Queens and Workers Contribute Differently to Adaptive Evolution in Bumble Bees and Honey Bees

Leaf-damaging behavior by queens is widespread among bumblebee species

Phenological mismatches and resource limitations resulting from ongoing environmental change can have severe impacts on pollinator fitness. Recent findings show that bumblebee workers respond to pollen scarcity by damaging plant leaves in ways that can accelerate flowering, suggesting a mechanism by which direct information transfer from bees to plants might influence the timing of flower production. However, the ecological and adaptive significance of this interaction remains uncertain. Here we report that mated and unmated queens of Bombus terrestris also damage leaves, with similar effects on flowering. Furthermore, we document leaf damage by wild-caught queens from 12 species, spanning seven subgenera, indicating damaging behavior is widespread among Bombus species. Leaf damage by bumblebee queens may have particular relevance in the context of colony founding and early development, where the timely availability of local floral resources can be critical for colony success and fitness.

An integrative genomic toolkit for studying the genetic, evolutionary, and molecular underpinnings of eusociality in insects

While genomic resources for social insects have vastly increased over the past two decades, we are still far from understanding the genetic and molecular basis of eusociality. Here, we briefly review three scientific advancements that, when integrated, can be highly synergistic for advancing our knowledge of the genetics and evolution of eusocial traits. Population genomics provides a natural way to quantify the strength of natural selection on coding and regulatory sequences, highlighting genes that have undergone adaptive evolution during the evolution or maintenance of eusociality. Genome-wide association studies (GWAS) can be used to characterize the complex genetic architecture underlying eusocial traits and identify candidate causal variants. Concurrently, CRISPR/Cas9 enables the precise manipulation of gene function to both validate genotype-phenotype associations and study the molecular biology underlying interesting traits. While each approach has its own advantages and disadvantages, which we discuss herein, we argue that their combination will ultimately help us better understand the genetics and evolution of eusocial behavior. Specifically, by triangulating across these three different approaches, researchers can directly identify and study loci that have a causal association with key phenotypes and have evidence of positive selection over the relevant timescales associated with the evolution and maintenance of eusociality in insects.

The impact of geography and climate on the population structure and local adaptation in a wild bee

Deciphering processes that contribute to genetic differentiation and divergent selection of natural populations is useful for evaluating the adaptive potential and resilience of organisms faced with various anthropogenic stressors. Insect pollinator species, including wild bees, provide critical ecosystem services but are highly susceptible to biodiversity declines. Here, we use population genomics to infer the genetic structure and test for evidence of local adaptation in an economically important native pollinator, the small carpenter bee (Ceratina calcarata). Using genome-wide SNP data (n = 8302), collected from specimens across the species' entire distribution, we evaluated population differentiation and genetic diversity and identified putative signatures of selection in the context of geographic and environmental variation. Results of the analyses of principal component and Bayesian clustering were concordant with the presence of two to three genetic clusters, associated with landscape features and inferred phylogeography of the species. All populations examined in our study demonstrated a heterozygote deficit, along with significant levels of inbreeding. We identified 250 robust outlier SNPs, corresponding to 85 annotated genes with known functional relevance to thermoregulation, photoperiod, and responses to various abiotic and biotic stressors. Taken together, these data provide evidence for local adaptation in a wild bee and highlight genetic responses of native pollinators to landscape and climate features.

Thrice out of Asia and the adaptive radiation of the western honey bee

The origin of the western honey bee Apis mellifera has been intensely debated. Addressing this knowledge gap is essential for understanding the evolution and genetics of one of the world’s most important pollinators. By analyzing 251 genomes from 18 native subspecies, we found support for an Asian origin of honey bees with at least three expansions leading to African and European lineages. The adaptive radiation of honey bees involved selection on a few genomic “hotspots.” We found 145 genes with independent signatures of selection across all bee lineages, and these genes were highly associated with worker traits. Our results indicate that a core set of genes associated with worker and colony traits facilitated the adaptive radiation of honey bees across their vast distribution.

The genomic basis of evolutionary differentiation among honey bees

In contrast to the western honey bee, Apis mellifera, other honey bee species have been largely neglected despite their importance and diversity. The genetic basis of the evolutionary diversification of honey bees remains largely unknown. Here, we provide a genome-wide comparison of three honey bee species, each representing one of the three subgenera of honey bees, namely the dwarf (Apis florea), giant (A. dorsata), and cavity-nesting (A. mellifera) honey bees with bumblebees as an outgroup. Our analyses resolve the phylogeny of honey bees with the dwarf honey bees diverging first. We find that evolution of increased eusocial complexity in Apis proceeds via increases in the complexity of gene regulation, which is in agreement with previous studies. However, this process seems to be related to pathways other than transcriptional control. Positive selection patterns across Apis reveal a trade-off between maintaining genome stability and generating genetic diversity, with a rapidly evolving piRNA pathway leading to genomes depleted of transposable elements, and a rapidly evolving DNA repair pathway associated with high recombination rates in all Apis species. Diversification within Apis is accompanied by positive selection in several genes whose putative functions present candidate mechanisms for lineage-specific adaptations, such as migration, immunity, and nesting behavior.

