Molecular determinants of caste differentiation in the highly eusocial honeybee Apis mellifera

Reminiscences on the honeybee genome project and the rise of epigenetic concepts in insect science

The sequencing of the honeybee genome in 2006 was an important technological and logistic achievement experience. But what benefits have flown from the honeybee genome project? What does the annotated genomic assembly mean for the study of behavioural complexity and organismal function in honeybees? Here, I discuss several lines of research that have arisen from this project and highlight the rapidly expanding studies on insect epigenomics, emergent properties of royal jelly, the mechanism of nutritional control of development and the contribution of epigenomic regulation to the evolution of sociality. I also argue that the term 'insect epigenetics' needs to be carefully redefined to reflect the diversity of epigenomic toolkits in insects and the impact of lineage-specific innovations on organismal outcomes. The honeybee genome project helped pioneer advances in social insect molecular biology, and fuelled breakthrough research into the role of flexible epigenomic control systems in linking genotype to phenotype.

Post-invasion selection acts on standing genetic variation despite a severe founding bottleneck

Invasive populations often have lower genetic diversity relative to the native-range populations from which they derive.1,2 Despite this, many biological invaders succeed in their new environments, in part due to rapid adaptation.3,4,5,6 Therefore, the role of genetic bottlenecks in constraining the adaptation of invaders is debated.7,8,9,10 Here, we use whole-genome resequencing of samples from a 10-year time-series dataset, representing the natural invasion of the Asian honey bee (Apis cerana) in Australia, to investigate natural selection occurring in the aftermath of a founding event. We find that Australia's A. cerana population was founded by as few as one colony, whose arrival was followed by a period of rapid population expansion associated with an increase of rare variants.11 The bottleneck resulted in a steep loss of overall genetic diversity, yet we nevertheless detected loci with signatures of positive selection during the first years post-invasion. When we investigated the origin of alleles under selection, we found that selection acted primarily on the variation introduced by founders and not on the variants that arose post-invasion by mutation. In all, our data highlight that selection on standing genetic variation can occur in the early years post-invasion, even where founding bottlenecks are severe.

Transcriptional signature of host shift in the seed beetle Zabrotes subfasciatus

In phytophagous insects, adaptation to a new host is a dynamic process, in which early and later steps may be underpinned by different features of the insect genome. Here, we tested the hypothesis that early steps of this process are underpinned by a shift in gene expression patterns. We set up a short-term artificial selection experiment (10 generations) for the use of an alternative host (Cicer arietinum) on populations of the bean beetle Zabrotes subfasciatus. Using Illumina sequencing on young adult females, we show the selected populations differ in the expression of genes associated to stimuli, signalling, and developmental processes. Particularly, the "C. arietinum" population shows upregulation of histone methylation genes, which may constitute a strategy for fine-tuning the insect global gene expression network. Using qPCR on body regions, we demonstrated that the "Phaseolus vulgaris" population upregulates the genes polygalacturonase and egalitarian and that the expression of an odorant receptor transcript variant changes over generations. Moreover, in this population we detected the existence of vitellogenin (Vg) variants in both males and females, possibly harbouring canonical reproductive function in females and extracellular unknown functions in males. This study provides the basis for future genomic investigations seeking to shed light on the nature of the proximate mechanisms involved in promoting differential gene expression associated to insect development and adaptation to new hosts.

DNA methylation extends lifespan in the bumblebee Bombus terrestris

Epigenetic alterations are a primary hallmark of ageing. In mammals, age-related epigenetic changes alter gene expression profiles, disrupt cellular homeostasis and physiological functions and, therefore, promote ageing. It remains unclear whether ageing is also driven by epigenetic mechanisms in invertebrates. Here, we used a pharmacological hypomethylating agent (RG108) to evaluate the effects of DNA methylation (DNAme) on lifespan in an insect-the bumblebee Bombus terrestris. RG108 extended mean lifespan by 43% and induced the differential methylation of genes involved in hallmarks of ageing, including DNA damage repair and chromatin organization. Furthermore, the longevity gene sirt1 was overexpressed following the treatment. Functional experiments demonstrated that SIRT1 protein activity was positively associated with lifespan. Overall, our study indicates that epigenetic mechanisms are conserved regulators of lifespan in both vertebrates and invertebrates and provides new insights into how DNAme is involved in the ageing process in insects.

Epigenetics Mechanisms of Honeybees: Secrets of Royal Jelly

Early diets in honeybees have effects on epigenome with consequences on their phenotype. Depending on the early larval diet, either royal jelly (RJ) or royal worker, 2 different female castes are generated from identical genomes, a long-lived queen with fully developed ovaries and a short-lived functionally sterile worker. To generate these prominent physiological and morphological differences between queen and worker, honeybees utilize epigenetic mechanisms which are controlled by nutritional input. These mechanisms include DNA methylation and histone post-translational modifications, mainly histone acetylation. In honeybee larvae, DNA methylation and histone acetylation may be differentially altered by RJ. This diet has biologically active ingredients with inhibitory effects on the de novo methyltransferase DNMT3A or the histone deacetylase 3 HDAC3 to create and maintain the epigenetic state necessary for developing larvae to generate a queen. DNMT and HDAC enzymes work together to induce the formation of a compacted chromatin structure, repressing transcription. Such dialog could be coordinated by their association with other epigenetic factors including the ubiquitin-like containing plant homeodomain (PHD) and really interesting new gene (RING) finger domains 1 (UHRF1). Through its multiple functional domains, UHRF1 acts as an epigenetic reader of both DNA methylation patterns and histone marks. The present review discusses the epigenetic regulation of honeybee's chromatin and how the early diets in honeybees can affect the DNA/histone modifying types of machinery that are necessary to stimulate the larvae to turn into either queen or worker. The review also looks at future directions in epigenetics mechanisms of honeybees, mainly the potential role of UHRF1 in these mechanisms.

The Juvenile-Hormone-Responsive Factor AmKr-h1 Regulates Caste Differentiation in Honey Bees

Honey bees are typical model organisms for the study of caste differentiation, and the juvenile hormone (JH) is a crucial link in the regulatory network of caste differentiation in honey bees. To investigate the mechanism of JH-mediated caste differentiation, we analyzed the effect of the JH response gene AmKr-h1 on this process. We observed that AmKr-h1 expression levels were significantly higher in queen larvae than in worker larvae at the 48 h, 84 h, and 120 h larval stages, and were regulated by JH. Inhibiting AmKr-h1 expression in honey bee larvae using RNAi could lead to the development of larvae toward workers. We also analyzed the transcriptome changes in honey bee larvae after AmKr-h1 RNAi and identified 191 differentially expressed genes (DEGs) and 682 differentially expressed alternative splicing events (DEASEs); of these, many were related to honey bee caste differentiation. Our results indicate that AmKr-h1 regulates caste differentiation in honey bees by acting as a JH-responsive gene.

Phenotypic dimorphism between honeybee queen and worker is regulated by complicated epigenetic modifications

Phenotypic dimorphism between queens and workers is an important biological characteristic of honeybees that has been the subject of intensive research. The enormous differences in morphology, lifespan, physiology, and behavior between queens and workers are caused by a complicated set of factors. Epigenetic modifications are considered to play an important role in this process. In this study, we analyzed the differences in chromosome interactions and H3K27ac and H3K4me1 modifications between the queens and workers using high-throughput chromosome conformation capture (Hi-C) and Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) technologies. We found that the queens contain more chromosome interactions and more unique H3K27ac modifications than workers; in contrast, workers have more H3K4me1 modifications than queens. Moreover, we identified Map3k15 as a potential caste gene in queen-worker differentiation. Our results suggest that chromosomal conformation and H3K27ac and H3K4me1 modifications are involved in regulating queen-worker differentiation, which reveals that the queen-worker phenotypic dimorphism is regulated by multiple epigenetic modifications.

