Environmental regulation of the neural epigenome

Parental effects are a major source of phenotypic plasticity. Moreover, there is evidence from studies with a wide range of species that the relevant parental signals are influenced by the quality of the parental environment. The link between the quality of the environment and the nature of the parental signal is consistent with the idea that parental effects, whether direct or indirect, might serve to influence the phenotype of the offspring in a manner that is consistent with the prevailing environmental demands. In this review we explore recent studies from the field of 'environmental epigenetics' that suggest that (1) DNA methylation states are far more variable than once thought and that, at least within specific regions of the genome, there is evidence for both demethylation and remethylation in post-mitotic cells and (2) that such remodeling of DNA methylation can occur in response to environmentally-driven, intracellular signaling pathways. Thus, studies of variation in mother-offspring interactions in rodents suggest that parental signals operate during pre- and/or post-natal life to influence the DNA methylation state at specific regions of the genome leading to sustained changes in gene expression and function. We suggest that DNA methylation is a candidate mechanism for parental effects on phenotypic variation.     

Transgenerational effects of stress exposure on offspring phenotypes in apomictic dandelion

Heritable epigenetic modulation of gene expression is a candidate mechanism to explain parental environmental effects on offspring phenotypes, but current evidence for environment-induced epigenetic changes that persist in offspring generations is scarce. In apomictic dandelions, exposure to various stresses was previously shown to heritably alter DNA methylation patterns. In this study we explore whether these induced changes are accompanied by heritable effects on offspring phenotypes. We observed effects of parental jasmonic acid treatment on offspring specific leaf area and on offspring interaction with a generalist herbivore; and of parental nutrient stress on offspring root-shoot biomass ratio, tissue P-content and leaf morphology. Some of the effects appeared to enhance offspring ability to cope with the same stresses that their parents experienced. Effects differed between apomictic genotypes and were not always consistently observed between different experiments, especially in the case of parental nutrient stress. While this context-dependency of the effects remains to be further clarified, the total set of results provides evidence for the existence of transgenerational effects in apomictic dandelions. Zebularine treatment affected the within-generation response to nutrient stress, pointing at a role of DNA methylation in phenotypic plasticity to nutrient environments. This study shows that stress exposure in apomictic dandelions can cause transgenerational phenotypic effects, in addition to previously demonstrated transgenerational DNA methylation effects.     

Environmental enrichment induces intergenerational behavioural and epigenetic effects on fish

Parental effects influence offspring phenotypes through pre‐ and post‐natal routes but little is known about their molecular basis, and therefore their adaptive significance. Epigenetic modifications, which control gene expression without changes in the DNA sequence and are influenced by the environment, may contribute to parental effects. We investigated the effects of environmental enrichment on the behaviour, metabolic rate and brain DNA methylation patterns of parents and offspring of the highly inbreed mangrove killifish (Kryptolebias marmoratus). Parental fish reared in enriched environments had lower cortisol levels, lower metabolic rates and were more active and neophobic than those reared in barren environments. They also differed in 1,854 methylated cytosines (DMCs). Offspring activity and neophobia were determined by the parental environment. Among the DMCs of the parents, 98 followed the same methylation patterns in the offspring, three of which were significantly influenced by parental environments irrespective of their own rearing environment. Our results suggest that parental environment influences the behaviour and, to some extent, the brain DNA methylation patterns of the offspring.     

Effects of parental light environment on growth and morphological responses of clonal offspring

• Environments experienced by parent ramets of clonal plants can potentially influence fitness of clonal offspring ramets. Such clonal parental effects may result from heritable epigenetic changes, such as DNA methylation, which can be removed by application of DNA de‐methylation agents such as 5‐azacytidine.
• To test whether parental shading effects occur via clonal generation and whether DNA methylation plays a role in such effects, parent plants of the clonal herb Alternanthera philoxeroides were first subjected to two levels of light intensity (high versus low) crossed with two levels of DNA de‐methylation (no or with de‐methylation by application of 5‐azacytidine), and then clonal offspring taken from each of these four types of parent plant were subjected to the same two light levels.
• Parental shading effects transmitted via clonal generation decreased growth and modified morphology of clonal offspring. Offspring responses were also influenced by DNA methylation level of parent plants. For clonal offspring growing under low light, parental shading effects on growth and morphology were always negative, irrespective of the parental de‐methylation treatment. For clonal offspring growing under high light, parental shading effects on offspring growth and morphology were negative when the parents were not treated with 5‐azacytidine, but neutral when they were treated with 5‐azacytidine.
• Overall, parental shading effects on clonal offspring performance of A. philoxeroides were found, and DNA methylation is likely to be involved in such effects. However, parental shading effects contributed little to the tolerance of clonal offspring to shading.

