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

Genetic differentiation and adaptive evolution of buff-tailed bumblebees in Asia

Bumblebees are important pollinating insects, so their declines resulting from environmental change have received intensive attention. Understanding how environmental factors shape the genetic structure of natural populations and identifying the genetic basis of local adaptation will provide insights into how bumblebees cope with environmental change. The buff-tailed bumblebee (Bombus terrestris) has a wide natural distribution range and has been domesticated to produce commercial colonies for greenhouse pollination. Previous population genetics studies on B. terrestris have mainly focused on its European populations; however, its Asian populations, representing the eastern side of its natural distribution, remain largely unsampled. To fill this gap, we collected wild B. terrestris samples from Asia, as well as wild B. terrestris samples from Europe and samples from domesticated colonies. We conducted whole-genome resequencing for 77 collected B. terrestris and performed population genomics analysis. Our results indicate that distinct genetic differentiation (FST = 0.076) exists between B. terrestris in Europe and Asia, with substantial morphological and physiological differences detected between them; B. terrestris in Asia should represent a distinct genetic resource. Demographic analysis suggests that the effective population size of B. terrestris has increased during historic cold periods, indicating their cold-adapted characteristics. Selective sweep analysis identified 331 genes under selection in the genomes of Asian B. terrestris, likely involved in their adaptation to the high ultraviolet radiation, low temperature and low precipitation of their habitats. Our research provides insights into the population genetic structure and genetic basis of local adaptation in the buff-tailed bumblebee, which will be useful for its conservation and management.

Cytogenetics of insects in the era of chromosome-level genome assemblies

Over the past few years, a revolution has occurred in cytogenetics, driven by the emergence and spread of methods for obtaining high-quality chromosome-level genome assemblies. In fact, this has led to a new tool for studying chromosomes and chromosomal rearrangements, and this tool is thousands of times more powerful than light microscopy. This tool has revolutionized the cytogenetics of many groups of insects for which previously karyotype information, if available at all, was limited to the chromosome number. Even more impressive are the achievements of the genomic approach for studying the general patterns of chromosome organization and evolution in insects. Thus, it has been shown that rapid transformations of chromosomal numbers, which are often found in the order Lepidoptera, are most often carried out in the most parsimonious way, as a result of simple fusions and fissions of chromosomes. It has been established that these fusions and fissions are not random and occur independently in different phylogenetic lineages due to the reuse of the same ancestral chromosomal breakpoints. It has been shown that the tendency for chromosome fissions is correlated with the presence in chromosomes of the so-called interstitial telomeres, i. e. telomere-like structures located not at the ends of chromosomes, but inside them. It has been revealed that, in most insects, telomeric DNA is not just a set of short repeats, but a very long sequence consisting of (TTAGG)n (or other telomeric motifs), regularly and specifically interrupted by retrotransposons, and the telomeric motifs are diverse in terms of their length and nucleotide composition. The number of high-quality chromosome-level genome assemblies available for insects in the GenBank database is growing exponentially and now exceeds a thousand species. Therefore, the exceptional prospects for using genomic data for karyotype analysis are beyond doubt.

Localized Tissue-Specific Gene Expression and Gene Duplications are Important Sources of Social Morph Differences in a Social Bumblebee

Understanding the expression of multiple behaviorally and morphologically distinct phenotypes from a single genome represents a fundamental topic in evolutionary biology. Central to the complication of expressing phenotypes, which may differ in their optima, is the sharing of largely the same genome, which is predicted to manifest in conflict at the genomic level. This is particularly true for social insects where molecular mechanisms, such as differential gene expression, contribute to observed phenotypic differences between reproductive and nonreproductive morphs. In comparison, other mechanisms, such as tissue-specific expression and gene duplications, have been posited as contributing to social morph differences yet formal investigations are limited. Here, using a combination of transcriptomics for multiple tissues and comparative genomics, we show that in a social bumblebee, the strongest differences in gene expression are found in reproductive tissues, such as the spermatheca, an organ previously believed as vestigial in workers but recently shown as functional. In comparison, we find modest expression differences in genes between queens and workers for the brain, fat body, and ovary, which are traditionally investigated in social evolution. Interestingly, morph-biased genes in these three tissues display higher tissue-specificity suggesting that while social morphs may express a shared core transcriptome, localized expression profiles may contribute to phenotypic differences. We also find evidence of differential usage of duplicated genes by queens and workers, highlighting structural variants as a contributing factor to morph differences. Collectively, our findings highlight how social insects can utilize tissue-specific gene regulation and structural variants to contribute to phenotypic differences.

Adapting to change: bee pollinator signatures in anthropized environments

Bees are essential pollinators for wild, ornamental, and agricultural plants, but human activities have disrupted their habitats, threatening their persistence. Although bees face numerous challenges in habitats heavily modified by human activities, certain species persist and thrive there. This review synthesizes recent literature on two types of traits that help bees survive in human-modified environments: preadaptive traits, which evolved before these environments existed, and adaptive traits, which have evolved in response to new conditions. This review highlights our limited understanding of adaptive traits and examines how trait combinations, including those influenced by epigenetics, contribute to bees' success in these altered habitats. Additionally, we discuss the promising use of genomic tools to reveal signatures of adaptation in these important pollinators.

Bumble bee gut microbial community structure differs between species and commercial suppliers, but metabolic potential remains largely consistent

Bumble bees are key pollinators for natural and agricultural plant communities. Their health and performance are supported by a core gut microbiota composed of a few bacterial taxa. However, the taxonomic composition and community structure of bumble bee gut microbiotas can vary with bee species, environment, and origin (i.e., whether colonies come from the wild or a commercial rearing facility), and it is unclear whether metabolic capabilities therefore vary as well. Here we used metagenomic sequencing to examine gut microbiota community composition, structure, and metabolic potential across bumble bees from two different commercial Bombus impatiens suppliers, wild B. impatiens, and three other wild bumble bee species sampled from sites within the native range of all four species. We found that the community structure of gut microbiotas varied between bumble bee species, between populations from different origins within species, and between commercial suppliers. Notably, we found that Apibacter is consistently present in some wild bumble bee species-suggesting it may be a previously unrecognized core phylotype of bumble bees-and that commercial B. impatiens colonies can lack core phylotypes consistently found in wild populations. However, despite variation in community structure, the high-level metabolic potential of gut microbiotas was largely consistent across all hosts, including for metabolic capabilities related to host performance, though metabolic activity remains to be investigated.IMPORTANCEOur study is the first to compare genome-level taxonomic structure and metabolic potential of whole bumble bee gut microbiotas between commercial suppliers and between commercial and wild populations. In addition, we profiled the full gut microbiotas of three wild bumble bee species for the first time. Overall, our results provide new insight into bumble bee gut microbiota community structure and function and will help researchers evaluate how well studies conducted in one bumble bee population will translate to other populations and species. Research on taxonomic and metabolic variation in bumble bee gut microbiotas across species and origins is of increasing relevance as we continue to discover new ways that social bee gut microbiotas influence host health, and as some bumble bee species decline in range and abundance.

The genome sequence of the Large Red Tailed Bumble Bee, Bombus lapidarius (Linnaeus, 1758)

We present a genome assembly from an individual female specimen of Bombus lapidarius (Large Red Tailed Bumble Bee; Arthropoda; Insecta; Hymenoptera; Apidae). The genome sequence has a total length of 368.50 megabases. Most of the assembly (81.04%) is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 28.11 kilobases in length.