H3K4me1 Modification Functions in Caste Differentiation in Honey Bees

Honey bees are important species for the study of epigenetics. Female honey bee larvae with the same genotype can develop into phenotypically distinct organisms (sterile workers and fertile queens) depending on conditions such as diet. Previous studies have shown that DNA methylation and histone modification can establish distinct gene expression patterns, leading to caste differentiation. It is unclear whether the histone methylation modification H3K4me1 can also impact caste differentiation. In this study, we analyzed genome-wide H3K4me1 modifications in both queen and worker larvae and found that H3K4me1 marks are more abundant in worker larvae than in queen larvae at both the second and fourth instars, and many genes associated with caste differentiation are differentially methylated. Notably, caste-specific H3K4me1 in promoter regions can direct worker development. Thus, our results suggest that H3K4me1 modification may act as an important regulatory factor in the establishment and maintenance of caste-specific transcriptional programs in honey bees; however, the potential influence of other epigenetic modifications cannot be excluded.

Chromatin accessibility-based characterisation of brain gene regulatory networks in three distinct honey bee polyphenisms

The honey bee genome has the capacity to produce three phenotypically distinct organisms (two diploid female castes: queen and worker, and a haploid male drone). Previous studies have implicated metabolic flux acting via epigenetic regulation in directing nutrition-driven phenotypic plasticity in the honey bee. However, the cis-acting DNA regulatory elements that establish tissue and polyphenism -specific epigenomes and gene expression programmes, remain unclear. Using a high resolution multiomic approach including assay for transposase-accessible chromatin by sequencing (ATAC-seq), RNA-seq and ChIP-seq, we produce the first genome-wide maps of the regulatory landscape across all three adult honey bee phenotypes identifying > 5000 regulatory regions in queen, 7500 in worker and 6500 in drone, with the vast majority of these sites located within intronic regions. These regions are defined by positive enrichment of H3K27ac and depletion of H3K4me3 and show a positive correlation with gene expression. Using ATAC-seq footprinting we determine queen, worker and drone -specific transcription factor occupancy and uncover novel phenotype-specific regulatory networks identifying two key nuclear receptors that have previously been implicated in caste-determination and adult behavioural maturation in honey bees; ecdysone receptor and ultraspiracle. Collectively, this study provides novel insights into key gene regulatory networks that are associated with these distinct polyphenisms in the honey bee.

Canalized gene expression during development mediates caste differentiation in ants

Ant colonies are higher-level organisms consisting of specialized reproductive and non-reproductive individuals that differentiate early in development, similar to germ-soma segregation in bilateral Metazoa. Analogous to diverging cell lines, developmental differentiation of individual ants has often been considered in epigenetic terms but the sets of genes that determine caste phenotypes throughout larval and pupal development remain unknown. Here, we reconstruct the individual developmental trajectories of two ant species, Monomorium pharaonis and Acromyrmex echinatior, after obtaining >1,400 whole-genome transcriptomes. Using a new backward prediction algorithm, we show that caste phenotypes can be accurately predicted by genome-wide transcriptome profiling. We find that caste differentiation is increasingly canalized from early development onwards, particularly in germline individuals (gynes/queens) and that the juvenile hormone signalling pathway plays a key role in this process by regulating body mass divergence between castes. We quantified gene-specific canalization levels and found that canalized genes with gyne/queen-biased expression were enriched for ovary and wing functions while canalized genes with worker-biased expression were enriched in brain and behavioural functions. Suppression in gyne larvae of Freja, a highly canalized gyne-biased ovary gene, disturbed pupal development by inducing non-adaptive intermediate phenotypes between gynes and workers. Our results are consistent with natural selection actively maintaining canalized caste phenotypes while securing robustness in the life cycle ontogeny of ant colonies.

Extent and complexity of RNA processing in honey bee queen and worker caste development

The distinct honeybee (Apis mellifera) worker and queen castes have become a model for the study of genomic mechanisms of phenotypic plasticity. Here we performed a nanopore-based direct RNA sequencing with exceptionally long reads to compare the mRNA transcripts between queen and workers at three points during their larval development. We found thousands of significantly differentially expressed transcript isoforms (DEIs) between queen and worker larvae. These DEIs were formatted by a flexible splicing system. We showed that poly(A) tails participated in this caste differentiation by negatively regulating the expression of DEIs. Hundreds of isoforms uniquely expressed in either queens or workers during their larval development, and isoforms were expressed at different points in queen and worker larval development demonstrating a dynamic relationship between isoform expression and developmental mechanisms. These findings show the full complexity of RNA processing and transcript expression in honey bee phenotypic plasticity.

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Honeybee caste differentiation has a complexity of RNA processing

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Isoforms differentially express between queens and workers during larval development

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Isoforms are formatted by a flexible alternative splicing system

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Poly(A) tails are negatively correlated with isoform expression

Ant phylogenomics reveals a natural selection hotspot preceding the origin of complex eusociality

The evolution of eusociality has allowed ants to become one of the most conspicuous and ecologically dominant groups of organisms in the world. A large majority of the current ∼14,000 ant species belong to the formicoids,¹ a clade of nine subfamilies that exhibit the most extreme forms of reproductive division of labor, large colony size,² worker polymorphism,³ and extended queen longevity.⁴ The eight remaining non-formicoid subfamilies are less well studied, with few genomes having been sequenced so far and unclear phylogenetic relationships.⁵ By sequencing 65 genomes, we provide a robust phylogeny of the 17 ant subfamilies, retrieving high support to the controversial leptanillomorph clade (Leptanillinae and Martialinae) as the sister group to all other extant ants. Moreover, our genomic analyses revealed that the emergence of the formicoids was accompanied by an elevated number of positive selection events. Importantly, the top three gene functions under selection are linked to key features of complex eusociality, with histone acetylation being implicated in caste differentiation, gene silencing by RNA in worker sterility, and autophagy in longevity. These results show that the key pathways associated with eusociality have been under strong selection during the Cretaceous, suggesting that the molecular foundations of complex eusociality may have evolved rapidly in less than 20 Ma.

Active genic machinery for epigenetic RNA modifications in bees

Epitranscriptomics is an emerging field of investigation dedicated to the study of post-transcriptional RNA modifications. RNA methylations regulate RNA metabolism and processing, including changes in response to environmental cues. Although RNA modifications are conserved from bacteria to eukaryotes, there is little evidence of an epitranscriptomic pathway in insects. Here we identified genes related to RNA m⁶ A (N6-methyladenine) and m⁵ C (5-methylcytosine) methylation machinery in seven bee genomes (Apis mellifera, Melipona quadrifasciata, Frieseomelitta varia, Eufriesea mexicana, Bombus terrestris, Megachile rotundata and Dufourea novaeangliae). In A. mellifera, we validated the expression of methyltransferase genes and found that the global levels of m⁶ A and m⁵ C measured in the fat body and brain of adult workers differ significantly. Also, m⁶ A levels were differed significantly mainly between the fourth larval instar of queens and workers. Moreover, we found a conserved m⁵ C site in the honeybee 28S rRNA. Taken together, we confirm the existence of epitranscriptomic machinery acting in bees and open avenues for future investigations on RNA epigenetics in a wide spectrum of hymenopteran species.

