Global decline of bumblebees is phylogenetically structured and inversely related to species range size and pathogen incidence

Conservation genomics analysis reveals recent population decline and possible causes in bumblebee Bombus opulentus

Bumblebees are a genus of pollinators (Bombus) that play important roles in natural ecosystem and agricultural production. Several bumblebee species have been recorded as under population decline, and the proportion of species experiencing population decline within subgenus Thoracobombus is higher than average. Bombus opulentus is 1 species in Thoracobombus, but little is known about its recent population dynamics. Here, we employed conservation genomics methods to investigate the population dynamics of B. opulentus during the recent past and identify the likely environmental factors that may cause population decline. Firstly, we placed the scaffold-level of B. opulentus reference genome sequence onto chromosome-level using Hi-C technique. Then, based on this reference genome and whole-genome resequencing data for 51 B. opulentus samples, we reconstructed the population structure and effective population size (Ne ) trajectories of B. opulentus and identified genes that were under positive selection. Our results revealed that the collected B. opulentus samples could be divided into 2 populations, and 1 of them experienced a recent population decline; the declining population also exhibited lower genetic diversity and higher inbreeding levels. Genes related to high-temperature tolerance, immune response, and detoxication showed signals of positive selection in the declining population, suggesting that climate warming and pathogen/pesticide exposures may contribute to the decline of this B. opulentus population. Taken together, our study provided insights into the demography of B. opulentus populations and highlighted that populations of the same bumblebee species could have contrasting Ne trajectories and population decline could be caused by a combination of various stressors.

Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis

BACKGROUND

Antimicrobial resistance (AMR) poses a significant global health threat, and an accurate prediction of bacterial resistance patterns is critical for effective treatment and control strategies. In recent years, machine learning (ML) approaches have emerged as powerful tools for analyzing large-scale bacterial AMR data. However, ML methods often ignore evolutionary relationships among bacterial strains, which can greatly impact performance of the ML methods, especially if resistance-associated features are attempted to be detected. Genome-wide association studies (GWAS) methods like linear mixed models accounts for the evolutionary relationships in bacteria, but they uncover only highly significant variants which have already been reported in literature.

RESULTS

In this work, we introduce a novel phylogeny-related parallelism score (PRPS), which measures whether a certain feature is correlated with the population structure of a set of samples. We demonstrate that PRPS can be used, in combination with SVM- and random forest-based models, to reduce the number of features in the analysis, while simultaneously increasing models' performance. We applied our pipeline to publicly available AMR data from PATRIC database for Mycobacterium tuberculosis against six common antibiotics.

CONCLUSIONS

Using our pipeline, we re-discovered known resistance-associated mutations as well as new candidate mutations which can be related to resistance and not previously reported in the literature. We demonstrated that taking into account phylogenetic relationships not only improves the model performance, but also yields more biologically relevant predicted most contributing resistance markers.

Genome-wide DNA methylation patterns in bumble bee (Bombus vosnesenskii) populations from spatial-environmental range extremes

Unraveling molecular mechanisms of adaptation to complex environments is crucial to understanding tolerance of abiotic pressures and responses to climatic change. Epigenetic variation is increasingly recognized as a mechanism that can facilitate rapid responses to changing environmental cues. To investigate variation in genetic and epigenetic diversity at spatial and thermal extremes, we use whole genome and methylome sequencing to generate a high-resolution map of DNA methylation in the bumble bee Bombus vosnesenskii. We sample two populations representing spatial and environmental range extremes (a warm southern low-elevation site and a cold northern high-elevation site) previously shown to exhibit differences in thermal tolerance and determine positions in the genome that are consistently and variably methylated across samples. Bisulfite sequencing reveals methylation characteristics similar to other arthropods, with low global CpG methylation but high methylation concentrated in gene bodies and in genome regions with low nucleotide diversity. Differentially methylated sites (n = 2066) were largely hypomethylated in the northern high-elevation population but not related to local sequence differentiation. The concentration of methylated and differentially methylated sites in exons and putative promoter regions suggests a possible role in gene regulation, and this high-resolution analysis of intraspecific epigenetic variation in wild Bombus suggests that the function of methylation in niche adaptation would be worth further investigation.

Unexpected worker mating and colony-founding in a superorganism

The emergence of caste-differentiated colonies, which have been defined as 'superorganisms', in ants, bees, and wasps represents a major transition in evolution. Lifetime mating commitment by queens, pre-imaginal caste determination and lifetime unmatedness of workers are key features of these animal societies. Workers in superorganismal species like honey bees and many ants have consequently lost, or retain only vestigial spermathecal structures. However, bumble bee workers retain complete spermathecae despite 25-40 million years since their origin of superorganismality, which remains an evolutionary mystery. Here, we show (i) that bumble bee workers retain queen-like reproductive traits, being able to mate and produce colonies, underlain by queen-like gene expression, (ii) the social conditions required for worker mating, and (iii) that these abilities may be selected for by early queen-loss in these annual species. These results challenge the idea of lifetime worker unmatedness in superorganisms, and provide an exciting new tool for the conservation of endangered bumble bee species.

