Landscape heterogeneity predicts gene flow in a widespread polymorphic bumble bee, Bombus bifarius (Hymenoptera: Apidae)

Does coevolution in refugia drive mimicry in bumble bees? Insights from a South Asian mimicry group

Müllerian mimicry was proposed to be an example of a coevolved mutualism promoted by population isolation in glacial refugia. This, however, has not been well supported in butterfly models. Here, we use genomic data to test this theory while examining the population genetics behind mimetic diversification in a pair of co-mimetic bumble bees, Bombus breviceps Smith and Bombus trifasciatus Smith. In both lineages, populations were structured by geography but not as much by color pattern, suggesting sharing of color alleles across regions of restricted gene flow and formation of mimicry complexes in the absence of genetic differentiation. Demographic analyses showed mismatches between historical effective population size changes and glacial cycles, and niche modeling revealed only mild habitat retraction during glaciation. Moreover, mimetic subpopulations of the same color form in the two lineages only in some cases exhibit similar population history and genetic divergence. Therefore, the current study supports a more complex history in this comimicry than a simple refugium-coevolution model.

Biology, Genetic Diversity, and Conservation of Wild Bees in Tree Fruit Orchards

Different species of bees provide essential ecosystem services by pollinating various agricultural crops, including tree fruits. Many fruits and nuts depend on insect pollination, primarily by wild and managed bees. In different geographical regions where orchard crops are grown, fruit growers rely on wild bees in the farmscape and use orchard bees as alternative pollinators. Orchard crops such as apples, pears, plums, apricots, etc., are mass-flowering crops and attract many different bee species during their bloom period. Many bee species found in orchards emerge from overwintering as the fruit trees start flowering in spring, and the active duration of these bees aligns very closely with the blooming time of fruit trees. In addition, most of the bees in orchards are short-range foragers and tend to stay close to the fruit crops. However, the importance of orchard bee communities is not well understood, and many challenges in maintaining their populations remain. This comprehensive review paper summarizes the different types of bees commonly found in tree fruit orchards in the fruit-growing regions of the United States, their bio-ecology, and genetic diversity. Additionally, recommendations for the management of orchard bees, different strategies for protecting them from multiple stressors, and providing suitable on-farm nesting and floral resource habitats for propagation and conservation are discussed.

Maine's Bumble Bees (Hymenoptera: Apidae)-Part 2: Comparisons of a Common (Bombus ternarius) and a Rare (Bombus terricola) Species

As part of a quantitative survey of Maine's bumble bee fauna (Butler et al. 2021), we compared and contrasted genetic diversity, parasite and pathogen burdens, and pesticide exposure of the relatively common Bombus ternarius Say, 1937 and the spatially rare Bombus terricola Kirby, 1837. We recorded 11 Bombus species at 40 survey sites across three Maine ecoregions, and B. ternarius was the most common species, while B. terricola was spatially rare. Nonmetric multidimensional scaling indicated that B. terricola was associated with higher elevation sites in Maine, while B. ternarius was more broadly distributed in the state. Pollinator networks constructed for each bee indicated B. ternarius foraged on more plant species than B. terricola, but that there was considerable overlap (73%) in plant species visited. Genetic diversity was greater in the spatially restricted B. terricola, whereas the widely distributed B. ternarius was characterized by greater genetic differentiation among regions. Bombus terricola had higher molecular marker levels of the microsporidian fungi Nosema spp. and the trypanosome Crithidia spp., and both species had high levels of Trypanosoma spp. exposure. No Western Honey Bee (Apis mellifera, Linnaeus, 1758) viruses were detected in either species. Pesticides were not detected in pollen samples collected from workers of either species, and B. ternarius worker tissue samples exhibited only trace levels of diflubenzuron.

A genomic and morphometric analysis of alpine bumblebees: Ongoing reductions in tongue length but no clear genetic component

Over the last six decades, populations of the bumblebees Bombus sylvicola and Bombus balteatus in Colorado have experienced decreases in tongue length, a trait important for plant-pollinator mutualisms. It has been hypothesized that this observation reflects selection resulting from shifts in floral composition under climate change. Here we used morphometrics and population genomics to determine whether morphological change is ongoing, investigate the genetic basis of morphological variation, and analyse population structure in these populations. We generated a genome assembly of B. balteatus. We then analysed whole-genome sequencing data and morphometric measurements of 580 samples of both species from seven high-altitude localities. Out of 281 samples originally identified as B. sylvicola, 67 formed a separate genetic cluster comprising a newly-discovered cryptic species ("incognitus"). However, an absence of genetic structure within species suggests that gene flow is common between mountains. We found a significant decrease in tongue length between bees collected between 2012-2014 and in 2017, indicating that morphological shifts are ongoing. We did not discover any genetic associations with tongue length, but a SNP related to production of a proteolytic digestive enzyme was implicated in body size variation. We identified evidence of covariance between kinship and both tongue length and body size, which is suggestive of a genetic component of these traits, although it is possible that shared environmental effects between colonies are responsible. Our results provide evidence for ongoing modification of a morphological trait important for pollination and indicate that this trait probably has a complex genetic and environmental basis.