miRNA-34 and miRNA-210 target hexamerin genes enhancing their differential expression during early brain development of honeybee (Apis mellifera) castes

During the honeybee larval stage, queens develop larger brains than workers, with morphological differentiation appearing at the fourth larval phase (L4), just after a boost in nutritional difference both prospective females experience. The molecular promoters of this caste-specific brain development are already ongoing in previous larval phases. Transcriptomic analyses revealed a set of differentially expressed genes in the L3 brains of queens and workers, which represents the early molecular response to differential feeding females receive during larval development. Three genes of this set, hex70b, hex70c and hex110, are more highly transcribed in the brain of workers than in queens. The microRNAs miR-34, miR-210 and miR-317 are in higher levels in the queens' brain at the same phase of larval development. Here, we tested the hypothesis that the brain of workers expresses higher levels of hexamerins than that of queens during key phases of larval development and that this differential hexamerin genes expression is further enhanced by the repressing activity of miR-34, miR-210 and miR-317. Our transcriptional analyses showed that hex70b, hex70c and hex110 genes are differentially expressed in the brain of L3 and L4 larval phases of honeybee queens and workers. In silico reconstructed miRNA-mRNA interaction networks were validated using luciferase assays, which showed miR-34 and miR-210 negatively regulate hex70b and hex110 genes by directly and redundantly binding their 3'UTR (untranslated region) sequences. Taken together, our results suggest that miR-34 and miR-210 act together promoting differential brain development in honeybee castes by downregulating the expression of the putative antineurogenic hexamerin genes hex70b and hex110.

Juvenile hormone and transcriptional changes in honey bee worker larvae when exposed to sublethal concentrations of thiamethoxam

Thiamethoxam, an insecticide with high usage and large amounts of environmental residues, has been reported to affect the pupation and survival of honey bee larvae at sublethal concentrations. The molecular mechanisms are not fully understood. In this study, we measured the response of juvenile hormone (JH) to environmental concentrations of thiamethoxam using liquid chromatography-tandem mass spectrometry (LC-MS/MS), monitored the dynamic changes in the transcription of genes encoding major JH metabolic enzymes (CYP15A1, FAMET, JHAMT and JHE) using RT-qPCR, and analysed the transcriptome changes in worker larvae under thiamethoxam stress using RNA-seq. Thiamethoxam significantly increased the levels of JH3 in honey bee larvae, but no significant changes in the transcript levels of the four major metabolic enzymes were observed. Thiamethoxam exposure resulted in 140 differentially expressed genes (DEGs). P450 CYP6AS5 was upregulated, and some ion-related, odourant-related and gustatory receptors for sugar taste genes were altered significantly. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that amino acid metabolism and protein digestion and absorption were influenced by thiamethoxam. These changes may do harm to honey bee caste differentiation, foraging behaviour related to sensory perception and nutrient levels of bee colonies. These results represent the first assessment of the effects of thiamethoxam on JH in honey bee larvae and provides a new perspective and molecular basis for the study of JH regulation and thiamethoxam toxicity to honey bees.

Reproductive Potential Accelerates Preimaginal Development of Rebel Workers in Apis mellifera

Simple Summary

All female honeybee larvae may develop into workers or queens, depending on the food they receive. During this period, queen mandibular pheromones (QMP) perform a regulatory function in inhibiting ovarian development in adult workers. These pheromones are transmitted (via trophallaxis) by workers to pass information to larvae on the presence or absence of the queen. Queen-less conditions are conducive to the emergence of rebel workers that are set to reproduce, and do not participate in the rearing of successive bee generations in contrast to the sterile, normal workers. We posited that rebels are not only similar to queens in some anatomical features, but also develop in a shorter time in comparison to normal workers. Therefore, the aim of this study was to compare the duration of preimaginal development in rebel and normal workers. Our results confirmed that the workers who develop in a queen-less colony undergo a shorter preimaginal development than those in a queen-right colony.

Abstract

Rebel workers develop from eggs laid by the previous queen, before it went swarming and left the colony orphaned, until the emergence of a new queen. In contrast to normal workers developing in the queen’s presence, rebels are set to reproduce and avoid rearing of successive bee generations. They have more ovarioles in their ovaries, as well as more developed mandibular glands and underdeveloped hypopharyngeal glands, just like the queen. We posited that rebels are not only similar to queens in some anatomical features, but also develop in a shorter time in comparison to normal workers. Therefore, the aim of this study was to compare preimaginal development duration in rebel and normal workers. The results show that rebels, i.e., workers with a higher reproductive potential, had a significantly shorter preimaginal development period (mean ± SD, 19.24 ± 0.07 days) than normal workers (22.29 ± 0.32 days). Our result confirmed that workers who develop in a queen-less colony undergo a shorter preimaginal development than those in a queen-right colony.

Transcriptome dynamics during metamorphosis of imaginal discs into wings and thoracic dorsum in Apis mellifera castes

BACKGROUND

Much of the complex anatomy of a holometabolous insect is built from disc-shaped epithelial structures found inside the larva, i.e., the imaginal discs, which undergo a rapid differentiation during metamorphosis. Imaginal discs-derived structures, like wings, are built through the action of genes under precise regulation.

RESULTS

We analyzed 30 honeybee transcriptomes in the search for the gene expression needed for wings and thoracic dorsum construction from the larval wing discs primordia. Analyses were carried out before, during, and after the metamorphic molt and using worker and queen castes. Our RNA-seq libraries revealed 13,202 genes, representing 86.2% of the honeybee annotated genes. Gene Ontology analysis revealed functional terms that were caste-specific or shared by workers and queens. Genes expressed in wing discs and descendant structures showed differential expression profiles dynamics in premetamorphic, metamorphic and postmetamorphic developmental phases, and also between castes. At the metamorphic molt, when ecdysteroids peak, the wing buds of workers showed maximal gene upregulation comparatively to queens, thus underscoring differences in gene expression between castes at the height of the larval-pupal transition. Analysis of small RNA libraries of wing buds allowed us to build miRNA-mRNA interaction networks to predict the regulation of genes expressed during wing discs development.

CONCLUSION

Together, these data reveal gene expression dynamics leading to wings and thoracic dorsum formation from the wing discs, besides highlighting caste-specific differences during wing discs metamorphosis.

Amsp3 may act upstream of Amdnmt3 in female caste differentiation in the honeybee (Apis mellifera)

In honey bees, the process of producing two female castes, including queens and workers, is nutritionally controlled by differential feeding royal jelly to newly emerged larvae. Although they have almost identical genetic blueprints, these castes show striking differences in their morphologies, longevities and reproductive capabilities. DNA methyltransferase 3 (Amdnmt3) gene is involved in the regulatory network for honeybee caste differentiation. Due to the role of two zinc fingers containing transcription factors, SP1 and SP3 in controlling mammalian Dnmts, this study aimed to determine a similar interaction of SPs with Amdnmt3 in the honeybee. We confirmed that the promoter region of Amdnmt3 contained multiple predicted SP1/SP3 binding sites and then investigated the role of AmSP3 in queen-worker differentiation network. We observed that the expression level of Amsp3 was significantly higher in worker larvae than that in queen larvae at 48 h, 84 h and 120 h. Knockdown of Amsp3 expression by RNAi in worker larvae significantly reduced the expression level of Amdnmt3 and caused morphological changes in adult bees towards a queen-like phenotype. However, the expression levels of Amsp3 and Amdnmt3 were repressed by juvenile hormone (JH). Our results suggest that AmSP3 is an important part of the queen-worker differentiation network and supports the role of Amdnmt3 in determining the phenotypic outcome of developing larvae.

