Bridging the Gap between Field Experiments and Machine Learning: The EC H2020 B-GOOD Project as a Case Study towards Automated Predictive Health Monitoring of Honey Bee Colonies.

Honey bee colonies have great societal and economic importance. The main challenge that beekeepers face is keeping bee colonies healthy under ever-changing environmental conditions. In the past two decades, beekeepers that manage colonies of Western honey bees (Apis mellifera) have become increasingly concerned by the presence of parasites and pathogens affecting the bees, the reduction in pollen and nectar availability, and the colonies' exposure to pesticides, among others. Hence, beekeepers need to know the health condition of their colonies and how to keep them alive and thriving, which creates a need for a new holistic data collection method to harmonize the flow of information from various sources that can be linked at the colony level for different health determinants, such as bee colony, environmental, socioeconomic, and genetic statuses. For this purpose, we have developed and implemented the B-GOOD (Giving Beekeeping Guidance by computational-assisted Decision Making) project as a case study to categorize the colony's health condition and find a Health Status Index (HSI). Using a 3-tier setup guided by work plans and standardized protocols, we have collected data from inside the colonies (amount of brood, disease load, honey harvest, etc.) and from their environment (floral resource availability). Most of the project's data was automatically collected by the BEEP Base Sensor System. This continuous stream of data served as the basis to determine and validate an algorithm to calculate the HSI using machine learning. In this article, we share our insights on this holistic methodology and also highlight the importance of using a standardized data language to increase the compatibility between different current and future studies. We argue that the combined management of big data will be an essential building block in the development of targeted guidance for beekeepers and for the future of sustainable beekeeping.

Evolutionarily diverse origins of deformed wing viruses in western honey bees.

Novel transmission routes can allow infectious diseases to spread, often with devastating consequences. Ectoparasitic varroa mites vector a diversity of RNA viruses, having switched hosts from the eastern to western honey bees (Apis cerana to Apis mellifera). They provide an opportunity to explore how novel transmission routes shape disease epidemiology. As the principal driver of the spread of deformed wing viruses (mainly DWV-A and DWV-B), varroa infestation has also driven global honey bee health declines. The more virulent DWV-B strain has been replacing the original DWV-A strain in many regions over the past two decades. Yet, how these viruses originated and spread remains poorly understood. Here, we use a phylogeographic analysis based on whole-genome data to reconstruct the origins and demography of DWV spread. We found that, rather than reemerging in western honey bees after varroa switched hosts, as suggested by previous work, DWV-A most likely originated in East Asia and spread in the mid-20th century. It also showed a massive population size expansion following the varroa host switch. By contrast, DWV-B was most likely acquired more recently from a source outside East Asia and appears absent from the original varroa host. These results highlight the dynamic nature of viral adaptation, whereby a vector's host switch can give rise to competing and increasingly virulent disease pandemics. The evolutionary novelty and rapid global spread of these host-virus interactions, together with observed spillover into other species, illustrate how increasing globalization poses urgent threats to biodiversity and food security.

Population Genomics for Insect Conservation.

Insects constitute vital components of ecosystems. There is alarming evidence for global declines in insect species diversity, abundance, and biomass caused by anthropogenic drivers such as habitat degradation or loss, agricultural practices, climate change, and environmental pollution. This raises important concerns about human food security and ecosystem functionality and calls for more research to assess insect population trends and identify threatened species and the causes of declines to inform conservation strategies. Analysis of genetic diversity is a powerful tool to address these goals, but so far animal conservation genetics research has focused strongly on endangered vertebrates, devoting less attention to invertebrates, such as insects, that constitute most biodiversity. Insects' shorter generation times and larger population sizes likely necessitate different analytical methods and management strategies. The availability of high-quality reference genome assemblies enables population genomics to address several key issues. These include precise inference of past demographic fluctuations and recent declines, measurement of genetic load levels, delineation of evolutionarily significant units and cryptic species, and analysis of genetic adaptation to stressors. This enables identification of populations that are particularly vulnerable to future threats, considering their potential to adapt and evolve. We review the application of population genomics to insect conservation and the outlook for averting insect declines.