Chromosome-level genome of Osmia excavata (Hymenoptera: Megachilidae) provides insights into low-temperature tolerance of Osmia pollinator

The solitary bee Osmia excavata (Hymenoptera: Megachilidae) is a key pollinator managed on a large scale. It has been widely used for commercial pollination of fruit trees, vegetables, and other crops with high efficiency in increasing the crop seeding rate, yield, and seed quality in Northern hemisphere. Here, a high-quality chromosome-level genome of O. excavata was generated using PacBio sequencing along with Hi-C technology. The genome size was 207.02 Mb, of which 90.25% of assembled sequences were anchored to 16 chromosomes with a contig N50 of 9,485 kb. Approximately 186.83 Mb, accounting for 27.93% of the genome, was identified as repeat sequences. The genome comprises 12,259 protein-coding genes, 96.24% of which were functionally annotated. Comparative genomics analysis suggested that the common ancestor of O. excavata and Osmia bicornis (Hymenoptera: Megachilidae) lived 8.54 million years ago. Furthermore, cytochrome P450 family might be involved in the responses of O. excavata to low-temperature stress. Taken together, the chromosome-level genome assembly of O. excavata provides in-depth knowledge and will be a helpful resource for the pollination biology research.

The Genomic Landscape, Causes, and Consequences of Extensive Phylogenomic Discordance in Murine Rodents

A species tree is a central concept in evolutionary biology whereby a single branching phylogeny reflects relationships among species. However, the phylogenies of different genomic regions often differ from the species tree. Although tree discordance is widespread in phylogenomic studies, we still lack a clear understanding of how variation in phylogenetic patterns is shaped by genome biology or the extent to which discordance may compromise comparative studies. We characterized patterns of phylogenomic discordance across the murine rodents-a large and ecologically diverse group that gave rise to the laboratory mouse and rat model systems. Combining recently published linked-read genome assemblies for seven murine species with other available rodent genomes, we first used ultraconserved elements (UCEs) to infer a robust time-calibrated species tree. We then used whole genomes to examine finer-scale patterns of discordance across ∼12 million years of divergence. We found that proximate chromosomal regions tended to have more similar phylogenetic histories. There was no clear relationship between local tree similarity and recombination rates in house mice, but we did observe a correlation between recombination rates and average similarity to the species tree. We also detected a strong influence of linked selection whereby purifying selection at UCEs led to appreciably less discordance. Finally, we show that assuming a single species tree can result in substantial deviation from the results with gene trees when testing for positive selection under different models. Collectively, our results highlight the complex relationship between phylogenetic inference and genome biology and underscore how failure to account for this complexity can mislead comparative genomic studies.

Building a reliable 16S mini-barcode library of wild bees from Occitania, south-west of France

Background

DNA barcoding and metabarcoding are now powerful tools for studying biodiversity and especially the accurate identification of large sample collections belonging to diverse taxonomic groups. Their success depends largely on the taxonomic resolution of the DNA sequences used as barcodes and on the reliability of the reference databases. For wild bees, the barcode sequences coverage is consistently growing in volume, but some incorrect species annotations need to be cared for. The COI (Cytochrome Oxydase subunit 1) gene, the most used in barcoding/metabarcoding of arthropods, suffers from primer bias and difficulties for covering all wild bee species using the classical Folmer primers.

New information

We present here a curated database for a 250 bp mini-barcode region of the 16S rRNA gene, suitable for low-cost metabarcoding wild bees in applications, such as eDNA analysis or for sequencing ancient or degraded DNA. Sequenced specimens were captured in Occitania (south-west of France) and morphologically identified by entomologists, with a total of 530 individuals belonging to 171 species and 19 genera. A customised workflow including distance-tree inferences and a second round of entomologist observations, when necessary, was used for the validation of 348 mini-barcodes covering 148 species. Amongst them, 93 species did not have any 16S reference barcode available before our contribution. This high-quality reference library data are freely available to the scientific community, with the aim of facilitating future large-scale characterisation of wild bee communities in a context of pollinators' decline.

The nuclear and mitochondrial genomes of the bellicose bumblebee (Bombus bellicosus, Hymenoptera: Apidae), a threatened pollinator in a changing South American landscape

We present the first genome of a Brazilian bumblebee species, the bellicose bumblebee (Bombus bellicosus). This is an endemic species in southern South America facing local extinction due to habitat loss and climate change. During the COVID-19 social distancing in Brazil, we launched a citizen science initiative via social media to locate remaining bellicose bumblebee populations, leading to the collection of a specimen for genome sequencing. Analysis of the novel genome revealed lower genetic diversity in the bellicose bumblebee compared to a widespread related species (Bombus pascuorum). However, the absence of extensive runs of homozygosity indicated a lack of recent inbreeding, offering a promising perspective for the conservation of this species. Furthermore, demographic history analysis indicates population expansion during past glacial periods, in contrast to Palearctic bumblebees that suffered a stark decline during glaciations. Our findings provide invaluable information for the conservation of this species and for further studies about its biology and evolution, particularly under a scenario of rapid environmental change.

Cuticular Hydrocarbon Profiles of Himalayan Bumble Bees (Hymenoptera: Bombus Latreille) are Species-Specific and Show Elevational Variation

Bumble bees are important pollinators in natural environments and agricultural farmlands, and they are in particular adapted to harsh environments like high mountain habitats. In these environments, animals are exposed to low temperature and face the risk of desiccation. The Eastern Himalayas are one of the recognized biodiversity hotspots worldwide. The area covers subtropical rainforest with warm temperature and high precipitation as well as high mountain ranges with peaks reaching up to 7,000 m, shaping a diverse floral and faunal community at the different elevational zones. To identify possible adaptation strategies, we investigated the cuticular hydrocarbon profiles of four bumble bee species occurring at different elevational ranges in Arunachal Pradesh, the northeastern most state in India. At 17 locations along an elevational gradient, we collected workers of two species from lower elevations (B. albopleuralis and B. breviceps; ~ 100 m - 3,000 m asl) and two species from higher elevations (B. prshewalskyi and B. mirus; ~ 2,800 m - 4,500 m asl). The CHC profiles of all four species showed a significant degree of variation in the composition of hydrocarbons, indicating species specificity. We also found clear correlation with elevation. The weighted mean chain length of the hydrocarbons significantly differed between the low and high elevation species, and the proportion of saturated hydrocarbons in CHC profiles significantly increased with the elevational range of the bumble bee species. Our results indicate that bumble bees living at high elevations reduce the risk of water loss by adapting their CHC composition on their cuticle, a phenomenon that has also been found in other insects like ants and fruit flies.