Female developmental environment delays development of male honeybee (Apis mellifera)

Background

Nutrition and cell size play an important role in the determination of caste differentiation in queen and worker of honeybees (Apis mellifera), whereas the haploid genome dominates the differentiation of drones. However, the effects of female developmental environment on the development of males remain unclear. In this study, young drone larvae were transferred into worker cells (WCs) or remained in drone cells (DCs) to rear drones. The drone larvae were also grafted into queen cells (QCs) for 48 h and then transplanted into drone cells until emerging. Morphological indexes and reproductive organs of these three types of newly emerged drones were measured. Newly emerged drones and third instar drone larvae from WCs, DCs and QCs were sequenced by RNA sequencing (RNA-Seq).

Results

The amount of food remaining in cells of the QC and WC groups was significantly different to that in the DC group at the early larval stage. Morphological results showed that newly emerged DC drones had bigger body sizes and more well-developed reproductive tissues than WC and QC drones, whereas the reproductive tissues of QC drones were larger than those of WC drones. Additionally, whole body gene expression results showed a clear difference among three groups. At larval stage there were 889, 1761 and 1927 significantly differentially expressed genes (DEGs) in WC/DC, QC/DC and WC/QC comparisons, respectively. The number of DEGs decreased in adult drones of these three comparisons [678 (WC/DC), 338 (QC/DC) and 518 (WC/QC)]. A high number of DEGs were involved in sex differentiation, growth, olfaction, vision, mammalian target of rapamycin (mTOR), Wnt signaling pathways, and other processes.

Conclusions

This study demonstrated that the developmental environment of honeybee females can delay male development, which may serve as a model for understanding the regulation of sex differentiation and male development in social insects by environmental factors.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08014-1.

Vitellogenin regulates estrogen-related receptor expression by crosstalk with the JH and IIS-TOR signaling pathway in Polyrhachis vicina Roger (Hymenoptera, Formicidae)

The Estrogen-related receptor (ERR) can regulate the growth and development, metabolism, reproduction, and other physiological activities of insects, but its specific mechanism of action is still unclear. The aim of this study was to explore the relationship between expression of ERR and Vitellogenins (Vg) and the juvenile hormone (JH) and insulin/insulin-like growth factor/target of rapamycin (IIS/TOR) signaling pathways in Polyrhachis vicina Roger. P. vicina was used as the experimental model to clone the PvVg gene, perform double-stranded RNA synthesis and delivery and observe the effects of pharmacological treatments. The full-length PvVg cDNA product is 5586 bp. Higher PvVg mRNA expression was seen in the pupa and adults, and varying levels were seen in the different body parts of three different castes. RNA interference of PvVg expression led to disturbed development, an abnormal phenotype, and high mortality. PvVg RNAi also led to a reduction in mRNA levels of PvERR, ultraspiracle (PvUSP), forkhead box protein O (PvFOXO) and PvTOR genes in fourth instar larval, but a significant increase was seen in pupa and females. No significant change was seen in workers and males. After PvVg knockdown, application of exogenous JHIII reduced the expression of these genes in pupa and females, increased expression in workers, and decreased PvUSP mRNA expression in males. Both protein and mRNA expression levels of PvFOXO were affected by PvVg RNAi. PvERR RNAi increased PvVg expression in pupa and females and Kruppel-homolog 1 (PvKr-h1) and PvFOXO expression in males. The results of this study suggest that there is an interaction between PvERR and PvVg, and that crosstalk with the JH and IIS/TOR signaling pathways can affect development and reproduction. This effect is caste and developmental stage specific. We also speculate that the FOXO/USP complex participates in JH regulation of PvVg in P. vicina.

Pairwise interactions in gene expression determine a hierarchical transcriptional profile in the human brain

The orchestrated expression of thousands of genes gives rise to the complexity of the human brain. However, the structures governing these myriad gene-gene interactions remain unclear. By analyzing transcription data from more than 2000 sites in six human brains, we found that pairwise interactions between genes, without considering any higher-order interactions, are sufficient to predict the transcriptional pattern of the genome for individual brain regions and the transcriptional profile of the entire brain consisting of more than 200 areas. These findings suggest a quadratic complexity of transcriptional patterns in the human brain, which is much simpler than expected. In addition, using a pairwise interaction model, we revealed that the strength of gene-gene interactions in the human brain gives rise to the nearly maximal number of transcriptional clusters, which may account for the functional and structural richness of the brain.

Molecular underpinnings of the early brain developmental response to differential feeding in the honey bee Apis mellifera

Brain differential morphogenesis in females is one of the major phenotypic manifestations of caste development in honey bees. Brain diphenism appears at the fourth larval phase as a result of the differential feeding regime developing females are submitted during early phases of larval development. Here, we used a forward genetics approach to test the early brain molecular response to differential feeding leading to the brain diphenism observed at later developmental phases. Using RNA sequencing analysis, we identified 53 differentially expressed genes (DEGs) between the brains of queens and workers at the third larval phase. Since miRNAs have been suggested to play a role in caste differentiation after horizontal and vertical transmission, we tested their potential participation in regulating the DEGs. The miRNA-mRNA interaction network, including the DEGs and the royal- and worker-jelly enriched miRNA populations, revealed a subset of miRNAs potentially involved in regulating the expression of DEGs. The interaction of miR-34, miR-210, and miR-317 with Takeout, Neurotrophin-1, Forked, and Masquerade genes was experimentally confirmed using a luciferase reporter system. Taken together, our results reconstruct the regulatory network that governs the development of the early brain diphenism in honey bees.

10-hydroxy-2E-decenoic acid (10HDA) does not promote caste differentiation in Melipona scutellaris stingless bees

In bees from genus Melipona, differential feeding is not enough to fully explain female polyphenism. In these bees, there is a hypothesis that in addition to the environmental component (food), a genetic component is also involved in caste differentiation. This mechanism has not yet been fully elucidated and may involve epigenetic and metabolic regulation. Here, we verified that the genes encoding histone deacetylases HDAC1 and HDAC4 and histone acetyltransferase KAT2A were expressed at all stages of Melipona scutellaris, with fluctuations between developmental stages and castes. In larvae, the HDAC genes showed the same profile of Juvenile Hormone titers-previous reported-whereas the HAT gene exhibited the opposite profile. We also investigated the larvae and larval food metabolomes, but we did not identify the putative queen-fate inducing compounds, geraniol and 10-hydroxy-2E-decenoic acid (10HDA). Finally, we demonstrated that the histone deacetylase inhibitor 10HDA-the major lipid component of royal jelly and hence a putative regulator of honeybee caste differentiation-was unable to promote differentiation in queens in Melipona scutellaris. Our results suggest that epigenetic and hormonal regulations may act synergistically to drive caste differentiation in Melipona and that 10HDA is not a caste-differentiation factor in Melipona scutellaris.

The trophocytes and oenocytes of worker and queen honey bees (Apis mellifera) exhibit distinct age-associated transcriptome profiles

Despite the identical genomic context, trophocytes and oenocytes in worker bees exhibit aging-related phenotypes, in contrast to the longevity phenotypes in queen bees. To explore this phenomenon at the molecular level, we evaluated the age-associated transcriptomes of trophocytes and oenocytes in worker bees and queen bees using high-throughput RNA-sequencing technology (RNA-seq). The results showed that (i) while gene expression profiles were different between worker and queen bees, they remained similar between young and old counterparts; (ii) worker bees express a high proportion of low-abundance genes, whereas queen bee transcriptomes display a high proportion of moderate-expression genes; (iii) genes were upregulated to a greater extent in queen bees vs. worker bees; and (iv) distinct aging-related and longevity-related candidate genes were found in worker and queen bees. These results provide new insights into the cellular aging and longevity of trophocytes and oenocytes in honey bees. Identification of aging-associated biomarker genes also constitutes a basis for translational research of aging in higher organisms.

