Ewan Harney

The P-element, a DNA transposon, has independently invaded two Drosophila species, accompanied by rapid evolution of suppression. In the germline, suppression is mediated primarily by maternally expressed piRNAs, a class of regulatory small RNAs associated with PIWI proteins. The offspring of females that lack P-element-specific piRNAs and males that contain P-elements suffer a syndrome of deleterious phenotypes, including sterility, genome rearrangements, gonadal atrophy, and mutations, while the offspring of the reciprocal cross are normal. These effects, collectively termed hybrid dysgenesis, have been investigated primarily in female Drosophila melanogaster. Here, we study hybrid dysgenesis in male Drosophila simulans. Using an attached-X chromosome stock, we generated genetically identical F1 males that differed only in maternal suppression of the P-element. Using targeted sequencing of P-element breakpoints, we show that P-element transposition is elevated in dysgenic males and confirm a preference for insertion near origins of replication. Using transcriptomics, we show that dysgenic males have elevated P-element expression and reduced splicing suppression, with patterns of gene expression suggesting the loss of mature sperm cells. Fertility assays show higher rates of male sterility but otherwise modest effects on fertility. In conjunction with the transcriptomic data, small RNA sequencing confirms that the piRNA pathway functions in testes. Our results suggest that the P-element may spread more readily through males than females, as transposition rates are similar while fertility defects are less severe in males.

Heat stress will increasingly affect populations as climate change leads to higher temperatures and more frequent heat waves. Recent work suggests that interactions between the epigenome and transposable elements (TEs) could link environmental acclimation with rapid evolution. Yet little is known about how these processes interact in natural genetic backgrounds or shape evolutionarily relevant phenotypes. To investigate these interactions, we carried out laboratory experiments measuring gene expression and chromatin accessibility responses to heat shock in female D. melanogaster from arid and cold climates, their associations with population variation in TEs, and fitness-related phenotypes including viability and development time in the offspring. We also measured expression, accessibility and phenotypic traits three generations later to explore transgenerational inheritance. Expression and accessibility responses to heat shock varied between populations and were influenced by TE presence, with more upregulated responses in the arid population. Effects of heat shock on transcription were detected three generations later, especially in the arid population, although this was not driven by chromatin accessibility. Among offspring of heat shocked flies, phenotypes of the initial cohort (eggs laid within 2 d of heat shock) were negatively affected in both populations, but later cohorts (eggs laid more than 2 d after heat shock) from the arid population developed quicker than controls, indicating hormesis. This effect was still present four generations after the heat shock in the great-great-grandoffspring, demonstrating transgenerational inheritance of potentially beneficial phenotypes and gene expression in a natural insect population.

A particularly well-studied evolutionary model is the vinegar fly Drosophila melanogaster, a cosmopolitan insect of ancestral southern-central African origin. Recent work suggests that it expanded out of Africa ∼9,000 years ago, and spread from the Middle East into Europe ∼1,800 years ago. During its global expansion, this human commensal adapted to novel climate zones and habitats. Despite much work on phenotypic differentiation and adaptation on several continents (especially North America and Australia), typically in the context of latitudinal clines, little is known about phenotypic divergence among European populations. Here, we sought to provide a continent-wide study of phenotypic differentiation among European populations of D. melanogaster. In a consortium-wide phenomics effort, we assayed 16 fitness-related traits on a panel of 173 isofemale lines from 9 European populations, with the majority of traits measured by several groups using semi-standardized protocols. For most fitness-related traits, we found significant differentiation among populations on a continental scale. Despite inevitable differences in assay conditions among labs, the reproducibility and hence robustness of our measurements were overall remarkably good. Several fitness components (e.g., viability, development time) exhibited significant latitudinal or longitudinal clines, and populations differed markedly in multivariate trait structure. Notably, populations experiencing higher humidity/rainfall and lower maximum temperature showed higher viability, fertility, starvation resistance, and lifespan at the expense of lower heat-shock survival, suggesting a pattern of local adaptation. Our results indicate that derived populations of this tropical fly have been shaped by pervasive spatially varying multivariate selection and adaptation to different climates on the European continent.

