epigenetics: Definition, mechanisms and clinical perspective. Semin. Reprod. Med. 2009, 27, 351-357.
15. Guerrero-Bosagna, C.M, Skinner, M.K. Epigenetic transgenerational effects of endocrine disruptors on male reproduction. Semin. Reprod. Med. 2009, 27, 403-408. [CrossRef] [PubMed]
16. Verhoeven, K.J, von Holdt, B.M, Sork, V.L. Epigenetics in ecology and evolution: What we know and what we need to know. Mol. Ecol. 2016. [CrossRef]
17. Martos, S.N, Tang, W.Y, Wang, Z. Elusive inheritance: Transgenerational effects and epigenetic inheritance in human environmental disease. Prog. Biophys. Mol. Biol. 2015, 118, 44-54. [CrossRef] [PubMed]
18. Gissis, S, Jablonka, E. Trarnsformations of Lamarckism; MIT Press: Cambridge, MA, USA, 2011; pp. 1-457.
19. Bateson, P. The impact of the organism on its descendants. Genet. Res. Int. 2012. [CrossRef] [PubMed]
20. Popper, K. Objective Knowledge: An evolutionary approach; Oxford University Press: Oxford, UK, 1979.
21. Nelson, T.C, Groth, K.D, Sotherland, P.R. Maternal investment and nutrient use affect phenotype of American alligator and domestic chicken hatchlings. Comp. Biochem. Physiol. A. Mol. Integr. Physiol. 2010, 157, 19-27.
22. Reed, W.L, Clark, M.E. Beyond maternal effects in birds: Responses of the embryo to the environment. Integr. Comp. Biol. 2011, 51, 73-80. [CrossRef] [PubMed]
23. Ho, D.H. Transgenerational epigenetics: The role of maternal effects in cardiovascular development. Integr. Comp. Biol. 2014, 54, 43-51. [CrossRef] [PubMed]
24. Seemann, F, Peterson, D.R, Witten, P.E, Guo, B.S, Shanthanagouda, A.H, Ye, R.R, Zhang, G, Au, D.W. Insight into the transgenerational effect of benzo[a]pyrene on bone formation in a teleost fish (Oryzias latipes). Comp. Biochem. Physiol. C. Toxicol. Pharmacol. 2015, 178, 60-67. [CrossRef] [PubMed]
25. Clarke, H.J, Vieux, K.F. Epigenetic inheritance through the female germ-line: The known, the unknown, and the possible. Semin. Cell Dev. Biol. 2015, 43, 106-116. [CrossRef] [PubMed]
26. Jinha, A.E. Article 50 million: An estimate of the number of scholarly articles in existince. Learn. Publ. 2010, 23, 258-263. [CrossRef]
27. Prokopuk, L, Western, P.S, Stringer, J.M. Transgenerational epigenetic inheritance: Adaptation through the germline epigenome? Epigenomics 2015, 7, 829-846. [CrossRef] [PubMed]
28. Jimenez-Chillaron, J.C, Ramon-Krauel, M, Ribo, S, Diaz, R. Transgenerational epigenetic inheritance of diabetes risk as a consequence of early nutritional imbalances. Proc. Nutr. Soc. 2016, 75, 78-89. [CrossRef] [PubMed]
29. Not all would agree with these taxonomic choices of search terms, but, again, the purpose of this meta-analysis is to determine relative frequencies and patterns of various taxa in epigenetic studies, not to provide a comprehensive quantitative analysis.
