DNA methyltransferase 3a mediates developmental thermal plasticity

DNA methylase 1 influences temperature responses and development in the invasive pest Tuta absoluta

DNA methylase 1 (Dnmt1) is an important regulatory factor associated with biochemical signals required for insect development. It responds to changes in the environment and triggers phenotypic plasticity. Meanwhile, Tuta absoluta Meyrick (Lepidoptera: Gelechiidae)-a destructive invasive pest-can rapidly invade and adapt to different habitats; however, the role of Dnmt1 in this organism has not been elucidated. Accordingly, this study investigates the mechanism(s) underlying the rapid adaptation of Tuta absoluta to temperature stress. Potential regulatory genes were screened via RNAi (RNA interference), and the DNA methylase in Tuta absoluta was cloned by RACE (Rapid amplification of cDNA ends). TaDnmt1 was identified as a potential regulatory gene via bioinformatics; its expression was evaluated in response to temperature stress and during different development stages using real-time polymerase chain reaction. Results revealed that TaDnmt1 participates in hot/cold tolerance, temperature preference and larval development. The full-length cDNA sequence of TaDnmt1 is 3765 bp and encodes a 1254 kDa protein with typical Dnmt1 node-conserved structural features and six conserved DNA-binding active motifs. Moreover, TaDnmt1 expression is significantly altered by temperature stress treatments and within different development stages. Hence, TaDnmt1 likely contributes to temperature responses and organismal development. Furthermore, after treating with double-stranded RNA and exposing Tuta absoluta to 35°C heat shock or -12°C cold shock for 1 h, the survival rate significantly decreases; the preferred temperature is 2°C lower than that of the control group. In addition, the epidermal segments become enlarged and irregularly folded while the surface dries up. This results in a significant increase in larval mortality (57%) and a decrease in pupation (49.3%) and eclosion (50.9%) rates. Hence, TaDnmt1 contributes to temperature stress responses and temperature perception, as well as organismal growth and development, via DNA methylation regulation. These findings suggest that the rapid geographic expansion of T absoluta has been closely associated with TaDnmt1-mediated temperature tolerance. This study advances the research on 'thermos Dnmt' and provides a potential target for RNAi-driven regulation of Tuta absoluta.

Epigenetics and environmental health

Epigenetic modifications including DNA methylation, histone modifications, chromatin remodeling, and RNA modifications complicate gene regulation and heredity and profoundly impact various physiological and pathological processes. In recent years, accumulating evidence indicates that epigenetics is vulnerable to environmental changes and regulates the growth, development, and diseases of individuals by affecting chromatin activity and regulating gene expression. Environmental exposure or induced epigenetic changes can regulate the state of development and lead to developmental disorders, aging, cardiovascular disease, Alzheimer's disease, cancers, and so on. However, epigenetic modifications are reversible. The use of specific epigenetic inhibitors targeting epigenetic changes in response to environmental exposure is useful in disease therapy. Here, we provide an overview of the role of epigenetics in various diseases. Furthermore, we summarize the mechanism of epigenetic alterations induced by different environmental exposures, the influence of different environmental exposures, and the crosstalk between environmental variation epigenetics, and genes that are implicated in the body's health. However, the interaction of multiple factors and epigenetics in regulating the initiation and progression of various diseases complicates clinical treatments. We discuss some commonly used epigenetic drugs targeting epigenetic modifications and methods to prevent or relieve various diseases regulated by environmental exposure and epigenetics through diet.

Thyroid hormone links environmental signals to DNA methylation

Environmental conditions experienced within and across generations can impact individual phenotypes via so-called 'epigenetic' processes. Here we suggest that endocrine signalling acts as a 'sensor' linking environmental inputs to epigenetic modifications. We focus on thyroid hormone signalling and DNA methylation, but other mechanisms are likely to act in a similar manner. DNA methylation is one of the most important epigenetic mechanisms, which alters gene expression patterns by methylating cytosine bases via DNA methyltransferase enzymes. Thyroid hormone is mechanistically linked to DNA methylation, at least partly by regulating the activity of DNA methyltransferase 3a, which is the principal enzyme that mediates epigenetic responses to environmental change. Thyroid signalling is sensitive to natural and anthropogenic environmental impacts (e.g. light, temperature, endocrine-disrupting pollution), and here we propose that thyroid hormone acts as an environmental sensor to mediate epigenetic modifications. The nexus between thyroid hormone signalling and DNA methylation can integrate multiple environmental signals to modify phenotypes, and coordinate phenotypic plasticity at different time scales, such as within and across generations. These dynamics can have wide-ranging effects on health and fitness of animals, because they influence the time course of phenotypic adjustments and potentially the range of environmental stimuli that can elicit epigenetic responses. This article is part of the theme issue 'Endocrine responses to environmental variation: conceptual approaches and recent developments'.

