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

A Field Trial to Demonstrate the Potential of a Vitamin B Diet Supplement in Reducing Oxidative Stress and Improving Hygienic and Grooming Behaviors in Honey Bees

The honey bee is an important insect pollinator that provides critical pollination services for natural and agricultural systems worldwide. However, inadequate food weakens honey bee colonies, making them vulnerable to various biotic and abiotic factors. In this study, we examined the impact of supplementary feeding on bees' genes for antioxidative enzymes and vitellogenin, oxidative stress parameters, and the hygienic and grooming behavior. The colonies were divided into two experimental groups (with ten hives each): a treatment group that received the plant-based supplement and a control group. The experiment was conducted in two seasons, spring and summer. After the treatment, in both seasons, all the monitored parameters in the treatment group differed from those in the control group. The expression levels of genes for antioxidative enzymes were significantly lower, but the vitellogenin gene transcript level was significantly higher. Values of oxidative stress parameters were significantly lower. The levels of hygienic and grooming behavior were significantly higher. Therefore, our field study indicates that the tested supplement exerted beneficial effects on bees, reflected in reduced oxidative stress and enhanced hygienic and grooming behavior.

Accurate Detection of scutellata-Hybrids (Africanized Bees) Using a SNP-Based Diagnostic Assay

Hybrid populations of Africanized honey bees (scutellata-hybrids), notable for their defensive behaviour, have spread rapidly throughout South and North America since their unintentional introduction. Although their migration has slowed, the large-scale trade and movement of honey bee queens and colonies raise concern over the accidental importation of scutellata-hybrids to previously unoccupied areas. Therefore, developing an accurate and robust assay to detect scutellata-hybrids is an important first step toward mitigating risk. Here, we used an extensive population genomic dataset to assess the genomic composition of Apis mellifera native populations and patterns of genetic admixture in North and South American commercial honey bees. We used this dataset to develop a SNP assay, where 80 markers, combined with machine learning classification, can accurately differentiate between scutellata-hybrids and non-scutellata-hybrid commercial colonies. The assay was validated on 1263 individuals from colonies located in Canada, the United States, Australia and Brazil. Notably, we demonstrate that using a reduced SNP set of as few as 10 loci can still provide accurate results.

An integrative genomic toolkit for studying the genetic, evolutionary, and molecular underpinnings of eusociality in insects

While genomic resources for social insects have vastly increased over the past two decades, we are still far from understanding the genetic and molecular basis of eusociality. Here, we briefly review three scientific advancements that, when integrated, can be highly synergistic for advancing our knowledge of the genetics and evolution of eusocial traits. Population genomics provides a natural way to quantify the strength of natural selection on coding and regulatory sequences, highlighting genes that have undergone adaptive evolution during the evolution or maintenance of eusociality. Genome-wide association studies (GWAS) can be used to characterize the complex genetic architecture underlying eusocial traits and identify candidate causal variants. Concurrently, CRISPR/Cas9 enables the precise manipulation of gene function to both validate genotype-phenotype associations and study the molecular biology underlying interesting traits. While each approach has its own advantages and disadvantages, which we discuss herein, we argue that their combination will ultimately help us better understand the genetics and evolution of eusocial behavior. Specifically, by triangulating across these three different approaches, researchers can directly identify and study loci that have a causal association with key phenotypes and have evidence of positive selection over the relevant timescales associated with the evolution and maintenance of eusociality in insects.

HBeeID: a molecular tool that identifies honey bee subspecies from different geographic populations

BACKGROUND

Honey bees are the principal commercial pollinators. Along with other arthropods, they are increasingly under threat from anthropogenic factors such as the incursion of invasive honey bee subspecies, pathogens and parasites. Better tools are needed to identify bee subspecies. Genomic data for economic and ecologically important organisms is increasing, but in its basic form its practical application to address ecological problems is limited.