Ensemble evaluation of the potential risk areas of yellow-legged hornet distribution

Invasion of alien species facilitated by climate change and human assistant is one of global threats that cause irreversible damages on the local flora and fauna. One of these issued species, Vespa velutina nigrithorax du Buysson, 1905 (Hymenoptera:Vespidae), is a significant threat to entomofauna, including honeybees, in the introduced regions. This wasp is still expanding its habitats, prioritizing the development of a reliable species distribution model based on recently updated occurrence data. Therefore, the aim of this study was to evaluate the potential areas that are climatically exposed to V. v. nigrithorax invasion globally and in South Korea, where the wasp has caused severe damage to local ecosystems and apiculture after its recent introduction. We developed a new global scale ensemble model based on CLIMEX and Maxent models and applied it to South Korea using field survey data. As a result, risky areas were predicted to be temperate and subtropical climate regions, including the eastern USA, western Europe, Far East Asia, and small areas in South America and Australia. In particular, South Korea has a high potential risk throughout the country. We expect that this study would provide fundamental data for monitoring the environmental risks caused by V. v. nigrithorax using advanced species distribution modeling.

rasterdiv-An Information Theory tailored R package for measuring ecosystem heterogeneity from space: To the origin and back

Ecosystem heterogeneity has been widely recognized as a key ecological indicator of several ecological functions, diversity patterns and change, metapopulation dynamics, population connectivity or gene flow.In this paper, we present a new R package-rasterdiv-to calculate heterogeneity indices based on remotely sensed data. We also provide an ecological application at the landscape scale and demonstrate its power in revealing potentially hidden heterogeneity patterns.The rasterdiv package allows calculating multiple indices, robustly rooted in Information Theory, and based on reproducible open-source algorithms.

Conservation insights from wild bee genetic studies: Geographic differences, susceptibility to inbreeding, and signs of local adaptation

Conserving bees are critical both ecologically and economically. Genetic tools are valuable for monitoring these vital pollinators since tracking these small, fast-flying insects by traditional means is difficult. By surveying the current state of the literature, this review discusses how recent advances in landscape genetic and genomic research are elucidating how wild bees respond to anthropogenic threats. Current literature suggests that there may be geographic differences in the vulnerability of bee species to landscape changes. Populations of temperate bee species are becoming more isolated and more genetically depauperate as their landscape becomes more fragmented, but tropical bee species appear unaffected. These differences may be an artifact of historical differences in land-use, or it suggests that different management plans are needed for temperate and tropical bee species. Encouragingly, genetic studies on invasive bee species indicate that low levels of genetic diversity may not lead to rapid extinction in bees as once predicted. Additionally, next-generation sequencing has given researchers the power to identify potential genes under selection, which are likely critical to species' survival in their rapidly changing environment. While genetic studies provide insights into wild bee biology, more studies focusing on a greater phylogenetic and life-history breadth of species are needed. Therefore, caution should be taken when making broad conservation decisions based on the currently few species examined.

Bark beetle outbreak enhances biodiversity and foraging habitat of native bees in alpine landscapes of the southern Rocky Mountains

Landscape-scale bark beetle outbreaks alter forest structure with direct and indirect effects on plants and animals in forest ecosystems. Using alpine spruce forest and a native bee community as a study system, we tested how tree mortality from bark beetles impacts bee foraging habitats and populations. Bees were collected across the growing season (early-, middle-, and late-season) for two years using passive trapping methods, and collections were used to analyze patterns in species abundances and diversity. Three important findings emerged: (1) forest stands that were post-outbreak had 62% higher floral density and 68% more floral species during peak bloom, respectively, than non-affected stands; (2) bee captures were highest early-season (June) and were not strongly affected by bark beetle outbreak; however, mean number of bee species and Shannon–Weiner diversity were significantly higher in post-outbreak stands and this effect was pronounced early in the growing season. Corresponding analysis of β-diversity indicated higher accumulation of bee biodiversity in post-outbreak stands and a turnover in the ratio of Bombus: Osmia; (3) bee captures were linked to variation in foraging habitat, but number of bee species and diversity were more strongly predicted by forest structure. Our results provide evidence of increased alpine bee biodiversity in post-outbreak stands and increased availability of floral resources. We conclude that large-scale disturbance from bark beetle outbreaks may drive shifts in pollinator community composition through cascading effects on floral resources, mediated via mortality of overstory trees.