Cuticular hydrocarbons of alpine bumble bees (Hymenoptera: Bombus) are species-specific, but show little evidence of elevation-related climate adaptation

Alpine bumble bees are the most important pollinators in temperate mountain ecosystems. Although they are used to encounter small-scale successions of very different climates in the mountains, many species respond sensitively to climatic changes, reflected in spatial range shifts and declining populations worldwide. Cuticular hydrocarbons (CHCs) mediate climate adaptation in some insects. However, whether they predict the elevational niche of bumble bees or their responses to climatic changes remains poorly understood. Here, we used three different approaches to study the role of bumble bees’ CHCs in the context of climate adaptation: using a 1,300 m elevational gradient, we first investigated whether the overall composition of CHCs, and two potentially climate-associated chemical traits (proportion of saturated components, mean chain length) on the cuticle of six bumble bee species were linked to the species’ elevational niches. We then analyzed intraspecific variation in CHCs of Bombus pascuorum along the elevational gradient and tested whether these traits respond to temperature. Finally, we used a field translocation experiment to test whether CHCs of Bombus lucorum workers change, when translocated from the foothill of a cool and wet mountain region to (a) higher elevations, and (b) a warm and dry region. Overall, the six species showed distinctive, species-specific CHC profiles. We found inter- and intraspecific variation in the composition of CHCs and in chemical traits along the elevational gradient, but no link to the elevational distribution of species and individuals. According to our expectations, bumble bees translocated to a warm and dry region tended to express longer CHC chains than bumble bees translocated to cool and wet foothills, which could reflect an acclimatization to regional climate. However, chain lengths did not further decrease systematically along the elevational gradient, suggesting that other factors than temperature also shape chain lengths in CHC profiles. We conclude that in alpine bumble bees, CHC profiles and traits respond at best secondarily to the climate conditions tested in this study. While the functional role of species-specific CHC profiles in bumble bees remains elusive, limited plasticity in this trait could restrict species’ ability to adapt to climatic changes.

Plant-pollinator network change across a century in the subarctic

Animal-mediated pollination is a vital ecosystem service to crops and wild plants, and long-term stability of plant-pollinator interactions is therefore crucial for maintaining plant biodiversity and food security. However, it is unknown how the composition of pollinators and the structure of pollinator interactions have changed across longer time spans relevant to examining responses to human activities such as climate change. We resampled an historical dataset of plant-pollinator interactions across several orders of pollinating insects in a subarctic location in Finland that has already experienced substantial climate warming but little land use change. Our results reveal a dramatic turnover in pollinator species and rewiring of plant-pollinator interactions, with only 7% of the interactions shared across time points. The relative abundance of moth and hoverfly pollinators declined between time points, whereas muscoid flies, a group for which little is known regarding conservation status and responses to climate, became more common. Specialist pollinators disproportionately declined, leading to a decrease in network-level specialization, which could have harmful consequences for pollination services. Our results exemplify the changes in plant-pollinator networks that might be expected in other regions as climate change progresses.

Impact of climate change on parasite infection of an important pollinator depends on host genotypes

Climate change is predicted to affect host-parasite interactions, and for some hosts, parasite infection is expected to increase with rising temperatures. Global population declines of important pollinators already have been attributed to climate change and parasitism. However, the role of climate in driving parasite infection and the genetic basis for pollinator hosts to respond often remain obscure. Based on decade-long field data, we investigated the association between climate and Nosema bombi (Microsporidia) infection of buffed-tailed bumblebees (Bombus terrestris), and whether host genotypes play a role. For this, we genotyped 876 wild bumblebee queens and screened for N. bombi infection of those queens between 2000 and 2010. We recorded seven climate parameters during those 11 years and tested for correlations between climate and infection prevalence. Here we show that climatic factors drive N. bombi infection and that the impact of climate depends on mitochondrial DNA cytochrome oxidase I (COI) haplotypes of the host. Infection prevalence was correlated with climatic variables during the time when queens emerge from hibernation. Remarkably, COI haplotypes best predict this association between climatic factors and infection. In particular, two host haplotypes ("A" and "B") displayed phenotypic plasticity in response to climatic variation: Temperature was positively correlated with infection of host haplotype B, but not haplotype A. The likelihood of infection of haplotype A was associated with moisture, conferring greater resistance to parasite infection during wetter years. In contrast, infection of haplotype B was unrelated to moisture. To the best of our knowledge, this is the first study that identifies specific host genotypes that confer differential parasite resistance under variable climatic conditions. Our results underscore the importance of mitochondrial haplotypes to ward off parasites in a changing climate. More broadly, this also suggests that COI may play a pertinent role in climate change adaptations of insect pollinators.

Transcriptomic Analyses Suggest the Adaptation of Bumblebees to High Altitudes

Determining the adaptive mechanisms by which bumblebees adapt to high altitudes can help us to better understand their distribution, providing a basis for the future protection and utilization of bumblebee resources. For this study, the adaptive mechanisms of two dominant bumblebee species in the northeastern Qinghai-Tibet Plateau-Bombus kashmirensis and B. waltoni-were studied through transcriptomics methods. For each species, enrichment analysis of the differentially expressed genes and gene set enrichment analysis were carried out between samples collected at different altitudes (4000 m, 4500 m, and 5000 m). The results indicate that these bumblebees tend to up-regulate energy metabolism-related genes when facing extremely high-altitude environments. Of the enriched pathways up-regulated in higher altitudes, the pentose and glucuronate interconversions pathway presented the most severe up-regulation in multiple comparisons of different altitudes for B. kashmirensis, as well as the AMPK signaling pathway, which was found to be up-regulated in both species. Notably, limited by the extreme hypoxic conditions in this study, oxidative phosphorylation was found to be down-regulated with increasing altitude, which is uncommon in studies on bumblebee adaptation to high altitudes.

