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.

Molecular tools and bumble bees: revealing hidden details of ecology and evolution in a model system.

Bumble bees are a longstanding model system for studies on behaviour, ecology and evolution, due to their well-studied social lifestyle, invaluable role as wild and managed pollinators, and ubiquity and diversity across temperate ecosystems. Yet despite their importance, many aspects of bumble bee biology have remained enigmatic until the rise of the genetic and, more recently, genomic eras. Here, we review and synthesize new insights into the ecology, evolution and behaviour of bumble bees that have been gained using modern genetic and genomic techniques. Special emphasis is placed on four areas of bumble bee biology: the evolution of eusociality in this group, population-level processes, large-scale evolutionary relationships and patterns, and immunity and resistance to pesticides. We close with a prospective on the future of bumble bee genomics research, as this rapidly advancing field has the potential to further revolutionize our understanding of bumble bees, particularly in regard to adaptation and resilience. Worldwide, many bumble bee populations are in decline. As such, throughout the review, connections are drawn between new molecular insights into bumble bees and our understanding of the causal factors involved in their decline. Ongoing and potential applications to bumble bee management and conservation are also included to demonstrate how genetics- and genomics-enabled research aids in the preservation of this threatened group.

Host specific social parasites (Psithyrus) indicate chemical recognition system in bumblebees.

Semiochemicals influence many aspects of insect behavior, including interactions between parasites and their hosts. We studied the chemical recognition system of bumblebees (Bombus) by examining the cuticular hydrocarbon cues of 14 species, including five species of social parasites, known as cuckoo bees (subgenus Psithyrus). We found that bumblebees possess species-specific alkene positional isomer profiles that are stable over large geographical regions and are mimicked by three host-specific cuckoo parasites. In three host-cuckoo associations where mimicry is poor, possibly due to recent host shifts, these cuckoos produce dodecyl acetate a known chemical repellent that allows the cuckoos to invade their host colonies. Our findings indicate cuckoos use two chemical mechanisms, mimicry and repellents, to invade their hosts, and this may reflect different stages of an ongoing dynamic arms race.

Contribution to the knowledge of the bumblebee fauna of Afghanistan (Hymenoptera, Apidae, Bombus Latreille).

Bumblebees (Hymenoptera: Apidae: genus Bombus Latreille, 1802) constitute an important group of pollinators for many wild plants and crops in north temperate regions and South America. Although knowledge of these insects has been increasing over the last decades, some geographic areas remain poorly studied and additions to the knowledge of their faunas are infrequent. Afghanistan is one example of a country that is currently underrepresented in the scientific literature despite its high species diversity. For this study, more than 420 new occurrence records were gathered for 17 bumblebee species belonging to all eight subgenera recorded in the country, including the first record of a species closely related to the B longipennis group. Additionally, the first standardized database for Afghan bees is launched, which we hope will be enriched in the future to allow further assessments of population trends for the bumblebees of Afghanistan. Finally, the previously published species records for the country are discussed considering the most recent taxonomic revisions of the genus and key perspectives are highlighted for further work in this understudied country and neighboring regions.

Prevalence of infection by the microsporidian Nosema spp. in native bumblebees (Bombus spp.) in northern Thailand.

Bumblebees (tribe Bombini, genus Bombus Latreille) play a pivotal role as pollinators in mountain regions for both native plants and for agricultural systems. In our survey of northern Thailand, four species of bumblebees (Bombus (Megabombus) montivagus Smith, B. (Alpigenobombus) breviceps Smith, B. (Orientalibombus) haemorrhoidalis Smith and B. (Melanobombus) eximius Smith), were present in 11 localities in 4 provinces (Chiang Mai, Mae Hong Son, Chiang Rai and Nan). We collected and screened 280 foraging worker bumblebees for microsporidia (Nosema spp.) and trypanosomes (Crithidia spp.). Our study is the first to demonstrate the parasite infection in bumblebees in northern Thailand. We found N. ceranae in B. montivagus (5.35%), B. haemorrhoidalis (4.76%), and B. breviceps (14.28%) and N. bombi in B. montivagus (14.28%), B. haemorrhoidalis (11.64%), and B. breviceps (28.257%).

