DNA methylation as a mechanism of nutritional plasticity: limited support from horned beetles

A role of epigenetic mechanisms in regulating female reproductive responses to temperature in a pest beetle

Many species are threatened by climate change and must rapidly respond to survive in changing environments. Epigenetic modifications, such as DNA methylation, can facilitate plastic responses by regulating gene expression in response to environmental cues. Understanding epigenetic responses is therefore essential for predicting species' ability to rapidly adapt in the context of global environmental change. Here, we investigated the functional significance of different methylation-associated cellular processes on temperature-dependent life history in seed beetles, Callosobruchus maculatus Fabricius 1775 (Coleoptera: Bruchidae). We assessed changes under thermal stress in (1) DNA methyltransferase (Dnmt1 and Dnmt2) expression levels, (2) genome-wide methylation and (3) reproductive performance, with (2) and (3) following treatment with 3-aminobenzamide (3AB) and zebularine (Zeb) over two generations. These drugs are well-documented to alter DNA methylation across the tree of life. We found that Dnmt1 and Dnmt2 were expressed throughout the body in males and females, but were highly expressed in females compared with males and exhibited temperature dependence. However, whole-genome methylation did not significantly vary with temperature, and only marginally or inconclusively with drug treatment. Both 3AB and Zeb led to profound temperature-dependent shifts in female reproductive life history trade-off allocation, often increasing fitness compared with control beetles. Mismatch between magnitude of treatment effects on DNA methylation versus life history effects suggest potential of 3AB and Zeb to alter reproductive trade-offs via changes in DNA repair and recycling processes, rather than or in addition to (subtle) changes in DNA methylation. Together, our results suggest that epigenetic mechanisms relating to Dnmt expression, DNA repair and recycling pathways, and possibly DNA methylation, are strongly implicated in modulating insect life history trade-offs in response to temperature change.

Spatial covariation between genetic and epigenetic diversity in wild plant and animal populations: a meta-analysis

Epigenetic variation may be crucial in understanding the structure of wild populations, thereby aiding in their management and conservation. However, the relationship between epigenetic and genetic variation remains poorly understood, especially in wild populations. To address this, we conducted a meta-analysis of studies that examined the genetic and epigenetic structures of wild plant and animal populations. We aimed to determine whether epigenetic variation is spatially independent of genetic variation in the wild and to highlight the conditions under which epigenetic variation might be informative. We show a significant positive correlation between genetic and epigenetic pairwise differentiation, indicating that in wild populations, epigenetic diversity is closely linked to genetic differentiation. The correlation was weaker for population pairs that were weakly differentiated genetically, suggesting that in such cases, epigenetic marks might be independent of genetic marks. Additionally, we found that global levels of genetic and epigenetic differentiation were similar across plant and animal populations, except when populations were weakly differentiated genetically. In such cases, epigenetic differentiation was either higher or lower than genetic differentiation. Our results suggest that epigenetic information is particularly relevant in populations that have recently diverged genetically or are connected by gene flow. Future studies should consider the genetic structure of populations when inferring the role of epigenetic diversity in local adaptation in wild populations. Furthermore, there is a need to identify the factors that sustain the links between genetic and epigenetic diversity to improve our understanding of the interplay between these two forms of variation in wild populations.

Gene regulatory networks underlying the development and evolution of plasticity in horned beetles

Horned beetles have emerged as a powerful study system with which to investigate the developmental mechanisms underlying environment-responsive development and its evolution. We begin by reviewing key advances in our understanding of the diverse roles played by transcription factors, endocrine regulators, and signal transduction pathways in the regulation of horned beetle plasticity. We then explore recent efforts aimed at understanding how such condition-specific expression may be regulated in the first place, as well as how the differential expression of master regulators may instruct conditional expression of downstream target genes. Here, we focus on the significance of chromatin remodeling as a powerful but thus far understudied mechanism able to facilitate trait-, sex-, and species-specific responses to environmental conditions.

