Epimutation markers as a tool 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.