A framework for understanding gene expression plasticity and its influence on stress tolerance

Phenotypic plasticity can serve as a stepping stone towards adaptation. Recently, studies have shown that gene expression contributes to emergent stress responses such as thermal tolerance, with tolerant and susceptible populations showing distinct transcriptional profiles. However, given the dynamic nature of gene expression, interpreting transcriptomic results in a way that elucidates the functional connection between gene expression and the observed stress response is challenging. Here, we present a conceptual framework to guide interpretation of gene expression reaction norms in the context of stress tolerance. We consider the evolutionary and adaptive potential of gene expression reaction norms and discuss the influence of sampling timing, transcriptomic resilience, as well as complexities related to life history when interpreting gene expression dynamics and how these patterns relate to host tolerance. We highlight corals as a case study to demonstrate the value of this framework for non-model systems. As species face rapidly changing environmental conditions, modulating gene expression can serve as a mechanistic link from genetic and cellular processes to the physiological responses that allow organisms to thrive under novel conditions. Interpreting how or whether a species can employ gene expression plasticity to ensure short-term survival will be critical for understanding the global impacts of climate change across diverse taxa.

Caste-specific gene expression underlying the differential adult brain development in the honeybee Apis mellifera

Apis mellifera adult workers feature more developed key brain regions than queens, which allows them to cope with the broad range of duties they need to perform in a colony. However, at the end of larval development, the brain of queens is largely more developed than that of workers. Major morphogenetic changes take place after metamorphosis that shift caste-specific brain development. Here, we tested the hypothesis that this phenomenon is hormonally governed and involves differential gene expression. Our molecular screening approach revealed a set of differentially expressed genes in Pp (first pharate-adult phase) brains between castes mainly coding for tissue remodelling and energy-converting proteins (e.g. hex 70a and ATPsynβ). An in-depth qPCR analysis of the transcriptional behaviour during pupal and pharate-adult developmental stage in both castes and in response to artificially augmented hormone titres of 18 genes/variants revealed that: i. subtle differences in hormone titres between castes might be responsible for the differential expression of the EcR and insulin/insulin-like signalling (IIS) pathway genes; ii. the morphogenetic activity of the IIS in brain development must be mediated by ILP-2, iii. which together with the tum, mnb and caspase system, can constitute the molecular effectors of the caste-specific opposing brain developmental trajectories.

Novel Insight Into the Development and Function of Hypopharyngeal Glands in Honey Bees

Hypopharyngeal glands (HGs) are the most important organ of hymenopterans which play critical roles for the insect physiology. In honey bees, HGs are paired structures located bilaterally in the head, in front of the brain between compound eyes. Each gland is composed of thousands of secretory units connecting to secretory duct in worker bees. To better understand the recent progress made in understanding the structure and function of these glands, we here review the ontogeny of HGs, and the factors affecting the morphology, physiology, and molecular basis of the functionality of the glands. We also review the morphogenesis of HGs in the pupal and adult stages, and the secretory role of the glands across the ages for the first time. Furthermore, recent transcriptome, proteome, and phosphoproteome analyses have elucidated the potential mechanisms driving the HGs development and functionality. This adds a comprehensive novel knowledge of the development and physiology of HGs in honey bees over time, which may be helpful for future research investigations.

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.

Transgenerational accumulation of methylome changes discovered in commercially reared honey bee (Apis mellifera) queens

Whether a female honey bee (Apis mellifera) develops into a worker or a queen depends on her nutrition during development, which changes the epigenome to alter the developmental trajectory. Beekeepers typically exploit this developmental plasticity to produce queen bee by transplanting worker larvae into queen cells to be reared as queens, thus redirecting a worker developmental pathway to a queen developmental pathway. We studied the consequences of this manipulation for the queen phenotype and methylome over four generations. Queens reared from worker larvae consistently had fewer ovarioles than queens reared from eggs. Over four generations the methylomes of lines of queens reared from eggs and worker larvae diverged, accumulating increasing differences in exons of genes related to caste differentiation, growth and immunity. We discuss the consequences of these cryptic changes to the honey bee epigenome for the health and viability of honey bee stocks.

First Draft Genome Assembly of the Malaysian Stingless Bee, Heterotrigona itama (Apidae, Meliponinae)

The Malaysian stingless bee industry is hugely dependent on wild colonies. Nevertheless, the availability of new queens to establish new colonies is insufficient to meet the growing demand for hives in the industry. Heterotrigona itama is primarily utilized for honey production in the region and the major source of stingless bee colonies comes from the wild. To propagate new colonies domestically, a fundamental understanding of the biology of queen development, especially from the genomics aspect, is necessary. The whole genome was sequenced using a paired-end 150 strategy on the Illumina HiSeq X platform. The shotgun sequencing generated approximately 89 million raw pair-end reads with a total output of 13.37 Gb and a GC content of 37.31%. The genome size of the species was estimated to be approximately 272 Mb. Phylogenetic analysis showed H. itama are much more closely related to the bumble bee (Bombus spp.) than they are to the modern honey bee (Apis spp.). The genome data provided here are expected to contribute to a better understanding of the genetic aspect of queen differentiation as well as of important molecular pathways which are crucial for stingless bee biology, management and conservation.

Epigenetic Molecular Mechanisms in Insects

Insects are the largest animal group on Earth both in biomass and diversity. Their outstanding success has inspired genetics and developmental research, allowing the discovery of dynamic process explaining extreme phenotypic plasticity and canalization. Epigenetic molecular mechanisms (EMMs) are vital for several housekeeping functions in multicellular organisms, regulating developmental, ontogenetic trajectories and environmental adaptations. In Insecta, EMMs are involved in the development of extreme phenotypic divergences such as polyphenisms and eusocial castes. Here, we review the history of this research field and how the main EMMs found in insects help to understand their biological processes and diversity. EMMs in insects confer them rapid response capacity allowing insect either to change with plastic divergence or to keep constant when facing different stressors or stimuli. EMMs function both at intra as well as transgenerational scales, playing important roles in insect ecology and evolution. We discuss on how EMMs pervasive influences in Insecta require not only the control of gene expression but also the dynamic interplay of EMMs with further regulatory levels, including genetic, physiological, behavioral, and environmental among others, as was earlier proposed by the Probabilistic Epigenesis model and Developmental System Theory.

