Sources of epigenetic variation and their applications in natural populations

Abstract

Epigenetic processes manage gene expression and products in a real‐time manner, allowing a single genome to display different phenotypes. In this paper, we discussed the relevance of assessing the different sources of epigenetic variation in natural populations. For a given genotype, the epigenetic variation could be environmentally induced or occur randomly. Strategies developed by organisms to face environmental fluctuations such as phenotypic plasticity and diversified bet‐hedging rely, respectively, on these different sources. Random variation can also represent a proxy of developmental stability and can be used to assess how organisms deal with stressful environmental conditions. We then proposed the microbiome as an extension of the epigenotype of the host to assess the factors determining the establishment of the community of microorganisms. Finally, we discussed these perspectives in the applied context of conservation.

Phenotypic Responses, Reproduction Mode and Epigenetic Patterns under Temperature Treatments in the Alpine Plant Species Ranunculus kuepferi (Ranunculaceae)

“…Seed set is negatively affected by cold conditions, with diploids having significantly lower abortion rates under both temperature conditions, while tetraploids produced only a handful of well-developed seeds under warm conditions. Cold and frost conditions decrease seed set and injure the reproductive tissues of alpine plants, e.g., in Saxifraga bryoides [ 120 ] and Ranunculus hirtellus [ 121 ]. Moreover, Ladinig et al [ 122 ] suggested that the repeated moderate frost treatment, applied also here, mimics temperature conditions occurring in high mountains and provokes frost injury in reproductive shoots, which could also result in full fruit loss.…”

The epiallelic potential of transposable elements and its evolutionary significance in plants

“…On the one hand, pronounced and stable epialleles resulting from spontaneous loss of DNA methylation can generate heritable phenotypic variation and can be seen as a form of diversified bet-hedging strategy. On the other hand, moderate and transient epialleles induced by the environment provide a means to generate rapid and transient phenotypic plasticity [140]. However, this second flavour of epimutations appears to be of little adaptive potential in the face of abrupt environmental changes, except perhaps when environments fluctuate.…”

“…However, this second flavour of epimutations appears to be of little adaptive potential in the face of abrupt environmental changes, except perhaps when environments fluctuate. Indeed, modelling suggests that by enabling a rapid loss of stress memory, transient epimutations may be advantageous in the latter context [141][142][143], and especially when environmental changes are relatively predictable [140,[144][145][146][147].…”

Sources of variation of DNA methylation in rainbow trout: combined effects of temperature and genetic background

“…To date however, there has been only a limited number of studies in fish because it is difficult to disentangle the different effects due to genetic variation among individuals. In this context, the use of asexual fish vertebrate models, such as the clonal fish Chrosomus eos-neogaeus (Cyprinidea), that reproduces asexually through gynogenesis, has been pioneering as it allowed to have biological replicates without genetic variation (reviewed in Angers et al, 2020). Several studies using this biological model in natural populations have revealed that i) levels of DNA methylation variation were higher than genetic variation (Massicotte et al, 2011); ii) both environmentally induced and stochastic modifications of DNA methylation were sources of epigenetic variation (Massicotte and Angers, 2012;Leung et al, 2016); iii) the relative abundance of environmentally induced and randomly established epigenetic marks was correlated to the predictability of environmental conditions, both in natural sites and common garden experiments (Leung et al, 2016).…”

“…The role of epigenetic processes such as DNA methylation in mediating environmentally induced phenotypic variation has been reviewed in Angers et al (2010). To date, only a limited number of studies in fish could independently analyse genetic and epigenetic variations, using asexual fish vertebrate model systems such as the clonal fish Chrosomus eos-neogaeus (Cyprinidea) (Angers et al, 2020) or the naturally self-fertilizing hermaphroditic mangrove killifish Kryptolebias marmoratus (Ellison et al, 2015;Berbel-Filho et al, 2019). However, the aforementioned studies were limited to a single or a few genotypes.…”