Heat stress will increasingly affect populations as climate change leads to higher temperatures and more extreme events such as heat waves. Adaptation is predicted to occur over long evolutionary timescales, but recent work suggests that interactions between the epigenome and transposable elements (TEs) could link environmental acclimation with rapid adaptation. Yet combining all these factors in a tractable model system remains challenging; consequently little is known about how these processes interact in natural genetic backgrounds or shape evolutionarily relevant phenotypes. To investigate these interactions, we carried out laboratory experiments measuring gene expression and chromatin accessibility responses to heat shock in female D. melanogaster from arid and temperate climates and their associations with population variation in TEs. The consequences for fitness-related phenotypes were characterised in the offspring, and we also measured expression, chromatin accessibility and phenotypic traits three generations later to explore transgenerational inheritance. Expression and accessibility responses to heat shock varied between populations and were influenced by the presence of TEs, with more upregulated responses in the arid population. Effects of heat shock on transcription were detected three generations later, especially in the arid population, with many epigenetic genes transgenerationally expressed, although this was not driven by chromatin accessibility. Heat shock negatively affected phenotypes in the initial offspring cohort, but later arid population cohorts developed quicker than controls, indicating hormesis, an effect still present in the great-great- grandoffspring. These results demonstrate the transgenerational inheritance of a potentially beneficial hormetic phenotype and associated patterns of gene expression in a natural insect population. Significance Statement Global warming will lead to heat stress for many organisms. Interactions between the epigenome (the machinery controlling gene expression) and transposable elements, (TEs; mobile elements within the genome) are likely to influence the response to stress. In transgenerational laboratory heat shock experiments we investigated how the epigenome and TEs affected gene expression and phenotypes of arid and temperate populations of Drosophila melanogaster. The arid population showed clearer upregulation of epigenome and gene expression and transgenerational inheritance of gene expression following heat shock, and we identified TE insertions associated with stress-responsive genes. We also observed potentially beneficial transgenerational phenotypic responses in this population. Integrating molecular systems and measuring relevant phenotypes improves our understanding of acclimatory and evolutionary responses to environmental stress.

The epigenome is the suite of interacting chemical marks and molecules that helps to shape patterns of development, phenotypic plasticity and gene regulation, in part due to its responsiveness to environmental stimuli. There is increasing interest in understanding the functional and evolutionary importance of this sensitivity under ecologically realistic conditions. Observations that epigenetic variation abounds in natural populations have prompted speculation that it may facilitate evolutionary responses to rapid environmental perturbations, such as those occurring under climate change. A frequent point of contention is whether epigenetic variants reflect genetic variation or are independent of it. The genome and epigenome often appear tightly linked and interdependent. While many epigenetic changes are genetically determined, the converse is also true, with DNA sequence changes influenced by the presence of epigenetic marks. Understanding how the epigenome, genome and environment interact with one another is therefore an essential step in explaining the broader evolutionary consequences of epigenomic variation. Drawing on results from experimental and comparative studies carried out in diverse plant and animal species, we synthesize our current understanding of how these factors interact to shape phenotypic variation in natural populations, with a focus on identifying similarities and differences between taxonomic groups. We describe the main components of the epigenome and how they vary within and between taxa. We review how variation in the epigenome interacts with genetic features and environmental determinants, with a focus on the role of transposable elements (TEs) in integrating the epigenome, genome and environment. And we look at recent studies investigating the functional and evolutionary consequences of these interactions. Although epigenetic differentiation in nature is likely often a result of drift or selection on stochastic epimutations, there is growing evidence that a significant fraction of it can be stably inherited and could therefore contribute to evolution independently of genetic change.

Ocean acidification and warming are key stressors for many marine organisms. Some organisms display physiological acclimatization or plasticity, but this may vary across species ranges, especially if populations are adapted to local climatic conditions. Understanding how acclimatization potential varies among populations is therefore important in predicting species responses to climate change. We carried out a common garden experiment to investigate how different populations of the economically important great scallop (Pecten maximus) from France and Norway responded to variation in temperature and PCO2 concentration. After acclimation, post-larval scallops (spat) were reared for 31 days at one of two temperatures (13°C or 19°C) under either ambient or elevated PCO2 (pH 8.0 and pH 7.7). We combined measures of proteomic, metabolic and phenotypic traits to produce an integrative picture of how physiological plasticity varies between the populations. The proteome of French spat showed significant sensitivity to environmental variation, with 12 metabolic, structural and stress-response proteins responding to temperature and/or PCO2. Principal component analysis revealed seven energy metabolism proteins in French spat that were consistent with countering ROS stress under elevated temperature. Oxygen uptake in French spat did not change under elevated temperature but increased under elevated PCO2. In contrast, Norwegian spat reduced oxygen uptake under both elevated temperature and PCO2. Metabolic plasticity allows French scallops to maintain greater energy availability for growth compared with Norwegian spat. However, increased physiological plasticity and growth in French spat may come at a cost, as they showed reduced survival compared with Norwegian scallops under elevated temperature.