Genome-Wide Differential DNA Methylation in Reproductive, Morphological, and Visual System Differences Between Queen Bee and Worker Bee (Apis mellifera)

There are many differences in external morphology and internal physiology between the Apis mellifera queen bee and worker bee, some of which are relevant to beekeeping production. These include reproductive traits, body size, royal jelly secreting properties, and visual system development, among others. The identification of candidate genes that control the differentiation of these traits is critical for selective honeybee breeding programs. In this study, we compared the genomic methylation of queen bee and worker bee larvae at 3, 4, and 5 days of age by whole-genome bisulfite sequencing, and found that the basic characteristics of genomic methylation in queen and worker larvae were the same. There were approximately 49 million cytosines in the Apis larvae genome, of which about 90,000 were methylated. Methylated CpG sites accounted for 99% of the methylated cytosines, and methylation mainly occurred in exons. However, methylation levels of queen and worker larvae showed different trends with age: the methylation level of queen larvae varied with age in an inverted parabola, while the corresponding trend for worker larvae with resembled an exponential curve with a platform. The methylation level of queen larvae was higher than that of worker larvae at 3 days of age, lower than that of worker larvae at 4 days of age, and similar to that of worker larvae at 5 days old. The top 10 differentially methylated genes (DMGs) and 13 caste-specific methylated genes were listed, and correlations with caste determination were speculated. We additionally screened 38 DMGs between queen larvae and worker larvae involved in specific organ differentiation as well as reproduction, morphology, and vision differentiation during caste determination. These genes are potential molecular markers for selective breeding of A. mellifera to improve fecundity, royal jelly production, body size, and foraging, and represent candidate genes for investigating specialized functional segregation during the process of caste differentiation.

Chromatin accessibility and transcriptome landscapes of Monomorium pharaonis brain

The emergence of social organization (eusociality) is a major event in insect evolution. Although previous studies have investigated the mechanisms underlying caste differentiation and social behavior of eusocial insects including ants and honeybees, the molecular circuits governing sociality in these insects remain obscure. In this study, we profiled the transcriptome and chromatin accessibility of brain tissues in three Monomorium pharaonis ant castes: queens (including mature and un-mated queens), males and workers. We provide a comprehensive dataset including 16 RNA-sequencing and 16 assay for transposase accessible chromatin (ATAC)-sequencing profiles. We also demonstrate strong reproducibility of the datasets and have identified specific genes and open chromatin regions in the genome that may be associated with the social function of these castes. Our data will be a valuable resource for further studies of insect behaviour, particularly the role of brain in the control of eusociality.

The modular nature of protein evolution: domain rearrangement rates across eukaryotic life

BACKGROUND

Modularity is important for evolutionary innovation. The recombination of existing units to form larger complexes with new functionalities spares the need to create novel elements from scratch. In proteins, this principle can be observed at the level of protein domains, functional subunits which are regularly rearranged to acquire new functions.

RESULTS

In this study we analyse the mechanisms leading to new domain arrangements in five major eukaryotic clades (vertebrates, insects, fungi, monocots and eudicots) at unprecedented depth and breadth. This allows, for the first time, to directly compare rates of rearrangements between different clades and identify both lineage specific and general patterns of evolution in the context of domain rearrangements. We analyse arrangement changes along phylogenetic trees by reconstructing ancestral domain content in combination with feasible single step events, such as fusion or fission. Using this approach we explain up to 70% of all rearrangements by tracing them back to their precursors. We find that rates in general and the ratio between these rates for a given clade in particular, are highly consistent across all clades. In agreement with previous studies, fusions are the most frequent event leading to new domain arrangements. A lineage specific pattern in fungi reveals exceptionally high loss rates compared to other clades, supporting recent studies highlighting the importance of loss for evolutionary innovation. Furthermore, our methodology allows us to link domain emergences at specific nodes in the phylogenetic tree to important functional developments, such as the origin of hair in mammals.

CONCLUSIONS

Our results demonstrate that domain rearrangements are based on a canonical set of mutational events with rates which lie within a relatively narrow and consistent range. In addition, gained knowledge about these rates provides a basis for advanced domain-based methodologies for phylogenetics and homology analysis which complement current sequence-based methods.

Impact of sublethal exposure to synthetic and natural acaricides on honey bee (Apis mellifera) memory and expression of genes related to memory

Acaricides are used by beekeepers in honey bee (Apis mellifera L.) colonies to control parasitic mites, but may also have adverse effects to honey bees. In this study, five commonly used acaricides were tested for their sublethal effects on memory and expression of neural-related genes in honey bees. Memory measured with the proboscis extension reflex (PER) assay was significantly reduced by topical treatment of bees with a single LD₀₅ dose of formic acid at 2 and 24 h post treatment (hpt). However, tau-fluvalinate, amitraz, coumaphos, and formic acid, but not thymol, resulted in memory loss at 48 hpt. The LD₀₅ doses of the acraricides did not affect expression of neuroligin-1, related to memory, or expression of major royal jelly protein-1, related to both memory and development, although expression of both genes was affected at LD₅₀ doses. The LD₀₅ doses of thymol, formic acid, amitraz and coumaphos increased defensin-1 expression, which is related to both memory and immunity. The effect of thymol, however, may have been due to its impact on the immune response rather than memory. This study demonstrates that acaricides vary in their effects on bee's memory, and that the widely used acaricide, formic acid, is particularly damaging.

Effects of larval Age at Grafting and Juvenile Hormone on Morphometry and Reproductive Quality Parameters of in Vitro Reared Honey Bees (Hymenoptera: Apidae)

The honey bee queen plays a central role in the Apis mellifera L. (Hymenoptera: Apidae) colony, and her high reproductive capacity is fundamental for building up the workforce of a colony. Caste development in honey bee females involves elaborate physiological pathways unleashed at the beginning of the first larval instars, with juvenile hormone (JH) playing a crucial role. Here we took advantage of established in vitro rearing techniques to conduct a 2 × 2 experimental design and test initial rearing age (young vs old) and JH treatment (JH III vs solvent control) to enlighten the role of nutrient quality and JH in shaping honey bee female fertility, morphological features related to queenliness, and key physiological parameters (hemolymph vitellogenin/Vg, sugar levels, and Vg transcript levels). Our results show that while the age at initial larval rearing had major impacts on external morphology development, where younger larvae exhibited a higher probability to develop into queen-like adults morphotypes, the JH application during the larval stage improved physiological pathways related to ovary development and metabolism during the ontogenic development. We detected that the supplementation of queen larvae with JH promoted important benefits regarding queen fertility as the increase of ovariole number and vg levels at hemolymph, both crucial factors at eggs production. The data presented here provide guidance in efforts to improve honey bee queen quality, especially in light of frequent episodes of queen failures in the beekeeping industry.

A comparison of honeybee (Apis mellifera) queen, worker and drone larvae by RNA-Seq

Honeybees (Apis mellifera) have haplodiploid sex determination: males develop from unfertilized eggs and females develop from fertilized ones. The differences in larval food also determine the development of females. Here we compared the total somatic gene expression profiles of 2-day and 4-day-old drone, queen and worker larvae by RNA-Seq. The results from a co-expression network analysis on all expressed genes showed that 2-day-old drone and worker larvae were closer in gene expression profiles than 2-day-old queen larvae. This indicated that for young larvae (2-day-old) environmental factors such as larval diet have a greater effect on gene expression profiles than ploidy or sex determination. Drones had the most distinct gene expression profiles at the 4-day larval stage, suggesting that haploidy, or sex dramatically affects the gene expression of honeybee larvae. Drone larvae showed fewer differences in gene expression profiles at the 2-day and 4-day time points than the worker and queen larval comparisons (598 against 1190 and 1181), suggesting a different pattern of gene expression regulation during the larval development of haploid males compared to diploid females. This study indicates that early in development the queen caste has the most distinct gene expression profile, perhaps reflecting the very rapid growth and morphological specialization of this caste compared to workers and drones. Later in development the haploid male drones have the most distinct gene expression profile, perhaps reflecting the influence of ploidy or sex determination on gene expression.