30. Ronsseray, S. Paramutation phenomena in non-vertebrate animals. Semin. Cell Dev. Biol. 2015, 44, 39-46. [CrossRef] [PubMed]
31. Andrewartha, S.J, Burggren, W.W. Transgenerational variation in metabolism and life-history traits induced by maternal hypoxia in Daphnia magna. Physiol. Biochem. Zool. 2012, 85, 625-634. [CrossRef] [PubMed]
32. Mukherjee, K, Twyman, R.M, Vilcinskas, A. Insects as models to study the epigenetic basis of disease. Prog. Biophys. Mol. Biol. 2015, 118, 69-78. [CrossRef] [PubMed]
33. Wei, Y, Schatten, H, Sun, Q.Y. Environmental epigenetic inheritance through gametes and implications for human reproduction. Hum. Reprod. Update 2015, 21, 194-208. [CrossRef] [PubMed]
34. Padilla, P.A, Garcia, A.M, Ladage, M.L, Toni, L.S. Caenorhabditis elegans: An old genetic model can learn new epigenetic tricks. Integr. Comp. Biol. 2014, 54, 52-60. [CrossRef] [PubMed]
35. Perfus-Barbeoch, L, Castagnone-Sereno, P, Reichelt, M, Fneich, S, Roquis, D, Pratx, L, Cosseau, C, Grunau, C, Abad, P. Elucidating the molecular bases of epigenetic inheritance in non-model invertebrates: The case of the root-knot nematode Meloidogyne incognita. Front. Physiol. 2014, 5. [CrossRef] [PubMed]
36. Iglesias, S, Thompson, M.B, Seebacher, F. Energetic cost of a meal in a frequent feeding lizard. Comp. Biochem. Physiol. 2003, 135, 377-382. [CrossRef]
37. Iglesias, F.M, Cerdan, P.D. Maintaining Epigenetic Inheritance During DNA Replication in Plants. Front. Plant Sci. 2016, 7. [CrossRef] [PubMed]
38. Guo, S, Sun, B, Looi, L, Xu, Y, Gan, E.S, Huang, J, Ito, T. Co-ordination of Flower Development Through Epigenetic Regulation in Two Model Species: Rice and Arabidopsis. Plant Cell Physiol. 2015, 56, 830-842. [CrossRef] [PubMed]
39. Jobson, M.A, Jordan, J.M, Sandrof, M.A, Hibshman, J.D, Lennox, A.L, Baugh, L.R. Transgenerational Effects of Early Life Starvation on Growth, Reproduction, and Stress Resistance in Caenorhabditis elegans. Genetics 2015, 201, 201-212. [CrossRef] [PubMed]
40. Burggren, W.W. Epigenetics as a source of variation in comparative animal physiology—or—Lamarck is lookin’ pretty good these days. J. Exp. Biol. 2014, 217, 682-689. [CrossRef] [PubMed]
41. Burggren, W.W. Dynamics of epigenetic phenomena: Intergenerational and intragenerational phenotype 'washout'. J. Exp. Biol. 2015, 218, 80-87. [CrossRef] [PubMed]
42. Corrales, J, Thornton, C, White, M, Willett, K.L. Multigenerational effects of benzo[a]pyrene exposure on survival and developmental deformities in zebrafish larvae. Aquat. Toxicol. 2014, 148, 16-26. [CrossRef] [PubMed]
43. Saab, B.J, Mansuy, I.M. Neurobiological disease etiology and inheritance: An epigenetic perspective. J. Exp. Biol. 2014, 217, 94-101. [CrossRef] [PubMed]
44. Vaiserman, A.M. Epigenetic engineering and its possible role in anti-aging intervention. Rejuvenation Res. 2008, 11, 39-42. [CrossRef] [PubMed]
45. Felling, R.J, Song, H. Epigenetic mechanisms of neuroplasticity and the implications for stroke recovery. Exp. Neurol. 2015, 268, 37-45. [CrossRef] [PubMed]
46. Goddard, M.E, Whitelaw, E. The use of epigenetic phenomena for the improvement of sheep and cattle. Front Genet. 2014, 5. [CrossRef] [PubMed]
47. Bilichak, A, Kovalchuk, I. Transgenerational response to stress in plants and its application for breeding. J. Exp. Bot. 2016, 67, 2081-2092. [CrossRef] [PubMed]
48. López-Arredondo, D, González-Morales, S.I, Bello-Bello, E, Alejo-Jacuinde, G, Herrera, L. Engineering food crops to grow in harsh environments. F1000Res. 2015, 4. [CrossRef] [PubMed]
49. Wu, Y, Sun, Y, Shen, K, Sun, S, Wang, J, Jiang, T, Cao, S, Josiah, S.M, Pang, J, Lin, X, et al. Immediate Genetic and Epigenetic Changes in F1 Hybrids Parented by Species with Divergent Genomes in the Rice Genus (Oryza). PLoS ONE 2015, 10, e0132911. [CrossRef] [PubMed]
50. Springer, N.M, McGinnis, K.M. Paramutation in evolution, population genetics and breeding. Semin. Cell Dev. Biol. 2015, 44, 33-38. [CrossRef] [PubMed]