Evolution of resource generalism via generalized stress response confers increased reproductive thermal tolerance in a pest beetle

Generalism should be favoured evolutionarily when there is no genetic constraint or loss of fitness across alternative environments. However, evolution of generalism can require substantial evolutionary change, which can confer a general stress response to other aspects of the environment. We created generalist lineages from an ancestral, resource-specialized laboratory population of seed beetles (Callosobruchus maculatus) by rearing lines over 60 generations on a mixture of both ancestral and novel host species to test for costs associated with the evolution of generalism involving evolutionary changes in gene expression and correlated phenotypic responses during a shift to generalism. Evolved lines had higher fitness on the novel resource, with no loss of fitness on the ancestral resource, indicating that they overcame initial fitness trade-offs. This involved upregulation of major stress response (heat shock protein) genes and genes coding for metabolic enzymes, suggesting an underpinning metabolic and physiological cost. Resource generalist populations also evolved greater thermal tolerance breadth, highlighting that the evolution of resource generalism might pre-adapt species to respond favourably to other environmental stressors, following selection for generalized stress response gene upregulation. The rapid gain of novel hosts during a pest invasion might also confer greater thermal resilience to ongoing climate change.

Phenotypic Plasticity: What Has DNA Methylation Got to Do with It?

How does one genome give rise to multiple, often markedly different, phenotypes in response to an environmental cue? This phenomenon, known as phenotypic plasticity, is common amongst plants and animals, but arguably the most striking examples are seen in insects. Well-known insect examples include seasonal morphs of butterfly wing patterns, sexual and asexual reproduction in aphids, and queen and worker castes of eusocial insects. Ultimately, we need to understand how phenotypic plasticity works at a mechanistic level; how do environmental signals alter gene expression, and how are changes in gene expression translated into novel morphology, physiology and behaviour? Understanding how plasticity works is of major interest in evolutionary-developmental biology and may have implications for understanding how insects respond to global change. It has been proposed that epigenetic mechanisms, specifically DNA methylation, are the key link between environmental cues and changes in gene expression. Here, we review the available evidence on the function of DNA methylation of insects, the possible role(s) for DNA methylation in phenotypic plasticity and also highlight key outstanding questions in this field as well as new experimental approaches to address these questions.

Insecticide exposure affects intergenerational patterns of DNA methylation in the Colorado potato beetle, Leptinotarsa decemlineata

Insecticide use is pervasive as a selective force in modern agroecosystems. Insect herbivores exposed to these insecticides have been able to rapidly evolve resistance to them, but how they are able to do so is poorly understood. One possible but largely unexplored explanation is that exposure to sublethal doses of insecticides may alter epigenetic patterns that are heritable. For instance, epigenetic mechanisms, such as DNA methylation that modifies gene expression without changing the underlying genetic code, may facilitate the emergence of resistant phenotypes in complex ways. We assessed the effects of sublethal insecticide exposure, with the neonicotinoid imidacloprid, on DNA methylation in the Colorado potato beetle, Leptinotarsa decemlineata, examining both global changes in DNA methylation and specific changes found within genes and transposable elements. We found that exposure to insecticide led to decreases in global DNA methylation for parent and F2 generations and that many of the sites of changes in methylation are found within genes associated with insecticide resistance, such as cytochrome P450s, or within transposable elements. Exposure to sublethal doses of insecticide caused heritable changes in DNA methylation in an agricultural insect herbivore. Therefore, epigenetics may play a role in insecticide resistance, highlighting a fundamental mechanism of evolution while informing how we might better coexist with insect species in agroecosystems.

Host use diversification during range shifts shapes global variation in Lepidopteran dietary breadth

Niche breadths tend to be greater at higher latitudes. This pattern is frequently assumed to emerge from the cumulative effects of multiple, independent local adaptation events along latitudinal environmental gradients, although evidence that generalization is more beneficial at higher-latitude locations remains equivocal. Here I propose an alternative hypothesis: that latitudinal variation in niche breadths emerges as a non-adaptive consequence of range shift dynamics. Based on analysis of a global dataset comprising more than 6,934 globally distributed dietary records from 4,410 Lepidopteran species, this hypothesis receives robust support. Population-level dietary niche breadths are better explained by the relative position of the population within its geographic range and the species' poleward range extent than by the latitude of diet observation. Broader diets are observed closer to poleward range limits and in species that have attained higher latitudes. Moreover, latitudinal variation in diet breadth is more prominent within and among species undergoing rapid, contemporary range shifts than for species with more stable ranges. Together these results suggest that latitudinal patterns in niche breadth represent a transient and emergent property of recent geographic range dynamics and need not require underlying gradients in selective agents or fitness trade-offs. The results have wide-ranging implications for global ecology and for anticipating changes in host use during ongoing distributional shifts of pests and disease vectors.

