Large-scale coding sequence change underlies the evolution of postdevelopmental novelty in honey bees

Ancient Secretory Pathways Contributed to the Evolutionary Origin of an Ecologically Impactful Bioluminescence System

Evolutionary innovations in chemical secretion-such as the production of secondary metabolites, pheromones, and toxins-profoundly impact ecological interactions across a broad diversity of life. These secretory innovations may involve a "legacy-plus-innovation" mode of evolution, whereby new biochemical pathways are integrated with conserved secretory processes to create novel products. Among secretory innovations, bioluminescence is important because it evolved convergently many times to influence predator-prey interactions, while often producing courtship signals linked to increased rates of speciation. However, whether or not deeply conserved secretory genes are used in secretory bioluminescence remains unexplored. Here, we show that in the ostracod Vargula tsujii, the evolutionary novel c-luciferase gene is co-expressed with many conserved genes, including those related to toxin production and high-output protein secretion. Our results demonstrate that the legacy-plus-innovation mode of secretory evolution, previously applied to sensory modalities of olfaction, gustation, and nociception, also encompasses light-producing signals generated by bioluminescent secretions. This extension broadens the paradigm of secretory diversification to include not only chemical signals but also bioluminescent light as an important medium of ecological interaction and evolutionary innovation.

Fundamental Patterns of Structural Evolution Revealed by Chromosome-Length Genomes of Cactophilic Drosophila

A thorough understanding of adaptation and speciation requires model organisms with both a history of ecological and phenotypic study as well as a complete set of genomic resources. In particular, high-quality genome assemblies of ecological model organisms are needed to assess the evolution of genome structure and its role in adaptation and speciation. Here, we generate new genomes of cactophilic Drosophila, a crucial model clade for understanding speciation and ecological adaptation in xeric environments. We generated chromosome-level genome assemblies and complete annotations for seven populations across Drosophila mojavensis, Drosophila arizonae, and Drosophila navojoa. We use these data first to establish the most robust phylogeny for this clade to date, and to assess patterns of molecular evolution across the phylogeny, showing concordance with a priori hypotheses regarding adaptive genes in this system. We then show that structural evolution occurs at constant rate across the phylogeny, varies by chromosome, and is correlated with molecular evolution. These results advance the understanding of the D. mojavensis clade by demonstrating core evolutionary genetic patterns and integrating those patterns to generate new gene-level hypotheses regarding adaptation. Our data are presented in a new public database (cactusflybase.arizona.edu), providing one of the most in-depth resources for the analysis of inter- and intraspecific evolutionary genomic data. Furthermore, we anticipate that the patterns of structural evolution identified here will serve as a baseline for future comparative studies to identify the factors that influence the evolution of genome structure across taxa.

Expression of honey bee (Apis mellifera) sterol homeostasis genes in food jelly producing glands of workers

Adult workers of Western honey bees (Apis mellifera L.) acquire sterols from their pollen diet. These food sterols are transported by the hemolymph to peripheral tissues such as the mandibular and the hypopharyngeal glands in the worker bees' heads that secrete food jelly which is fed to developing larvae. As sterols are obligatory components of biological membranes and essential precursors for molting hormone synthesis in insects, they are indispensable to normal larval development. Thus, the study of sterol delivery to larvae is important for a full understanding of honey bee larval nutrition and development. Whereas hypopharyngeal glands only require sterols for their membrane integrity, mandibular glands add sterols, primarily 24-methylenecholesterol, to its secretion. For this, sterols must be transported through the glandular epithelial cells. We have analyzed for the first time in A. mellifera the expression of genes which are involved in intracellular movement of sterols. Mandibular and hypopharyngeal glands were dissected from newly emerged bees, 6-day-old nurse bees that feed larvae and 26-day-old forager bees. The expression of seven genes involved in intracellular sterol metabolism was measured with quantitative real-time PCR. Relative transcript abundance of sterol metabolism genes was significantly influenced by the age of workers and specific genes but not by gland type. Newly emerged bees had significantly more transcripts for six out of seven genes than older bees indicating that the bulk of the proteins needed for sterol metabolism are produced directly after emergence.

Gene regulation supporting sociality shared across lineages and variation in complexity

Across evolutionary lineages, insects vary in social complexity, from those that exhibit extended parental care to those with elaborate divisions of labor. Here, we synthesize the sociogenomic resources from hundreds of species to describe common gene regulatory mechanisms in insects that regulate social organization across phylogeny and levels of social complexity. Different social phenotypes expressed by insects can be linked to the organization of co-expressing gene networks and features of the epigenetic landscape. Insect sociality also stems from processes like the emergence of parental care and the decoupling of ancestral genetic programs. One underexplored avenue is how variation in a group's social environment affects the gene expression of individuals. Additionally, an experimental reduction of gene expression would demonstrate how the activity of specific genes contributes to insect social phenotypes. While tissue specificity provides greater localization of the gene expression underlying social complexity, emerging transcriptomic analysis of insect brains at the cellular level provides even greater resolution to understand the molecular basis of social insect evolution.

A chromosome-level genome for the nudibranch gastropod Berghia stephanieae helps parse clade-specific gene expression in novel and conserved phenotypes

BACKGROUND

How novel phenotypes originate from conserved genes, processes, and tissues remains a major question in biology. Research that sets out to answer this question often focuses on the conserved genes and processes involved, an approach that explicitly excludes the impact of genetic elements that may be classified as clade-specific, even though many of these genes are known to be important for many novel, or clade-restricted, phenotypes. This is especially true for understudied phyla such as mollusks, where limited genomic and functional biology resources for members of this phylum have long hindered assessments of genetic homology and function. To address this gap, we constructed a chromosome-level genome for the gastropod Berghia stephanieae (Valdés, 2005) to investigate the expression of clade-specific genes across both novel and conserved tissue types in this species.

