References

Alonso, Conchita, Ricardo Pérez, Pilar Bazaga, and Carlos M. Herrera. 2015. “Global DNA Cytosine Methylation as an Evolving Trait: Phylogenetic Signal and Correlated Evolution with Genome Size in Angiosperms.” Frontiers in Genetics 6.

Audergon, Pauline N. C. B., Sandra Catania, Alexander Kagansky, Pin Tong, Manu Shukla, Alison L. Pidoux, and Robin C. Allshire. 2015. “Restricted Epigenetic Inheritance of H3K9 Methylation.” Science 348 (6230): 132–35.

Becker, Claude, Jörg Hagmann, Jonas Müller, Daniel Koenig, Oliver Stegle, Karsten Borgwardt, and Detlef Weigel. 2011. “Spontaneous Epigenetic Variation in the Arabidopsis Thaliana Methylome.” Nature 480 (7376): 245–49.

Bossdorf, Oliver, Christina Richards, and Massimo Pigliucci. 2008. “Epigenetics for Ecologists.” Ecology Letters 11 (2): 106–15.

Cambareri, E. B., B. C. Jensen, E. Schabtach, and E. U. Selker. 1989. “Repeat-Induced G-C to A-T Mutations in Neurospora.” Science 244 (4912): 1571–75.

Castonguay, Emilie, and Bernard Angers. 2012. “The Key Role of Epigenetics in the Persistence of Asexual Lineages.” Research article. Genetics Research International. 2012.

Cortijo, Sandra, René Wardenaar, Maria Colomé-Tatché, Arthur Gilly, Mathilde Etcheverry, Karine Labadie, Erwann Caillieux, et al. 2014. “Mapping the Epigenetic Basis of Complex Traits.” Science 343 (6175): 1145–48.

Cubas, Pilar, Coral Vincent, and Enrico Coen. 1999. “An Epigenetic Mutation Responsible for Natural Variation in Floral Symmetry.” Nature 401 (6749): 157–61.

Darwin, Charles. 1859. “On the Origin of Species, 1859.” Taylor & Francis. 1859. https://www.taylorfrancis.com/books/9781134439928.

Dickins, T. E., and R. A. Barton. 2013. “Reciprocal Causation and the Proximate–Ultimate Distinction.” Biology & Philosophy 28 (5): 747–56.

Dubin, Manu J, Pei Zhang, Dazhe Meng, Marie-Stanislas Remigereau, Edward J Osborne, Francesco Paolo Casale, Philipp Drewe, et al. 2015. “DNA Methylation in Arabidopsis Has a Genetic Basis and Shows Evidence of Local Adaptation.” ELife 4.

Fisher, R. A. 1919. The Correlation between Relatives on the Supposition of Mendelian Inheritance. Earth and Environmental Science Transactions of the Royal Society of Edinburgh. 1919; 52 (02): 399–433.

Flood, Pádraic J., Joost van Heerwaarden, Frank Becker, C. Bastiaan de Snoo, Jeremy Harbinson, and Mark G. M. Aarts. 2016. “Whole-Genome Hitchhiking on an Organelle Mutation.” Current Biology 26 (10): 1306–11.

Frankham, Richard. 1996. “Introduction to Quantitative Genetics (4th Edn): By Douglas S. Falconer and Trudy F.C. Mackay Longman, 1996. £24.99 Pbk (Xv and 464 Pages) ISBN 0582 24302 5.” Trends in Genetics 12 (7): 280.

Furci, Leonardo, Ritushree Jain, Joost Stassen, Oliver Berkowitz, James Whelan, David Roquis, Victoire Baillet, Vincent Colot, Frank Johannes, and Jurriaan Ton. 2019. “Identification and Characterisation of Hypomethylated DNA Loci Controlling Quantitative Resistance in Arabidopsis.” Edited by Daniel J Kliebenstein and Christian S Hardtke. ELife 8 (January): e40655.

Futuyma, Douglas J. 1998. “Evolutionary Biology. Sunderland.” Mass.: Sinauer Associates. 2017. “Evolutionary Biology Today and the Call for an Extended Synthesis.” Interface Focus 7 (5): 20160145.

Gao, Dongying, Jinfeng Chen, Mingsheng Chen, Blake C. Meyers, and Scott Jackson. 2012. “A Highly Conserved, Small LTR Retrotransposon That Preferentially Targets Genes in Grass Genomes.” PLOS ONE 7 (2): e32010.

