Genes involved in convergent evolution of eusociality in bees

Eusociality has arisen independently at least 11 times in insects. Despite this convergence, there are striking differences among eusocial lifestyles, ranging from species living in small colonies with overt conflict over reproduction to species in which colonies contain hundreds of thousands of highly specialized sterile workers produced by one or a few queens. Although the evolution of eusociality has been intensively studied, the genetic changes involved in the evolution of eusociality are relatively unknown. We examined patterns of molecular evolution across three independent origins of eusociality by sequencing transcriptomes of nine socially diverse bee species and combining these data with genome sequence from the honey bee Apis mellifera to generate orthologous sequence alignments for 3,647 genes. We found a shared set of 212 genes with a molecular signature of accelerated evolution across all eusocial lineages studied, as well as unique sets of 173 and 218 genes with a signature of accelerated evolution specific to either highly or primitively eusocial lineages, respectively. These results demonstrate that convergent evolution can involve a mosaic pattern of molecular changes in both shared and lineage-specific sets of genes. Genes involved in signal transduction, gland development, and carbohydrate metabolism are among the most prominent rapidly evolving genes in eusocial lineages. These findings provide a starting point for linking specific genetic changes to the evolution of eusociality.

Nutritional regulation of division of labor in honey bees: toward a systems biology perspective

Organisms adapt their behavior and physiology to environmental conditions through processes of phenotypic plasticity. In one well-studied example, the division of labor among worker honey bees involves a stereotyped yet plastic pattern of behavioral and physiological maturation. Early in life, workers perform brood care and other in-hive tasks and have large internal nutrient stores; later in life, they forage for nectar and pollen outside the hive and have small nutrient stores. The pace of maturation depends on colony conditions, and the environmental, physiological, and genomic mechanisms by which this occurs are being actively investigated. Here we review current knowledge of the mechanisms by which a key environmental variable, nutritional status, influences worker honey bee division of labor. These studies demonstrate that changes in individual nutritional status and conserved food-related molecular and hormonal pathways regulate the age at which individual bees begin to forage. We then outline ways in which systems biology approaches, enabled by the sequencing of the honey bee genome, will allow researchers to gain deeper insight into nutritional regulation of honey bee behavior, and phenotypic plasticity in general.

Brain transcriptomic analysis in paper wasps identifies genes associated with behaviour across social insect lineages

Comparative sociogenomics has the potential to provide important insights into how social behaviour evolved. We examined brain gene expression profiles of the primitively eusocial wasp Polistes metricus and compared the results with a growing base of brain gene expression information for the advanced eusocial honeybee, Apis mellifera. We studied four female wasp groups that show variation in foraging/provisioning behaviour and reproductive status, using our newly developed microarray representing approximately 3248 P. metricus genes based on sequences generated from high-throughput pyrosequencing. We found differences in the expression of approximately 389 genes across the four groups. Pathways known from Drosophila melanogaster to be related to lipid metabolism, heat and stress response, and various forms of solitary behaviour were associated with behavioural differences among wasps. Forty-five per cent of differentially expressed transcripts showed significant associations with foraging/provisioning status, and 14 per cent with reproductive status. By comparing these two gene lists with lists of genes previously shown to be differentially expressed in association with honeybee division of labour, we found a significant overlap of genes associated with foraging/provisioning, but not reproduction, across the two species. These results suggest common molecular roots for foraging division of labour in two independently evolved social insect species and the possibility of more lineage-specific roots of reproductive behaviour. We explore the implications of these findings for the idea that there is a conserved 'genetic toolkit' for division of labour across multiple lineages.

Functional characterization of transcription factor motifs using cross-species comparison across large evolutionary distances

We address the problem of finding statistically significant associations between cis-regulatory motifs and functional gene sets, in order to understand the biological roles of transcription factors. We develop a computational framework for this task, whose features include a new statistical score for motif scanning, the use of different scores for predicting targets of different motifs, and new ways to deal with redundancies among significant motif–function associations. This framework is applied to the recently sequenced genome of the jewel wasp, Nasonia vitripennis, making use of the existing knowledge of motifs and gene annotations in another insect genome, that of the fruitfly. The framework uses cross-species comparison to improve the specificity of its predictions, and does so without relying upon non-coding sequence alignment. It is therefore well suited for comparative genomics across large evolutionary divergences, where existing alignment-based methods are not applicable. We also apply the framework to find motifs associated with socially regulated gene sets in the honeybee, Apis mellifera, using comparisons with Nasonia, a solitary species, to identify honeybee-specific associations.

