Patterns of Epigenetic Diversity in Two Sympatric Fish Species: Genetic vs. Environmental Determinants

Abstract

Epigenetic components are hypothesized to be sensitive to the environment, which should permit species to adapt to environmental changes. In wild populations, epigenetic variation should therefore be mainly driven by environmental variation. Here, we tested whether epigenetic variation (DNA methylation) observed in wild populations is related to their genetic background, and/or to the local environment. Focusing on two sympatric freshwater fish species (Gobio occitaniae and Phoxinus phoxinus), we tested the relationships between epigenetic differentiation, genetic differentiation (using microsatellite and single nucleotide polymorphism (SNP) markers), and environmental distances between sites. We identify positive relationships between pairwise genetic and epigenetic distances in both species. Moreover, epigenetic marks better discriminated populations than genetic markers, especially in G. occitaniae. In G. occitaniae, both pairwise epigenetic and genetic distances were significantly associated to environmental distances between sites. Nonetheless, when controlling for genetic differentiation, the link between epigenetic differentiation and environmental distances was not significant anymore, indicating a noncausal relationship. Our results suggest that fish epigenetic variation is mainly genetically determined and that the environment weakly contributed to epigenetic variation. We advocate the need to control for the genetic background of populations when inferring causal links between epigenetic variation and environmental heterogeneity in wild populations.

Genome‐wide DNA methylation patterns harbour signatures of hatchling sex and past incubation temperature in a species with environmental sex determination

“…The utility of these DNAm marks as a conservation tool depends on validation using more targeted approaches (e.g., bisulphite sequencing PCR) across many samples originating from multiple geographical sites. Given the links between genomic sequence variation and epigenomic variation (Fargeot et al, 2021 ; Foust et al, 2016 ; Wogan et al, 2020 ), incorporating samples from distinct populations is crucial to develop a generalizable tool for use in conservation contexts. Further, a quantitative comparison of the reliability and cost‐efficiency of different potential molecular markers of sex, for example blood DNAm patterns, sex‐biased protein levels (Tezak et al, 2020 ), and high‐sensitivity steroid hormone quantitation (Bae et al, 2021 ), in TSD species is warranted.…”

Genetic Diversity and Population Structure of Hemiculter leucisculus (Basilesky, 1855) in Xinjiang Tarim River

“…This could be because Taitema Lake is located at the end of the Tarim River, and the alluvial plain formed by three water systems of Tarim River, Qarqan River and Altun Rivers, with frequent water exchange [ 35 ]. There was increased gene flow between populations during floods [ 38 , 39 , 40 ].…”

Population Epigenetics: The Extent of DNA Methylation Variation in Wild Animal Populations

“…Based on their degree of autonomy from the underlying genotype, epialleles are categorized into three types: obligatory, which is completely dependent on the genetic variation; facilitated, which is directed or loosely potentiated by the genotype; pure, which is independent of the genetic variation and is generated by stochastic events or environmental changes [ 73 ]. To identify which epialleles categories are encountered in natural populations, the correlation between the genetic and epigenetic profiles can be estimated, mostly by using a Mantel test [ 50 , 63 , 74 , 75 ]. A significant (positive or negative) correlation suggests that the epigenetic and genetic variations are interdependent, which corresponds to the presence of obligatory epialleles.…”