Modeling the extinction risk of European butterflies and odonates

Insect populations have become increasingly threatened during the last decades due to climate change and landuse intensification. Species characteristics driving these threats remain poorly understood. Trait‐based analyses provide a straight‐forward approach to gain a mechanistic understanding of species' extinction risk, guiding the development of conservation strategies. We combined morphological traits and phylogenetic relationship for 332 European species of butterflies and 115 species of odonates (dragon and damselflies) to model their red list status via phylogenetically controlled ordered logistic regression. We hypothesized that extinction risk increases with increasing body volume and wing area, decreasing range size, and is larger for brighter species. All investigated traits exhibited a strong phylogenetic signal. When controlling for phylogenetic relationship, we found that extinction risk of butterflies increased with decreasing range size. The extinction risk of odonates showed no relationship with the selected traits. Our results show that there is no universal trait defining the extinction risk of our investigated insect taxa. Furthermore, evolutionary history, measured as the phylogenetically predicted part of our analyzed traits, poorly predicted extinction risk. Our study confirms the focus of conservation measures on European butterfly species with small range sizes.

Bumble bees exhibit body size clines across an urban gradient despite low genetic differentiation

Environmental heterogeneity resulting from human-modified landscapes can increase intraspecific trait variation. However, less known is whether such phenotypic variation is driven by plastic or adaptive responses to local environments. Here, we study five bumble bee (Apidae: Bombus) species across an urban gradient in the greater Saint Louis, Missouri region in the North American Midwest and ask: (1) Can urban environments induce intraspecific spatial structuring of body size, an ecologically consequential functional trait? And, if so, (2) is this body size structure the result of plasticity or adaptation? We additionally estimate genetic diversity, inbreeding, and colony density of these species—three factors that affect extinction risk. Using ≥ 10 polymorphic microsatellite loci per species and measurements of body size, we find that two of these species (Bombus impatiens, Bombus pensylvanicus) exhibit body size clines across the urban gradient, despite a lack of population genetic structure. We also reaffirm reports of low genetic diversity in B. pensylvanicus and find evidence that Bombus griseocollis, a species thought to be thriving in North America, is inbred in the greater Saint Louis region. Collectively, our results have implications for conservation in urban environments and suggest that plasticity can cause phenotypic clines across human-modified landscapes.

A contemporary survey of bumble bee diversity across the state of California

Bumble bees (genus Bombus) are important pollinators with more than 260 species found worldwide, many of which are in decline. Twenty-five species occur in California with the highest species abundance and diversity found in coastal, northern, and montane regions. No recent studies have examined California bumble bee diversity across large spatial scales nor explored contemporary community composition patterns across the state. To fill these gaps, we collected 1740 bumble bee individuals, representing 17 species from 17 sites (~100 bees per site) in California, using an assemblage monitoring framework. This framework is intended to provide an accurate estimate of relative abundance of more common species without negatively impacting populations through overcollection. Our sites were distributed across six ecoregions, with an emphasis on those that historically hosted high bumble bee diversity. We compared bumble bee composition among these sites to provide a snapshot of California bumble bee biodiversity in a single year. Overall, the assemblage monitoring framework that we employed successfully captured estimated relative abundance of species for most sites, but not all. This shortcoming suggests that bumble bee biodiversity monitoring in California might require multiple monitoring approaches, including greater depth of sampling in some regions, given the variable patterns in bumble bee abundance and richness throughout the state. Our study sheds light on the current status of bumble bee diversity in California, identifies some areas where greater sampling effort and conservation action should be focused in the future, and performs the first assessment of an assembly monitoring framework for bumble bee communities in the state.

Nocturnal Pollinators Significantly Contribute to Apple Production

Agricultural dependency on insect-mediated pollination is increasing at the same time that pollinator populations are experiencing declines in diversity and abundance. Current pollinator research in agriculture focuses largely on diurnal pollinators, yet the evidence for pollination by moths and other nocturnal pollinators is growing. Apples are one of the most valuable and important fruits produced globally, and apple production is dependent on insect-mediated cross-pollination to generate a profitable crop. We examined contributions to apple production provided by nocturnal insects via an exclusion experiment. We compared the relative contributions to apple production provided by nocturnal and diurnal pollinators using fruit set, the likelihood of cluster pollination, and seed set. We found nocturnal pollinators capable of facilitating the production of as many apples at similar levels of pollination as diurnal pollinators. We further found evidence that nocturnal and diurnal pollinators pollinate synergistically, with pollination contributions being additive in one year of our study. Our research identifies significant contributions to apple production provided by nocturnal pollinators, which may interact with diurnal pollinators in ways that are currently unrecognized. Expansions of this research into additional pollinator-dependent crops and focused investigations on specific nocturnal insects will provide more accurate assessments of nocturnal-pollinator roles in agriculture and improve our overall understanding of pollination in agriculture.