We develop a computational pipeline for predicting the functions of transcription factor motifs, through DNA sequence analysis. The pipeline is applied to the newly sequenced genome of the jewel wasp, Nasonia vitripennis. It exploits the wealth of molecular data available in another insect species, the fruitfly Drosophila melanogaster, and uses cross-species comparison to its advantage. Our main contribution is to show how this can be done despite the large evolutionary divergence between the two species. The methodology presented here may be applied more generally to other scenarios (genomes) where comparative regulatory genomics must deal with large evolutionary divergences.

Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse

We present new approaches to cis-regulatory module (CRM) discovery in the common scenario where relevant transcription factors and/or motifs are unknown. Beginning with a small list of CRMs mediating a common gene expression pattern, we search genome-wide for CRMs with similar functionality, using new statistical scores and without requiring known motifs or accurate motif discovery. We cross-validate our predictions on 31 regulatory networks in Drosophila and through correlations with gene expression data. Five predicted modules tested using an in vivo reporter gene assay all show tissue-specific regulatory activity. We also demonstrate our methods' ability to predict mammalian tissue-specific enhancers. Finally, we predict human CRMs that regulate early blood and cardiovascular development. In vivo transgenic mouse analysis of two predicted CRMs demonstrates that both have appropriate enhancer activity. Overall, 7/7 predictions were validated successfully in vivo, demonstrating the effectiveness of our approach for insect and mammalian genomes.

Evo-devo and the evolution of social behavior: brain gene expression analyses in social insects

Studies of genes and social behavior, aided by new genomic resources, are coming of age. Here, we show how some of the insights that have emerged from research on the evolution of development (evo-devo) also provide a useful framework for studying the evolution of social behavior at the molecular level. These insights include co-opting old genes for new functions, phenotypic modularity, genetic tool kits, the importance of gene regulation in evolutionary change, and the influences of some genes over multiple timescales. We next outline a few differences between development and behavior that pose challenges for an evo-devo approach to behavior. For the remainder of this chapter, we review several studies that illustrate the relevance of evo-devo insights to our understanding of the evolution of behaviors related to eusociality in the insect societies.

Modulatory communication signal performance is associated with a distinct neurogenomic state in honey bees

Studies of animal communication systems have revealed that the perception of a salient signal can cause large-scale changes in brain gene expression, but little is known about how communication affects the neurogenomic state of the sender. We explored this issue by studying honey bees that produce a vibratory modulatory signal. We chose this system because it represents an extreme case of animal communication; some bees perform this behavior intensively, effectively acting as communication specialists. We show large differences in patterns of brain gene expression between individuals producing vibratory signal as compared with carefully matched non-senders. Some of the differentially regulated genes have previously been implicated in the performance of other motor activities, including courtship behavior in Drosophila melanogaster and Parkinson's Disease in humans. Our results demonstrate for the first time a neurogenomic brain state associated with sending a communication signal and provide suggestive glimpses of molecular roots for motor control.

Effects of cocaine on honey bee dance behaviour

The role of cocaine as an addictive drug of abuse in human society is hard to reconcile with its ecological role as a natural insecticide and plant-protective compound, preventing herbivory of coca plants (Erythroxylum spp.). This paradox is often explained by proposing a fundamental difference in mammalian and invertebrate responses to cocaine, but here we show effects of cocaine on honey bees (Apis mellifera L.) that parallel human responses. Forager honey bees perform symbolic dances to advertise the location and value of floral resources to their nest mates. Treatment with a low dose of cocaine increased the likelihood and rate of bees dancing after foraging but did not otherwise increase locomotor activity. This is consistent with cocaine causing forager bees to overestimate the value of the floral resources they collected. Further, cessation of chronic cocaine treatment caused a withdrawal-like response. These similarities likely occur because in both insects and mammals the biogenic amine neuromodulator systems disrupted by cocaine perform similar roles as modulators of reward and motor systems. Given these analogous responses to cocaine in insects and mammals, we propose an alternative solution to the paradox of cocaine reinforcement. Ecologically, cocaine is an effective plant defence compound via disruption of herbivore motor control but, because the neurochemical systems targeted by cocaine also modulate reward processing, the reinforcing properties of cocaine occur as a ;side effect'.

