A depauperate immune repertoire precedes evolution of sociality in bees

Mechanisms of Pathogen and Pesticide Resistance in Honey Bees

Bees are the most important insect pollinators of the crops humans grow, and Apis mellifera, the Western honey bee, is the most commonly managed species for this purpose. In addition to providing agricultural services, the complex biology of honey bees has been the subject of scientific study since the 18th century, and the intricate behaviors of honey bees and ants, fellow hymenopterans, inspired much sociobiological inquest. Unfortunately, honey bees are constantly exposed to parasites, pathogens, and xenobiotics, all of which pose threats to their health. Despite our curiosity about and dependence on honey bees, defining the molecular mechanisms underlying their interactions with biotic and abiotic stressors has been challenging. The very aspects of their physiology and behavior that make them so important to agriculture also make them challenging to study, relative to canonical model organisms. However, because we rely on A. mellifera so much for pollination, we must continue our efforts to understand what ails them. Here, we review major advancements in our knowledge of honey bee physiology, focusing on immunity and detoxification, and highlight some challenges that remain.

Insects' essential role in understanding and broadening animal medication

Like humans, animals use plants and other materials as medication against parasites. Recent decades have shown that the study of insects can greatly advance our understanding of medication behaviors. The ease of rearing insects under laboratory conditions has enabled controlled experiments to test critical hypotheses, while their spectrum of reproductive strategies and living arrangements - ranging from solitary to eusocial communities - has revealed that medication behaviors can evolve to maximize inclusive fitness through both direct and indirect fitness benefits. Studying insects has also demonstrated in some cases that medication can act through modulation of the host's innate immune system and microbiome. We highlight outstanding questions, focusing on costs and benefits in the context of inclusive host fitness.

Social life results in social stress protection: a novel concept to explain individual life-history patterns in social insects

Resistance to and avoidance of stress slow aging and confer increased longevity in numerous organisms. Honey bees and other superorganismal social insects have two main advantages over solitary species to avoid or resist stress: individuals can directly help each other by resource or information transfer, and they can cooperatively control their environment. These benefits have been recognised in the context of pathogen and parasite stress as the concept of social immunity, which has been extensively studied. However, we argue that social immunity is only a special case of a general concept that we define here as social stress protection to include group-level defences against all biotic and abiotic stressors. We reason that social stress protection may have allowed the evolution of reduced individual-level defences and individual life-history optimization, including the exceptional aging plasticity of many social insects. We describe major categories of stress and how a colonial lifestyle may protect social insects, particularly against temporary peaks of extreme stress. We use the honey bee (Apis mellifera L.) to illustrate how patterns of life expectancy may be explained by social stress protection and how modern beekeeping practices can disrupt social stress protection. We conclude that the broad concept of social stress protection requires rigorous empirical testing because it may have implications for our general understanding of social evolution and specifically for improving honey bee health.

Influence of social lifestyles on host-microbe symbioses in the bees

Microbiomes are increasingly recognised as critical for the health of an organism. In eusocial insect societies, frequent social interactions allow for high-fidelity transmission of microbes across generations, leading to closer host-microbe coevolution. The microbial communities of bees with other social lifestyles are less studied, and few comparisons have been made between taxa that vary in social structure. To address this gap, we leveraged a cloud-computing resource and publicly available transcriptomic data to conduct a survey of microbial diversity in bee samples from a variety of social lifestyles and taxa. We consistently recover the core microbes of well-studied corbiculate bees, supporting this method's ability to accurately characterise microbial communities. We find that the bacterial communities of bees are influenced by host location, phylogeny and social lifestyle, although no clear effect was found for fungal or viral microbial communities. Bee genera with more complex societies tend to harbour more diverse microbes, with Wolbachia detected more commonly in solitary tribes. We present a description of the microbiota of Euglossine bees and find that they do not share the "corbiculate core" microbiome. Notably, we find that bacteria with known anti-pathogenic properties are present across social bee genera, suggesting that symbioses that enhance host immunity are important with higher sociality. Our approach provides an inexpensive means of exploring microbiomes of a given taxa and identifying avenues for further research. These findings contribute to our understanding of the relationships between bees and their associated microbial communities, highlighting the importance of considering microbiome dynamics in investigations of bee health.

Double trouble: trypanosomatids with two hosts have lower infection prevalence than single host trypanosomatids

Trypanosomatids are a diverse family of protozoan parasites, some of which cause devastating human and livestock diseases. There are two distinct infection life cycles in trypanosomatids; some species complete their entire life cycle in a single host (monoxenous) while others infect two hosts (dixenous). Dixenous trypanosomatids are mostly vectored by insects, and the human trypanosomatid diseases are caused mainly by vectored parasites. While infection prevalence has been described for subsets of hosts and trypanosomatids, little is known about whether monoxenous and dixenous trypanosomatids differ in infection prevalence. Here, we use meta-analyses to synthesise all published evidence of trypanosomatid infection prevalence for the last two decades, encompassing 931 unique host-trypansomatid systems. In examining 584 studies that describe infection prevalence, we find, strikingly, that monoxenous species are two-fold more prevalent than dixenous species across all hosts. We also find that dixenous trypanosomatids have significantly lower infection prevalence in insects than their non-insect hosts. To our knowledge, these results reveal for the first time, a fundamental difference in infection prevalence according to host specificity where vectored species might have lower infection prevalence as a result of a potential 'jack of all trades, master of none' style trade-off between the vector and subsequent hosts.

Differential bumble bee gene expression associated with pathogen infection and pollen diet

BACKGROUND

Diet and parasitism can have powerful effects on host gene expression. However, how specific dietary components affect host gene expression that could feed back to affect parasitism is relatively unexplored in many wild species. Recently, it was discovered that consumption of sunflower (Helianthus annuus) pollen reduced severity of gut protozoan pathogen Crithidia bombi infection in Bombus impatiens bumble bees. Despite the dramatic and consistent medicinal effect of sunflower pollen, very little is known about the mechanism(s) underlying this effect. However, sunflower pollen extract increases rather than suppresses C. bombi growth in vitro, suggesting that sunflower pollen reduces C. bombi infection indirectly via changes in the host. Here, we analyzed whole transcriptomes of B. impatiens workers to characterize the physiological response to sunflower pollen consumption and C. bombi infection to isolate the mechanisms underlying the medicinal effect. B. impatiens workers were inoculated with either C. bombi cells (infected) or a sham control (un-infected) and fed either sunflower or wildflower pollen ad libitum. Whole abdominal gene expression profiles were then sequenced with Illumina NextSeq 500 technology.

RESULTS

Among infected bees, sunflower pollen upregulated immune transcripts, including the anti-microbial peptide hymenoptaecin, Toll receptors and serine proteases. In both infected and un-infected bees, sunflower pollen upregulated putative detoxification transcripts and transcripts associated with the repair and maintenance of gut epithelial cells. Among wildflower-fed bees, infected bees downregulated immune transcripts associated with phagocytosis and the phenoloxidase cascade.

