Molecular characterization of the gene feminizer in the stingless bee Melipona interrupta (Hymenoptera: Apidae) reveals association to sex and caste development

Sex- and caste-specific transcriptomes of larval honey bee (Apis mellifera L.) gonads: DMRT A2 and Hsp83 are differentially expressed and regulated by juvenile hormone

The gonads of honey bee, Apis mellifera, queens and drones are each composed of hundreds of serial units, the ovarioles and testioles, while the ovaries of the adult subfertile workers consist of only few ovarioles. We performed a comparative RNA-seq analysis on early fifth-instar (L5F1) larval gonads, which is a critical stage in gonad development of honey bee larvae. A total of 1834 genes were identified as differentially expressed (Padj < 0.01) among the three sex and caste phenotypes. The Gene Ontology analysis showed significant enrichment for metabolism, protein or ion binding, and oxidoreductase activity, and a KEGG analysis revealed metabolic pathways as enriched. In a principal component analysis for the total transcriptomes and hierarchical clustering of the DEGs, we found higher similarity between the queen and worker ovary transcriptomes compared to the drone testis, despite the onset of programmed cell death in the worker ovaries. Four DEGs were selected for RT-qPCR analyses, including their response to juvenile hormone (JH), which is a critical factor in the caste-specific development of the ovaries. Among these, DMRT A2 and Hsp83 were found upregulated by JH and, thus, emerged as potential molecular markers for sex- and caste-specific gonad development in honey bees.

Expression of methyl farnesoate epoxidase (mfe) and juvenile hormone esterase (jhe) genes and their relation to social organization in the stingless bee Melipona interrupta (Hymenoptera: Apidae)

Social organization in highly eusocial bees relies upon two important processes: caste differentiation in female larvae, and age polyethism in adult workers. Juvenile Hormone (JH) is a key regulator of both processes. Here we investigated the expression of two genes involved in JH metabolism - mfe (biosynthesis) and jhe (degradation) - in the context of social organization in the stingless bee Melipona interrupta. We found evidence that the expression of mfe and jhe genes is related to changes in JH levels during late larval development, where caste determination occurs. Also, both mfe and jhe were upregulated when workers engage in intranidal tasks, but only jhe expression was downregulated at the transition from nursing to foraging activities. This relation is different than expected, considering recent reports of lower JH levels in foragers than nurses in the closely related species Melipona scutellaris. Our findings suggest that highly eusocial bees have different mechanisms to regulate JH and, thus, to maintain their level of social organization.

The nuclear and mitochondrial genomes of Frieseomelitta varia - a highly eusocial stingless bee (Meliponini) with a permanently sterile worker caste

BACKGROUND

Most of our understanding on the social behavior and genomics of bees and other social insects is centered on the Western honey bee, Apis mellifera. The genus Apis, however, is a highly derived branch comprising less than a dozen species, four of which genomically characterized. In contrast, for the equally highly eusocial, yet taxonomically and biologically more diverse Meliponini, a full genome sequence was so far available for a single Melipona species only. We present here the genome sequence of Frieseomelitta varia, a stingless bee that has, as a peculiarity, a completely sterile worker caste.

RESULTS

The assembly of 243,974,526 high quality Illumina reads resulted in a predicted assembled genome size of 275 Mb composed of 2173 scaffolds. A BUSCO analysis for the 10,526 predicted genes showed that these represent 96.6% of the expected hymenopteran orthologs. We also predicted 169,371 repetitive genomic components, 2083 putative transposable elements, and 1946 genes for non-coding RNAs, largely long non-coding RNAs. The mitochondrial genome comprises 15,144 bp, encoding 13 proteins, 22 tRNAs and 2 rRNAs. We observed considerable rearrangement in the mitochondrial gene order compared to other bees. For an in-depth analysis of genes related to social biology, we manually checked the annotations for 533 automatically predicted gene models, including 127 genes related to reproductive processes, 104 to development, and 174 immunity-related genes. We also performed specific searches for genes containing transcription factor domains and genes related to neurogenesis and chemosensory communication.

