Morphological and epigenetic variation in mussels from contrasting environments

Watson, Ralph; Baldanzi, Simone; Pérez‐Figueroa, Andrés; Gouws, Gavin; Porri, Francesca

doi:10.1007/s00227-018-3310-6

Cited by 10 publications

(9 citation statements)

References 67 publications

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“…Our results might have been different with other tissues like muscle [ 33 , 74 , 75 , 76 ], blood [ 34 , 77 , 78 ], liver [ 79 , 80 ], or gill tissue [ 81 ]. Some authors made different choices to avoid tissue-specific differences such as gonads [ 56 ] or even whole organism when it is relatively small in body size [ 36 , 82 , 83 , 84 ]. Second, we used a MS-AFLP protocol, which is currently the most widely used approach for inferring epigenetic diversity in wild populations [ 37 , 78 , 81 , 85 ].…”

Section: Discussionmentioning

confidence: 99%

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

Fargeot

Loot

Prunier

et al. 2021

Genes

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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.

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Section: Discussionmentioning

confidence: 99%

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

Fargeot

Loot

Prunier

et al. 2021

Genes

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“…For MSAP, this package detects the activity of each restriction enzyme and classifies each locus depending on the methylation state of the cytosines present in the target sequence (Supplementary Data Table S2 ). Thus, the loci were classified as Methylation-Susceptible Loci (MSL), which are used to assess epigenetic variation, or Non-Methylated Loci (NML), used as a proxy to assess genetic variation (Watson et al 2018 ). Variations among MSL were also calculated with the Shannon’s diversity index ( S ), and epigenetic variations among plots and climatic treatments were also explored by principal coordinate analyses (PCoA) based on Euclidean distance matrix, implemented in the msap package.…”

Section: Methodsmentioning

confidence: 99%

“…Furthermore, an analysis of the molecular variance (AMOVA) was used for the estimation of variance components and the Phi -statistic (analogue to the F-statistic for binary data) to reflect genetic and epigenetic diversity (Excoffier et al 1992 ). In order to determine those loci showing non-randomly distributed methylation patterns between treatments (h for hemimethylation, i for methylation of inner cytosines, u for non-methylation, and f for uninformative state, which may be due to full methylation or changes in the nucleotide sequence of the target), a locus -by- locus Chi -squared test was performed using the MSL, following the reproducible example script for R found in Watson et al ( 2018 ). To control the false discovery rate (FDR), a BH multitest adjustment was adopted (Benjamini and Hochberg 1995 ), and those MSL with p-value < 0.001 were considered as significantly differentiated.…”

Section: Methodsmentioning

confidence: 99%

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Epigenetic responses of hare barley (Hordeum murinum subsp. leporinum) to climate change: an experimental, trait-based approach

et al. 2021

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The impact of reduced rainfall and increased temperatures forecasted by climate change models on plant communities will depend on the capacity of plant species to acclimate and adapt to new environmental conditions. The acclimation process is mainly driven by epigenetic regulation, including structural and chemical modifications on the genome that do not affect the nucleotide sequence. In plants, one of the best-known epigenetic mechanisms is cytosine-methylation. We evaluated the impact of 30% reduced rainfall (hereafter “drought” treatment; D), 3 °C increased air temperature (“warming”; W), and the combination of D and W (WD) on the phenotypic and epigenetic variability of Hordeum murinum subsp. leporinum L., a grass species of high relevance in Mediterranean agroforestry systems. A full factorial experiment was set up in a savannah-like ecosystem located in southwestern Spain. H. murinum exhibited a large phenotypic plasticity in response to climatic conditions. Plants subjected to warmer conditions (i.e., W and WD treatments) flowered earlier, and those subjected to combined stress (WD) showed a higher investment in leaf area per unit of leaf mass (i.e., higher SLA) and produced heavier seeds. Our results also indicated that both the level and patterns of methylation varied substantially with the climatic treatments, with the combination of D and W inducing a clearly different epigenetic response compared to that promoted by D and W separately. The main conclusion achieved in this work suggests a potential role of epigenetic regulation of gene expression for the maintenance of homoeostasis and functional stability under future climate change scenarios.

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“…Most of these studies focused on plants with the genome reference at the individual level (e.g., Colicchio et al, 2018 ; Jueterbock et al, 2020 ). However, roles of epigenetic variation in plastic responses of natural populations to specific environment changes is still largely unknown, especially for non-traditional model organisms lacking the genome reference ( Paun et al, 2010 ; Abratowska et al, 2012 ; Rico et al, 2014 ; Watson et al, 2018 ).…”

Section: Introductionmentioning

confidence: 99%

DNA Methylation Correlates With Responses of Experimental Hydrocotyle vulgaris Populations to Different Flood Regimes

et al. 2022

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Epigenetic mechanisms such as DNA methylation are considered as an important pathway responsible for phenotypic responses and rapid acclimation of plants to different environments. To search for empirical evidence that DNA methylation is implicated in stress-responses of non-model species, we exposed genetically uniform, experimental populations of the wetland clonal plant Hydrocotyle vulgaris to two manipulated flood regimes, i.e., semi-submergence vs. submergence, measured phenotypic traits, and quantified different types of DNA methylation using MSAP (methylation-sensitive amplified polymorphism). We found different epi-phenotypes and significant epigenetic differentiation between semi-submerged and submerged populations. Compared to subepiloci (denoting DNA methylation conditions) for the CG-methylated state, unmethylation and CHG-hemimethylation subepiloci types contribute more prominently to the epigenetic structure of experimental populations. Moreover, we detected some epimarker outliers potentially facilitate population divergence between two flood regimes. Some phenotypic variation was associated with flood-induced DNA methylation variation through different types of subepiloci. Our study provides the indication that DNA methylation might be involved in plant responses to environmental variation without altering DNA sequences.

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Morphological and epigenetic variation in mussels from contrasting environments

Cited by 10 publications

References 67 publications

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

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

Epigenetic responses of hare barley (Hordeum murinum subsp. leporinum) to climate change: an experimental, trait-based approach

DNA Methylation Correlates With Responses of Experimental Hydrocotyle vulgaris Populations to Different Flood Regimes

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