Network robustness and structure depend on the phenological characteristics of plants and pollinators

Many structural patterns have been found to be important for the stability and robustness of mutualistic plant-pollinator networks. These structural patterns are impacted by a suite of variables, including species traits, species abundances, their spatial configuration, and their phylogenetic history. Here, we consider a specific trait: phenology, or the timing of life history events. We expect that timing and duration of activity of pollinators, or of flowering in plants, could greatly affect the species' roles within networks in which they are embedded. Using plant-pollinator networks from 33 sites in southern British Columbia, Canada, we asked (a) how phenological species traits, specifically timing of first appearance in the network and duration of activity in a network, were related to species' roles within a network, and (b) how those traits affected network robustness to phenologically biased species loss. We found that long duration of activity increased connection within modules for both pollinators and plants and among modules for plants. We also found that date of first appearance was positively related to interaction strength asymmetry in plants but negatively related to pollinators. Networks were generally more robust to the loss of pollinators than plants, and robustness increased if the models allow new interactions to form when old ones are lost, constrained by overlapping phenology of plants and pollinators. Robustness declined with the loss of late-flowering plants, which tended to have higher interaction strength asymmetry. In addition, robustness declined with loss of early-flying or long-duration pollinators. These pollinators tended to be among-module connectors. Our results point to networks being limited by early-flying pollinators. If plants flower earlier due to climate change, plant fitness may decline as they will depend on early emerging pollinators, unless pollinators also emerge earlier.

Global effects of extreme temperatures on wild bumblebees

Climate plays a key role in shaping population trends and determining the geographic distribution of species because of limits in species' thermal tolerance. An evaluation of species tolerance to temperature change can therefore help predict their potential spatial shifts and population trends triggered by ongoing global warming. We assessed inter- and intraspecific variations in heat resistance in relation to body mass, local mean temperatures, and evolutionary relationships in 39 bumblebee species, a major group of pollinators in temperate and cold ecosystems, across 3 continents, 6 biomes, and 20 regions (2386 male specimens). Based on experimental bioassays, we measured the time before heat stupor of bumblebee males at a heatwave temperature of 40 °C. Interspecific variability was significant, in contrast to interpopulational variability, which was consistent with heat resistance being a species-specific trait. Moreover, cold-adapted species are much more sensitive to heat stress than temperate and Mediterranean species. Relative to their sensitivity to extreme temperatures, our results help explain recent population declines and range shifts in bumblebees following climate change.

Microplastic Polystyrene Ingestion Promotes the Susceptibility of Honeybee to Viral Infection

Microplastics (MPs) are an emerging threat to ecological conservation and biodiversity; however, little is known of the types and possible impacts of MPs in pollinators. To examine whether MPs were present in honeybees, we analyzed the honeybee samples collected in fields from six provinces in China. Four types MPs were identified in honeybee including polystyrene (PS) by Raman spectroscopic analysis, and these plastic polymers were detected in 66.7% bee samples. Then, we assessed the physical and biological impacts of PS of three sizes (0.5, 5, and 50 μm) on bees for 21 days. Next, we measured how the presence of PS affected the Israeli acute paralysis virus proliferation, a small RNA virus associated with bee colony decline. Experimental evidence showed that a large mass of PS was ingested and accumulated within the midgut and enhanced the susceptibility of bees to viral infection. Not only histological analysis showed that PS, especially 0.5 μm PS, damaged the midgut tissue and was subsequently transferred to the hemolymph, trachea, and Malpighian tubules, but also qPCR and transcriptomic results indicated that genes correlated with membrane lipid metabolism, immune response, detoxification, and the respiratory system were significantly regulated after PS ingestion. Our results highlight neglected MP contamination to the bees, a pollination ecosystem stressed by the anthropogenic pollution, and have implications for human health via ingestion of bee products.

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

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

Global patterns in bumble bee pollen collection show phylogenetic conservation of diet

Bumble bees (Bombus) are a group of eusocial bees with a strongly generalised feeding pattern, collecting pollen from many different botanical families. Though predominantly generalists, some bumble bee species seem to have restricted dietary choices. It is unclear whether restricted diets in bumble bees are inherent or a function of local conditions due to a lack of data for many species across different regions. The objective of this study was to determine whether bumble bee species displayed specific patterns of pollen collection, and whether patterns were influenced by phylogenetic relatedness or tongue length, a trait known to be associated with structuring floral visitation. Bumble bee pollen collection patterns were quantified from 4,132 pollen loads taken from 58 bumble bee species, representing 24% of the pollen-collecting diversity of this genus. Phylogenetic trait mapping showed a conserved pattern of dietary dissimilarity across species, but not for dietary breadth. Dietary dissimilarity was driven by collection of Fabaceae, with the most similar species collecting around 50%-60% of their diet from this botanical family. The proportion of the diet collected from Fabaceae also showed a conserved phylogenetic signal. Greater collection of Fabaceae was associated with longer tongue lengths, with shorter tongued species focusing on alternative botanical families. However, this result was largely driven by phylogenetic relatedness, not tongue length per se. These results demonstrate that, though generalists, bumble bees are still subject to dietary restrictions that constrain their foraging choices. These dietary constraints have implications for their persistence should their core resources decline in abundance.