RESULTS

We introduce HBeeID a means to identify honey bees. The tool utilizes a knowledge-based network and diagnostic SNPs identified by discriminant analysis of principle components and hierarchical agglomerative clustering. Tests of HBeeID showed that it identifies African, Americas-Africanized, Asian, and European honey bees with a high degree of certainty even when samples lack the full 272 SNPs of HBeeID. Its prediction capacity decreases with highly admixed samples.

CONCLUSION

HBeeID is a high-resolution genomic, SNP based tool, that can be used to identify honey bees and screen species that are invasive. Its flexible design allows for future improvements via sample data additions from other localities.

Population-wide modelling reveals prospects of marker-assisted selection for parasitic mite resistance in honey bees

In 2019, a joint eight-variant model was published in which eight single nucleotide polymorphisms (SNPs) in seven Apis mellifera genes were associated with Varroa destructor drone brood resistance (DBR, i.e. mite non-reproduction in drone brood). As this model was derived from only one Darwinian Black Bee Box colony, it could not directly be applied on a population-overarching scale in the northern part of Belgium (Flanders), where beekeepers prefer the carnica subspecies. To determine whether these eight SNPs remained associated with the DBR trait on a Flemish colony-broad scope, we performed population-wide modelling through sampling of various A. mellifera carnica colonies, DBR scoring of Varroa-infested drone brood and variant genotyping. Novel eight-variant modelling was performed and the classification performance of the eight SNPs was evaluated. Besides, we built a reduced three-variant model retaining only three genetic variants and found that this model classified 76% of the phenotyped drones correctly. To examine the spread of beneficial alleles and predict the DBR probability distribution in Flanders, we determined the allelic frequencies of the three variants in 292 A. mellifera carnica queens. As such, this research reveals prospects of marker-assisted selection for Varroa drone brood resistance in honeybees.

AmelHap: Leveraging drone whole-genome sequence data to create a honey bee HapMap

Honey bee, Apis mellifera, drones are typically haploid, developing from an unfertilized egg, inheriting only their queen's alleles and none from the many drones she mated with. Thus the ordered combination or 'phase' of alleles is known, making drones a valuable haplotype resource. We collated whole-genome sequence data for 1,407 drones, including 45 newly sequenced Scottish drones, collectively representing 19 countries, 8 subspecies and various hybrids. Following alignment to Amel_HAv3.1, variant calling and quality filtering, we retained 17.4 M high quality variants across 1,328 samples with a genotyping rate of 98.7%. We demonstrate the utility of this haplotype resource, AmelHap, for genotype imputation, returning >95% concordance when up to 61% of data is missing in haploids and up to 12% of data is missing in diploids. AmelHap will serve as a useful resource for the community for imputation from low-depth sequencing or SNP chip data, accurate phasing of diploids for association studies, and as a comprehensive reference panel for population genetic and evolutionary analyses.

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.

Host-pathogen protein-nucleic acid interactions: A comprehensive review

Recognition of pathogen-derived nucleic acids by host cells is an effective host strategy to detect pathogenic invasion and trigger immune responses. In the context of pathogen-specific pharmacology, there is a growing interest in mapping the interactions between pathogen-derived nucleic acids and host proteins. Insight into the principles of the structural and immunological mechanisms underlying such interactions and their roles in host defense is necessary to guide therapeutic intervention. Here, we discuss the newest advances in studies of molecular interactions involving pathogen nucleic acids and host factors, including their drug design, molecular structure and specific patterns. We observed that two groups of nucleic acid recognizing molecules, Toll-like receptors (TLRs) and the cytoplasmic retinoic acid-inducible gene (RIG)-I-like receptors (RLRs) form the backbone of host responses to pathogen nucleic acids, with additional support provided by absent in melanoma 2 (AIM2) and DNA-dependent activator of Interferons (IFNs)-regulatory factors (DAI) like cytosolic activity. We review the structural, immunological, and other biological aspects of these representative groups of molecules, especially in terms of their target specificity and affinity and challenges in leveraging host-pathogen protein-nucleic acid interactions (HP-PNI) in drug discovery.