Phylogenomic insights into the worldwide evolutionary relationships of the stingless bees (Apidae, Meliponini)

Stingless bees (tribe Meliponini) are remarkable for their characteristically large social colonies, their capacity to produce honey and other useful products, and their morphological and behavioral diversity. They have a disjunct pan-tropical distribution, primarily occurring in warm and humid environments in the Neotropical, Afrotropical, and Indo-Australasian regions. Even though phylogenetic hypotheses have been proposed for Meliponini based on morphology and molecular data, many questions are still unsolved regarding the evolutionary relationships and systematics of the tribe. In this contribution, we present a large phylogenomic dataset comprising over 2500 ultra-conserved element (UCE) loci sequenced for 153 species of Meliponini, representing all known genera of stingless bees. The genera Camargoia, Paratrigonoides, Plectoplebeia, Cleptotrigona, Ebaiotrigona, Papuatrigona, Pariotrigona, Platytrigona, and Sahulotrigona were included in molecular phylogenetic analyses for the first time. Concatenated and species-tree analyses were performed using different partitioning strategies and summary methods. We performed gene-genealogy interrogation (GGI) on several recalcitrant nodes to resolve discordances among recovered tree topologies. Results were mostly consistent among analyses, recovering three main lineages of Meliponini congruent with the biogeographic domains to which they are associated. Within major clades, discordances were found in relation to previous works. The genus Frieseomelitta was recovered as paraphyletic in relation to Trichotrigona, and the genus Lepidotrigona was revealed to be composed of two independent lineages. Even though concatenated and weighted ASTRAL analyses were mostly effective in recovering the relationships favored by GGI, they retrieved different results in relation to the phylogenetic placements of Oxytrigona and Cephalotrigona. The most favored hypothesis in GGI analyses was not found in any other analyses, being more congruent with morphological evidence and highlighting the relevance of exploring the support given to alternative hypotheses through topological tests. Recent advances in our capacity to generate molecular sequences from old specimens using modern sequencing methods allowed for unparalleled sampling across genera, yielding a backbone for the phylogenetic relationships of stingless bees, which will further investigations into their systematics and evolution.

Genome assembly of an endemic butterfly (Minois Aurata) shed light on the genetic mechanisms underlying ecological adaptation to arid valley habitat

BACKGROUND

The Hengduan Mountains, one of the global biodiversity hotspots with exceptional species richness and high endemism, contains numerous arid valleys that create a distinctive geographical and ecological landscape. However, the adaptive evolutionary mechanisms of organism in the arid valley remain poorly understood. Minois aurata, an endemic butterfly species found exclusively in the arid valley of the upper Minjiang River, represents an attractive model system for studying adaptive evolutionary mechanisms to arid valley environments.

RESULTS

Here, we present the first chromosome-level genome assembly for Minois aurata, with a total size of approximately 609.17 Mb, and a scaffold N50 size of 23.88 Mb. These scaffolds were further clustered and anchored onto 29 chromosomes based on Hi-C data. A total of 16,163 protein-coding genes were predicted, of which 91.83% were functionally annotated. The expansion of transposable elements (TEs) accounts for the relatively large genome size of M. aurata, potentially aiding its adaptation to environmental conditions. Phylogenomic analyses based on 3,785 single-copy genes revealed that M. aurata is most closely related to Hipparchia semele. Further mitochondrial genome analysis of four Minois species placed M. aurata in a basal position within the genus, supporting it as an independent species. A total of 185 rapidly evolving and 232 specific gene families were identified in M. aurata. Functional enrichment analysis indicated that these gene families were mainly associated with ultraviolet radiation, heat and hypoxia responses. We also identified 234 positive selected genes in M. aurata, some of which are related to compound eye photoreceptor development, osmotic stress, and light stimulus response. Demographic analysis indicated that the effective population size of M. aurata decreased around 0.4 and 0.04 million years ago, respectively, coinciding with the localized sub-glaciation.

CONCLUSION

The chromosome-level genome offers a comprehensive genomic basis for understanding the evolutionary and adaptive strategies of Minois aurata in the unique arid valley environment of the Hengduan Mountains, while also providing valuable insights into the broader mechanisms of organism adaptation to such habitats.

Perception, regulation, and effects on longevity of pollen fatty acids in the honey bee, Apis mellifera

For successful cross-pollination, most flowering plants rely on insects as pollinators and attract them by offering rewards, predominantly nectar and pollen. Bees-a highly important pollinator group-are especially dependent on pollen as their main source of essential nutrients, including proteins, lipids, and sterols. Fatty acids (FAs) in particular play a pivotal role as fundamental energy source, contributing to membrane structure integrity, cellular homeostasis, and cognitive processes. However, overconsumption of FAs can have detrimental effects on fitness and survival. Thus, bees need to precisely modulate FA intake. To better understand how Apis mellifera, the globally predominant managed pollinator, regulate FA intake, we conducted controlled feeding experiments with newly hatched honey bee workers by providing pollen with different FA concentrations. We additionally investigated the honey bee's capacity to perceive individual FAs by means of chemotactile proboscis extension response (PER) conditioning. We tested both natural concentrations and concentrations exceeding those typically found in pollen. Given the dose-dependent importance of FAs observed in other bee species, we hypothesized that (i) a high FA concentration in pollen would reduce honey bee longevity, and (ii) honey bees are able to perceive individual FAs and differentiate between different FA concentrations via antennal sensation prior to consumption. Our study revealed that elevated FA concentrations in pollen resulted in reduced consumption rates and increased mortality in Apis mellifera. Workers can detect and discriminate between saturated and unsaturated FAs utilizing their antennae. Moreover, they were able to distinguish between individual FAs and also between different concentrations of the same FAs. Our results suggest a high sensitivity of A. mellifera towards both the concentration and composition of individual FAs, which greatly impacts their foraging decisions and fitness. These insights contribute to the growing evidence highlighting the importance of balanced nutrient ratios, in particular of FAs, for bees and other organisms.

New genomic resources inform transcriptomic responses to heavy metal toxins in the common Eastern bumble bee Bombus impatiens

BACKGROUND

The common Eastern bumble bee Bombus impatiens is native to North America and is the main commercially reared pollinator in the Americas. There has been extensive research on this species related to its social biology, applied pollination, and genetics. The genome of this species was previously sequenced using short-read technology, but recent technological advances provide an opportunity for substantial improvements. This species is common in agricultural and urban environments, and heavy metal contaminants produced by industrial processes can negatively impact it. To begin to identify possible mechanisms underlying responses to these toxins, we used RNA-sequencing to examine how exposure to a cocktail of four heavy metals at field-realistic levels from industrial areas affected B. impatiens worker gene expression.

RESULTS

PacBio long-read sequencing resulted in 544x coverage of the genome, and HiC technology was used to map chromatin contacts. Using Juicer and manual curation, the genome was scaffolded into 18 main pseudomolecules, representing a high quality, chromosome-level assembly. The sequenced genome size is 266.6 Mb and BRAKER3 annotation produced 13,938 annotated genes. The genome and annotation show high completeness, with ≥ 96% of conserved Eukaryota and Hymenoptera genes present in both the assembly and annotated genes. RNA sequencing of heavy metal exposed workers revealed 603 brain and 34 fat body differentially expressed genes. In the brain, differentially expressed genes had biological functions related to chaperone activity and protein folding.

CONCLUSIONS

Our data represent a large improvement in genomic resources for this important model species-with 10% more genome coverage than previously available, and a high-quality assembly into 18 chromosomes, the expected karyotype for this species. The new gene annotation added 777 new genes. Altered gene expression in response to heavy metal exposure suggests a possible mechanism for how these urban toxins are negatively impacting bee health, specifically by altering protein folding in the brain. Overall, these data are useful as a general high quality genomic resource for this species, and provide insight into mechanisms underlying tissue-specific toxicological responses of bumble bees to heavy metals.

