Stage-specific genotype-by-environment interactions for cold and heat hardiness in Drosophila melanogaster

Naturally segregating genetic variants contribute to thermal tolerance in a Drosophila melanogaster model system

Thermal tolerance is a fundamental physiological complex trait for survival in many species. For example, everyday tasks such as foraging, finding a mate, and avoiding predation are highly dependent on how well an organism can tolerate extreme temperatures. Understanding the general architecture of the natural variants within the genes that control this trait is of high importance if we want to better comprehend thermal physiology. Here, we take a multipronged approach to further dissect the genetic architecture that controls thermal tolerance in natural populations using the Drosophila Synthetic Population Resource as a model system. First, we used quantitative genetics and Quantitative Trait Loci mapping to identify major effect regions within the genome that influences thermal tolerance, then integrated RNA-sequencing to identify differences in gene expression, and lastly, we used the RNAi system to (1) alter tissue-specific gene expression and (2) functionally validate our findings. This powerful integration of approaches not only allows for the identification of the genetic basis of thermal tolerance but also the physiology of thermal tolerance in a natural population, which ultimately elucidates thermal tolerance through a fitness-associated lens.

Seasonal energetics: are insects constrained by energy during dormancy?

In seasonal environments, many animals, including insects, enter dormancy, where they are limited to a fixed energy budget. The inability to replenish energetic stores during these periods suggests insects should be constrained by pre-dormancy energy stores. Over the last century, the community of researchers working on survival during dormancy has operated under the strong assumption that energy limitation is a key fitness trait driving the evolution of seasonal strategies. That is, energy use has to be minimized during dormancy because insects otherwise run out of energy and die during dormancy, or are left with too little energy to complete development, reproductive maturation or other costly post-dormancy processes such as dispersal or nest building. But if energy is so strongly constrained during dormancy, how can some insects - even within the same species and population - be dormant in very warm environments or show prolonged dormancy for many successive years? In this Commentary, we discuss major assumptions regarding dormancy energetics and outline cases where insects appear to align with our assumptions and where they do not. We then highlight several research directions that could help link organismal energy use with landscape-level changes. Overall, the optimal energetic strategy during dormancy might not be to simply minimize metabolic rate, but instead to maintain a level that matches the demands of the specific life-history strategy. Given the influence of temperature on energy use rates of insects in winter, understanding dormancy energetic strategies is critical in order to determine the potential impacts of climate change on insects in seasonal environments.

Harnessing thermal plasticity to enhance the performance of mass-reared insects: opportunities and challenges

Insects are mass-reared for release for biocontrol including the sterile insect technique. Insects are usually reared at temperatures that maximize the number of animals produced, are chilled for handling and transport, and released into the field, where temperatures may be considerably different to those experienced previously. Insect thermal biology is phenotypically plastic (i.e. flexible), which means that there may exist opportunities to increase the performance of these programmes by modifying the temperature regimes during rearing, handling, and release. Here we synthesize the literature on thermal plasticity in relation to the opportunities to reduce temperature-related damage and increase the performance of released insects. We summarize how and why temperature affects insect biology, and the types of plasticity shown by insects. We specifically identify aspects of the production chain that might lead to mismatches between the thermal acclimation of the insect and the temperatures it is exposed to, and identify ways to harness physiological plasticity to reduce that potential mismatch. We address some of the practical (especially engineering) challenges to implementing some of the best-supported thermal regimes to maximize performance (e.g. fluctuating thermal regimes), and acknowledge that a focus only on thermal performance may lead to unwanted trade-offs with other traits that contribute to the success of the programme. Together, it appears that thermal physiological plasticity is well-enough understood to allow its implementation in release programmes.

