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

Knock down to level up: Reframing RNAi for invertebrate ecophysiology

Comparative ecophysiologists strive to understand physiological problems in non-model organisms, but molecular tools such as RNA interference (RNAi) are under-used in our field. Here, we provide a framework for invertebrate ecophysiologists to use RNAi to answer questions focused on physiological processes, rather than as a tool to investigate gene function. We specifically focus on non-model invertebrates, in which the use of other genetic tools (e.g., genetic knockout lines) is less likely. We argue that because RNAi elicits a temporary manipulation of gene expression, and resources to carry out RNAi are technically and financially accessible, it is an effective tool for invertebrate ecophysiologists. We cover the terminology and basic mechanisms of RNA interference as an accessible introduction for "non-molecular" physiologists, include a suggested workflow for identifying RNAi gene targets and validating biologically relevant gene knockdowns, and present a hypothesis-testing framework for using RNAi to answer common questions in the realm of invertebrate ecophysiology. This review encourages invertebrate ecophysiologists to use these tools and workflows to explore physiological processes and bridge genotypes to phenotypes in their animal(s) of interest.

Timing-dependent effects of elevated temperature on reproductive traits in the European corn borer moth

Elevated temperature often has life stage-specific effects on ectotherms because thermal tolerance varies throughout ontogeny. Impacts of elevated temperature may extend beyond the exposed life stage if developmental plasticity causes early exposure to carry-over or if exposure at multiple life stages cumulatively produces effects. Reproductive traits may be sensitive to different thermal environments experienced during development, but such effects have not been comprehensively measured in Lepidoptera. In this study, we investigate how elevated temperature at different life stages alters reproduction in the European corn borer moth, Ostrinia nubilalis. We tested effects of exposure to elevated temperature (28 °C) separately or additively during larval, pupal, and adult life stages compared to control temperatures (23 °C). We found that exposure to elevated pupal and adult temperature decreased the number of egg clusters produced, but exposure limited to a single stage did not significantly impact reproductive output. Furthermore, elevated temperature during the pupal stage led to a faster transition to the adult stage and elevated larval temperature altered synchrony of adult eclosion, either by itself or combined with pupal temperature exposure. These results suggest that exposure to elevated temperature during development alters reproduction in corn borers in multiple ways, including through carry-over and additive effects. Additive effects of temperature across life stages are thought to be less common than stage-specific or carry-over effects, but our results suggest thermal environments experienced at all life stages need to be considered when predicting reproductive responses of insects to heatwaves.

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.

Interaction models matter: an efficient, flexible computational framework for model-specific investigation of epistasis

PURPOSE

Epistasis, the interaction between two or more genes, is integral to the study of genetics and is present throughout nature. Yet, it is seldom fully explored as most approaches primarily focus on single-locus effects, partly because analyzing all pairwise and higher-order interactions requires significant computational resources. Furthermore, existing methods for epistasis detection only consider a Cartesian (multiplicative) model for interaction terms. This is likely limiting as epistatic interactions can evolve to produce varied relationships between genetic loci, some complex and not linearly separable.

METHODS

We present new algorithms for the interaction coefficients for standard regression models for epistasis that permit many varied models for the interaction terms for loci and efficient memory usage. The algorithms are given for two-way and three-way epistasis and may be generalized to higher order epistasis. Statistical tests for the interaction coefficients are also provided. We also present an efficient matrix based algorithm for permutation testing for two-way epistasis. We offer a proof and experimental evidence that methods that look for epistasis only at loci that have main effects may not be justified. Given the computational efficiency of the algorithm, we applied the method to a rat data set and mouse data set, with at least 10,000 loci and 1,000 samples each, using the standard Cartesian model and the XOR model to explore body mass index.

RESULTS

This study reveals that although many of the loci found to exhibit significant statistical epistasis overlap between models in rats, the pairs are mostly distinct. Further, the XOR model found greater evidence for statistical epistasis in many more pairs of loci in both data sets with almost all significant epistasis in mice identified using XOR. In the rat data set, loci involved in epistasis under the XOR model are enriched for biologically relevant pathways.

CONCLUSION

Our results in both species show that many biologically relevant epistatic relationships would have been undetected if only one interaction model was applied, providing evidence that varied interaction models should be implemented to explore epistatic interactions that occur in living systems.

Life cycle complexity and body mass drive erratic changes in climate vulnerability across ontogeny in a seasonally migrating butterfly

Physiological traits are often used for vulnerability assessments of organismal responses to climate change. Trait values can change dramatically over the life cycle of organisms but are typically assessed at a single developmental stage. Reconciling ontogenetic changes in physiological traits with vulnerability assessments often reveals early life-stage vulnerabilities. The degree to which ontogenetic changes in physiological traits are due to changes in body mass over development versus stage-specific responses determines the degree to which mass can be used as a proxy for vulnerability. Here, we use the painted lady butterfly, Vanessa cardui, to test ontogenetic changes in two physiological traits, the acute thermal sensitivity of routine metabolic rate (RMR Q10) and the critical thermal maximum (CTmax). RMR Q10 generally followed ontogenetic changes in body mass, with stages characterized by smaller body mass exhibiting lower acute thermal sensitivity. However, CTmax was largely decoupled from ontogenetic changes in body mass. In contrast with trends from other studies showing increasing vulnerability among progressively earlier developmental stages, our study revealed highly erratic patterns of vulnerability across ontogeny. Specifically, we found the lowest joint-trait vulnerability (both RMR Q10 and CTmax) in the earliest developmental stage we tested (3rd instar larvae), the highest vulnerabilities in the next two developmental stages (4th and 5th instar larvae), and reduced vulnerability into the pupal and adult stages. Our study supports growing evidence of mechanistic decoupling of physiology across developmental stages and suggests that body mass is not a universal proxy for all physiological trait indicators of climate vulnerability.