An Evaluation of Habitat Uses and Their Implications for the Conservation of the Chinese Bumblebee Bombus pyrosoma (Hymenoptera: Apidae)

Bumblebees are important pollinators for many wild plants and crops. However, the bumblebee populations are seriously declining in many parts of the world. Hence, the bumblebee conservation strategy should be urgently addressed, and the species distribution modeling approach can effectively evaluate the potentially suitable areas for their conservation. Here, one of the most abundant and endemic species of bumblebee in China, Bombus pyrosoma, was selected to assess current and future climates’ influence on its distribution with MaxEnt. Nine high-resolution bioclimatic/environmental variables with high contribution rates and low correlations were used. Four of the nine bioclimatic/environmental variables, min temperature of the coldest month (bio_06), annual mean temperature (bio_01), precipitation of wettest month (bio_13) and radiation of warmest quarter (bio_26), were found to be the most critical factors influencing the distribution of B. pyrosoma. The modeling results showed that the areas with high and moderate suitability for B. pyrosoma covered 141,858 and 186,198 km2 under the current climate conditions. More than 85% of the sampling sites in 2019 were found to be suitable under the current scenario. Under the future A1B and A2 scenarios in 2050 and 2100, the areas with low and moderate suitability for B. pyrosoma increased. However, alarmingly, the high suitability areas decreased under the future A1B and A2 scenarios in 2050 and 2100. Furthermore, regions covering seven provinces of northern China were the most crucial for developing nature reserves for B. pyrosoma, with the following order of suitable areas: Gansu, Shanxi, Ningxia, Qinghai, Shaanxi, Hebei and Beijing. Our study highlights the impact of future climate changes on the distribution of B. pyrosoma, and conservation strategies should mitigate the threats posed by environmental changes, particularly in the current high suitability areas.

Metatranscriptome Analysis of Sympatric Bee Species Identifies Bee Virus Variants and a New Virus, Andrena-Associated Bee Virus-1

Bees are important plant pollinators in agricultural and natural ecosystems. High average annual losses of honey bee (Apis mellifera) colonies in some parts of the world, and regional population declines of some mining bee species (Andrena spp.), are attributed to multiple factors including habitat loss, lack of quality forage, insecticide exposure, and pathogens, including viruses. While research has primarily focused on viruses in honey bees, many of these viruses have a broad host range. It is therefore important to apply a community level approach in studying the epidemiology of bee viruses. We utilized high-throughput sequencing to evaluate viral diversity and viral sharing in sympatric, co-foraging bees in the context of habitat type. Variants of four common viruses (i.e., black queen cell virus, deformed wing virus, Lake Sinai virus 2, and Lake Sinai virus NE) were identified in honey bee and mining bee samples, and the high degree of nucleotide identity in the virus consensus sequences obtained from both taxa indicates virus sharing. We discovered a unique bipartite + ssRNA Tombo-like virus, Andrena-associated bee virus-1 (AnBV-1). AnBV-1 infects mining bees, honey bees, and primary honey bee pupal cells maintained in culture. AnBV-1 prevalence and abundance was greater in mining bees than in honey bees. Statistical modeling that examined the roles of ecological factors, including floral diversity and abundance, indicated that AnBV-1 infection prevalence in honey bees was greater in habitats with low floral diversity and abundance, and that interspecific virus transmission is strongly modulated by the floral community in the habitat. These results suggest that land management strategies that aim to enhance floral diversity and abundance may reduce AnBV-1 spread between co-foraging bees.

Validating Morphometrics with DNA Barcoding to Reliably Separate Three Cryptic Species of Bombus Cresson (Hymenoptera: Apidae)

Despite their large size and striking markings, the identification of bumble bees (Bombus spp.) is surprisingly difficult. This is particularly true for three North American sympatric species in the subgenus Pyrobombus that are often misidentified: B. sandersoni Franklin, B. vagans Smith B. perplexus Cresson. Traditionally, the identification of these cryptic species was based on observations of differences in hair coloration and pattern and qualitative comparisons of morphological characters including malar length. Unfortunately, these characteristics do not reliably separate these species. We present quantitative morphometric methods to separate these species based on the malar length to width ratio (MRL) and the ratios of the malar length to flagellar segments 1 (MR1) and 3 (MR3) for queens and workers, and validated our determinations based on DNA barcoding. All three measurements discriminated queens of B. sandersoni and B. vagans with 100% accuracy. For workers, we achieved 99% accuracy by combining both MR1 and MR3 measurements, and 100% accuracy differentiating workers using MRL. Moreover, measurements were highly repeatable within and among both experienced and inexperienced observers. Our results, validated by genetic evidence, demonstrate that malar measurements provide accurate identifications of B. vagans and B. sandersoni. There was considerable overlap in the measurements between B. perplexus and B. sandersoni. However, these species can usually be reliably separated by combining malar ratio measurements with other morphological features like hair color. The ability to identify bumble bees is key to monitoring the status and trends of their populations, and the methods we present here advance these efforts.

