Agricultural insect pests as models for studying stress-induced evolutionary processes.

Agricultural insect pests (AIPs) are widely successful in adapting to natural and anthropogenic stressors, repeatedly overcoming population bottlenecks and acquiring resistance to intensive management practices. Although they have been largely overlooked in evolutionary studies, AIPs are ideal systems for understanding rapid adaptation under novel environmental conditions. Researchers have identified several genomic mechanisms that likely contribute to adaptive stress responses, including positive selection on de novo mutations, polygenic selection on standing allelic variation and phenotypic plasticity (e.g., hormesis). However, new theory suggests that stress itself may induce epigenetic modifications, which may confer heritable physiological changes (i.e., stress-resistant phenotypes). In this perspective, we discuss how environmental stress from agricultural management generates the epigenetic and genetic modifications that are associated with rapid adaptation in AIPs. We summarise existing evidence for stress-induced evolutionary processes in the context of insecticide resistance. Ultimately, we propose that studying AIPs offers new opportunities and resources for advancing our knowledge of stress-induced evolution.

Evolution of chemosensory genes in Colorado potato beetle, Leptinotarsa decemlineata.

Associating with plant hosts is thought to have elevated the diversification of insect herbivores, which comprise the majority of global species diversity. In particular, there is considerable interest in understanding the genetic changes that allow host-plant shifts to occur in pest insects and in determining what aspects of functional genomic diversity impact host-plant breadth. Insect chemoreceptors play a central role in mediating insect-plant interactions, as they directly influence plant detection and sensory stimuli during feeding. Although chemosensory genes evolve rapidly, it is unclear how they evolve in response to host shifts and host specialization. We investigate whether selection at chemosensory genes is linked to host-plant expansion from the buffalo burr, Solanum rostratum, to potato, Solanum tuberosum, in the super-pest Colorado potato beetle (CPB), Leptinotarsa decemlineata (Coleoptera: Chrysomelidae). First, to refine our knowledge of CPB chemosensory genes, we developed novel gene expression data for the antennae and maxillary-labial palps. We then examine patterns of selection at these loci within CPB, as well as compare whether rates of selection vary with respect to 9 closely related, non-pest Leptinotarsa species that vary in diet breadth. We find that rates of positive selection on olfactory receptors are higher in host-plant generalists, and this signal is particularly strong in CPB. These results provide strong candidates for further research on the genetic basis of variation in insect chemosensory performance and novel targets for pest control of a notorious super-pest.

Transposable elements differ between geographic populations of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae).

Agricultural insect herbivores show a remarkable ability to adapt to modern agroecosystems, making them ideal for the study of the mechanisms underlying rapid evolution. The mobilization of transposable elements is one mechanism that may help explain this ability. The Colorado potato beetle, Leptinotarsa decemlineata, is a highly adaptable species, as shown by its wide host range, broad geographic distribution, and tolerance to insecticides. However, beetle populations vary in insecticide tolerance, with Eastern US beetle populations being more adaptable than Western US ones. Here, we use a community ecology approach to examine how the abundance and diversity of transposable elements differs in 88 resequenced genomes of L. decemlineata collected throughout North America. We tested if assemblages and mobilization of transposable elements differed between populations of L. decemlineata based on the beetle's geography, host plant, and neonicotinoid insecticide resistance. Among populations of North American L. decemlineata, individuals collected in Mexico host more transposable elements than individuals collected in the United States. Transposable element insertion locations differ among geographic populations, reflecting the evolutionary history of this species. Total transposable element diversity between L. decemlineata individuals is enough to distinguish between populations, with more TEs found in beetles collected in Mexico than in the United States. Transposable element diversity does not appear to differ between beetles found on different host plants, or relate to different levels of insecticide resistance.

Cross-protection interactions in insect pests: Implications for pest management in a changing climate.