Comparative transcriptomics of social insect queen pheromones

Queen pheromones are chemical signals that mediate reproductive division of labor in eusocial animals. Remarkably, queen pheromones are composed of identical or chemically similar compounds in some ants, wasps and bees, even though these taxa diverged >150MYA and evolved queens and workers independently. Here, we measure the transcriptomic consequences of experimental exposure to queen pheromones in workers from two ant and two bee species (genera: Lasius, Apis, Bombus), and test whether they are similar across species. Queen pheromone exposure affected transcription and splicing at many loci. Many genes responded consistently in multiple species, and the set of pheromone-sensitive genes was enriched for functions relating to lipid biosynthesis and transport, olfaction, production of cuticle, oogenesis, and histone (de)acetylation. Pheromone-sensitive genes tend to be evolutionarily ancient, positively selected, peripheral in the gene coexpression network, hypomethylated, and caste-specific in their expression. Our results reveal how queen pheromones achieve their effects, and suggest that ants and bees use similar genetic modules to achieve reproductive division of labor.

A genetic switch for worker nutrition-mediated traits in honeybees

Highly social insects are characterized by caste dimorphism, with distinct size differences of reproductive organs between fertile queens and the more or less sterile workers. An abundance of nutrition or instruction via diet-specific compounds has been proposed as explanations for the nutrition-driven queen and worker polyphenism. Here, we further explored these models in the honeybee (Apis mellifera) using worker nutrition rearing and a novel mutational screening approach using the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) method. The worker nutrition-driven size reduction of reproductive organs was restricted to the female sex, suggesting input from the sex determination pathway. Genetic screens on the sex determination genes in genetic females for size polyphenism revealed that doublesex (dsx) mutants display size-reduced reproductive organs irrespective of the sexual morphology of the organ tissue. In contrast, feminizer (fem) mutants lost the response to worker nutrition-driven size control. The first morphological worker mutants in honeybees demonstrate that the response to nutrition relies on a genetic program that is switched “ON” by the fem gene. Thus, the genetic instruction provided by the fem gene provides an entry point to genetically dissect the underlying processes that implement the size polyphenism.

In honeybees, nutrition drives dimorphic size development of reproductive organs in fertile queens and sterile workers. A study using the first induced morphological mutants in honeybees demonstrates that this developmental plasticity requires a genetic program that is switched on by the “feminizer” gene.

In honeybees, nutrition drives dimorphic size development of reproductive organs in fertile queens and sterile workers. The first induced morphological mutants in honeybees demonstrate that this developmental plasticity requires a genetic program that is switched “ON” by the feminizer (fem) gene.

One-Carbon Metabolism Links Nutrition Intake to Embryonic Development via Epigenetic Mechanisms

Beyond energy production, nutrient metabolism plays a crucial role in stem cell lineage determination. Changes in metabolism based on nutrient availability and dietary habits impact stem cell identity. Evidence suggests a strong link between metabolism and epigenetic mechanisms occurring during embryonic development and later life of offspring. Metabolism regulates epigenetic mechanisms such as modifications of DNA, histones, and microRNAs. In turn, these epigenetic mechanisms regulate metabolic pathways to modify the metabolome. One-carbon metabolism (OCM) is a crucial metabolic process involving transfer of the methyl groups leading to regulation of multiple cellular activities. OCM cycles and its related micronutrients are ubiquitously present in stem cells and feed into the epigenetic mechanisms. In this review, we briefly introduce the OCM process and involved micronutrients and discuss OCM-associated epigenetic modifications, including DNA methylation, histone modification, and microRNAs. We further consider the underlying OCM-mediated link between nutrition and epigenetic modifications in embryonic development.

Environmental and Evolutionary Drivers of the Modular Gene Regulatory Network Underlying Phenotypic Plasticity for Stress Resistance in the Nematode Caenorhabditis remanei

Organisms can cope with stressful environments via a combination of phenotypic plasticity at the individual level and adaptation at the population level. Changes in gene expression can play an important role in both. Significant advances in our understanding of gene regulatory plasticity and evolution have come from comparative studies in the field and laboratory. Experimental evolution provides another powerful path by which to learn about how differential regulation of genes and pathways contributes to both acclimation and adaptation. Here we present results from one such study using the nematode Caenorhabditis remanei We selected one set of lines to withstand heat stress and another oxidative stress. We then compared transcriptional responses to acute heat stress of both and an unselected control to the ancestral population using a weighted gene coexpression network analysis, finding that the transcriptional response is primarily dominated by a plastic response that is shared in the ancestor and all evolved populations. In addition, we identified several modules that respond to artificial selection by (1) changing the baseline level of expression, (2) altering the magnitude of the plastic response, or (3) a combination of the two. Our findings therefore reveal that while patterns of transcriptional response can be perturbed with short bouts of intense selection, the overall ancestral structure of transcriptional plasticity is largely maintained over time.

Hormonal control and target genes of ftz-f1 expression in the honeybee Apis mellifera: a positive loop linking juvenile hormone, ftz-f1, and vitellogenin

Ftz-f1 is an orphan member of the nuclear hormone receptor superfamily. A 20-hydroxyecdysone pulse allows ftz-f1 gene expression, which then regulates the activity of downstream genes involved in major developmental progression events. In honeybees, the expression of genes like vitellogenin (vg), prophenoloxidase and juvenile hormone-esterase during late pharate-adult development is known to be hormonally controlled in both queens and workers by increasing juvenile hormone (JH) titres in the presence of declining levels of ecdysteroids. Since Ftz-f1 is known for mediating intracellular JH signalling, we hypothesized that ftz-f1 could mediate JH action during the pharate-adult development of honeybees, thus controlling the expression of these genes. Here, we show that ftz-f1 has caste-specific transcription profiles during this developmental period, with a peak coinciding with the increase in JH titre, and that its expression is upregulated by JH and downregulated by ecdysteroids. RNAi-mediated knock down of ftz-f1 showed that the expression of genes essential for adult development (e.g. vg and cuticular genes) depends on ftz-f1 expression. Finally, a double-repressor hypothesis-inspired vg gene knock-down experiment suggests the existence of a positive molecular loop between JH, ftz-f1 and vg.

Reproductive capacity and castes in eusocial stingless bees (Hymenoptera: Apidae)

Eusocial lifestyle is one of the most important transitions in the evolutionary history of some groups of organisms. In bees, there are only two eusocial groups: the honey bees (Apini) and the stingless bees (Meliponini). Despite similarities on the eusocial lifestyles of these taxa, they present profound differences related to caste determination, development, behavior, and reproductive capacity of their members. In most of them the queen has a monopoly on reproduction. However, even though workers are tipically sterile, they can contribute to producing haploid eggs that generate males, or trophic eggs, used as an additional nutrition by the queen.

Genetic accommodation and the role of ancestral plasticity in the evolution of insect eusociality

For over a century, biologists have proposed a role for phenotypic plasticity in evolution, providing an avenue for adaptation in addition to 'mutation-first' models of evolutionary change. According to the various versions of this idea, the ability of organisms to respond adaptively to their environment through phenotypic plasticity may lead to novel phenotypes that can be screened by natural selection. If these initially environmentally induced phenotypes increase fitness, then genetic accommodation can lead to allele frequency change, influencing the expression of those phenotypes. Despite the long history of 'plasticity-first' models, the importance of genetic accommodation in shaping evolutionary change has remained controversial - it is neither fully embraced nor completely discarded by most evolutionary biologists. We suggest that the lack of acceptance of genetic accommodation in some cases is related to a lack of information on its molecular mechanisms. However, recent reports of epigenetic transgenerational inheritance now provide a plausible mechanism through which genetic accommodation may act, and we review this research here. We also discuss current evidence supporting a role for genetic accommodation in the evolution of eusociality in social insects, which have long been models for studying the influence of the environment on phenotypic variation, and may be particularly good models for testing hypotheses related to genetic accommodation. Finally, we introduce 'eusocial engineering', a method by which novel social phenotypes are first induced by environmental modification and then studied mechanistically to understand how environmentally induced plasticity may lead to heritable changes in social behavior. We believe the time is right to incorporate genetic accommodation into models of the evolution of complex traits, armed with new molecular tools and a better understanding of non-genetic heritable elements.