DNA Methylation in Anopheles albimanus Modulates the Midgut Immune Response Against Plasmodium berghei

Epigenetic mechanisms such as DNA methylation and histone post-translational modifications are fundamental for the phenotypic plasticity of insects during their interaction with the environment. In response to environmental cues, the methylation pattern in DNA is dynamically remodeled to achieve an epigenetic control of gene expression. DNA methylation is the focus of study in insects for its evolutionarily conserved character; however, there is scant knowledge about the epigenetic regulation in vector mosquitoes, especially during their infection by parasites. The aim of the present study was to evaluate the participation of DNA methylation in the immune response of Anopheles albimanus to a Plasmodium infection. For this, we first investigated the presence of a fully functional DNA methylation system in A. albimanus by assessing its potential role in larval development. Subsequently, we evaluated the transcriptional response to Plasmodium berghei of two mosquito phenotypes with different degrees of susceptibility to the parasite, in a scenario where their global DNA methylation had been pharmacologically inhibited. Our study revealed that A. albimanus has a functional DNA methylation system that is essential to larval viability, and that is also responsive to feeding and parasite challenges. The pharmacological erasure of the methylome with azacytidine or decitabine abolished the divergent responses of both mosquito phenotypes, leading to a transcriptionally similar response upon parasite challenge. This response was more specific, and the infection load in both phenotypes was lowered. Our findings suggest that DNA methylation may constitute a key factor in vector competence, and a promising target for preventing malaria transmission.

Nutrient Stress During Ontogeny Alters Patterns of Resource Allocation in two Species of Horned Beetles

The elaboration of exaggerated, sexually selected weapons and ornaments often comes at a cost to other traits. For instance, by sustaining the growth of an exaggerated weapon during development, shared and limited resources such as morphogens, growth factors, and nutrients may become depleted and limit the size to which other structures can grow. Such interactions are characteristic of resource allocation trade-offs, which can constrain the production of phenotypic variation and bias evolutionary trajectories. Across many species of Onthophagus beetles, males produce extravagant horns that are used as weapons in male-male competition over mates. Previous studies have reported resource allocation trade-offs between horns and both proximally and distally developing structures. However, more recent studies have largely failed to recover these patterns, leading to the hypothesis that trade-offs may manifest only in certain species, populations, or environmental conditions. Here, we investigate (i) patterns of resource allocation into horns, eyes, and genitalia in Onthophagus gazella and O. taurus, and assess (ii) how these patterns of resource allocation are influenced by nutrient stress during larval development. We find that nutrient stress alters patterns of resource allocation within and among traits, but recover a trade-off only in the species that invests most heavily into horn production (O. taurus), and in individuals of that species that invested a disproportionately large or small amount of resources into horn growth. These results suggest that resource allocation trade-offs may not be as prevalent as previously described, and that their presence and magnitude may instead be highly context dependent.

Novel Insights into Insect-Microbe Interactions-Role of Epigenomics and Small RNAs

It has become increasingly clear that microbes form close associations with the vast majority of animal species, especially insects. In fact, an array of diverse microbes is known to form shared metabolic pathways with their insect hosts. A growing area of research in insect-microbe interactions, notably for hemipteran insects and their mutualistic symbionts, is to elucidate the regulation of this inter-domain metabolism. This review examines two new emerging mechanisms of gene regulation and their importance in host-microbe interactions. Specifically, we highlight how the incipient areas of research on regulatory "dark matter" such as epigenomics and small RNAs, can play a pivotal role in the evolution of both insect and microbe gene regulation. We then propose specific models of how these dynamic forms of gene regulation can influence insect-symbiont-plant interactions. Future studies in this area of research will give us a systematic understanding of how these symbiotic microbes and animals reciprocally respond to and regulate their shared metabolic processes.