Multiple mating by both sexes in an invasive insect species, Aethina tumida (Coleoptera: Nitidulidae).

Multiple mating by both sexes is common among sexually reproducing animals. Small hive beetles (SHB), Aethina tumida, are parasites of bee nests endemic to sub-Saharan Africa and have become a widespread invasive species. Despite the considerable economic damages they can cause, their basic biology remains poorly understood. Here we show that male and female small hive beetles can mate multiple times, suggesting that costs for mating are low in this species. In an invasive A. tumida population in the United States, a combination of laboratory experiments for males and paternity analysis with eight polymorphic DNA microsatellite markers for field-caught females were used to estimate the number of mating by both sexes. The data show that females and males can mate multiple times-females mated with up to eight males, whereas males mated with at least seven females. The results also showed that A. tumida displayed a skewed paternity, although this was not consistent among the tested females. Thus, first or last male advantage seem to be unlikely in A. tumida. Our observations that individuals of both sexes of A. tumida can mate multiple times opens new research avenues for examining drivers of multiple mating and determining the role it may play in promoting biological invasions.

Genetic diversification of an invasive honey bee ectoparasite across sympatric and allopatric host populations.

Invasive parasites are major threats to biodiversity. The honey bee ectoparasite, Varroa destructor, has shifted host and spread almost globally several decades ago. This pest is generally considered to be the main global threat to Western honey bees, Apis mellifera, although the damages it causes are not equivalent in all its new host's populations. Due to the high virulence of this parasite and the viruses it vectors, beekeepers generally rely on acaricide treatments to keep their colonies alive. However, some populations of A. mellifera can survive without anthropogenic mite control, through the expression of diverse resistance and tolerance traits. Such surviving colonies are currently found throughout the globe, with the biggest populations being found in Sub-Saharan Africa and Latin America. Recently, genetic differences between mite populations infesting surviving and treated A. mellifera colonies in Europe were found, suggesting that adaptations of honey bees drive mite evolution. Yet, the prevalence of such co-evolutionary adaptations in other invasive populations of V. destructor remain unknown. Using the previous data from Europe and novel genetic data from V. destructor populations in South America and Africa, we here investigated whether mites display signs of adaptations to different host populations of diverse origins and undergoing differing management. Our results show that, contrary to the differences previously documented in Europe, mites infesting treated and untreated honey bee populations in Africa and South America are genetically similar. However, strong levels of genetic differentiation were found when comparing mites across continents, suggesting ongoing allopatric speciation despite a recent spread from genetically homogenous lineages. This study provides novel insights into the co-evolution of V. destructor and A. mellifera, and confirms that these species are ideal to investigate coevolution in newly established host-parasite systems.

Chito-Oligosaccharide and Propolis Extract of Stingless Bees Reduce the Infection Load of Nosema ceranae in Apis dorsata (Hymenoptera: Apidae).

Nosema ceranae is a microsporidian that infects Apis species. Recently, natural compounds have been proposed to control nosemosis and reduce its transmission among honey bees. We investigated how ethanolic extract of Tetrigona apicalis's propolis and chito-oligosaccharide (COS) impact the health of N. ceranae-infected Apis dorsata workers. Nosema ceranae spores were extracted from the guts of A. florea workers and fed 106 spores dissolved in 2 µL 50% (w/v) sucrose solution to A. dorsata individually. These bees were then fed a treatment consisting either of 0% or 50% propolis extracts or 0 ppm to 0.5 ppm COS. We found that propolis and COS significantly increased the number of surviving bees and lowered the infection ratio and spore loads of N. ceranae-infected bees 14 days post-infection. Our results suggest that propolis extract and COS could be possible alternative treatments to reduce N. ceranae infection in A. dorsata. Moreover, N. ceranae isolated from A. florea can damage the ventricular cells of A. dorsata, thereby lowering its survival. Our findings highlight the importance of considering N. ceranae infections and using alternative treatments at the community level where other honey bee species can act as a reservoir and readily transmit the pathogen among the honey bee species.