Coordinated responses to developmental hormones in the Kenyon cells of the adult worker honey bee brain (Apis mellifera L.)

The brains of experienced forager honey bees exhibit predictable changes in structure, including significant growth of the neuropil of the mushroom bodies. In vertebrates, members of the superfamily of nuclear receptors function as key regulators of neuronal structure. The adult insect brain expresses many members of the nuclear receptor superfamily, suggesting that insect neurons are also likely important targets of developmental hormones. The actions of developmental hormones (the ecdysteroids and the juvenile hormones) in insects have been primarily explored in the contexts of metamorphosis and vitellogenesis. The cascade of gene expression activated by 20-hydroxyecdysone and modulated by juvenile hormone is strikingly conserved in these different physiological contexts. We used quantitative RT-PCR to measure, in the mushroom bodies of the adult worker honey bee brain, relative mRNA abundances of key members of the nuclear receptor superfamily (EcR, USP, E75, Ftz-f1, and Hr3) that participate in the metamorphosis/vitellogenesis cascade. We measured responses to endogenous peaks of hormones experienced early in adult life and to exogenous hormones. Our studies demonstrate that a population of adult insect neurons is responsive to endocrine signals through the use of conserved portions of the canonical ecdysteroid transcriptional cascade previously defined for metamorphosis and vitellogenesis.

Genes and social behavior

What genes and regulatory sequences contribute to the organization and functioning of neural circuits and molecular pathways in the brain that support social behavior? How does social experience interact with information in the genome to modulate brain activity? Here, we address these questions by highlighting progress that has been made in identifying and understanding two key "vectors of influence" that link genes, the brain, and social behavior: (i) Social information alters gene expression in the brain to influence behavior, and (ii) genetic variation influences brain function and social behavior. We also discuss how evolutionary changes in genomic elements influence social behavior and outline prospects for a systems biology of social behavior.

Genetic and genomic analyses of the division of labour in insect societies

Division of labour--individuals specializing in different activities--features prominently in the spectacular success of the social insects. Until recently, genetic and genomic analyses of division of labour were limited to just a few species. However, research on an ever-increasing number of species has provided new insight, from which we highlight two results. First, heritable influences on division of labour are more pervasive than previously imagined. Second, different forms of division of labour, in lineages in which eusociality has arisen independently, have evolved through changes in the regulation of highly conserved molecular pathways associated with several basic life-history traits, including nutrition, metabolism and reproduction.

Pilocarpine improves recognition of nestmates in young honey bees

Honey bees can distinguish nestmates from non-nestmates, directing aggressive responses toward non-nestmates and rarely attacking nestmates. Here we provide evidence that treatment with pilocarpine, a muscarinic agonist, significantly reduced the number of aggressive responses directed toward nestmates. By contrast, treatment with scopolamine, a muscarinic antagonist, significantly increased attacks on nestmates. Locomotor activity was not altered by these pharmacological treatments. When interpreted in light of known cholinergic pathways in the insect brain, our results provide the first evidence that cholinergic signaling via muscarinic receptors plays a role in olfaction-based social behavior in honey bees.

The utility of behavioral models and modules in molecular analyses of social behavior

It is extremely difficult to trace the causal pathway relating gene products or molecular pathways to the expression of behavior. This is especially true for social behavior, which being dependent on interactions and communication between individuals is even further removed from molecular-level events. In this review, we discuss how behavioral models can aid molecular analyses of social behavior. Various models of behavior exist, each of which suggest strategies to dissect complex behavior into simpler behavioral 'modules.' The resulting modules are easier to relate to neural processes and thus suggest hypotheses for neural and molecular function. Here we discuss how three different models of behavior have facilitated understanding the molecular bases of aspects of social behavior. We discuss the response threshold model and two different approaches to modeling motivation, the state space model and models of reinforcement and reward processing. The examples we have chosen illustrate how models can generate testable hypotheses for neural and molecular function and also how molecular analyses probe the validity of a model of behavior. We do not champion one model over another; rather, our examples illustrate how modeling and molecular analyses can be synergistic in exploring the molecular bases of social behavior.

