Tribolium beetles as a model system in evolution and ecology

Tests of evolutionary and genetic rescue using flour beetles, Tribolium castaneum, experimentally evolved to thermal conditions

Small, isolated populations are often characterised by low levels of genetic diversity. This can result in inbreeding depression and reduced capacity to adapt to changes in the environment, and therefore higher risk of extinction. However, sometimes these populations can be rescued if allowed to increase in size or if migrants enter, bringing in new allelic variation and thus increasing genetic diversity. This study uses experimental manipulation of population size and migration to quantify their effects on fitness in a challenging environment to better understand genetic rescue. Using small, replicated populations of Tribolium castaneum experimentally evolved to different temperature regimes we tested genetic and demographic rescue, by performing large-scale manipulations of population size and migration and examining fitness consequences over multiple generations. We measured fitness in high temperature (38°C) thermal lines maintained at their usual 'small' population size of N = 100 individuals, and with 'large' scaled up duplicates containing N≈10,000 individuals. We compared these large lines with and without migration (m = 0.1) for 10 generations. Additionally, we assessed the effects of outcrossing at an individual level, by comparing fitness of hybrid (thermal line × stock) offspring with within-line crosses. We found that, at the population level, a rapid increase in the number of individuals in the population resulted in reduced fitness (represented by reproductive output and survival through heatwave conditions), regardless of migration. However, at an individual level, the hybrid offspring of migrants with native individuals generally demonstrated increased longevity in high temperature conditions compared with individuals from thermal selection lines. Overall, these populations showed no evidence that demographic manipulations led to genetic or evolutionary rescue. Following the effects of migration in individuals over several generations may be the next step in unravelling these conflicting results. We discuss these findings in the context of conservation intervention.

Anatomical changes of Tenebrio molitor and Tribolium castaneum during complete metamorphosis

In holometabolous insects, extensive reorganisation of tissues and cells occurs at the pupal stage. The remodelling of the external exoskeleton and internal organs that intervenes during metamorphosis has been traditionally studied in many insect species based on histological or ultrastructural methods. This study demonstrates the use of synchrotron X-ray phase-contrast micro-computed tomography as a powerful, non-destructive tool for in situ morphological observation of anatomical structures at the pupal stage in two Tenebrionid beetles, i.e. Tribolium castaneum and Tenebrio molitor, known as important pests, as well as emerging and promising models in experimental biology. Virtual sections and three-dimensional reconstructions were performed on both males and females at early, intermediate, and late pupal stage. The dataset allowed us to observe the remodelling of the gut and nervous system as well as the shaping of the female and male reproductive system at different pupal ages in both mealworm and red flour beetles. Moreover, we observed that the timing and duration pattern of organ development varied between the species analysed, likely related to the species-specific adaptations of the pre-imaginal stages to environmental conditions, which ultimately affect their life cycle. This research provides new knowledge on the morphological modifications that occur during the pupal stage of holometabolous insects and provides a baseline set of information on beetle metamorphosis that may support future research in forensics, physiology, and ecology as well as an image atlas for educational purposes.

scRNA-seq Reveals Novel Genetic Pathways and Sex Chromosome Regulation in Tribolium Spermatogenesis

Spermatogenesis is critical to sexual reproduction yet evolves rapidly in many organisms. High-throughput single-cell transcriptomics promises unparalleled insight into this important process but understanding can be impeded in nonmodel systems by a lack of known genes that can reliably demarcate biologically meaningful cell populations. Tribolium castaneum, the red flour beetle, lacks known markers for spermatogenesis found in insect species like Drosophila melanogaster. Using single-cell sequencing data collected from adult beetle testes, we implement a strategy for elucidating biologically meaningful cell populations by using transient expression stage identification markers, weighted principal component clustering, and SNP-based haploid/diploid phasing. We identify populations that correspond to observable points in sperm differentiation and find species specific markers for each stage. Our results indicate that molecular pathways underlying spermatogenesis in Coleoptera are substantially diverged from those in Diptera. We also show that most genes on the X chromosome experience meiotic sex chromosome inactivation. Temporal expression of Drosophila MSL complex homologs coupled with spatial analysis of potential chromatin entry sites further suggests that the dosage compensation machinery may mediate escape from meiotic sex chromosome inactivation and postmeiotic reactivation of the X chromosome.