Agricultural insect pests display an exceptional ability to adapt quickly to natural and anthropogenic stressors. Emerging evidence suggests that frequent and varied sources of stress play an important role in driving protective physiological responses; therefore, intensively managed agroecosystems combined with climatic shifts might be an ideal crucible for stress adaptation. Cross-protection, where responses to one stressor offers protection against another type of stressor, has been well documented in many insect species, yet the molecular and epigenetic underpinnings that drive overlapping protective responses in insect pests remain unclear. In this perspective, we discuss cross-protection mechanisms and provide an argument for its potential role in increasing tolerance to a wide range of natural and anthropogenic stressors in agricultural insect pests. By drawing from existing literature on single and multiple stressor studies, we outline the processes that facilitate cross-protective interactions, including epigenetic modifications, which are understudied in insect stress responses. Finally, we discuss the implications of cross-protection for insect pest management, focusing on the consequences of cross-protection between insecticides and elevated temperatures associated with climate change. Given the multiple ways that insect pests are intensively managed in agroecosystems, we suggest that examining the role of multiple stressors can be important in understanding the wide adaptability of agricultural insect pests. © 2022 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Rapid evolution of insecticide resistance in the Colorado potato beetle, Leptinotarsa decemlineata.

Despite considerable research, efforts to manage insecticide resistance continue to fail. The Colorado potato beetle (CPB), Leptinotarsa decemlineata Say (Coleoptera: Chrysomelidae), epitomizes this problem, as it has repeatedly and rapidly evolved resistance to>50 insecticides. The patterns of resistance evolution are intriguing, as they defy models where resistance evolves from rare mutations. Here, we synthesize recent research on insecticide resistance in CPB showing that polygenic resistance drawn from standing genetic diversity explains genomic patterns of insecticide resistance evolution. However, rapid gene regulatory evolution suggests that other mechanisms might also facilitate adaptive change. We explore the hypothesis that sublethal stress from insecticide exposure could alter heritable epigenetic modifications, and discuss the range of experimental approaches needed to fully understand insecticide resistance evolution in this super pest.

Evidence of hard-selective sweeps suggests independent adaptation to insecticides in Colorado potato beetle (Coleoptera: Chrysomelidae) populations.

Pesticide resistance provides one of the best examples of rapid evolution to environmental change. The Colorado potato beetle (CPB) has a long and noteworthy history as a super-pest due to its ability to repeatedly develop resistance to novel insecticides and rapidly expand its geographic and host plant range. Here, we investigate regional differences in demography, recombination, and selection using whole-genome resequencing data from two highly resistant CPB populations in the United States (Hancock, Wisconsin and Long Island, New York). Demographic reconstruction corroborates historical records for a single pest origin during the colonization of the Midwestern and Eastern United States in the mid- to late-19th century and suggests that the effective population size might be higher in Long Island, NY than Hancock, WI despite contemporary potato acreage of Wisconsin being far greater. Population-based recombination maps show similar background recombination rates between these populations, as well as overlapping regions of low recombination that intersect with important metabolic detoxification genes. In both populations, we find compelling evidence for hard selective sweeps linked to insecticide resistance with multiple sweeps involving genes associated with xenobiotic metabolism, stress response, and defensive chemistry. Notably, only two candidate insecticide resistance genes are shared among both populations, but both appear to be independent hard selective sweep events. This suggests that repeated, rapid, and independent evolution of genes may underlie CPB's pest status among geographically distinct populations.

Genome Resequencing Reveals Rapid, Repeated Evolution in the Colorado Potato Beetle.