Intergenerational plasticity aligns with temperature-dependent selection on offspring metabolic rates

Metabolic rates are linked to key life-history traits that are thought to set the pace of life and affect fitness, yet the role that parents may have in shaping the metabolism of their offspring to enhance survival remains unclear. Here, we investigated the effect of temperature (24°C or 30°C) and feeding frequency experienced by parent zebrafish (Danio rerio) on offspring phenotypes and early survival at different developmental temperatures (24°C or 30°C). We found that embryo size was larger, but survival lower, in offspring from the parental low food treatment. Parents exposed to the warmer temperature and lower food treatment also produced offspring with lower standard metabolic rates-aligning with selection on embryo metabolic rates. Lower metabolic rates were correlated with reduced developmental and growth rates, suggesting selection for a slow pace of life. Our results show that intergenerational phenotypic plasticity on offspring size and metabolic rate can be adaptive when parent and offspring temperatures are matched: the direction of selection on embryo size and metabolism aligned with intergenerational plasticity towards lower metabolism at higher temperatures, particularly in offspring from low-condition parents. These findings provide evidence for adaptive parental effects, but only when parental and offspring environments match. This article is part of the theme issue 'The evolutionary significance of variation in metabolic rates'.

Warming and pollution interact to alter energy transfer efficiency, performance and fitness across generations in zebrafish (Danio rerio)

Energy transfer efficiency across different trophic levels, from food to new biomass, can determine population dynamics and food-web function. Here we show that the energy needed to produce a unit of new biomass increases with warming and exposure to bisphenol A (BPA), an endocrine disrupting compound. These environmental effects are at least partially transmitted across generations via DNA methylation. We raised parental (F0) and their offspring (F1) zebrafish (Danio rerio) of two genotypes (DNA methyltransferase 3a knock-out [DNMT3a-/-] and wild type [DNMT3a+/+]) at different temperatures (24 and 30 °C), with and without BPA (0 and 10 μg l-1) to test whether the effects of BPA are i) temperature specific, ii) mediated by DNA methylation, and iii) transmitted across generations even if offspring are not exposed. All experimental factors interacted to influence growth in length and mass, and metabolic rates with the result that wild-type F0 and F1 fish experienced the greatest energetic cost of growth under warm conditions in the presence of BPA. However, this response was not observed in DNMT3a-/- fish, indicating that DNA methylation is at least partly responsible for mediating these effects. Under the same conditions (warm + BPA) wild-type parents had reduced swimming performance, and reduced fecundity, and offspring embryonic survival was reduced significantly; genotype affected these responses significantly. Our results indicate that the conditions that are becoming increasingly common globally - warming and endocrine disrupting compounds from plastic pollution and production - can have detrimental effects on energy transfer efficiency and thereby potentially on food-web structure. These effects can be transmitted across generations even if offspring are not exposed to the pollutant, and are likely to have ramifications for conservation and fisheries.

Plasticity and associated epigenetic mechanisms play a role in thermal evolution during range expansion

Due to global change, many species are shifting their distribution and are thereby confronted with novel thermal conditions at the moving range edges. Especially during the initial phases of exposure to a new environment, it has been hypothesized that plasticity and associated epigenetic mechanisms enable species to cope with environmental change. We tested this idea by capitalizing on the well-documented southward range expansion of the damselfly Ischnura elegans from France into Spain where the species invaded warmer regions in the 1950s in eastern Spain (old edge region) and in the 2010s in central Spain (new edge region). Using a common garden experiment at rearing temperatures matching the ancestral and invaded thermal regimes, we tested for evolutionary changes in (thermal plasticity in) larval life history and heat tolerance in these expansion zones. Through the use of de- and hypermethylating agents, we tested whether epigenetic mechanisms play a role in enabling heat tolerance during expansion. We used the phenotype of the native sister species in Spain, I. graellsii, as proxy for the locally adapted phenotype. New edge populations converged toward the phenotype of the native species through plastic thermal responses in life history and heat tolerance while old edge populations (partly) constitutively evolved a faster life history and higher heat tolerance than the core populations, thereby matching the native species. Only the heat tolerance of new edge populations increased significantly when exposed to the hypermethylating agent. This suggests that the DNA methylation machinery is more amenable to perturbation at the new edge and shows it is able to play a role in achieving a higher heat tolerance. Our results show that both (evolved) plasticity as well as associated epigenetic mechanisms are initially important when facing new thermal regimes but that their importance diminishes with time.