Diet Supplementation Helps Honey Bee Colonies in Combat Infections by Enhancing their Hygienic Behaviour

The hygienic behavior in honey bees is a complex polygenic trait that serves as a natural defense mechanism against bacterial and fungal brood diseases and Varroa destructor mites infesting brood cells. The aim of this study was to evaluate the effect of a dietary amino acids and vitamins supplement “BEEWELL AminoPlus” on hygienic behavior of Apis mellifera colonies combating microsporidial and viral infections. The experiment was performed during a one-year period on 40 colonies alloted to five groups: one supplemented and infected with Nosema ceranae and four viruses (Deformed wing virus - DWV, Acute bee paralysis virus - ABPV, Chronic bee paralysis virus - CBPV and Sacbrood virus – SBV), three not supplemented, but infected with N. ceranae and/ or viruses, and one negative control group. Beside the l isted pathogens, honey bee trypanosomatids were also monitored in all groups.

The supplement “BEEWELL AminoPlus” induced a significant and consistent increase of the hygienic behavior in spite of the negative effects of N. ceranae and viral infections. N. ceranae and viruses significantly and consistently decreased hygienic behavior, but also threatened the survival of bee colonies. The tested supplement showed anti-Nosema effect, since the N. ceranae infection level significantly and consistently declined only in the supplemented group. Among infected groups, only the supplemented one remained Lotmaria passim-free throughout the study. In conclusion, diet supplementation enhances hygienic behavior of honey bee colonies and helps them fight the most common infections of honey bees.

OUP accepted manuscript

Many species have separate haploid and diploid phases. Theory predicts that each phase should experience the effects of evolutionary forces (like selection) differently. In the haploid phase, all fitness-affecting alleles are exposed to selection, whereas in the diploid phase, those same alleles can be masked by homologous alleles. This predicts that selection acting on genes expressed in haploids should be more effective than diploid-biased genes. Unfortunately, in arrhenotokous species, this prediction can be confounded with the effects of sex-specific expression, as haploids are usually reproductive males. Theory posits that, when accounting for ploidal- and sex-specific expression, selection should be equally efficient on haploid- and diploid-biased genes relative to constitutive genes. Here, we used a multiomic approach in honey bees to quantify the evolutionary rates of haploid-biased genes and test the relative effects of sexual- and haploid-expression on molecular evolution. We found that 16% of the honey bee’s protein-coding genome is highly expressed in haploid tissue. When accounting for ploidy and sex, haploid- and diploid-biased genes evolve at a lower rate than expected, indicating that they experience strong negative selection. However, the rate of molecular evolution of haploid-biased genes was higher than diploid-based genes. Genes associated with sperm storage are a clear exception to this trend with evidence of strong positive selection. Our results provide an important empirical test of theory outlining how selection acts on genes expressed in arrhenotokous species. We propose the haploid life history stage affects genome-wide patterns of diversity and divergence because of both sexual and haploid selection.

Thrice out of Asia and the adaptive radiation of the western honey bee

The origin of the western honey bee Apis mellifera has been intensely debated. Addressing this knowledge gap is essential for understanding the evolution and genetics of one of the world’s most important pollinators. By analyzing 251 genomes from 18 native subspecies, we found support for an Asian origin of honey bees with at least three expansions leading to African and European lineages. The adaptive radiation of honey bees involved selection on a few genomic “hotspots.” We found 145 genes with independent signatures of selection across all bee lineages, and these genes were highly associated with worker traits. Our results indicate that a core set of genes associated with worker and colony traits facilitated the adaptive radiation of honey bees across their vast distribution.