     

Epigenetic effects of infection on the phenotype of host offspring: parasites reaching across host generations

Parasite‐induced changes in host phenotype are now well‐documented from a wide range of taxa. There is a growing body of evidence indicating that parasites can also have trans‐generational consequences, with infection of a host leading to changes in the phenotype of its offspring, though the latter are not parasitised. Several proximate mechanisms have been put forward to explain these ‘maternal’ effects, most involving hormonal or other physiological pathways, ultimately leading to offspring that are pre‐adapted to the parasites they are most likely to encounter based on their mother's experience. Here, we propose that all these trans‐generational effects on offspring phenotype must involve epigenetic phenomena. Epigenetics concerns the appearance and inheritance of seemingly new phenotypic traits without changes in the underlying DNA sequence. Since diet and other environmental factors experienced by a mother can affect gene expression in her offspring by turning genes ‘on’ or ‘off’ (for example, via DNA methylation), why couldn't parasites do it? Although epigenetic effects have not been explicitly invoked to account for trans‐generational impacts of parasites on the phenotype of host offspring, the existing evidence is fully compatible with their involvement. We argue that epigenetic mechanisms must play a central role; we also discuss their evolutionary implications and suggest questions for future investigations in this new and exciting research direction.     

Transgenerational plasticity of inducible defences: Combined effects of grand‐parental,parental and current environments

Phenotypic plasticity can occur across generations (transgenerational plasticity) when environments experienced by the previous generations influenced offspring phenotype. The evolutionary importance of transgenerational plasticity, especially regarding within‐generational plasticity, is a currently hot topic in the plasticity framework. How long an environmental effect can persist across generations and whether multigenerational effects are cumulative are primordial—for the evolutionary significance of transgenerational plasticity—but still unresolved questions. In this study, we investigated how the grand‐parental, parental and offspring exposures to predation cues shape the predator‐induced defences of offspring in the Physa acuta snail. We expected that the offspring phenotypes result from a three‐way interaction among grand‐parental, parental and offspring environments. We exposed three generations of snails without and with predator cues according to a full factorial design and measured offspring inducible defences. We found that both grand‐parental and parental exposures to predator cues impacted offspring antipredator defences, but their effects were not cumulative and depended on the defences considered. We also highlighted that the grand‐parental environment did alter reaction norms of offspring shell thickness, demonstrating an interaction between the grand‐parental transgenerational plasticity and the within‐generational plasticity. We concluded that the effects of multigenerational exposure to predator cues resulted on complex offspring phenotypic patterns which are difficult to relate to adaptive antipredator advantages.     

Weak evidence for anticipatory parental effects in plants and animals

The evolution of adaptive phenotypic plasticity relies on the presence of cues that enable organisms to adjust their phenotype to match local conditions. Although mostly studied with respect to nonsocial cues, it is also possible that parents transmit information about the environment to their offspring. Such ‘anticipatory parental effects’ or ‘adaptive transgenerational plasticity’ can have important consequences for the dynamics and adaptive potential of populations in heterogeneous environments. Yet, it remains unknown how widespread this form of plasticity is. Using a meta‐analysis of experimental studies with a fully factorial design, we show that there is only weak evidence for higher offspring performance when parental and offspring environments are matched compared with when they are mismatched. Estimates of heterogeneity among studies suggest that effects, when they occur, are subtle. Study features, environmental context, life stage and trait categories all failed to explain significant amounts of variation in effect sizes. We discuss theoretical and methodological reasons for the limited evidence for anticipatory parental effects and suggest ways to improve our understanding of the prevalence of this form of plasticity in nature.     