CONCLUSIONS

The total genome size for F. varia is similar to the sequenced genomes of other bees. Using specific prediction methods, we identified a large number of repetitive genome components and long non-coding RNAs, which could provide the molecular basis for gene regulatory plasticity, including worker reproduction. The remarkable reshuffling in gene order in the mitochondrial genome suggests that stingless bees may be a hotspot for mtDNA evolution. Hence, while being just the second stingless bee genome sequenced, we expect that subsequent targeting of a selected set of species from this diverse clade of highly eusocial bees will reveal relevant evolutionary signals and trends related to eusociality in these important pollinators.

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

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

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

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.

Impact of environmental temperatures on mortality, sex and caste ratios in Melipona interrupta Latreille (Hymenoptera, Apidae)

Temperature is a major driver of biological phenomena, from metabolism to ecological interactions and rates of evolutionary diversification. However, species vary greatly in their thermal tolerance, as well as the temperature under which they perform best. This study aimed to investigate the effect of experimental manipulation of environmental temperatures on the individual mortality and phenotypic composition of colonies of Melipona interrupta. To fulfill these objectives, 30 colonies in equivalent developmental conditions were artificially subjected to different temperatures. Temperatures were monitored by thermo-hygrometers, and immature mortality and sex and caste ratios were observed in brood combs during 14 months. A strong effect of external temperature on immatures was detected on deviations from 28 to 30 °C (the natural average temperature inside the colony), causing an increase in mortality. Likewise, a significant effect of temperature on sex ratio was detected, with male:female ratio decreasing at temperatures below and above 28-30 °C. Lastly, there was no clear evidence for an effect of temperature on caste ratio, although queens appeared to become relatively more frequent at warmer temperatures. The results of this study allow us to conclude that anthropogenic changes, whose effect can be extrapolated to the similar natural changes, that modify the environmental temperatures to which M. interrupta colonies are exposed are likely to compromise their survival, mainly through individual mortality.

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.

Building a new research framework for social evolution: intralocus caste antagonism

The breeding and non‐breeding ‘castes’ of eusocial insects provide a striking example of role‐specific selection, where each caste maximises fitness through different morphological, behavioural and physiological trait values. Typically, queens are long‐lived egg‐layers, while workers are short‐lived, largely sterile foragers. Remarkably, the two castes are nevertheless produced by the same genome. The existence of inter‐caste genetic correlations is a neglected consequence of this shared genome, potentially hindering the evolution of caste dimorphism: alleles that increase the productivity of queens may decrease the productivity of workers and vice versa, such that each caste is prevented from reaching optimal trait values. A likely consequence of this ‘intralocus caste antagonism’ should be the maintenance of genetic variation for fitness and maladaptation within castes (termed ‘caste load’), analogous to the result of intralocus sexual antagonism. The aim of this review is to create a research framework for understanding caste antagonism, drawing in part upon conceptual similarities with sexual antagonism. By reviewing both the social insect and sexual antagonism literature, we highlight the current empirical evidence for caste antagonism, discuss social systems of interest, how antagonism might be resolved, and challenges for future research. We also introduce the idea that sexual and caste antagonism could interact, creating a three‐way antagonism over gene expression. This includes unpacking the implications of haplodiploidy for the outcome of this complex interaction.

