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1. Examining the Effects of Environment, Geography, and Elevation on Patterns of DNA Methylation Across Populations of Two Widespread Bumble Bee Species

   https://doi.org/10.1093/gbe/evae207  

   Heraghty, Sam D; Rahman, Sarthok Rasique; Verble, Kelton M; Lozier, Jeffrey D (October 2024, Genome Biology and Evolution)

   Abstract Understanding the myriad avenues through which spatial and environmental factors shape evolution is a major focus in biological research. From a molecular perspective, much work has been focused on genomic sequence variation; however, recently there has been increased interest in how epigenetic variation may be shaped by different variables across the landscape. DNA methylation has been of particular interest given that it is dynamic and can alter gene expression, potentially offering a path for a rapid response to environmental change. We utilized whole genome enzymatic methyl sequencing to evaluate the distribution of CpG methylation across the genome and to analyze patterns of spatial and environmental association in the methylomes of two broadly distributed montane bumble bees (Bombus vancouverensis Cresson and Bombus vosnesenskii Radoszkowski) across elevational gradients in the western US. Methylation patterns in both species are similar at the genomic scale with ∼1% of CpGs being methylated and most methylation being found in exons. At the landscape scale, neither species exhibited strong spatial or population structuring in patterns of methylation, although some weak relationships between methylation and distance or environmental variables were detected. Differential methylation analysis suggests a stronger environment association in B. vancouverensis given the larger number of differentially methylated CpG's compared to B. vosnesenskii. We also observed only a handful of genes with both differentially methylated CpGs and previously detected environmentally associated outlier SNPs. Overall results reveal a weak but present pattern in variation in methylation over the landscape in both species. 

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2. Developmental programming of DNA methylation and gene expression patterns is associated with extreme cardiovascular tolerance to anoxia in the common snapping turtle

   https://doi.org/10.1186/s13072-021-00414-7  

   Ruhr, Ilan; Bierstedt, Jacob; Rhen, Turk; Das, Debojyoti; Singh, Sunil Kumar; Miller, Soleille; Crossley, Dane A.; Galli, Gina L. (December 2021, Epigenetics & Chromatin)

   Abstract Background Environmental fluctuation during embryonic and fetal development can permanently alter an organism’s morphology, physiology, and behaviour. This phenomenon, known as developmental plasticity, is particularly relevant to reptiles that develop in subterranean nests with variable oxygen tensions. Previous work has shown hypoxia permanently alters the cardiovascular system of snapping turtles and may improve cardiac anoxia tolerance later in life. The mechanisms driving this process are unknown but may involve epigenetic regulation of gene expression via DNA methylation. To test this hypothesis, we assessed in situ cardiac performance during 2 h of acute anoxia in juvenile turtles previously exposed to normoxia (21% oxygen) or hypoxia (10% oxygen) during embryogenesis. Next, we analysed DNA methylation and gene expression patterns in turtles from the same cohorts using whole genome bisulfite sequencing, which represents the first high-resolution investigation of DNA methylation patterns in any reptilian species. Results Genome-wide correlations between CpG and CpG island methylation and gene expression patterns in the snapping turtle were consistent with patterns observed in mammals. As hypothesized, developmental hypoxia increased juvenile turtle cardiac anoxia tolerance and programmed DNA methylation and gene expression patterns. Programmed differences in expression of genes such as SCN5A may account for differences in heart rate, while genes such as TNNT2 and TPM3 may underlie differences in calcium sensitivity and contractility of cardiomyocytes and cardiac inotropy. Finally, we identified putative transcription factor-binding sites in promoters and in differentially methylated CpG islands that suggest a model linking programming of DNA methylation during embryogenesis to differential gene expression and cardiovascular physiology later in life. Binding sites for hypoxia inducible factors (HIF1A, ARNT, and EPAS1) and key transcription factors activated by MAPK and BMP signaling (RREB1 and SMAD4) are implicated. Conclusions Our data strongly suggests that DNA methylation plays a conserved role in the regulation of gene expression in reptiles. We also show that embryonic hypoxia programs DNA methylation and gene expression patterns and that these changes are associated with enhanced cardiac anoxia tolerance later in life. Programming of cardiac anoxia tolerance has major ecological implications for snapping turtles, because these animals regularly exploit anoxic environments throughout their lifespan. 