Parental effects and the evolution of phenotypic memory

Despite growing evidence for nongenetic inheritance, the ecological conditions that favour the evolution of heritable parental or grandparental effects remain poorly understood. Here, we systematically explore the evolution of parental effects in a patch‐structured population with locally changing environments. When selection favours the production of a mix of offspring types, this mix differs according to the parental phenotype, implying that parental effects are favoured over selection for bet‐hedging in which the mixture of offspring phenotypes produced does not depend on the parental phenotype. Positive parental effects (generating a positive correlation between parental and offspring phenotype) are favoured in relatively stable habitats and when different types of local environment are roughly equally abundant, and can give rise to long‐term parental inheritance of phenotypes. By contrast, unstable habitats can favour negative parental effects (generating a negative correlation between parental and offspring phenotype), and under these circumstances, even slight asymmetries in the abundance of local environmental states select for marked asymmetries in transmission fidelity.     

EFFECTS OF MATERNAL AND PATERNAL ENVIRONMENT AND GENOTYPE ON OFFSPRING PHENOTYPE IN SOLIDAGO ALTISSIMA L.

To predict the possible evolutionary response of a plant species to a new environment, it is necessary to separate genetic from environmental sources of phenotypic variation. In a case study of the invader Solidago altissima, the influences of several kinds of parental effects and of direct inheritance and environment on offspring phenotype were separated. Fifteen genotypes were crossed in three 5 × 5 diallels excluding selfs. Clonal replicates of the parental genotypes were grown in two environments such that each diallel could be made with maternal/paternal plants from sand/sand, sand/soil, soil/sand, and soil/soil. In a first experiment (1989) offspring were raised in the experimental garden and in a second experiment (1990) in the glasshouse. Parent plants growing in sand invested less biomass in inflorescences but produced larger seeds than parent plants growing in soil. In the garden experiment, phenotypic variation among offspring was greatly influenced by environmental heterogeneity. Direct genetic variation (within diallels) was found only for leaf characters and total leaf mass. Germination probability and early seedling mass were significantly affected by phenotypic differences among maternal plants because of genotype ( genetic maternal effects ) and soil environment ( general environmental maternal effects ). Seeds from maternal plants in sand germinated better and produced bigger seedlings than seeds from maternal plants in soil. They also grew taller with time, probably because competition accentuated the initial differences. Height growth and stem mass at harvest (an integrated account of individual growth history) of offspring varied significantly among crosses within parental combinations ( specific environmental maternal effects ). In the glasshouse experiment, the influence of environmental heterogeneity and competition could be kept low. Except for early characters, the influence of direct genetic variation was large but again leaf characters (= basic module morphology) seemed to be under stricter genetic control than did size characters. Genetic maternal effects, general environmental maternal effects, and specific environmental maternal effects dominated in early characters. The maternal effects were exerted both via seed mass and directly on characters of young offspring. Persistent effects of the general paternal environment ( general environmental paternal effects ) were found for leaf length and stem and leaf mass at harvest. They were opposite in direction to the general environmental maternal effects, that is the same genotypes produced “better mothers” in sand but “better fathers” in soil. The general environmental paternal effects must have been due to differences in pollen quality, resulting from pollen selection within the male parent or leading to pre- or postzygotic selection within the female parent. The ranking of crosses according to mean offspring phenotypes was different in the two experiments, suggesting strong interaction of the observed effects with the environment. The correlation structure among characters changed less between experiments than did the pattern of variation of single characters, but under the competitive conditions in the garden plant height seemed to be more directly related to fitness than in the glasshouse. Reduced competition could also explain why maternal effects were less persistent in the glasshouse than in the garden experiment. Evolution via selection of maternal effects would be possible in the study population because these effects are in part due to genetic differences among parents.     