Transcriptomic and functional genetic evidence for distinct ecophysiological responses across complex life cycle stages

Organisms with complex life cycles demonstrate a remarkable ability to change their phenotypes across development, presumably as an evolutionary adaptation to developmentally variable environments. Developmental variation in environmentally sensitive performance, and thermal sensitivity in particular, has been well documented in holometabolous insects. For example, thermal performance in adults and juvenile stages exhibit little genetic correlation (genetic decoupling) and can evolve independently, resulting in divergent thermal responses. Yet, we understand very little about how this genetic decoupling occurs. We tested the hypothesis that genetic decoupling of thermal physiology is driven by fundamental differences in physiology between life stages, despite a potentially conserved Cellular Stress Response. We used RNAseq to compare transcript expression in response to a cold stressor in Drosophila melanogaster larvae and adults and used RNAi (RNA interference) to test whether knocking down nine target genes differentially affected larval and adult cold tolerance. Transcriptomic responses of whole larvae and adults during and following exposure to -5°C were largely unique both in identity of responding transcripts and in temporal dynamics. Further, we analyzed the tissue-specificity of differentially-expressed transcripts from FlyAtlas 2 data, and concluded that stage-specific differences in transcription were not simply driven by differences in tissue composition. In addition, RNAi of target genes resulted in largely stage-specific and sometimes sex-specific effects on cold tolerance. The combined evidence suggests that thermal physiology is largely stage-specific at the level of gene expression, and thus natural selection may be acting on different loci during the independent thermal adaptation of different life stages.

Genotype-by-Diet Interactions for Larval Performance and Body Composition Traits in the Black Soldier Fly, Hermetia illucens

Simple Summary

The bioconversion of organic waste into valuable insect protein as an alternative animal feed ingredient has the potential to improve agricultural sustainability and may become a key element of future circular economy. However, while insects farmed for feed production are considered livestock from a regulatory perspective, systematic linking of genetic resource characterisations and fundamental phenotyping, crucial for precision breeding and feeding schemes, remains scarce even for prime insect candidates, such as the black soldier fly (BSF). The present study initiated to fill this knowledge gap by experimentally assessing BSF genotype-by-diet interactions for a number of economically and ecologically relevant larval phenotypic traits. Besides pervasive diet effects, strong impact of BSF genetic background and ubiquitous environment-mediated interactions were found. This implies some of the so-far unexplained response variation across global BSF studies could be driven by previously neglected mechanisms of genetic specificity, and thus that the concept of broad conspecific plasticity in this insect is likely too simplistic. Instead, it is emphasised that matching BSF genetics to dietary contexts is vital for purposive production optimisation, particularly when extrapolated to large-scale operations. These insights highlight that establishing tailored BSF breeding as an independent branch offers veritable opportunities to efficiently support this growing agricultural sector.

Abstract

Further advancing black soldier fly (BSF) farming for waste valorisation and more sustainable global protein supplies critically depends on targeted exploitation of genotype-phenotype associations in this insect, comparable to conventional livestock. This study used a fully crossed factorial design of rearing larvae of four genetically distinct BSF strains (F_ST: 0.11–0.35) on three nutritionally different diets (poultry feed, food waste, poultry manure) to investigate genotype-by-environment interactions. Phenotypic responses included larval growth dynamics over time, weight at harvest, mortality, biomass production with respective contents of ash, fat, and protein, including amino acid profiles, as well as bioconversion and nitrogen efficiency, reduction of dry matter and relevant fibre fractions, and dry matter loss (emissions). Virtually all larval performance and body composition traits were substantially influenced by diet but also characterised by ample BSF genetic variation and, most importantly, by pronounced interaction effects between the two. Across evaluated phenotypes, variable diet-dependent rankings and the lack of generally superior BSF strains indicate the involvement of trade-offs between traits, as their relationships may even change signs. Conflicting resource allocation in light of overall BSF fitness suggests anticipated breeding programs will require complex and differential selection strategies to account for pinpointed trait maximisation versus multi-purpose resilience.

Direct and indirect effects of altered temperature regimes and phenological mismatches on insect populations

Climate change is transforming ecosystems by altering species ranges, the composition of communities, and trophic interactions. Here, we synthesize recent reviews and subsequent developments to provide an overview of insect ecological and evolutionary responses to altered temperature regimes. We discuss both direct responses to thermal stress and indirect responses arising from phenological mismatches, altered host quality, and changes in natural enemy activity. Altered temperature regimes can increase exposure to both cold and heat stress and result in phenological and morphological mismatches with adjacent trophic levels. Host plant quality varies in a heterogenous way in response to altered temperatures with both increases and decreases observed. Density-dependent effects, spatial heterogeneity, and rapid evolutionary change provide some resilience to these threats.