Transcriptomic comparison between populations selected for higher and lower mobility in the red flour beetle Tribolium castaneum

Movement is an important behavior observed in a wide range of taxa. Previous studies have examined genes controlling movement using wing polymorphic insects and genes controlling wing size. However, few studies have investigated genes controlling movement activity rather than morphological traits. In the present study, we conducted RNA sequencing using populations with higher (WL) and lower (WS) mobility established by artificial selection in the red flour beetle Tribolium castaneum and compared gene expression levels between selected populations with two replicate lines. As a result, we found significant differences between the selected populations in 677 genes expressed in one replicate line and 1198 genes expressed in another replicate line, of which 311 genes were common to the two replicate lines. Furthermore, quantitative PCR focusing on 6 of these genes revealed that neuropeptide F receptor gene (NpF) was significantly more highly expressed in the WL population than in the WS population, which was common to the two replicate lines. We discuss differences in genes controlling movement between walking activity and wing polymorphism.

A life-history allele of large effect shortens developmental time in a wild insect population

Developmental time is a key life-history trait with large effects on Darwinian fitness. In many insects, developmental time is currently under strong selection to minimize ecological mismatches in seasonal timing induced by climate change. The genetic basis of responses to such selection, however, is poorly understood. To address this problem, we set up a long-term evolve-and-resequence experiment in the beetle Tribolium castaneum and selected replicate, outbred populations for fast or slow embryonic development. The response to this selection was substantial and embryonic developmental timing of the selection lines started to diverge during dorsal closure. Pooled whole-genome resequencing, gene expression analysis and an RNAi screen pinpoint a 222 bp deletion containing binding sites for Broad and Tramtrack upstream of the ecdysone degrading enzyme Cyp18a1 as a main target of selection. Using CRISPR/Cas9 to reconstruct this allele in the homogenous genetic background of a laboratory strain, we unravel how this single deletion advances the embryonic ecdysone peak inducing dorsal closure and show that this allele accelerates larval development but causes a trade-off with fecundity. Our study uncovers a life-history allele of large effect and reveals the evolvability of developmental time in a natural insect population.

Genetic architecture of dispersal behaviour in the post-harvest pest and model organism Tribolium castaneum

Dispersal behaviour is an important aspect of the life-history of animals. However, the genetic architecture of dispersal-related traits is often obscure or unknown, even in well studied species. Tribolium castaneum is a globally significant post-harvest pest and established model organism, yet studies of its dispersal have shown ambiguous results and the genetic basis of this behaviour remains unresolved. We combine experimental evolution and agent-based modelling to investigate the number of loci underlying dispersal in T. castaneum, and whether the trait is sex-linked. Our findings demonstrate rapid evolution of dispersal behaviour under selection. We find no evidence of sex-biases in the dispersal behaviour of the offspring of crosses, supporting an autosomal genetic basis of the trait. Moreover, simulated data approximates experimental data under simulated scenarios where the dispersal trait is controlled by one or few loci, but not many loci. Levels of dispersal in experimentally inbred lines, compared with simulations, indicate that a single locus model is not well supported. Taken together, these lines of evidence support an oligogenic architecture underlying dispersal in Tribolium castaneum. These results have implications for applied pest management and for our understanding of the evolution of dispersal in the coleoptera, the world's most species-rich order.

