A Tissue Comparison of DNA Methylation of the Glucocorticoid Receptor Gene (Nr3c1) in European Starlings

Lasting benefits of embryonic eavesdropping on parent-parent communication

Developing embryos have traditionally been viewed as passive agents in the evolution of family conflicts, with maternal substances within the uterus or eggs as main factors modulating later expression of offspring solicitation behaviors. Yet, parent-offspring conflict theory predicts that offspring might also rely on alternative cues to adjust demand in response to prenatal cues of parental capacity for resource provisioning. Here, we show how embryonic experience with vocalizations carried out by parents during nest-relief displays at incubation adaptively shapes avian offspring development, providing lasting benefits to offspring. Genetic siblings prenatally exposed to different levels of parent-parent communication showed differences in epigenetic patterns, adrenocortical responsiveness, development, and food solicitation behavior. The correspondence between prenatal acoustic experience and parental context positively influenced the nutritional status and growth rate of offspring reared by communicative parents. Offspring can thus retain strong control over their own development by gathering prenatal acoustic information about parental generosity.

The impact of parental and developmental stress on DNA methylation in the avian hypothalamic-pituitary-adrenal axis

The hypothalamic-pituitary-adrenal (HPA) axis coordinates an organism's response to environmental stress. The responsiveness and sensitivity of an offspring's stress response may be shaped not only by stressors encountered in their early post-natal environment but also by stressors in their parent's environment. Yet, few studies have considered how stressors encountered in both of these early life environments may function together to impact the developing HPA axis. Here, we manipulated stressors in the parental and post-natal environments in a population of house sparrows (Passer domesticus) to assess their impact on changes in DNA methylation (and corresponding gene expression) in a suite of genes within the HPA axis. We found that nestlings that experienced early life stress across both life-history periods had higher DNA methylation in a critical HPA axis gene, the glucocorticoid receptor (NR3C1). In addition, we found that the life-history stage when stress was encountered impacted some genes (HSD11B1, NR3C1 and NR3C2) differently. We also found evidence for the mitigation of parental stress by post-natal stress (in HSD11B1 and NR3C2). Finally, by assessing DNA methylation in both the brain and blood, we were able to evaluate cross-tissue patterns. While some differentially methylated regions were tissue-specific, we found cross-tissue changes in NR3C2 and NR3C1, suggesting that blood is a suitable tissue for assessing DNA methylation as a biomarker of early life stress. Our results provide a crucial first step in understanding the mechanisms by which early life stress in different life-history periods contributes to changes in the epigenome of the HPA axis.

Covariation between glucocorticoid levels and receptor expression modulates embryo development and postnatal phenotypes in gulls

The hypothalamic-pituitary-adrenocortical axis can translate, through glucocorticoid secretion, the prenatal environment to development to produce phenotypes that match prevailing environmental conditions. However, whether developmental plasticity is modulated by the interaction between circulating glucocorticoids and receptor expression remains unclear. Here, we tested whether covariation between plasma corticosterone (CORT) and glucocorticoid receptor gene (Nr3c1) expression in blood underlies embryonic developmental programming in yellow-legged gulls (Larus michahellis). We examined variations in circulating levels of CORT and the expression and DNA methylation patterns of Nr3c1 in response to two ecologically relevant prenatal factors: adult alarm calls (a cue of predator presence) and changes in prenatal light environment (a cue of competitive disadvantage). We then determined whether embryonic development and postnatal phenotypes were associated with CORT levels and Nr3c1 expression, and explored direct and indirect relationships between the prenatal environment, hormone-receptor covariation, and postnatal phenotypes. Prenatal exposure to alarm calls increased CORT levels and up-regulated Nr3c1 expression in gull chicks, while exposure to light cues reduced both hormone levels and receptor expression. Chicks prenatally exposed to alarm calls showed altered DNA methylation profiles in the Nr3c1 regulatory region, but patterns varied throughout the breeding season and between years. Moreover, our results suggest a negative relationship between DNA methylation and expression in Nr3c1 , at least at specific CpG sites. The interplay between circulating CORT and Nr3c1 expression affected embryo developmental timing and vocalizations, as well as hatchling mass and fitness-relevant behaviours. These findings provide a link between prenatal inputs, glucocorticoid function and phenotypic outcomes, suggesting that hormone-receptor interaction may underlie developmental programming in free-living animals.