51. Martinez Bautista, N, Burggren, W.W, University of North Texas, Denton, TX, USA. Unpublished data. 2016.
52. Rando, O.J, Verstrepen, K.J. Timescales of genetic and epigenetic inheritance. Cell 2007, 128, 655-668. [CrossRef] [PubMed]
53. Klironomos, F.D, Berg, J, Collins, S. How epigenetic mutations can affect genetic evolution: Model and mechanism. Bioessays 2013, 35, 571-578. [CrossRef] [PubMed]
54. Smith, T.A, Martin, M.D, Nguyen, M, Mendelson, T.C. Epigenetic divergence as a potential first step in darter speciation. Mol. Ecol. 2016, 25, 1883-1894. [CrossRef] [PubMed]
55. Herrera, C.M, Medrano, M, Bazaga, P. Comparative spatial genetics and epigenetics of plant populations: Heuristic value and a proof of concept. Mol. Ecol. 2016, 25, 1653-1664. [CrossRef] [PubMed]
56. Flatscher, R, Frajman, B, Schönswetter, P, Paun, O. Environmental heterogeneity and phenotypic divergence: Can heritable epigenetic variation aid speciation? Genet. Res. Int. 2012, 2012. [CrossRef] [PubMed]
57. Eichten, S.R, Briskine, R, Song, J, Li, Q, Swanson-Wagner, R, Hermanson, P.J, Waters, A.J, Starr, E, West, P.T, Tiffin, F, et al. Epigenetic and genetic influences on DNA methylation variation in maize populations. Plant Cell 2013, 25, 2783-2797. [CrossRef] [PubMed]
58. Vastenhouw, N.L, Brunschwig, K, Okihara, K.L, Müller, F, Tijsterman, M, Plasterk, R.H. Gene expression: Long-term gene silencing by RNAi. Nature 2006, 442. [CrossRef] [PubMed]
59. Cubas, P, Vincent, C, Coen, E. An epigenetic mutation responsible for natural variation in floral symmetry. Nature 1999, 401, 157-161. [PubMed]
60. Richards, C.L, Bossdorf, O, Pigliucci, M. What role does heritable epigenetic variation play in phenotypic evolution? BioScience 2010, 60, 232-237. [CrossRef]
61. Hartl, D.L, Clark, A.G. Principles of Population Genetics; Sinauer Associates: Sunderland, MA, USA, 2007.
62. Dubin, M.J, Zhang, P, Meng, D, Remigereau, M.S, Osborne, E.J, Paolo, C.F, Drewe, P, Kahles, A, Jean, G, Vilhjálmsson, B, et al. DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation. Elife 2015, 4, e05255. [CrossRef] [PubMed]
63. Gutierrez-Arcelus, M, Lappalainen, T, Montgomery, S.B, Buil, A, Ongen, H, Yurovsky, A, Bryois, J, Giger, T, Romano, L, Planchon, A, et al. Passive and active DNA methylation and the interplay with genetic variation in gene regulation. Elife 2013, 2, e00523. [PubMed]
64. Schmitz, R.J, Schultz, M.D, Urich, M.A, Nery, J.R, Pelizzola, M, Libiger, O, Alix, A, McCosh, R.B, Chen, H, Schork, N.J, et al. Patterns of population epigenomic diversity. Nature 2013, 495, 193-198. [CrossRef] [PubMed]
65. Brandvain, Y, Wright, S.I. The Limits of Natural Selection in a Nonequilibrium World. Trends Genet. 2016, 32, 201-210. [CrossRef] [PubMed]
66. Taute, K.M, Gude, S, Nghe, P, Tans, S.J. Evolutionary constraints in variable environments, from proteins to networks. Trends Genet. 2014, 30, 192-198. [CrossRef] [PubMed]
67. Bell, G. Fluctuating selection: The perpetual renewal of adaptation in variable environments. Philos. Trans. R. Soc. Lond. B. 2010, 365, 87-97. [CrossRef] [PubMed]
68. 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, 1283-1295. [CrossRef] [PubMed]