CONCLUSIONS

Taken together, these results indicate dissimilar immune responses between sunflower- and wildflower-fed bumble bees infected with C. bombi, a response to physical damage to gut epithelial cells caused by sunflower pollen, and a strong detoxification response to sunflower pollen consumption. Identifying host responses that drive the medicinal effect of sunflower pollen in infected bumble bees may broaden our understanding of plant-pollinator interactions and provide opportunities for effective management of bee pathogens.

Differential Gene Expression of Innate Immune Response Genes Consequent to Solenopsis invicta Virus-3 Infection

The red imported fire ant Solenopsis invicta Buren (fire ant hereafter) is a global pest that inflicts billions of dollars in damages to the United States economy and poses a major threat on a global scale. Concerns with the broad-spectrum application of insecticides have facilitated the hunt for natural enemy-mediated controls. One of these, the virus Solenopsis invicta virus-3 (SINV-3 hereafter) is exceptionally virulent in laboratory settings. However, despite high mortality rates in the laboratory and documented widespread SINV-3 prevalence in the southern United States, the fire ant remains a major pest. To explore this paradox, we document the immune response elicited by the fire ant when infected with SINV-3. We sequence the fire ant transcriptome prior to and following infection with SINV-3, and identify and discuss in detail genes in immune response pathways differentially expressed following infection with SINV-3. This information provides insights into genes and pathways involved in the SINV-3 infection response in the fire ant and offers avenues to pursue, to suppress key immune response genes and force the fire ant to succumb to SINV-3 infection in the field.

Impaired immune function accompanies social evolution in spiders

An efficient immune system is essential to the survival of many animals. Sociality increases risk of pathogen transmission, which should select for enhanced immune function. However, two hypotheses instead predict a weakened immune function: relaxed selection caused by social immunity/protection, and reduced efficacy of selection due to inbreeding, reproductive skew and female bias in social species that reduce effective population size and accelerate genetic drift. We assessed the effect of social evolution on immune function in a comparative study of two social spider species and their closely related subsocial sister species (genus Stegodyphus). The haemolymph of social species was less efficient in inhibiting bacterial growth of the potentially pathogenic bacteria Bacillus subtilis than that of subsocial species. Reduced efficacy of selection in social species was supported by comparative genomic analysis showing substantially elevated non-synonymous substitutions in immune genes in one of the social species. We propose that impaired immune function results from reduced efficacy of selection because the evolution of sociality in spiders is accompanied by demographic processes that elevate genetic drift. Positive feedback between pathogen-induced local extinctions and the resulting elevation of genetic drift may further weaken responses to selection by pathogens, and threaten species persistence.

Genomic architecture and sexually dimorphic expression underlying immunity in the red mason bee, Osmia bicornis

Insect pollinators provide crucial ecosystem services yet face increasing environmental pressures. The challenges posed by novel and reemerging pathogens on bee health means we need to improve our understanding of the immune system, an important barrier to infections and disease. Despite the importance of solitary bees, which are ecologically relevant, our understanding of the genomic basis and molecular mechanisms underlying their immune potential, and how intrinsic and extrinsic factors may influence it is limited. To improve our understanding of the genomic architecture underlying immunity of a key solitary bee pollinator, we characterized putative immune genes of the red mason bee, Osmia bicornis. In addition, we used publicly available RNA-seq datasets to determine how sexes differ in immune gene expression and splicing but also how pesticide exposure may affect immune gene expression in females. Through comparative genomics, we reveal an evolutionarily conserved set of more than 500 putative immune-related genes. We found genome-wide patterns of sex-biased gene expression, with greater enrichment of immune-related processes among genes with higher constitutive expression in males than females. Our results also suggest an up-regulation of immune-related genes in response to exposure to two common neonicotinoids, thiacloprid and imidacloprid. Collectively, our study provides important insights into the gene repertoire, regulation and expression differences in the sexes of O. bicornis, as well as providing additional support for how neonicotinoids can affect immune gene expression, which may affect the capacity of solitary bees to respond to pathogenic threats.

Current Knowledge on Bee Innate Immunity Based on Genomics and Transcriptomics

As important pollinators, bees play a critical role in maintaining the balance of the ecosystem and improving the yield and quality of crops. However, in recent years, the bee population has significantly declined due to various pathogens and environmental stressors including viruses, bacteria, parasites, and increased pesticide application. The above threats trigger or suppress the innate immunity of bees, their only immune defense system, which is essential to maintaining individual health and that of the colony. In addition, bees can be divided into solitary and eusocial bees based on their life traits, and eusocial bees possess special social immunities, such as grooming behavior, which cooperate with innate immunity to maintain the health of the colony. The omics approach gives us an opportunity to recognize the distinctive innate immunity of bees. In this regard, we summarize innate bee immunity from a genomic and transcriptomic perspective. The genetic characteristics of innate immunity were revealed by the multiple genomes of bees with different kinds of sociality, including honeybees, bumblebees, wasps, leaf-cutter bees, and so on. Further substantial transcriptomic data of different tissues from diverse bees directly present the activation or suppression of immune genes under the infestation of pathogens or toxicity of pesticides.

Complex networks of parasites and pollinators: moving towards a healthy balance

Parasites are viewed as a major threat to wild pollinator health. While this may be true for epidemics driven by parasite spillover from managed or invasive species, the picture is more complex for endemic parasites. Wild pollinator species host and share a species-rich, generalist parasite community. In contrast to the negative health impacts that these parasites impose on individual hosts, at a community level they may act to reduce competition from common and abundant pollinator species. By providing rare species with space in which to exist, this will act to support and maintain a diverse and thus healthier pollinator community. At this level, and perhaps paraxodically, parasites may be good for pollinators. This stands in clear contrast to the obvious negative impacts of epidemic and spillover parasites on wild pollinator communities. Research into floral resources that control parasites could be best employed to help design landscapes that provide pollinators with the opportunity to moderate their parasite community, rather than attempting to eliminate specific parasites from wild pollinator communities. This article is part of the theme issue 'Natural processes influencing pollinator health: from chemistry to landscapes'.

Short and long-term costs of inbreeding in the lifelong-partnership in a termite

Social life and lifelong partner commitments are expected to favor thorough partner choice, as an ill-suited partnership may have long-term consequences, adversely affecting the parents and spanning several cohorts of offspring. Here, we used ~1400 termite incipient colonies to estimate the short- and long-term costs of inbreeding upon the survival of the parents over a 15-month period, their productivity, and the resistance of their offspring toward pathogen pressure. We observed that foundation success was not influenced by the relatedness of partners, but by their levels of microbial load. We showed faster growth in inbred colonies with low levels of microbial load, revealing a potential tradeoff between pathogen defense and offspring production. Yet, inbreeding takes its toll later in colony development when offspring from incipient colonies face pathogen pressure. Although the success of a lifetime partnership is initially determined by the partner’s health, the cost of inbreeding in incipient colonies favors outbred colonies reaching maturity.