The Meaning and Measure of Concordance Factors in Phylogenomics

As phylogenomic datasets have grown in size, researchers have developed new ways to measure biological variation and to assess statistical support for specific branches. Larger datasets have more sites and loci and therefore less sampling variance. While we can more accurately measure the mean signal in these datasets, lower sampling variance is often reflected in uniformly high measures of branch support-such as the bootstrap and posterior probability-limiting their utility. Larger datasets have also revealed substantial biological variation in the topologies found across individual loci, such that the single species tree inferred by most phylogenetic methods represents a limited summary of the data for many purposes. In contrast to measures of statistical support, the degree of underlying topological variation among loci should be approximately constant regardless of the size of the dataset. "Concordance factors" (CFs) and similar statistics have therefore become increasingly important tools in phylogenetics. In this review, we explain why CFs should be thought of as descriptors of topological variation rather than as measures of statistical support, and argue that they provide important information about the predictive power of the species tree not contained in measures of support. We review a growing suite of statistics for measuring concordance, compare them in a common framework that reveals their interrelationships, and demonstrate how to calculate them using an example from birds. We also discuss how measures of topological variation might change in the future as we move beyond estimating a single "tree of life" toward estimating the myriad evolutionary histories underlying genomic variation.

Examining the Effects of Environment, Geography, and Elevation on Patterns of DNA Methylation Across Populations of Two Widespread Bumble Bee Species

Understanding the myriad avenues through which spatial and environmental factors shape evolution is a major focus in biological research. From a molecular perspective, much work has been focused on genomic sequence variation; however, recently there has been increased interest in how epigenetic variation may be shaped by different variables across the landscape. DNA methylation has been of particular interest given that it is dynamic and can alter gene expression, potentially offering a path for a rapid response to environmental change. We utilized whole genome enzymatic methyl sequencing to evaluate the distribution of CpG methylation across the genome and to analyze patterns of spatial and environmental association in the methylomes of two broadly distributed montane bumble bees (Bombus vancouverensis Cresson and Bombus vosnesenskii Radoszkowski) across elevational gradients in the western US. Methylation patterns in both species are similar at the genomic scale with ∼1% of CpGs being methylated and most methylation being found in exons. At the landscape scale, neither species exhibited strong spatial or population structuring in patterns of methylation, although some weak relationships between methylation and distance or environmental variables were detected. Differential methylation analysis suggests a stronger environment association in B. vancouverensis given the larger number of differentially methylated CpG's compared to B. vosnesenskii. We also observed only a handful of genes with both differentially methylated CpGs and previously detected environmentally associated outlier SNPs. Overall results reveal a weak but present pattern in variation in methylation over the landscape in both species.

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.

Tracking Existing Factors Directly Affecting the Reproduction of Bumblebees: Current Knowledge

Bumblebees are primary social insects and a vital class of pollinating insects. Their distinctive reproductive mode is characterized by the independent initiation and construction of the nest by the queen and the subsequent production of sufficient workers, males, and gynes following colony development. After successful mating, the queen transitions to the first phase of its annual life cycle. The reproductive processes are directly influenced by environmental factors, including floral resources and pesticides. Moreover, the reproductive level is regulated by biological factors, particularly the role of workers, who participate in egg laying and pass on their genetic material to the next generation of queens. Successful reproduction can only be achieved by maintaining colony development under natural or artificial breeding conditions. Consequently, understanding the known factors that influence bumblebee reproduction is essential for developing conservation strategies for wild bumblebees and for successfully breeding diverse bumblebee species. Breeding various bumblebee species is crucial for in-depth research into known factors and for further exploration of other potential factors, which will also help to meet the demand for pollination in agricultural facilities globally.

Chromosome-Level Assembly and Annotation of the Genome of the Endangered Giant Patagonian Bumble Bee Bombus dahlbomii

This article describes a genome assembly and annotation for Bombus dahlbomii, the giant Patagonian bumble bee. DNA from a single, haploid male collected in Argentina was used for PacBio (HiFi) sequencing, and Hi-C technology was then used to map chromatin contacts. Using Juicer and manual curation, the genome was scaffolded into 18 main pseudomolecules, representing a high-quality, near chromosome-level assembly. The sequenced genome size is estimated at 265 Mb. The genome was annotated based on RNA sequencing data of another male from Argentina, and BRAKER3 produced 15,767 annotated genes. The genome and annotation show high completeness, with >95% BUSCO scores for both the genome and annotated genes (based on conserved genes from Hymenoptera). This genome provides a valuable resource for studying the biology of this iconic and endangered species, as well as for understanding the impacts of its decline and designing strategies for its preservation.

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.

Bumblebee Foraging Dynamics and Pollination Outcomes for Cherry Tomato and Pear Varieties in Northern China

Bumblebees (Bombus terrestris) have strong environmental adaptability and high pollen transfer efficiency, making them well-suited pollinators of economic crops. However, bumblebee pollination is still not widely applied in northern China due to the lack of data on foraging behavior and pollination effects. We conducted a three-year experiment involving cherry tomatoes (Solanum lycopersicum L.) and pears (Pyrus spp.) treated with bumblebee pollination to evaluate the foraging behavior and pollination effects on these two crops. Results showed that B. terrestris had enhanced foraging activities as daytime temperatures rose from 18 °C to 26 °C, as indicated by the increased number of bees leaving the hive and returning bees carrying pollen in greenhouses in winter. There were two peaks in the foraging activity of bumblebees in pear orchards in early spring, which was closely related to the temperature change in the daytime. Undoubtedly, cherry tomatoes treated with B. terrestris had higher fruit setting rate, weight, seed number, and fruit yields compared to those with hormone 2,4-dichlorophenoxyacetic acid treatments, as well as a lower rate of deformed fruits. B. terrestris pollination can significantly increase the fruit setting rate and fruit yield of pears, compared with open pollination, and can fully achieve the effect of hand pollination. B. terrestris pollination can improve cultivation efficiency, increase yield, and produce more economic benefits. Moreover, it can also contribute to reducing hormone residues and ensure the safety of agricultural products. We recommend its application to cherry tomatoes in greenhouses in winter and potential application to pears in orchards in early spring in northern China. However, the risk to local bumblebee species of introducing commercially available bumblebees into orchards should be considered and evaluated in future research. This study provides both empirical support and a theoretical basis for the selection of bumblebees as pollinators in the production of economically important crops and the improvement of crop cultivation management in northern China.