Evolutionarily stable levels of aposematic defence in prey populations

Our understanding of aposematism (the conspicuous signalling of a defence for the deterrence of predators) has advanced notably since its first observation in the late nineteenth century. Indeed, it extends the scope of a well-established game-theoretical model of this very same process both from the analytical standpoint (by considering regimes of varying background mortality and colony size) and from the practical standpoint (by assessing its efficacy and limitations in predicting the evolution of prey traits in finite simulated populations). The nature of the manuscript at hand is more mathematical and its aim is two-fold: first, to determine the relationship between evolutionarily stable levels of defence and signal strength under various regimes of background mortality and colony size. Second, to compare these predictions with simulations of finite prey populations that are subject to random local mutation. We compare the roles of absolute resident fitness, mutant fitness and stochasticity in the evolution of prey traits and discuss the importance of population size in the above.

Model worms: knowledge gains and risks associated with the use of model species in parasitological research

Model parasite species, whose entire life cycle can be completed in the laboratory and maintained for multiple generations, have played a fundamental role in our understanding of host–parasite interactions. Yet, keeping parasites in laboratory conditions may expose them to unnatural evolutionary pressures, and using laboratory cultures for research is therefore not without limitations. Using 2 widely-used model helminth species, the cestode Hymenolepis diminuta and the nematode Heligmosomoides polygyrus, I illustrate the caution needed when interpreting experimental results on model species. I first review more than 1200 experimental studies published on these species in the past 4 decades, to determine which research areas they have contributed to. This is followed by an examination of the institutional laboratory cultures that have provided the parasites used in these studies. Some of these have persisted for decades and accounted for a substantial proportion of published studies, whereas others have been short-lived. Using information provided by the curators of active cultures, I summarize data on their origins and maintenance conditions. Finally, I discuss how laboratory cultures may have been subject to the influence of evolutionary genetic processes, such as founder effects, genetic drift and inbreeding. I also address the possibility that serial passage through laboratory hosts across multiple generations has exerted artificial selection on several parasite traits, resulting in genetic and phenotypic divergence among laboratory cultures, and between these cultures and natural parasite populations. I conclude with recommendations for the continued usage of laboratory helminth cultures aimed at maximizing their important contribution to parasitological research.

Influence of diverse storage conditions of double-stranded RNA in vitro on the RNA interference efficiency in vivo insect Tribolium castaneum

BACKGROUND

A significant variation in RNA interference (RNAi) efficiency hinders further functional gene studies and pest control application in many insects. The available double-stranded RNA (dsRNA) molecules introduced into the target cells are regarded as the crucial factor for efficient RNAi response. However, numerous studies have only focused on dsRNA stability in vivo; it is uncertain whether different dsRNA storage conditions in vitro play a role in variable RNAi efficiency among insects.

RESULTS

A marker gene cardinal, which leads to white eyes when knocked-down in the red flour beetle Tribolium castaneum, was used to evaluate the effects of RNAi efficiency under different dsRNA storage conditions. We demonstrated that the dsRNA molecule is very stable under typical cryopreservation temperatures (-80 and -20 °C) within 180 days, and RNAi efficiency shows no significant differences under either low temperature. Unexpectedly, while dsRNA molecules were treated with multiple freeze-thaw cycles up to 50 times between -80/-20 °C and room temperature, we discovered that dsRNA integrity and RNAi efficiency were comparable with fresh dsRNA. Finally, when the stability of dsRNA was further measured under refrigerated storage conditions (4 °C), we surprisingly found that dsRNA is still stable within 180 days and can induce an efficient RNAi response as that of initial dsRNA.

CONCLUSION

Our results indicate that dsRNA is extraordinarily stable under various temperature storage conditions that did not significantly impact RNAi efficiency in vivo insects. © 2022 Society of Chemical Industry.