Preadult life history variation determines adult transcriptome expression

Preadult determinants of adult fitness and behaviour have been documented in a variety of organisms with complex life cycles, but little is known about expression patterns of genes underlying these adult traits. We explored the effects of differences in egg-to-adult development time on adult transcriptome and cuticular hydrocarbon variation in order to understand the nature of the genetic correlation between preadult development time and premating isolation between populations of Drosophila mojavensis reared in different host cactus environments. Transcriptome variation was analysed separately in flies reared on each host and revealed that hundreds of genes in adults were differentially expressed (FDR P < 0.05) due to development time differences. For flies reared on pitaya agria cactus, longer preadult development times caused increased expression of genes in adults enriched for ribosome production, protein metabolism, chromatin remodelling and regulation of alternate splicing and transcription. Baja California flies reared on organ pipe cactus showed fewer differentially expressed genes in adults due to longer preadult development time, but these were enriched for ATP synthesis and the TCA cycle. Mainland flies reared on organ pipe cactus with shorter development times showed increased transcription of genes enriched for mitochondria and energy production, protein synthesis and glucose metabolism: adults with longer development times had increased expression of genes enriched for adult life span, cuticle proteins and ion binding, although most differentially expressed genes were unannotated. Differences due to population, sex, mating status and their interactions were also assessed. Adult cuticular hydrocarbon profiles also showed shifts due to egg-to-adult development time and were influenced by population and mating status. These results help to explain why preadult life history variation determines subsequent expression of the adult transcriptome along with traits involved with reproductive isolation and revealed previously undocumented connections between genetic and environmental influences over the entire life cycle in this desert insect.

The Genome and Methylome of a Beetle with Complex Social Behavior, Nicrophorus vespilloides (Coleoptera: Silphidae)

Testing for conserved and novel mechanisms underlying phenotypic evolution requires a diversity of genomes available for comparison spanning multiple independent lineages. For example, complex social behavior in insects has been investigated primarily with eusocial lineages, nearly all of which are Hymenoptera. If conserved genomic influences on sociality do exist, we need data from a wider range of taxa that also vary in their levels of sociality. Here, we present the assembled and annotated genome of the subsocial beetle Nicrophorus vespilloides, a species long used to investigate evolutionary questions of complex social behavior. We used this genome to address two questions. First, do aspects of life history, such as using a carcass to breed, predict overlap in gene models more strongly than phylogeny? We found that the overlap in gene models was similar between N. vespilloides and all other insect groups regardless of life history. Second, like other insects with highly developed social behavior but unlike other beetles, does N. vespilloides have DNA methylation? We found strong evidence for an active DNA methylation system. The distribution of methylation was similar to other insects with exons having the most methylated CpGs. Methylation status appears highly conserved; 85% of the methylated genes in N. vespilloides are also methylated in the hymentopteran Nasonia vitripennis. The addition of this genome adds a coleopteran resource to answer questions about the evolution and mechanistic basis of sociality and to address questions about the potential role of methylation in social behavior.

The nutritionally responsive transcriptome of the polyphenic beetle Onthophagus taurus and the importance of sexual dimorphism and body region

Developmental responses to nutritional variation represent one of the ecologically most important classes of adaptive plasticity. However, knowledge of genome-wide patterns of nutrition-responsive gene expression is limited. Here, we studied genome-wide transcriptional responses to nutritional variation and their dependency on trait and sex in the beetle Onthophagus taurus. We find that averaged across the transcriptome, nutrition contributes less to overall variation in gene expression than do sex or body region, but that for a modest subset of genes nutrition is by far the most important determinant of expression variation. Furthermore, our results reject the hypothesis that a common machinery may underlie nutrition-sensitive development across body regions. Instead, we find that magnitude (measured by number of differentially expressed contigs), composition (measured by functional enrichment) and evolutionary consequences (measured by patterns of sequence variation) are heavily dependent on exactly which body region is considered and the degree of sexual dimorphism observed on a morphological level. More generally, our findings illustrate that studies into the developmental mechanisms and evolutionary consequences of nutrition-biased gene expression must take into account the dynamics and complexities imposed by other sources of variation in gene expression such as sexual dimorphism and trait type.