Comparative genomics suggests local adaptations in the invasive small hive beetle.

Invasive species are a major driver of ecological and environmental changes that affect human health, food security, and natural biodiversity. The success and impact of biological invasions depend on adaptations to novel abiotic and biotic selective pressures. However, the molecular mechanisms underlying adaptations in invasive parasitic species are inadequately understood. Small hive beetles, Aethina tumida, are parasites of bee nests. Originally endemic to sub-Saharan Africa, they are now found nearly globally. Here, we investigated the molecular bases of the adaptations to novel environments underlying their invasion routes. Genomes of historic and recent adults A. tumida from both the endemic and introduced ranges were compared. Analysis of gene-environment association identified 3049 candidate loci located in 874 genes. Functional annotation showed a significant bias toward genes linked to growth and reproduction. One of the genes from the apoptosis pathway encodes an "ecdysone-related protein," which is a crucial regulator in controlling body size in response to environmental cues for holometabolous insects during cell death and renewal. Genes whose proteins regulate organ size, ovary activation, and oviposition were also detected. Functions of these enriched pathways parallel behavioral differences between introduced and native A. tumida populations, which may reflect patterns of local adaptation. The results considerably improve our understanding of the underlying mechanisms and ecological factors driving adaptations of invasive species. Deep functional investigation of these identified loci will help clarify the mechanisms of local adaptation in A. tumida.

Using Citizen Science to Scout Honey Bee Colonies That Naturally Survive Varroa destructor Infestations.

Citizen Science contributes significantly to the conservation of biodiversity, but its application to honey bee research has remained minimal. Even though certain European honey bee (Apis mellifera) populations are known to naturally survive Varroa destructor infestations, it is unclear how widespread or common such populations are. Such colonies are highly valuable for investigating the mechanisms enabling colony survival, as well as for tracking the conservation status of free-living honey bees. Here, we use targeted Citizen Science to identify potentially new cases of managed or free-living A. mellifera populations that survive V. destructor without mite control strategies. In 2018, a survey containing 20 questions was developed, translated into 13 languages, and promoted at beekeeping conferences and online. After three years, 305 reports were collected from 28 countries: 241 from managed colonies and 64 from free-living colonies. The collected data suggest that there could be twice as many naturally surviving colonies worldwide than are currently known. Further, online and personal promotion seem to be key for successful recruitment of participants. Although the survivor status of these colonies still needs to be confirmed, the volume of reports and responses already illustrate how effectively Citizen Science can contribute to bee research by massively increasing generated data, broadening opportunities for comparative research, and fostering collaboration between scientists, beekeepers, and citizens. The success of this survey spurred the development of a more advanced Citizen Science platform, Honey Bee Watch, that will enable a more accurate reporting, confirmation, and monitoring of surviving colonies, and strengthen the ties between science, stakeholders, and citizens to foster the protection of both free-living and managed honey bees.

Intra-Colonial Viral Infections in Western Honey Bees (Apis Mellifera).

RNA viruses play a significant role in the current high losses of pollinators. Although many studies have focused on the epidemiology of western honey bee (Apis mellifera) viruses at the colony level, the dynamics of virus infection within colonies remains poorly explored. In this study, the two main variants of the ubiquitous honey bee virus DWV as well as three major honey bee viruses (SBV, ABPV and BQCV) were analyzed from Varroa-destructor-parasitized pupae. More precisely, RT-qPCR was used to quantify and compare virus genome copies across honey bee pupae at the individual and subfamily levels (i.e., patrilines, sharing the same mother queen but with different drones as fathers). Additionally, virus genome copies were compared in cells parasitized by reproducing and non-reproducing mite foundresses to assess the role of this vector. Only DWV was detected in the samples, and the two variants of this virus significantly differed when comparing the sampling period, colonies and patrilines. Moreover, DWV-A and DWV-B exhibited different infection patterns, reflecting contrasting dynamics. Altogether, these results provide new insight into honey bee diseases and stress the need for more studies about the mechanisms of intra-colonial disease variation in social insects.