Endophytic Diaporthe as Promising Leads for the Development of Biopesticides and Biofertilizers for a Sustainable Agriculture

Plant pathogens are responsible for causing economic and production losses in several crops worldwide, thus reducing the quality and quantity of agricultural supplies. To reduce the usage of chemically synthesized pesticides, strategies and approaches using microorganisms are being used in plant disease management. Most of the studies concerning plant-growth promotion and biological agents to control plant diseases are mainly focused on bacteria. In addition, a great portion of registered and commercialized biopesticides are bacterial-based products. Despite fungal endophytes having been identified as promising candidates for their use in biological control, it is of the utmost importance to develop and improve the existing knowledge on this research field. The genus Diaporthe, encompasses plant pathogens, saprobes and endophytes that have been screened for secondary metabolite, mainly due to their production of polyketides and a variety of unique bioactive metabolites with agronomic importance. Some of these metabolites exhibit antifungal and antibacterial activity for controlling plant pathogens, and phytotoxic activity for the development of potential mycoherbicides. Moreover, species of Diaporthe are reported as promising agents in the development of biofertilizers. For this reason, in this review we summarize the potential of Diaporthe species to produce natural products with application in agriculture and describe the benefits of these fungi to promote their host plant's growth.

Generating and testing the efficacy of transgenic Cas9 in Tribolium castaneum

CRISPR/Cas9 genome editing has now expanded to many insect species, including Tribolium castaneum. However, compared to Drosophila melanogaster, the CRISPR toolkit of T. castaneum is limited. A particularly apparent gap is the lack of Cas9 transgenic animals, which generally offer higher editing efficiency. We address this by creating and testing transgenic beetles expressing Cas9. We generated two different constructs bearing basal heat shock promoter-driven Cas9, two distinct 3' UTRs, and one containing Cas9 fused to EGFP by a T2A peptide. Analyses of Cas9 activity in each transgenic line demonstrated that both designs are capable of inducing CRISPR- mediated changes in the genome in the absence of heat induction. Overall, these resources enhance the accessibility of CRISPR/Cas9 genome editing for the Tribolium research community and provide a benchmark against which to compare future transgenic Cas9 lines.

The red flour beetle T. castaneum: elaborate genetic toolkit and unbiased large scale RNAi screening to study insect biology and evolution

The red flour beetle Tribolium castaneum has emerged as an important insect model system for a variety of topics. With respect to studying gene function, it is second only to the vinegar fly D. melanogaster. The RNAi response in T. castaneum is exceptionally strong and systemic, and it appears to target all cell types and processes. Uniquely for emerging model organisms, T. castaneum offers the opportunity of performing time- and cost-efficient large-scale RNAi screening, based on commercially available dsRNAs targeting all genes, which are simply injected into the body cavity. Well established transgenic and genome editing approaches are met by ease of husbandry and a relatively short generation time. Consequently, a number of transgenic tools like UAS/Gal4, Cre/Lox, imaging lines and enhancer trap lines are already available. T. castaneum has been a genetic experimental system for decades and now has become a workhorse for molecular and reverse genetics as well as in vivo imaging. Many aspects of development and general biology are more insect-typical in this beetle compared to D. melanogaster. Thus, studying beetle orthologs of well-described fly genes has allowed macro-evolutionary comparisons in developmental processes such as axis formation, body segmentation, and appendage, head and brain development. Transgenic approaches have opened new ways for in vivo imaging. Moreover, this emerging model system is the first choice for research on processes that are not represented in the fly, or are difficult to study there, e.g. extraembryonic tissues, cryptonephridial organs, stink gland function, or dsRNA-based pesticides.