Landscape composition and local floral resources influence foraging behavior but not the size of Bombus impatiens Cresson (Hymenoptera: Apidae) workers

Bumble bee communities are strongly disrupted worldwide through the population decline of many species; a phenomenon that has been generally attributed to landscape modification, pesticide use, pathogens, and climate change. The mechanisms by which these causes act on bumble bee colonies are, however, likely to be complex and to involve many levels of organization spanning from the community down to the least understood individual level. Here, we assessed how the morphology, weight and foraging behavior of individual workers are affected by their surrounding landscape. We hypothesized that colonies established in landscapes showing high cover of intensive crops and low cover of flowering crops, as well as low amounts of local floral resources, would produce smaller workers, which would perform fewer foraging trips and collect pollen loads less constant in species composition. We tested these predictions with 80 colonies of commercially reared Bombus impatiens Cresson placed in 20 landscapes spanning a gradient of agricultural intensification in southern Québec, Canada. We estimated weekly rate at which workers entered and exited colonies and captured eight workers per colony over a period of 14 weeks during the spring and summer of 2016. Captured workers had their wing, thorax, head, tibia, and dry weight measured, as well as their pollen load extracted and identified to the lowest possible taxonomic level. We did not detect any effect of landscape habitat composition on worker morphology or body weight, but found that foraging activity decreased with intensive crops. Moreover, higher diversity of local floral resources led to lower pollen constancy in intensively cultivated landscapes. Finally, we found a negative correlation between the size of workers and the diversity of their pollen load. Our results provide additional evidence that conservation actions regarding pollinators in arable landscapes should be made at the landscape rather than at the farm level.

Rapid Gastrointestinal Passage May Protect Bombus terrestris from Becoming a True Host for Nosema ceranae

Pollination provided by managed honey bees as well as by all the wild bee species is a crucial ecosystem service contributing to the conservation of biodiversity and human food security. Therefore, it is not only the health status of honey bees but also the health status of wild bees that concerns us all. In this context, recent field studies suggesting interspecies transmission of the microsporidium parasite Nosema ceranae from honey bees (Apis mellifera) to bumblebees (Bombus spp.) were alarming. On the basis of these studies, N. ceranae was identified as an emerging infectious agent (EIA) of bumblebees, although knowledge of its impact on its new host was still elusive. In order to investigate the infectivity, virulence, and pathogenesis of N. ceranae infections in bumblebees, we performed controlled laboratory exposure bioassays with Bombus terrestris by orally inoculating the bees with infectious N. ceranae spores. We comprehensively analyzed the infection status of the bees via microscopic analysis of squash preparations, PCR-based detection of N. ceranae DNA, histology of Giemsa-stained tissue sections, and species-specific fluorescence in situ hybridization. We did not find any evidence for a true infection of bumblebees by N. ceranae Through a series of experiments, we ruled out the possibility that spore infectivity, spore dosage, incubation time, or age and source of the bumblebees caused these negative results. Instead, our results clearly demonstrate that no infection and production of new spores took place in bumblebees after they ingested N. ceranae spores in our experiments. Thus, our results question the classification of N. ceranae as an emerging infectious agent for bumblebees.IMPORTANCE Emerging infectious diseases (EIDs) pose a major health threat to both humans and animals. EIDs include, for instance, those that have spread into hitherto naive populations. Recently, the honey bee-specific microsporidium Nosema ceranae has been detected by molecular methods in field samples of bumblebees. This detection of N. ceranae DNA in bumblebees led to the assumption that N. ceranae infections represent an EID of bumblebees and resulted in speculations on the role of this pathogen in driving bumblebee declines. In order to address the issue of whether N. ceranae is an emerging infectious agent for bumblebees, we experimentally analyzed host susceptibility and pathogen reproduction in this new host-pathogen interaction. Surprisingly, we did not find any evidence for a true infection of Bombus terrestris by N. ceranae, questioning the classification of N. ceranae infections as EIDs of bumblebees and demonstrating that detection of microsporidian DNA does not equal detection of microsporidian infection.

Imidacloprid impairs performance on a model flower handling task in bumblebees (Bombus impatiens)

Bumblebees exposed to neonicotinoid pesticides collect less pollen on foraging trips. Exposed bumblebees are also slower to learn to handle flowers, which may account for reduced pollen collection. It is unclear, however, why neonicotinoid exposure slows learning to handle flowers. We investigated the effect of imidacloprid, a neonicotinoid pesticide, on bumblebee motor learning using a lab model of flower handling. Bumblebees learned to invert inside a narrow tube and lift a petal-shaped barrier to reach a reward chamber. Imidacloprid-exposed bumblebees showed a dose-dependent delay to solve the task, which resulted from reduced switching between behavioural strategies and a subsequent delay in use of the successful strategy. This effect was consistent in colonies exposed at 10 but not 2.6 ppb, suggesting a variable effect on individuals at lower doses. These results help to explain why exposed bumblebees are slow to learn to handle flowers and collect less pollen on foraging trips.

Brood parasitism in eusocial insects (Hymenoptera): role of host geographical range size and phylogeny

Interspecific brood parasitism is common in many animal systems. Brood parasites enter the nests of other species and divert host resources for producing their own offspring, which can lead to strong antagonistic parasite-host coevolution. Here, we look at commonalities among social insect species that are victims of brood parasites, and use phylogenetic data and information on geographical range size to predict which species are most probably to fall victims to brood parasites in the future. In our analyses, we focus on three eusocial hymenopteran groups and their brood parasites: (i) bumblebees, (ii) Myrmica ants, and (iii) vespine and polistine wasps. In these groups, some, but not all, species are parasitized by obligate workerless inquilines that only produce reproductive-caste descendants. We find phylogenetic signals for geographical range size and the presence of parasites in bumblebees, but not in ants and wasps. Phylogenetic logistic regressions indicate that the probability of being attacked by one or more brood parasite species increases with the size of the geographical range in bumblebees, but the effect is statistically only marginally significant in ants. However, non-phylogenetic logistic regressions suggest that bumblebee species with the largest geographical range sizes may have a lower likelihood of harbouring social parasites than do hosts with medium-sized ranges. Our results provide new insights into the ecology and evolution of host-social parasite systems, and indicate that host phylogeny and geographical range size can be used to predict threats posed by social parasites, as well to design efficient conservation measures for both hosts and their parasites. This article is part of the theme issue 'The coevolutionary biology of brood parasitism: from mechanism to pattern'.