Gáspár, Bence, Oliver Bossdorf, and Walter Durka. 2018. “Structure, Stability and Ecological Significance of Natural Epigenetic Variation: A Large-Scale Survey in Plantago Lanceolata.” New Phytologist 0 (0).

Gugger, Paul F., Sorel Fitz‐Gibbon, Matteo Pellegrini, and Victoria L. Sork. 2016. “Species-Wide Patterns of DNA Methylation Variation in Quercus Lobata and Their Association with Climate Gradients.” Molecular Ecology 25 (8): 1665–80.

Haig, David. 2007. “Weismann Rules! OK? Epigenetics and the Lamarckian Temptation.” Biology & Philosophy 22 (3): 415–28.

Heer, Katrin, Kristian K. Ullrich, Manuel Hiss, Sascha Liepelt, Ralf Schulze Brüning, Jiabin Zhou, Lars Opgenoorth, and Stefan A. Rensing. 2018. “Detection of Somatic Epigenetic Variation in Norway Spruce via Targeted Bisulfite Sequencing.” Ecology and Evolution 8 (19): 9672–82.

Herrera, Carlos M., and Pilar Bazaga. 2013. “Epigenetic Correlates of Plant Phenotypic Plasticity: DNA Methylation Differs between Prickly and Nonprickly Leaves in Heterophyllous Ilex Aquifolium (Aquifoliaceae) Trees.” Botanical Journal of the Linnean Society 171 (3): 441–52.

Huxley, Julian Sorell. 1943. “Evolution, the Modern Synthesis.” London Georg Allen Unwin.

Ingouff, Mathieu, Svenja Rademacher, Sarah Holec, Lucija Šoljić, Nie Xin, Anne Readshaw, Shi Hui Foo, Benoît Lahouze, Stefanie Sprunck, and Frédéric Berger. 2010. “Zygotic Resetting of the HISTONE 3 Variant Repertoire Participates in Epigenetic Reprogramming in Arabidopsis.” Current Biology 20 (23): 2137–43.

Johannes, Frank, Emmanuelle Porcher, Felipe K. Teixeira, Vera Saliba-Colombani, Matthieu Simon, Nicolas Agier, Agnès Bulski, et al. 2009. “Assessing the Impact of Transgenerational Epigenetic Variation on Complex Traits.” PLOS Genetics 5 (6): e1000530.

Johannes, Frank, and Robert J. Schmitz. 2018. “Spontaneous Epimutations in Plants.” New Phytologist, September.

Kalisz, Susan, and Michael D. Purugganan. 2004. “Epialleles via DNA Methylation: Consequences for Plant Evolution.” Trends in Ecology & Evolution 19 (6): 309–14.

Kawakatsu, Taiji, Shao-shan Carol Huang, Florian Jupe, Eriko Sasaki, Robert J. Schmitz, Mark A. Urich, Rosa Castanon, et al. 2016. “Epigenomic Diversity in a Global Collection of Arabidopsis Thaliana Accessions.” Cell 166 (2): 492–505.

Kinoshita, Tetsu, and Motoaki Seki. 2014. “Epigenetic Memory for Stress Response and Adaptation in Plants.” Plant and Cell Physiology 55 (11): 1859–63.

Koo, Dal-Hoe, William T. Molin, Christopher A. Saski, Jiming Jiang, Karthik Putta, Mithila Jugulam, Bernd Friebe, and Bikram S. Gill. 2018. “Extrachromosomal Circular DNA-Based Amplification and Transmission of Herbicide Resistance in Crop Weed Amaranthus Palmeri.” Proceedings of the National Academy of Sciences 115 (13): 3332–37.

Kooke, Rik, Frank Johannes, René Wardenaar, Frank Becker, Mathilde Etcheverry, Vincent Colot, Dick Vreugdenhil, and Joost J. B. Keurentjes. 2015. “Epigenetic Basis of Morphological Variation and Phenotypic Plasticity in Arabidopsis Thaliana.” The Plant Cell, February, tpc.114.133025.

Laland, Kevin N., Tobias Uller, Marcus W. Feldman, Kim Sterelny, Gerd B. Müller, Armin Moczek, Eva Jablonka, and John Odling-Smee. 2015. “The Extended Evolutionary Synthesis: Its Structure, Assumptions and Predictions.” Proc. R. Soc. B 282 (1813): 20151019.

Lämke, Jörn, and Isabel Bäurle. 2017. “Epigenetic and Chromatin-Based Mechanisms in Environmental Stress Adaptation and Stress Memory in Plants.” Genome Biology 18 (1): 124.