Prior parental experience attenuates hormonal stress responses and alters hippocampal glucocorticoid receptors in biparental rock doves

In the face of challenges, animals must balance investments in reproductive effort versus their own survival. Physiologically, this trade-off may be mediated by glucocorticoid release by the hypothalamic-pituitary-adrenal axis and prolactin release from the pituitary to maintain parental care. The degree to which animals react to and recover from stressors likely affects maintenance of parental behavior and, ultimately, fitness. However, less is known about how gaining parental experience may alter hormonal stress responses and their underlying neuroendocrine mechanisms. To address this gap, we measured the corticosterone (CORT) and prolactin (PRL) stress response in individuals of both sexes of the biparental rock dove (Columba livia) that had never raised chicks versus birds that had fledged at least one chick. We measured both CORT and PRL at baseline and after an acute stressor (30 min restraint). We also measured negative feedback ability by administering dexamethasone, a synthetic glucocorticoid that suppresses CORT release, and measured CORT and PRL after 60 min. All hormones were measured when birds were not actively nesting to assess whether effects of parental experience extend beyond the breeding bout. Experienced birds had lower stress-induced and negative-feedback CORT, and higher stress-induced PRL than inexperienced birds. In a separate experiment, we measured glucocorticoid receptor subtype expression in the hippocampus, a key site of negative feedback regulation. Experienced birds showed higher glucocorticoid receptor expression than inexperienced controls, which may mediate their ability to attenuate CORT release. Together, these results shed light on potential mechanisms by which gaining experience may improve parental performance and fitness.

Associations between DNA methylation and telomere length during early life: Insight from wild zebra finches (Taeniopygia guttata)

Telomere length and DNA methylation (DNAm) are two promising biomarkers of biological age. Environmental factors and life history traits are known to affect variation in both these biomarkers, especially during early life, yet surprisingly little is known about their reciprocal association, especially in natural populations. Here, we explore how variation in DNAm, growth rate, and early-life conditions are associated with telomere length changes during development. We tested these associations by collecting data from wild, nestling zebra finches in the Australian desert. We found that increases in the level of DNAm were negatively correlated with telomere length changes across early life. We also confirm previously documented effects of post hatch growth rate and clutch size on telomere length in a natural ecological context for a species that has been extensively studied in the laboratory. However, we did not detect any effect of ambient temperature during developmental on telomere length dynamics. We also found that the absolute telomere length of wild zebra finches, measured using the in-gel TRF method, was similar to that of captive birds. Our findings highlight exciting new opportunities to link and disentangle potential relationships between DNA based biomarkers of ageing, and of physiological reactions to environmental change.

Epigenetics in Ecology, Evolution, and Conservation

Epigenetic variation is often characterized by modifications to DNA that do not alter the underlying nucleotide sequence, but can influence behavior, morphology, and physiological phenotypes by affecting gene expression and protein synthesis. In this review, we consider how the emerging field of ecological epigenetics (eco-epi) aims to use epigenetic variation to explain ecologically relevant phenotypic variation and predict evolutionary trajectories that are important in conservation. Here, we focus on how epigenetic data have contributed to our understanding of wild populations, including plants, animals, and fungi. First, we identified published eco-epi literature and found that there was limited taxonomic and ecosystem coverage and that, by necessity of available technology, these studies have most often focused on the summarized epigenome rather than locus- or nucleotide-level epigenome characteristics. We also found that while many studies focused on adaptation and heritability of the epigenome, the field has thematically expanded into topics such as disease ecology and epigenome-based ageing of individuals. In the second part of our synthesis, we discuss key insights that have emerged from the epigenetic field broadly and use these to preview the path toward integration of epigenetics into ecology. Specifically, we suggest moving focus to nucleotide-level differences in the epigenome rather than whole-epigenome data and that we incorporate several facets of epigenome characterization (e.g., methylation, chromatin structure). Finally, we also suggest that incorporation of behavior and stress data will be critical to the process of fully integrating eco-epi data into ecology, conservation, and evolutionary biology.