Studies of termite colonies over 15 months show that inbred colonies exhibit faster initial growth with low levels of microbial load, but higher mortality toward pathogens later in colony development.

Parasite resistance and immunity across female castes in a social insect

Abstract

Living in a social group increases the risks of parasitism, especially in highly-related groups. In homogenous groups, with no reproductive division of labour, the impact of parasitism is unlikely to vary with host identity. Many social systems, however, do exhibit division of reproductive labour, most famously in social insects with their reproductive queens and generally infertile workers. In such systems, the impact of parasitism will differ for each group. Consequently, we predict that susceptibility to parasites will vary to reflect such differential impact. We tested this prediction using a trypanosome-bumble bee system, where Crithidia bombi infects both gynes and workers of Bombus terrestris. We studied both susceptibility to the parasite and relevant measures of the immune function. As predicted, gynes were significantly less susceptible to the parasite than workers, but while gynes and workers expressed different immune profiles, how these link to differential susceptibility remains unclear. In conclusion, our results suggest that differential selection pressures exerted by parasites may produce multiple phenotypes from a single genotype in order to maximise fitness in a social group context.

Significance statement

Social insect colonies dominate terrestrial ecology, and as such are targets for parasites. How they defend themselves against such threats is a key question. Here, we show that bumble bee gynes — the reproductive individuals that overwinter and found colonies in this annual social system — are more resistant to a parasite that disproportionately affects reproductive fitness than their sister workers. Differential patterns of susceptibility may help to explain the success of these social insects.

Understanding effects of floral products on bee parasites: Mechanisms, synergism, and ecological complexity

Floral nectar and pollen commonly contain diverse secondary metabolites. While these compounds are classically thought to play a role in plant defense, recent research indicates that they may also reduce disease in pollinators. Given that parasites have been implicated in ongoing bee declines, this discovery has spurred interest in the potential for 'medicinal' floral products to aid in pollinator conservation efforts. We review the evidence for antiparasitic effects of floral products on bee diseases, emphasizing the importance of investigating the mechanism underlying antiparasitic effects, including direct or host-mediated effects. We discuss the high specificity of antiparasitic effects of even very similar compounds, and highlight the need to consider how nonadditive effects of multiple compounds, and the post-ingestion transformation of metabolites, mediate the disease-reducing capacity of floral products. While the bulk of research on antiparasitic effects of floral products on bee parasites has been conducted in the lab, we review evidence for the impact of such effects in the field, and highlight areas for future research at the floral product-bee disease interface. Such research has great potential both to enhance our understanding of the role of parasites in shaping plant-bee interactions, and the role of plants in determining bee-parasite dynamics. This understanding may in turn reveal new avenues for pollinator conservation.

Critical View on the Importance of Host Defense Strategies on Virus Distribution of Bee Viruses: What Can We Learn from SARS-CoV-2 Variants?

Bees, both wild and domesticated ones, are hosts to a plethora of viruses, with most of them infecting a wide range of bee species and genera. Although viral discovery and research on bee viruses date back over 50 years, the last decade is marked by a surge of new studies, new virus discoveries, and reports on viral transmission in and between bee species. This steep increase in research on bee viruses was mainly initiated by the global reports on honeybee colony losses and the worldwide wild bee decline, where viruses are regarded as one of the main drivers. While the knowledge gained on bee viruses has significantly progressed in a short amount of time, we believe that integration of host defense strategies and their effect on viral dynamics in the multi-host viral landscape are important aspects that are currently still missing. With the large epidemiological dataset generated over the last two years on the SARS-CoV-2 pandemic, the role of these defense mechanisms in shaping viral dynamics has become eminent. Integration of these dynamics in a multi-host system would not only greatly aid the understanding of viral dynamics as a driver of wild bee decline, but we believe bee pollinators and their viruses provide an ideal system to study the multi-host viruses and their epidemiology.

Functional constraints on insect immune system components govern their evolutionary trajectories

Roles of constraints in shaping evolutionary outcomes are often considered in the contexts of developmental biology and population genetics, in terms of capacities to generate new variants and how selection limits or promotes consequent phenotypic changes. Comparative genomics also recognizes the role of constraints, in terms of shaping evolution of gene and genome architectures, sequence evolutionary rates, and gene gains or losses, as well as on molecular phenotypes. Characterizing patterns of genomic change where putative functions and interactions of system components are relatively well described offers opportunities to explore whether genes with similar roles exhibit similar evolutionary trajectories. Using insect immunity as our test case system, we hypothesize that characterizing gene evolutionary histories can define distinct dynamics associated with different functional roles. We develop metrics that quantify gene evolutionary histories, employ these to characterize evolutionary features of immune gene repertoires, and explore relationships between gene family evolutionary profiles and their roles in immunity to understand how different constraints may relate to distinct dynamics. We identified three main axes of evolutionary trajectories characterized by gene duplication and synteny, maintenance/stability and sequence conservation, and loss and sequence divergence, highlighting similar and contrasting patterns across these axes amongst subsets of immune genes. Our results suggest that where and how genes participate in immune responses limit the range of possible evolutionary scenarios they exhibit. The test case study system of insect immunity highlights the potential of applying comparative genomics approaches to characterize how functional constraints on different components of biological systems govern their evolutionary trajectories.

Sociality and parasite transmission

Parasites and their social hosts form many different relationships. But what kind of selection regimes are important? A look at the parameters that determine fitness of the two parties suggests that social hosts differ from solitary ones primarily in the structure of transmission pathways. Because transmission is, both, the physical encounter of a new host and infecting it, several different elements determine parasite transmission success. These include spatial distance, genetic distance, or the temporal and ecological niche overlaps. Combing these elements into a ‘generalized transmission distance’ that determines parasite fitness aids in the identification of the critical steps. For example, short-distance transmission to genetically similar hosts within the social group is the most frequent process under sociality. Therefore, spatio-genetical distances are the main driver of parasite fitness. Vice versa, the generalized distance identifies the critical host defences. In this case, host defences should be primarily selected to defend against the within-group spread of an infection, especially among closely related group members.

Cuticle melanization and the expression of immune-related genes in the honeybee Apis mellifera (Hymenoptera: Apidae) adult workers

The global decline of bee populations has several factors, including pathogens, which need overcome the insect defenses such as the physical barriers, the body cuticle and peritrophic matrix (primary defenses), as well as the secondary defenses with antimicrobial peptides (AMPs) and the enzyme lysozyme. The regulation of immune defenses according to the infection risks raises questions about the immunity of social bees due to their exposition to different pathogens pressures during the adult lifespan and tasks performed. This study evaluated the primary (body cuticle melanization, peritrophic matrix and cpr14 expression) and secondary (AMPs and lysozyme expression) defenses of the honeybee Apis mellifera workers according to the age and tasks. The expression of malvolio was used to detect precocious forage tasks outside the colony. Forager workers have higher amount of cuticular melanization in the body cuticle than nurse, but not when the age effect is retired, indicating the gradual acquisition of this compound in the integument of adult bees. The relative value of chitin in the peritrophic matrix and cpr14 mRNA are similar in all bees evaluated, suggesting that these components of primary defenses do not change according to the task and age. Differential expression of genes for AMPs in workers performing different tasks, within the same age group, indicates that the behavior stimulates expression of genes related to secondary immune defense. The expression of malvolio gene, accelerating the change in workers behavior, and those related to immune defense suggest the investment in secondary defense mechanisms when the primary defense of the body cuticle is not yet completed.

