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.

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.

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.

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.

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.

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.

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.

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.

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.