Pattern of population structuring between Belgian and Estonian bumblebees

Several population genetic studies investigated the extent of gene flow and population connectivity in bumblebees. In general, no restriction in gene flow is considered for mainland populations of common bumblebee species. Whether this assumption holds true for all species is not known. An assessment of bumblebee genetic structure in the context of their geographic distribution is needed to prioritize conservation and management needs. Here, we conducted a genetic study on seven bumblebee species occurring in Belgium and Estonia. Using 16 microsatellite markers, we investigated genetic diversity and population structuring in each species. This is the first study investigating population structuring of both declining and stable bumblebee species on both small and large geographic scales. Our results showed no or only low population structuring between the populations of the restricted and declining bumblebee species on both scales, while significant structuring was found for populations of the common species on the larger scale. The latter result, which may be due to human or environmental changes in the landscape, implies the need for the conservation of also widespread bumblebee species. Conservation strategies to improve gene flow and connectivity of populations could avoid the isolation and future losses of populations of these important species.

Circuit-theory applications to connectivity science and conservation

Conservation practitioners have long recognized ecological connectivity as a global priority for preserving biodiversity and ecosystem function. In the early years of conservation science, ecologists extended principles of island biogeography to assess connectivity based on source patch proximity and other metrics derived from binary maps of habitat. From 2006 to 2008, the late Brad McRae introduced circuit theory as an alternative approach to model gene flow and the dispersal or movement routes of organisms. He posited concepts and metrics from electrical circuit theory as a robust way to quantify movement across multiple possible paths in a landscape, not just a single least-cost path or corridor. Circuit theory offers many theoretical, conceptual, and practical linkages to conservation science. We reviewed 459 recent studies citing circuit theory or the open-source software Circuitscape. We focused on applications of circuit theory to the science and practice of connectivity conservation, including topics in landscape and population genetics, movement and dispersal paths of organisms, anthropogenic barriers to connectivity, fire behavior, water flow, and ecosystem services. Circuit theory is likely to have an effect on conservation science and practitioners through improved insights into landscape dynamics, animal movement, and habitat-use studies and through the development of new software tools for data analysis and visualization. The influence of circuit theory on conservation comes from the theoretical basis and elegance of the approach and the powerful collaborations and active user community that have emerged. Circuit theory provides a springboard for ecological understanding and will remain an important conservation tool for researchers and practitioners around the globe.

Characterizing bumble bee (Bombus) communities in the United States and assessing a conservation monitoring method

AIM

Bumble bees (Hymenoptera: Apidae: Bombus) are economically and ecologically important pollinators in agroecosystems and wildland habitats. In the Nearctic region, there are approximately 41 species, of which the IUCN lists twelve species as vulnerable, endangered, or critically endangered. We conducted a standardized faunal survey to inform ongoing conservation efforts including petitions under review for the Endangered Species Act. Furthermore, we test the appropriateness of a methodology for accurately sampling bumble bee communities.

LOCATION

The United States of America, including 31 sites in 15 states.

METHODS

We surveyed 15 states in the summer of 2015 to assess community composition and relative species abundance at agricultural and seminatural sites throughout the United States. We collected approximately 100 bees, using aerial nets, from each of 31 sites and identified specimens to species, totaling 3,252 bees. We assessed our survey methodology to understand whether it accurately sampled the potential community of bumble bees at each site for utility in future monitoring efforts.

RESULTS

Average site species richness was 5.1 ± 2.05, and we detected 30 of the 41 species documented historically within the contiguous United States. Sampling a site beyond 100 bees rarely added additional species detections, whereas adding additional sampling sites within an ecoregion frequently increased the species richness for the ecoregion. Thirteen of the 30 species we detected each accounted for <1% of the total fauna, and two species accounted for 49.02% of all bees captured. Species richness and evenness increased with increasing latitude across communities.

MAIN CONCLUSIONS

Species diversity and evenness in bumble bees increases in northern latitudes and increasing elevation in the United States; however, a few common species tend to dominate communities while many species occur only in low numbers. The results of this survey effort can inform current conservation evaluations and planning.