69. Bonduriansky, R, Crean, A.J, Day, T. The implications of nongenetic inheritance for evolution in changing environments. Evol. Appl. 2012, 5, 192-201. [CrossRef] [PubMed]
70. Dolinoy, D.C, Huang, D, Jirtle, R.L. Maternal nutrient supplementation counteracts bisphenol A-induced DNA hypomethylation in early development. Proc. Natl. Acad. Sci. USA 2007, 104, 13056-13061. [CrossRef] [PubMed]
71. Gao, L, Geng, Y, Li, B, Chen, J, Yang, J. Genome-wide DNA methylation alterations of Alternanthera philoxeroides in natural and manipulated habitats: Implications for epigenetic regulation of rapid responses to environmental fluctuation and phenotypic variation. Plant Cell Environ. 2010, 33, 1820-1827. [CrossRef] [PubMed]
72. Soubry, A. Epigenetic inheritance and evolution: A paternal perspective on dietary influences. Prog. Biophys. Mol. Biol. 2015, 118, 79-85. [CrossRef] [PubMed]
73. Jablonka, E. Epigenetic inheritance and plasticity: The responsive germline. Prog. Biophys. Mol. Biol. 2013, 111, 99-107. [CrossRef] [PubMed]
74. Badyaev, A.V. Epigenetic resolution of the 'curse of complexity' in adaptive evolution of complex traits. J. Physiol. 2014, 592, 2251-2260. [CrossRef] [PubMed]
75. Roux, F, Colomé-Tatché, M, Edelist, C, Wardenaar, R, Guerche, P, Hospital, F, Colot, V, Jansen, R.C, Johannes, F. Genome-wide epigenetic perturbation jump-starts patterns of heritable variation found in nature. Genetics 2011, 188, 1015-1017. [CrossRef] [PubMed]
76. De Vos, M.G, Poelwijk, F.J, Battich, N, Ndika, J.D, Tans, S.J. Environmental dependence of genetic constraint. PLoS Genet. 2013, 9, e1003580. [PubMed]
77. Ho, D.H, Burggren,W.W. Parental hypoxic exposure confers offspring hypoxia resistance in zebrafish (Danio rerio). J. Exp. Biol. 2012, 215, 4208-4216. [CrossRef] [PubMed]
78. Schrey, A.W, Richards, C.L. Within-genotype epigenetic variation enables broad niche width in a flower living yeast. Mol. Ecol. 2012, 21, 2559-2561. [CrossRef] [PubMed]
79. Herrera, C.M, Pozo, M.I, 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, 2602-2616. [CrossRef] [PubMed]
80. Preite, V, Snoek, L.B, Oplaat, C, Biere, A, van der Putten, W.H, Verhoeven, K.J.F. The epigenetic footprint of poleward range-expanding plants in apomictic dandelions. Mol. Ecol. 2015, 24, 4406-4418. [CrossRef] [PubMed]
81. Kilvitis, H.J, Alvarez, M, Foust, C.M, Schrey, A.W, Robertson, M, Richards, C.L. Ecological epigenetics. Adv. Exp. Med. Biol. 2014, 781, 191-210. [PubMed]
82. Robertson, M, Richards, C. Opportunities and challenges of next-generation sequencing applications in ecological epigenetics. Mol. Ecol. 2015, 24, 3799-3801. [CrossRef] [PubMed]
83. Richards, E.J. Population epigenetics. Curr. Opin. Genet. Dev. 2008, 18, 221-226. [CrossRef] [PubMed]
84. Bossdorf, O, Richards, C.L, Pigliucci, M. Epigenetics for ecologists. Ecol. Lett. 2008, 11, 106-115. [CrossRef] [PubMed]
85. Kaiser, J. The epigenetics heretic. Science 2014, 343, 361-363. [CrossRef] [PubMed]
86. Heard, E, Martienssen, R.A. Transgenerational epigenetic inheritance: myths and mechanisms. Cell 2014, 157, 95-109. [CrossRef] [PubMed]
87. Jablonka, E, Lamb, M.J, Zeligowski, A. Evolution in Four Dimensions: Genetics, Epigenetic, Behavioral, and Symbolic Variation in the History of Life; MIT Press: Cambridge, MA, USA, 2006; pp. 1-472.
