Introduction: From genetic diversity to epigenetic diversity

Genetic variation provides the baseline for phenotypic variation on which evolutionary processes like natural selection can act (Fisher, 1930; Hughes et al., 2008). The magnitude of genetic variation within a population can be quantified in many ways, and it is a fundamental source of biodiversity (Hughes et al., 2008). Although we know relatively little about the range of potential ecological effects (Hughes et al., 2008), there is plenty of evidence that genetic diversity can affect population dynamics (Reusch et al., 2005; Johnson et al., 2006), species interactions (Kagiya et al., 2017), community composition (Booth & Grime, 2003), and ecosystem processes (Hughes & Stachowicz, 2004; Schweitzer et al., 2005; Madritch et al., 2006).

However, recent advances in molecular biology and genomics have shown that genetic variation is not the only cause of phenotypic variation among individuals (Rapp & Wendel, 2005). One of these additional sources of phenotypic plasticity is epigenetic variation (Zhang et al., 2013). Several studies have suggested that epigenetic diversity has a more significant role in phenotypic plasticity than previously thought (Bossdorf et al., 2008; Heer et al., 2018a). It can create variation (heritable or non-heritable) in ecologically important traits such as tree growth, phenology, plant defense responses to herbivory, or even niche width and habitat differentiation (for further details, see chapter 1: "Phenotypic plasticity and adaptation").

In plants, heritable epialleles frequently arise de novo through epimutations in the germline, that is, through stochastic losses or gain of DNA methylation. These heritable epimutations seem to occur mainly at CpG dinucleotides and are highly dependent on genomic context (Taudt et al., 2016), suggesting that genetic variability in plants can influence the levels of DNA methylation (Dubin et al., 2015). Therefore, high genetic diversity can potentially translate into high epigenetic diversity. On the other hand, if epigenetic variation can create heritable variation in functional traits, then epigenetic diversity can, in principle, have positive effects similar to those of DNA sequence diversity on the functioning of populations and ecosystems (Latzel et al., 2013). Epigenetic changes can also be independent of genetic structure and could, in theory, trigger the formation of novel epialleles and promote the movement of DNA transposons that are commonly found in plant genomes. Therefore, novel 'epigenetically induced' heritable phenotypes can increase the ability of plants to adapt to environmental challenges (Richards, 2006; Mirouze & Paszkowski, 2011). Despite recent advances in the field, the effects of epigenetic variation across different ecological organization levels remain poorly understood. However, thanks to modern genomic techniques becoming more affordable and accessible, new efforts have been made to understand the relationship between genetic, epigenetic, and phenotypic variation and the range of effects of epigenetic variation at ecosystem and landscape levels. This chapter will discuss the known effects of genetic and epigenetic diversity and argue that even though more research on the topic is needed, it is safe to assume that epigenetic diversity across large-scale systems may have consequences similar to those of genetic diversity.