Law, Julie A., and Steven E. Jacobsen. 2010. “Establishing, Maintaining and Modifying DNA Methylation Patterns in Plants and Animals.” Nature Reviews Genetics 11 (3): 204–20.

Lira-Medeiros, Catarina Fonseca, Christian Parisod, Ricardo Avancini Fernandes, Camila Souza Mata, Monica Aires Cardoso, and Paulo Cavalcanti Gomes Ferreira. 2010. “Epigenetic Variation in Mangrove Plants Occurring in Contrasting Natural Environment.” PLOS ONE 5 (4): e10326.

Manning, Kenneth, Mahmut Tör, Mervin Poole, Yiguo Hong, Andrew J. Thompson, Graham J. King, James J. Giovannoni, and Graham B. Seymour. 2006. “A Naturally Occurring Epigenetic Mutation in a Gene Encoding an SBP-Box Transcription Factor Inhibits Tomato Fruit Ripening.” Nature Genetics 38 (8): 948–52.

Martin, Antoine, Christelle Troadec, Adnane Boualem, Mazen Rajab, Ronan Fernandez, Halima Morin, Michel Pitrat, Catherine Dogimont, and Abdelhafid Bendahmane. 2009. “A Transposon-Induced Epigenetic Change Leads to Sex Determination in Melon.” Nature 461 (7267): 1135–38.

Masel J (October 2011). "Genetic drift". Current Biology. Cell Press. 21 (20): R837–8.

Mendel, Gregor. 1865. “Versuche Über Pflanzen-Hybriden. Verhandlungen Des Naturforschenden Vereines in Brünn.,” no. 4: 3–47.

Mesoudi, Alex, Simon Blanchet, Anne Charmantier, Étienne Danchin, Laurel Fogarty, Eva Jablonka, Kevin N. Laland, et al. 2013. “Is Non-Genetic Inheritance Just a Proximate Mechanism? A Corroboration of the Extended Evolutionary Synthesis.” Biological Theory 7 (3): 189–95.

Mette, M.f., W. Aufsatz, J. van der Winden, M.a. Matzke, and A.j.m. Matzke. 2000. “Transcriptional Silencing and Promoter Methylation Triggered by Double-Stranded RNA.” The EMBO Journal 19 (19): 5194–5201.

Mittelsten Scheid, Ortrun, Karin Afsar, and Jerzy Paszkowski. 2003. “Formation of Stable Epialleles and Their Paramutation-like Interaction in Tetraploid Arabidopsis Thaliana.” Nature Genetics 34 (4): 450–54.

Müller, Gerd B. 2007. “Evo–Devo: Extending the Evolutionary Synthesis.” Nature Reviews Genetics 8 (12): 943–49.

Münzbergová, Zuzana, Vít Latzel, Maria Šurinová, and Věroslava Hadincová. 2019. “DNA Methylation as a Possible Mechanism Affecting Ability of Natural Populations to Adapt to Changing Climate.” Oikos 128 (1): 124–34.

Noshay, Jaclyn M., Sarah N. Anderson, Peng Zhou, Lexiang Ji, William Ricci, Zefu Lu, Michelle C. Stitzer, et al. 2019. “Monitoring the Interplay between Transposable Element Families and DNA Methylation in Maize.” PLOS Genetics 15 (9): e1008291.

Ong-Abdullah, Meilina, Jared M. Ordway, Nan Jiang, Siew-Eng Ooi, Sau-Yee Kok, Norashikin Sarpan, Nuraziyan Azimi, et al. 2015. “Loss of Karma Transposon Methylation Underlies the Mantled Somaclonal Variant of Oil Palm.” Nature 525 (7570): 533–37.

Pecinka, Ales, and Ortrun Mittelsten Scheid. 2012. “Stress-Induced Chromatin Changes: A Critical View on Their Heritability.” Plant and Cell Physiology 53 (5): 801–8.

Pfeifer, G. P. 2006. “Mutagenesis at Methylated CpG Sequences.” In DNA Methylation: Basic Mechanisms, edited by Walter Doerfler and Petra Böhm, 259–81. Current Topics in Microbiology and Immunology. Berlin, Heidelberg: Springer Berlin Heidelberg.

Pigliucci, Massimo. 2009. “An Extended Synthesis for Evolutionary Biology.” Annals of the New York Academy of Sciences 1168 (1): 218–28.

Pigliucci, Massimo, and Leonard Finkelman. 2014. “The Extended (Evolutionary) Synthesis Debate: Where Science Meets Philosophy.” BioScience 64 (6): 511–16.