Secretion and Detection of Defensive Compounds by the Red Flour Beetle Tribolium castaneum Interacting with the Insect Pathogenic Fungus Beauveria bassiana

Entomopathogenic fungi such as Beauveria bassiana are extensively used for the control of insect pests worldwide. They infect mostly by adhesion to the insect surface and penetration through the cuticle. However, some insects, such as the red flour beetle Tribolium castaneum (Herbst), have evolved resistance by embedding their cuticle with antifungal compounds. Thus, they avoid fungal germination on the cuticle, which result in low susceptibility to entomopathogenic fungi. In adult T. castaneum, these antifungals are the well-known defensive compounds methyl-1,4- and ethyl-1,4-benzoquinone. In this study, we added B. bassiana conidia on the diet of adult beetles to study the effect of the entomopathogen on the secretion and detection of the beetle volatile blend containing both benzoquinones. The compounds were analyzed by solid phase microextraction coupled to gas chromatography–flame ionization detection, and were detected by electroantennography. In addition, we measured the expression level of four genes encoding for two odorant-binding proteins (OBP), one chemosensory protein (CSP), and one odorant receptor (OR) in both healthy and fungus-treated insects. Significant alterations in the secretion of both benzoquinones, as well as in the perception of methyl-1,4-benzoquinone, were found in fungus-treated insects. TcOBP7D, TcOBP0A and TcCSP3A genes were down-regulated in insects fed conidia for 12 and 48 h, and the latter gene was up-regulated in 72 h samples. TcOR1 expression was not altered at the feeding times studied. We conclude that fungus-treated insects alter both secretion and perception of benzoquinones, but additional functional and genetic studies are needed to fully understand the effects of fungal infection on the insect chemical ecology.

Whole-Genome Sequence of the Wolbachia Strain wTcon, an Endosymbiont of the Confused Flour Beetle, Tribolium confusum

Up to 60% of insects are infected with symbiont intracellular alphaproteobacteria of the genus Wolbachia, which are often able to manipulate their host’s reproduction. Here, we report the annotated draft genome sequence of strain wTcon from the confused flour beetle, Tribolium confusum, based on long- and short-read sequence data. The assembled genome is located on 12 contigs with a total size of 1,418,452 bp.

Negative effects of fluctuating temperatures around the optimal temperature on reproduction and survival of the red flour beetle

Whereas the vast majority of animals in nature experience daily or seasonal thermal fluctuations, most laboratory experiments use constant temperatures. We examined the effect of fluctuating temperatures on reproduction and survival under starvation, two important components of fitness. We used the red flour beetle as a model organism, which is a significant pest in grain mills around the world. Fluctuations around the optimal temperature were always negative for the adult survival under starvation. The effect of thermal fluctuations on the number of offspring reaching adulthood was negative as well but increased with the extent of exposure. It was the strongest when the adult parents were kept and the offspring were raised under fluctuating temperatures. However, the later the offspring were exposed to fluctuations during their development, the weaker the effect of fluctuating temperatures was. Moreover, raising the parents under fluctuating temperatures but keeping them after pupation at constant temperatures fully alleviated the negative effects of fluctuations on the offspring. Finally, we demonstrate that keeping the parents a few days under fluctuating temperatures is required to induce negative effects on the number of offspring reaching adulthood. Our study disentangles between the effects of thermal fluctuations experienced during the parental and offspring stage thus contributing to the ongoing research of insects under fluctuating temperatures.

Tribolium castaneum: A Model Insect for Fundamental and Applied Research

Tribolium castaneum has a long history as a model species in many distinct subject areas, but improved connections among the genetics, genomics, behavioral, ecological, and pest management fields are needed to fully realize this species' potential as a model. Tribolium castaneum was the first beetle whose genome was sequenced, and a new genome assembly and enhanced annotation, combined with readily available genomic research tools, have facilitated its increased use in a wide range of functional genomics research. Research into T. castaneum's sensory systems, response to pheromones and kairomones, and patterns of movement and landscape utilization has improved our understanding of behavioral and ecological processes. Tribolium castaneum has also been a model in the development of pest monitoring and management tactics, including evaluation of insecticide resistance mechanisms. Application of functional genomics approaches to behavioral, ecological, and pest management research is in its infancy but offers a powerful tool that can link mechanism with function and facilitate exploitation of these relationships to better manage this important food pest.