Morphometric analysis of fossil bumble bees (Hymenoptera, Apidae, Bombini) reveals their taxonomic affinities.

Bumble bees (Bombus spp.) are a widespread corbiculate lineage (Apinae: Corbiculata: Bombini), mostly found among temperate and alpine ecosystems. Approximately 260 species have been recognized and grouped recently into a simplified system of 15 subgenera. Most of the species are nest-building and primitively eusocial. Species of Bombus have been more intensely studied than any other lineages of bees with the exception of the honey bees. However, most bumble bee fossils are poorly described and documented, making their placement relative to other Bombus uncertain. A large portion of the known and presumed bumble bee fossils were re-examined in an attempt to better understand their affinities with extant Bombini. The taxonomic affinities of fossil specimens were re-assessed based on morphological features and previous descriptions, and for 13 specimens based on geometric morphometrics of forewing shape. None of the specimens coming from Eocene and Oligocene deposits were assigned within the contemporary shape space of any subgenus of Bombus. It is shown that Calyptapis florissantensis Cockerell, 1906 (Eocene-Oligocene boundary, Florissant shale, Colorado, USA) and Oligobombus cuspidatus Antropov, 2014 (Late Eocene, Bembridge Marls) likely belong to stem-group Bombini. Bombus anacolus Zhang, 1994, B. dilectus Zhang, 1994, B. luianus Zhang, 1990 (Middle Miocene, Shanwang Formation), as well as B. vetustus Rasnitsyn & Michener, 1991 (Miocene, Botchi Formation) are considered as species inquirenda. In the Miocene, affinities of fossils with derived subgenera of Bombus s. l. increased, and some are included in the shape space of contemporary subgenera: Cullumanobombus (i.e., B. pristinus Unger, 1867, B. randeckensis Wappler & Engel, 2012, and B. trophonius Prokop, Dehon, Michez & Engel, 2017), Melanobombus (i.e., B. cerdanyensis Dehon, De Meulemeester & Engel, 2014), and Mendacibombus (i.e., B. beskonakensis (Nel & Petrulevicius, 2003), new combination), agreeing with previous estimates of diversification.

The arctic and alpine bumblebees of the subgenus Alpinobombus revised from integrative assessment of species' gene coalescents and morphology (Hymenoptera, Apidae, Bombus).

The bumblebees of the subgenus Alpinobombus of the genus Bombus are unusual among bees for specialising in many of the most northerly vegetated arctic habitats on Earth. Most named taxa in this group (37 available names from a total of 67 names) were described originally from differences in the colour patterns of the hair. Previous revisions have shown unusually little agreement, recognising a range of 6‒9 species, in part because of pronounced intraspecific variation in both skeletal morphology and in the colour patterns of the hair. Here we examine variation among 4622 specimens from throughout the group's global range. Bayesian inference of the gene tree for the fast evolving mitochondrial COI gene combined with Poisson-tree-process analysis of this tree shows support for 10 gene lineages as candidates for being putative species lineages. Integrative assessment shows that the interpretation of these results is not straightforward. Evidence from the fast evolving mitochondrial 16S ribosomal RNA gene supports two of the COI gene alleles (from the samples B. kluanensis s. str. and 'unnamed2') as being associated with just one 16S allele. Double COI bands on the PCR gels for these individuals and double peaks on sequence traces (in one case with both COI alleles sequenced from one individual) identifies this as a likely case of COI paralogy that has resulted in mitochondrial heteroplasmy. Evidence from morphology also supports only the remaining nine lineages as separate. Evidence from extracts of cephalic labial gland secretions (CLGS, with components believed to function as sex pheromones) reported by others shows small diagnostic differences between all of the candidate species examined (although B. kluanensis s. l. was not examined) and shows larger differences between all of the species pairs that we find are likely to have co-occurred at least in the past, revealing a likely limitation to the CLGS approach in cases of recent and continuously allopatric species. Consequently we infer nine species in the subgenus Alpinobombus (so that B. kluanensis s. str. and 'unnamed2' are interpreted as conspecific, as B. kluanensis s. l.). We provide distribution maps and identification keys for the nine species. The morphology of the male of B. kluanensis is described for the first time, including a unique, unusually dense pad of short hair on the mandible that may have a function involving CLGS in mate-searching behaviour. In seeking to identify the valid names for these species, seven new lectotypes are designated and support is provided for synonymizing 10 names as proposed in a recent summary table of names. The prevailing usage of Bombus balteatus Dahlbom is maintained as valid by proposing Bombus nivalis Dahlbom and Bombus tricolor Dahlbom as nomina oblita and by proposing Bombus balteatus Dahlbom as a nomen protectum. The prevailing usage of Bombus hyperboreus Schönherr is maintained as valid by supporting Apis arctica Quensel as a nomen oblitum and by supporting Bombus hyperboreus Schönherr as a nomen protectum. We then use sequence data from COI and 16S together with nuclear PEPCK and opsin genes to estimate dated phylogenetic relationships among the nine species, allowing for incongruent gene trees with *BEAST. If crown-group divergence within the subgenus Alpinobombus coincided with the global climate cooling and with the growth of the northern ice sheets at the end of the Miocene at ca 7.2 Ma, then divergences between each of the three pairs of sister species are likely to have coincided with fluctuations in vegetated land connections across the Bering Strait after ca 2.5 Ma.