The adaptation of bumblebees to extremely high elevation associated with their gut microbiota

Bumblebees are among the most abundant and important pollinators for sub-alpine and alpine flowering plant species in the Northern Hemisphere, but little is known about their adaptations to high elevations. In this article, we focused on two bumblebee species, Bombus friseanus and Bombus prshewalskyi, and their respective gut microbiota. The two species, distributed through the Hengduan Mountains of southwestern China, show species replacement at different elevations. We performed genome sequencing based on 20 worker bee samples of each species. Applying evolutionary population genetics and metagenomic approaches, we detected genes under selection and analyzed functional pathways between bumblebees and their gut microbes. We found clear genetic differentiation between the two host species and significant differences in their microbiota. Species replacement occurred in both hosts and their bacteria (Snodgrassella) with an increase in elevation. These extremely high-elevation bumblebees show evidence of positive selection related to diverse biological processes. Positively selected genes involved in host immune systems probably contributed to gut microbiota changes, while the butyrate generated by gut microbiota may influence both host energy metabolism and immune systems. This suggests a close association between the genomes of the host species and their microbiomes based on some degree of natural selection.IMPORTANCETwo closely related and dominant bumblebee species, distributed at different elevations through the Hengduan Mountains of southwestern China, showed a clear genomic signature of adaptation to elevation at the molecular level and significant differences in their respective microbiota. Species replacement occurred in both hosts and their bacteria (Snodgrassella) with an increase in elevation. Bumblebees' adaptations to higher elevations are closely associated with their gut microbiota through two biological processes: energy metabolism and immune response. Information allowing us to understand the adaptive mechanisms of species to extreme conditions is implicit if we are to conserve them as their environments change.

DrosOMA: the Drosophila Orthologous Matrix browser

Background

Comparative genomic analyses to delineate gene evolutionary histories inform the understanding of organismal biology by characterising gene and gene family origins, trajectories, and dynamics, as well as enabling the tracing of speciation, duplication, and loss events, and facilitating the transfer of gene functional information across species. Genomic data are available for an increasing number of species from the genus Drosophila, however, a dedicated resource exploiting these data to provide the research community with browsable results from genus-wide orthology delineation has been lacking.

Methods

Using the OMA Orthologous Matrix orthology inference approach and browser deployment framework, we catalogued orthologues across a selected set of Drosophila species with high-quality annotated genomes. We developed and deployed a dedicated instance of the OMA browser to facilitate intuitive exploration, visualisation, and downloading of the genus-wide orthology delineation results.

Results

DrosOMA - the Drosophila Orthologous Matrix browser, accessible from https://drosoma.dcsr.unil.ch/ - presents the results of orthology delineation for 36 drosophilids from across the genus and four outgroup dipterans. It enables querying and browsing of the orthology data through a feature-rich web interface, with gene-view, orthologous group-view, and genome-view pages, including comprehensive gene name and identifier cross-references together with available functional annotations and protein domain architectures, as well as tools to visualise local and global synteny conservation.

Conclusions

The DrosOMA browser demonstrates the deployability of the OMA browser framework for building user-friendly orthology databases with dense sampling of a selected taxonomic group. It provides the Drosophila research community with a tailored resource of browsable results from genus-wide orthology delineation.

Genetic Modification of a Hox Locus Drives Mimetic Color Pattern Variation in a Highly Polymorphic Bumble Bee

Müllerian mimicry provides natural replicates ideal for exploring mechanisms underlying adaptive phenotypic divergence and convergence, yet the genetic mechanisms underlying mimetic variation remain largely unknown. The current study investigates the genetic basis of mimetic color pattern variation in a highly polymorphic bumble bee, Bombus breviceps (Hymenoptera, Apidae). In South Asia, this species and multiple comimetic species converge onto local Müllerian mimicry patterns by shifting the abdominal setal color from orange to black. Genetic crossing between the orange and black phenotypes suggested the color dimorphism being controlled by a single Mendelian locus, with the orange allele being dominant over black. Genome-wide association suggests that a locus at the intergenic region between 2 abdominal fate-determining Hox genes, abd-A and Abd-B, is associated with the color change. This locus is therefore in the same intergenic region but not the same exact locus as found to drive red black midabdominal variation in a distantly related bumble bee species, Bombus melanopygus. Gene expression analysis and RNA interferences suggest that differential expression of an intergenic long noncoding RNA between abd-A and Abd-B at the onset setal color differentiation may drive the orange black color variation by causing a homeotic shift late in development. Analysis of this same color locus in comimetic species reveals no sequence association with the same color shift, suggesting that mimetic convergence is achieved through distinct genetic routes. Our study establishes Hox regions as genomic hotspots for color pattern evolution in bumble bees and demonstrates how pleiotropic developmental loci can drive adaptive radiations in nature.

Influence of social lifestyles on host-microbe symbioses in the bees

Microbiomes are increasingly recognised as critical for the health of an organism. In eusocial insect societies, frequent social interactions allow for high-fidelity transmission of microbes across generations, leading to closer host-microbe coevolution. The microbial communities of bees with other social lifestyles are less studied, and few comparisons have been made between taxa that vary in social structure. To address this gap, we leveraged a cloud-computing resource and publicly available transcriptomic data to conduct a survey of microbial diversity in bee samples from a variety of social lifestyles and taxa. We consistently recover the core microbes of well-studied corbiculate bees, supporting this method's ability to accurately characterise microbial communities. We find that the bacterial communities of bees are influenced by host location, phylogeny and social lifestyle, although no clear effect was found for fungal or viral microbial communities. Bee genera with more complex societies tend to harbour more diverse microbes, with Wolbachia detected more commonly in solitary tribes. We present a description of the microbiota of Euglossine bees and find that they do not share the "corbiculate core" microbiome. Notably, we find that bacteria with known anti-pathogenic properties are present across social bee genera, suggesting that symbioses that enhance host immunity are important with higher sociality. Our approach provides an inexpensive means of exploring microbiomes of a given taxa and identifying avenues for further research. These findings contribute to our understanding of the relationships between bees and their associated microbial communities, highlighting the importance of considering microbiome dynamics in investigations of bee health.

Prevalent bee venom genes evolved before the aculeate stinger and eusociality

BACKGROUND

Venoms, which have evolved numerous times in animals, are ideal models of convergent trait evolution. However, detailed genomic studies of toxin-encoding genes exist for only a few animal groups. The hyper-diverse hymenopteran insects are the most speciose venomous clade, but investigation of the origin of their venom genes has been largely neglected.

RESULTS

Utilizing a combination of genomic and proteo-transcriptomic data, we investigated the origin of 11 toxin genes in 29 published and 3 new hymenopteran genomes and compiled an up-to-date list of prevalent bee venom proteins. Observed patterns indicate that bee venom genes predominantly originate through single gene co-option with gene duplication contributing to subsequent diversification.

CONCLUSIONS

Most Hymenoptera venom genes are shared by all members of the clade and only melittin and the new venom protein family anthophilin1 appear unique to the bee lineage. Most venom proteins thus predate the mega-radiation of hymenopterans and the evolution of the aculeate stinger.

Whole genome analyses reveal weak signatures of population structure and environmentally associated local adaptation in an important North American pollinator, the bumble bee Bombus vosnesenskii

Studies of species that experience environmental heterogeneity across their distributions have become an important tool for understanding mechanisms of adaptation and predicting responses to climate change. We examine population structure, demographic history and environmentally associated genomic variation in Bombus vosnesenskii, a common bumble bee in the western USA, using whole genome resequencing of populations distributed across a broad range of latitudes and elevations. We find that B. vosnesenskii exhibits minimal population structure and weak isolation by distance, confirming results from previous studies using other molecular marker types. Similarly, demographic analyses with Sequentially Markovian Coalescent models suggest that minimal population structure may have persisted since the last interglacial period, with genomes from different parts of the species range showing similar historical effective population size trajectories and relatively small fluctuations through time. Redundancy analysis revealed a small amount of genomic variation explained by bioclimatic variables. Environmental association analysis with latent factor mixed modelling (LFMM2) identified few outlier loci that were sparsely distributed throughout the genome and although a few putative signatures of selective sweeps were identified, none encompassed particularly large numbers of loci. Some outlier loci were in genes with known regulatory relationships, suggesting the possibility of weak selection, although compared with other species examined with similar approaches, evidence for extensive local adaptation signatures in the genome was relatively weak. Overall, results indicate B. vosnesenskii is an example of a generalist with a high degree of flexibility in its environmental requirements that may ultimately benefit the species under periods of climate change.