RESULTS

The final assembled and filtered Berghia genome is comparable to other high-quality mollusk genomes in terms of size (1.05 Gb) and number of predicted genes (24,960 genes) and is highly contiguous. The proportion of upregulated, clade-specific genes varied across tissues, but with no clear trend between the proportion of clade-specific genes and the novelty of the tissue. However, more complex tissue like the brain had the highest total number of upregulated, clade-specific genes, though the ratio of upregulated clade-specific genes to the total number of upregulated genes was low.

CONCLUSIONS

Our results, when combined with previous research on the impact of novel genes on phenotypic evolution, highlight the fact that the complexity of the novel tissue or behavior, the type of novelty, and the developmental timing of evolutionary modifications will all influence how novel and conserved genes interact to generate diversity.

A chromosome-level genome for the nudibranch gastropod Berghia stephanieae helps parse clade-specific gene expression in novel and conserved phenotypes

How novel phenotypes originate from conserved genes, processes, and tissues remains a major question in biology. Research that sets out to answer this question often focuses on the conserved genes and processes involved, an approach that explicitly excludes the impact of genetic elements that may be classified as clade-specific, even though many of these genes are known to be important for many novel, or clade-restricted, phenotypes. This is especially true for understudied phyla such as mollusks, where limited genomic and functional biology resources for members of this phylum has long hindered assessments of genetic homology and function. To address this gap, we constructed a chromosome-level genome for the gastropod Berghia stephanieae (Valdés, 2005) to investigate the expression of clade-specific genes across both novel and conserved tissue types in this species. The final assembled and filtered Berghia genome is comparable to other high quality mollusk genomes in terms of size (1.05 Gb) and number of predicted genes (24,960 genes), and is highly contiguous. The proportion of upregulated, clade-specific genes varied across tissues, but with no clear trend between the proportion of clade-specific genes and the novelty of the tissue. However, more complex tissue like the brain had the highest total number of upregulated, clade-specific genes, though the ratio of upregulated clade-specific genes to the total number of upregulated genes was low. Our results, when combined with previous research on the impact of novel genes on phenotypic evolution, highlight the fact that the complexity of the novel tissue or behavior, the type of novelty, and the developmental timing of evolutionary modifications will all influence how novel and conserved genes interact to generate diversity.

Comparative transcriptomics reveals that a novel form of phenotypic plasticity evolved via lineage-specific changes in gene expression

Novel forms of phenotypic plasticity may evolve by lineage-specific changes or by co-opting mechanisms from more general forms of plasticity. Here, we evaluated whether a novel resource polyphenism in New World spadefoot toads (genus Spea) evolved by co-opting mechanisms from an ancestral form of plasticity common in anurans-accelerating larval development rate in response to pond drying. We compared overlap in differentially expressed genes between alternative trophic morphs constituting the polyphenism in Spea versus those found between tadpoles of Old World spadefoot toads (genus Pelobates) when experiencing different pond-drying regimes. Specifically, we (1) generated a de novo transcriptome and conducted differential gene expression analysis in Spea multiplicata, (2) utilized existing gene expression data and a recently published transcriptome for Pelobates cultripes when exposed to different drying regimes, and (3) identified unique and overlapping differentially expressed transcripts. We found thousands of differentially expressed genes between S. multiplicata morphs that were involved in major developmental reorganization, but the vast majority of these were not differentially expressed in P. cultripes. Thus, S. multiplicata's novel polyphenism appears to have arisen primarily through lineage-specific changes in gene expression and not by co-opting existing patterns of gene expression involved in pond-drying plasticity. Therefore, although ancestral stress responses might jump-start evolutionary innovation, substantial lineage-specific modification might be needed to refine these responses into more complex forms of plasticity.

Convergent and complementary selection shaped gains and losses of eusociality in sweat bees

Sweat bees have repeatedly gained and lost eusociality, a transition from individual to group reproduction. Here we generate chromosome-length genome assemblies for 17 species and identify genomic signatures of evolutionary trade-offs associated with transitions between social and solitary living. Both young genes and regulatory regions show enrichment for these molecular patterns. We also identify loci that show evidence of complementary signals of positive and relaxed selection linked specifically to the convergent gains and losses of eusociality in sweat bees. This includes two pleiotropic proteins that bind and transport juvenile hormone (JH)-a key regulator of insect development and reproduction. We find that one of these proteins is primarily expressed in subperineurial glial cells that form the insect blood-brain barrier and that brain levels of JH vary by sociality. Our findings are consistent with a role of JH in modulating social behaviour and suggest that eusocial evolution was facilitated by alteration of the proteins that bind and transport JH, revealing how an ancestral developmental hormone may have been co-opted during one of life's major transitions. More broadly, our results highlight how evolutionary trade-offs have structured the molecular basis of eusociality in these bees and demonstrate how both directional selection and release from constraint can shape trait evolution.

Expression of subunits of an insecticide target receptor varies across tissues, life stages, castes, and species of social bees

Global losses of insects jeopardize ecosystem stability and crop pollination. Robust evidence indicates that insecticides have contributed to these losses. Notably, insecticides targeting nicotinic acetylcholine receptors (nAChRs) have neurotoxic effects on beneficial insects. Because each nAChR consists of five subunits, the alternative arrangements of subunits could create a multitude of receptors differing in structure and function. Therefore, understanding whether the use of subunits varies is essential for evaluating and predicting the effects of insecticides targeting such receptors. To better understand how the use and composition of nAChRs differ within and between insect pollinators, we analysed RNA-seq gene expression data from tissues and castes of Apis mellifera honey bees and life stages and castes of the Bombus terrestris bumble bees. We reveal that all analysed tissues express nAChRs and that relative expression levels of nAChR subunits vary widely across almost all comparisons. Our work thus shows fine-tuned spatial and temporal expression of nAChRs. Given that coexpression of subunits underpins the compositional diversity of functional receptors and that the affinities of insecticides depend on nAChR composition, our findings provide a likely mechanism for the various damaging effects of nAChR-targeting insecticides on insects. Furthermore, our results indicate that the appraisal of insecticide risks should carefully consider variation in molecular targets.

