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As genetic diversity in conservation genetics, epigenetic diversity will be at the core of any conservation epigenetic approach. If it will prove to be relevant in various taxa, functional epigenetic diversity would be bound to environmental priming. Consequently, one essential principle to sustain epigenetic functional diversity would be to focus on environmental heterogeneity in conservation strategies. This principle is scalable, meaning that it would refer on the one side to range-wide heterogeneity e.g. strengthening rear edges conservation analogous to the genetic diversity (Hampe and Petit 2005). But it would also refer to microenvironmental heterogeneity. In other words, conservation epigenetics should aim to diversify habitat heterogeneity and welcome stress as well as disturbances as important factors to strengthen or sustain the acclimation potential of a population or species. This principle could also be reflected in ex-situ and breeding strategies. Especially for the latter, it would mean a clear deviation from current management strategies. For example, tree seeds are normally harvested in orchards or from so called plus-trees. The former normally are placed under ideal habitat situations in productive sites. In both cases seed donors normally have favorable phenotypes. If epigenetic diversity is the ultimate goal, it would mean that seeds should also come from edge populations, stressed populations, and not-perfect phenotypes, in other words selecting seeds to increase plasticity.

The human-induced 6th mass extinction threatens more species with global extinction than ever before with an average of around 25 % of species in assessed animal and plant groups being threatened. That means, that up to one million species already face extinction, many of which in the next decades, unless action is taken to reduce the intensity of drivers of biodiversity loss (Díaz et al. 2019). Conservation biology has been the research field that deals with this biodiversity crisis. It studies the conservation of biodiversity by investigating the biology of species, communities, and ecosystems that are directly or indirectly threatened by human activities or other agents. Its goal is to provide principles and tools for preserving all levels of biodiversity including its evolutionary potential (Soulé 1985). Conservation genetics in turn, is a well-established scientific field within conservation biology and is dedicated to shedding light on the evolutionary dimension of conservation biology. Large numbers of scientific studies are published each year in dedicated scientific journals as well as journals targeting broader scientific audiences (Holderegger et al. 2019). Conservation genetics has impacted conservation on two levels. First, it established mechanistic principles that have acted as conservation guidelines already for decades – from the core principle that genetic diversity is crucial for the well-being of populations to central concepts such as inbreeding depression, accumulation and loss of deleterious mutations, loss of genetic variation in small populations, genetic adaptation to captivity and its effect on reintroduction success, outbreeding depression (Frankham 1996), minimum viable populations (Menges 1991), and the distinctness of rear edge populations in conservation (Hampe and Petit 2005). Besides such textbook principles, the availability of conservation genetic tools directly empowers conservation managers on the ground including barcoding and metabarcoding for species identification or monitoring or with genetic studies on gene flow to assess fragmentation and connectivity to assess the success of connectivity measures (Holderegger et al. 2019). Still, Holderegger and co-workers attest that conservation genetics still remains a largely academic field and that real‐world examples with a clear focus on application would largely be restricted to emblematic vertebrate fauna. They observe, that this gap between conservation genetic sciences and the practical conservation yet increases through the rapid development of high‐throughput genotyping technologies and thus the use of genomic information as new challenges emerge with regards to data analyses. Undeniably, despite these initial gaps between science and management, the genomic revolution will provide valuable information for conservation genetic approaches, as it will allow to focus on a species’ or population’s adaptive potential to respond to stress by means of molecular changes (Eizaguirre & Baltazar-Soares, 2014).