Uncovering the Changing Gene Expression Profile of Honeybee (Apis mellifera) Worker Larvae Transplanted to Queen Cells

The reproductive division of labor, based on caste differentiation in social insects, is of great significance in evolution. Generally, a healthy bee colony consists of a queen and numerous workers and drones. Despite being genetically identical, the queen and workers exhibit striking differences in morphology, behavior, and lifespan. The fertilized eggs and larvae selectively develop into queen and worker bees depending on the local nutrition and environment. Bee worker larvae that are transplanted within 3 days of age to queen cells of a bee colony can develop into queens with mature ovaries. This phenomenon is important to understand the regulatory mechanisms of caste differentiation. In this study, we transplanted worker larvae (Apis mellifera) at the age of 1 (L1), 2 (L2), and 3 days (L3) into queen cells until the age of 4 days. Subsequently, genetic changes in these larvae were evaluated. The results revealed that the number of differentially expressed genes (DEGs) in L1 vs. L3 was more than that in L1 vs. L2. Furthermore, many of the genes that were downregulated are mostly involved in metabolism, body development, reproductive ability, and longevity, indicating that these functions decreased with the age of transplantation of the larvae. Moreover, these functions may be critical for worker larvae to undergo the developmental path to become queens. We also found that the DEGs of L1 vs. L2 and L1 vs. L3 were enriched in the MAPK, FoxO, mTOR, Wnt, TGF-beta Hedgehog Toll and Imd, and Hippo signaling pathways. Gene ontology analysis indicated that some genes are simultaneously involved in different biological pathways; through these genes, the pathways formed a mutual regulatory network. Casein kinase 1 (CK 1) was predicted to participate in the FoxO, Wnt, Hedgehog, and Hippo signaling pathways. The results suggest that these pathways cross talked through the network to modify the development of larvae and that CK 1 is an important liaison. The results provide valuable information regarding the regulatory mechanism of environmental factors affecting queen development, thus, amplifying the understanding of caste differentiation in bees.

Towards reconstructing the ancestral brain gene-network regulating caste differentiation in ants

Specialized queens and life-time unmated workers evolved once in the common ancestor of all ants, but whether caste development across ants continues to be at least partly regulated by a single core set of genes remains obscure. We analysed brain transcriptomes from five ant species (three subfamilies) and reconstructed the origins of genes with caste-biased expression. Ancient genes predating the Neoptera were more likely to regulate gyne (virgin queen) phenotypes, while caste differentiation roles of younger, ant-lineage-specific genes varied. Transcriptome profiling showed that the ancestral network for caste-specific gene-regulation has been maintained, but that signatures of common ancestry are obscured by later modifications. Adjusting for such differences, we identified a core gene-set that: 1. consistently displayed similar directions and degrees of caste-differentiated expression, and 2. have mostly not been reported as being involved in caste differentiation. These core regulatory genes exist in the genomes of ant species that secondarily lost the queen caste, but expression differences for reproductive and sterile workers are minor and similar to social paper wasps that lack differentiated castes. Many caste-biased ant genes have caste-differentiated expression in honeybees, but directions of caste bias were uncorrelated, as expected when permanent castes evolved independently in both lineages.

Phenotypically distinct female castes in honey bees are defined by alternative chromatin states during larval development

The capacity of the honey bee to produce three phenotypically distinct organisms (two female castes; queens and sterile workers, and haploid male drones) from one genotype represents one of the most remarkable examples of developmental plasticity in any phylum. The queen-worker morphological and reproductive divide is environmentally controlled during post-embryonic development by differential feeding. Previous studies implicated metabolic flux acting via epigenetic regulation, in particular DNA methylation and microRNAs, in establishing distinct patterns of gene expression underlying caste-specific developmental trajectories. We produce the first genome-wide maps of chromatin structure in the honey bee at a key larval stage in which developmental canalization into queen or worker is virtually irreversible. We find extensive genome-wide differences in H3K4me3, H3K27ac, and H3K36me3, many of which correlate with caste-specific transcription. Furthermore, we identify H3K27ac as a key chromatin modification, with caste-specific regions of intronic H3K27ac directing the worker caste. These regions may harbor the first examples of caste-specific enhancer elements in the honey bee. Our results demonstrate a key role for chromatin modifications in the establishment and maintenance of caste-specific transcriptional programs in the honey bee. We show that at 96 h of larval growth, the queen-specific chromatin pattern is already established, whereas the worker determination is not, thus providing experimental support for the perceived timing of this critical point in developmental heterochrony in two types of honey bee females. In a broader context, our study provides novel data on environmentally regulated organismal plasticity and the molecular foundation of the evolutionary origins of eusociality.

Clonal raider ant brain transcriptomics identifies candidate molecular mechanisms for reproductive division of labor

BACKGROUND

Division of labor between reproductive queens and workers that perform brood care is a hallmark of insect societies. However, studies of the molecular basis of this fundamental dichotomy are limited by the fact that the caste of an individual cannot typically be experimentally manipulated at the adult stage. Here we take advantage of the unique biology of the clonal raider ant, Ooceraea biroi, to study brain gene expression dynamics during experimentally induced transitions between reproductive and brood care behavior.

RESULTS

Introducing larvae that inhibit reproduction and induce brood care behavior causes much faster changes in adult gene expression than removing larvae. In addition, the general patterns of gene expression differ depending on whether ants transition from reproduction to brood care or vice versa, indicating that gene expression changes between phases are cyclic rather than pendular. Finally, we identify genes that could play upstream roles in regulating reproduction and behavior because they show large and early expression changes in one or both transitions.

CONCLUSIONS

Our analyses reveal that the nature and timing of gene expression changes differ substantially depending on the direction of the transition, and identify a suite of promising candidate molecular regulators of reproductive division of labor that can now be characterized further in both social and solitary animal models. This study contributes to understanding the molecular regulation of reproduction and behavior, as well as the organization and evolution of insect societies.

The Role of Brood in Eusocial Hymenoptera

Study of social traits in offspring traditionally reflects on interactions in simple family groups, with famous examples including parent-offspring conflict and sibling rivalry in birds and mammals. In contrast, studies of complex social groups such as the societies of ants, bees, and wasps focus mainly on adults and, in particular, on traits and interests of queens and workers. The social role of developing individuals in complex societies remains poorly understood. We attempt to fill this gap by illustrating that development in social Hymenoptera constitutes a crucial life stage with important consequences for the individual as well as the colony. We begin by describing the complex social regulatory network that modulates development in Hymenoptera societies. By highlighting the inclusive fitness interests of developing individuals, we show that they may differ from those of other colony members. We then demonstrate that offspring have evolved specialized traits that allow them to play a functional, cooperative role within colonies and give them the potential power to act toward increasing their inclusive fitness. We conclude by providing testable predictions for investigating the role of brood in colony interactions and giving a general outlook on what can be learned from studying offspring traits in hymenopteran societies.