Practical Applications of Genomics in Managing Honey bee Health

The honey bee Apis mellifera is a model organism for sociogenomics and one of the most important managed pollinators. High mortalities experienced by honey bee colonies over the past several decades are expected to have a substantive effect on crop pollination and global food security. These threats and the availability of a growing number of genomic resources for the honey bee have motivated research on how genetics and genomics can be practically applied to manage bee health. The authors review 3 such applications: (1) Certification of bee lineages using single-polymorphism markers; (2) breeding bees using marker-assisted selection; (3) diagnosing honey bee stressors using biomarkers.

A brief history and popularity of methods and tools used to estimate micro-evolutionary forces

Population genetics is a field of research that predates the current generations of sequencing technology. Those approaches, that were established before massively parallel sequencing methods, have been adapted to these new marker systems (in some cases involving the development of new methods) that allow genome-wide estimates of the four major micro-evolutionary forces-mutation, gene flow, genetic drift, and selection. Nevertheless, classic population genetic markers are still commonly used and a plethora of analysis methods and programs is available for these and high-throughput sequencing (HTS) data. These methods employ various and diverse theoretical and statistical frameworks, to varying degrees of success, to estimate similar evolutionary parameters making it difficult to get a concise overview across the available approaches. Presently, reviews on this topic generally focus on a particular class of methods to estimate one or two evolutionary parameters. Here, we provide a brief history of methods and a comprehensive list of available programs for estimating micro-evolutionary forces. We furthermore analyzed their usage within the research community based on popularity (citation bias) and discuss the implications of this bias for the software community. We found that a few programs received the majority of citations, with program success being independent of both the parameters estimated and the computing platform. The only deviation from a model of exponential growth in the number of citations was found for the presence of a graphical user interface (GUI). Interestingly, no relationship was found for the impact factor of the journals, when the tools were published, suggesting accessibility might be more important than visibility.

Improved Apis mellifera reference genome based on the alternative long-read-based assemblies

Apis mellifera L., the western honey bee is a major crop pollinator that plays a key role in beekeeping and serves as an important model organism in social behavior studies. Recent efforts have improved on the quality of the honey bee reference genome and developed a chromosome-level assembly of 16 chromosomes, two of which are gapless. However, the rest suffer from 51 gaps, 160 unplaced/unlocalized scaffolds, and the lack of 2 distal telomeres. The gaps are located at the hard-to-assemble extended highly repetitive chromosomal regions that may contain functional genomic elements. Here, we use de novo re-assemblies from the most recent reference genome Amel_HAv_3.1 raw reads and other long-read-based assemblies (INRA_AMelMel_1.0, ASM1384120v1, and ASM1384124v1) of the honey bee genome to resolve 13 gaps, five unplaced/unlocalized scaffolds and, the lacking telomeres of the Amel_HAv_3.1. The total length of the resolved gaps is 848,747 bp. The accuracy of the corrected assembly was validated by mapping PacBio reads and performing gene annotation assessment. Comparative analysis suggests that the PacBio-reads-based assemblies of the honey bee genomes failed in the same highly repetitive extended regions of the chromosomes, especially on chromosome 10. To fully resolve these extended repetitive regions, further work using ultra-long Nanopore sequencing would be needed. Our updated assembly facilitates more accurate reference-guided scaffolding and marker/sequence mapping in honey bee genomics studies.

Bidirectional interactions between host social behaviour and parasites arise through ecological and evolutionary processes

An animal's social behaviour both influences and changes in response to its parasites. Here we consider these bidirectional links between host social behaviours and parasite infection, both those that occur from ecological vs evolutionary processes. First, we review how social behaviours of individuals and groups influence ecological patterns of parasite transmission. We then discuss how parasite infection, in turn, can alter host social interactions by changing the behaviour of both infected and uninfected individuals. Together, these ecological feedbacks between social behaviour and parasite infection can result in important epidemiological consequences. Next, we consider the ways in which host social behaviours evolve in response to parasites, highlighting constraints that arise from the need for hosts to maintain benefits of sociality while minimizing fitness costs of parasites. Finally, we consider how host social behaviours shape the population genetic structure of parasites and the evolution of key parasite traits, such as virulence. Overall, these bidirectional relationships between host social behaviours and parasites are an important yet often underappreciated component of population-level disease dynamics and host-parasite coevolution.