Insects and their pathogens in a changing climate

The complex nature of climate change-mediated multitrophic interaction is an underexplored area, but has the potential to dramatically shift transmission and distribution of many insects and their pathogens, placing some populations closer to the brink of extinction. However, for individual insect-pathogen interactions climate change will have complicated hard-to-anticipate impacts. Thus, both pathogen virulence and insect host immunity are intrinsically linked with generalized stress responses, and in both pathogen and host have extensive trade-offs with nutrition (e.g., host plant quality), growth and reproduction. Potentially alleviating or exasperating these impacts, some pathogens and hosts respond genetically and rapidly to environmental shifts. This review identifies many areas for future research including a particular need to identify how altered global warming interacts with other environmental changes and stressors, and how consistent these impacts are across pathogens and hosts. With that achieved we would be closer to producing an overarching framework to integrate knowledge on all environmental interplay and infectious disease events.

Plasticity of cold hardiness in the eastern spruce budworm, Choristoneura fumiferana

High latitude insect populations must cope with extreme conditions, particularly low temperatures. Insects use a variety of cold hardiness mechanisms to withstand this temperature stress, and these can drive geographic distributions through overwintering mortality. The degree of cold hardiness can be altered by two evolved responses: phenotypic plasticity and local adaptation. Phenotypic plasticity can occur within or between generations (transgenerational plasticity; TGP), and local adaptation can evolve through directional selection in response to regional climatic differences. We used the eastern spruce budworm, Choristoneura fumiferana (Lepidoptera: Tortricidae) as a model to explore the role that variable winter temperatures play in inducing two aspects of plasticity in cold hardiness: TGP and local adaptation in phenotypic plasticity. This species is one of the most destructive boreal forest pests in North America, therefore accurately predicting overwintering survival is essential for effective management. While we found no evidence of TGP in cold hardiness, there was a long term fitness cost to larvae that experienced repeated cold exposures. We also found evidence of local adaptation in both seasonal and short-term plasticity of cold hardiness, as our more northerly populations that would experience lower overwintering temperatures had more plastic responses to cold exposure. These findings provide evidence for the importance of phenotypic plasticity and local adaptation when modelling species distributions.

Characterizing the genetic basis of copper toxicity in Drosophila reveals a complex pattern of allelic, regulatory, and behavioral variation

A range of heavy metals are required for normal cell function and homeostasis. However, the anthropogenic release of metal compounds into soil and water sources presents a pervasive health threat. Copper is one of many heavy metals that negatively impacts diverse organisms at a global scale. Using a combination of quantitative trait locus (QTL) mapping and RNA sequencing in the Drosophila Synthetic Population Resource, we demonstrate that resistance to the toxic effects of ingested copper in D. melanogaster is genetically complex and influenced by allelic and expression variation at multiple loci. QTL mapping identified several QTL that account for a substantial fraction of heritability. Additionally, we find that copper resistance is impacted by variation in behavioral avoidance of copper and may be subject to life-stage specific regulation. Gene expression analysis further demonstrated that resistant and sensitive strains are characterized by unique expression patterns. Several of the candidate genes identified via QTL mapping and RNAseq have known copper-specific functions (e.g., Ccs, Sod3, CG11825), and others are involved in the regulation of other heavy metals (e.g., Catsup, whd). We validated several of these candidate genes with RNAi suggesting they contribute to variation in adult copper resistance. Our study illuminates the interconnected roles that allelic and expression variation, organism life stage, and behavior play in copper resistance, allowing a deeper understanding of the diverse mechanisms through which metal pollution can negatively impact organisms.