Insecticide resistance and rapid pest evolution threatens food security and the development of sustainable agricultural practices, yet the evolutionary mechanisms that allow pests to rapidly adapt to control tactics remains unclear. Here, we examine how a global super-pest, the Colorado potato beetle (CPB), Leptinotarsa decemlineata, rapidly evolves resistance to insecticides. Using whole-genome resequencing and transcriptomic data focused on its ancestral and pest range in North America, we assess evidence for three, nonmutually exclusive models of rapid evolution: pervasive selection on novel mutations, rapid regulatory evolution, and repeated selection on standing genetic variation. Population genomic analysis demonstrates that CPB is geographically structured, even among recently established pest populations. Pest populations exhibit similar levels of nucleotide diversity, relative to nonpest populations, and show evidence of recent expansion. Genome scans provide clear signatures of repeated adaptation across CPB populations, with especially strong evidence of selection on insecticide resistance genes in different populations. Analyses of gene expression show that constitutive upregulation of candidate insecticide resistance genes drives distinctive population patterns. CPB evolves insecticide resistance repeatedly across agricultural regions, leveraging similar genetic pathways but different genes, demonstrating a polygenic trait architecture for insecticide resistance that can evolve from standing genetic variation. Despite expectations, we do not find support for strong selection on novel mutations, or rapid evolution from selection on regulatory genes. These results suggest that integrated pest management practices must mitigate the evolution of polygenic resistance phenotypes among local pest populations, in order to maintain the efficacy and sustainability of novel control techniques.

Sequence variation and regulatory variation in acetylcholinesterase genes contribute to insecticide resistance in different populations of Leptinotarsa decemlineata.

Although insect herbivores are known to evolve resistance to insecticides through multiple genetic mechanisms, resistance in individual species has been assumed to follow the same mechanism. While both mutations in the target site insensitivity and increased amplification are known to contribute to insecticide resistance, little is known about the degree to which geographic populations of the same species differ at the target site in a response to insecticides. We tested structural (e.g., mutation profiles) and regulatory (e.g., the gene expression of Ldace1 and Ldace2, AChE activity) differences between two populations (Vermont, USA and Belchow, Poland) of the Colorado potato beetle, Leptinotarsa decemlineata in their resistance to two commonly used groups of insecticides, organophosphates, and carbamates. We established that Vermont beetles were more resistant to azinphos-methyl and carbaryl insecticides than Belchow beetles, despite a similar frequency of resistance-associated alleles (i.e., S291G) in the Ldace2 gene. However, the Vermont population had two additional amino acid replacements (G192S and F402Y) in the Ldace1 gene, which were absent in the Belchow population. Moreover, the Vermont population showed higher expression of Ldace1 and was less sensitive to AChE inhibition by azinphos-methyl oxon than the Belchow population. Therefore, the two populations have evolved different genetic mechanisms to adapt to organophosphate and carbamate insecticides.

De Novo Whole-Genome Assembly of the Swede Midge (Contarinia nasturtii), a Specialist of Brassicaceae, Using Linked-Read Sequencing.

The swede midge, Contarinia nasturtii, is a cecidomyiid fly that feeds specifically on plants within the Brassicaceae. Plants in this family employ a glucosinolate-myrosinase defense system, which can be highly toxic to nonspecialist feeders. Feeding by C. nasturtii larvae induces gall formation, which can cause substantial yield losses thus making it a significant agricultural pest. A lack of genomic resources, in particular a reference genome, has limited deciphering the mechanisms underlying glucosinolate tolerance in C. nasturtii, which is of particular importance for managing this species. Here, we present an annotated, scaffolded reference genome of C. nasturtii using linked-read sequencing from a single individual and explore systems involved in glucosinolate detoxification. The C. nasturtii genome is similar in size and annotation completeness to that of the Hessian fly, Mayetiola destructor, but has greater contiguity. Several genes encoding enzymes involved in glucosinolate detoxification in other insect pests, including myrosinases, sulfatases, and glutathione S-transferases, were found, suggesting that C. nasturtii has developed similar strategies for feeding on Brassicaceae. The C. nasturtii genome will, therefore, be integral to continued research on plant-insect interactions in this system and contribute to effective pest management strategies.

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.

Elevated rates of positive selection drive the evolution of pestiferousness in the Colorado potato beetle (Leptinotarsa decemlineata, Say).