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3. Biogeographic parallels in thermal tolerance and gene expression variation under temperature stress in a widespread bumble bee

   https://doi.org/10.1038/s41598-020-73391-8  

   Pimsler, Meaghan L.; Oyen, Kennan J.; Herndon, James D.; Jackson, Jason M.; Strange, James P.; Dillon, Michael E.; Lozier, Jeffrey D. (December 2020, Scientific Reports)

   null (Ed.)

   Abstract Global temperature changes have emphasized the need to understand how species adapt to thermal stress across their ranges. Genetic mechanisms may contribute to variation in thermal tolerance, providing evidence for how organisms adapt to local environments. We determine physiological thermal limits and characterize genome-wide transcriptional changes at these limits in bumble bees using laboratory-reared Bombus vosnesenskii workers. We analyze bees reared from latitudinal (35.7–45.7°N) and altitudinal (7–2154 m) extremes of the species’ range to correlate thermal tolerance and gene expression among populations from different climates. We find that critical thermal minima (CT MIN ) exhibit strong associations with local minimums at the location of queen origin, while critical thermal maximum (CT MAX ) was invariant among populations. Concordant patterns are apparent in gene expression data, with regional differentiation following cold exposure, and expression shifts invariant among populations under high temperatures. Furthermore, we identify several modules of co-expressed genes that tightly correlate with critical thermal limits and temperature at the region of origin. Our results reveal that local adaptation in thermal limits and gene expression may facilitate cold tolerance across a species range, whereas high temperature responses are likely constrained, both of which may have implications for climate change responses of bumble bees. 

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4. Divergent gametic thermal performance and floral warming across an elevation gradient

   https://doi.org/10.1093/evolut/qpad237  

   Heiling, Jacob M; Koski, Matthew H (January 2024, Evolution)

   Friedman, Jannice; Connallon, Tim (Ed.)

   Abstract Thermal environments vary widely across species ranges, establishing the potential for local adaptation of thermal performance optima and tolerance. In the absence of local adaptation, selection should favor mechanisms to meet thermal optima. Floral temperature is a major determinant of reproductive success in angiosperms, yet whether gametic thermal performance shows signatures of local adaptation across temperature gradients, and how variation in gametic thermal performance influences floral evolution, is unknown. We characterized flowering season temperatures for the forb, Argentina anserina, at extremes of a 1000 m elevation gradient and generated thermal performance curves for pollen and ovule performance in populations at each extreme. Thermal optima fell between mean and maximum intrafloral temperatures. However, cooler high-elevation populations had ~4 °C greater pollen thermal optima than warmer low-elevation populations, while tolerance breadths did not differ. We then tested whether plants at elevational extremes differentially warmed the floral microenvironment. High-elevation flowers warmed significantly more than low, bringing intrafloral temperatures nearer the pollen optima. A manipulative experiment demonstrated that stronger warming in high elevation was conferred by floral tissues. Elevational divergence in floral warming may be driven, in part, by selection on flowers to meet different thermal demands of the gametophytes. 

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5. Symbiont shuffling induces differential DNA methylation responses to thermal stress in the coral Montastraea cavernosa

   https://doi.org/10.1111/mec.16246  

   Rodriguez‐Casariego, Javier A.; Cunning, Ross; Baker, Andrew C.; Eirin‐Lopez, Jose M. (October 2021, Molecular Ecology)

   null (Ed.)

   Algal symbiont shuffling in favour of more thermotolerant species has been shown to enhance coral resistance to heat-stress. Yet, the mechanistic underpinnings and long-term implications of these changes are poorly understood. This work studied the modifications in coral DNA methylation, an epigenetic mechanism involved in coral acclimatization, in response to symbiont manipulation and subsequent heat stress exposure. Symbiont composition was manipulated in the great star coral Montastraea cavernosa through controlled thermal bleaching and recovery, producing paired ramets of three genets dominated by either their native symbionts (genus Cladocopium) or the thermotolerant species (Durusdinium trenchi). Single-base genome-wide analyses showed significant modifications in DNA methylation concentrated in intergenic regions, introns and transposable elements. Remarkably, DNA methylation changes in response to heat stress were dependent on the dominant symbiont, with twice as many differentially methylated regions found in heat-stressed corals hosting different symbionts (Cladocopium vs. D. trenchii) compared to all other comparisons. Interestingly, while differential gene body methylation was not correlated with gene expression, an enrichment in differentially methylated regions was evident in repetitive genome regions. Overall, these results suggest that changes in algal symbionts favouring heat tolerant associations are accompanied by changes in DNA methylation in the coral host. The implications of these results for coral adaptation, along with future avenues of research based on current knowledge gaps, are discussed in the present work. 

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