Adaptive parental effects: the importance of estimating environmental predictability and offspring fitness appropriately

Anticipatory parental effects (APE's) occur when parents adjust the phenotype of their offspring to match the local environment, so as to increase the fitness of both parents and offspring. APE's, as in the evolution of adaptive phenotypic plasticity more generally, are predicated on the idea that the parental environment is a reliable predictor of the offspring environment. Most studies on APE's fail to explicitly consider environmental predictability so risk searching for APE's under circumstances where they are unlikely to occur. This failure is perhaps one of the major reasons for mixed evidence for APE's in a recent meta‐analysis. Here, we highlight some often‐overlooked assumptions in studies of APE's and provide a framework for identifying and testing APE's. Our review highlights the importance of measuring environmental predictability, outlines the minimal requirements for experimental designs, explains the important differences between relative and absolute measures of offspring fitness, and highlights some potential issues in assigning components of offspring fitness to parental fitness. Our recommendations should result in more targeted and effective tests of APE's. Synthesis A decent set of theory is available to understand when certain kinds of parental effects might act to increase parental fitness (i.e. be ‘adaptive’). This theory could be better incorporated into empirical studies on anticipatory parental effects (APE's). Here, we provide practical advice for how empirical studies can more closely align with the theoretical underpinnings of adaptive parental effects. In short, robust inferences on APE's require quantitative estimates of environmental predictability in the field over the space and time scales relevant to the life history of the study organism as well as an understanding of when to use absolute or relative offspring fitness.     

Structural (UV) and carotenoid‐based plumage coloration – signals for parental investment?

Parental care increases parental fitness through improved offspring condition and survival but comes at a cost for the caretaker(s). To increase life‐time fitness, caring parents are, therefore, expected to adjust their reproductive investment to current environmental conditions and parental capacities. The latter is thought to be signaled via ornamental traits of the bearer. We here investigated whether pre‐ and/or posthatching investment of blue tit (Cyanistes caeruleus) parents was related to ornamental plumage traits (UV crown coloration and carotenoid‐based plumage coloration) expressed by either the individual itself (i.e. “good parent hypothesis”) or its partner (i.e. “differential allocation hypothesis”). Our results show that neither prehatching (that is clutch size and offspring begging intensity) nor posthatching parental investment (provisioning rate, offspring body condition at fledging) was related to an individual's UV crown coloration or to that of its partner. Similar observations were made for carotenoid‐based plumage coloration, except for a consistent positive relationship between offspring begging intensity and maternal carotenoid‐based plumage coloration. This sex‐specific pattern likely reflects a maternal effect mediated via maternally derived egg substances, given that the relationship persisted when offspring were cross‐fostered. This suggests that females adjust their offspring's phenotype toward own phenotype, which may facilitate in particular mother‐offspring co‐adaptation. Overall, our results contribute to the current state of evidence that structural or pigment‐based plumage coloration of blue tits are inconsistently correlated with central life‐history traits.     

A paternal environmental legacy: Evidence for epigenetic inheritance through the male germ line

Literature on maternal exposures and the risk of epigenetic changes or diseases in the offspring is growing. Paternal contributions are often not considered. However, some animal and epidemiologic studies on various contaminants, nutrition, and lifestyle‐related conditions suggest a paternal influence on the offspring's future health. The phenotypic outcomes may have been attributed to DNA damage or mutations, but increasing evidence shows that the inheritance of environmentally induced functional changes of the genome, and related disorders, are (also) driven by epigenetic components. In this essay we suggest the existence of epigenetic windows of susceptibility to environmental insults during sperm development. Changes in DNA methylation, histone modification, and non‐coding RNAs are viable mechanistic candidates for a non‐genetic transfer of paternal environmental information, from maturing germ cell to zygote. Inclusion of paternal factors in future research will ultimately improve the understanding of transgenerational epigenetic plasticity and health‐related effects in future generations.     

Molecular insights into the transgenerational inheritance of stress memory

There is accumulating evidence to show that environmental stressors can regulate a variety of phenotypes in descendants through germline-mediated epigenetic inheritance. Studies of model organisms exposed to environmental cues (e.g., diet, heat stress, toxins) indicate that altered DNA methylations, histone modifications, or non-coding RNAs in the germ cells are responsible for the transgenerational effects. In addition, it has also become evident that maternal provision could provide a mechanism for the transgenerational inheritance of stress adaptations that result from ancestral environmental cues. However, how the signal of environmentally-induced stress response transmits from the soma to the germline, which may influence offspring fitness, remains largely elusive. Small RNAs could serve as signaling molecules that transmit between tissues and even across generations. Furthermore, a recent study revealed that neuronal mitochondrial perturbations induce a transgenerational induction of the mitochondrial unfolded protein response mediated by a Wnt-dependent increase in mitochondrial DNA levels. Here, we review recent work on the molecular mechanism by which parental experience can affect future generations and the importance of soma-to-germline signaling for transgenerational inheritance.     