Global cytosine methylation in Daphnia magna depends on genotype, environment, and their interaction

The authors characterized global cytosine methylation levels in 2 different genotypes of the ecotoxicological model organism Daphnia magna after exposure to a wide array of biotic and abiotic environmental stressors. The present study aimed to improve the authors' understanding of the role of cytosine methylation in the organism's response to environmental conditions. The authors observed a significant genotype effect, an environment effect, and a genotype × environment effect. In particular, global cytosine methylation levels were significantly altered after exposure to Triops predation cues, Microcystis, and sodium chloride compared with control conditions. Significant differences between the 2 genotypes were observed when animals were exposed to Triops predation cues, Microcystis, Cryptomonas, and sodium chloride. Despite the low global methylation rate under control conditions (0.49-0.52%), global cytosine methylation levels upon exposure to Triops demonstrated a 5-fold difference between the genotypes (0.21% vs 1.02%). No effects were found in response to arsenic, cadmium, fish, lead, pH of 5.5, pH of 8, temperature, hypoxia, and white fat cell disease. The authors' results point to the potential role of epigenetic effects under changing environmental conditions such as predation (i.e., Triops), diet (i.e., Cryptomonas and Microcystis), and salinity. The results of the present study indicate that, despite global cytosine methylation levels being low, epigenetic effects may be important in environmental studies on Daphnia.

What do studies of insect polyphenisms tell us about nutritionally-triggered epigenomic changes and their consequences?

Many insects are capable of remarkable changes in biology and form in response to their environment or diet. The most extreme example of these are polyphenisms, which are when two or more different phenotypes are produced from a single genotype in response to the environment. Polyphenisms provide a fascinating opportunity to study how the environment affects an animal’s genome, and how this produces changes in form. Here we review the current state of knowledge of the molecular basis of polyphenisms and what can be learnt from them to understand how nutrition may influence our own genomes.

Eusocial insects as emerging models for behavioural epigenetics

Understanding the molecular basis of how behavioural states are established, maintained and altered by environmental cues is an area of considerable and growing interest. Epigenetic processes, including methylation of DNA and post-translational modification of histones, dynamically modulate activity-dependent gene expression in neurons and can therefore have important regulatory roles in shaping behavioural responses to environmental cues. Several eusocial insect species - with their unique displays of behavioural plasticity due to age, morphology and social context - have emerged as models to investigate the genetic and epigenetic underpinnings of animal social behaviour. This Review summarizes recent studies in the epigenetics of social behaviour and offers perspectives on emerging trends and prospects for establishing genetic tools in eusocial insects.

Fine-scale population epigenetic structure in relation to gastrointestinal parasite load in red grouse (Lagopus lagopus scotica)

Epigenetic modification of cytosine methylation states can be elicited by environmental stresses and may be a key process affecting phenotypic plasticity and adaptation. Parasites are potent stressors with profound physiological and ecological effects on their host, but there is little understanding in how parasites may influence host methylation states. Here, we estimate epigenetic diversity and differentiation among 21 populations of red grouse (Lagopus lagopus scotica) in north-east Scotland and test for association of gastrointestinal parasite load (caecal nematode Trichostrongylus tenuis) with hepatic genome-wide and locus-specific methylation states. Following methylation-sensitive AFLP (MSAP), 129 bands, representing 73 methylation-susceptible and 56 nonmethylated epiloci, were scored across 234 individuals. The populations differed significantly in genome-wide methylation levels and were also significantly epigenetically (F_SC = 0.0227; P < 0.001) and genetically (F_SC = 0.0058; P < 0.001) differentiated. Parasite load was not associated with either genome-wide methylation levels or epigenetic differentiation. Instead, we found eight disproportionately differentiated epilocus-specific methylation states (F_ST outliers) using bayescan software and significant positive and negative association of 35 methylation states with parasite load from bespoke generalized estimating equations (GEE), simple logistic regression (sam) and Bayesian environmental analysis (bayenv2). Following Sanger sequencing, genome mapping and geneontology (go) annotation, some of these epiloci were linked to genes involved in regulation of cell cycle, signalling, metabolism, immune system and notably rRNA methylation, histone acetylation and small RNAs. These findings demonstrate an epigenetic signature of parasite load in populations of a wild bird and suggest intriguing physiological effects of parasite-associated cytosine methylation.

