No evidence for large differences in genomic methylation between wild and hatchery steelhead (Oncorhynchus mykiss)

Blouin, Michael S.; Thuillier, Virginie; Cooper, Becky; Amarasinghe, Vindhya; Cluzel, Laura CluzelL.; Araki, Hideki; Grunau, Christoph

doi:10.1139/f09-174

Cited by 37 publications

(32 citation statements)

References 33 publications

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“…First investigations into epigenetic variation in wild animal populations involved the salmonid, Oncorhynchus mykiss (Blouin et al, 2010). The authors tested if distinct levels of DNA methylation variation could explain differential survival rates between fish in two different habitats, but found no significant differences, possibly due to small sample size (six fish in total) and low-resolution methods (MS-AFLP).…”

Section: Population Epigenetics In the Wildmentioning

confidence: 99%

Epigenetics in natural animal populations

Barrett

2017

J of Evolutionary Biology

137

127

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Phenotypic plasticity is an important mechanism for populations to buffer themselves from environmental change. While it has long been appreciated that natural populations possess genetic variation in the extent of plasticity, a surge of recent evidence suggests that epigenetic variation could also play an important role in shaping phenotypic responses. Compared with genetic variation, epigenetic variation is more likely to have higher spontaneous rates of mutation and a more sensitive reaction to environmental inputs. In our review, we first provide an overview of recent studies on epigenetically encoded thermal plasticity in animals to illustrate environmentally-mediated epigenetic effects within and across generations. Second, we discuss the role of epigenetic effects during adaptation by exploring population epigenetics in natural animal populations. Finally, we evaluate the evolutionary potential of epigenetic variation depending on its autonomy from genetic variation and its transgenerational stability. Although many of the causal links between epigenetic variation and phenotypic plasticity remain elusive, new data has explored the role of epigenetic variation in facilitating evolution in natural populations. This recent progress in ecological epigenetics will be helpful for generating predictive models of the capacity of organisms to adapt to changing climates.

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Section: Population Epigenetics In the Wildmentioning

confidence: 99%

Epigenetics in natural animal populations

Barrett

2017

J of Evolutionary Biology

137

127

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“…Genomic DNA was prepared from soft tissues of the foot of pooled snails. The biological samples for methyl cytosine positive and negative controls were obtained from Oncorhynchus mykiss (see [23]), Hela cells and from S. mansoni adult worms Brazilian strain ( Sm Bre; see Theron et al 1997). S. mansoni indeed displays no or very low levels of DNA methylation [24-26].…”

Section: Methodsmentioning

confidence: 99%

5-methyl-cytosine and 5-hydroxy-methyl-cytosine in the genome of Biomphalaria glabrata, a snail intermediate host of Schistosoma mansoni

et al. 2013

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BackgroundBiomphalaria glabrata is the mollusc intermediate host for Schistosoma mansoni, a digenean flatworm parasite that causes human intestinal schistosomiasis. An estimated 200 million people in 74 countries suffer from schistosomiasis, in terms of morbidity this is the most severe tropical disease after malaria. Epigenetic information informs on the status of gene activity that is heritable, for which changes are reversible and that is not based on the DNA sequence. Epigenetic mechanisms generate variability that provides a source for potentially heritable phenotypic variation and therefore could be involved in the adaptation to environmental constraint. Phenotypic variations are particularly important in host-parasite interactions in which both selective pressure and rate of evolution are high. In this context, epigenetic changes are expected to be major drivers of phenotypic plasticity and co-adaptation between host and parasite. Consequently, with characterization of the genomes of invertebrates that are parasite vectors or intermediate hosts, it is also essential to understand how the epigenetic machinery functions to better decipher the interplay between host and parasite.MethodsThe CpGo/e ratios were used as a proxy to investigate the occurrence of CpG methylation in B. glabrata coding regions. The presence of DNA methylation in B. glabrata was also confirmed by several experimental approaches: restriction enzymatic digestion with isoschizomers, bisulfite conversion based techniques and LC-MS/MS analysis.ResultsIn this work, we report that DNA methylation, which is one of the carriers of epigenetic information, occurs in B. glabrata; approximately 2% of cytosine nucleotides are methylated. We describe the methylation machinery of B. glabrata. Methylation occurs predominantly at CpG sites, present at high ratios in coding regions of genes associated with housekeeping functions. We also demonstrate by bisulfite treatment that methylation occurs in multiple copies of Nimbus, a transposable element.ConclusionsThis study details DNA methylation for the first time, one of the carriers of epigenetic information in B. glabrata. The general characteristics of DNA methylation that we observed in the B. glabrata genome conform to what epigenetic studies have reported from other invertebrate species.