Social and nonsocial stimuli and juvenile hormone titer in a male burying beetle, Nicrophorus orbicollis

We investigated the interaction of social and nonsocial stimuli on juvenile hormone (JH) titer in male burying beetles (Nicrophorus orbicollis). The initial JH response to discovery of a carcass was substantial (10-15-fold increase over controls) and rapid (<1h), and occurred whether or not a female was present. By 3h after discovery, JH titers were declining, the decline being more pronounced when a female was not present. We also tested the effect of larval stimulation on JH titer in care-giving males by removing a male's brood and replacing it with a brood of first or third instar larvae. Males initially providing care for begging first instar larvae continued to maintain high titers of JH when the replacement broods were first but not third instars. Males caring for third instar larvae (normally low JH titers) maintained low levels of JH regardless of the developmental stage of the replacement brood. This suggests that once males begin to care for nutritionally independent third instar larvae, JH titers remain low regardless of subsequent larval stimulation. Burying beetles are socially and hormonally complex organisms in which stimuli from a breeding resource, mating partners, rivals and young interact to alter the JH profile of breeding adults.

Alarm pheromone induces immediate-early gene expression and slow behavioral response in honey bees

Primer and releaser pheromones are molecules used for communication that induce species-specific responses. In contrast to primer pheromones, it is not known whether the quicker-acting releaser pheromones can affect brain gene expression. We show here that isopentyl acetate (IPA), a releaser pheromone that communicates alarm in honey bees, not only provokes a quick defensive response but also influences behavior for a longer period of time and affects brain gene expression. Exposure to IPA affected behavioral responsiveness to subsequent exposures to IPA and induced the expression of the immediate early gene and transcription factor c-Jun in the antennal lobes. Our findings blur the long-standing distinction between primer and releaser pheromone and highlight the pervasiveness of environmental regulation of brain gene expression.

Identification and characterization of a juvenile hormone response element and its binding proteins

Juvenile hormones (JH) regulate a wide variety of developmental and physiological processes in insects. Comparison of microarray data on JH-induced genes in the fruit fly, Drosophila melanogaster, L57 cells and in the honey bee, Apis mellifera, identified 16 genes that are induced in both species. Analysis of promoter regions of these 16 D. melanogaster genes identified DmJHRE1 (D. melanogaster JH response element 1). In L57 cells, the reporter gene regulated by DmJHRE1 was induced by JH III. Two proteins (FKBP39 and Chd64) that bind to DmJHRE1 were identified. FKBP39 and Chd64 double-stranded RNA inhibited JH III induction of a reporter gene regulated by DmJHRE1. FKBP39 and Chd64 proteins expressed in yeast bound to DmJHRE1. Two-hybrid and pull-down assays showed that these two proteins interact with each other as well as with ecdysone receptor, ultraspiracle, and methoprene-tolerant protein. Developmental expression profiles and JH induction of mRNA for FKBP39 and Chd64 proteins and their interaction with proteins known to be involved in both JH (methoprene-tolerant protein) and ecdysteroid action (ecdysone receptor and ultraspiracle) suggest that these proteins probably play important roles in cross-talk between JH and ecdysteroids.