Climate change contributes to widespread declines among bumble bees across continents

Climate change could increase species’ extinction risk as temperatures and precipitation begin to exceed species’ historically observed tolerances. Using long-term data for 66 bumble bee species across North America and Europe, we tested whether this mechanism altered likelihoods of bumble bee species’ extinction or colonization. Increasing frequency of hotter temperatures predicts species’ local extinction risk, chances of colonizing a new area, and changing species richness. Effects are independent of changing land uses. The method developed in this study permits spatially explicit predictions of climate change–related population extinction-colonization dynamics within species that explains observed patterns of geographical range loss and expansion across continents. Increasing frequencies of temperatures that exceed historically observed tolerances help explain widespread bumble bee species decline. This mechanism may also contribute to biodiversity loss more generally.

Global Trends in Bumble Bee Health

Bumble bees (Bombus) are unusually important pollinators, with approximately 260 wild species native to all biogeographic regions except sub-Saharan Africa, Australia, and New Zealand. As they are vitally important in natural ecosystems and to agricultural food production globally, the increase in reports of declining distribution and abundance over the past decade has led to an explosion of interest in bumble bee population decline. We summarize data on the threat status of wild bumble bee species across biogeographic regions, underscoring regions lacking assessment data. Focusing on data-rich studies, we also synthesize recent research on potential causes of population declines. There is evidence that habitat loss, changing climate, pathogen transmission, invasion of nonnative species, and pesticides, operating individually and in combination, negatively impact bumble bee health, and that effects may depend on species and locality. We distinguish between correlational and causal results, underscoring the importance of expanding experimental research beyond the study of two commercially available species to identify causal factors affecting the diversity of wild species.

Phylogenetic signals in pest abundance and distribution range of spider mites

Background

Attributes of pest species like host range are frequently reported as being evolutionarily constrained and showing phylogenetic signal. Because these attributes in turn could influence the abundance and impact of species, phylogenetic information could be useful in predicting the likely status of pests. In this study, we used regional (China) and global datasets to investigate phylogenetic patterns in occurrence patterns and host ranges of spider mites, which constitute a pest group of many cropping systems worldwide.

Results

We found significant phylogenetic signal in relative abundance and distribution range both at the regional and global scales. Relative abundance and range size of spider mites were positively correlated with host range, although these correlations became weaker after controlling for phylogeny.

Conclusions

The results suggest that pest impacts are evolutionarily constrained. Information that is easily obtainable – including the number of known hosts and phylogenetic position of the mites – could therefore be useful in predicting future pest risk of species.

Agriculturally dominated landscapes reduce bee phylogenetic diversity and pollination services

Land-use change threatens global biodiversity and may reshape the tree of life by favoring some lineages over others. Whether phylogenetic diversity loss compromises ecosystem service delivery remains unknown. We address this knowledge gap using extensive genomic, community, and crop datasets to examine relationships among land use, pollinator phylogenetic structure, and crop production. Pollinator communities in highly agricultural landscapes contain 230 million fewer years of evolutionary history; this loss was strongly associated with reduced crop yield and quality. Our study links landscape-mediated changes in the phylogenetic structure of natural communities to the disruption of ecosystem services. Measuring conservation success by species counts alone may fail to protect ecosystem functions and the full diversity of life from which they are derived.

A neonicotinoid pesticide impairs foraging, but not learning, in free-flying bumblebees

Neonicotinoids are widely-used pesticides implicated in the decline of bees, known to have sub-lethal effects on bees’ foraging and colony performance. One proposed mechanism for these negative effects is impairment to bees’ ability to learn floral associations. However, the effects of neonicotinoids on learning performance have largely been addressed using a single protocol, where immobilized bees learn an association based on a single sensory modality. We thus have an incomplete understanding of how these pesticides affect bee learning in more naturalistic foraging scenarios. We carried out the first free-foraging study into the effects of acute exposure of a neonicotinoid (imidacloprid) on bumblebees’ (Bombus impatiens) ability to learn associations with visual stimuli. We uncovered dose-dependent detrimental effects on motivation to initiate foraging, amount of nectar collected, and initiation of subsequent foraging bouts. However, we did not find any impairment to bees’ ability to learn visual associations. While not precluding the possibility that other forms of learning are impaired, our findings suggest that some of the major effects of acute neonicotinoid exposure on foraging performance may be due to motivational and/or sensory impairments. In light of these findings, we discuss more broadly how pesticide effects on pollinator cognition might be studied.

Climate change-driven range losses among bumblebee species are poised to accelerate

Climate change has shaped bee distributions over the past century. Here, we conducted the first species-specific assessment of future climate change impacts on North American bumblebee distributions, using the most recent global change scenarios developed in the Fifth Assessment Report of the Intergovernmental Panel on Climate Change (IPCC). We assessed potential shifts in bumblebee species distributions with models generated using Maxent. We tested different assumptions about bumblebee species’ dispersal capacities, drawing on observed patterns of range shifts to date, dispersal rates observed for bumblebee queens, and, lastly, assuming unlimited dispersal. Models show significant contractions of current ranges even under scenarios in which dispersal rates were high. Results suggest that dispersal rates may not suffice for bumblebees to track climate change as rapidly as required under any IPCC scenario for future climate change. Areas where species losses are projected overlap for many species and climate scenarios, and are concentrated in eastern parts of the continent. Models also show overlap for range expansions across many species, suggesting the presence of “hotspots” where management activities could benefit many species, across all climate scenarios. Broad-scale strategies are likely to be necessary to improve bumblebee conservation prospects under climate change.