Methylation patterns at fledging predict delayed dispersal in a cooperatively breeding bird

Individuals may delay dispersing from their natal habitat, even after maturation to adulthood. Such delays can have broad consequences from determining population structure to allowing an individual to gain indirect fitness by helping parents rear future offspring. Dispersal in species that use delayed dispersal is largely thought to be opportunistic; however, how individuals, particularly inexperienced juveniles, assess their environments to determine the appropriate time to disperse is unknown. One relatively unexplored possibility is that dispersal decisions are the result of epigenetic mechanisms interacting between a genome and environment during development to generate variable dispersive phenotypes. Here, we tested this using epiRADseq to compare genome-wide levels of DNA methylation of blood in cooperatively breeding chestnut-crowned babblers (Pomatostomus ruficeps). We measured dispersive and philopatric individuals at hatching, before fledging, and at 1 year (following when first year dispersal decisions would be made). We found that individuals that dispersed in their first year had a reduced proportion of methylated loci than philopatric individuals before fledging, but not at hatching or as adults. Further, individuals that dispersed in the first year had a greater number of loci change methylation state (i.e. gain or lose) between hatching and fledging. The existence and timing of these changes indicate some influence of development on epigenetic changes that may influence dispersal behavior. However, further work needs to be done to address exactly how developmental environments may be associated with dispersal decisions and which loci in particular are manipulated to generate such changes.

Urbanization is associated with modifications in DNA methylation in a small passerine bird

Urbanization represents a fierce driver of phenotypic change, yet the molecular mechanisms underlying observed phenotypic patterns are poorly understood. Epigenetic changes are expected to facilitate more rapid adaption to changing or novel environments, such as our towns and cities, compared with slow changes in gene sequence. A comparison of liver and blood tissue from great tits Parus major originating from an urban and a forest site demonstrated that urbanization is associated with variation in genome-wide patterns of DNA methylation. Combining reduced representation bisulphite sequencing with transcriptome data, we revealed habitat differences in DNA methylation patterns that suggest a regulated and coordinated response to the urban environment. In the liver, genomic sites that were differentially methylated between urban- and forest-dwelling birds were over-represented in regulatory regions of the genome and more likely to occur in expressed genes. DNA methylation levels were also inversely correlated with gene expression at transcription start sites. Furthermore, differentially methylated CpG sites, in liver, were over-represented in pathways involved in (i) steroid biosynthesis, (ii) superoxide metabolism, (iii) secondary alcohol metabolism, (iv) chylomicron remodelling, (v) cholesterol transport, (vi) reactive oxygen species (ROS) metabolic process and (vii) epithelial cell proliferation. This corresponds with earlier studies identifying diet and exposure to ROS as two of the main drivers of divergence between organisms in urban and nonurban environments. Conversely, in blood, sites that were differentially methylated between urban- and forest-dwelling birds were under-represented in regulatory regions, more likely to occur in nonexpressed genes and not over-represented in specific biological pathways. It remains to be determined whether diverging patterns of DNA methylation represent adaptive evolutionary responses and whether the conclusions can be more widely attributed to urbanization.