Early-diverging bumblebees from across the roof of the world: the high-mountain subgenus Mendacibombus revised from species' gene coalescents and morphology (Hymenoptera, Apidae).

The bumblebees of the subgenus Mendacibombus of the genus Bombus are the sister group to all other extant bumblebees and are unusual among bees for specialising in some of the highest elevation habitats with entomophilous plants on Earth. Most named taxa in this group (24 available names, from a total of 49 published names) were described originally from small differences in the colour pattern of the hair, many as parts (e.g. subspecies) of just one species. Subsequent taxonomic treatments recognised multiple species, but have described very few morphological characters, most of which are in the male genitalia. We examined 4413 specimens representing all of the named taxa from throughout the group's global range to describe variation in DNA, in skeletal morphology, and in the colour patterns of the hair. Using Bayesian inference of the phylogeny from an evolutionary model for the fast-evolving COI gene, and fitting either general mixed Yule/coalescent models or Poisson tree process models, we identify COI gene coalescents, which are expected to characterise species as evolutionarily independent lineages. None of the conditions most likely to compromise this interpretation (biased sampling, paralogy, introgression, heteroplasmy, incomplete lineage sorting) appears to be a substantial problem in this case. In an integrative analysis, we show that colour patterns are often variable within these groups and do not diagnose the same groups as we recognise from genes; in contrast, the groups recognised from gene coalescents can also be diagnosed from differences we identify in morphology. We infer that the 12 groups with coalescents in the COI gene that are corroborated by morphology constitute species, whereas many of these species are polymorphic in colour pattern. Lectotypes are designated for 15 taxa in order to reduce uncertainty in the identity and application of the names. We provide new morphological keys and distribution maps for the species. Then we use four genes (fast-evolving mitochondrial COI and 16S; and slower nuclear PEPCK and opsin) to obtain an absolute chronogram of phylogenetic relationships among the species. From published estimates that the most recent common ancestor of the subgenus Mendacibombus diverged from the other bumblebees at the beginning of the Oligocene, our results support the crown group of Mendacibombus as having diversified in the late Miocene, events that both appear to have been associated with periods of climate cooling. Relative conservatism in the alpine/subalpine climate niche of Mendacibombus, as compared with the much more diversified climate niches in the sister group of all other bumblebees, may have contributed to constraining the number of Mendacibombus species to just one twentieth of the total number of extant bumblebee species.

Extreme food-plant specialisation in Megabombus bumblebees as a product of long tongues combined with short nesting seasons.