Insights into the development and evolution of exaggerated traits using de novo transcriptomes of two species of horned scarab beetles

Scarab beetles exhibit an astonishing variety of rigid exo-skeletal outgrowths, known as “horns”. These traits are often sexually dimorphic and vary dramatically across species in size, shape, location, and allometry with body size. In many species, the horn exhibits disproportionate growth resulting in an exaggerated allometric relationship with body size, as compared to other traits, such as wings, that grow proportionately with body size. Depending on the species, the smallest males either do not produce a horn at all, or they produce a disproportionately small horn for their body size. While the diversity of horn shapes and their behavioural ecology have been reasonably well studied, we know far less about the proximate mechanisms that regulate horn growth. Thus, using 454 pyrosequencing, we generated transcriptome profiles, during horn growth and development, in two different scarab beetle species: the Asian rhinoceros beetle, Trypoxylus dichotomus, and the dung beetle, Onthophagus nigriventris. We obtained over half a million reads for each species that were assembled into over 6,000 and 16,000 contigs respectively. We combined these data with previously published studies to look for signatures of molecular evolution. We found a small subset of genes with horn-biased expression showing evidence for recent positive selection, as is expected with sexual selection on horn size. We also found evidence of relaxed selection present in genes that demonstrated biased expression between horned and horn-less morphs, consistent with the theory of developmental decoupling of phenotypically plastic traits.

Ecological epigenetics: an introduction to the symposium

Phenotypic variation arises from interactions between environmental and genetic variation, and the emergence of such variation is, in part, mediated by epigenetic mechanisms: factors that modify gene expression but do not change the gene sequence, per se. The role of epigenetic variation and inheritance in natural populations, however, remains poorly understood. The budding field of Ecological Epigenetics seeks to extend our knowledge of epigenetic mechanisms and processes to natural populations, and recent conceptual and technical advances have made progress toward this goal more feasible. In light of these breakthroughs, now is a particularly opportune time to develop a framework that will guide and facilitate exceptional studies in Ecological Epigenetics. Toward this goal, the Ecological Epigenetics symposium brought together researchers with diverse strengths in theory, developmental genetics, ecology, and evolution, and the proceedings from their talks are presented in this issue. By characterizing environmentally dependent epigenetic variation in natural populations, we will enhance our understanding of developmental, ecological, and evolutionary phenomena. In particular, ecological epigenetics has the potential to explain how populations endure (or fail to endure) profound and rapid environmental change. Here, my goal is to introduce some of the common goals and challenges shared by those pursuing this critical field.

The function of intragenic DNA methylation: insights from insect epigenomes

Epigenetic inheritance plays a fundamentally important role in mediating gene regulation and phenotypic plasticity. DNA methylation, in particular, has been the focus of many recent studies aimed at understanding the function of epigenetic information in insects. An understanding of DNA methylation, however, requires knowledge of its context in relation to other epigenetic modifications. Here, we review recent insights into the localization of DNA methylation in insect genomes and further discuss the functional significance of these insights in the context of the greater eukaryotic epigenome. In particular, we highlight the complementarity of the eukaryotic epigenetic landscape. We focus on the importance of DNA methylation to nucleosome stability, which may explain the context-dependent associations of DNA methylation with gene expression. Ultimately, we suggest that the integration of diverse epigenetic modifications in studies of insects will greatly advance our understanding of the evolution of epigenetic systems and epigenetic contributions to developmental regulation.

Beetle horns and horned beetles: emerging models in developmental evolution and ecology

Many important questions in developmental biology increasingly interface with related questions in other biological disciplines such as evolutionary biology and ecology. In this article, we review and summarize recent progress in the development of horned beetles and beetle horns as study systems amenable to the integration of a wide range of approaches, from gene function analysis in the laboratory to population ecological and behavioral studies in the field. Specifically, we focus on three key questions at the current interface of developmental biology, evolutionary biology and ecology: (1) the developmental mechanisms underlying the origin and diversification of novel, complex traits, (2) the relationship between phenotypic diversification and the diversification of genes and transcriptomes, and (3) the role of behavior as a leader or follower in developmental evolution. For each question we discuss how work on horned beetles is contributing to our current understanding of key issues, as well as highlight challenges and opportunities for future studies.