Ocean acidification and warming are key stressors for many marine organisms. Some organisms display physiological acclimatisation or plasticity, but this may vary across species ranges, especially if populations are adapted to local climatic conditions. Understanding how acclimatisation potential varies among populations is therefore important in predicting species responses to climate change. We carried out a common garden experiment to investigate how different populations of the economically important great scallop ( Pecten maximus ) from France and Norway responded to variation in temperature and p CO ₂ concentration. After acclimation, post-larval scallops (spat) were reared for 31 days at one of two temperatures (13°C and 19°C) under either ambient or elevated p CO ₂ (pH 8.0 and pH 7.7). We combined measures of proteomic, metabolic, and phenotypic traits to produce an integrative picture of how physiological plasticity varies between the populations. The proteome of French spat showed significant sensitivity to environmental variation, with 12 metabolic, structural and stress-response proteins responding to temperature and/or p CO ₂ . Principal component analysis revealed seven energy metabolism proteins in French spat that were consistent with countering ROS stress under elevated temperature. Oxygen uptake in French spat did not change under elevated temperature, but increased under elevated p CO ₂ . In contrast, Norwegian spat reduced oxygen uptake under both elevated temperature and p CO ₂ . Metabolic plasticity seemingly allowed French scallops to maintain greater energy availability for growth than Norwegian spat. However, increased physiological plasticity and growth in French spat may come at a cost, as French (but not Norwegian) spat showed reduced survival under elevated temperature. Summary Statement: Juvenile scallops from France and Norway differ in their response to warming and acidification. French scallops show more physiological plasticity, adjusting their proteome and metabolism in order to maintain growth.

It has been hypothesized that the effects of pollutants on phenotypes can be passed to subsequent generations through epigenetic inheritance, affecting populations long after the removal of a pollutant. But there is still little evidence that pollutants can induce persistent epigenetic effects in animals. Here, we show that low doses of commonly used pollutants induce genome-wide differences in cytosine methylation in the freshwater crustacean Daphnia pulex. Uniclonal populations were either continually exposed to pollutants or switched to clean water, and methylation was compared to control populations that did not experience pollutant exposure. Although some direct changes to methylation were only present in the continually exposed populations, others were present in both the continually exposed and switched to clean water treatments, suggesting that these modifications had persisted for 7 months (>15 generations). We also identified modifications that were only present in the populations that had switched to clean water, indicating a long-term legacy of pollutant exposure distinct from the persistent effects. Pollutant-induced differential methylation tended to occur at sites that were highly methylated in controls. Modifications that were observed in both continually and switched treatments were highly methylated in controls and showed reduced methylation in the treatments. On the other hand, modifications found just in the switched treatment tended to have lower levels of methylation in the controls and showed increase methylation in the switched treatment. In a second experiment, we confirmed that sublethal doses of the same pollutants generate effects on life histories for at least three generations following the removal of the pollutant. Our results demonstrate that even low doses of pollutants can induce transgenerational epigenetic effects that are stably transmitted over many generations. Persistent effects are likely to influence phenotypic development, which could contribute to the rapid adaptation, or extinction, of populations confronted by anthropogenic stressors.

Significance: We show that female insects can subtly change the management of their immune system contingent on infradian feeding cycles that act as cues to immune insult during mating. We experimentally reject the possibility that this is learned behavior, and show instead that it is dependent on the predictability of feeding which in turn is a cue for mating-induced infection. Although evidence exists for insect immune anticipation over life-time scales, this study links the temporal features of feeding to the insect’s mating behavior in the context of a system with infection caused by traumatic insemination. We predict similar mating ecology in other animals is likely to select for similar reproductive immune anticipation (RIA).