Social complexity, life-history and lineage influence the molecular basis of castes in vespid wasps

A key mechanistic hypothesis for the evolution of division of labour in social insects is that a shared set of genes co-opted from a common solitary ancestral ground plan (a genetic toolkit for sociality) regulates caste differentiation across levels of social complexity. Using brain transcriptome data from nine species of vespid wasps, we test for overlap in differentially expressed caste genes and use machine learning models to predict castes using different gene sets. We find evidence of a shared genetic toolkit across species representing different levels of social complexity. We also find evidence of additional fine-scale differences in predictive gene sets, functional enrichment and rates of gene evolution that are related to level of social complexity, lineage and of colony founding. These results suggest that the concept of a shared genetic toolkit for sociality may be too simplistic to fully describe the process of the major transition to sociality.

Gene transcriptional profiles in gonads of Bacillus taxa (Phasmida) with different cytological mechanisms of automictic parthenogenesis

The evolution of automixis - i.e., meiotic parthenogenesis - requires several features, including ploidy restoration after meiosis and maintenance of fertility. Characterizing the relative contribution of novel versus pre-existing genes and the similarities in their expression and sequence evolution is fundamental to understand the evolution of reproductive novelties. Here we identify gonads-biased genes in two Bacillus automictic stick-insects and compare their expression profile and sequence evolution with a bisexual congeneric species. The two parthenogens restore ploidy through different cytological mechanisms: in Bacillus atticus, nuclei derived from the first meiotic division fuse to restore a diploid egg nucleus, while in Bacillus rossius, diploidization occurs in some cells of the haploid blastula through anaphase restitution. Parthenogens' gonads transcriptional program is found to be largely assembled from genes that were already present before the establishment of automixis. The three species transcriptional profiles largely reflect their phyletic relationships, yet we identify a shared core of genes with gonad-biased patterns of expression in parthenogens which are either male gonads-biased in the sexual species or are not differentially expressed there. At the sequence level, just a handful of gonads-biased genes were inferred to have undergone instances of positive selection exclusively in the parthenogen species. This work is the first to explore the molecular underpinnings of automixis in a comparative framework: it delineates how reproductive novelties can be sustained by genes whose origin precedes the establishment of the novelty itself and shows that different meiotic mechanisms of reproduction can be associated with a shared molecular ground plan.

Convergent Loss of Prothoracicotropic Hormone, A Canonical Regulator of Development, in Social Bee Evolution

The evolution of insect sociality has repeatedly involved changes in developmental events and their timing. Here, we propose the hypothesis that loss of a canonical regulator of moulting and metamorphosis, prothoracicotropic hormone (PTTH), and its receptor, Torso, is associated with the evolution of sociality in bees. Specifically, we posit that the increasing importance of social influences on early developmental timing in social bees has led to their decreased reliance on PTTH, which connects developmental timing with abiotic cues in solitary insects. At present, the evidence to support this hypothesis includes the absence of genes encoding PTTH and Torso from all fully-sequenced social bee genomes and its presence in all available genomes of solitary bees. Based on the bee phylogeny, the most parsimonious reconstruction of evolutionary events is that this hormone and its receptor have been lost multiple times, across independently social bee lineages. These gene losses shed light on possible molecular and cellular mechanisms that are associated with the evolution of social behavior in bees. We outline the available evidence for our hypothesis, and then contextualize it in light of what is known about developmental cues in social and solitary bees, and the multiple precedences of major developmental changes in social insects.

Genetic Drift and Purifying Selection Shaped Mitochondrial Genome Variation in the High Royal Jelly-Producing Honeybee Strain (Apis mellifera ligustica)

Mitochondrial genomes (mitogenomes) are involved in cellular energy metabolism and have been shown to undergo adaptive evolution in organisms with increased energy-consuming activities. The genetically selected high royal jelly-producing bees (RJBs, Apis mellifera ligustica) in China can produce 10 times more royal jelly, a highly nutritional and functional food, relative to unselected Italian bees (ITBs). To test for potential adaptive evolution of RJB mitochondrial genes, we sequenced mitogenomes from 100 RJBs and 30 ITBs. Haplotype network and phylogenetic analysis indicate that RJBs and ITBs are not reciprocally monophyletic but mainly divided into the RJB- and ITB-dominant sublineages. The RJB-dominant sublineage proportion is 6-fold higher in RJBs (84/100) than in ITBs (4/30), which is mainly attributable to genetic drift rather than positive selection. The RJB-dominant sublineage exhibits a low genetic diversity due to purifying selection. Moreover, mitogenome abundance is not significantly different between RJBs and ITBs, thereby rejecting the association between mitogenome copy number and royal jelly-producing performance. Our findings demonstrate low genetic diversity levels of RJB mitogenomes and reveal genetic drift and purifying selection as potential forces driving RJB mitogenome evolution.

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.

Reproductive activation in honeybee (Apis mellifera) workers protects against abiotic and biotic stress

Social insect reproductives exhibit exceptional longevity instead of the classic trade-off between somatic maintenance and reproduction. Even normally sterile workers experience a significant increase in life expectancy when they assume a reproductive role. The mechanisms that enable the positive relation between the antagonistic demands of reproduction and somatic maintenance are unclear. To isolate the effect of reproductive activation, honeybee workers were induced to activate their ovaries. These reproductively activated workers were compared to controls for survival and gene expression patterns after exposure to Israeli Acute Paralysis Virus or the oxidative stressor paraquat. Reproductive activation increased survival, indicating better immunity and oxidative stress resistance. After qPCR analysis confirmed our experimental treatments at the physiological level, whole transcriptome analysis revealed that paraquat treatment significantly changed the expression of 1277 genes in the control workers but only two genes in reproductively activated workers, indicating that reproductive activation preemptively protects against oxidative stress. Significant overlap between genes that were upregulated by reproductive activation and in response to paraquat included prominent members of signalling pathways and anti-oxidants known to affect ageing. Thus, while our results confirm a central role of vitellogenin, they also point to other mechanisms to explain the molecular basis of the lack of a cost of reproduction and the exceptional longevity of social insect reproductives. Thus, socially induced reproductive activation preemptively protects honeybee workers against stressors, explaining their longevity. This article is part of the theme issue 'Ageing and sociality: why, when and how does sociality change ageing patterns?'