Provine, W. B. 1978. “The Role of Mathematical Population Geneticists in the Evolutionary Synthesis of the 1930s and 1940s.” Studies in History of Biology 2: 167–92.

Rangwala, Sanjida H., Rangasamy Elumalai, Cheryl Vanier, Hakan Ozkan, David W. Galbraith, and Eric J. Richards. 2006. “Meiotically Stable Natural Epialleles of Sadhu, a Novel Arabidopsis Retroposon.” PLOS Genetics 2 (3): e36.

Richards, Christina L., Conchita Alonso, Claude Becker, Oliver Bossdorf, Etienne Bucher, Maria Colomé-Tatché, Walter Durka, et al. 2017. “Ecological Plant Epigenetics: Evidence from Model and Non-Model Species, and the Way Forward.” Ecology Letters 20 (12): 1576–90.

Richards, Eric J. 2006. “Inherited Epigenetic Variation — Revisiting Soft Inheritance.” Nature Reviews Genetics 7 (5): 395–401.

Riddle, Nicole C., and Eric J. Richards. 2002. “The Control of Natural Variation in Cytosine Methylation in Arabidopsis.” Genetics 162 (1): 355–63.

Secco, David, Chuang Wang, Huixia Shou, Matthew D Schultz, Serge Chiarenza, Laurent Nussaume, Joseph R Ecker, James Whelan, and Ryan Lister. 2015. “Stress Induced Gene Expression Drives Transient DNA Methylation Changes at Adjacent Repetitive Elements.” ELife 4.

Shindo, Chikako, Maria Jose Aranzana, Clare Lister, Catherine Baxter, Colin Nicholls, Magnus Nordborg, and Caroline Dean. 2005. “Role of FRIGIDA and FLOWERING LOCUS C in Determining Variation in Flowering Time of Arabidopsis.” Plant Physiology 138 (2): 1163–73.

Shindo, Chikako, Clare Lister, Pedro Crevillen, Magnus Nordborg, and Caroline Dean. 2006. “Variation in the Epigenetic Silencing of FLC Contributes to Natural Variation in Arabidopsis Vernalization Response.” Genes & Development 20 (22): 3079–83.

Smocovitis, Vassiliki Betty. 1997. “G. Ledyard Stebbins, Jr. and the Evolutionary Synthesis (1924–1950).” American Journal of Botany 84 (12): 1625–37.

Stebbins, C. L. 1950. “Variation and Evolution in Plants.” Variation and Evolution in Plants. https://www.cabdirect.org/cabdirect/abstract/19510302133.

Vanden Broeck, An, Karen Cox, Rein Brys, Stefano Castiglione, Angela Cicatelli, Francesco Guarino, Berthold Heinze, Marijke Steenackers, and Kristine Vander Mijnsbrugge. 2018. “Variability in DNA Methylation and Generational Plasticity in the Lombardy Poplar, a Single Genotype Worldwide Distributed Since the Eighteenth Century.” Frontiers in Plant Science 9.

Vaughn, Matthew W., Miloš Tanurdžić, Zachary Lippman, Hongmei Jiang, Robert Carrasquillo, Pablo D. Rabinowicz, Neilay Dedhia, et al. 2007. “Epigenetic Natural Variation in Arabidopsis Thaliana.” PLOS Biology 5 (7): e174.

Wallace, Alfred Russel. 1858. Contributions to the Theory of Natural Selection: A Series of Essays. 2nd ed. Cambridge: Cambridge University Press.

Whitelaw, Nadia C., and Emma Whitelaw. 2006. “How Lifetimes Shape Epigenotype within and across Generations.” Human Molecular Genetics 15 (suppl_2): R131–37.

Wilkins, Adam S. 2008. “Waddington’s Unfinished Critique of Neo-Darwinian Genetics: Then and Now.” Biological Theory 3 (3): 224–32.

Zhang, Jianmin, Zhen Yang, Pei Feng, Xiao Zhong, Qiqi Ma, Qi Su, Xiangping Wang, Chuanren Li, and Yazhen Yang. 2019. “Identification and the Potential Roles of Long Non-Coding RNAs in Cotton Leaves Damaged by Aphis Gossypii.” Plant Growth Regulation 88 (3): 215–25.

Zicola, Johan, Liangyu Liu, Petra Tänzler, and Franziska Turck. 2019. “Targeted DNA Methylation Represses Two Enhancers of FLOWERING LOCUS T in Arabidopsis Thaliana.” Nature Plants 5 (3): 300–307.

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