Dynamic changes in DNA methylation during embryonic and postnatal development of an altricial wild bird

DNA methylation could shape phenotypic responses to environmental cues and underlie developmental plasticity. Environmentally induced changes in DNA methylation during development can give rise to stable phenotypic traits and thus affect fitness. In the laboratory, it has been shown that the vertebrate methylome undergoes dynamic reprogramming during development, creating a critical window for environmentally induced epigenetic modifications. Studies of DNA methylation in the wild are lacking, yet are essential for understanding how genes and the environment interact to affect phenotypic development and ultimately fitness. Furthermore, our knowledge of the establishment of methylation patterns during development in birds is limited. We quantified genome‐wide DNA methylation at various stages of embryonic and postnatal development in an altricial passerine bird, the great tit Parus major. While, there was no change in global DNA methylation in embryonic tissue during the second half of embryonic development, a twofold increase in DNA methylation in blood occurred between 6 and 15 days posthatch. Though not directly comparable, DNA methylation levels were higher in the blood of nestlings compared with embryonic tissue at any stage of prenatal development. This provides the first evidence that DNA methylation undergoes global change during development in a wild bird, supporting the hypothesis that methylation mediates phenotypic development. Furthermore, the plasticity of DNA methylation demonstrated during late postnatal development, in the present study, suggests a wide window during which DNA methylation could be sensitive to environmental influences. This is particularly important for our understanding of the mechanisms by which early‐life conditions influence later‐life performance. While, we found no evidence for differences in genome‐wide methylation in relation to habitat of origin, environmental variation is likely to be an important driver of variation in methylation at specific loci.     

The effect of maternal and paternal environments on seed characters in the herbaceous plant Campanula Americana (Campanulaceae)

Maternal environments typically influence the phenotype of their offspring. However, the effect of the paternal environment or the potential for joint effects of both parental environments on offspring characters is poorly understood. Two populations of Campanula americana, a woodland herb with a variable life history, were used to determine the influence of maternal and paternal light and nutrient environments on offspring seed characters. Families were grown in the greenhouse in three levels of light or three levels of nutrients. Crosses were conducted within each environmental gradient to produce seeds with all combinations of maternal and paternal environments. On average, increasing maternal nutrient and light levels increased seed mass and decreased percentage germination. The paternal environment affected seed mass, germination time, and percentage germination. However, the influence of the paternal environment varied across maternal environments, suggesting that paternal environmental effects should be evaluated in the context of maternal environments. Significant interactions between family and the parental environments for offspring characters suggest that parental environmental effects are genetically variable. In C. americana, the timing of germination determines life history. Therefore parental environmental effects on germination timing, and genetic variation in those parental effects, suggest that parental environments may influence life history evolution in this system.     

Genome methylation patterns across castes and generations in a parasitoid wasp

Environmental influences shape phenotypes within and across generations, often through DNA methylations that modify gene expression. Methylations were proposed to mediate caste and task allocation in some eusocial insects, but how an insect's environment affects DNA methylation in its offspring is yet unknown. We characterized parental effects on methylation profiles in the polyembryonic parasitoid wasp Copidosoma koehleri, as well as methylation patterns associated with its simple caste system. We used methylation‐sensitive amplified fragment length polymorphism (MS‐AFLP) to compare methylation patterns, among (1) reproductive and soldier larvae; and (2) offspring (larvae, pupae, and adults) of wasps that were reared at either high or low larval density and mated in the four possible combinations. Methylation frequencies were similar across castes, but the profiles of methylated fragments differed significantly. Parental rearing density did not affect methylation frequencies in the offspring at any developmental stage. Principal coordinate analysis indicated no significant differences in methylation profiles among the four crossbreeding groups and the three developmental stages. Nevertheless, a clustering analysis, performed on a subset of the fragments, revealed similar methylation patterns in larvae, pupae, and adults in two of the four parental crosses. Nine fragments were methylated at two cytosine sites in all larvae, and five others were methylated at two sites in all adults. Thus, DNA methylations correlate with within‐generation phenotypic plasticity due to caste. However, their association with developmental stage and with transgenerational epigenetic effects is not clearly supported.     