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.

Gene expression during larval caste determination and differentiation in intermediately eusocial bumblebees, and a comparative analysis with advanced eusocial honeybees

The queen‐worker caste system of eusocial insects represents a prime example of developmental polyphenism (environmentally‐induced phenotypic polymorphism) and is intrinsic to the evolution of advanced eusociality. However, the comparative molecular basis of larval caste determination and subsequent differentiation in the eusocial Hymenoptera remains poorly known. To address this issue within bees, we profiled caste‐associated gene expression in female larvae of the intermediately eusocial bumblebee Bombus terrestris. In B. terrestris, female larvae experience a queen‐dependent period during which their caste fate as adults is determined followed by a nutrition‐sensitive period also potentially affecting caste fate but for which the evidence is weaker. We used mRNA‐seq and qRT‐PCR validation to isolate genes differentially expressed between each caste pathway in larvae at developmental stages before and after each of these periods. We show that differences in gene expression between caste pathways are small in totipotent larvae, then peak after the queen‐dependent period. Relatively few novel (i.e., taxonomically‐restricted) genes were differentially expressed between castes, though novel genes were significantly enriched in late‐instar larvae in the worker pathway. We compared sets of caste‐associated genes in B. terrestris with those reported from the advanced eusocial honeybee, Apis mellifera, and found significant but relatively low levels of overlap of gene lists between the two species. These results suggest both the existence of low numbers of shared toolkit genes and substantial divergence in caste‐associated genes between Bombus and the advanced eusocial Apis since their last common eusocial ancestor.

Injection of seminal fluid into the hemocoel of honey bee queens (Apis mellifera) can stimulate post-mating changes

Honey bee queens undergo dramatic behavioral (e.g., reduced sexual receptivity), physiological (e.g., ovary activation, ovulation, and modulation of pheromone production) and transcriptional changes after they complete mating. To elucidate how queen post-mating changes are influenced by seminal fluid, the non-spermatozoa-containing component of semen, we injected queens with semen or seminal fluid alone. We assessed queen sexual receptivity (as measured by likelihood to take mating flights), ovary activation, worker retinue response (which is influenced by queen pheromone production), and transcriptional changes in queen abdominal fat body and brain tissues. Injection with either seminal fluid or semen resulted in decreased sexual receptivity, increased attractiveness of queens to workers, and altered expression of several genes that are also regulated by natural mating in queens. The post-mating and transcriptional changes of queens receiving seminal fluid were not significantly different from queens injected with semen, suggesting that components in seminal fluid, such as seminal fluid proteins, are largely responsible for stimulating post-mating changes in queens.

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.

Distributed physiology and the molecular basis of social life in eusocial insects

The traditional focus of physiological and functional genomic research is on molecular processes that play out within a single multicellular organism. In the colonial (eusocial) insects such as ants, bees, and termites, molecular and behavioral responses of interacting nestmates are tightly linked, and key physiological processes are regulated at the scale of the colony. Such colony-level physiological processes regulate nestmate physiology in a distributed fashion, through various social communication mechanisms. As a result of physiological decentralization over evolutionary time, organismal mechanisms, for example related to pheromone detection, hormone signaling, and neural signaling pathways, are deployed in novel contexts to influence nestmate and colony traits. Here we explore how functional genomic, physiological, and behavioral studies can benefit from considering the traits of eusocial insects in this light. We highlight functional genomic work exploring how nestmate-level and colony-level traits arise and are influenced by interactions among physiologically-specialized nestmates of various developmental stages. We also consider similarities and differences between nestmate-level (organismal) and colony-level (superorganismal) physiological processes, and make specific hypotheses regarding the physiology of eusocial taxa. Integrating theoretical models of distributed systems with empirical functional genomics approaches will be useful in addressing fundamental questions related to the evolution of eusociality and collective behavior in natural systems.

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.

Gene expression variation in the brains of harvester ant foragers is associated with collective behavior

Natural selection on collective behavior acts on variation among colonies in behavior that is associated with reproductive success. In the red harvester ant (Pogonomyrmex barbatus), variation among colonies in the collective regulation of foraging in response to humidity is associated with colony reproductive success. We used RNA-seq to examine gene expression in the brains of foragers in a natural setting. We find that colonies differ in the expression of neurophysiologically-relevant genes in forager brains, and a fraction of these gene expression differences are associated with two colony traits: sensitivity of foraging activity to humidity, and forager brain dopamine to serotonin ratio. Loci that were correlated with colony behavioral differences were enriched in neurotransmitter receptor signaling & metabolic functions, tended to be more central to coexpression networks, and are evolving under higher protein-coding sequence constraint. Natural selection may shape colony foraging behavior through variation in gene expression.

Molecular Profiling of the Drosophila Antenna Reveals Conserved Genes Underlying Olfaction in Insects

Repellent odors are widely used to prevent insect-borne diseases, making it imperative to identify the conserved molecular underpinnings of their olfactory systems. Currently, little is known about the molecules supporting odor signaling beyond the odor receptors themselves. Most known molecules function in one of two classes of olfactory sensilla, single-walled or double-walled, which have differing morphology and odor response profiles. Here, we took two approaches to discover novel genes that contribute to insect olfaction in the periphery. We transcriptionally profiled Drosophila melanogasteramos mutants that lack trichoid and basiconic sensilla, the single-walled sensilla in this species. This revealed 187 genes whose expression is enriched in these sensilla, including pickpocket ion channels and neuromodulator GPCRs that could mediate signaling pathways unique to single-walled sensilla. For our second approach, we computationally identified 141 antennal-enriched (AE) genes that are more than ten times as abundant in D. melanogaster antennae as in other tissues or whole-body extracts, and are thus likely to play a role in olfaction. We identified unambiguous orthologs of AE genes in the genomes of four distantly related insect species, and most identified orthologs were expressed in the antenna of these species. Further analysis revealed that nearly half of the 141 AE genes are localized specifically to either single or double-walled sensilla. Functional annotation suggests the AE genes include signaling molecules and enzymes that could be involved in odorant degradation. Together, these two resources provide a foundation for future studies investigating conserved mechanisms of odor signaling.

