Growing evidence shows that epigenetic mechanisms contribute to complex traits, with implications across many fields of biology. In plant ecology, recent studies have attempted to merge ecological experiments with epigenetic analyses to elucidate the contribution of epigenetics to plant phenotypes, stress responses, adaptation to habitat, and range distributions. While there has been some progress in revealing the role of epigenetics in ecological processes, studies with non-model species have so far been limited to describing broad patterns based on anonymous markers of DNA methylation. In contrast, studies with model species have benefited from powerful genomic resources, which contribute to a more mechanistic understanding but have limited ecological realism. Understanding the significance of epigenetics for plant ecology requires increased transfer of knowledge and methods from model species research to genomes of evolutionarily divergent species, and examination of responses to complex natural environments at a more mechanistic level. This requires transforming genomics tools specifically for studying non-model species, which is challenging given the large and often polyploid genomes of plants. Collaboration among molecular geneticists, ecologists and bioinformaticians promises to enhance our understanding of the mutual links between genome function and ecological processes.

BIOSS Centre for Biological Signaling Studies University of Freiburg 79098 Freiburg Germany

Conservation Biology Philipps University of Marburg 35037 Marburg Germany

Department of Biological and Environmental Sciences Center of Excellence in Biological Interactions University of Jyväskylä 40014 Jyväskylän yliopisto Finland

Department of Community Ecology Helmholtz Centre for Environmental Research UFZ 06120 Halle Germany

Department of Ecology Philipps University Marburg 35037 Marburg Germany

Department of Integrative Biology University of South Florida Tampa FL 33620 USA

Estación Biológica de Doñana CSIC 41092 Sevilla Spain

European Research Institute for the Biology of Ageing University Medical Center Groningen 9713 Groningen The Netherlands

German Centre for Integrative Biodiversity Research Halle Jena Leipzig 04103 Leipzig Germany

Gregor Mendel Institute of Molecular Plant Biology 1030 Vienna Austrian Academy of Sciences Vienna Biocenter Austria

Institut de Recherche en Horticulture et Semences 49071 Beaucouzé Cedex France

Institut de Recherche pour le Développement Laboratoire Génome et Développement des Plantes 66860 Perpignan France

Institut für Informatik University of Leipzig 04107 Leipzig Germany

Institute of Botany The Czech Academy of Sciences 25243 Průhonice Czech Republic

Institute of Computational Biology Helmholtz Zentrum München 85764 Neuherberg Germany

Institute of Computer Science University of Halle 06120 Halle Germany

Institute of Plant Breeding Seed Science and Population Genetics 70599 Stuttgart Germany

Max Planck Institute for Mathematics in the Sciences 04103 Leipzig Germany

Netherlands Institute of Ecology Wageningen The Netherlands

Plant Cell Biology Philipps University Marburg 35037 Marburg Germany

Plant Ecological Genomics University of Vienna 1030 Vienna Austria

Plant Evolutionary Ecology University of Tübingen 72076 Tübingen Germany

School of Life Sciences Weihenstephan Technical University of Munich 85354 Freising Germany

The Santa Fe Institute Santa Fe NM 87501 USA

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