Potential Role of DNA Methylation as a Driver of Plastic Responses to the Environment Across Cells, Organisms, and Populations

There is great interest in exploring epigenetic modifications as drivers of adaptive organismal responses to environmental change. Extending this hypothesis to populations, epigenetically driven plasticity could influence phenotypic changes across environments. The canonical model posits that epigenetic modifications alter gene regulation and subsequently impact phenotypes. We first discuss origins of epigenetic variation in nature, which may arise from genetic variation, spontaneous epimutations, epigenetic drift, or variation in epigenetic capacitors. We then review and synthesize literature addressing three facets of the aforementioned model: (i) causal effects of epigenetic modifications on phenotypic plasticity at the organismal level, (ii) divergence of epigenetic patterns in natural populations distributed across environmental gradients, and (iii) the relationship between environmentally induced epigenetic changes and gene expression at the molecular level. We focus on DNA methylation, the most extensively studied epigenetic modification. We find support for environmentally associated epigenetic structure in populations and selection on stable epigenetic variants, and that inhibition of epigenetic enzymes frequently bears causal effects on plasticity. However, there are pervasive confounding issues in the literature. Effects of chromatin-modifying enzymes on phenotype may be independent of epigenetic marks, alternatively resulting from functions and protein interactions extrinsic of epigenetics. Associations between environmentally induced changes in DNA methylation and expression are strong in plants and mammals but notably absent in invertebrates and nonmammalian vertebrates. Given these challenges, we describe emerging approaches to better investigate how epigenetic modifications affect gene regulation, phenotypic plasticity, and divergence among populations.

Epigenetic Diversity Underlying Seasonal and Annual Variations in Brown Planthopper (BPH) Populations as Revealed by Methylation- sensitive Restriction Assay

Background

The brown planthopper (BPH) is a monophagous sap-sucking insect pest of rice that is responsible for massive yield loss. BPH populations, even when genetically homogenous, can display a vast range of phenotypes, and the development of effective pest-management strategies requires a good understanding of what generates this phenotypic variation. One potential source could be epigenetic differences.

Methods

With this premise, we explored epigenetic diversity, structure and differentiation in field populations of BPH collected across the rice-growing seasons over a period of two consecutive years. Using a modified methylation-sensitive restriction assay (MSRA) and CpG island amplification-representational difference analysis, site-specific cytosine methylation of five stress-responsive genes (CYP6AY1, CYP6ER1, Carboxylesterase, Endoglucanase, Tf2-transposon) was estimated, for identifying methylation-based epiallelic markers and epigenetic variation across BPH populations.

Results

Using a cost-effective and rapid protocol, our study, for the first time, revealed the epigenetic component of phenotypic variations in the wild populations of BPH. Besides, results showed that morphologically indistinguishable populations of BPH can be epigenetically distinct.

Conclusion

Screening field-collected BPH populations revealed the presence of previously unreported epigenetic polymorphisms and provided a platform for future studies aimed at investigating their significance for BPH. Furthermore, these findings can form the basis for understanding the contribution(s) of DNA methylation in providing phenotypic plasticity to BPH.

Warming during embryogenesis induces a lasting transcriptomic signature in fishes

Exposure to elevated temperatures during embryogenesis can influence the plasticity of tissues in later life. Despite these long-term changes in plasticity, few differentially expressed genes are ever identified, suggesting that the developmental programming of later life plasticity may occur through the modulation of other aspects of transcriptomic architecture, such as gene network organisation. Here, we use network modelling approaches to demonstrate that warm temperatures during embryonic development (developmental warming) have consistent effects in later life on the organisation of transcriptomic networks across four diverse species of fishes: Scyliorhinus canicula, Danio rerio, Dicentrarchus labrax, and Gasterosteus aculeatus. The transcriptomes of developmentally warmed fishes are characterised by an increased entropy of their pairwise gene interaction networks, implying a less structured, more 'random' set of gene interactions. We also show that, in zebrafish subject to developmental warming, the entropy of an individual gene within a network is associated with that gene's probability of expression change during temperature acclimation in later life. However, this association is absent in animals reared under 'control' conditions. Thus, the thermal environment experienced during embryogenesis can alter transcriptomic organisation in later life, and these changes may influence an individual's responsiveness to future temperature challenges.

Associations between DNA methylation and gene regulation depend on chromatin accessibility during transgenerational plasticity

BACKGROUND

Epigenetic processes are proposed to be a mechanism regulating gene expression during phenotypic plasticity. However, environmentally induced changes in DNA methylation exhibit little-to-no association with differential gene expression in metazoans at a transcriptome-wide level. It remains unexplored whether associations between environmentally induced differential methylation and expression are contingent upon other epigenomic processes such as chromatin accessibility. We quantified methylation and gene expression in larvae of the purple sea urchin Strongylocentrotus purpuratus exposed to different ecologically relevant conditions during gametogenesis (maternal conditioning) and modeled changes in gene expression and splicing resulting from maternal conditioning as functions of differential methylation, incorporating covariates for genomic features and chromatin accessibility. We detected significant interactions between differential methylation, chromatin accessibility, and genic feature type associated with differential expression and splicing.