Megabombus bumblebees have unusually long tongues and are generally more specialised than other bumblebees in their choice of food plants. The phylogeny of Megabombus bumblebees shows that speciation was concentrated in two periods. Speciation in the first period (ca 4.25-1.5 Ma) is associated with the late rise of the Hengduan Mountains at the eastern end of the Qinghai-Tibetan plateau. Speciation in the second period (1.2-0.3 Ma) is associated with climatic cooling in the northern forests. The most extreme food-specialist species belong to the second period, which may point to climate as a factor in specialisation. These extreme specialist species occur either in the far north (Bombus consobrinus), or at high elevations (Bombus gerstaeckeri), in situations where long tongues coincide with the shortest nesting seasons. Species with the longest tongues but occurring further south (even at high elevations) use a broader range of food plants.

Genes Suggest Ancestral Colour Polymorphisms Are Shared across Morphologically Cryptic Species in Arctic Bumblebees.

Our grasp of biodiversity is fine-tuned through the process of revisionary taxonomy. If species do exist in nature and can be discovered with available techniques, then we expect these revisions to converge on broadly shared interpretations of species. But for the primarily arctic bumblebees of the subgenus Alpinobombus of the genus Bombus, revisions by some of the most experienced specialists are unusual for bumblebees in that they have all reached different conclusions on the number of species present. Recent revisions based on skeletal morphology have concluded that there are from four to six species, while variation in colour pattern of the hair raised questions as to whether at least seven species might be present. Even more species are supported if we accept the recent move away from viewing species as morphotypes to viewing them instead as evolutionarily independent lineages (EILs) using data from genes. EILs are recognised here in practice from the gene coalescents that provide direct evidence for their evolutionary independence. We show from fitting both general mixed Yule/coalescent (GMYC) models and Poisson-tree-process (PTP) models to data for the mitochondrial COI gene that there is support for nine species in the subgenus Alpinobombus. Examination of the more slowly evolving nuclear PEPCK gene shows further support for a previously unrecognised taxon as a new species in northwestern North America. The three pairs of the most morphologically similar sister species are separated allopatrically and prevented from interbreeding by oceans. We also find that most of the species show multiple shared colour patterns, giving the appearance of mimicry among parts of the different species. However, reconstructing ancestral colour-pattern states shows that speciation is likely to have cut across widespread ancestral polymorphisms, without or largely without convergence. In the particular case of Alpinobombus, morphological, colour-pattern, and genetic groups show little agreement, which may help to explain the lack of agreement among previous taxonomic revisions.

Managed bumblebees outperform honeybees in increasing peach fruit set in China: different limiting processes with different pollinators.

Peach Prunus persica (L.) Batsch is self-compatible and largely self-fertile, but under greenhouse conditions pollinators must be introduced to achieve good fruit set and quality. Because little work has been done to assess the effectiveness of different pollinators on peach trees under greenhouse conditions, we studied 'Okubo' peach in greenhouse tunnels near Beijing between 2012 and 2014. We measured pollen deposition, pollen-tube growth rates, ovary development, and initial fruit set after the flowers were visited by either of two managed pollinators: bumblebees, Bombus patagiatus Nylander, and honeybees, Apis mellifera L. The results show that B. patagiatus is more effective than A. mellifera as a pollinator of peach in greenhouses because of differences in two processes. First, B. patagiatus deposits more pollen grains on peach stigmas than A. mellifera, both during a single visit and during a whole day of open pollination. Second, there are differences in the fertilization performance of the pollen deposited. Half of the flowers visited by B. patagiatus are fertilized 9-11 days after bee visits, while for flowers visited by A. mellifera, half are fertilized 13-15 days after bee visits. Consequently, fruit development is also accelerated by bumblebees, showing that the different pollinators have not only different pollination efficiency, but also influence the subsequent time course of fertilization and fruit set. Flowers visited by B. patagiatus show faster ovary growth and ultimately these flowers produce more fruit. Our work shows that pollinators may influence fruit production beyond the amount of pollen delivered. We show that managed indigenous bumblebees significantly outperform introduced honeybees in increasing peach initial fruit set under greenhouse conditions.

