A selective sweep in a Varroa destructor resistant honeybee (Apis mellifera) population

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.

Changes in capture availability due to infection can lead to detectable biases in population-level infectious disease parameters

Correctly identifying the strength of selection that parasites impose on hosts is key to predicting epidemiological and evolutionary outcomes of host-parasite interactions. However, behavioral changes due to infection can alter the capture probability of infected hosts and thereby make selection difficult to estimate by standard sampling techniques. Mark-recapture approaches, which allow researchers to determine if some groups in a population are less likely to be captured than others, can be used to identify infection-driven capture biases. If a metric of interest directly compares infected and uninfected populations, calculated detection probabilities for both groups may be useful in identifying bias. Here, we use an individual-based simulation to test whether changes in capture rate due to infection can alter estimates of three key metrics: 1) reduction in the reproductive success of infected parents relative to uninfected parents, 2) the relative risk of infection for susceptible genotypes compared to resistant genotypes, and 3) changes in allele frequencies between generations. We explore the direction and underlying causes of the biases that emerge from these simulations. Finally, we argue that short series of mark-recapture sampling bouts, potentially implemented in under a week, can yield key data on detection bias due to infection while not adding a significantly higher burden to disease ecology studies.

Prospects, challenges and perspectives in harnessing natural selection to solve the ‘varroa problem’ of honey bees

Honey bees, Apis mellifera, of European origin are major pollinators of crops and wild flora. Their endemic and exported populations are threatened by a variety of abiotic and biotic factors. Among the latter, the ectoparasitic mite Varroa destructor is the most important single cause behind colony mortality. The selection of mite resistance in honey bee populations has been deemed a more sustainable solution to its control than varroacidal treatments. Because natural selection has led to the survival of some European and African honey bee populations to V. destructor infestations, harnessing its principles has recently been highlighted as a more efficient way to provide honey bee lineages that survive infestations when compared with conventional selection on resistance traits against the parasite. However, the challenges and drawbacks of harnessing natural selection to solve the varroa problem have only been minimally addressed. We argue that failing to consider these issues could lead to counterproductive results, such as increased mite virulence, loss of genetic diversity reducing host resilience, population collapses or poor acceptance by beekeepers. Therefore, it appears timely to evaluate the prospects for the success of such programmes and the qualities of the populations obtained. After reviewing the approaches proposed in the literature and their outcomes, we consider their advantages and drawbacks and propose perspectives to overcome their limitations. In these considerations, we not only reflect on the theoretical aspects of host-parasite relationships but also on the currently largely neglected practical constraints, that is, the requirements for productive beekeeping, conservation or rewilding objectives. To optimize natural selection-based programmes towards these objectives, we suggest designs based on a combination of nature-driven phenotypic differentiation and human-directed selection of traits. Such a dual strategy aims at allowing field-realistic evolutionary approaches towards the survival of V. destructor infestations and the improvement of honey bee health.

Population Structure and Diversity in European Honey Bees (Apismellifera L.)-An Empirical Comparison of Pool and Individual Whole-Genome Sequencing

BACKGROUND

Whole-genome sequencing has become routine for population genetic studies. Sequencing of individuals provides maximal data but is rather expensive and fewer samples can be studied. In contrast, sequencing a pool of samples (pool-seq) can provide sufficient data, while presenting less of an economic challenge. Few studies have compared the two approaches to infer population genetic structure and diversity in real datasets. Here, we apply individual sequencing (ind-seq) and pool-seq to the study of Western honey bees (Apis mellifera).

METHODS

We collected honey bee workers that belonged to 14 populations, including 13 subspecies, totaling 1347 colonies, who were individually (139 individuals) and pool-sequenced (14 pools). We compared allele frequencies, genetic diversity estimates, and population structure as inferred by the two approaches.

RESULTS

Pool-seq and ind-seq revealed near identical population structure and genetic diversities, albeit at different costs. While pool-seq provides genome-wide polymorphism data at considerably lower costs, ind-seq can provide additional information, including the identification of population substructures, hybridization, or individual outliers.

CONCLUSIONS

If costs are not the limiting factor, we recommend using ind-seq, as population genetic structure can be inferred similarly well, with the advantage gained from individual genetic information. Not least, it also significantly reduces the effort required for the collection of numerous samples and their further processing in the laboratory.

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.

Integrated Pest Management Control of Varroa destructor (Acari: Varroidae), the Most Damaging Pest of (Apis mellifera L. (Hymenoptera: Apidae)) Colonies

Varroa destructor is among the greatest biological threats to western honey bee (Apis mellifera L.) health worldwide. Beekeepers routinely use chemical treatments to control this parasite, though overuse and mismanagement of these treatments have led to widespread resistance in Varroa populations. Integrated Pest Management (IPM) is an ecologically based, sustainable approach to pest management that relies on a combination of control tactics that minimize environmental impacts. Herein, we provide an in-depth review of the components of IPM in a Varroa control context. These include determining economic thresholds for the mite, identification of and monitoring for Varroa, prevention strategies, and risk conscious treatments. Furthermore, we provide a detailed review of cultural, mechanical, biological, and chemical control strategies, both longstanding and emerging, used against Varroa globally. For each control type, we describe all available treatments, their efficacies against Varroa as described in the primary scientific literature, and the obstacles to their adoption. Unfortunately, reliable IPM protocols do not exist for Varroa due to the complex biology of the mite and strong reliance on chemical control by beekeepers. To encourage beekeeper adoption, a successful IPM approach to Varroa control in managed colonies must be an improvement over conventional control methods and include cost-effective treatments that can be employed readily by beekeepers. It is our intention to provide the most thorough review of Varroa control options available, ultimately framing our discussion within the context of IPM. We hope this article is a call-to-arms against the most damaging pest managed honey bee colonies face worldwide.