Contextualizing evolutionary history and identifying genomic features of an insect that might contribute to its pest status is important in developing early detection and control tactics. In order to understand the evolution of pestiferousness, which we define as the accumulation of traits that contribute to an insect population's success in an agroecosystem, we tested the importance of known genomic properties associated with rapid adaptation in the Colorado potato beetle (CPB), Leptinotarsa decemlineata Say. Within the leaf beetle genus Leptinotarsa, only CPB, and a few populations therein, has risen to pest status on cultivated nightshades, Solanum. Using whole genomes from ten closely related Leptinotarsa species native to the United States, we reconstructed a high-quality species tree and used this phylogenetic framework to assess evolutionary patterns in four genomic features of rapid adaptation: standing genetic variation, gene family expansion and contraction, transposable element abundance and location, and positive selection at protein-coding genes. Throughout approximately 20 million years of history, Leptinotarsa species show little evidence of gene family turnover and transposable element variation. However, there is a clear pattern of CPB experiencing higher rates of positive selection on protein-coding genes. We determine that these rates are associated with greater standing genetic variation due to larger effective population size, which supports the theory that the demographic history contributes to rates of protein evolution. Furthermore, we identify a suite of coding genes under positive selection that are putatively associated with pestiferousness in the Colorado potato beetle lineage. They are involved in the biological processes of xenobiotic detoxification, chemosensation and hormone function.

Synthetic pheromone exposure increases calling and reduces subsequent mating in female Contarinia nasturtii (Diptera: Cecidomyiidae).

BACKGROUND: Pheromone-mediated mating disruption, which uses large amounts of synthetic female pheromones to interrupt insect reproductive behavior, has been successful for managing important agricultural pests. While multiple mechanisms have been discovered explaining how synthetic pheromone treatments prevent males from finding females, it is less clear how unnaturally large doses of synthetic sex pheromone impact the behavior of female insects, particularly nonlepidopteran females. In some species, 'autodetecting' females possess pheromone receptors and respond to ambient pheromones by altering their mating behavior. Here, we test whether exposure to stereospecific and racemic synthetic pheromones influences calling and subsequent propensity to mate in female swede midge (Contarinia nasturtii Kieffer; Diptera: Cecidomyiidae), a pest of Brassica crops. RESULTS: In both laboratory and field settings, females exposed to stereospecific and racemic three-component pheromone blends called significantly more frequently and for longer durations than midges in control treatments. In the field, midges were twice as likely to call in pheromone-treated plots versus nontreated plots. Additionally, pheromone pre-exposure reduced subsequent mating: while 68% of female midges mated following control conditions, only 42% and 35% of females pre-exposed to stereospecific and racemic three-component blends mated, respectively. CONCLUSION: While more frequent calling within pheromone-treated backgrounds may increase the likelihood that females are detected by males, a reduction in female propensity to mate would increase the efficacy of a pheromone-mediated mating disruption system. Our work presents the first known investigation of autodetection behavior in Cecidomyiidae. Additional research is necessary to understand the implications of female autodetection for swede midge management.

Gene content evolution in the arthropods.

BACKGROUND: Arthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recorded in adaptive changes in the genome. Dissection of the genomic record of sequence change enables broad questions regarding genome evolution to be addressed, even across hyper-diverse taxa within arthropods. RESULTS: Using 76 whole genome sequences representing 21 orders spanning more than 500 million years of arthropod evolution, we document changes in gene and protein domain content and provide temporal and phylogenetic context for interpreting these innovations. We identify many novel gene families that arose early in the evolution of arthropods and during the diversification of insects into modern orders. We reveal unexpected variation in patterns of DNA methylation across arthropods and examples of gene family and protein domain evolution coincident with the appearance of notable phenotypic and physiological adaptations such as flight, metamorphosis, sociality, and chemoperception. CONCLUSIONS: These analyses demonstrate how large-scale comparative genomics can provide broad new insights into the genotype to phenotype map and generate testable hypotheses about the evolution of animal diversity.

Odors from phylogenetically-distant plants to Brassicaceae repel an herbivorous Brassica specialist.