88. Smith, G.D. Epidemiology, epigenetics and the 'Gloomy Prospect': Embracing randomness in population health research and practice. Int. J. Epidemiol. 2011, 40, 537-562. [CrossRef] [PubMed]
89. Weigel, D, Colot, V. Epialleles in plant evolution. Genome Biol. 2012, 13. [CrossRef] [PubMed]
90. Stotz, K. Extended evolutionary psychology: The importance of transgenerational developmental plasticity. Front. Psychol. 2014, 5. [CrossRef] [PubMed]
91. Dickins, T.E, Rahman, Q. The extended evolutionary synthesis and the role of soft inheritance in evolution. Proc. Biol. Sci. 2012, 279, 2913-2921. [CrossRef] [PubMed]
92. Danchin, E, Charmantier, A, Champagne, F.A, Mesoudi, A, Pujol, B, Blanchet, S. Beyond DNA: Integrating inclusive inheritance into an extended theory of evolution. Nat. Rev. Genet. 2011, 12, 475-486. [CrossRef] [PubMed]
93. Danchin, E, Pocheville, A. Inheritance is where physiology meets evolution. J. Physiol. 2014, 592, 2307-2317. [CrossRef] [PubMed]
94. Laland, K.N, Uller, T, Feldman, M.W, Sterelny, K, Müller, G.B, Moczek, A, Jablonka, E, John Odling-Smee, J. The extended evolutionary synthesis: Its structure, assumptions and predictions. Proc. Biol. Sci. 2015, 282. [CrossRef] [PubMed]
95. Boero, F. From Darwin's Origin of Species toward a theory of natural history. F1000Prime Rep. 2015, 7. [CrossRef] [PubMed]
96. Noble, D. Evolution beyond neo-Darwinism: A new conceptual framework. J. Exp. Biol. 2015. [CrossRef] [PubMed]
97. Tricker, P.J. Transgenerational inheritance or resetting of stress-induced epigenetic modifications: Two sides of the same coin. Front. Plant Sci. 2015, 6. [CrossRef] [PubMed]
98. Reznick, D. Hard and Soft Selection Revisited: How Evolution by Natural SelectionWorks in the Real World. J. Hered. 2016, 107, 3-14. [CrossRef] [PubMed]
99. Pigliucci, M. An extended synthesis for evolutionary biology. Ann. N. Y. Acad. Sci. 2009, 1168, 218-228. [CrossRef] [PubMed]
100. Holland, M.L, Rakyan, V.K. Transgenerational inheritance of non-genetically determined phenotypes. Biochem. Soc. Trans. 2013, 41, 769-776. [CrossRef] [PubMed]
101. Anava, S, Posner, R, Rechavi, O. The soft genome. Worm 2014, 3, e989798. [CrossRef] [PubMed]
102. Moya, C, Boyd, R, Henrich, J. Reasoning About Cultural and Genetic Transmission: Developmental and Cross-Cultural Evidence From Peru, Fiji, and the United States on How People Make Inferences About Trait Transmission. Top. Cogn. Sci. 2015, 7, 595-610. [CrossRef] [PubMed]
103. Torday, J.S. On the evolution of development. Trends Dev. Biol. 2014, 8, 17-37. [PubMed]
104. Laland, K, Uller, T, Feldman, M, Sterelny, K, Müller, G.B, Moczek, A, Jablonka, E, Odling-Smee, J, Wray, G.A, Hoekstra, H.E, et al. Does evolutionary theory need a rethink? Nature 2014, 514, 161-164. [CrossRef] [PubMed]
105. Day, T, Bonduriansky, R. A unified approach to the evolutionary consequences of genetic and nongenetic inheritance. Am. Nat. 2011, 178, E18-E36. [CrossRef] [PubMed]
106. Hauser, M.T, Aufsatz, W, Jonak, C, Luschnig, C. Transgenerational epigenetic inheritance in plants. Biochim. Biophys. Acta 2011, 1809, 459-468. [CrossRef] [PubMed]
107. Mendizabal, I, Keller, T.E, Zeng, J, Yi, S.V. Epigenetics and evolution. Integr. Comp. Biol. 2014, 54, 31-42. [CrossRef] [PubMed]
108. Gilbert, S. The decline of soft inheritance. In Transformations of Lamarckism; Gissis, S., Jablonka, E., Eds, MIT Press: Cambridge, MA, USA, 2011; pp. 121-126.