The ecology of nutrient sensation and perception in insects

Insects are equipped with neurological, physiological, and behavioral tools to locate potential food sources and assess their nutritional quality based on volatile and chemotactile cues. We summarize current knowledge on insect taste perception and the different modalities of reception and perception. We suggest that the neurophysiological mechanisms of reception and perception are closely linked to the species-specific ecology of different insects. Understanding these links consequently requires a multidisciplinary approach. We also highlight existing knowledge gaps, especially in terms of the exact ligands of receptors, and provide evidence for a perceptional hierarchy suggesting that insects have adapted their reception and perception to preferentially perceive nutrient stimuli that are important for their fitness.

Evolution of five environmentally responsive gene families in a pine-feeding sawfly, Neodiprion lecontei (Hymenoptera: Diprionidae)

A central goal in evolutionary biology is to determine the predictability of adaptive genetic changes. Despite many documented cases of convergent evolution at individual loci, little is known about the repeatability of gene family expansions and contractions. To address this void, we examined gene family evolution in the redheaded pine sawfly Neodiprion lecontei, a noneusocial hymenopteran and exemplar of a pine-specialized lineage evolved from angiosperm-feeding ancestors. After assembling and annotating a draft genome, we manually annotated multiple gene families with chemosensory, detoxification, or immunity functions before characterizing their genomic distributions and molecular evolution. We find evidence of recent expansions of bitter gustatory receptor, clan 3 cytochrome P450, olfactory receptor, and antimicrobial peptide subfamilies, with strong evidence of positive selection among paralogs in a clade of gustatory receptors possibly involved in the detection of bitter compounds. In contrast, these gene families had little evidence of recent contraction via pseudogenization. Overall, our results are consistent with the hypothesis that in response to novel selection pressures, gene families that mediate ecological interactions may expand and contract predictably. Testing this hypothesis will require the comparative analysis of high-quality annotation data from phylogenetically and ecologically diverse insect species and functionally diverse gene families. To this end, increasing sampling in under-sampled hymenopteran lineages and environmentally responsive gene families and standardizing manual annotation methods should be prioritized.

'Junk' that matters: the role of transposable elements in bumblebee genome evolution

Transposable elements (TEs) are mobile DNA sequences that are widely distributed in eukaryotic genomes, where they are known to serve as a major force in genome evolution. The phenotypic impacts of TEs, while less well-studied, have also been discovered. Bumblebees are globally important pollinators in natural ecosystems and agriculture. Although TEs comprise a small fraction of bumblebee genomes, emerging evidence suggests that TEs are the major contributor of genome size variation across species and are involved in the formation of new coding and regulatory sequences. We review recent discoveries related to TEs in bumblebees, as well as outlining three key questions for the future of the field. In the future, we argue long-read sequencing technologies and genome editing techniques will help us identify TEs in bumblebees, unveil mechanisms that could account for their silencing and limited abundance, and uncover their contributions to phenotypic diversification, ecological adaptation, and speciation.

Evolutionary dynamics of genome size and content during the adaptive radiation of Heliconiini butterflies

Heliconius butterflies, a speciose genus of Müllerian mimics, represent a classic example of an adaptive radiation that includes a range of derived dietary, life history, physiological and neural traits. However, key lineages within the genus, and across the broader Heliconiini tribe, lack genomic resources, limiting our understanding of how adaptive and neutral processes shaped genome evolution during their radiation. Here, we generate highly contiguous genome assemblies for nine Heliconiini, 29 additional reference-assembled genomes, and improve 10 existing assemblies. Altogether, we provide a dataset of annotated genomes for a total of 63 species, including 58 species within the Heliconiini tribe. We use this extensive dataset to generate a robust and dated heliconiine phylogeny, describe major patterns of introgression, explore the evolution of genome architecture, and the genomic basis of key innovations in this enigmatic group, including an assessment of the evolution of putative regulatory regions at the Heliconius stem. Our work illustrates how the increased resolution provided by such dense genomic sampling improves our power to generate and test gene-phenotype hypotheses, and precisely characterize how genomes evolve.

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.

PhyloAcc-GT: A Bayesian Method for Inferring Patterns of Substitution Rate Shifts on Targeted Lineages Accounting for Gene Tree Discordance

An important goal of evolutionary genomics is to identify genomic regions whose substitution rates differ among lineages. For example, genomic regions experiencing accelerated molecular evolution in some lineages may provide insight into links between genotype and phenotype. Several comparative genomics methods have been developed to identify genomic accelerations between species, including a Bayesian method called PhyloAcc, which models shifts in substitution rate in multiple target lineages on a phylogeny. However, few methods consider the possibility of discordance between the trees of individual loci and the species tree due to incomplete lineage sorting, which might cause false positives. Here, we present PhyloAcc-GT, which extends PhyloAcc by modeling gene tree heterogeneity. Given a species tree, we adopt the multispecies coalescent model as the prior distribution of gene trees, use Markov chain Monte Carlo (MCMC) for inference, and design novel MCMC moves to sample gene trees efficiently. Through extensive simulations, we show that PhyloAcc-GT outperforms PhyloAcc and other methods in identifying target lineage-specific accelerations and detecting complex patterns of rate shifts, and is robust to specification of population size parameters. PhyloAcc-GT is usually more conservative than PhyloAcc in calling convergent rate shifts because it identifies more accelerations on ancestral than on terminal branches. We apply PhyloAcc-GT to two examples of convergent evolution: flightlessness in ratites and marine mammal adaptations, and show that PhyloAcc-GT is a robust tool to identify shifts in substitution rate associated with specific target lineages while accounting for incomplete lineage sorting.

The genomic landscape, causes, and consequences of extensive phylogenomic discordance in Old World mice and rats

A species tree is a central concept in evolutionary biology whereby a single branching phylogeny reflects relationships among species. However, the phylogenies of different genomic regions often differ from the species tree. Although tree discordance is often widespread in phylogenomic studies, we still lack a clear understanding of how variation in phylogenetic patterns is shaped by genome biology or the extent to which discordance may compromise comparative studies. We characterized patterns of phylogenomic discordance across the murine rodents (Old World mice and rats) - a large and ecologically diverse group that gave rise to the mouse and rat model systems. Combining new linked-read genome assemblies for seven murine species with eleven published rodent genomes, we first used ultra-conserved elements (UCEs) to infer a robust species tree. We then used whole genomes to examine finer-scale patterns of discordance and found that phylogenies built from proximate chromosomal regions had similar phylogenies. However, there was no relationship between tree similarity and local recombination rates in house mice, suggesting that genetic linkage influences phylogenetic patterns over deeper timescales. This signal may be independent of contemporary recombination landscapes. We also detected a strong influence of linked selection whereby purifying selection at UCEs led to less discordance, while genes experiencing positive selection showed more discordant and variable phylogenetic signals. Finally, we show that assuming a single species tree can result in high error rates when testing for positive selection under different models. Collectively, our results highlight the complex relationship between phylogenetic inference and genome biology and underscore how failure to account for this complexity can mislead comparative genomic studies.