RESULTS

Differential gene body methylation had significantly stronger effects on expression among genes with poorly accessible transcriptional start sites while baseline transcript abundance influenced the direction of this effect. Transcriptional responses to maternal conditioning were 4-13 × more likely when accounting for interactions between methylation and chromatin accessibility, demonstrating that the relationship between differential methylation and gene regulation is partially explained by chromatin state.

CONCLUSIONS

DNA methylation likely possesses multiple associations with gene regulation during transgenerational plasticity in S. purpuratus and potentially other metazoans, but its effects are dependent on chromatin accessibility and underlying genic features.

Sex-specific transgenerational plasticity: developmental temperatures of mothers and fathers have different effects on sons and daughters

Each parent can influence offspring phenotype via provisioning of the zygote or sex-specific DNA methylation. Transgenerational plasticity may therefore depend on the environmental conditions experienced by each parent. We tested this hypothesis by conducting a fully factorial experiment across three generations of guppies (Poecilia reticulata), determining the effects of warm (28°C) and cold (21°C) thermal backgrounds of mothers and fathers on mass and length, and thermal performance (sustained and sprint swimming speeds, citrate synthase and lactate dehydrogenase activities; 18, 24, 28, 32 and 36°C test temperatures) of sons and daughters. Offspring sex was significant for all traits except for sprint speed. Warmer mothers produced sons and daughters with reduced mass and length, and warmer fathers produced shorter sons. Sustained swimming speed (Ucrit) of male offspring was greatest when both parents were raised at 28°C, and warmer fathers produced daughters with greater Ucrit. Similarly, warmer fathers produced sons and daughters with greater metabolic capacity. We show that the thermal variation experienced by parents can modify offspring phenotype, and that predicting the impacts of environmental change on populations would require knowledge of the thermal background of each mother and father, particularly where sexes are spatially segregated.

How can physiology best contribute to wildlife conservation in a warming world?

Global warming is now predicted to exceed 1.5°C by 2033 and 2°C by the end of the 21st century. This level of warming and the associated environmental variability are already increasing pressure on natural and human systems. Here we emphasize the role of physiology in the light of the latest assessment of climate warming by the Intergovernmental Panel on Climate Change. We describe how physiology can contribute to contemporary conservation programmes. We focus on thermal responses of animals, but we acknowledge that the impacts of climate change are much broader phylogenetically and environmentally. A physiological contribution would encompass environmental monitoring, coupled with measuring individual sensitivities to temperature change and upscaling these to ecosystem level. The latest version of the widely accepted Conservation Standards designed by the Conservation Measures Partnership includes several explicit climate change considerations. We argue that physiology has a unique role to play in addressing these considerations. Moreover, physiology can be incorporated by institutions and organizations that range from international bodies to national governments and to local communities, and in doing so, it brings a mechanistic approach to conservation and the management of biological resources.

Transgenerational effects of intertidal environment on physiological phenotypes and DNA methylation in Pacific oysters

Climate change and intensifying human activity are posing serious threats to marine organisms. The fluctuating intertidal zone forms a miniature ecosystem of a rapidly changing environment for studying biological adaptation. Transgenerational plasticity (TGP), an evolutionary phenomenon in which parental experience influences offspring phenotypes, provides an avenue for adaptation, but the molecular mechanism was poorly understood in marine molluscs. In this study, wild Pacific oysters (Crassostrea gigas), which were collected from intertidal zones, were used to conduct two-generation breeding in a subtidal area combined with a heat shock experiment in the laboratory to investigate the intertidal environment-induced TGP under temperate subtidal condition and thermally exposed condition, respectively. We showed that TGP could influence the physiological phenotypes related to the status of oxidation and energy in non-stress-exposed subtidal offspring for at least two generations. Genomic DNA methylation exhibited heritable divergence between intertidal and subtidal oysters, and 1655 (or 42.83 %) differentially methylated genes (DMGs) in F₀ were continuously reserved to F₂, which may mediate physiological TGP by participating in biological processes including macromolecule metabolism, cellular responses to stress, and the positive regulation of molecular function, especially fatty acid metabolism. The intertidal experience also influenced the thermal plasticity of physiological phenotypes within and across generations. Totally, 320 (or 14.74 %) specific thermal response DMGs in the intertidal F₀ generation were identified in F₁ and F₂, participating in pathways including carbohydrate, lipid, and energy metabolism, signal transduction, and the organismal immune system, which suggested transgenerational intertidal effect mediated by these genes could positively contribute to stress adaptation and had potential applications for aquaculture. This study demonstrates an epigenetic mechanism for TGP in stress adaptation in marine molluscs, and provides new avenues to improve the stress adaptation for marine resource conservation and aquaculture.