Mathematical modeling of positron emission tomography (PET) data to assess radiofluoride transport in living plants following petiolar administration.

BACKGROUND: Ion transport is a fundamental physiological process that can be studied non-invasively in living plants with radiotracer imaging methods. Fluoride is a known phytotoxic pollutant and understanding its transport in plants after leaf absorption is of interest to those in agricultural areas near industrial sources of airborne fluoride. Here we report the novel use of a commercial, high-resolution, animal positron emission tomography (PET) scanner to trace a bolus of [(18)F]fluoride administered via bisected petioles of Brassica oleracea, an established model species, to simulate whole plant uptake of atmospheric fluoride. This methodology allows for the first time mathematical compartmental modeling of fluoride transport in the living plant. Radiotracer kinetics in the stem were described with a single-parameter free- and trapped-compartment model and mean arrival times at different stem positions were calculated from the free-compartment time-activity curves. RESULTS: After initiation of administration at the bisected leaf stalk, [(18)F] radioactivity climbed for approximately 10 minutes followed by rapid washout from the stem and equilibration within leaves. Kinetic modeling of transport in the stem yielded a trapping rate of 1.5 +/- 0.3%/min (mean +/- s.d., n = 3), velocity of 2.2 +/- 1.1 cm/min, and trapping fraction of 0.8 +/- 0.5%/cm. CONCLUSION: Quantitative assessment of physiologically meaningful transport parameters of fluoride in living plants is possible using standard positron emission tomography in combination with petiolar radiotracer administration. Movement of free fluoride was observed to be consistent with bulk flow in xylem, namely a rapid and linear change in position with respect to time. Trapping, likely in the apoplast, was observed. Future applications of the methods described here include studies of transport of other ions and molecules of interest in plant physiology.

Dynamics of extinction and the selection of nature reserves.

Familiar quantitative reserve-selection techniques are tailored to simple decision problems, where the representation of species is sought at minimum cost. However, conservationists have begun to ask whether representing species in reserve networks is sufficient to avoid local extinctions within selected areas. An attractive, but previously untested idea is to model current species' probabilities of occurrence as an estimate of local persistence in the near future. Using distribution data for passerine birds in Great Britain, we show that (i) species' probabilities of occurrence are negatively related to local probabilities of extinction, at least when a particular 20-year period is considered, and (ii) local extinctions can be reduced if areas are selected to maximize current species' probabilities of occurrence We suggest that more extinctions could be avoided if even a simple treatment of persistence were to be incorporated within reserve selection methods.

Assessment of Genetic Variation Among Leptosphaeria maculans Isolates Using Pathogenicity Data and AFLP Analysis.

Increased production of rapeseed in the north central and southeastern regions of the United States has been accompanied by an increase in the incidence of blackleg disease caused by Leptosphaeria maculans. In order to assess the genetic variability and relatedness of isolates from these regions to others from around the world, we analyzed 49 aggressive isolates representing three pathogenicity groups (PG2, 3, and 4) of L. maculans from North Dakota, Georgia, Ontario, Western Canada, the United Kingdom (UK), France, Germany, and Australia using pathogenicity data and amplified fragment length polymorphism (AFLP). Approximately 10% of the 400 amplified fragments were polymorphic, scored as discrete characters and analyzed by cluster analysis. The isolates from North Dakota, Western Canada, Georgia, and PHW1252 from the UK formed one tightly clustered group and were mostly of the same pathogenicity group; whereas isolates from Ontario, Australia, France, Germany, and the remaining isolates from the UK formed a second group, which exhibited greater variation and consisted of three pathogenicity groups. The similarity between North Dakota isolates collected in 1995-96 and Western Canadian isolates collected in the 1980s suggests that L. maculans was introduced into North Dakota from Western Canada, and that the populations have remained relatively unchanged over the past 10 years.

Beyond Punnett squares: Student word association and explanations of phenotypic variation through an integrative quantitative genetics unit investigating anthocyanin inheritance and expression in Brassica rapa Fast plants.