From phenotype to genotype: the precursor hypothesis predicts genetic influences that facilitate transitions in social behavior

Parental care is expected to be one of the key evolutionary precursors to advanced social behavior. This suggests that there could be common genetic underpinnings to both parental care and sociality. However, little is known of the genetics underlying care. Here, we suggest that ethological predictions of behavioral precursors to care along with a genetic toolkit for behavior provide testable hypotheses and a defined approach to investigating genetics of sociality. We call this the 'precursor hypothesis'.

Integrative Genomics Reveals the Genetics and Evolution of the Honey Bee's Social Immune System

Social organisms combat pathogens through individual innate immune responses or through social immunity—behaviors among individuals that limit pathogen transmission within groups. Although we have a relatively detailed understanding of the genetics and evolution of the innate immune system of animals, we know little about social immunity. Addressing this knowledge gap is crucial for understanding how life-history traits influence immunity, and identifying if trade-offs exist between innate and social immunity. Hygienic behavior in the Western honey bee, Apis mellifera, provides an excellent model for investigating the genetics and evolution of social immunity in animals. This heritable, colony-level behavior is performed by nurse bees when they detect and remove infected or dead brood from the colony. We sequenced 125 haploid genomes from two artificially selected highly hygienic populations and a baseline unselected population. Genomic contrasts allowed us to identify a minimum of 73 genes tentatively associated with hygienic behavior. Many genes were within previously discovered QTLs associated with hygienic behavior and were predictive of hygienic behavior within the unselected population. These genes were often involved in neuronal development and sensory perception in solitary insects. We found that genes associated with hygienic behavior have evidence of positive selection within honey bees (Apis), supporting the hypothesis that social immunity contributes to fitness. Our results indicate that genes influencing developmental neurobiology and behavior in solitary insects may have been co-opted to give rise to a novel and adaptive social immune phenotype in honey bees.

Convergent eusocial evolution is based on a shared reproductive groundplan plus lineage-specific plastic genes

Eusociality has convergently evolved multiple times, but the genomic basis of caste-based division of labor and degree to which independent origins of eusociality have utilized common genes remain largely unknown. Here we characterize caste-specific transcriptomic profiles across development and adult body segments from pharaoh ants (Monomorium pharaonis) and honey bees (Apis mellifera), representing two independent origins of eusociality. We identify a substantial shared core of genes upregulated in the abdomens of queen ants and honey bees that also tends to be upregulated in mated female flies, suggesting that these genes are part of a conserved insect reproductive groundplan. Outside of this shared groundplan, few genes are differentially expressed in common. Instead, the majority of the thousands of caste-associated genes are plastically expressed, rapidly evolving, and relatively evolutionarily young. These results emphasize that the recruitment of both highly conserved and lineage-specific genes underlie the convergent evolution of novel traits such as eusociality.

Eusocial caste systems have evolved independently multiple times. Here, Warner et al. investigate the amount of shared vs. lineage-specific genes involved in the evolution of caste in pharaoh ants and honey bees by comparing transcriptomes across tissues, developmental stages, and castes.

Taxonomically Restricted Genes Are Fundamental to Biology and Evolution

Genes limited to particular clades, taxonomically restricted genes (TRGs), are common in all sequenced genomes. TRGs have recently become associated with the evolution of novelty, as numerous studies across the tree of life have now linked expression of TRGs with novel phenotypes. However, TRGs that underlie ancient lineage specific traits have been largely omitted from discussions of the general importance of TRGs. Here it is argued that when all TRGs are considered, it is apparent that TRGs are fundamental to biology and evolution and likely play many complementary roles to the better understood toolkit genes. Genes underlying photosynthesis and skeletons, for example, are examples of commonplace fundamental TRGs. Essentially, although basic cell biology has a highly conserved genetic basis across the tree of life, most major clades also have lineage specific traits central to their biology and these traits are often based on TRGs. In short, toolkit genes underlie what is conserved across organisms, while TRGs define in many cases what is unique. An appreciation of the importance of TRGs will improve our understanding of evolution by triggering the study of neglected topics in which TRGs are of paramount importance.

A morphological novelty evolved by co-option of a reduced gene regulatory network and gene recruitment in a beetle

The mechanisms underlying the evolution of morphological novelties have remained enigmatic but co-option of existing gene regulatory networks (GRNs), recruitment of genes and the evolution of orphan genes have all been suggested to contribute. Here, we study a morphological novelty of beetle pupae called gin-trap. By combining the classical candidate gene approach with unbiased screening in the beetle Tribolium castaneum, we find that 70% of the tested components of the wing network were required for gin-trap development. However, many downstream and even upstream components were not included in the co-opted network. Only one gene was recruited from another biological context, but it was essential for the anteroposterior symmetry of the gin-traps, which represents a gin-trap-unique morphological innovation. Our data highlight the importance of co-option and modification of GRNs. The recruitment of single genes may not be frequent in the evolution of morphological novelties, but may be essential for subsequent diversification of the novelties. Finally, after having screened about 28% of annotated genes in the Tribolium genome to identify the genes required for gin-trap development, we found none of them are orphan genes, suggesting that orphan genes may have played only a minor, if any, role in the evolution of gin-traps.

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.