Experimental DNA Demethylation Reduces Expression Plasticity and Thermal Tolerance in Pacific Oysters

Increasing seawater temperatures pose a great threat to marine organisms, especially those settled in fluctuating intertidal areas. DNA methylation, which can be induced by environmental variation, can influence gene expression and mediate phenotypic plasticity. However, the regulatory mechanisms of DNA methylation in gene expression-mediated adaptation to environmental stress have rarely been elucidated. In this study, DNA demethylation experiments were conducted on a typical intertidal species, the Pacific oyster (Crassostrea gigas), to determine the direct role of DNA methylation in regulating gene expression and adaptability under thermal stress. The global methylation level and the expression level of DNA methyltransferases (DNMT1, DNMT3a) showed an accordant variation trend under high temperatures, supporting that the genomic methylation status was catalyzed by DNMTs. DNA methylation inhibitor 5-Azacytidine (5-Aza) effectively inhibited DNA methylation level and decreased methylation plasticity at the 6th hour in thermal conditions. In total, 88 genes were identified as candidate DNA methylation-regulated thermal response genes; they exhibited reduced expression plasticity in response to heat stress, possibly caused by the decreased methylation plasticity. Post-heat shock, the thermal tolerance indicated by the survival curve was reduced when oysters were pretreated with 5-Aza, meaning that DNA demethylation negatively affected thermal adaptation in oysters. This study provides direct evidence for the crucial role of DNA methylation in mediating stress adaptation in marine invertebrates and contributes to the theoretical foundations underlying marine resource conservation and aquaculture.

Biological mechanisms matter in contemporary wildlife conservation

Given limited resources for wildlife conservation paired with an urgency to halt declines and rebuild populations, it is imperative that management actions are tactical and effective. Mechanisms are about how a system works and can inform threat identification and mitigation such that conservation actions that work can be identified. Here, we call for a more mechanistic approach to wildlife conservation and management where behavioral and physiological tools and knowledge are used to characterize drivers of decline, identify environmental thresholds, reveal strategies that would restore populations, and prioritize conservation actions. With a growing toolbox for doing mechanistic conservation research as well as a suite of decision-support tools (e.g., mechanistic models), the time is now to fully embrace the concept that mechanisms matter in conservation ensuring that management actions are tactical and focus on actions that have the potential to directly benefit and restore wildlife populations.

Genetic and epigenetic regulation of growth, reproduction, disease resistance and stress responses in aquaculture

Major progress has been made with genomic and genetic studies in aquaculture in the last decade. However, research on epigenetic regulation of aquaculture traits is still at an early stage. It is apparent that most, if not all, aquaculture traits are regulated at both genetic and epigenetic levels. This paper reviews recent progress in understanding of genetic and epigenetic regulation of important aquaculture traits such as growth, reproduction, disease resistance, and stress responses. Although it is challenging to make generalized statements, DNA methylation is mostly correlated with down-regulation of gene expression, especially when at promoters and enhancers. As such, methylation of growth factors and their receptors is negatively correlated with growth; hypomethylation of genes important for stress tolerance is correlated with increased stress tolerance; hypomethylation of genes important for male or female sex differentiation leads to sex differentiation into males or females, respectively. It is apparent that environmental regulation of aquaculture traits is mediated at the level of epigenetic regulation, and such environment-induced epigenetic changes appeared to be intergenerationally inherited, but evidences for transgenerational inheritance are still limited.

Evolution of plasticity: metabolic compensation for fluctuating energy demands at the origin of life

Phenotypic plasticity of physiological functions enables rapid responses to changing environments and may thereby increase the resilience of organisms to environmental change. Here, we argue that the principal hallmarks of life itself, self-replication and maintenance, are contingent on the plasticity of metabolic processes ('metabolic plasticity'). It is likely that the Last Universal Common Ancestor (LUCA), 4 billion years ago, already possessed energy-sensing molecules that could adjust energy (ATP) production to meet demand. The earliest manifestation of metabolic plasticity, switching cells from growth and storage (anabolism) to breakdown and ATP production (catabolism), coincides with the advent of Darwinian evolution. Darwinian evolution depends on reliable translation of information from information-carrying molecules, and on cell genealogy where information is accurately passed between cell generations. Both of these processes create fluctuating energy demands that necessitate metabolic plasticity to facilitate replication of genetic material and (proto)cell division. We propose that LUCA possessed rudimentary forms of these capabilities. Since LUCA, metabolic networks have increased in complexity. Generalist founder enzymes formed the basis of many derived networks, and complexity arose partly by recruiting novel pathways from the untapped pool of reactions that are present in cells but do not have current physiological functions (the so-called 'underground metabolism'). Complexity may thereby be specific to environmental contexts and phylogenetic lineages. We suggest that a Boolean network analysis could be useful to model the transition of metabolic networks over evolutionary time. Network analyses can be effective in modelling phenotypic plasticity in metabolic functions for different phylogenetic groups because they incorporate actual biochemical regulators that can be updated as new empirical insights are gained.