Methyl farnesoate epoxidase (mfe) gene expression and juvenile hormone titers in the life cycle of a highly eusocial stingless bee, Melipona scutellaris

In social insects, juvenile hormone (JH) has acquired novel functions related to caste determination and division of labor among workers, and this is best evidenced in the honey bee. In contrast to honey bees, stingless bees are a much more diverse group of highly eusocial bees, and the genus Melipona has long called special attention due to a proposed genetic mechanism of caste determination. Here, we examined methyl farnesoate epoxidase (mfe) gene expression, encoding an enzyme relevant for the final step in JH biosynthesis, and measured the hemolymph JH titers for all life cycle stages of Melipona scutellaris queens and workers. We confirmed that mfe is exclusively expressed in the corpora allata. The JH titer is high in the second larval instar, drops in the third, and rises again as the larvae enter metamorphosis. During the pupal stage, mfe expression is initialy elevated, but then gradually drops to low levels before adult emergence. No variation was, however, seen in the JH titer. In adult virgin queens, mfe expression and the JH titer are significantly elevated, possibly associated with their reproductive potential. For workers we found that JH titers are lower in foragers than in nurse bees, while mfe expression did not differ. Stingless bees are, thus, distinct from honey bee workers, suggesting that they have maintained the ancestral gonadotropic function for JH. Hence, the physiological circuitries underlying a highly eusocial life style may be variable, even within a monophyletic clade such as the corbiculate bees.

Selection of reference genes for expression analysis using RT-qPCR in the dissemination system of Heliothis virescens ascovirus 3 h (HvAV-3h)

Ascoviruses are double-stranded DNA viruses that mainly infect noctuid larvae, and are transmitted by the parasitoid wasp Microplitis similis Lyle. Ascovirus-parasitoids wasp-noctuid insects constitute the dissemination system. Selection of suitable reference genes for the dissemination system could play an important role in elucidating the pathogenic molecular mechanisms of ascovirus. Unfortunately, such studies on potential reference genes in the dissemination system of ascoviruses are lacking. In the present study, we evaluated 11 candidate reference genes: β-actin1 (ACT1), β-actin2 (ACT2), elongation factor 1 (EF1), elongation factor 2 (EF2), ribosomal protein L10 (L10), ribosomal protein L17A (L17A), superoxide dismutase (SOD), 28S ribosome (28S), Tubulin (TUB) and 18S ribosome (18S). The samples were originally from various virus concentrations and points-in-time of experimental treatments using RefFinder and four algorithms. The results showed that EF1 was the most stable internal gene in S. exigua and M. similis and that EF2 was the most stable in the IOZCAS-Spex-II-A cell line, and the stability of reference genes were confirmed via the expression levels of two inhibitor of apoptosis-like (iap-like) genes from Heliothis virescens ascovirus 3 h (HvAV-3h). This study provides a crucial basis for future research that explores the molecular mechanisms of the pathogenesis of ascoviruses.

Pleistocene climate changes shaped the population structure of Partamona seridoensis (Apidae, Meliponini), an endemic stingless bee from the Neotropical dry forest

Partamona seridoensis is an endemic stingless bee from the Caatinga, a Neotropical dry forest in northeastern Brazil. Like other stingless bees, this species plays an important ecological role as a pollinator. The aim of the present study was to investigate the genetic structure and evolutionary history of P. seridoensis across its current geographic range. Workers from 84 nests from 17 localities were analyzed for COI and Cytb genic regions. The population structure tests (Bayesian phylogenetic inference, AMOVA and haplotype network) consistently characterized two haplogroups (northwestern and eastern), with little gene flow between them, generating a high differentiation between them as well as among the populations within each haplogroup. The Mantel test revealed no isolation by distance. No evidence of a potential geographic barrier in the present that could explain the diversification between the P. seridoensis haplogroups was found. However, Pleistocene climatic changes may explain this differentiation, since the initial time for the P. seridoensis lineages diversification took place during the mid-Pleistocene, specifically the interglacial period, when the biota is presumed to have been more associated with dry conditions and had more restricted, fragmented geographical distribution. This event may have driven diversification by isolating the two haplogroups. Otherwise, the climatic changes in the late Pleistocene must not have drastically affected the population dynamics of P. seridoensis, since the Bayesian Skyline Plot did not reveal any substantial fluctuation in effective population size in either haplogroup. Considering its importance and the fact that it is an endemic bee from a very threatened Neotropical dry forest, the results herein could be useful to the development of conservation strategies for P. seridoensis.