109. Wilkins, A. Why did the Modern Synthesis give short shrift to "Soft Inheritance"? In Transformations of Lamarckism; Gissis, S., Jablonka, E., Eds, MIT Press: Cambridge, MA, USA, 2011; pp. 127-132.
110. Katz, D.J, Edwards, T.M, Reinke, V, Kelly, W.G. A C. elegans LSD1 demethylase contributes to germline immortality by reprogramming epigenetic memory. Cell 2009, 137, 308-320. [CrossRef] [PubMed]
111. Rechavi, O, Houri-Ze’evi, L, Anava, S, Goh, W.S, Kerk, S.Y, Hannon, G.J, Hobert, O. Starvation-induced transgenerational inheritance of small RNAs in C. elegans. Cell 2014, 158, 277-287. [CrossRef] [PubMed]
112. Pilu, R. Paramutation phenomena in plants. Semin. Cell Dev. Biol. 2015, 44, 2-10. [CrossRef] [PubMed]
113. Borges, F, Martienssen, R.A. The expanding world of small RNAs in plants. Nat. Rev. Mol. Cell. Biol. 2015, 16, 727-741. [CrossRef] [PubMed]
114. Boffelli, D, Martin, D.I. Epigenetic inheritance: A contributor to species differentiation? DNA Cell Biol. 2012, 31, S11-S16. [CrossRef] [PubMed]
115. Brown, J.D, O'Neill, R.J. Chromosomes, conflict, and epigenetics: Chromosomal speciation revisited. Annu. Rev. Genomics Hum. Genet. 2010, 11, 291-316. [CrossRef] [PubMed]
116. Rebollo, R, Horard, B, Hubert, B, Vieira, C. Jumping genes and epigenetics: Towards new species. Gene 2010, 454, 1-7. [CrossRef] [PubMed]
117. Holliday, R. The inheritance of epigenetic defects. Science 1987, 238, 163-170. [CrossRef] [PubMed]
118. Bonduriansky, R, Day, T. Nongenetic inheritance and the evolution of costly female preference. J. Evol. Biol. 2013, 26, 76-87. [PubMed]
119. Rehan, V.K, Liu, J, Naeem, E, Tian, J, Sakurai, R, Kwong, K, Akbari, O, Torday, J.S. Perinatal nicotine exposure induces asthma in second generation offspring. BMC Med. 2012, 10. [CrossRef] [PubMed]
120. Schorderet, D.F, Gartler, S.M. Analysis of CpG suppression in methylated and nonmethylated species. Proc. Natl. Acad. Sci. USA 1992, 89, 957-961. [CrossRef] [PubMed]
121. Misawa, K, Kamatani, N, Kikuno, R.F. The universal trend of amino acid gain-loss is caused by CpG hypermutability. J. Mol. Evol. 2008, 67, 334-342. [CrossRef] [PubMed]
122. Mugal, C.F, Arndt, P.F, Holm, L, Ellegren, H. Evolutionary consequences of DNA methylation on the GC content in vertebrate genomes. G3 (Bethesda) 2015, 5, 441-447. [CrossRef] [PubMed]
123. Borstnik, B, Pumpernik, D. The apparent enhancement of CpG transversions in primate lineage is a consequence of multiple replacements. J. Bioinform. Comput. Biol. 2014, 12. [CrossRef] [PubMed]