Validating measurements of acclimation for climate change adaptation

Acclimation and other forms of plasticity that can increase stress resistance feature strongly in discussions surrounding climate change impacts or vulnerability projections of insects and other ectotherms. There is interest in compiling databases for assessing the adequacy of acclimation for dealing with climate change. Here, we argue that the nature of acclimation is context dependent and therefore that estimates summarised across studies, especially those that have assayed stress using diverse methods, are limited in their utility when applied as a standardized metric or to a single general context such as average climate warming. Moreover, the dynamic nature of tolerances and acclimation drives important variation that is quickly obscured through many summary statistics or even in effect size analyses; retaining a strong focus on the temporal-level, population-level and treatment-level variance in forecasting climate change impacts on insects is essential. We summarise recent developments within the context of climate change and propose how future studies might validate the role of acclimation by integration across field studies and mechanistic modelling. Despite arguments to the contrary, to date no studies have convincingly demonstrated an important role for acclimation in recent climate change adaptation of insects. Paramount to these discussions is i) developing a strong conceptual framework for acclimation in the focal trait(s), ii) obtaining novel empirical data dissecting the fitness benefits and consequences of acclimation across diverse contexts and timescales, with iii) better coverage of under-represented geographic regions and taxa.

Evolutionary impacts of winter climate change on insects

Overwintering is a serious challenge for insects, and winters are rapidly changing as climate shifts. The capacity for phenotypic plasticity and evolutionary adaptation will determine which species profit or suffer from these changes. Here we discuss current knowledge on the potential and evidence for evolution in winter-relevant traits among insect species and populations. We conclude that the best evidence for evolutionary shifts in response to changing winters remain those related to changes in phenology, but all evidence points to cold hardiness as also having the potential to evolve in response to climate change. Predicting future population sizes and ranges relies on understanding to what extent evolution in winter-related traits is possible, and remains a serious challenge.

Ontogenetic variation in thermal sensitivity shapes insect ecological responses to climate change

Insects have distinct life stages that can differ in their responses to environmental factors. We discuss empirical evidence and theoretical models for ontogenetic variation in thermal sensitivity and performance curves (TPCs). Data on lower thermal limits for development (T₀) demonstrate variation between stages within a species that is of comparable magnitude to variation among species; we illustrate the consequences of such ontogenetic variation for developmental responses to changing temperature. Ontogenetic variation in optimal temperatures and upper thermal limits has been reported in some systems, but current data are too limited to identify general patterns. The shapes of TPCs for different fitness components such as juvenile survival, adult fecundity, and generation time differ in characteristic ways, with important consequences for understanding fitness in varying thermal environments. We highlight a theoretical framework for incorporating ontogenetic variation into process-based models of population responses to seasonal variation and climate change.

Rejection of the beneficial acclimation hypothesis (BAH) for short term heat acclimation in Drosophila nepalensis

Beneficial acclimation hypothesis (BAH) is the phenotypic plasticity in response to changing environments which enables organisms to enhance their fitness. In recent years, however, BAH has received vigorous criticism and is still debatable. In this study, we tested thermal hardiness phenotypes (melanization, chill coma recovery, heat knockdown and percentage survival) on adult and pre-adult stages of Drosophila nepalensis, reared in different thermal environments (14, 17, 21 and 25 °C) to check whether increasing natural surrounding temperature and acclimation limit towards environmental change is detrimental or beneficial. Results showed that rearing D. nepalensis at higher temperatures (21 and 25 °C) reduces its melanization and cold hardiness but improves heat knockdown times. When temperature was raised to 26.2 °C (0.6 °C above the upper thermal maxima), to determine the short-term acclimation effects, survival and fitness of adults diminished approximately 1.5 to 2 folds. These results suggest that D. nepalensis has long-term developmental acclimation to both heat and cold which would be extremely beneficial as temperatures and climates alter in the region due to global warming. However, a lack of short-term heat acclimation suggests that rapid shifts in thermal extreme could be detrimental to D. nepalensis.

Integrating GWAS and Transcriptomics to Identify the Molecular Underpinnings of Thermal Stress Responses in Drosophila melanogaster