On the Use of Blood Samples for Measuring DNA Methylation in Ecological Epigenetic Studies

There is increasing interest in understanding the potential for epigenetic factors to contribute to phenotypic diversity in evolutionary biology. One well studied epigenetic mechanism is DNA methylation, the addition of a methyl group to cytosines, which have the potential to alter gene expression depending on the genomic region in which it takes place. Obtaining information about DNA methylation at genome-wide scale has become straightforward with the use of bisulfite treatment in combination with reduced representation or whole-genome sequencing. While it is well recognized that methylation is tissue specific, a frequent limitation for many studies is that sampling-specific tissues may require sacrificing individuals, something which is generally undesirable and sometimes impossible. Instead, information about DNA methylation patterns in the blood is frequently used as a proxy tissue. This can obviously be problematic if methylation patterns in the blood do not reflect that in the relevant tissue. Understanding how, or if, DNA methylation in blood reflect DNA methylation patterns in other tissues is therefore of utmost importance if we are to make inferences about how observed differences in methylation or temporal changes in methylation can contribute to phenotypic variation. The aim of this review is to examine what we know about the potential for using blood samples in ecological epigenetic studies. I briefly outline some methods by which we can measure DNA methylation before I examine studies that have compared DNA methylation patterns across different tissues and, finally, examine how useful blood samples may be for ecological studies of DNA methylation. Ecological epigenetic studies are in their infancy, but it is paramount for the field to move forward to have detailed information about tissue and time dependence relationships in methylation to gain insights into if blood DNA methylation patterns can be a reliable bioindicator for changes in methylation that generate phenotypic variation in ecologically important traits.

A supergene-linked estrogen receptor drives alternative phenotypes in a polymorphic songbird

Behavioral evolution relies on genetic changes, yet few behaviors can be traced to specific genetic sequences in vertebrates. Here we provide experimental evidence showing that differentiation of a single gene has contributed to the evolution of divergent behavioral phenotypes in the white-throated sparrow, a common backyard songbird. In this species, a series of chromosomal inversions has formed a supergene that segregates with an aggressive phenotype. The supergene has captured ESR1, the gene that encodes estrogen receptor α (ERα); as a result, this gene is accumulating changes that now distinguish the supergene allele from the standard allele. Our results show that in birds of the more aggressive phenotype, ERα knockdown caused a phenotypic change to that of the less aggressive phenotype. We next showed that in a free-living population, aggression is predicted by allelic imbalance favoring the supergene allele. Finally, we identified cis-regulatory features, both genetic and epigenetic, that explain the allelic imbalance. This work provides a rare illustration of how genotypic divergence has led to behavioral phenotypic divergence in a vertebrate.

Developmental conditions modulate DNA methylation at the glucocorticoid receptor gene with cascading effects on expression and corticosterone levels in zebra finches

Developmental conditions can impact the adult phenotype via epigenetic changes that modulate gene expression. In mammals, methylation of the glucocorticoid receptor gene Nr3c1 has been implicated as mediator of long-term effects of developmental conditions, but this evidence is limited to humans and rodents, and few studies have simultaneously tested for associations between DNA methylation, gene expression and phenotype. Adverse environmental conditions during early life (large natal brood size) or adulthood (high foraging costs) exert multiple long-term phenotypic effects in zebra finches, and we here test for effects of these manipulations on DNA methylation and expression of the Nr3c1 gene in blood. Having been reared in a large brood induced higher DNA methylation of the Nr3c1 regulatory region in adulthood, and this effect persisted over years. Nr3c1 expression was negatively correlated with methylation at 2 out of 8 CpG sites, and was lower in hard foraging conditions, despite foraging conditions having no effect on Nr3c1 methylation at our target region. Nr3c1 expression also correlated with glucocorticoid traits: higher expression level was associated with lower plasma baseline corticosterone concentrations and enhanced corticosterone reactivity. Our results suggest that methylation of the Nr3c1 regulatory region can contribute to the mechanisms underlying the emergence of long-term effects of developmental conditions in birds, but in our system current adversity dominated over early life experiences with respect to receptor expression.