A combined RAD-Seq and WGS approach reveals the genomic basis of yellow color variation in bumble bee Bombus terrestris

Bumble bees exhibit exceptional diversity in their segmental body coloration largely as a result of mimicry. In this study we sought to discover genes involved in this variation through studying a lab-generated mutant in bumble bee Bombus terrestris, in which the typical black coloration of the pleuron, scutellum, and first metasomal tergite is replaced by yellow, a color variant also found in sister lineages to B. terrestris. Utilizing a combination of RAD-Seq and whole-genome re-sequencing, we localized the color-generating variant to a single SNP in the protein-coding sequence of transcription factor cut. This mutation generates an amino acid change that modifies the conformation of a coiled-coil structure outside DNA-binding domains. We found that all sequenced Hymenoptera, including sister lineages, possess the non-mutant allele, indicating different mechanisms are involved in the same color transition in nature. Cut is important for multiple facets of development, yet this mutation generated no noticeable external phenotypic effects outside of setal characteristics. Reproductive capacity was reduced, however, as queens were less likely to mate and produce female offspring, exhibiting behavior similar to that of workers. Our research implicates a novel developmental player in pigmentation, and potentially caste, thus contributing to a better understanding of the evolution of diversity in both of these processes.

Connecting social polymorphism to single nucleotide polymorphism: population genomics of the small carpenter bee, Ceratina australensis

How do social insects expand and adapt to new ranges and how does sociality per se contribute to their success (or failure)? These questions can become tractable with the use of population genomics. We explored the population genomics of the socially polymorphic small carpenter bee, Ceratina australensis, across its range in eastern and southern Australia to search for evidence of selection and identify loci associated with social nesting. We sampled and sequenced fully the genomes of 54 socially and solitarily nesting C. australensis within Queensland, Victoria and South Australia, yielding 2 061 234 single nucleotide polymorphisms across the genome. We found strong evidence of population-specific selection and evidence of genetic variants associated with social nesting behaviour. Both the sets of associated loci and differentially expressed ‘social’ genes had evidence of positive selection, suggesting that alleles at genes associated with social nesting might provide different fitness benefits.

Gene expression and epigenetics reveal species-specific mechanisms acting upon common molecular pathways in the evolution of task division in bees

A striking feature of advanced insect societies is the existence of workers that forgo reproduction. Two broad types of workers exist in eusocial bees: nurses who care for their young siblings and the queen, and foragers who guard the nest and forage for food. Comparisons between these two worker subcastes have been performed in honeybees, but data from other bees are scarce. To understand whether similar molecular mechanisms are involved in nurse-forager differences across distinct species, we compared gene expression and DNA methylation profiles between nurses and foragers of the buff-tailed bumblebee Bombus terrestris and the stingless bee Tetragonisca angustula. These datasets were then compared to previous findings from honeybees. Our analyses revealed that although the expression pattern of genes is often species-specific, many of the biological processes and molecular pathways involved are common. Moreover, the correlation between gene expression and DNA methylation was dependent on the nucleotide context, and non-CG methylation appeared to be a relevant factor in the behavioral changes of the workers. In summary, task specialization in worker bees is characterized by a plastic and mosaic molecular pattern, with species-specific mechanisms acting upon broad common pathways across species.

Non-Destructive Genotyping of Honeybee Queens to Support Selection and Breeding

In traditional bee breeding, the honeybee queen is chosen for breeding based on the performance of the colony produced by its mother. However, we cannot be entirely certain that a specific queen will produce offspring with desirable traits until we observe the young queen's new colony. Collecting the queen's genetic material enables quick and reliable determination of the relevant information. We sampled exuviae, feces, and wingtips for DNA extraction to avoid fatally injuring the queen when using tissue samples. Quantity and purity of extracted DNA were measured. Two mitochondrial markers were used to determine the lineage affiliation and exclude possible contamination of DNA extracts with non-honeybee DNA. dCAPS (derived Cleaved Amplified Polymorphic Sequences) markers allowed detection of single nucleotide polymorphisms (SNPs) in nuclear DNA regions presumably associated with Varroa sensitive hygiene and set the example of successful development of genotyping protocol from non-destructive DNA sources. One of the logical future steps in honeybee breeding is introducing genomic selection and non-destructive sampling methods of genetic material may be the prerequisite for successful genotyping. Our results demonstrate that the extraction of DNA from feces and exuviae can be introduced into practice. The advantage of these two sources over wingtips is reducing the time window for processing the samples, thus enabling genotyping directly after the queen's emergence.