Adaptive population structure shifts in invasive parasitic mites, Varroa destructor.

Comparative studies of genetic diversity and population structure can shed light on the ecological and evolutionary factors governing host-parasite interactions. Even though invasive parasites are considered of major biological importance, little is known about their adaptative potential when infesting the new hosts. Here, the genetic diversification of Varroa destructor, a novel parasite of Apis mellifera originating from Asia, was investigated using population genetics to determine how the genetic structure of the parasite changed in distinct European populations of its new host. To do so, mites infesting two categories of hosts in four European regions were compared: (a) adapted hosts surviving through means of natural selection, thereby expected to impose strong selective pressure on the mites, and (b) treated host populations, surviving mite infestations because acaricides are applied, therefore characterized by a relaxed selection imposed by the host on the mites. Significant genetic divergence was found across regions, partially reflecting the invasion pattern of V. destructor throughout Europe and indicating local adaptation of the mite to the host populations. Additionally, varying degrees of genotypic changes were found between mites from adapted and treated colonies. Altogether, these results indicate that V. destructor managed to overcome the genetic bottlenecks following its introduction in Europe and that host-mediated selection fostered changes in the genetic structure of this mite at diverse geographic scales. These findings highlight the potential of parasites to adapt to their local host populations and confirm that adaptations developed within coevolutionary dynamics are a major determinant of population genetic changes.

Gene Expression and Functional Analyses of Odorant Receptors in Small Hive Beetles (Aethina tumida).

Olfaction is key to many insects. Odorant receptors (ORs) stand among the key chemosensory receptors mediating the detection of pheromones and kairomones. Small hive beetles (SHBs), Aethina tumida, are parasites of social bee colonies and olfactory cues are especially important for host finding. However, how interactions with their hosts may have shaped the evolution of ORs in the SHB remains poorly understood. Here, for the first time, we analyzed the evolution of SHB ORs through phylogenetic and positive selection analyses. We then tested the expression of selected OR genes in antennae, heads, and abdomens in four groups of adult SHBs: colony odor-experienced/-naive males and females. The results show that SHBs experienced both OR gene losses and duplications, thereby providing a first understanding of the evolution of SHB ORs. Additionally, three candidate ORs potentially involved in host finding and/or chemical communication were identified. Significantly different downregulations of ORs between the abdomens of male and female SHBs exposed to colony odors may reflect that these expression patterns might also reflect other internal events, e.g., oviposition. Altogether, these results provide novel insights into the evolution of SHB ORs and provide a valuable resource for analyzing the function of key genes, e.g., for developing biological control. These results will also help in understanding the chemosensory system in SHBs and other beetles.

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.

Diversity and Global Distribution of Viruses of the Western Honey Bee, Apis mellifera.

In the past centuries, viruses have benefited from globalization to spread across the globe, infecting new host species and populations. A growing number of viruses have been documented in the western honey bee, Apis mellifera. Several of these contribute significantly to honey bee colony losses. This review synthetizes the knowledge of the diversity and distribution of honey-bee-infecting viruses, including recent data from high-throughput sequencing (HTS). After presenting the diversity of viruses and their corresponding symptoms, we surveyed the scientific literature for the prevalence of these pathogens across the globe. The geographical distribution shows that the most prevalent viruses (deformed wing virus, sacbrood virus, black queen cell virus and acute paralysis complex) are also the most widely distributed. We discuss the ecological drivers that influence the distribution of these pathogens in worldwide honey bee populations. Besides the natural transmission routes and the resulting temporal dynamics, global trade contributes to their dissemination. As recent evidence shows that these viruses are often multihost pathogens, their spread is a risk for both the beekeeping industry and the pollination services provided by managed and wild pollinators.

Behavioral Genetics of the Interactions between Apis mellifera and Varroa destructor.