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.

Genetic markers for the resistance of honey bee to Varroa destructor

In the mid-20th century, the first case of infection of European bees Apis mellifera L. with the ectoparasite mite Varroa destructor was recorded. The original host of this mite is the Asian bee Apis cerana. The mite V. destructor was widespread throughout Europe, North and South America, and Australia remained the only continent free from this parasite. Without acaricide treatment any honeybee colony dies within 1–4 years. The use of synthetic acaricides has not justified itself – they make beekeeping products unsuitable and mites develop resistance to them, which forces the use of even greater concentrations that can be toxic to the bees. Therefore, the only safe measure to combat the mite is the use of biological control methods. One of these methods is the selection of bee colonies with natural mite resistance. In this article we summarize publications devoted to the search for genetic markers associated with resistance to V. destructor. The first part discusses the basic mechanisms of bee resistance (Varroa sensitive hygienic behavior and grooming) and methods for their assessment. The second part focuses on research aimed at searching for loci and candidate genes associated with resistance to varroosis by mapping quantitative traits loci and genome-wide association studies. The third part summarizes studies of the transcriptome profile of Varroa resistant bees. The last part discusses the most likely candidate genes – potential markers for breeding Varroa resistant bees. Resistance to the mite is manifested in a variety of phenotypes and is under polygenic control. The establishing of gene pathways involved in resistance to Varroa will help create a methodological basis for the selection of Varroa resistant honeybee colonies.

Genome-wide patterns of differentiation within and among U.S. commercial honey bee stocks

BACKGROUND

The population genetics of U.S. honey bee stocks remain poorly characterized despite the agricultural importance of Apis mellifera as the major crop pollinator. Commercial and research-based breeding programs have made significant improvements of favorable genetic traits (e.g. production and disease resistance). The variety of bees produced by artificial selection provides an opportunity to characterize the genetic diversity and regions of the genome undergoing selection in commonly managed stocks.

RESULTS

Pooled sequencing of eight honey bee stocks found strong genetic similarity among six of the stocks. Two stocks, Pol-line and Hilo, showed significant differentiation likely due to their intense and largely closed breeding for resistance to the parasitic Varroa mite. Few variants were identified as being specific to any one stock, indicating potential admixture among the sequenced stocks. Juxtaposing the underlying genetic variation of stocks selected for disease- and parasite-resistance behavior, we identified genes and candidate regions putatively associated with resistance regulated by hygienic behavior.

CONCLUSION

This study provides important insights into the distinct genetic characteristics and population diversity of honey bee stocks used in the United States, and provides further evidence of high levels of admixture in commercially managed honey bee stocks. Furthermore, breeding efforts to enhance parasite resistance in honey bees may have created unique genetic profiles. Genomic regions of interest have been highlighted for potential future work related to developing genetic markers for selection of disease and parasite resistance traits. Due to the vast genomic similarities found among stocks in general, our findings suggest that additional data regarding gene expression, epigenetic and regulatory information are needed to more fully determine how stock phenotypic diversity is regulated.

Ultraconserved Non-coding DNA Within Diptera and Hymenoptera

This study has taken advantage of the availability of the assembled genomic sequence of flies, mosquitos, ants and bees to explore the presence of ultraconserved sequence elements in these phylogenetic groups. We compared non-coding sequences found within and flanking Drosophila developmental genes to homologous sequences in Ceratitis capitata and Musca domestica. Many of the conserved sequence blocks (CSBs) that constitute Drosophila cis-regulatory DNA, recognized by EvoPrinter alignment protocols, are also conserved in Ceratitis and Musca. Also conserved is the position but not necessarily the orientation of many of these ultraconserved CSBs (uCSBs) with respect to flanking genes. Using the mosquito EvoPrint algorithm, we have also identified uCSBs shared among distantly related mosquito species. Side by side comparison of bee and ant EvoPrints of selected developmental genes identify uCSBs shared between these two Hymenoptera, as well as less conserved CSBs in either one or the other taxon but not in both. Analysis of uCSBs in these dipterans and Hymenoptera will lead to a greater understanding of their evolutionary origin and function of their conserved non-coding sequences and aid in discovery of core elements of enhancers.