Windows of opportunity: Ocean warming shapes temperature-sensitive epigenetic reprogramming and gene expression across gametogenesis and embryogenesis in marine stickleback

Rapid climate change is placing many marine species at risk of local extinction. Recent studies show that epigenetic mechanisms (e.g. DNA methylation, histone modifications) can facilitate both within and transgenerational plasticity to cope with changing environments. However, epigenetic reprogramming (erasure and re-establishment of epigenetic marks) during gamete and early embryo development may hinder transgenerational epigenetic inheritance. Most of our knowledge about reprogramming stems from mammals and model organisms, whereas the prevalence and extent of reprogramming among non-model species from wild populations is rarely investigated. Moreover, whether reprogramming dynamics are sensitive to changing environmental conditions is not well known, representing a key knowledge gap in the pursuit to identify mechanisms underlying links between parental exposure to changing climate patterns and environmentally adapted offspring phenotypes. Here, we investigated epigenetic reprogramming (DNA methylation/hydroxymethylation) and gene expression across gametogenesis and embryogenesis of marine stickleback (Gasterosteus aculeatus) under three ocean warming scenarios (ambient, +1.5 and +4°C). We found that parental acclimation to ocean warming led to dynamic and temperature-sensitive reprogramming throughout offspring development. Both global methylation/hydroxymethylation and expression of genes involved in epigenetic modifications were strongly and differentially affected by the increased warming scenarios. Comparing transcriptomic profiles from gonads, mature gametes and early embryonic stages showed sex-specific accumulation and temperature sensitivity of several epigenetic actors. DNA methyltransferase induction was primarily maternally inherited (suggesting maternal control of remethylation), whereas induction of several histone-modifying enzymes was shaped by both parents. Importantly, massive, temperature-specific changes to the epigenetic landscape occurred in blastula, a critical stage for successful embryo development, which could, thus, translate to substantial consequences for offspring phenotype resilience in warming environments. In summary, our study identified key stages during gamete and embryo development with temperature-sensitive reprogramming and epigenetic gene regulation, reflecting potential 'windows of opportunity' for adaptive epigenetic responses under future climate change.

The effects of population and thermal acclimation on the growth, condition and cold responsive mRNA expression of age-0 lake sturgeon (Acipenser fulvescens)

In Manitoba, Canada, wild lake sturgeon (Acipenser fulvescens) populations exist along a latitudinal gradient and are reared in hatcheries to bolster threatened populations. We reared two populations of lake sturgeon, one from each of the northern and southern ends of Manitoba and examined the effects of typical hatchery temperatures (16°C) as well as 60-day acclimation to elevated rearing temperatures (20°C) on mortality, growth and condition throughout early development. Additionally, we examined the cold shock response, which may be induced during stocking, through the hepatic mRNA expression of genes involved in the response to cold stress and homeoviscous adaptation (HSP70, HSP90a, HSP90b, CIRP and SCD). Sturgeon were sampled after 1 day and 1 week following stocking into temperatures of 8, 6 and 4°C in a controlled laboratory environment. The southern population showed lower condition and higher mortality during early life than the northern population while increased rearing temperature impacted the growth and condition of developing northern sturgeon. During the cold shock, HSP70 and HSP90a mRNA expression increased in all sturgeon treatments as stocking temperature decreased, with higher expression observed in the southern population. Expression of HSP90b, CIRP and SCD increased as stocking temperature decreased in northern sturgeon with early acclimation to 20°C. Correlation analyses indicated the strongest molecular relationships were in the expression of HSP90b, CIRP and SCD, across all treatments, with a correlation between HSP90b and body condition in northern sturgeon with early acclimation to 20°C. Together, these observations highlight the importance of population and rearing environment throughout early development and on later cellular responses induced by cold stocking temperatures.

Two Locomotor Traits Show Different Patterns of Developmental Plasticity Between Closely Related Clonal and Sexual Fish