Specialist insect herbivores are constrained by highly specific odor recognition systems to accept suitable host plants. Given that odor recognition leads specialist insects to accept a limited range of plants, we hypothesized that phylogenetically distant plants produce odors that are physicochemically different from host odors and would be less attractive or even repellent to a specialist herbivore. We tested this hypothesis by examining behavioral and ovipositional responses of swede midge (Contarinia nasturtii, Diptera: Cecidomyiidae), a specialist of brassicas, to broccoli sprayed with non-host essential oils. Specifically, we asked: (1) How do essential oils from different plant species influence host-seeking and oviposition behaviors of swede midge? (2) Do odors from non-host plants that are not phylogenetically related or physicochemically similar to host plants affect host-seeking or ovipositional behavior of swede midge? In oviposition assays, we found that non-host odors varied in their ability to modify female midge behavior and that phylogenetic relatedness was negatively correlated with larval density. In y-tube assays, we found that female midges most frequently avoided non-host odors that were more similar to brassica odors. Females were less likely to oviposit on or choose any treated host plants, but particularly avoided garlic, spearmint, thyme, eucalyptus lemon, and cinnamon bark treatments. Overall, we found that plant phylogenetic relatedness and odor similarity are related to repellency. Therefore, altering the diversity of plant odors by explicitly accounting for plant phylogenetic distance and odor similarity, relative to host plants, may be an important, underexploited tactic for sustainably managing challenging pests.

Racemic Pheromone Blends Disrupt Mate Location in the Invasive Swede Midge, Contarinia nasturtii.

Swede midge, Contarinia nasturtii Kieffer, is an invasive cecidomyiid pest that causes serious losses of Brassica oilseed and vegetable crops in the Northeastern U.S. and Canada. Currently, few alternatives to systemic insecticides exist for its management. Because a single feeding larva can render heading Brassica crops unmarketable, management strategies that prevent oviposition are needed urgently. Pheromone-mediated mating disruption is a promising management approach for swede midge because it prevents mating and subsequent crop damage. While the swede midge pheromone has been identified, one of the major barriers to using it in mating disruption is the high cost of synthesis. Racemic blends, consisting of natural and non-natural stereoisomers, could be useful for mating disruption because they are cheaper to produce. However, it is not clear whether racemic pheromone blends attract males and/or prevent them from locating and mating with females. Here, we studied the behavior of male swede midge in Y-tube and wind tunnel bioassays to pheromone blends. Specifically, we tested whether males: (1) are attracted to different doses of pheromone, (2) discriminate between blends comprising natural stereospecific or racemic components, or a combination thereof, and (3) are able to locate and copulate with females in pheromone-permeated olfactometers. We found that picogram amounts of pheromone attracted males and prevented them from locating females in y-tube olfactometers. While males were more attracted to stereospecific blends, compared to racemic blends, all blends tested prevented nearly all males mating with females. Therefore, low dose racemic blends may be promising for pheromone-mediated mating disruption.

Did maize domestication and early spread mediate the population genetics of corn leafhopper?

Investigating how crop domestication and early farming mediated crop attributes, distributions, and interactions with antagonists may shed light on today's agricultural pest problems. Crop domestication generally involved artificial selection for traits desirable to early farmers, for example, increased productivity or yield, and enhanced qualities, though invariably it altered the interactions between crops and insects, and expanded the geographical ranges of crops. Thus, some studies suggest that with crop domestication and spread, insect populations on wild crop ancestors gave rise to pestiferous insect populations on crops. Here, we addressed whether the emergence of corn leafhopper (Dalbulus maidis) as an agricultural pest may be associated with domestication and early spread of maize (Zea mays mays). We used AFLP markers and mitochondrial COI sequences to assess population genetic structuring and haplotype relationships among corn leafhopper samples from maize and its wild relative Zea diploperennis from multiple locations in Mexico and Argentina. We uncovered seven corn leafhopper haplotypes contained within two haplogroups, one haplogroup containing haplotypes associated with maize and the other containing haplotypes associated with Z. diploperennis in a mountainous habitat. Within the first haplogroup, one haplotype was predominant across Mexican locations, and another across Argentinean locations; both were considered pestiferous. We suggested that the divergence times of the maize-associated haplogroup and of the "pestiferous" haplotypes are correlated with the chronology of maize spread following its domestication. Overall, our results support a hypothesis positing that maize domestication favored corn leafhopper genotypes preadapted for exploiting maize so that they became pestiferous, and that with the geographical expansion of maize farming, corn leafhopper colonized Z. diploperennis, a host exclusive to secluded habitats that serves as a refuge for archaic corn leafhopper genotypic diversity. Broadly, our results help explain the extents to which crop domestication and early spread may have mediated the emergence of today's agricultural pests.