Thermal stress induces tissue damage and a broad shift in regenerative signaling pathways in the honey bee digestive tract

Honey bee colonies in the USA have suffered from increased die-off in the last few years with a complex set of interacting stresses playing a key role. With changing climate, an increase in the frequency of severe weather events, such as heat waves, is anticipated. Understanding how these changes may contribute to stress in honey bees is crucial. Individual honey bees appear to have a high capacity to endure thermal stress. One reason for this high-level endurance is likely their robust heat shock response (HSR), which contributes to thermotolerance at the cellular level. However, less is known about other mechanisms of thermotolerance, especially those operating at the tissue level. To elucidate other determinants of resilience in this species, we used thermal stress coupled with RNAseq and identified broad transcriptional remodeling of a number of key signaling pathways in the honey bee, including those pathways known to be involved in digestive tract regeneration in the fruit fly such as the Hippo and JAK/STAT pathways. We also observed cell death and shedding of epithelial cells, which likely leads to induction of this regenerative transcriptional program. We found that thermal stress affects many of these pathways in other tissues, suggesting a shared program of damage response. This study provides important foundational characterization of the tissue damage response program in this key pollinating species. In addition, our data suggest that a robust regeneration program may also be a critical contributor to thermotolerance at the tissue level, a possibility which warrants further exploration in this and other species.

Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera

The tremendous diversity of Hymenoptera is commonly attributed to the evolution of parasitoidism in the last common ancestor of parasitoid sawflies (Orussidae) and wasp-waisted Hymenoptera (Apocrita). However, Apocrita and Orussidae differ dramatically in their species richness, indicating that the diversification of Apocrita was promoted by additional traits. These traits have remained elusive due to a paucity of sawfly genome sequences, in particular those of parasitoid sawflies. Here, we present comparative analyses of draft genomes of the primarily phytophagous sawfly Athalia rosae and the parasitoid sawfly Orussus abietinus. Our analyses revealed that the ancestral hymenopteran genome exhibited traits that were previously considered unique to eusocial Apocrita (e.g., low transposable element content and activity) and a wider gene repertoire than previously thought (e.g., genes for CO₂ detection). Moreover, we discovered that Apocrita evolved a significantly larger array of odorant receptors than sawflies, which could be relevant to the remarkable diversification of Apocrita by enabling efficient detection and reliable identification of hosts.

Conservation genomics reveals pesticide and pathogen exposure in the declining bumble bee Bombus terricola

In recent years, many pollinators have experienced large population declines, which threaten food security and the stability of natural ecosystems. Bumble bees are particularly important because their ability to “buzz” pollinate and tolerate cooler conditions make them critical pollinators for certain plants and regions. Here, we apply a conservation genomics approach to study the vulnerable Bombus terricola. We sequenced RNA from 30 worker abdomens, 18 of which were collected from agricultural sites and 12 of which were collected from nonagricultural sites. We found transcriptional signatures associated with exposure to insecticides, with gene expression patterns suggesting that bumble bees were exposed to neonicotinoids and/or fipronil—two compounds known to negatively impact bees. We also found transcriptional signatures associated with pathogen infections. In addition to the transcriptomic analysis, we carried out a metatranscriptomic analysis and detected five pathogens in the abdomens of workers, three of which are common in managed honey bee and bumble bee colonies. Our conservation genomics study provides functional support for the role of pesticides and pathogen spillover in the decline of B. terricola. We demonstrate that conservation genomics is an invaluable tool which allows researchers to quantify the effects of multiple stressors that impact pollinator populations in the wild.

Genus-Wide Characterization of Bumblebee Genomes Provides Insights into Their Evolution and Variation in Ecological and Behavioral Traits

Bumblebees are a diverse group of globally important pollinators in natural ecosystems and for agricultural food production. With both eusocial and solitary life-cycle phases, and some social parasite species, they are especially interesting models to understand social evolution, behavior, and ecology. Reports of many species in decline point to pathogen transmission, habitat loss, pesticide usage, and global climate change, as interconnected causes. These threats to bumblebee diversity make our reliance on a handful of well-studied species for agricultural pollination particularly precarious. To broadly sample bumblebee genomic and phenotypic diversity, we de novo sequenced and assembled the genomes of 17 species, representing all 15 subgenera, producing the first genus-wide quantification of genetic and genomic variation potentially underlying key ecological and behavioral traits. The species phylogeny resolves subgenera relationships, whereas incomplete lineage sorting likely drives high levels of gene tree discordance. Five chromosome-level assemblies show a stable 18-chromosome karyotype, with major rearrangements creating 25 chromosomes in social parasites. Differential transposable element activity drives changes in genome sizes, with putative domestications of repetitive sequences influencing gene coding and regulatory potential. Dynamically evolving gene families and signatures of positive selection point to genus-wide variation in processes linked to foraging, diet and metabolism, immunity and detoxification, as well as adaptations for life at high altitudes. Our study reveals how bumblebee genes and genomes have evolved across the Bombus phylogeny and identifies variations potentially linked to key ecological and behavioral traits of these important pollinators.

Avoidance of Contaminated Food Correlates With Low Protozoan Infection in Bonobos

Intense selection pressure from parasites on free-living animals has resulted in behavioral adaptations that help potential hosts avoid sources of infection. In primates, such “behavioral immunity” is expressed in different contexts and may vary according to the ecology of the host, the nature of the infectious agent, and the individual itself. In this study, we investigated whether avoidance of contaminated food was associated with reduced parasite infection in sanctuary-housed bonobos. To do this, we used bonobos’ responses to soil- and fecally-contaminated food in behavioral experiments, and then compared the results with an estimate of protozoan infection across individuals. We found that avoidance of contaminated food correlated negatively with Balantioides coli infection, a potentially pathogenic protozoan transmitted through the fecal-oral route. The association between avoidance responses and parasitism were most evident in experiments in which subjects were offered a choice of food items falling along a gradient of fecal contamination. In the case of experiments with more limited options and a high degree of contamination, most subjects were averse to the presented food item and this may have mitigated any relationship between feeding decisions and infection. In experiments with low perceived levels of contamination, most subjects consumed previously contaminated food items, which may also have obscured such a relationship. The behavioral immunity observed may be a consequence of the direct effects of parasites (infection), reflecting the first scale of a landscape of disgust: individual responses. Indirect effects of parasites, such as modulation of feeding decisions and reduced social interactions—and their potential trade-offs with physiological immunity—are also discussed in light of individual fitness and primate evolution. This study builds on previous work by showing that avoidance behaviors may be effective in limiting exposure to a wide diversity of oro-fecally transmitted parasites.