The Complexity of Social Complexity: A Quantitative Multidimensional Approach for Studies of Social Organization

AbstractThe rapid increase in "big data" during the postgenomic era makes it crucial to appropriately measure the level of social complexity in comparative studies. We argue that commonly used qualitative classifications lump together species showing a broad range of social complexity and falsely imply that social evolution always progresses along a single linear stepwise trajectory that can be deduced from comparing extant species. To illustrate this point, we compared widely used social complexity measures in "primitively eusocial" bumble bees with "advanced eusocial" stingless bees, honey bees, and attine ants. We find that a single species can have both higher and lower levels of complexity compared with other taxa, depending on the social trait measured. We propose that measuring the complexity of individual social traits switches focus from semantic discussions and offers several directions for progress. First, quantitative social traits can be correlated with molecular, developmental, and physiological processes within and across lineages of social animals. This approach is particularly promising for identifying processes that influence or have been affected by social evolution. Second, key social complexity traits can be combined into multidimensional lineage-specific quantitative indices, enabling fine-scale comparison across species that are currently bundled within the same level of social complexity.

Eusociality influences the strength of negative selection on insect genomes

While much of the focus of sociobiology concerns identifying genomic changes that influence social behaviour, we know little about the consequences of social behaviour on genome evolution. It has been hypothesized that social evolution can influence the strength of negative selection via two mechanisms. First, division of labour can influence the efficiency of negative selection in a caste-specific manner; indirect negative selection on worker traits is theoretically expected to be weaker than direct selection on queen traits. Second, increasing social complexity is expected to lead to relaxed negative selection because of its influence on effective population size. We tested these two hypotheses by estimating the strength of negative selection in honeybees, bumblebees, paper wasps, fire ants and six other insects that span the range of social complexity. We found no consistent evidence that negative selection was significantly stronger on queen-biased genes relative to worker-biased genes. However, we found strong evidence that increased social complexity reduced the efficiency of negative selection. Our study clearly illustrates how changes in behaviour can influence patterns of genome evolution by modulating the strength of natural selection.

Brain microRNAs among social and solitary bees

Evolutionary transitions to a social lifestyle in insects are associated with lineage-specific changes in gene expression, but the key nodes that drive these regulatory changes are unknown. We examined the relationship between social organization and lineage-specific microRNAs (miRNAs). Genome scans across 12 bee species showed that miRNA copy-number is mostly conserved and not associated with sociality. However, deep sequencing of small RNAs in six bee species revealed a substantial proportion (20-35%) of detected miRNAs had lineage-specific expression in the brain, 24-72% of which did not have homologues in other species. Lineage-specific miRNAs disproportionately target lineage-specific genes, and have lower expression levels than shared miRNAs. The predicted targets of lineage-specific miRNAs are not enriched for genes with caste-biased expression or genes under positive selection in social species. Together, these results suggest that novel miRNAs may coevolve with novel genes, and thus contribute to lineage-specific patterns of evolution in bees, but do not appear to have significant influence on social evolution. Our analyses also support the hypothesis that many new miRNAs are purged by selection due to deleterious effects on mRNA targets, and suggest genome structure is not as influential in regulating bee miRNA evolution as has been shown for mammalian miRNAs.

Developmental plasticity shapes social traits and selection in a facultatively eusocial bee

Developmental processes are an important source of phenotypic variation, but the extent to which this variation contributes to evolutionary change is unknown. We used integrative genomic analyses to explore the relationship between developmental and social plasticity in a bee species that can adopt either a social or solitary lifestyle. We find genes regulating this social flexibility also regulate development, and positive selection on these genes is influenced by their function during development. This suggests that developmental plasticity may influence the evolution of sociality. Our additional finding of genetic variants linked to differences in social behavior sheds light on how phenotypic variation derived from development may become encoded into the genome, and thus contribute to evolutionary change.