124. Bird, A.P. DNA methylation and the frequency of CpG in animal DNA. Nucleic Acids Res. 1980, 8, 1499-1504.
125. Dubrovina, A.S, Kiselev, K.V. Age-associated alterations in the somatic mutation and DNA methylation levels in plants. Plant Biol. (Stuttg) 2016, 18, 185-196. [CrossRef] [PubMed]
126. Kumar, S, Kumari, R, Sharma, V, Sharma, V. Roles, and establishment, maintenance and erasing of the epigenetic cytosine methylation marks in plants. J. Genet. 2013, 92, 629-666. [CrossRef] [PubMed]
127. Cheng, D.T, Kim, D.K, Cockayne, D.A, Belousov, A, Bitter, H, Cho, M.H, Duvoix, A, Edwards, L.D, Lomas, D.A, Miller, B.E, et al. Systemic soluble receptor for advanced glycation endproducts is a biomarker of emphysema and associated with AGER genetic variants in patients with chronic obstructive pulmonary disease. Am. J. Respir. Crit. Care Med. 2013, 188, 948-957. [CrossRef] [PubMed]
128. Meng, H, Cao, Y, Qin, J, Song, X, Zhang, Q, Shi, Y, Cao, L. DNA methylation, its mediators and genome integrity. Int. J. Biol. Sci. 2015, 11, 604-617. [CrossRef] [PubMed]
129. Meng, H.X, Hackett, J.A, Nestor, C, Dunican, D.S, Madej, M, Reddington, J.P, Pennings, S, Harrison, D.J, Meehan, R.R. Apoptosis and DNA methylation. Cancers 2011, 3, 1798-1820. [CrossRef] [PubMed]
130. Putiri, E.L, Robertson, K.D. Epigenetic mechanisms and genome stability. Clin. Epigenetics 2011, 2, 299-314.
131. Zhao, N, Zhu, B, Li, M, Wang, L, Xu, L, Zhang, H, Zheng, S, Qi, B, Han, F, Liu, B. Extensive and heritable epigenetic remodeling and genetic stability accompany allohexaploidization of wheat. Genetics 2011, 188, 499-510. [CrossRef] [PubMed]
132. Zhang, Y.Y, Fischer, M, Colot, V, Bossdorf, O. Epigenetic variation creates potential for evolution of plant phenotypic plasticity. New Phytol. 2013, 197, 314-322. [CrossRef] [PubMed]
133. Sznajder, B, Sabelis, M.W, Egas, M. How Adaptive Learning Affects Evolution: Reviewing Theory on the Baldwin Effect. Evol. Biol. 2012, 39, 301-310. [CrossRef] [PubMed]
134. Liu, S, Sun, K, Jiang, T, Feng, J. Natural epigenetic variation in bats and its role in evolution. J. Exp. Biol. 2015, 218, 100-106. [CrossRef] [PubMed]
135. Tabansky, I, Stern, J.N, Pfaff, D.W. Implications of Epigenetic Variability within a Cell Population for "Cell Type" Classification. Front Behav. Neurosci. 2015, 9. [CrossRef] [PubMed]
136. Alonso, C, Pérez, R, Bazaga, P, Medrano, M, Herrera, C.M. Individual variation in size and fecundity is correlated with differences in global DNA cytosine methylation in the perennial herb Helleborus foetidus (Ranunculaceae). Am. J. Bot. 2014, 101, 1309-1313. [CrossRef] [PubMed]
137. Oey, H, Isbel, L, Hickey, P, Ebaid, B, Whitelaw, E. Genetic and epigenetic variation among inbred mouse littermates: Identification of inter-individual differentially methylated regions. Epigenetics Chromatin. 2015, 8. [CrossRef] [PubMed]
138. Lévesque, M.L, Casey, K.F, Szyf, M, Ismaylova, E, Ly, V, Verner, M.P, Suderman, M, Brendgen, M, Vitaro, F, Dionne, G, et al. Genome-wide DNA methylation variability in adolescent monozygotic twins followed since birth. Epigenetics 2014, 9, 1410-1421. [CrossRef] [PubMed]
139. Lemmers, R.J, Goeman, J.J, van der Vliet, P.J, van Nieuwenhuizen, M.P, Balog, J, Vos-Versteeg, M, Camano, P, Ramos Arroyo, M.A, Jerico, I, Rogers, M.T, et al. Inter-individual differences in CpG methylation at D4Z4 correlate with clinical variability in FSHD1 and FSHD2. Hum. Mol. Genet. 2015, 24, 659-669. [CrossRef] [PubMed]
140. Mathers, J.C. Session 2: Personalised nutrition. Epigenomics: A basis for understanding individual differences? Proc. Nutr. Soc. 2008, 67, 390-394. [CrossRef] [PubMed]
141. Stevens, J.B, Abdallah, B.Y, Horne, S.D, Liu, G, Bremer, S.W, Heng, H.H. Genetic and Epigenetic heterogeneity in Cancer; JohnWiley and Sons Ltd.: Chichester, UK, 2011.