A combined RAD-Seq and WGS approach reveals the genomic basis of yellow color variation in bumble bee Bombus terrestris

Bumble bees exhibit exceptional diversity in their segmental body coloration largely as a result of mimicry. In this study we sought to discover genes involved in this variation through studying a lab-generated mutant in bumble bee Bombus terrestris, in which the typical black coloration of the pleuron, scutellum, and first metasomal tergite is replaced by yellow, a color variant also found in sister lineages to B. terrestris. Utilizing a combination of RAD-Seq and whole-genome re-sequencing, we localized the color-generating variant to a single SNP in the protein-coding sequence of transcription factor cut. This mutation generates an amino acid change that modifies the conformation of a coiled-coil structure outside DNA-binding domains. We found that all sequenced Hymenoptera, including sister lineages, possess the non-mutant allele, indicating different mechanisms are involved in the same color transition in nature. Cut is important for multiple facets of development, yet this mutation generated no noticeable external phenotypic effects outside of setal characteristics. Reproductive capacity was reduced, however, as queens were less likely to mate and produce female offspring, exhibiting behavior similar to that of workers. Our research implicates a novel developmental player in pigmentation, and potentially caste, thus contributing to a better understanding of the evolution of diversity in both of these processes.

Exposure to low doses of pesticides induces an immune response and the production of nitric oxide in honeybees

Honeybees are essential pollinators of many agricultural crops and wild plants. However, the number of managed bee colonies has declined in some regions of the world over the last few decades, probably caused by a combination of factors including parasites, pathogens and pesticides. Exposure to these diverse biotic and abiotic stressors is likely to trigger immune responses and stress pathways that affect the health of individual honeybees and hence their contribution to colony survival. We therefore investigated the effects of an orally administered bacterial pathogen (Pseudomonas entomophila) and low-dose xenobiotic pesticides on honeybee survival and intestinal immune responses. We observed stressor-dependent effects on the mean lifespan, along with the induction of genes encoding the antimicrobial peptide abaecin and the detoxification factor cytochrome P450 monooxygenase CYP9E2. The pesticides also triggered the immediate induction of a nitric oxide synthase gene followed by the delayed upregulation of catalase, which was not observed in response to the pathogen. Honeybees therefore appear to produce nitric oxide as a specific defense response when exposed to xenobiotic stimuli. The immunity-related and stress-response genes we tested may provide useful stressor-dependent markers for ecotoxicological assessment in honeybee colonies.

The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control

Background

The stable fly, Stomoxys calcitrans, is a major blood-feeding pest of livestock that has near worldwide distribution, causing an annual cost of over $2 billion for control and product loss in the USA alone. Control of these flies has been limited to increased sanitary management practices and insecticide application for suppressing larval stages. Few genetic and molecular resources are available to help in developing novel methods for controlling stable flies.

Results

This study examines stable fly biology by utilizing a combination of high-quality genome sequencing and RNA-Seq analyses targeting multiple developmental stages and tissues. In conjunction, 1600 genes were manually curated to characterize genetic features related to stable fly reproduction, vector host interactions, host-microbe dynamics, and putative targets for control. Most notable was characterization of genes associated with reproduction and identification of expanded gene families with functional associations to vision, chemosensation, immunity, and metabolic detoxification pathways.

Conclusions

The combined sequencing, assembly, and curation of the male stable fly genome followed by RNA-Seq and downstream analyses provide insights necessary to understand the biology of this important pest. These resources and new data will provide the groundwork for expanding the tools available to control stable fly infestations. The close relationship of Stomoxys to other blood-feeding (horn flies and Glossina) and non-blood-feeding flies (house flies, medflies, Drosophila) will facilitate understanding of the evolutionary processes associated with development of blood feeding among the Cyclorrhapha.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-021-00975-9.

Exposure to Inactivated Deformed Wing Virus Leads to Trans-Generational Costs but Not Immune Priming in Honeybees (Apis mellifera)

Pathogens are identified as one of the major drivers behind the honeybee colony losses, as well as one of the reasons for the reported declines in terrestrial insect abundances in recent decades. To fight infections, animals rely on their immune system. The immune system of many invertebrates can be primed by exposure to a pathogen, so that upon further exposure the animal is better protected. The protective priming effect can even extend to the next generation, but the species capable of priming the immune system of their offspring are still being investigated. Here we studied whether honeybees could prime their offspring against a viral pathogen, by challenging honeybee queens orally with an inactivated deformed wing virus (DWV), one of the most devastating honeybee viruses. The offspring were then infected by viral injection. The effects of immune priming were assayed by measuring viral loads and two typical symptoms of the virus, pupal mortality, and abnormal wing phenotype. We saw a low amount of wing deformities and low pupal mortality. While no clear priming effect against the virus was seen, we found that the maternal immune challenge, when combined with the stress caused by an injection during development, manifested in costs in the offspring, leading to an increased number of deformed wings.

Evidence for reduced immune gene diversity and activity during the evolution of termites

The evolution of biological complexity is associated with the emergence of bespoke immune systems that maintain and protect organism integrity. Unlike the well-studied immune systems of cells and individuals, little is known about the origins of immunity during the transition to eusociality, a major evolutionary transition comparable to the evolution of multicellular organisms from single-celled ancestors. We aimed to tackle this by characterizing the immune gene repertoire of 18 cockroach and termite species, spanning the spectrum of solitary, subsocial and eusocial lifestyles. We find that key transitions in termite sociality are correlated with immune gene family contractions. In cross-species comparisons of immune gene expression, we find evidence for a caste-specific social defence system in termites, which appears to operate at the expense of individual immune protection. Our study indicates that a major transition in organismal complexity may have entailed a fundamental reshaping of the immune system optimized for group over individual defence.

Thiamethoxam exposure deregulates short ORF gene expression in the honey bee and compromises immune response to bacteria

Maximizing crop yields relies on the use of agrochemicals to control insect pests. One of the most widely used classes of insecticides are neonicotinoids that interfere with signalling of the neurotransmitter acetylcholine, but these can also disrupt crop-pollination services provided by bees. Here, we analysed whether chronic low dose long-term exposure to the neonicotinoid thiamethoxam alters gene expression and alternative splicing in brains of Africanized honey bees, Apis mellifera, as adaptation to altered neuronal signalling. We find differentially regulated genes that show concentration-dependent responses to thiamethoxam, but no changes in alternative splicing. Most differentially expressed genes have no annotated function but encode short Open Reading Frames, a characteristic feature of anti-microbial peptides. As this suggested that immune responses may be compromised by thiamethoxam exposure, we tested the impact of thiamethoxam on bee immunity by injecting bacteria. We show that intrinsically sub-lethal thiamethoxam exposure makes bees more vulnerable to normally non-pathogenic bacteria. Our findings imply a synergistic mechanism for the observed bee population declines that concern agriculturists, conservation ecologists and the public.