The western honeybee Apis mellifera exhibits a diverse set of adaptations in response to infestations by its most virulent disease-causing agent, the ectoparasitic mite Varroa destructor. In this study, we investigated the effect of honeybee pupae genotype on the expression of four host and parasite traits that are associated with the reproductive phase of the mite in the brood of its host. We first phenotyped cells containing bee pupae to assess their infestation status, their infestation level, the reproductive status of the mites, and the recapping of cells by adult workers. We then genotyped individual pupae with five microsatellites markers to compare these phenotypes across full sister groups. We found that the four phenotypes varied significantly in time but did not across the subfamilies within the colonies. These findings show that V. destructor mites do not differentially infest or reproduce on some particular honeybee patrilines, and that workers do not target preferentially specific pupae genotypes when performing recapping. These findings bring new insights that can help designing sustainable mite control strategies through breeding and provide new insights into the interactions between A. mellifera and V. destructor.

Population genetics of ectoparasitic mites suggest arms race with honeybee hosts.

The ectoparasitic mite, Varroa destructor, is the most severe biotic threat to honeybees (Apis mellifera) globally, usually causing colony death within a few years without treatments. While it is known that a few A. mellifera populations survive mite infestations by means of natural selection, the possible role of mite adaptations remains unclear. To investigate potential changes in mite populations in response to host adaptations, the genetic structure of V. destructor in the mite-resistant A. mellifera population on Gotland, Sweden, was studied. Spatio-temporal genetic changes were assessed by comparing mites collected in these colonies, as well as from neighboring mite-susceptible colonies, in historic (2009) and current (2017/2018) samples. The results show significant changes in the genetic structure of the mite populations during the time frame of this study. These changes were more pronounced in the V. destructor population infesting the mite-resistant honeybee colonies than in the mite-susceptible colonies. These results suggest that V. destructor populations are reciprocating, in a coevolutionary arms race, to the selection pressure induced by their honeybee host. Our data reveal exciting new insights into host-parasite interactions between A. mellifera and its major parasite.

Population genetics of ectoparasitic mites Varroa spp. in Eastern and Western honey bees.

Host shifts of parasites are often causing devastating effects in the new hosts. The Varroa genus is known for a lineage of Varroa destructor that shifted to the Western honey bee, Apis mellifera, with disastrous effects on wild populations and the beekeeping industry. Despite this, the biology of Varroa spp. remains poorly understood in its native distribution range, where it naturally parasitizes the Eastern honey bee, Apis cerana. Here, we combined mitochondrial and nuclear DNA analyses with the assessment of mite reproduction to determine the population structure and host specificity of V. destructor and Varroa jacobsonii in Thailand, where both hosts and several Varroa species and haplotypes are sympatric. Our data confirm previously described mite haplogroups, and show three novel haplotypes. Multiple infestations of single host colonies by both mite species and introgression of alleles between V. destructor and V. jacobsonii suggest that hybridization occurs between the two species. Our results indicate that host specificity and population genetic structure in the genus Varroa is more labile than previously thought. The ability of the host shifted V. destructor haplotype to spillback to A. cerana and to hybridize with V. jacobsonii could threaten honey bee populations of Asia and beyond.

Association of Varroa destructor females in multiply infested cells of the honeybee Apis mellifera.

The genetic diversity of Varroa destructor (Anderson & Trueman) is limited outside its natural range due to population bottlenecks and its propensity to inbreed. In light of the arms race between V. destructor and its honeybee (Apis mellifera L.) host, any mechanism enhancing population admixture of the mite may be favored. One way that admixture can occur is when two genetically dissimilar mites coinvade a brood cell, with the progeny of the foundresses admixing. We determined the relatedness of 393 pairs of V. destructor foundresses, each pair collected from a single bee brood cell (n = five colonies). We used six microsatellites to identify the genotypes of mites coinvading a cell and calculated the frequency of pairs with different or the same genotypes. We found no deviation from random coinvasion, but the frequency of cells infested by mites with different genotypes was high. This rate of recombination, coupled with a high transmission rate of mites, homogenized the allelic pool of mites within the apiary.