Quaternary climate instability is correlated with patterns of population genetic variability in Bombus huntii

Climate oscillations have left a significant impact on the patterns of genetic diversity observed in numerous taxa. In this study, we examine the effect of Quaternary climate instability on population genetic variability of a bumble bee pollinator species, Bombus huntii in western North America. Pleistocene and contemporary B. huntii habitat suitability (HS) was estimated with an environmental niche model (ENM) by associating 1,035 locality records with 10 bioclimatic variables. To estimate genetic variability, we genotyped 380 individuals from 33 localities at 13 microsatellite loci. Bayesian inference was used to examine population structure with and without a priori specification of geographic locality. We compared isolation by distance (IBD) and isolation by resistance (IBR) models to examine population differentiation within and among the Bayesian inferred genetic clusters. Furthermore, we tested for the effect of environmental niche stability (ENS) on population genetic diversity with linear regression. As predicted, high-latitude B. huntii habitats exhibit low ENS when compared to low-latitude habitats. Two major genetic clusters of B. huntii inhabit western North America: (a) a north genetic cluster predominantly distributed north of 28°N and (b) a south genetic cluster distributed south of 28°N. In the south genetic cluser, both IBD and IBR models are significant. However, in the north genetic cluster, IBD is significant but not IBR. Furthermore, the IBR models suggest that low-latitude montane populations are surrounded by habitat with low HS, possibly limiting dispersal, and ultimately gene flow between populations. Finally, we detected high genetic diversity across populations in regions that have been climatically unstable since the last glacial maximum (LGM), and low genetic diversity across populations in regions that have been climatically stable since the LGM. Understanding how species have responded to climate change has the potential to inform management and conservation decisions of both ecological and economic concerns.

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.

Genetic variations of DNA barcoding region of bumble bees (Hymenoptera: Apidae) from South Korea

We reassessed species diversity and genetic structure in Korean bumble bees using DNA barcode analyses of 484 cytochrome c oxidase subunit I (COI) sequences from 24 morphospecies. Based on COI, all of the Korean species formed distinct clades in the phylogenetic trees, except for Bombus (Megabombus) koreanus in the maximum likelihood tree. Five species exhibited low interspecific genetic distances (range: 1.2-2.7%), indicating that they are recently diverged species. COI data could not be used to identify bumble bees at the subspecies level. For the dominant species, most local populations in Korea were panmictic and were more closely related to continental populations than to allopatric populations. Furthermore, sympatric haplotypes within Korea could be distinguished. We detected B. (Megabombus) diversus in South Korea for the first time. Our results demonstrate that DNA barcoding is a useful technique for species recognition and for allopatric and sympatric haplotype detection in bumble bees.

Population genomics reveals a candidate gene involved in bumble bee pigmentation

Variation in bumble bee color patterns is well‐documented within and between species. Identifying the genetic mechanisms underlying such variation may be useful in revealing evolutionary forces shaping rapid phenotypic diversification. The widespread North American species Bombus bifarius exhibits regional variation in abdominal color forms, ranging from red‐banded to black‐banded phenotypes and including geographically and phenotypically intermediate forms. Identifying genomic regions linked to this variation has been complicated by strong, near species level, genome‐wide differentiation between red‐ and black‐banded forms. Here, we instead focus on the closely related black‐banded and intermediate forms that both belong to the subspecies B. bifarius nearcticus. We analyze an RNA sequencing (RNAseq) data set and identify a cluster of single nucleotide polymorphisms (SNPs) within one gene, Xanthine dehydrogenase/oxidase‐like, that exhibit highly unusual differentiation compared to the rest of the sequenced genome. Homologs of this gene contribute to pigmentation in other insects, and results thus represent a strong candidate for investigating the genetic basis of pigment variation in B. bifarius and other bumble bee mimicry complexes.

Landscape genetics of a pollinator longhorn beetle [Typocerus v. velutinus (Olivier)] on a continuous habitat surface

Landscape connectivity, the degree to which the landscape structure facilitates or impedes organismal movement and gene flow, is increasingly important to conservationists and land managers. Metrics for describing the undulating shape of continuous habitat surfaces can expand the usefulness of continuous gradient surfaces that describe habitat and predict the flow of organisms and genes. We adopted a landscape gradient model of habitat and used surface metrics of connectivity to model the genetic continuity between populations of the banded longhorn beetle [Typocerus v. velutinus (Olivier)] collected at 17 sites across a fragmentation gradient in Indiana, USA. We tested the hypothesis that greater habitat connectivity facilitates gene flow between beetle populations against a null model of isolation by distance (IBD). We used next-generation sequencing to develop 10 polymorphic microsatellite loci and genotype the individual beetles to assess the population genetic structure. Isolation by distance did not explain the population genetic structure. The surface metrics model of habitat connectivity explained the variance in genetic dissimilarities 30 times better than the IBD model. We conclude that surface metrology of habitat maps is a powerful extension of landscape genetics in heterogeneous landscapes.