The capacity to compensate for environmental change determines population persistence and biogeography. In ectothermic organisms, performance at different temperatures can be strongly affected by temperatures experienced during early development. Such developmental plasticity is mediated through epigenetic mechanisms that induce phenotypic changes within the animal's lifetime. However, epigenetic modifiers themselves are encoded by DNA so that developmental plasticity could itself be contingent on genetic diversity. In this study, we test the hypothesis that the capacity for developmental plasticity depends on a species' among-individual genetic diversity. To test this, we exploited a unique species complex that contains both the clonal, genetically identical Amazon molly (Poecilia formosa), and the sexual, genetically diverse Atlantic molly (Poecilia mexicana). We predicted that the greater among-individual genetic diversity in the Atlantic molly may increase their capacity for developmental plasticity. We raised both clonal and sexual mollies at either warm (28°C) or cool (22°C) temperatures and then measured locomotor capacity (critical sustained swimming performance) and unforced movement in an open field across a temperature gradient that simulated environmental conditions often experienced by these species in the wild. In the clonal Amazon molly, differences in the developmental environment led to a shift in the thermal performance curve of unforced movement patterns, but much less so in maximal locomotor capacity. In contrast, the sexual Atlantic mollies exhibited the opposite pattern: developmental plasticity was present in maximal locomotor capacity, but not in unforced movement. Thus our data show that developmental plasticity in clones and their sexual, genetically more diverse sister species is trait dependent. This points toward mechanistic differences in how genetic diversity mediates plastic responses exhibited in different traits.

Plasticity of Performance Curves in Ectotherms: Individual Variation Modulates Population Responses to Environmental Change

Many ectothermic animals can respond to changes in their environment by altering the sensitivities of physiological rates, given sufficient time to do so. In other words, thermal acclimation and developmental plasticity can shift thermal performance curves so that performance may be completely or partially buffered against the effects of environmental temperature changes. Plastic responses can thereby increase the resilience to temperature change. However, there may be pronounced differences between individuals in their capacity for plasticity, and these differences are not necessarily reflected in population means. In a bet-hedging strategy, only a subsection of the population may persist under environmental conditions that favour either plasticity or fixed phenotypes. Thus, experimental approaches that measure means across individuals can not necessarily predict population responses to temperature change. Here, we collated published data of 608 mosquitofish (Gambusia holbrooki) each acclimated twice, to a cool and a warm temperature in random order, to model how diversity in individual capacity for plasticity can affect populations under different temperature regimes. The persistence of both plastic and fixed phenotypes indicates that on average, neither phenotype is selectively more advantageous. Fish with low acclimation capacity had greater maximal swimming performance in warm conditions, but their performance decreased to a greater extent with decreasing temperature in variable environments. In contrast, the performance of fish with high acclimation capacity decreased to a lesser extent with a decrease in temperature. Hence, even though fish with low acclimation capacity had greater maximal performance, high acclimation capacity may be advantageous when ecologically relevant behaviour requires submaximal locomotor performance. Trade-offs, developmental effects and the advantages of plastic phenotypes together are likely to explain the observed population variation.

Systematic review of climate change impact research in Nigeria: implication for sustainable development

There is evidence that Nigeria is already experiencing environmental challenges attributed to climate change (CC) and its impacts. This has clearly highlighted the need for knowledge-based strategies to help plan adequate mitigation and adaptation measures for the country. One of the basic requirements to ensure such strategies is the development of a database of national CC research. This will aid in the assessment of past and present scientific publications from which directions for future study can be mapped. The present study used standard, systematic, and bibliographic literature reviews to analyse the trend, focus, spatial variability, and effectiveness of published research on CC impacts in Nigeria. Four thematic areas of CC impact research were defined: Agriculture, Environment, Human and Multi-disciplinary study. A total of 701 articles were found to be relevant and the review shows that CC impacts and adaptations in the literature vary across research categories and locations. The period between 2011 (68 studies) and 2015 (80 studies) showed a tremendous rise in CC impact research with a peak in 2014 (84 studies). Studies in the agriculture category had the highest publications in 23 States of Nigeria. The review revealed three research gaps: (1) lack of research that investigated the magnitude of present and potential future impacts in the aquatic environment (2) little attention on CC impacts and adaptation in the Northern regions of Nigeria (3) absence of study investigating the effects of multiple variables of CC at the same time. The findings suggest that it would be useful to advance CC research in Nigeria beyond perceptive approaches to more quantitative ones. This is particularly important for highly vulnerable animals, crops, locations, and for better planning of adaptation strategies.

Dnmt3aa but Not Dnmt3ab Is Required for Maintenance of Gametogenesis in Nile Tilapia (Oreochromis niloticus)