Genetics instruction in introductory biology is often confined to Mendelian genetics and avoids the complexities of variation in quantitative traits. Given the driving question "What determines variation in phenotype (Pv)? (Pv=Genotypic variation Gv + environmental variation Ev)," we developed a 4-wk unit for an inquiry-based laboratory course focused on the inheritance and expression of a quantitative trait in varying environments. We utilized Brassica rapa Fast Plants as a model organism to study variation in the phenotype anthocyanin pigment intensity. As an initial curriculum assessment, we used free word association to examine students' cognitive structures before and after the unit and explanations in students' final research posters with particular focus on variation (Pv = Gv + Ev). Comparison of pre- and postunit word frequency revealed a shift in words and a pattern of co-occurring concepts indicative of change in cognitive structure, with particular focus on "variation" as a proposed threshold concept and primary goal for students' explanations. Given review of 53 posters, we found ∼50% of students capable of intermediate to high-level explanations combining both Gv and Ev influence on expression of anthocyanin intensity (Pv). While far from "plug and play," this conceptually rich, inquiry-based unit holds promise for effective integration of quantitative and Mendelian genetics.

The bumblebees of North China (Apidae, Bombus Latreille).

Bumblebees are important pollinators for wild flowers and agricultural crops. North China is a region of varied geomorphology and vegetation, with plateaus, plains, mountains and deserts, and is part of the greatest hotspot of bumblebee diversity worldwide. We report on a field survey of the bumblebees of North China made between 2005-2012. A sample of 21,636 bumblebee specimens are assigned to 76 species. One older specimen held in London added one more species to this list. Together, these 77 species represent 10 subgenera of the genus Bombus. Seven species are recorded from North China for the first time: B. (St.) distinguendus, B. (Th.) anachoreta, B. (Th.) pseudobaicalensis, B. (Th.) exil, B. (Ps.) campestris, B. (Pr.) infirmus and B. (Ag.) validus. We provide identification keys for both males and females, photographs of the common colour patterns, and distribution maps for all species. We describe variation in local species richness and abundance, and list the food plants used by bumblebees in North China. The most abundant 10 bumblebee species are: B. (Ml.) pyrosoma, B. (Bo.) lantschouensis, B. (Bo.) patagiatus, B. (St.) melanurus, B. (Sb.) sibiricus, B. (Bo.) ignitus, B. (Th.) hedini, B. (Pr.) picipes, B. (Mg.) trifasciatus and B. (Mg.) longipes. Bumblebees are distributed widely within North China, from low elevations near the edge of the North-China plain to high elevations at the edge of the east Qinghai-Tibetan plateau (65-4011 m). The highest species richness is found in meadows of the high elevation east Qinghai-Tibetan plateau and in forests of the Qilianshan mountains in southwestern Gansu. The 337 food plant species recorded here belong to 49 families, showing that bumblebees play an important role in interconnecting agricultural and natural ecosystems in North China. 

Cryptic bumblebee species: consequences for conservation and the trade in greenhouse pollinators.

Commercial greenhouse growers in both Japan and China are increasingly using reared orange-tailed bumblebees known previously as Bombus hypocrita Pérez as pollinators. Phylogenetic analysis of the DNA (COI) barcodes with Bayesian methods shows that this "species" is a long-standing confusion of two cryptic species. We find that the orange-tailed bumblebees in North China are actually part of the widespread Russian (otherwise white-tailed) B. patagiatus Nylander (as B. patagiatus ganjsuensis Skorikov, n. comb.), whereas the orange-tailed bees in Japan are true B. hypocrita. This situation has been further complicated because two other cryptic species from North China that were previously confused with the Russian B. patagiatus are now recognised as separate: B. lantschouensis Vogt n. stat. and B. minshanensis Bischoff n. stat.. As demand for pollination services by greenhouse growers inevitably increases, these bees are more likely to be transported between countries. In order to conserve genetic resources of pollinator species for their option value for future food security, we advocate preventing trade and movement of B. patagiatus from China into Japan and of B. hypocrita from Japan into China.