Genetics and Genomics of Social Behavior in a Chicken Model

The identification of genes affecting sociality can give insights into the maintenance and development of sociality and personality. In this study, we used the combination of an advanced intercross between wild and domestic chickens with a combined QTL and eQTL genetical genomics approach to identify genes for social reinstatement, a social and anxiety-related behavior. A total of 24 social reinstatement QTL were identified and overlaid with over 600 eQTL obtained from the same birds using hypothalamic tissue. Correlations between overlapping QTL and eQTL indicated five strong candidate genes, with the gene TTRAP being strongly significantly correlated with multiple aspects of social reinstatement behavior, as well as possessing a highly significant eQTL.

Differential expression of a fructose receptor gene in honey bee workers according to age and behavioral role

Honey bee (Apis mellifera) workers contribute to the maintenance of colonies in various ways. The primary functions of workers are divided into two types depending on age: young workers (nurses) primarily engage in such behaviors as cleaning and food handling within the hive, whereas older workers (foragers) acquire floral nutrients beyond the colony. Concomitant with this age-dependent change in activity, physiological changes occur in the tissues and organs of workers. Nurses supply younger larvae with honey containing high levels of glucose and supply older larvae with honey containing high levels of fructose. Given that nurses must determine both the concentration and type of sugar used in honey, gustatory receptors (Gr) expressed in the chemosensory organs likely play a role in distinguishing between sugars. Glucose is recognized by Gr1 in honey bees (AmGr1); however, it remains unclear which Gr are responsible for fructose recognition. This study aimed to identify fructose receptors in honey bees and reported that AmGr3, when transiently expressed in Xenopus oocytes, responded only to fructose, and to no other sugars. We analyzed expression levels of AmGr3 to identify which tissues and organs of workers are involved in fructose recognition and determined that expression of AmGr3 was particularly high in the antennae and legs of nurses. Our results suggest that nurses use their antennae and legs to recognize fructose, and that AmGr3 functions as an accurate nutrient sensor used to maintain food quality in honey bee hives.

Taxon-restricted genes at the origin of a novel trait allowing access to a new environment

Taxon-restricted genes make up a considerable proportion of genomes, yet their contribution to phenotypic evolution is poorly understood. We combined gene expression with functional and behavioral assays to study the origin and adaptive value of an evolutionary innovation exclusive to the water strider genus Rhagovelia: the propelling fan. We discovered that two taxon-restricted genes, which we named geisha and mother-of-geisha, specifically control fan development. geisha originated through a duplication event at the base of the Rhagovelia lineage, and both duplicates acquired a novel expression in a specific cell population prefiguring fan development. These gene duplicates played a central role in Rhagovelia's adaptation to a new physical environment, demonstrating that the evolution of taxon-restricted genes can contribute directly to evolutionary novelties that allow access to unexploited ecological niches.

Gene duplication and the evolution of phenotypic diversity in insect societies

Gene duplication is an important evolutionary process thought to facilitate the evolution of phenotypic diversity. We investigated if gene duplication was associated with the evolution of phenotypic differences in a highly social insect, the honeybee Apis mellifera. We hypothesized that the genetic redundancy provided by gene duplication could promote the evolution of social and sexual phenotypes associated with advanced societies. We found a positive correlation between sociality and rate of gene duplications across the Apoidea, indicating that gene duplication may be associated with sociality. We also discovered that genes showing biased expression between A. mellifera alternative phenotypes tended to be found more frequently than expected among duplicated genes than singletons. Moreover, duplicated genes had higher levels of caste-, sex-, behavior-, and tissue-biased expression compared to singletons, as expected if gene duplication facilitated phenotypic differentiation. We also found that duplicated genes were maintained in the A. mellifera genome through the processes of conservation, neofunctionalization, and specialization, but not subfunctionalization. Overall, we conclude that gene duplication may have facilitated the evolution of social and sexual phenotypes, as well as tissue differentiation. Thus this study further supports the idea that gene duplication allows species to evolve an increased range of phenotypic diversity.

Fire ant social chromosomes: Differences in number, sequence and expression of odorant binding proteins

Variation in social behavior is common yet our knowledge of the mechanisms underpinning its evolution is limited. The fire ant Solenopsis invicta provides a textbook example of a Mendelian element controlling social organization: alternate alleles of a genetic element first identified as encoding an odorant binding protein (OBP) named Gp-9 determine whether a colony accepts one or multiple queens. The potential roles of such a protein in perceiving olfactory cues and evidence of positive selection on its amino acid sequence made it an appealing candidate gene. However, we recently showed that recombination is suppressed between Gp-9 and hundreds of other genes as part of a >19 Mb supergene-like region carried by a pair of social chromosomes. This finding raises the need to reassess the potential role of Gp-9. We identify 23 OBPs in the fire ant genome assembly, including nine located in the region of suppressed recombination with Gp-9. For six of these, the alleles carried by the two variants of the supergene-like region differ in protein-coding sequence and thus likely in function, with Gp-9 showing the strongest evidence of positive selection. We identify an additional OBP specific to the Sb variant of the region. Finally, we find that 14 OBPs are differentially expressed between single- and multiple-queen colonies. These results are consistent with multiple OBPs playing a role in determining social structure.

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

Eusociality represents a major transition in evolution and is typified by cooperative brood care and reproductive division of labor between generations. In bees, this division of labor allows queens and workers to phenotypically specialize. Worker traits associated with helping are thought to be crucial to the fitness of a eusocial lineage, and recent studies of honey bees (genus Apis) have found that adaptively evolving genes often have worker-biased expression patterns. It is unclear however if worker-biased genes are disproportionately acted on by strong positive selection in all eusocial insects. We undertook a comparative population genomics study of bumble bees (Bombus) and honey bees to quantify natural selection on queen- and worker-biased genes across two levels of social complexity. Despite sharing a common eusocial ancestor, genes, and gene groups with the highest levels of positive selection were often unique within each genus, indicating that life history and the environment, but not sociality per se, drives patterns of adaptive molecular evolution. We uncovered differences in the contribution of queen- and worker-biased genes to adaptive evolution in bumble bees versus honey bees. Unlike honey bees, where worker-biased genes are enriched for signs of adaptive evolution, genes experiencing positive selection in bumble bees were predominately expressed by reproductive foundresses during the initial solitary-founding stage of colonies. Our study suggests that solitary founding is a major selective pressure and that the loss of queen totipotency may cause a change in the architecture of selective pressures upon the social insect genome.