This study applies the phylogenetic footprinting program EvoPrinter to detection of ultraconserved non-coding sequence elements in Diptera, including flies and mosquitos, and Hymenoptera, including ants and bees. EvoPrinter outputs an interspecies comparison as a single sequence in terms of the input reference sequence. Ultraconserved sequences flanking known developmental genes were detected in Ceratitis and Musca when compared with Drosophila species, in Aedes and Culex when compared with Anopheles, and between ants and bees. Our methods are useful in detecting and understanding the core evolutionarily hardened sequences required for gene regulation.

Honey bee survival mechanisms against the parasite Varroa destructor: a systematic review of phenotypic and genomic research efforts

The ectoparasitic mite Varroa destructor is the most significant pathological threat to the western honey bee, Apis mellifera, leading to the death of most colonies if left untreated. An alternative approach to chemical treatments is to selectively enhance heritable honey bee traits of resistance or tolerance to the mite through breeding programs, or select for naturally surviving untreated colonies. We conducted a literature review of all studies documenting traits of A. mellifera populations either selectively bred or naturally selected for resistance and tolerance to mite parasitism. This allowed us to conduct an analysis of the diversity, distribution and importance of the traits in different honey bee populations that can survive V. destructor globally. In a second analysis, we investigated the genetic bases of these different phenotypes by comparing 'omics studies (genomics, transcriptomics, and proteomics) of A. mellifera resistance and tolerance to the parasite. Altogether, this review provides a detailed overview of the current state of the research projects and breeding efforts against the most devastating parasite of A. mellifera. By highlighting the most promising traits of Varroa-surviving bees and our current knowledge on their genetic bases, this work will help direct future research efforts and selection programs to control this pest. Additionally, by comparing the diverse populations of honey bees that exhibit those traits, this review highlights the consequences of anthropogenic and natural selection in the interactions between hosts and parasites.

Natural selection, selective breeding, and the evolution of resistance of honeybees (Apis mellifera) against Varroa

We examine evidence for natural selection resulting in Apis mellifera becoming tolerant or resistant to Varroa mites in different bee populations. We discuss traits implicated in Varroa resistance and how they can be measured. We show that some of the measurements used are ambiguous, as they measure a combination of traits. In addition to behavioural traits, such as removal of infested pupae, grooming to remove mites from bees or larval odours, small colony size, frequent swarming, and smaller brood cell size may also help to reduce reproductive rates of Varroa. Finally, bees may be tolerant of high Varroa infections when they are resistant or tolerant to viruses implicated in colony collapse. We provide evidence that honeybees are an extremely outbreeding species. Mating structure is important for how natural selection operates. Evidence for successful natural selection of resistance traits against Varroa comes from South Africa and from Africanized honeybees in South America. Initially, Varroa was present in high densities and killed about 30% of the colonies, but soon after its spread, numbers per hive decreased and colonies survived without treatment. This shows that natural selection can result in resistance in large panmictic populations when a large proportion of the population survives the initial Varroa invasion. Natural selection in Europe and North America has not resulted in large-scale resistance. Upon arrival of Varroa, the frequency of traits to counter mites and associated viruses in European honey bees was low. This forced beekeepers to protect bees by chemical treatment, hampering natural selection. In a Swedish experiment on natural selection in an isolated mating population, only 7% of the colonies survived, resulting in strong inbreeding. Other experiments with untreated, surviving colonies failed because outbreeding counteracted the effects of selection. If loss of genetic variation is prevented, colony level selection in closed mating populations can proceed more easily, as natural selection is not counteracted by the dispersal of resistance genes. In large panmictic populations, selective breeding can be used to increase the level of resistance to a threshold level at which natural selection can be expected to take over.