Transcriptomic, Morphological, and Developmental Comparison of Adult Honey Bee Queens (Apis mellifera) Reared From Eggs or Worker Larvae of Differing Ages

Queens and workers are very distinct phenotypes that develop from the same genome. Larvae from worker cells up to 3.5 d old can be transferred to larger queen cells and will subsequently be reared as queens and develop into functional queens. This has become a very popular queen rearing practice in contemporary apiculture. Here we used RNA-Seq to study the consequences of rearing queens from transplanted worker larvae on the transcriptome of the adult queens. We found that queens reared from transferred older larvae developed slower, weighted less, and had fewer ovarioles than queens reared from transferred eggs, indicating queens were cryptically intercaste. RNA-Seq analysis revealed differentially expressed genes between queens reared from transferred larvae compared with queens reared from transferred eggs: the older the larvae transferred, the greater the number of differentially expressed genes. Many of the differentially expressed genes had functions related to reproduction, longevity, immunity, or metabolism, suggesting that the health and long-term viability of queens was compromised. Our finds verify the previous studies that adult queens reared from older transferred larvae were of lower quality than queens reared from transferred eggs or younger larvae.

Transgenerational accumulation of methylome changes discovered in commercially reared honey bee (Apis mellifera) queens

Whether a female honey bee (Apis mellifera) develops into a worker or a queen depends on her nutrition during development, which changes the epigenome to alter the developmental trajectory. Beekeepers typically exploit this developmental plasticity to produce queen bee by transplanting worker larvae into queen cells to be reared as queens, thus redirecting a worker developmental pathway to a queen developmental pathway. We studied the consequences of this manipulation for the queen phenotype and methylome over four generations. Queens reared from worker larvae consistently had fewer ovarioles than queens reared from eggs. Over four generations the methylomes of lines of queens reared from eggs and worker larvae diverged, accumulating increasing differences in exons of genes related to caste differentiation, growth and immunity. We discuss the consequences of these cryptic changes to the honey bee epigenome for the health and viability of honey bee stocks.

Multiple stressors interact to impair the performance of bumblebee Bombus terrestris colonies

Bumblebees are constantly exposed to a wide range of biotic and abiotic stresses which they must defend themselves against to survive. Pathogens and pesticides represent important stressors that influence bumblebee health, both when acting alone or in combination. To better understand bumblebee health, we need to investigate how these factors interact, yet experimental studies to date generally focus on only one or two stressors. The aim of this study is to evaluate how combined effects of four important stressors (the gut parasite Nosema ceranae, the neonicotinoid insecticide thiamethoxam, the pyrethroid insecticide cypermethrin and the EBI fungicide tebuconazole) interact to affect bumblebees at the individual and colony levels. We established seven treatment groups of colonies that we pulse exposed to different combinations of these stressors for 2 weeks under laboratory conditions. Colonies were subsequently placed in the field for 7 weeks to evaluate the effect of treatments on the prevalence of N. ceranae in inoculated bumblebees, expression levels of immunity and detoxification-related genes, food collection, weight gain, worker and male numbers, and production of worker brood and reproductives. Exposure to pesticide mixtures reduced food collection by bumblebees. All immunity-related genes were upregulated in the bumblebees inoculated with N. ceranae when they had not been exposed to pesticide mixtures, and bumblebees exposed to the fungicide and the pyrethroid were less likely to have N. ceranae. Combined exposure to the three-pesticide mixture and N. ceranae reduced bumblebee colony growth, and all treatments had detrimental effects on brood production. The groups exposed to the neonicotinoid insecticide produced 40%-76% fewer queens than control colonies. Our findings show that exposure to combinations of stressors that bumblebees frequently come into contact with have detrimental effects on colony health and performance and could therefore have an impact at the population level. These results also have significant implications for current practices and policies for pesticide risk assessment and use as the combinations tested here are frequently applied simultaneously in the field. Understanding the interactions between different stressors will be crucial for improving our ability to manage bee populations and for ensuring pollination services into the future.

Parasite defense mechanisms in bees: behavior, immunity, antimicrobials, and symbionts

Parasites are linked to the decline of some bee populations; thus, understanding defense mechanisms has important implications for bee health. Recent advances have improved our understanding of factors mediating bee health ranging from molecular to landscape scales, but often as disparate literatures. Here, we bring together these fields and summarize our current understanding of bee defense mechanisms including immunity, immunization, and transgenerational immune priming in social and solitary species. Additionally, the characterization of microbial diversity and function in some bee taxa has shed light on the importance of microbes for bee health, but we lack information that links microbial communities to parasite infection in most bee species. Studies are beginning to identify how bee defense mechanisms are affected by stressors such as poor-quality diets and pesticides, but further research on this topic is needed. We discuss how integrating research on host traits, microbial partners, and nutrition, as well as improving our knowledge base on wild and semi-social bees, will help inform future research, conservation efforts, and management.

The Importance of Males to Bumble Bee (Bombus Species) Nest Development and Colony Viability

Bumble bee population declines over the last decade have stimulated strong interest in determining causative factors and necessary conservation measures. Research attention has largely been directed toward bumble bee worker and queen health and their contributions to population stability, while male bees (i.e., drones) have typically been overlooked regarding their role in influencing colony fitness and longevity. In this review we assess existing literature on the diverse role of males within bumble bee nests and their importance to queen health and fitness, as well as to overall nest success. The implications of reproductive measures, including sperm transfer, mating behavior, mating plugs, and male immunity, among other topics, are examined. Overall, bumble bee males are found to drive colony function in a unique manner. Current knowledge gaps pertaining to the role of males are discussed. We highlight the importance of drones to queen success and fitness in many ways, and suggest future research exploring impacts of this often-neglected caste.

Identification of reference markers for characterizing honey bee (Apis mellifera) hemocyte classes

Cell mediated immunity of the honey bee (Apis mellifera) involves the activity of several hemocyte populations, currently defined by morphological features and lectin binding characteristics. The objective of the present study was to identify molecular markers capable of characterizing subsets of honey bee hemocytes. We developed and employed monoclonal antibodies with restricted reactions to functionally distinct hemocyte subpopulations. Melanizing cells, known as oenocytoids, were defined by an antibody to prophenoloxidase, aggregating cells were identified by the expression of Hemolectin, and phagocytic cells were identified by a marker expressed on granulocytes. We anticipate that this combination of antibodies not only allows for the detection of functionally distinct hemocyte subtypes, but will help to further the exploration of hematopoietic compartments, as well as reveal details of the honey bee cellular immune defense against parasites and microbes.

