IDEA AND PERSPECTIVE Epigenetics for ecologists Oliver Bossdorf, 1 * Christina L. Richards 2 and Massimo Pigliucci 3 1 Department of Community Ecology, Helmholtz Centre for Environmental Research-UFZ, Theodor-Lieser-Str. 4, D-06120 Halle, Germany 2 Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA 3 Department of Ecology & Evolution, Stony Brook University, Stony Brook, NY 11794, USA *Correspondence: E-mail: oliver.bossdorf@ufz.de Abstract There is now mounting evidence that heritable variation in ecologically relevant traits can be generated through a suite of epigenetic mechanisms, even in the absence of genetic variation. Moreover, recent studies indicate that epigenetic variation in natural populations can be independent from genetic variation, and that in some cases environmentally induced epigenetic changes may be inherited by future generations. These novel findings are potentially highly relevant to ecologists because they could significantly improve our understanding of the mechanisms underlying natural phenotypic variation and the responses of organisms to environmental change. To understand the full significance of epigenetic processes, however, it is imperative to study them in an ecological context. Ecologists should therefore start using a combination of experimental approaches borrowed from ecological genetics, novel techniques to analyse and manipulate epigenetic variation, and genomic tools, to investigate the extent and structure of epigenetic variation within and among natural populations, as well as the interrelations between epigenetic variation, phenotypic variation and ecological interactions. Keywords Adaptation, DNA methylation, ecological genetics, epialleles, inheritance, maternal effects, natural variation, rapid evolution. Ecology Letters (2008) 11: 106–115 INTRODUCTION Species and their traits are not fixed but are subject to genetic variation and evolutionary change. Not only are ecologically important traits often genetically differentiated in natural populations (Linhart & Grant 1996; Mousseau et al. 2000; Merila ¨ & Crnokrak 2001), there is also cumulating evidence that they can evolve rapidly (Thomp- son 1998; Hairston et al. 2005; Carroll et al. 2007). Genetic variation and microevolution are therefore increasingly recognized as relevant to basic ecological research (e.g. Whitham et al. 2006; Johnson & Stinchcombe 2007) and applied issues such as ecological restoration (Rice & Emery 2003; Bischoff et al. 2006), the invasion of exotic species (Mooney & Cleland 2001; Bossdorf et al. 2005; Strauss et al. 2006) and the response of ecological communities to global environmental change (Davis & Shaw 2001; Davis et al. 2005; Jump & Penuelas 2005; Parmesan 2006). However, while ecologists are still struggling to conceptually and methodologically incorporate genetics into their work, the situation is now likely to become even more complex, as recent research suggests that epigenetic processes, too, could play a significant role in natural variation and microevolution. The epigenetic code Epigenetics is the study of heritable changes in gene expression and function that cannot be explained by changes in DNA sequence (Richards 2006; Bird 2007). These epigenetic changes are based on a set of molecular processes that can activate, reduce or completely disable the activity of particular genes: (i) methylation of cytosine residues in the DNA, (ii) remodelling of chromatin structure through chemical modification, in particular acetylation or methylation, of histone proteins and (iii) regulatory pro- cesses mediated by small RNA molecules. The different classes of processes are not independent from each other but often regulate gene activity in a complex, interactive fashion (Grant-Downton & Dickinson 2005; Berger 2007). In the past, the term ÔepigeneticsÕ has sometimes also been used in a much broader sense to include all processes that determine how the genotype translates into the Ecology Letters, (2008) 11: 106–115 doi: 10.1111/j.1461-0248.2007.01130.x Ó 2007 Blackwell Publishing Ltd/CNRS