142. Heyn, H, Moran, S, Hernando-Herraez, I, Sergi Sayols, S, Gomez, A, Sandoval, J, Monk, D, Hata, K, Marques-Bonet, T, Wang, L, et al. DNA methylation contributes to natural human variation. Genome Res. 2013, 23, 1363-1372. [CrossRef] [PubMed]
143. Whitelaw, N.C, Whitelaw, E. How lifetimes shape epigenotype within and across generations. Hum. Mol. Genet. 2006, 15, R131-R137. [CrossRef] [PubMed]
144. Johnson, L.J, Tricker, P.J. Epigenomic plasticity within populations: Its evolutionary significance and potential. Heredity (Edinb) 2010, 105, 113-121. [CrossRef] [PubMed]
145. Van der Graaf, A, Wardenaar, R, Neumann, D.A, Taudt, A, Shaw, R.G, Jansen, R.C, Schmitz, R.J, Colomé-Tatché, M, Johannes, F. Rate, spectrum, and evolutionary dynamics of spontaneous epimutations. Proc. Natl. Acad. Sci. USA 2015, 112, 6676-6681. [CrossRef] [PubMed]
146. Fawcett, T.W, Frankenhuis, W.E. Adaptive explanations for sensitive windows in development. Front Zool. 2015, 12. [CrossRef] [PubMed]
147. Carretero, A, Ditrich, H, Pérez-Aparicio, F.J, Splechtna, H, Ruberte, J. Development and degeneration of the arterial system in the mesonephros and metanephros of chicken embryos. Anat. Rec. 1995, 243, 120-128.
148. Kopp, M, Matuszewski, S. Rapid evolution of quantitative traits: Theoretical perspectives. Evol. Appl. 2014, 7, 169-191. [CrossRef] [PubMed]
149. Diaz, S.A, Viney, M. The evolution of plasticity of dauer larva developmental arrest in the nematode Caenorhabditis elegans. Ecol. Evol. 2015, 5, 1343-1353. [CrossRef] [PubMed]
150. Hirsch, S, Baumberger, R, Grossniklaus, U. Epigenetic variation, inheritance, and selection in plant populations. Cold Spring Harb. Symp. Quant. Biol. 2012, 77, 97-104. [CrossRef] [PubMed]
151. Hernando-Herraez, I, Garcia-Perez, R, Sharp, A.J, Marques-Bonet, T. DNA Methylation: Insights into Human Evolution. PLoS Genet. 2015, 11, e1005661. [CrossRef] [PubMed]
152. Zhong, X. Comparative epigenomics: A powerful tool to understand the evolution of DNA methylation. New Phytol. 2016, 210, 76-80. [CrossRef] [PubMed]
153. Kooke, R, Keurentjes, J.J. Epigenetic variation contributes to environmental adaptation of Arabidopsis thaliana. Plant Signal Behav. 2015, 10, e1057368. [CrossRef] [PubMed]
154. Bintu, L, Yong, J, Antebil, Y.E, McCue, K, Kazuki, Y, Uno, N, Oshimura, M, Elowitz, M.B. Dynamics of epigenetic regulation at the single-cell level. Science 2016, 351, 720-724. [CrossRef] [PubMed]
155. Massah, S, Beischlag, T.V, Prefontaine, G.G. Epigenetic events regulating monoallelic gene expression. Crit. Rev. Biochem. Mol. Biol. 2015, 50, 337-358. [CrossRef] [PubMed]
156. Vogt, G. Stochastic developmental variation, an epigenetic source of phenotypic diversity with far-reaching biological consequences. J. Biosci. 2015, 40, 159-204. [CrossRef] [PubMed]