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.

Geographical Distribution and Selection of European Honey Bees Resistant to Varroa destructor

Developing resistance to the varroa mite in honey bees is a major goal for apicultural science and practice, the development of selection strategies and the availability of resistant stock. Here we present an extended literature review and survey of resistant populations and selection programs in the EU and elsewhere, including expert interviews. We illustrate the practical experiences of scientists, beekeepers, and breeders in search of resistant bees. We describe numerous resistant populations surviving without acaricide treatments, most of which developed under natural infestation pressure. Their common characteristics: reduced brood development; limited mite population growth; and low mite reproduction, may cause conflict with the interests of commercial beekeeping. Since environmental factors affect varroa mite resistance, particular honey bee strains must be evaluated under different local conditions and colony management. The resistance traits of grooming, hygienic behavior and mite reproduction, together with simple testing of mite population development and colony survival, are significant in recent selection programs. Advanced breeding techniques and genetic and physiological selection tools will be essential in the future. Despite huge demand, there is no well-established market for resistant stock in Europe. Moreover, reliable experience or experimental evidence regarding the resistance of stocks under different environmental and management conditions is still lacking.

Population abundance of Varroa destructor and its effects on Apis mellifera scutellata colonies in Kenya

The devastating effects of Varroa destructor Anderson and Trueman on Western honeybee colonies (Apis mellifera L.) have been well documented. Not only do these mites cause physical damage to parasitized individuals when they feed on them, but they also transmit viruses and other pathogens, weaken colonies and ultimately may cause their death. Unlike the subspecies of European origin, the honeybees of African origin suffer less from mite infestations. Absconding is one of the factors contributing to low V. destructor population in honeybee colonies as it creates a brood-free period. For a long time, researchers hypothesized that absconding was the main mechanism to control the parasite. The effects of V. destructor are well documented under temperate climatic conditions with a break during winter. Therefore, our study aimed at investigating the impact of V. destructor population growth on colony size, absconding and productivity under natural infestation levels of a tropical/subtropical climate with continuous brood production. We measured several characteristics related to the mite populations, the bee colonies and the resources of the bee colonies for a period of 8 months. The seven colonies that absconded during the study period were not influenced by densities of V. destructor. Absconding of the colonies occurred as a result of low numbers of capped brood. Mite densities were generally low throughout the study period (ranged between 26.9 and 59.8 mites per month) but were positively associated with adult bee densities. The amount of open and capped brood was positively associated with densities of V. destructor in the brood and negatively associated with denisities of V. destructor on screen boards, which appeared as extremely important factors that should be monitored regularly alongside colony stores and availability of pollen.

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.

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.

Drivers of colony losses

Over the past decade, in some regions of the world, honey bee (Apis mellifera L.) colonies have experienced rates of colony loss that are difficult for beekeepers to sustain. The reasons for losses are complex and interacting, with major drivers including Varroaand related viruses, pesticides, nutrition and beekeeper practices. In these endeavors it has also become apparent that defining a dead colony, and singling out the effects of specific drivers of loss, is not so straightforward. Using the class of neonicotinoid pesticides as an example we explain why quantifying risk factor impact at the colony level is at times elusive and in some cases unpractical. In this review, we discuss the caveats of defining and quantifying dead colonies. We also summarize the current leading drivers of colony losses, their interactions and the most recent research on their effects on colony mortality.

Isolation of oxalotrophic bacteria associated with Varroa destructor mites

Bacteria associated with varroa mites were cultivated and genotyped by 16S RNA. Under our experimental conditions, the cultivable bacteria were few in number, and most of them proved to be fastidious to grow. Cultivation with seven different media under O2 /CO2 conditions and selection for colony morphology yielded a panel of species belonging to 13 different genera grouped in two different phyla, proteobacteria and actinobacteria. This study identified one species of actinobacteria that is a known commensal of the honey bee. Some isolates are oxalotrophic, a finding that may carry ramifications into the use of oxalic acid to control the number of phoretic mites in the managed colonies of honey bees.

SIGNIFICANCE AND IMPACT OF THE STUDY

Oxalic acid, legally or brevi manu, is widely used to control phoretic Varroa destructor mites, a major drive of current honey bees' colony losses. Unsubstantiated by sanctioned research are rumours that in certain instances oxalic acid is losing efficacy, forcing beekeepers to increase the frequency of treatments. This investigation fathoms the hypothesis that V. destructor associates with bacteria capable of degrading oxalic acid. The data show that indeed oxalotrophy, a rare trait among bacteria, is common in bacteria that we isolated from V. destructor mites. This finding may have ramifications in the use of oxalic acid as a control agent.