Influence of incubation recess patterns on incubation period and hatchling traits in wood ducks Aix sponsa

Parental effects are influential sources of phenotypic variation in offspring. Incubation temperature in birds, which is largely driven by parental behavior and physiology, affects a suite of phenotypic traits in offspring including growth, immune function, stress endocrinology, and sex ratios. The importance of average incubation temperature on offspring phenotype has recently been described in birds, but parental incubation behaviors like the duration and frequency of recesses from the nest can be variable. There are few studies describing how or if thermal variation as a result of variable incubation affects offspring phenotype. We incubated wood duck Aix sponsa eggs under three different incubation regimes, based on patterns that occur in nature, which varied in off‐bout duration and/or temperature. We measured incubation period, morphometrics at hatching, and monitored growth and body condition for nine days post hatch. When average incubation temperature was allowed to drop from 35.9°C to 35.5°C as a result of doubled off‐bout duration, we found a significant 2 d extension in incubation period, but no effects on duckling hatch mass, or growth and body condition up to nine days post hatch. However, when average incubation temperatures were equivalent (35.9°C), doubling the duration of the simulated off‐bouts did not influence incubation period or any post hatch parameters. Our results suggest that if incubating parents can maintain favorable thermal environments in the nest via altered behavior (e.g. manipulating nest insulation) and/or physiology (e.g. heat production), parents may be able to avoid the costs of longer incubation periods resulting from increased off‐bout duration.     

Maternal eNOS deficiency determines a fatty liver phenotype of the offspring in a sex dependent manner

Maternal environmental factors can impact on the phenotype of the offspring via the induction of epigenetic adaptive mechanisms. The advanced fetal programming hypothesis proposes that maternal genetic variants may influence the offspring's phenotype indirectly via epigenetic modification, despite the absence of a primary genetic defect. To test this hypothesis, heterozygous female eNOS knockout mice and wild type mice were bred with male wild type mice. We then assessed the impact of maternal eNOS deficiency on the liver phenotype of wild type offspring. Birth weight of male wild type offspring born to female heterozygous eNOS knockout mice was reduced compared to offspring of wild type mice. Moreover, the offspring displayed a sex specific liver phenotype, with an increased liver weight, due to steatosis. This was accompanied by sex specific differences in expression and DNA methylation of distinct genes. Liver global DNA methylation was significantly enhanced in both male and female offspring. Also, hepatic parameters of carbohydrate metabolism were reduced in male and female offspring. In addition, male mice displayed reductions in various amino acids in the liver. Maternal genetic alterations, such as partial deletion of the eNOS gene, can affect liver metabolism of wild type offspring without transmission of the intrinsic defect. This occurs in a sex specific way, with more detrimental effects in females. This finding demonstrates that a maternal genetic defect can epigenetically alter the phenotype of the offspring, without inheritance of the defect itself. Importantly, these acquired epigenetic phenotypic changes can persist into adulthood.     

克隆和有性亲体效应及其调控机制

植物表型受自身基因型、所处环境及其亲体所经历环境的共同影响;其中,亲体环境对子代表型的影响被称为亲体效应。亲体效应不仅可通过有性繁殖产生的种子传递给后代（即有性亲体效应）,也可以通过克隆生长等无性繁殖产生的分株传递给后代（即克隆亲体效应）。亲体效应对植物种群,特别是对有性繁殖受限、缺乏遗传变异的克隆植物种群的长期进化可能发挥着极其重要的作用,因此,对亲体效应研究进展的梳理非常必要。对克隆亲体效应和有性亲体效应的内涵进行了阐释,并论述了克隆和有性亲体效应对子代表型、适合度、种内/种间竞争能力以及种群/群落结构和功能的潜在影响;阐述了亲体效应的潜在调控机制,包括供给机制、代谢物质调控机制、表观遗传机制等;论述了克隆亲体效应在克隆植物适应进化中的作用。未来可以就克隆亲体效应的遗传稳定性及其对克隆生活史性状变异的贡献程度,以及克隆和有性亲体效应引起的表型多样性对种内/种间关系、种群/群落多样性及生态系统结构、功能和稳定性的影响开展深入研究。