Developmental plasticity generates phenotypic variation, but how it contributes to evolutionary change is unclear. Phenotypes of individuals in caste-based (eusocial) societies are particularly sensitive to developmental processes, and the evolutionary origins of eusociality may be rooted in developmental plasticity of ancestral forms. We used an integrative genomics approach to evaluate the relationships among developmental plasticity, molecular evolution, and social behavior in a bee species (Megalopta genalis) that expresses flexible sociality, and thus provides a window into the factors that may have been important at the evolutionary origins of eusociality. We find that differences in social behavior are derived from genes that also regulate sex differentiation and metamorphosis. Positive selection on social traits is influenced by the function of these genes in development. We further identify evidence that social polyphenisms may become encoded in the genome via genetic changes in regulatory regions, specifically in transcription factor binding sites. Taken together, our results provide evidence that developmental plasticity provides the substrate for evolutionary novelty and shapes the selective landscape for molecular evolution in a major evolutionary innovation: Eusociality.

Coevolution of Genome Architecture and Social Behavior

Although social behavior can have a strong genetic component, it can also result in selection on genome structure and function, thereby influencing the evolution of the genome itself. Here we explore the bidirectional links between social behavior and genome architecture by considering variation in social and/or mating behavior among populations (social polymorphisms) and across closely related species. We propose that social behavior can influence genome architecture via associated demographic changes due to social living. We establish guidelines to exploit emerging whole-genome sequences using analytical approaches that examine genome structure and function at different levels (regulatory vs structural variation) from the perspective of both molecular biology and population genetics in an ecological context.

Draft Genome Assembly and Population Genetics of an Agricultural Pollinator, the Solitary Alkali Bee (Halictidae: Nomia melanderi)

Alkali bees (Nomia melanderi) are solitary relatives of the halictine bees, which have become an important model for the evolution of social behavior, but for which few solitary comparisons exist. These ground-nesting bees defend their developing offspring against pathogens and predators, and thus exhibit some of the key traits that preceded insect sociality. Alkali bees are also efficient native pollinators of alfalfa seed, which is a crop of major economic value in the United States. We sequenced, assembled, and annotated a high-quality draft genome of 299.6 Mbp for this species. Repetitive content makes up more than one-third of this genome, and previously uncharacterized transposable elements are the most abundant type of repetitive DNA. We predicted 10,847 protein coding genes, and identify 479 of these undergoing positive directional selection with the use of population genetic analysis based on low-coverage whole genome sequencing of 19 individuals. We found evidence of recent population bottlenecks, but no significant evidence of population structure. We also identify 45 genes enriched for protein translation and folding, transcriptional regulation, and triglyceride metabolism evolving slower in alkali bees compared to other halictid bees. These resources will be useful for future studies of bee comparative genomics and pollinator health research.

Conserved Genes Underlie Phenotypic Plasticity in an Incipiently Social Bee

Despite a strong history of theoretical work on the mechanisms of social evolution, relatively little is known of the molecular genetic changes that accompany transitions from solitary to eusocial forms. Here, we provide the first genome of an incipiently social bee that shows both solitary and social colony organization in sympatry, the Australian carpenter bee Ceratina australensis. Through comparative analysis, we provide support for the role of conserved genes and cis-regulation of gene expression in the phenotypic plasticity observed in nest-sharing, a rudimentary form of sociality. Additionally, we find that these conserved genes are associated with caste differences in advanced eusocial species, suggesting these types of mechanisms could pave the molecular pathway from solitary to eusocial living. Genes associated with social nesting in this species show signatures of being deeply conserved, in contrast to previous studies in other bees showing novel and faster-evolving genes are associated with derived sociality. Our data provide support for the idea that the earliest social transitions are driven by changes in gene regulation of deeply conserved genes.

Insects with similar social complexity show convergent patterns of adaptive molecular evolution

Eusociality has independently evolved multiple times in the hymenoptera, but the patterns of adaptive molecular evolution underlying the evolution and elaboration of eusociality remain uncertain. Here, we performed a population genomics study of primitively eusocial Polistes (paper wasps), and compared their patterns of molecular evolution to two social bees; Bombus (bumblebees), and Apis (honey bees). This species triad allowed us to study molecular evolution across a gradient of social complexity (Polistes < Bombus < Apis) and compare species pairs that have similar (i.e. Polistes and Bombus) or different (i.e. Polistes and Apis) life histories, while controlling for phylogenetic distance. We found that regulatory genes have high levels of positive selection in Polistes; consistent with the prediction that adaptive changes in gene regulation are important during early stages of social evolution. Polistes and Bombus exhibit greater similarity in patterns of adaptive evolution including greater overlap of genes experiencing positive selection, and greater positive selection on queen-biased genes. Our findings suggest that either adaptive evolution of a few key genes underlie the evolution of simpler forms of eusociality, or that the initial stages of social evolution lead to selection on a few key traits orchestrated by orthologous genes and networks.