Genetics and Evolution of Social Behavior in Insects

The study of insect social behavior has offered tremendous insight into the molecular mechanisms mediating behavioral and phenotypic plasticity. Genomic applications to the study of eusocial insect species, in particular, have led to several hypotheses for the processes underlying the molecular evolution of behavior. Advances in understanding the genetic control of social organization have also been made, suggesting an important role for supergenes in the evolution of divergent behavioral phenotypes. Intensive study of social phenotypes across species has revealed that behavior and caste are controlled by an interaction between genetic and environmentally mediated effects and, further, that gene expression and regulation mediate plastic responses to environmental signals. However, several key methodological flaws that are hindering progress in the study of insect social behavior remain. After reviewing the current state of knowledge, we outline ongoing challenges in experimental design that remain to be overcome in order to advance the field.

Accelerated Evolution of Developmentally Biased Genes in the Tetraphenic Ant Cardiocondyla obscurior

Plastic gene expression underlies phenotypic plasticity and plastically expressed genes evolve under different selection regimes compared with ubiquitously expressed genes. Social insects are well-suited models to elucidate the evolutionary dynamics of plastic genes for their genetically and environmentally induced discrete polymorphisms. Here, we study the evolution of plastically expressed genes in the ant Cardiocondyla obscurior—a species that produces two discrete male morphs in addition to the typical female polymorphism of workers and queens. Based on individual-level gene expression data from 28 early third instar larvae, we test whether the same evolutionary dynamics that pertain to plastically expressed genes in adults also pertain to genes with plastic expression during development. In order to quantify plasticity of gene expression over multiple contrasts, we develop a novel geometric measure. For genes expressed during development, we show that plasticity of expression is positively correlated with evolutionary rates. We furthermore find a strong correlation between expression plasticity and expression variation within morphs, suggesting a close link between active and passive plasticity of gene expression. Our results support the notion of relaxed selection and neutral processes as important drivers in the evolution of adaptive plasticity.

Evolutionary constraints shape caste-specific gene expression across 15 ant species

Development of polymorphic phenotypes from similar genomes requires gene expression differences. However, little is known about how morph-specific gene expression patterns vary on a broad phylogenetic scale. We hypothesize that evolution of morph-specific gene expression, and consequently morph-specific phenotypic evolution, may be constrained by gene essentiality and the amount of pleiotropic constraints. Here, we use comparative transcriptomics of queen and worker morphs, that is, castes, from 15 ant species to understand the constraints of morph-biased gene expression. In particular, we investigate how measures of evolutionary constraints at the sequence level (expression level, connectivity, and number of gene ontology [GO] terms) correlate with morph-biased expression. Our results show that genes indeed vary in their potential to become morph-biased. The existence of genes that are constrained in becoming caste-biased potentially limits the evolutionary decoupling of the caste phenotypes, that is, it might result in "caste load" occasioning from antagonistic fitness variation, similarly to sexually antagonistic fitness variation between males and females. On the other hand, we suggest that genes under low constraints are released from antagonistic variation and thus more likely to be co-opted for morph specific use. Overall, our results suggest that the factors that affect sequence evolutionary rates and evolution of plastic expression may largely overlap.

Gene expression and variation in social aggression by queens of the harvester ant Pogonomyrmex californicus

A key requirement for social cooperation is the mitigation and/or social regulation of aggression towards other group members. Populations of the harvester ant Pogonomyrmex californicus show the alternate social phenotypes of queens founding nests alone (haplometrosis) or in groups of unrelated yet cooperative individuals (pleometrosis). Pleometrotic queens display an associated reduction in aggression. To understand the proximate drivers behind this variation, we placed foundresses of the two populations into social environments with queens from the same or the alternate population, and measured their behaviour and head gene expression profiles. A proportion of queens from both populations behaved aggressively, but haplometrotic queens were significantly more likely to perform aggressive acts, and conflict escalated more frequently in pairs of haplometrotic queens. Whole-head RNA sequencing revealed variation in gene expression patterns, with the two populations showing moderate differentiation in overall transcriptional profile, suggesting that genetic differences underlie the two founding strategies. The largest detected difference, however, was associated with aggression, regardless of queen founding type. Several modules of coregulated genes, involved in metabolism, immune system and neuronal function, were found to be upregulated in highly aggressive queens. Conversely, nonaggressive queens exhibited a striking pattern of upregulation in chemosensory genes. Our results highlight that the social phenotypes of cooperative vs. solitary nest founding tap into a set of gene regulatory networks that seem to govern aggression level. We also present a number of highly connected hub genes associated with aggression, providing opportunity to further study the genetic underpinnings of social conflict and tolerance.

Do novel genes drive morphological novelty? An investigation of the nematosomes in the sea anemone Nematostella vectensis

BACKGROUND

The evolution of novel genes is thought to be a critical component of morphological innovation but few studies have explicitly examined the contribution of novel genes to the evolution of novel tissues. Nematosomes, the free-floating cellular masses that circulate through the body cavity of the sea anemone Nematostella vectensis, are the defining apomorphy of the genus Nematostella and are a useful model for understanding the evolution of novel tissues. Although many hypotheses have been proposed, the function of nematosomes is unknown. To gain insight into their putative function and to test hypotheses about the role of lineage-specific genes in the evolution of novel structures, we have re-examined the cellular and molecular biology of nematosomes.

RESULTS

Using behavioral assays, we demonstrate that nematosomes are capable of immobilizing live brine shrimp (Artemia salina) by discharging their abundant cnidocytes. Additionally, the ability of nematosomes to engulf fluorescently labeled bacteria (E. coli) reveals the presence of phagocytes in this tissue. Using RNA-Seq, we show that the gene expression profile of nematosomes is distinct from that of the tentacles and the mesenteries (their tissue of origin) and, further, that nematosomes (a Nematostella-specific tissue) are enriched in Nematostella-specific genes.