Inter and intra-population phenotypic and genotypic structuring in the European whitefish Coregonus lavaretus, a rare freshwater fish in Scotland

This study revealed between-lake genetic structuring between Coregonus lavaretus collected from the only two native populations of this species in Scotland, U.K. (Lochs Eck and Lomond) evidenced by the existence of private alleles (12 in Lomond and four in Eck) and significant genetic differentiation (FST = 0·056) across 10 microsatellite markers. Juvenile C. lavaretus originating from eggs collected from the two lakes and reared in a common-garden experiment showed clear phenotypic differences in trophic morphology (i.e. head and body shape) between these populations indicating that these characteristics were, at least partly, inherited. Microsatellite analysis of adults collected from different geographic regions within Loch Lomond revealed detectable and statistically significant but relatively weak genetic structuring (FST = 0·001-0·024) and evidence of private alleles related to the basin structure of the lake. Within-lake genetic divergence patterns suggest three possibilities for this observed pattern: (1) differential selection pressures causing divergence into separate gene pools, (2) a collapse of two formerly divergent gene pools and (3) a stable state maintained by balancing selection forces resulting from spatial variation in selection and lake heterogeneity. Small estimates of effective population sizes for the populations in both lakes suggest that the capacity of both populations to adapt to future environmental change may be limited.

Population genomics of divergence among extreme and intermediate color forms in a polymorphic insect

Geographic variation in insect coloration is among the most intriguing examples of rapid phenotypic evolution and provides opportunities to study mechanisms of phenotypic change and diversification in closely related lineages. The bumble bee Bombus bifarius comprises two geographically disparate color groups characterized by red‐banded and black‐banded abdominal pigmentation, but with a range of spatially and phenotypically intermediate populations across western North America. Microsatellite analyses have revealed that B. bifarius in the USA are structured into two major groups concordant with geography and color pattern, but also suggest ongoing gene flow among regional populations. In this study, we better resolve the relationships among major color groups to better understand evolutionary mechanisms promoting and maintaining such polymorphism. We analyze >90,000 and >25,000 single‐nucleotide polymorphisms derived from transcriptome (RNAseq) and double digest restriction site associated DNA sequencing (ddRAD), respectively, in representative samples from spatial and color pattern extremes in B. bifarius as well as phenotypic and geographic intermediates. Both ddRAD and RNAseq data illustrate substantial genome‐wide differentiation of the red‐banded (eastern) color form from both black‐banded (western) and intermediate (central) phenotypes and negligible differentiation among the latter populations, with no obvious admixture among bees from the two major lineages. Results thus indicate much stronger background differentiation among B. bifarius lineages than expected, highlighting potential challenges for revealing loci underlying color polymorphism from population genetic data alone. These findings will have significance for resolving taxonomic confusion in this species and in future efforts to investigate color‐pattern evolution in B. bifarius and other polymorphic bumble bee species.

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.

Fine-scale spatial genetic structure of common and declining bumble bees across an agricultural landscape

Land-use changes have threatened populations of many insect pollinators, including bumble bees. Patterns of dispersal and gene flow are key determinants of species' ability to respond to land-use change, but have been little investigated at a fine scale (<10 km) in bumble bees. Using microsatellite markers, we determined the fine-scale spatial genetic structure of populations of four common Bombus species (B. terrestris, B. lapidarius, B. pascuorum and B. hortorum) and one declining species (B. ruderatus) in an agricultural landscape in Southern England, UK. The study landscape contained sown flower patches representing agri-environment options for pollinators. We found that, as expected, the B. ruderatus population was characterized by relatively low heterozygosity, number of alleles and colony density. Across all species, inbreeding was absent or present but weak (FIS  = 0.01-0.02). Using queen genotypes reconstructed from worker sibships and colony locations estimated from the positions of workers within these sibships, we found that significant isolation by distance was absent in B. lapidarius, B. hortorum and B. ruderatus. In B. terrestris and B. pascuorum, it was present but weak; for example, in these two species, expected relatedness of queens founding colonies 1 m apart was 0.02. These results show that bumble bee populations exhibit low levels of spatial genetic structure at fine spatial scales, most likely because of ongoing gene flow via widespread queen dispersal. In addition, the results demonstrate the potential for agri-environment scheme conservation measures to facilitate fine-scale gene flow by creating a more even distribution of suitable habitats across landscapes.