Landscape predictors of pathogen prevalence and range contractions in US bumblebees

Several species of bumblebees have recently experienced range contractions and possible extinctions. While threats to bees are numerous, few analyses have attempted to understand the relative importance of multiple stressors. Such analyses are critical for prioritizing conservation strategies. Here, we describe a landscape analysis of factors predicted to cause bumblebee declines in the USA. We quantified 24 habitat, land-use and pesticide usage variables across 284 sampling locations, assessing which variables predicted pathogen prevalence and range contractions via machine learning model selection techniques. We found that greater usage of the fungicide chlorothalonil was the best predictor of pathogen (Nosema bombi) prevalence in four declining species of bumblebees. Nosema bombi has previously been found in greater prevalence in some declining US bumblebee species compared to stable species. Greater usage of total fungicides was the strongest predictor of range contractions in declining species, with bumblebees in the northern USA experiencing greater likelihood of loss from previously occupied areas. These results extend several recent laboratory and semi-field studies that have found surprising links between fungicide exposure and bee health. Specifically, our data suggest landscape-scale connections between fungicide usage, pathogen prevalence and declines of threatened and endangered bumblebees.

Pollinator decline - an ecological calamity in the making?

Since pollination by insects is vitally important for much of global crop production, and to provide pollination services more widely throughout the planetary ecosystems, the prospect of an imminent 'pollination crisis', due to a die-off of flying insects, is most disquieting, to say the least. Indeed, the term 'ecological Armageddon' has been used in the media. However, to know whether or not a wholesale decline in flying pollinators (including non-bee species) is occurring across the world is very difficult, due to an insufficiency of geographically widespread and long-term data. Bees, as the best documented species, can be seen to be suffering from chronic exposure to a range of stressors, which include: a loss of abundance and diversity of flowers, and a decline in suitable habitat for them to build nests; long-term exposure to agrochemicals, including pesticides such as neonicotinoids; and infection by parasites and pathogens, many inadvertently spread by the actions of humans. It is likely that climate change may impact further on particular pollinators, for example bumble bees, which are cool-climate specialists. Moreover, the co-operative element of various different stress factors should be noted; thus, for example, exposure to pesticides is known to diminish detoxification mechanisms and also immune responses, hence lowering the resistance of bees to parasitic infections. It is further conspicuous that for those wild non-bee insects - principally moths and butterflies - where data are available, the picture is also one of significant population losses. Alarmingly, a recent study in Germany indicated that a decline in the biomass of flying insects had occurred by 76% in less than three decades, as sampled in nature reserves across the country. Accordingly, to fully answer the question posed in the title of this article 'pollinator decline - an ecological calamity in the making?' will require many more detailed, more geographically encompassing, more species-inclusive, and longer-term studies, but the available evidence points to a clear 'probably', and the precautionary principle would suggest this is not a prospect we can afford to ignore.

A Nonlethal Method to Examine Non-Apis Bees for Mark-Capture Research

Studies of bee movement and activities across a landscape are important for developing an understanding of their behavior and their ability to withstand environmental stress. Recent research has shown that proteins, such as egg albumin, are effective for mass-marking bees. However, current protein mass-marking techniques require sacrificing individual bees during the data collection process. A nonlethal sampling method for protein mark-capture research is sorely needed, particularly for vulnerable, sensitive, or economically valuable species. This study describes a nonlethal sampling method, in which three non-Apis bee species (Bombus bifarius Cresson [Hymenoptera: Apidae], Osmia lignaria Say [Hymenoptera: Megachilidae], and Megachile rotundata Fabricius [Hymenoptera: Megachilidae]) were tested for a unique protein marker by immersing them momentarily in saline buffer and releasing them. Results showed that an egg albumin-specific enzyme-linked immunosorbent assay was 100% effective at detecting the protein on bees that were sampled nonlethally. Furthermore, this sampling method did not have an impact on bee survivorship, suggesting that immersing bees in buffer is a reliable and valid surrogate to traditional, destructive sampling methods for mark-capture bee studies.

Recently identified bee viruses and their impact on bee pollinators

Bees are agriculturally and ecologically important plant pollinators. Recent high annual losses of honey bee colonies, and reduced populations of native and wild bees in some geographic locations, may impact the availability of affordable food crops and the diversity and abundance of native and wild plant species. Multiple factors including viral infections affect pollinator health. The majority of well-characterized bee viruses are picorna-like RNA viruses, which may be maintained as covert infections or cause symptomatic infections or death. Next generation sequencing technologies have been utilized to identify additional bee-infecting viruses including the Lake Sinai viruses and Rhabdoviruses. In addition, sequence data is instrumental for defining specific viral strains and characterizing associated pathogenicity, such as the recent characterization of Deformed wing virus master variants (DWV-A, DWV-B, and DWV-C) and their impact on bee health.