Thermal tolerance of an organism depends on both the ability to dynamically adjust to a thermal stress and preparatory developmental processes that enhance thermal resistance. However, the extent to which standing genetic variation in thermal tolerance alleles influence dynamic stress responses vs. preparatory processes is unknown. Here, using the model species Drosophila melanogaster, we used a combination of Genome Wide Association mapping (GWAS) and transcriptomic profiling to characterize whether genes associated with thermal tolerance are primarily involved in dynamic stress responses or preparatory processes that influence physiological condition at the time of thermal stress. To test our hypotheses, we measured the critical thermal minimum (CTmin) and critical thermal maximum (CTmax) of 100 lines of the Drosophila Genetic Reference Panel (DGRP) and used GWAS to identify loci that explain variation in thermal limits. We observed greater variation in lower thermal limits, with CTmin ranging from 1.81 to 8.60°C, while CTmax ranged from 38.74 to 40.64°C. We identified 151 and 99 distinct genes associated with CTmin and CTmax, respectively, and there was strong support that these genes are involved in both dynamic responses to thermal stress and preparatory processes that increase thermal resistance. Many of the genes identified by GWAS were involved in the direct transcriptional response to thermal stress (72/151 for cold; 59/99 for heat), and overall GWAS candidates were more likely to be differentially expressed than other genes. Further, several GWAS candidates were regulatory genes that may participate in the regulation of stress responses, and gene ontologies related to development and morphogenesis were enriched, suggesting many of these genes influence thermal tolerance through effects on development and physiological status. Overall, our results suggest that thermal tolerance alleles can influence both dynamic plastic responses to thermal stress and preparatory processes that improve thermal resistance. These results also have utility for directly comparing GWAS and transcriptomic approaches for identifying candidate genes associated with thermal tolerance.

Dynamic genetic architecture of yeast response to environmental perturbation shed light on origin of cryptic genetic variation

Cryptic genetic variation could arise from, for example, Gene-by-Gene (G-by-G) or Gene-by-Environment (G-by-E) interactions. The underlying molecular mechanisms and how they influence allelic effects and the genetic variance of complex traits is largely unclear. Here, we empirically explored the role of environmentally influenced epistasis on the suppression and release of cryptic variation by reanalysing a dataset of 4,390 haploid yeast segregants phenotyped on 20 different media. The focus was on 130 epistatic loci, each contributing to segregant growth in at least one environment and that together explained most (69–100%) of the narrow sense heritability of growth in the individual environments. We revealed that the epistatic growth network reorganised upon environmental changes to alter the estimated marginal (additive) effects of the individual loci, how multi-locus interactions contributed to individual segregant growth and the level of expressed genetic variance in growth. The estimated additive effects varied most across environments for loci that were highly interactive network hubs in some environments but had few or no interactors in other environments, resulting in changes in total genetic variance across environments. This environmentally dependent epistasis was thus an important mechanism for the suppression and release of cryptic variation in this population. Our findings increase the understanding of the complex genetic mechanisms leading to cryptic variation in populations, providing a basis for future studies on the genetic maintenance of trait robustness and development of genetic models for studying and predicting selection responses for quantitative traits in breeding and evolution.

Many biological traits are polygenic, with complex interplay between underlying genes and the surrounding environment. As a result, individuals with the same allele might have distinctive phenotypes due to differences in the polygenic background and/or the environment. Such differences often create additional genetic variation that is highly relevant to quantitative and evolutionary genetics by limiting our ability to accurately predict the phenotypes in medical or agricultural applications and providing opportunities for long term evolution. Previously, yeast growth regulating genes were found to be organised in large interacting networks. Here, we found that these networks were reorganised upon environmental changes, and that this resulted in altered effect sizes of individual genes, and how the whole network contributed to growth and the level of total genetic variance, providing a basis for future studies on the genetic maintenance of trait robustness and development of genetic models for studying and predicting selection responses for quantitative traits.

Physiological and biochemical responses to thermal stress vary among genotypes in the parasitic wasp Nasonia vitripennis

In ectotherm species such as insects, thermal fluctuations represent a major environmental factor driving development, survival and reproduction of individuals. Reproductive traits are particularly sensitive to heat stress that can induce a permanent sterility, or at least hypofertility, of adult males. This study aims to compare physiological and biochemical responses associated to male performances to an exposure of 24 h to moderately high temperature (36 °C) among three inbred lines of N. vitripennis (AsymC, Cor, Oul). Cor males showed very specific metabolic adjustments compared to the two other lines. By contrast, Oul males showed stronger phenotypic adjustment of its life cycle, and produced metabolic water to compensate water loss by heat stress. Finally, AsymC males had probably more difficulties to acclimate at 36 °C, even for a short period, as their adult longevity was significantly reduced. Thus, the ability of developmental plasticity in N. vitripennis males exposed to heat stress appears to be dependent of their genotypes.