Roles of Drosophila Kruppel-homolog 1 in neuronal morphogenesis

The molecular mechanisms underlying remodeling of neural networks remain largely unknown. In Drosophila, widespread neural remodeling occurs during metamorphosis, and is regulated by ecdysone. Kruppel-homolog 1 (Kr-h1) is a zinc finger transcription factor known to play a role in orchestrating ecdysone-regulated transcriptional pathways and, furthermore, implicated in governing axon morphogenesis. Interestingly, in honey bee workers, neural expression of the Apis mellifera homolog of Kr-h1 is enhanced during their transition to foraging behavior when there is increased neurite outgrowth, branching, and synapse formation. Here, we assessed the role(s) of KR-H1 in Drosophila neuronal remodeling and morphology. We characterized the effect of Kr-h1 expression on neuronal morphology through Drosophila larval, pupal, and adult stages. Increased expression of Kr-h1 led to reduced branching in individual neurons and gross morphological changes in the mushroom bodies (MBs), while knocking down Kr-h1 did not produce any obvious changes in neural morphology. Drosophila Kr-h1 is normally expressed when MB neurons do not undergo active morphogenesis, suggesting that it may play a role in inhibiting morphogenesis. Further, loss of endogenous KR-H1 enhanced the neuronal morphogenesis that is otherwise delayed due to defective TGF-beta signaling. However, loss of KR-H1 alone did not affect neuronal morphogenesis. In addition, Kr-h1 expression remains strongly linked to ecdysone-regulated pathways: Kr-h1 expression is regulated by usp, which dimerizes to the ecdysone receptor, and Kr-h1 expression is essential for proper patterning of the ecdysone receptor isoforms in the late larval central nervous system. Thus, although KR-H1 has a potential for modulating neuronal morphogenesis, it appears physiologically involved in coordinating general ecdysone signaling.

Wasp Gene Expression Supports an Evolutionary Link Between Maternal Behavior and Eusociality

The presence of workers that forgo reproduction and care for their siblings is a defining feature of eusociality and a major challenge for evolutionary theory. It has been proposed that worker behavior evolved from maternal care behavior. We explored this idea by studying gene expression in the primitively eusocial wasp Polistes metricus. Because little genomic information existed for this species, we used 454 sequencing to generate 391,157 brain complementary DNA reads, resulting in robust hits to 3017 genes from the honey bee genome, from which we identified and assayed orthologs of 32 honey bee behaviorally related genes. Wasp brain gene expression in workers was more similar to that in foundresses, which show maternal care, than to that in queens and gynes, which do not. Insulin-related genes were among the differentially regulated genes, suggesting that the evolution of eusociality involved major nutritional and reproductive pathways.

Senescence in the worker honey bee Apis Mellifera

Honey bees are social insects that exhibit striking caste-specific differences in longevity. Queen honey bees live on average 1-2 years, whereas workers live 2-6 weeks in the summer and about 20 weeks in the winter. It is not clear whether queen-worker differences in longevity are due to intrinsic physiological differences in the rate of senescence, to differential exposure to extrinsic factors such as predation and adverse environmental conditions, or both. To determine if the relatively short lifespan of worker bees involves senescence, we measured age-specific resistance to three different physiological stressors (starvation, thermal, and oxidative stress) while eliminating age-related differences in foraging activity and minimizing age-related differences in energy expenditure. Despite these manipulations, older worker bees were still significantly less resistant to all three stressors than were younger bees. These results indicate that the regulation of worker bee lifespan involves senescence, in addition to extrinsic factors.

A statistical method for alignment-free comparison of regulatory sequences

MOTIVATION

The similarity of two biological sequences has traditionally been assessed within the well-established framework of alignment. Here we focus on the task of identifying functional relationships between cis-regulatory sequences that are non-orthologous or greatly diverged. 'Alignment-free' measures of sequence similarity are required in this regime.

RESULTS

We investigate the use of a new score for alignment-free sequence comparison, called the score. It is based on comparing the frequencies of all fixed-length words in the two sequences. An important, novel feature of the score is that it is comparable across sequence pairs drawn from arbitrary background distributions. We present a method that gives quadratic improvement in the time complexity of calculating the score, over the naïve method. We then evaluate the score on several tissue-specific families of cis-regulatory modules (in Drosophila and human). The new score is highly successful in discriminating functionally related regulatory sequences from unrelated sequence pairs. The performance of the score is compared to five other alignment-free similarity measures, and shown to be consistently superior to all of these measures.

AVAILABILITY

Our implementation of the score will be made freely available as source code, upon publication of this article, at: http://veda.cs.uiuc.edu/d2z/.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.