Dnmt3a, a de novo methyltransferase, is essential for mammalian germ line DNA methylation. Only one Dnmt3a is identified in mammals, and homozygous mutants of Dnmt3a are lethal, while two Dnmt3a paralogs, dnmt3aa and dnmt3ab, are identified in teleosts due to the third round of genome duplication, and homozygous mutants of dnmt3aa and dnmt3ab are viable in zebrafish. The expression patterns and roles of dnmt3aa and dnmt3ab in gonadal development remain poorly understood in teleosts. In this study, we elucidated the precise expression patterns of dnmt3aa and dnmt3ab in tilapia gonads. Dnmt3aa was highly expressed in oogonia, phase I and II oocytes and granulosa cells in ovaries and spermatogonia and spermatocytes in testes, while dnmt3ab was mainly expressed in ovarian granulosa cells and testicular spermatocytes. The mutation of dnmt3aa and dnmt3ab was achieved by CRISPR/Cas9 in tilapia. Lower gonadosomatic index (GSI), increased apoptosis of oocytes and spermatocytes and significantly reduced sperm quality were observed in dnmt3aa^−/− mutants, while normal gonadal development was observed in dnmt3ab^−/− mutants. Consistently, the expression of apoptotic genes was significantly increased in dnmt3aa^−/− mutants. In addition, the 5-methylcytosine (5-mC) level in dnmt3aa^−/− gonads was decreased significantly, compared with that of dnmt3ab^−/− and wild type (WT) gonads. Taken together, our results suggest that dnmt3aa, not dnmt3ab, plays important roles in maintaining gametogenesis in teleosts.

Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing - Review

Recent developments have revolutionized the study of biomolecules. Among them are molecular markers, amplification and sequencing of nucleic acids. The latter is classified into three generations. The first allows to sequence small DNA fragments. The second one increases throughput, reducing turnaround and pricing, and is therefore more convenient to sequence full genomes and transcriptomes. The third generation is currently pushing technology to its limits, being able to sequence single molecules, without previous amplification, which was previously impossible. Besides, this represents a new revolution, allowing researchers to directly sequence RNA without previous retrotranscription. These technologies are having a significant impact on different areas, such as medicine, agronomy, ecology and biotechnology. Additionally, the study of biomolecules is revealing interesting evolutionary information. That includes deciphering what makes us human, including phenomena like non-coding RNA expansion. All this is redefining the concept of gene and transcript. Basic analyses and applications are now facilitated with new genome editing tools, such as CRISPR. All these developments, in general, and nucleic-acid sequencing, in particular, are opening a new exciting era of biomolecule analyses and applications, including personalized medicine, and diagnosis and prevention of diseases for humans and other animals.

Thyroid hormone regulation of thermal acclimation in ectotherms: Physiological mechanisms and ecoevolutionary implications

The pathways that regulate adaptive thermal plasticity in ectothermic vertebrates have received little attention relative to those in birds and mammals. However, there is increasing evidence that thyroid hormone represents a critical regulator of thermal plasticity in both ectothermic and endothermic vertebrates. In this review, I summarize the evidence for thyroid hormone-mediated thermal compensation responses in ectothermic vertebrates, with specific focus on effects on the whole animal, skeletal muscle, and cardiac muscle. Interestingly, these effects can differ wildly between focal tissues and species. I move on to discuss what the role of thyroid hormone in ectotherm thermal plasticity can reveal about stressor interactions and central vs. peripheral levels of thyroid hormone regulation. Lastly, I focus on the conserved nature of thyroid hormone signaling in animal thermal responses, with specific reference to the ectotherm → endotherm spectrum. I use this framework to highlight research avenues that will further resolve the evolutionary trajectory of thyroid hormone actions across animals. I hope to emphasize what thyroid hormone-mediated cold acclimation in a 3 cm fish can contribute to ongoing debates surrounding the impacts of stressor interactions, the potential costs of plasticity, the evolution of endothermy, and the impacts of global change.

How does epigenetics influence the course of evolution?

Epigenetics is the study of changes in gene activity that can be transmitted through cell divisions but cannot be explained by changes in the DNA sequence. Epigenetic mechanisms are central to gene regulation, phenotypic plasticity, development and the preservation of genome integrity. Epigenetic mechanisms are often held to make a minor contribution to evolutionary change because epigenetic states are typically erased and reset at every generation, and are therefore, not heritable. Nonetheless, there is growing appreciation that epigenetic variation makes direct and indirect contributions to evolutionary processes. First, some epigenetic states are transmitted intergenerationally and affect the phenotype of offspring. Moreover, bona fide heritable 'epialleles' exist and are quite common in plants. Such epialleles could, therefore, be subject to natural selection in the same way as conventional DNA sequence-based alleles. Second, epigenetic variation enhances phenotypic plasticity and phenotypic variance and thus can modulate the effect of natural selection on sequence-based genetic variation. Third, given that phenotypic plasticity is central to the adaptability of organisms, epigenetic mechanisms that generate plasticity and acclimation are important to consider in evolutionary theory. Fourth, some genes are under selection to be 'imprinted' identifying the sex of the parent from which they were derived, leading to parent-of-origin-dependent gene expression and effects. These effects can generate hybrid disfunction and contribute to speciation. Finally, epigenetic processes, particularly DNA methylation, contribute directly to DNA sequence evolution, because they act as mutagens on the one hand and modulate genome stability on the other by keeping transposable elements in check. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'