Genomics of host-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales

Evolutionary genomics has recently entered a new era in the study of host-pathogen interactions. A variety of novel genomic techniques has transformed the identification, detection and classification of both hosts and pathogens, allowing a greater resolution that helps decipher their underlying dynamics and provides novel insights into their environmental context. Nevertheless, many challenges to a general understanding of host-pathogen interactions remain, in particular in the synthesis and integration of concepts and findings across a variety of systems and different spatiotemporal and ecological scales. In this perspective we aim to highlight some of the commonalities and complexities across diverse studies of host-pathogen interactions, with a focus on ecological, spatiotemporal variation, and the choice of genomic methods used. We performed a quantitative review of recent literature to investigate links, patterns and potential tradeoffs between the complexity of genomic, ecological and spatiotemporal scales undertaken in individual host-pathogen studies. We found that the majority of studies used whole genome resolution to address their research objectives across a broad range of ecological scales, especially when focusing on the pathogen side of the interaction. Nevertheless, genomic studies conducted in a complex spatiotemporal context are currently rare in the literature. Because processes of host-pathogen interactions can be understood at multiple scales, from molecular-, cellular-, and physiological-scales to the levels of populations and ecosystems, we conclude that a major obstacle for synthesis across diverse host-pathogen systems is that data are collected on widely diverging scales with different degrees of resolution. This disparity not only hampers effective infrastructural organization of the data but also data granularity and accessibility. Comprehensive metadata deposited in association with genomic data in easily accessible databases will allow greater inference across systems in the future, especially when combined with open data standards and practices. The standardization and comparability of such data will facilitate early detection of emerging infectious diseases as well as studies of the impact of anthropogenic stressors, such as climate change, on disease dynamics in humans and wildlife.

Defining Pollinator Health: A Holistic Approach Based on Ecological, Genetic, and Physiological Factors

Evidence for global bee population declines has catalyzed a rapidly evolving area of research that aims to identify the causal factors and to effectively assess the status of pollinator populations. The term pollinator health emerged through efforts to understand causes of bee decline and colony losses, but it lacks a formal definition. In this review, we propose a definition for pollinator health and synthesize the available literature on the application of standardized biomarkers to assess health at the individual, colony, and population levels. We focus on biomarkers in honey bees, a model species, but extrapolate the potential application of these approaches to monitor the health status of wild bee populations. Biomarker-guided health measures can inform beekeeper management decisions, wild bee conservation efforts, and environmental policies. We conclude by addressing challenges to pollinator health from a One Health perspective that emphasizes the interplay between environmental quality and human, animal, and bee health.

Honey bee predisposition of resistance to ubiquitous mite infestations

Host-parasite co-evolution history is lacking when parasites switch to novel hosts. This was the case for Western honey bees (Apis mellifera) when the ectoparasitic mite, Varroa destructor, switched hosts from Eastern honey bees (Apis cerana). This mite has since become the most severe biological threat to A. mellifera worldwide. However, some A. mellifera populations are known to survive infestations, largely by suppressing mite population growth. One known mechanism is suppressed mite reproduction (SMR), but the underlying genetics are poorly understood. Here, we take advantage of haploid drones, originating from one queen from the Netherlands that developed Varroa-resistance, whole exome sequencing and elastic-net regression to identify genetic variants associated with SMR in resistant honeybees. An eight variants model predicted 88% of the phenotypes correctly and identified six risk and two protective variants. Reproducing and non-reproducing mites could not be distinguished using DNA microsatellites, which is in agreement with the hypothesis that it is not the parasite but the host that adapted itself. Our results suggest that the brood pheromone-dependent mite oogenesis is disrupted in resistant hosts. The identified genetic markers have a considerable potential to contribute to a sustainable global apiculture.