Missing Microbes in Bees: How Systematic Depletion of Key Symbionts Erodes Immunity

Pesticide exposure, infectious disease, and nutritional stress contribute to honey bee mortality and a high rate of colony loss. This realization has fueled a decades-long investigation into the single and combined effects of each stressor and their overall bearing on insect physiology. However, one element largely missing from this research effort has been the evaluation of underlying microbial communities in resisting environmental stressors and their influence on host immunity and disease tolerance. In humans, multigenerational bombardment by antibiotics is linked with many contemporary diseases. Here, we draw a parallel conclusion for the case in honey bees and suggest that chronic exposure to antimicrobial xenobiotics can systematically deplete honey bees of their microbes and hamper cross-generational preservation of host-adapted symbionts that are crucial to health.

Cuticular pheromones stimulate hygienic behavior in the honey bee (Apis mellifera)

The health of western honey bee (Apis mellifera) colonies is challenged by the parasitic mite Varroa destructor and the numerous harmful pathogens it vectors. Selective breeding for the naturally occurring social immune trait "hygienic behavior" has emerged as one sustainable approach to reducing the mites' impact on honey bees. To expand our understanding of hygienic triggers and improve hygienic selection tools, we tested the hypothesis that the cuticular compounds (Z)-10-tritriacontene and (Z)-6-pentadecene, previously associated with unhealthy honey bee brood and/or brood targeted for hygiene, are triggers of honey bee hygienic behavior independent of brood health. In support of our hypothesis, application of synthetic (Z)-10-tritriacontene and (Z)-6-pentadecene onto brood and brood cell caps significantly increased hygienic behavior compared to application of similarly structured hydrocarbon controls (Z)-16-dotriacontene and (Z)-7-pentadecene. Furthermore, we demonstrate a significant positive correlation between colony-level hygienic responses to (Z)-10-tritriacontene and the traditional freeze-killed brood assay for selection of hygienic honey bee stocks. These results confirm biological activity of (Z)-6-pentadecene and reveal (Z)-10-tritriacontene as a novel hygiene trigger. They also support development of improved tools for honey bee colony monitoring and hygienic selection, and thus may accelerate development of honey bee stocks with greater resistance to Varroa and associated pathogens.

Infection by the castrating parasitic nematode Sphaerularia bombi changes gene expression in Bombus terrestris bumblebee queens

Parasitism can result in dramatic changes in host phenotype, which are themselves underpinned by genes and their expression. Understanding how hosts respond at the molecular level to parasites can therefore reveal the molecular architecture of an altered host phenotype. The entomoparasitic nematode Sphaerularia bombi is a parasite of bumblebee (Bombus) hosts where it induces complex behavioural changes and host castration. To examine this interaction at the molecular level, we performed genome-wide transcriptional profiling using RNA-Sequencing (RNA-Seq) of S. bombi-infected Bombus terrestris queens at two critical time-points: during and just after overwintering diapause. We found that infection by S. bombi affects the transcription of genes underlying host biological processes associated with energy usage, translation, and circadian rhythm. We also found that the parasite affects the expression of immune genes, including members of the Toll signalling pathway providing evidence for a novel interaction between the parasite and the host immune response. Taken together, our results identify host biological processes and genes affected by an entomoparasitic nematode providing the first steps towards a molecular understanding of this ecologically important host-parasite interaction.

Tissue Specificity in Social Context-Dependent lysozyme Expression in Bumblebees

Group living at high densities may result in the enhanced transmission of pathogens. Social insects are obligate group-living species, which often also exhibit high relatedness and frequent social interactions amongst individuals, resulting in a high risk of disease spread. Social species seem to exhibit immune systems that provide colonies of social insects with a certain level of flexibility for adjustment of immune activity according to the risk of disease spread. In bumblebees, Bombus terrestris, it was demonstrated that in group-kept individuals, immune component activity and immune gene expression is increased, potentially as a prophylactic adaptation. Here, I tested whether social environment influences the gene expression pattern of two lysozyme genes, which are components of the antimicrobial response of the bumblebee. In addition, I tested gene expression activation in different tissues (gut, fat body). The analysis revealed that the gene, the density of individuals, the tissue, and the interaction of the latter are the main factors that influence the expression of lysozyme genes. This is the first report of a tissue-specific response towards the social environment. This has implications for gene regulation, which must be responsive to social context-dependent information.

Mating precedes selective immune priming which is maintained throughout bumblebee queen diapause

Background

Understanding the mechanisms by which organisms adapt to unfavourable conditions is a fundamental question in ecology and evolutionary biology. One such mechanism is diapause, a period of dormancy typically found in nematodes, fish, crustaceans and insects. This state is a key life-history event characterised by arrested development, suppressed metabolism and increased stress tolerance and allows an organism to avoid prolonged periods of harsh and inhospitable environmental conditions. For some species, diapause is preceded by mating which can have a profound effect on female behaviour, physiology and key biological processes, including immunity. However, our understanding of how mating impacts long-term immunity and whether these effects persist throughout diapause is currently limited. To address this, we explored molecular changes in the haemolymph of the ecologically important pollinator, the buff-tailed bumblebee Bombus terrestris. B. terrestris queens mate prior to entering diapause, a non-feeding period of arrested development that can last 6–9 months. Using mass-spectrometry-based proteomics, we quantified changes in the pre-diapause queen haemolymph after mating, as well as the subsequent protein expression of mated queens during and post-diapause.

Results

Our analysis identified distinct proteome profiles associated with diapause preparation, maintenance and termination. More specifically, mating pre-diapause was followed by an increase in the abundance of antimicrobial peptides, key effectors of the immune system. Furthermore, we identified the elevated abundance of these proteins to be maintained throughout diapause. This finding was in contrast to the general reduction observed in immune proteins during diapause suggestive of selective immune priming and expression during diapause. Diapause also affected the expression of proteins involved in cuticular maintenance, olfaction, as well as proteins of unknown function, which may have roles in diapause regulation.

Conclusions

Our results provide clear molecular evidence for the consequences and benefits of mating at the immune level as it precedes the selective increased abundance of antimicrobial peptides that are sustained throughout diapause. In addition, our results provide novel insights into the molecular mechanisms by which bumblebees prepare for, survive, and recover from diapause, insights that may have implications for our general understanding of these processes in other insect groups.

Evaluation of reference genes for gene expression analysis by real-time quantitative PCR (qPCR) in three stingless bee species (Hymenoptera: Apidae: Meliponini)

Stingless bees are generalist pollinators distributed through the pantropical region. There is growing evidence that their wild populations are experiencing substantial decline in response to habitat degradation and pesticides. Policies for conservation of endangered species will benefit from studies focusing on genetic and molecular aspects of their development and behavior. The most common method for looking at gene expression is real-time quantitative polymerase chain reaction preceded by reverse transcription (RT-qPCR) of the mRNA of interest. This method requires the identification of reliable reference genes to correctly estimate fluctuations in transcript levels. To contribute to molecular studies on stingless bees, we used Frieseomelitta varia, Melipona quadrifasciata, and Scaptotrigona bipunctata species to test the expression stability of eight reference genes (act, ef1-α, gapdh, rpl32, rps5, rps18, tbp, and tbp-af) in RT-qPCR procedures in five physiological and experimental conditions (development, sex, tissues, bacteria injection, and pesticide exposure). In general, the rpl32, rps5 and rps18 ribosomal protein genes and tpb-af gene showed the highest stability, thus being identified as suitable reference genes for the three stingless bee species and defined conditions. Our results also emphasized the need to evaluate the stability of candidate genes for any designed experimental condition and stingless bee species.

