Alexander Archipelago wolves are an ecologically and genetically distinct subspecies of gray wolf endemic to the coastal regions of Southeast Alaska. Post-logging forest succession has led to the depletion of Alexander Archipelago wolves’ primary prey - Sitka black-tailed deer. The use of marine prey by some wolves has been suggested to increase population resilience to declines in ungulate prey, yet little is known about the molecular mechanisms mediating this dietary shift. Environmentally sensitive epigenetic modifications, such as DNA methylation, provide an important avenue through which ecological effects can impact animal behavior. Yet, the relationship between DNA methylation and diet has not been explored in wild carnivores, leaving questions about the sensitivity of epigenetic modifications to dietary processes unanswered. To address this gap, we profiled genome-wide DNA methylation among 152 Alexander Archipelago wolves and coupled this data with information on wolves’ diet. K-means clustering grouped wolves into three dietary clusters corresponding to wolves’ use of marine versus terrestrial sourced prey. We detected 1,263 differentially methylated regions (DMRs) between wolves from these dietary clusters. Compared to terrestrial wolves, marine-oriented wolves were hypermethylated at 96% of DMRs, possibly reflecting a higher consumption of marine derived polyunsaturated fatty acids. DMRs associated with diet were distinct from those associated with neutral genetic variation, suggesting that patterns of DNA methylation can distinguish between aspects of diversity related to diet versus genetic population structure. Our findings suggest that DNA methylation could represent an important molecular marker to investigate population differences in ecologically relevant behavioral traits.

Epigenetic mechanisms are increasingly understood to have major impacts across ecology. However, one molecular epigenetic mechanism, DNA methylation, currently dominates the literature. A second mechanism, histone modification, is likely important to ecologically relevant phenotypes and thus warrants investigation, especially because molecular interplay between methylation and histone acetylation can strongly affect gene expression. There are a limited number of histone acetylation studies on non-model organisms, yet those that exist show that it can impact gene expression and phenotypic plasticity. Wild birds provide an excellent system to investigate histone acetylation, as free-living individuals must rapidly adjust to environmental change. Here, we screen histone acetylation in the house sparrow (Passer domesticus); we studied this species because DNA methylation was important in the spread of this bird globally. This species has one of the broadest geographic distributions in the world, and part of this success is related to the way that it uses methylation to regulate its gene expression. Here, we verify that a commercially available assay that was developed for mammals can be used in house sparrows. We detected high variance in histone acetylation among individuals in both liver and spleen tissue. Further, house sparrows with higher epigenetic potential in the Toll Like Receptor-4 (TLR-4) promoter (i.e., CpG content) had higher histone acetylation in liver. Also, there was a negative correlation between histone acetylation in spleen and TLR-4 expression. In addition to validating a method for measuring histone acetylation in wild songbirds, this study also shows that histone acetylation varies in an ecologically relevant way, adding a new study option for ecological epigenetics.

Animals encounter many novel and unpredictable challenges when moving into new areas including pathogen exposure. Because effective immune defenses against such threats can be costly, plastic immune responses could be particularly advantageous, as such defenses can be engaged only when context warrants activation. DNA methylation is a key regulator of plasticity via its effects on gene expression. In vertebrates, DNA methylation occurs exclusively at CpG dinucleotides, and typically, high DNA methylation decreases gene expression. The CpG content of gene regulatory regions may therefore represent one form of epigenetic potential (EP), a genomic means to capacitate gene expression. Non-native populations of house sparrows (Passer domesticus) - one of the world’s most cosmopolitan species – have high EP in the promoter of a key microbial surveillance gene, Toll-like receptor 4 (TLR4), compared to native populations. We previously hypothesized that high EP may enable sparrows to balance the costs and benefits of immune responses well, a trait critical to success in novel environments. In the present study, we found support for this hypothesis. House sparrows with high EP in TLR4 were better able to resist a pathogenic Salmonella enterica infection than sparrows with low EP. These results support the premise that high EP contributes to adaptation in novel environments.

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. Here, we present the first study on a natural population to 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 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 environmental, epigenetic and telomere length dynamics during early life.