CONCLUSIONS

Despite the small number of cell types they contain, nematosomes are distinct among tissues, both functionally and molecularly. We provide the first evidence that nematosomes comprise part of the innate immune system in N. vectensis, and suggest that this tissue is potentially an important place to look for genes associated with pathogen stress. Finally, we demonstrate that Nematostella-specific genes comprise a significant proportion of the differentially expressed genes in all three of the tissues we examined and may play an important role in novel cell functions.

Ant Genetics: Reproductive Physiology, Worker Morphology, and Behavior

Many exciting studies have begun to elucidate the genetics of the morphological and physiological diversity of ants, but as yet few studies have investigated the genetics of ant behavior directly. Ant genomes are marked by extreme rates of gene turnover, especially in gene families related to olfactory communication, such as the synthesis of cuticular hydrocarbons and the perception of environmental semiochemicals. Transcriptomic and epigenetic differences are apparent between reproductive and sterile females, males and females, and workers that differ in body size. Quantitative genetic approaches suggest heritability of task performance, and population genetic studies indicate a genetic association with reproductive status in some species. Gene expression is associated with behavior including foraging, response to queens attempting to join a colony, circadian patterns of task performance, and age-related changes of task. Ant behavioral genetics needs further investigation of the feedback between individual-level physiological changes and socially mediated responses to environmental conditions.

Positive Selection and Centrality in the Yeast and Fly Protein-Protein Interaction Networks

Proteins within a molecular network are expected to be subject to different selective pressures depending on their relative hierarchical positions. However, it is not obvious what genes within a network should be more likely to evolve under positive selection. On one hand, only mutations at genes with a relatively high degree of control over adaptive phenotypes (such as those encoding highly connected proteins) are expected to be “seen” by natural selection. On the other hand, a high degree of pleiotropy at these genes is expected to hinder adaptation. Previous analyses of the human protein-protein interaction network have shown that genes under long-term, recurrent positive selection (as inferred from interspecific comparisons) tend to act at the periphery of the network. It is unknown, however, whether these trends apply to other organisms. Here, we show that long-term positive selection has preferentially targeted the periphery of the yeast interactome. Conversely, in flies, genes under positive selection encode significantly more connected and central proteins. These observations are not due to covariation of genes' adaptability and centrality with confounding factors. Therefore, the distribution of proteins encoded by genes under recurrent positive selection across protein-protein interaction networks varies from one species to another.

Comparative transcriptomics reveals the conserved building blocks involved in parallel evolution of diverse phenotypic traits in ants

BACKGROUND

Reproductive division of labor in eusocial insects is a striking example of a shared genetic background giving rise to alternative phenotypes, namely queen and worker castes. Queen and worker phenotypes play major roles in the evolution of eusocial insects. Their behavior, morphology and physiology underpin many ecologically relevant colony-level traits, which evolved in parallel in multiple species.

RESULTS

Using queen and worker transcriptomic data from 16 ant species we tested the hypothesis that conserved sets of genes are involved in ant reproductive division of labor. We further hypothesized that such sets of genes should also be involved in the parallel evolution of other key traits. We applied weighted gene co-expression network analysis, which clusters co-expressed genes into modules, whose expression levels can be summarized by their 'eigengenes'. Eigengenes of most modules were correlated with phenotypic differentiation between queens and workers. Furthermore, eigengenes of some modules were correlated with repeated evolution of key phenotypes such as complete worker sterility, the number of queens per colony, and even invasiveness. Finally, connectivity and expression levels of genes within the co-expressed network were strongly associated with the strength of selection. Although caste-associated sets of genes evolve faster than non-caste-associated, we found no evidence for queen- or worker-associated co-expressed genes evolving faster than one another.

CONCLUSIONS

These results identify conserved functionally important genomic units that likely serve as building blocks of phenotypic innovation, and allow the remarkable breadth of parallel evolution seen in ants, and possibly other eusocial insects as well.

Structure and function of gene regulatory networks associated with worker sterility in honeybees

A characteristic of eusocial bees is a reproductive division of labor in which one or a few queens monopolize reproduction, while her worker daughters take on reproductively altruistic roles within the colony. The evolution of worker reproductive altruism involves indirect selection for the coordinated expression of genes that regulate personal reproduction, but evidence for this type of selection remains elusive. In this study, we tested whether genes coexpressed under queen‐induced worker sterility show evidence of adaptive organization within a model brain transcriptional regulatory network (TRN). If so, this structured pattern would imply that indirect selection on nonreproductive workers has influenced the functional organization of genes within the network, specifically to regulate the expression of sterility. We found that literature‐curated sets of candidate genes for sterility, ranging in size from 18 to 267, show strong evidence of clustering within the three‐dimensional space of the TRN. This finding suggests that our candidate sets of genes for sterility form functional modules within the living bee brain's TRN. Moreover, these same gene sets colocate to a single, albeit large, region of the TRN's topology. This spatially organized and convergent pattern contrasts with a null expectation for functionally unrelated genes to be haphazardly distributed throughout the network. Our meta‐genomic analysis therefore provides first evidence for a truly “social transcriptome” that may regulate the conditional expression of honeybee worker sterility.

Genomic sources of phenotypic novelty in the evolution of eusociality in insects

Genomic resources are now available for closely related species that vary in social behavior, providing insight on the genomics of social evolution. Changes in the architecture of gene regulatory networks likely influence the evolutionary trajectory of social traits. Evolutionarily novel genes are likely important in the evolution of social diversity among insects, but it is unclear whether new genes played a driving role in the advent or elaboration of eusociality or if they were instead a result of other genomic features of eusociality. The worker phenotype appears to be the center of genetic novelty, but the mechanisms for this remain unresolved. Future studies are needed to understand how genetic novelty arises, becomes incorporated into existing gene regulatory networks, and the effects this has on the evolution of social traits in closely related social and solitary species.