The genomes of two parasitic wasps that parasitize the diamondback moth

BACKGROUND

Parasitic insects are well-known biological control agents for arthropod pests worldwide. They are capable of regulating their host's physiology, development and behaviour. However, many of the molecular mechanisms involved in host-parasitoid interaction remain unknown.

RESULTS

We sequenced the genomes of two parasitic wasps (Cotesia vestalis, and Diadromus collaris) that parasitize the diamondback moth Plutella xylostella using Illumina and Pacbio sequencing platforms. Genome assembly using SOAPdenovo produced a 178 Mb draft genome for C. vestalis and a 399 Mb draft genome for D. collaris. A total set that contained 11,278 and 15,328 protein-coding genes for C. vestalis and D. collaris, respectively, were predicted using evidence (homology-based and transcriptome-based) and de novo prediction methodology. Phylogenetic analysis showed that the braconid C. vestalis and the ichneumonid D. collaris diverged approximately 124 million years ago. These two wasps exhibit gene gains and losses that in some cases reflect their shared life history as parasitic wasps and in other cases are unique to particular species. Gene families with functions in development, nutrient acquisition from hosts, and metabolism have expanded in each wasp species, while genes required for biosynthesis of some amino acids and steroids have been lost, since these nutrients can be directly obtained from the host. Both wasp species encode a relative higher number of neprilysins (NEPs) thus far reported in arthropod genomes while several genes encoding immune-related proteins and detoxification enzymes were lost in both wasp genomes.

CONCLUSIONS

We present the annotated genome sequence of two parasitic wasps C. vestalis and D. collaris, which parasitize a common host, the diamondback moth, P. xylostella. These data will provide a fundamental source for studying the mechanism of host control and will be used in parasitoid comparative genomics to study the origin and diversification of the parasitic lifestyle.

Towards Precision Nutrition: A Novel Concept Linking Phytochemicals, Immune Response and Honey Bee Health

The high annual losses of managed honey bees (Apis mellifera) has attracted intensive attention, and scientists have dedicated much effort trying to identify the stresses affecting bees. There are, however, no simple answers; rather, research suggests multifactorial effects. Several works have been reported highlighting the relationship between bees' immunosuppression and the effects of malnutrition, parasites, pathogens, agrochemical and beekeeping pesticides exposure, forage dearth and cold stress. Here we analyze a possible connection between immunity-related signaling pathways that could be involved in the response to the stress resulted from Varroa-virus association and cold stress during winter. The analysis was made understanding the honey bee as a superorganism, where individuals are integrated and interacting within the colony, going from social to individual immune responses. We propose the term "Precision Nutrition" as a way to think and study bees' nutrition in the search for key molecules which would be able to strengthen colonies' responses to any or all of those stresses combined.

Integrative Genomics Reveals the Genetics and Evolution of the Honey Bee's Social Immune System

Social organisms combat pathogens through individual innate immune responses or through social immunity—behaviors among individuals that limit pathogen transmission within groups. Although we have a relatively detailed understanding of the genetics and evolution of the innate immune system of animals, we know little about social immunity. Addressing this knowledge gap is crucial for understanding how life-history traits influence immunity, and identifying if trade-offs exist between innate and social immunity. Hygienic behavior in the Western honey bee, Apis mellifera, provides an excellent model for investigating the genetics and evolution of social immunity in animals. This heritable, colony-level behavior is performed by nurse bees when they detect and remove infected or dead brood from the colony. We sequenced 125 haploid genomes from two artificially selected highly hygienic populations and a baseline unselected population. Genomic contrasts allowed us to identify a minimum of 73 genes tentatively associated with hygienic behavior. Many genes were within previously discovered QTLs associated with hygienic behavior and were predictive of hygienic behavior within the unselected population. These genes were often involved in neuronal development and sensory perception in solitary insects. We found that genes associated with hygienic behavior have evidence of positive selection within honey bees (Apis), supporting the hypothesis that social immunity contributes to fitness. Our results indicate that genes influencing developmental neurobiology and behavior in solitary insects may have been co-opted to give rise to a novel and adaptive social immune phenotype in honey bees.

The Mechanisms of Social Immunity Against Fungal Infections in Eusocial Insects

Entomopathogenic fungus as well as their toxins is a natural threat surrounding social insect colonies. To defend against them, social insects have evolved a series of unique disease defenses at the colony level, which consists of behavioral and physiological adaptations. These colony-level defenses can reduce the infection and poisoning risk and improve the survival of societal members, and is known as social immunity. In this review, we discuss how social immunity enables the insect colony to avoid, resist and tolerate fungal pathogens. To understand the molecular basis of social immunity, we highlight several genetic elements and biochemical factors that drive the colony-level defense, which needs further verification. We discuss the chemosensory genes in regulating social behaviors, the antifungal secretions such as some insect venoms in external defense and the immune priming in internal defense. To conclude, we show the possible driving force of the fungal toxins for the evolution of social immunity. Throughout the review, we propose several questions involved in social immunity extended from some phenomena that have been reported. We hope our review about social 'host-fungal pathogen' interactions will help us further understand the mechanism of social immunity in eusocial insects.

Comparative genomics and transcriptomics of host-pathogen interactions in insects: evolutionary insights and future directions

Classical evolutionary studies of protein-coding genes have established that genes in the canonical immune system are often among the most rapidly evolving within and between species. As more genomes and transcriptomes across insects are sequenced, it is becoming clear that duplications and losses of immune genes are also a likely consequence of host-pathogen interactions. Furthermore, particular species respond to diverse pathogenic challenges with a wide range of challenge-specific responses that are still poorly understood. Transcriptional studies, using RNA-seq to characterize the infection-regulated transcriptome of diverse insects, are crucial for additional progress in understanding the ecology and evolution of the full complexity of the host response.

Mining insect genomes for functionally affiliated genes

Several hundred insect genome assemblies are already publicly available, and this total grows on a weekly basis. A major challenge now confronting insect science is how best to use genomic data to improve our understanding of insect biology. We consider a framework for genome analysis based on functional affiliation, that is, groups of genes involved in the same biological process or pathway, and explore how such an approach furthers our understanding of several aspects of insect phenotype. We anticipate that this approach will prove useful for future research across the breadth of insect studies, whatever organism or trait it involves.