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“…Techniques like bisulphite sequencing, microarrays or next-generation sequencing may overcome the shortcomings of the MSAP technique. However, the MSAP technique is well suited for non-model species, and is applied widely to investigate natural epigenetic variance in wild populations (Blouin et al, 2010;Herrera and Bazaga, 2011;Lira-Medeiros et al, 2010;Richards et al, 2012). This is because it does not rely on genomic information and is able to provide several hundred epigenetic fingerprints of a larger number of individuals on a genome-wide scale concurrently, suggesting it could be a powerful detector of differentiation among populations (Bossdorf et al, 2008).…”

Section: Reviewmentioning

confidence: 99%

“…In the salmonid Oncorhynchus mykiss, fish raised in hatcheries have fewer surviving offspring than wild fish; Blouin et al (Blouin et al, 2010) attempted to explain the phenomenon in terms of epigenetic variation, but no significant difference in epigenetic patterns between the two populations was found. However, this work is the first to investigate the natural population epigenetic variation in animals.…”

Section: Introductionmentioning

confidence: 99%

“…This is because it does not rely on genomic information and is able to provide several hundred epigenetic fingerprints of a larger number of individuals on a genome-wide scale concurrently, suggesting it could be a powerful detector of differentiation among populations (Bossdorf et al, 2008). Additionally, the MSAP technique is sensitive in that band presence/absence is largely an all-or-nothing response (Blouin et al, 2010). Finally, epigenetic studies of natural populations based on the MSAP technique can detect environmentally induced variation in DNA methylation (Karan et al, 2012;Verhoeven et al, 2010).…”

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confidence: 99%

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Natural epigenetic variation in bats and its role in evolution

Liu

Sun

Jiang

et al. 2015

Journal of Experimental Biology

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When facing the challenges of environmental change, such as habitat fragmentation, organisms have to adjust their phenotype to adapt to various environmental stresses. Recent studies show that epigenetic modifications could mediate environmentally induced phenotypic variation, and this epigenetic variance could be inherited by future generations, indicating that epigenetic processes have potential evolutionary effects. Bats living in diverse environments show geographic variations in phenotype, and the females usually have natal philopatry, presenting an opportunity to explore how environments shape epigenetic marks on the genome and the evolutionary potential of epigenetic variance in bat populations for adaptation. We have explored the natural epigenetic diversity and structure of female populations of the great roundleaf bat (Hipposideros armiger), the least horseshoe bat (Rhinolophus pusillus) and the eastern bent-winged bat (Miniopterus fuliginosus) using a methylation-sensitive amplified polymorphism technique. We have also estimated the effects of genetic variance and ecological variables on epigenetic diversification. All three bat species have a low level of genomic DNA methylation and extensive epigenetic diversity that exceeds the corresponding genetic variance. DNA sequence divergence, epigenetic drift and environmental variables contribute to the epigenetic diversities of each species. Environmentinduced epigenetic variation may be inherited as a result of both mitosis and meiosis, and their potential roles in evolution for bat populations are also discussed in this review. KEY WORDS: DNA methylation, Chiroptera, Mammals, Environmental adaptation IntroductionWhen facing challenges from environmental changes or stresses, organisms have to adapt to the changed environment by genetic mechanisms, physiological adaptability, phenotypic plasticity or moving to a new, more suitable area. The genetic changes may support abundant phenotypic variation in organisms for environmental adaptation, but they occur slowly and cannot keep pace with the rapidly changing environment (Bonduriansky et al., 2012). Recent studies have suggested that epigenetic modifications in eukaryotes could affect genetic expression and thus may mediate phenotypical variation in response to rapid and unpredictable environmental changes without genetic divergence (Dolinoy et al., 2007;Gao et al., 2010; Kucharski et al., 2008). These environmentally induced epigenetic patterns may even be stably inherited by future generations (Grant-Downton and Dickinson, 2006; Jablonka and Lamb, 1998;Richards, 2006), which provides an additional pathway for environmental adaptation and produces a challenge to the Modern Evolutionary Synthesis (Bossdorf et al., 2008; Jablonka and Lamb, 1995; Jablonka et al., 2005), in that the epigenetic process is another source of random variation in natural populations in addition to genetic variance (Massicotte et al., 2011;Schmitz et al., 2011).DNA methylation, one of the key epigenetic markers, is a covalen...

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No evidence for large differences in genomic methylation between wild and hatchery steelhead (Oncorhynchus mykiss)

Cited by 37 publications

References 33 publications

Epigenetics in natural animal populations

Epigenetics in natural animal populations

5-methyl-cytosine and 5-hydroxy-methyl-cytosine in the genome of Biomphalaria glabrata, a snail intermediate host of Schistosoma mansoni

Natural epigenetic variation in bats and its role in evolution

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