In a recent review, Rey et al. propose to establish yet another research field that will contribute to conservation biology, namely conservation epigenetics. They argue that epigenetic marks – more particularly DNA methylation – and developmental reprogramming should be considered as an additional conservation level stating that DNA methylation is sensitive to the environment and is involved in organisms' plastic and adaptive responses to changing environments. As we have seen in previous chapters, epigenetic elements can act in conjunction with genetic information to modulate phenotypes during development (Allis & Jenuwein, 2016). Moreover, while some epigenetic patterns are under genetic determinism, some others are directly modulated by the surrounding environmental conditions (Feil & Fraga, 2012), particularly that of DNA methylation. Thus, DNA methylation induced by environmental stressors during development that produces maladaptive phenotypes can have negative consequences in populations (Piferrer, 2016). Rey et al. argue, that accounting for such epigenetic trap effect faced by some populations could be useful in a conservation context. Specifically, at the population level, modifications of DNA methylation patterns among individuals in response to changing environment could be associated with a phenotypic shift from suboptimal to optimal value in the resulting environment, hence leading to adaptive phenotypic plasticity corresponding to the environmentally induced phenotype variation (EPV) (Rey et al. 2019 and references therein). Alternatively, environmental changes could potentially induce spontaneous and random modifications in DNA methylation patterns potentially resulting in the broadening of phenotypic values around the original mean phenotype within populations corresponding to the stochastic developmental phenotype variation (SPV) (Rey et al. .2019 and references therein). They further argue, that those two processes can lead to phenotypic diversification, with EPV being expected to be selected when environmental changes are predictable allowing organisms to quickly respond and adjust their phenotypes to maximize their fitness while SPV could be considered a random and non-directional flexibilization of genome expression to new and/or unpredictable environments constituting a bet-hedging strategy resulting in the maintenance of few individuals harboring optimal phenotypes and most individuals expressing suboptimal phenotypes in the new environment (Rey et al. 2019 and references therein).

However, as we have seen throughout this book, the ecological importance of variation in DNA methylation relative to genetic variation has only been established in a few individual case studies and still needs to be empirically quantified in non-model plant species (Richards et al. 2017). That said, the growing body of literature shows that the distribution and especially function of DNA methylation variation varies strongly among taxa and its role in acclimation is not as straight forward as seen for genetic variation in adaptation. Therefore, it will likely take at least another decade to establish sound evidence for a large variety of conservation relevant taxa for conservation epigenetics to become effective. And given that sound epigenetic research is necessarily based on omics resources, a conservation epigenetic toolbox will likely not be available for conservation practitioners in the near future. As with the beginnings of conservation genetics decades ago, our current understanding of plant epigenetics might still be sufficient to establish basic principles for conservation management.

Aside from functional epigenetic diversity, conservation management could profit from epimutation markers as a new tool that could potentially replace SSR markers for some questions. The background is that heritable gains or losses of cytosine methylation can arise stochastically in plant genomes independently of DNA sequence changes. These are called ‘spontaneous epimutations’ and can be inherited across mitotic and meiotic cell divisions. They occur at rates four to five orders of magnitude higher than the DNA mutation rate per unit time and are neutral at the genome-wide scale accumulating in plant genomes in a ‘clock-like’ fashion (Yao et al. 2021). Emerging evidence indicates that these properties can be exploited for reconstructing and timing recent evolutionary events and for age dating long-lived perennials (see figure 1).

Figure 1: Epimutations have Clock-like Properties and can be used for example to date long-lived plants. Source: Yao et al. 2021.

Consequently, spontaneous epimutations can be used for the development of biomarkers to study wild populations' ecological structuring, and the study of landscape connectivity (Rey et al. 2019), in relation with conservation efforts of clonal plants, with reconstructing the dispersal of invasive clonal plant species and also help to differentiate between naturally dispersed plants and escaped garden plants.

One recent example of the usage of epigenetic biomarkers was shown in the pruning systems used in vineyards that induced detectable DNA methylation signatures in vines even at narrow geographical scales (Xie et al., 2017). In a conservation perspective, this example illustrates how methylation markers could be used to determine conservation units accounting not only for the long-term evolutionary history of organisms but also for some important fractions of their current ecological context.

Another example stems from well-illustrated populations of the perennial herb Helleborus foetidus of south-eastern Spain. Here Herrera and coworkers (2017) established the genetic, epigenetic and phenotypic structures of subpopulations on 10 geo-graphically distant sites. These sites had diverging environmental conditions and the genetic structure followed a classical isolation-by-distance pattern. The epigenetic structure in contrast, clearly followed an isolation-by-environment pattern, better reflecting the ecological processes that have shaped population phenotypic differentiation (Herrera et al., 2017).

It is very likely that in plants conservation epigenetics will never take on a central role in conservation biology as conservation genetics has. However, we do think that plant epigenetics will be a valuable complementation to conservation genetics possibly helping to put focus on the importance of microenvironmental heterogeneity in conservation and providing valuable tools based on spontaneous epimutations. It might be a stretch though, to invent yet another research field with the term Conservation Epigenetics.