Impacts of oxygen deficiency on embryo life-history traits of migratory locust Locusta migratoria from low and high altitudes

Hypoxia challenges aerobic organisms in numerous environments, and hypoxic conditions may become more severe under future climate-change scenarios. The impact of hypoxia on the development of terrestrial insect embryos is not well understood. Here, to address this gap, embryonic life-history traits of migratory locust Locusta migratoria from low-altitude and high-altitude regions were compared under 2 oxygen levels: normoxia (i.e., 21 kPa oxygen partial pressure and mild hypoxia (i.e., 10 kPa oxygen partial pressure). Our results demonstrated that, whether reared under normoxia or mild hypoxia, L. migratoria from high-altitude populations had longer developmental times, reduced weight, and lower mean relative growth rate as compared with those from low-altitude populations. When transferred from normoxia to mild hypoxia, nearly all the tested life-history traits presented significant negative changes in the low-altitude populations, but not in the high-altitude populations. The factor 'strain' alone explained 18.26%-54.59% of the total variation for traits, suggesting that the phenotypic differences between L. migratoria populations from the 2 altitudes could be driven by genetic variation. Significant genetic correlations were found between life-history traits, and most of these showed differentiation between the 2 altitudinal gradients. G-matrix comparisons showed significant structural differences between L. migratoria from the 2 regions, as well as several negative covariances (i.e., trade-offs) between traits in the low-altitude populations. Overall, our study provides clear evidence that evolutionary divergence of embryonic traits between L. migratoria populations from different altitudes has occurred.

Putting hornets on the genomic map

Hornets are the largest of the social wasps, and are important regulators of insect populations in their native ranges. Hornets are also very successful as invasive species, with often devastating economic, ecological and societal effects. Understanding why these wasps are such successful invaders is critical to managing future introductions and minimising impact on native biodiversity. Critical to the management toolkit is a comprehensive genomic resource for these insects. Here we provide the annotated genomes for two hornets, Vespa crabro and Vespa velutina. We compare their genomes with those of other social Hymenoptera, including the northern giant hornet Vespa mandarinia. The three hornet genomes show evidence of selection pressure on genes associated with reproduction, which might facilitate the transition into invasive ranges. Vespa crabro has experienced positive selection on the highest number of genes, including those putatively associated with molecular binding and olfactory systems. Caste-specific brain transcriptomic analysis also revealed 133 differentially expressed genes, some of which are associated with olfactory functions. This report provides a spring-board for advancing our understanding of the evolution and ecology of hornets, and opens up opportunities for using molecular methods in the future management of both native and invasive populations of these over-looked insects.

Expanding the Repertoire of the Plant-Infecting Ophioviruses through Metatranscriptomics Data

Ophioviruses (genus Ophiovirus, family Aspiviridae) are plant-infecting viruses with non-enveloped, filamentous, naked nucleocapsid virions. Members of the genus Ophiovirus have a segmented single-stranded negative-sense RNA genome (ca. 11.3–12.5 kb), encompassing three or four linear segments. In total, these segments encode four to seven proteins in the sense and antisense orientation, both in the viral and complementary strands. The genus Ophiovirus includes seven species with viruses infecting both monocots and dicots, mostly trees, shrubs and some ornamentals. From a genomic perspective, as of today, there are complete genomes available for only four species. Here, by exploring large publicly available metatranscriptomics datasets, we report the identification and molecular characterization of 33 novel viruses with genetic and evolutionary cues of ophioviruses. Genetic distance and evolutionary insights suggest that all the detected viruses could correspond to members of novel species, which expand the current diversity of ophioviruses ca. 4.5-fold. The detected viruses increase the tentative host range of ophioviruses for the first time to mosses, liverwort and ferns. In addition, the viruses were linked to several Asteraceae, Orchidaceae and Poaceae crops/ornamental plants. Phylogenetic analyses showed a novel clade of mosses, liverworts and fern ophioviruses, characterized by long branches, suggesting that there is still plenty of unsampled hidden diversity within the genus. This study represents a significant expansion of the genomics of ophioviruses, opening the door to future works on the molecular and evolutionary peculiarity of this virus genus.

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.

Testing the systematic status of Homalictus and Rostrohalictus with weakened cross-vein groups within Halictini (Hymenoptera: Halictidae) using low-coverage whole-genome sequencing

The halictid genus Lasioglossum, as one of the most species-rich bee groups with persistently contentious subgeneric boundaries, is one of the most challenging bee groups from a systematic standpoint. An enduring question is the relationship of Lasioglossum and Homalictus, whether all halictine bees with weakened distal wing venation comprise one or multiple genera. Here, we analyzed the phylogenetic relationships among the subgroups within Lasioglossum s.l. based on thousands of single-copy orthologs and ultraconserved elements, which were extracted from 23 newly sequenced low-coverage whole genomes alongside a published genome (22 ingroups plus 2 outgroups). Both marker sets provided consistent results across maximum likelihood and coalescent-based species tree approaches. The phylogenetic and topology test results show that the Lasioglossum and Hemihalictus series are reciprocally monophyletic and Homalictus and Rostrohalictus are valid subgenera of Lasioglossum. Consequently, we lower Homalictus to subgenus status within Lasioglossum again, and we also raise Rostrohalictus to subgenus status from its prior synonymy with subgenus Hemihalictus. Lasioglossum przewalskyi is also transferred to the subgenus Hemihalictus. Ultimately, we redefine Lasioglossum to include all halictine bees with weakened distal wing venation.

Current Knowledge on Bee Innate Immunity Based on Genomics and Transcriptomics

As important pollinators, bees play a critical role in maintaining the balance of the ecosystem and improving the yield and quality of crops. However, in recent years, the bee population has significantly declined due to various pathogens and environmental stressors including viruses, bacteria, parasites, and increased pesticide application. The above threats trigger or suppress the innate immunity of bees, their only immune defense system, which is essential to maintaining individual health and that of the colony. In addition, bees can be divided into solitary and eusocial bees based on their life traits, and eusocial bees possess special social immunities, such as grooming behavior, which cooperate with innate immunity to maintain the health of the colony. The omics approach gives us an opportunity to recognize the distinctive innate immunity of bees. In this regard, we summarize innate bee immunity from a genomic and transcriptomic perspective. The genetic characteristics of innate immunity were revealed by the multiple genomes of bees with different kinds of sociality, including honeybees, bumblebees, wasps, leaf-cutter bees, and so on. Further substantial transcriptomic data of different tissues from diverse bees directly present the activation or suppression of immune genes under the infestation of pathogens or toxicity of pesticides.