Crop domestication: anthropogenic effects on insect-plant interactions in agroecosystems.

Although crop domestication is considered a model system for understanding evolution, the eco-evolutionary effects of domesticated crops on higher trophic levels have rarely been discussed. Changes in size, shape, quality, or timing of plant traits during domestication can influence entire arthropod communities. The plant traits specific to crop plants can be rare in nature. In the face of such novelty, it is important to understand how species and trophic levels vary in their responses. Although the evidence is still limited, crop domestication can influence the ecology, genetics, and evolution of plants, insect herbivores, natural enemies, and pollinators. We call for more study on how eco-evolutionary processes operate under domestication to provide new insight on the sustainability of species interactions within agroecosystems.

A Single Swede Midge (Diptera: Cecidomyiidae) Larva Can Render Cauliflower Unmarketable.

Swede midge, Contarinia nasturtii Kieffer (Diptera: Cecidomyiidae), is an invasive pest causing significant damage on Brassica crops in the Northeastern United States and Eastern Canada. Heading brassicas, like cauliflower, appear to be particularly susceptible. Swede midge is difficult to control because larvae feed concealed inside meristematic tissues of the plant. In order to develop damage and marketability thresholds necessary for integrated pest management, it is important to determine how many larvae render plants unmarketable and whether the timing of infestation affects the severity of damage. We manipulated larval density (0, 1, 3, 5, 10, or 20) per plant and the timing of infestation (30, 55, and 80 d after seeding) on cauliflower in the lab and field to answer the following questions: 1) What is the swede midge damage threshold? 2) How many swede midge larvae can render cauliflower crowns unmarketable? and 3) Does the age of cauliflower at infestation influence the severity of damage and marketability? We found that even a single larva can cause mild twisting and scarring in the crown rendering cauliflower unmarketable 52% of the time, with more larvae causing more severe damage and additional losses, regardless of cauliflower age at infestation.

Transgenerational effects of insecticides-implications for rapid pest evolution in agroecosystems.

Although pesticides are a major selective force in driving the evolution of insect pests, the evolutionary processes that give rise to insecticide resistance remain poorly understood. Insecticide resistance has been widely observed to increase with frequent and intense insecticide exposure, but can be lost following the relaxation of insecticide use. One possible but rarely explored explanation is that insecticide resistance may be associated with epigenetic modifications, which influence the patterning of gene expression without changing underlying DNA sequence. Epigenetic modifications such as DNA methylation, histone modifications, and small RNAs have been observed to be heritable in arthropods, but their role in the context of rapid evolution of insecticide resistance remain poorly understood. Here, we discuss evidence supporting how: firstly, insecticide-induced effects can be transgenerationally inherited; secondly, epigenetic modifications are heritable; and thirdly, epigenetic modifications are responsive to pesticide and xenobiotic stress. Therefore, pesticides may drive the evolution of resistance via epigenetic processes. Moreover, insect pests primed by pesticides may be more tolerant of other stress, further enhancing their success in adapting to agroecosystems. Resolving the role of epigenetic modifications in the rapid evolution of insect pests has the potential to lead to new approaches for integrated pest management as well as improve our understanding of how anthropogenic stress may drive the evolution of insect pests.