Epigenetic modifications and their relation to caste and sex determination and adult division of labor in the stingless bee Melipona scutellaris

Stingless bees of the genus Melipona, have long been considered an enigmatic case among social insects for their mode of caste determination, where in addition to larval food type and quantity, the genotype also has a saying, as proposed over 50 years ago by Warwick E. Kerr. Several attempts have since tried to test his Mendelian two-loci/two-alleles segregation hypothesis, but only recently a single gene crucial for sex determination in bees was evidenced to be sex-specifically spliced and also caste-specifically expressed in a Melipona species. Since alternative splicing is frequently associated with epigenetic marks, and the epigenetic status plays a major role in setting the caste phenotype in the honey bee, we investigated here epigenetic chromatin modification in the stingless bee Melipona scutellaris. We used an ELISA-based methodology to quantify global methylation status and western blot assays to reveal histone modifications. The results evidenced DNA methylation/demethylation events in larvae and pupae, and significant differences in histone methylation and phosphorylation between newly emerged adult queens and workers. The epigenetic dynamics seen in this stingless bee species represent a new facet in the caste determination process in Melipona bees and suggest a possible mechanism that is likely to link a genotype component to the larval diet and adult social behavior of these bees.

Queens become workers: pesticides alter caste differentiation in bees

Bees are important for the world biodiversity and economy because they provide key pollination services in forests and crops. However, pesticide use in crops has adversely affected (decreased) queen production because of increased mortality among larvae. Here, we demonstrated that in vitro-reared queens of a neotropical social bee species (Plebeia droryana) also showed high larval mortality after exposure to an organophosphate pesticide (chlorpyrifos) via larval food. Moreover, most of the surviving larvae that were destined to develop into queens became workers more likely because they ate less food than expected without pesticide skewing thus caste differentiation in this bee species. This adverse effect has not been previously reported for any other social insects, such as honeybees or bumblebees. Queens are essential for breeding and colony growth. Therefore, if our data are applicable to other pantropical social bee species across the globe, it is likely that these bees are at a serious risk of failure to form new colonies.

Evolution of Social Insect Polyphenism Facilitated by the Sex Differentiation Cascade

The major transition to eusociality required the evolution of a switch to canalize development into either a reproductive or a helper, the nature of which is currently unknown. Following predictions from the ‘theory of facilitated variation’, we identify sex differentiation pathways as promising candidates because of their pre-adaptation to regulating development of complex phenotypes. We show that conserved core genes, including the juvenile hormone-sensitive master sex differentiation gene doublesex (dsx) and a krüppel homolog 2 (kr-h2) with putative regulatory function, exhibit both sex and morph-specific expression across life stages in the ant Cardiocondyla obscurior. We hypothesize that genes in the sex differentiation cascade evolved perception of alternative input signals for caste differentiation (i.e. environmental or genetic cues), and that their inherent switch-like and epistatic behavior facilitated signal transfer to downstream targets, thus allowing them to control differential development into morphological castes.

Division of labor into reproductive queens and helper workers in the societies of ants, bees and wasps is achieved by phenotypic plasticity, which allows individuals to embark on discrete developmental trajectories in response to variable signals. These signals can be genetic, epigenetic or environmental, thereby resembling the extreme variation in signals for sex determination across multicellular animals. We show that common developmental pathways downstream of these input signals, including the conserved sex differentiation gene doublesex, regulate sex and caste-specific phenotypic differentiation in the ant species Cardiocondyla obscurior. Many different mechanisms of gene regulation have been implicated in controlling caste-specific development in social insects but these all depend on a higher-level genetic switch. We propose that highly conserved hub genes such as dsx, which can translate variable input signals into large transcription differences using intermediate-level regulators, are tightly linked with the repeated evolutionary transition to eusociality and caste polyphenism.