Quantifying the uncertainty of assembly-free genome-wide distance estimates and phylogenetic relationships using subsampling

Computing distance between two genomes without alignments or even access to assemblies has many downstream analyses. However, alignment-free methods, including in the fast-growing field of genome skimming, are hampered by a significant methodological gap. While accurate methods (many k-mer-based) for assembly-free distance calculation exist, measuring the uncertainty of estimated distances has not been sufficiently studied. In this paper, we show that bootstrapping, the standard non-parametric method of measuring estimator uncertainty, is not accurate for k-mer-based methods that rely on k-mer frequency profiles. Instead, we propose using subsampling (with no replacement) in combination with a correction step to reduce the variance of the inferred distribution. We show that the distribution of distances using our procedure matches the true uncertainty of the estimator. The resulting phylogenetic support values effectively differentiate between correct and incorrect branches and identify controversial branches that change across alignment-free and alignment-based phylogenies reported in the literature.

Signals of adaptation to agricultural stress in the genomes of two European bumblebees

Human-induced environmental impacts on wildlife are widespread, causing major biodiversity losses. One major threat is agricultural intensification, typically characterised by large areas of monoculture, mechanical tillage, and the use of agrochemicals. Intensification leads to the fragmentation and loss of natural habitats, native vegetation, and nesting and breeding sites. Understanding the adaptability of insects to these changing environmental conditions is critical to predicting their survival. Bumblebees, key pollinators of wild and cultivated plants, are used as model species to assess insect adaptation to anthropogenic stressors. We investigated the effects of agricultural pressures on two common European bumblebees, Bombus pascuorum and B. lapidarius. Restriction-site Associated DNA Sequencing was used to identify loci under selective pressure across agricultural-natural gradients over 97 locations in Europe. 191 unique loci in B. pascuorum and 260 in B. lapidarius were identified as under selective pressure, and associated with agricultural stressors. Further investigation suggested several candidate proteins including several neurodevelopment, muscle, and detoxification proteins, but these have yet to be validated. These results provide insights into agriculture as a stressor for bumblebees, and signal for conservation action in light of ongoing anthropogenic changes.

Exploring new genomic territories with emerging model insects

Improvements in reference genome generation for insects and across the tree of life are extending the concept and utility of model organisms beyond traditional laboratory-tractable supermodels. Species or groups of species with comprehensive genome resources can be developed into model systems for studying a large variety of biological phenomena. Advances in sequencing and assembly technologies are supporting these emerging genome-enabled model systems by producing resources that are increasingly accurate and complete. Nevertheless, quality controls including assessing gene content completeness are required to ensure that these data can be included in expanding catalogues of high-quality references that will greatly advance understanding of insect biology and evolution.

Sex-differences in Phenology: A Tinbergian Perspective

Shifts in the timing of cyclic seasonal life-history events are among the most commonly reported responses to climate change, with differences in response rates among interacting species leading to phenological mismatches. Within a species, however, males and females can also exhibit differential sensitivity to environmental cues and may therefore differ in their responsiveness to climate change, potentially leading to phenological mismatches between the sexes. This occurs because males differ from females in when and how energy is allocated to reproduction, resulting in marked sex-differences in life-history timing across the annual cycle. In this review, we take a Tinbergian perspective and examine sex differences in timing of vertebrates from adaptive, ontogenetic, mechanistic, and phylogenetic viewpoints with the goal of informing and motivating more integrative research on sexually dimorphic phenologies. We argue that sexual and natural selection lead to sex-differences in life-history-timing and that understanding the ecological and evolutionary drivers of these differences is critical for connecting climate-driven phenological shifts to population resilience. Ontogeny may influence how and when sex differences in life-history timing arise because the early-life environment can profoundly affect developmental trajectory, rates of reproductive maturation, and seasonal timing. The molecular mechanisms underlying these organismal traits are relevant to identifying the diversity and genetic basis of population- and species-level responses to climate change, and promisingly, the molecular basis of phenology is becoming increasingly well-understood. However, because most studies focus on a single sex, the causes of sex-differences in phenology critical to population resilience often remain unclear. New sequencing tools and analyses informed by phylogeny may help generate hypotheses about mechanism as well as insight into the general "evolvability" of sex differences across phylogenetic scales, especially as trait and genome resources grow. We recommend that greater attention be placed on determining sex-differences in timing mechanisms and monitoring climate change responses in both sexes, and we discuss how new tools may provide key insights into sex-differences in phenology from all four Tinbergian domains.

Molecular (co)evolution of hymenopteran social parasites and their hosts

Social parasitism describes a fascinating way of life in which species exploit the altruistic behaviour of closely related, social species. Social parasites have repeatedly evolved in the social Hymenoptera, including ants, bees, and wasps. The common ancestry and shared (social) environment with their hosts facilitates the study of molecular adaptations to the parasitic lifestyle. Moreover, when social parasites are widespread and virulent, they exert strong selection pressure on their hosts, leading to the evolution of defense mechanisms and triggering a coevolutionary arms race. Recent advances in sequencing technology now make it possible to study the molecular basis of this coevolutionary process. In addition to describing the latest developments, we highlight open research questions that could be tackled with genomic, transcriptomic, or epigenetic data.

Chromosome-Level Genome Assembly of Anthidium xuezhongi Niu & Zhu, 2020 (Hymenoptera: Apoidea: Megachilidae: Anthidiini)

Anthidiini, a large bee tribe characterized by light-colored maculations, represents nearly 1,000 pollinator species, but no genomes are yet available for this tribe. Here, we report a chromosome-level genome assembly of Anthidium xuezhongi collected from the Tibetan Plateau. Using PacBio long reads and Hi-C data, we assembled a genome of 189.14 Mb with 99.94% of the assembly located in 16 chromosomes. Our assembly contains 23 scaffolds, with the scaffold N50 length of 12.53 Mb, and BUSCO completeness of 98.70% (n = 1,367). We masked 25.98 Mb (13.74%) of the assembly as repetitive elements, identified 385 noncoding RNAs, and predicted 10,820 protein-coding genes (99.20% BUSCO completeness). Gene family evolution analyses identified 9,251 gene families, of which 31 gene families experienced rapid evolution. Interspecific chromosomal variation among A. xuezhongi, Bombus terrestris, and Apis mellifera showed strong chromosomal syntenic relationships. This high-quality genome assembly is a valuable resource for evolutionary and comparative genomic analyses of bees.

Sunflower pollen reduces a gut pathogen in the model bee species, Bombus impatiens, but has weaker effects in three wild congeners

Commercial bumblebees have become popular models to understand stressors and solutions for pollinator health, but few studies test whether results translate to other pollinators. Consuming sunflower pollen dramatically reduces infection by the gut parasite Crithidia bombi in commercially reared Bombus impatiens. We assessed the effect of sunflower pollen on infection in wild B. impatiens, Bombus griseocollis, Bombus bimaculatus and Bombus vagans. We also asked how pollen diet (50% sunflower pollen versus wildflower pollen) and infection (yes/no) affected performance in wild B. impatiens microcolonies. Compared to controls, sunflower pollen dramatically reduced Crithidia infection in commercial and wild B. impatiens, had similar but less dramatic effects in B. bimaculatus and B. vagans, and no effect in B. griseocollis. Bombus impatiens, B. bimaculatus and B. vagans are in the same subgenus, suggesting that responses to sunflower pollen may be phylogenetically conserved. In microcolonies, 50% sunflower pollen reduced infection compared to wildflower pollen, but also reduced reproduction. Sunflower pollen could control Crithidia infections in B. impatiens and potentially close relatives, but may hinder reproduction if other resources are scarce. We caution that research using managed bee species, such as B. impatiens, be interpreted carefully as findings may not relate to all bee species.

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.