Preliminary Investigation of Species Diversity of Rice Hopper Parasitoids in Southeast Asia.

Ongoing intensification of rice production systems in Southeast Asia is causing devastating yield losses each year due to rice hoppers. Their continuing development of immunity to resistant rice varieties and pesticide applications further complicates this problem. Hence, there is a high demand for biological control agents of rice hoppers. Egg parasitoid wasps are among the most important natural enemies of rice hoppers, such as Nilaparvata lugens and Nephotettix spp. However, our knowledge of their diversity is still very limited, due to their small size and the lack of available morphological information. Classifying these parasitoids is the first step to properly understanding their role in the rice agroecosystem. We used traditional morphological identification, as well as DNA sequencing of the 28S rRNA and the COI genes, to investigate the diversity of four important hopper egg parasitoid genera in the Philippines. Parasitoids of the genera Anagrus, Oligosita, Gonatocerus, and Paracentrobia were collected in eight study landscapes located in Luzon. Our findings illustrate that characterization of species diversity using morphological and molecular analyses were concordant only for the genus Paracentrobia. The genera Anagrus and Gonatocerus exhibited more genetic diversity than estimated with the morphological analysis, while the opposite was observed for Oligosita. This is the first study investigating the molecular diversity of rice hopper parasitoids in the Philippines. More research combining morphological, behavioral, and molecular methods, as well as the establishment of a comprehensive DNA database, are urgently needed to assess the performance and suitability of these organisms as biocontrol agents.

Seasonal cycle of inbreeding and recombination of the parasitic mite Varroa destructor in honeybee colonies and its implications for the selection of acaricide resistance.

Varroa destructor is the most devastating parasite of the Western honeybee, Apis mellifera. In the light of the arm race opposing the host and its parasite, the population dynamics and genetic diversity of these organisms are key parameters. However, the life cycle of V. destructor is characterized by extreme inbreeding due to full sibling mating in the host brood cells. We here present an equation reflecting the evolution of inbreeding in such a clonal system, and compare our predictions with empirical data based on the analysis of seven microsatellite markers. This comparison revealed that the mites perform essentially incestuous mating in the beginning of the brood season. However, this pattern changes with the development of mite infestation. Despite the fact that the overall level of genetic diversity of the mites remained low through the season, multiple inbred lineages were identified in the mites we sampled in June. As a response to the decrease of brood availability and the increase of the parasite population in parallel in the colonies, these lineages recombined towards the end of the season as mites co-infest brood cells. Our results suggest that the ratio of the number of mite per brood cell in the colony determines the genetic structure of the populations of V. destructor. This intracolonial population dynamics has great relevance for the selection of acaricide resistance in V. destructor. If chemical treatments occur before the recombination phase, inbreeding will greatly enhance the fixation of resistance alleles at the colony level.

Host Specificity in the Honeybee Parasitic Mite, Varroa spp. in Apis mellifera and Apis cerana.

The ectoparasitic mite Varroa destructor is a major global threat to the Western honeybee Apis mellifera. This mite was originally a parasite of A. cerana in Asia but managed to spill over into colonies of A. mellifera which had been introduced to this continent for honey production. To date, only two almost clonal types of V. destructor from Korea and Japan have been detected in A. mellifera colonies. However, since both A. mellifera and A. cerana colonies are kept in close proximity throughout Asia, not only new spill overs but also spill backs of highly virulent types may be possible, with unpredictable consequences for both honeybee species. We studied the dispersal and hybridisation potential of Varroa from sympatric colonies of the two hosts in Northern Vietnam and the Philippines using mitochondrial and microsatellite DNA markers. We found a very distinct mtDNA haplotype equally invading both A. mellifera and A. cerana in the Philippines. In contrast, we observed a complete reproductive isolation of various Vietnamese Varroa populations in A. mellifera and A. cerana colonies even if kept in the same apiaries. In light of this variance in host specificity, the adaptation of the mite to its hosts seems to have generated much more genetic diversity than previously recognised and the Varroa species complex may include substantial cryptic speciation.