Phylogenomics Resolves Evolutionary Relationships among Ants, Bees, and Wasps

A Synopsis of Knowledge of the Rhopalosomatidae (Hymenoptera) in Brazil: an Annotated Checklist of the Family in the Country, with a Revised Key to the Brazilian Genera

This study is focused on the cricket leeches, Rhopalosomatidae, a family that is only poorly represented in entomological collections in Brazil. We provided a revised and updated key to the genera occurring in Brazil with the major traits of genera illustrated through high-resolution photomicrography. Also, we provided a synopsis of genera, a list of the species currently recorded from Brazil, the first country records for Rhopalosoma minus Townes, 1977 and Rhopalosoma breelandi Townes, 1977, which increases the diversity of these wasps in the country. Additionally, we provided information and a brief discussion about collection methods, flotation, and abundance of specimens collected. Maps with the geographical distribution of the studied species based on the previous and new records are also provided.

Evolutionary dynamics of mushroom body Kenyon cell types in hymenopteran brains from multifunctional type to functionally specialized types

Evolutionary dynamics of diversification of brain neuronal cell types that have underlain behavioral evolution remain largely unknown. Here, we compared transcriptomes and functions of Kenyon cell (KC) types that compose the mushroom bodies between the honey bee and sawfly, a primitive hymenopteran insect whose KCs likely have the ancestral properties. Transcriptome analyses show that the sawfly KC type shares some of the gene expression profile with each honey bee KC type, although unique gene expression profiles have also been acquired in each honey bee KC type. In addition, functional analysis of two sawfly genes suggested that the functions in learning and memory of the ancestral KC type were heterogeneously inherited among the KC types in the honey bee. Our findings strongly suggest that the functional evolution of KCs in Hymenoptera involved two previously hypothesized processes for evolution of cell function: functional segregation and divergence.

Biodiversity of hymenopteran parasitoids

Parasitoid wasps are the most successful group of insect parasitoids, comprising more than half the known diversity of Hymenoptera and probably most of the unknown diversity. This lifestyle has enabled them to be used as pest control agents conferring substantial economic benefits to global agriculture. Major lineages of parasitoid wasps include Ichneumonoidea, Ceraphronoidea, Proctotrupomorpha, and a number of aculeate families. The parasitoid lifestyle arose only once among basal Hymenoptera, in the common ancestor of the Orussidae and Apocrita some 200+ Ma ago. The ancestral parasitoid wasp was probably an idiobiont on wood-living beetle larvae. From this comparatively simple biology, Hymenoptera radiated into an incredible diversity of hosts and parasitoid lifestyles, including hyperparasitoidism, kleptoparasitoidism, egg parasitoidism, and polyembryony, in several instances co-opting viruses to subdue their hosts. Many lineages evolved beyond the parasitoid niche, becoming secondarily herbivorous or predatory nest provisioners and eventually giving rise to most instances of insect societies.

Subarachnoid hemorrhage following wasp stings: A case report

Three days after being stung by wasps in a rural area, a 60-year-old man was admitted to the emergency department with headaches. The physical examination showed that the patient was conscious, had moderate pain, had four head and back stings with local edema and erythema around the wounds, and had a stiff neck. Brain computed tomography upon admission revealed no abnormalities. Following lumbar puncture, the patient was diagnosed with subarachnoid hemorrhage (SAH) induced by wasp stings. No obvious aneurysms were found by either computed tomography angiography or three-dimensional rotational angiography. He received symptomatic treatment including antiallergy medication (chlorpheniramine and intravenous hydrocortisone), nimodipine for possible vasospasm, fluid infusion, and mannitol for intracranial pressure reduction and was discharged on the 14th day. This case of wasp sting-induced SAH is being reported to improve doctors' diagnostic abilities when encountering patients with wasp stings. It is important for emergency physicians to be aware that patients stung by wasps may develop rare complications such as SAH. Hymenoptera-induced SAH is an example of such a case.

Identification and Comparative Expression Profiles of Candidate Olfactory Receptors in the Transcriptomes of the Important Egg Parasitoid Wasp Anastatus japonicus Ashmead (Hymenoptera: Eupelmidae)

Anastatus japonicus Ashmead is an egg parasitoid wasp important for the biological control of fruit crop pests. The olfaction of parasitoids is crucial to searching for host pests in fruit crops. In this study, we sequenced and analyzed the antennal and abdominal transcriptomes of A. japonicus to better understand the olfactory mechanisms in this species. A total of 201 putative olfactory receptor genes were identified, including 184 odorant receptors (ORs) and 17 ionotropic receptors (IRs). Then, we assayed the tissue-specific and sex-biased expression profiles of those genes based on the transcriptional levels. In total, 165 ORs and 15 IRs had upregulated expression in the antennae. The expression levels of 133 ORs, including odorant receptor co-receptor (AjapORco), and 10 IRs, including AjapIR8a, were significantly different between the female and male antennae. Our results provide valuable information for further studies on the molecular mechanisms of the olfactory system in A. japonicus.

Low radiodensity μCT scans to reveal detailed morphology of the termite leg and its subgenual organ

Termites sense tiny substrate-borne vibrations through subgenual organs (SGOs) located within their legs' tibiae. Little is known about the SGOs' structure and physical properties. We applied high-resolution (voxel size 0.45 μm) micro-computed tomography (μCT) to Australian termites, Coptotermes lacteus and Nasutitermes exitiosus (Hill) to test two staining techniques. We compared the effectiveness of a single stain of Lugol's iodine solution (LS) to LS followed by Phosphotungstic acid (PTA) solutions (1% and 2%). We then present results of a soldier of Nasutitermes exitiosus combining μCT with LS + 2%PTS stains and scanning electron microscopy to exemplify the visualisation of their SGOs. The termite's SGO due to its approximately oval shape was shown to have a maximum diameter of 60 μm and a minimum of 48 μm, covering 60 ± 4% of the leg's cross-section and 90.4 ± 5% of the residual haemolymph channel. Additionally, the leg and residual haemolymph channel cross-sectional area decreased around the SGO by 33% and 73%, respectively. We hypothesise that this change in cross-sectional area amplifies the vibrations for the SGO. Since SGOs are directly connected to the cuticle, their mechanical properties and the geometric details identified here may enable new approaches to determine how termites sense micro-vibrations.

Highly contiguous genome assemblies of the Guinea paper wasp (Polistes exclamans) and Mischocyttarus mexicanus

Paper wasps are a model system for the study of social evolution due to a high degree of inter- and intraspecific variation in cooperation, aggression, and visual signals of social status. Increasing the taxonomic coverage of genomic resources for this diverse clade will aid comparative genomic approaches for testing predictions about the molecular basis of social evolution. Here, we provide draft genome assemblies for two well-studied species of paper wasps, Polistes exclamans and Mischocyttarus mexicanus. The P. exclamans genome assembly is 221.5 Mb in length with a scaffold N50 of 4.11 Mb. The M. mexicanus genome assembly is 227 Mb in length with a scaffold N50 of 1.1 Mb. Genomes have low repeat content (9.54–10.75%) and low GC content (32.06–32.4%), typical of other social hymenopteran genomes. The DNA methyltransferase gene, Dnmt3 , was lost early in the evolution of Polistinae. We identified a second independent loss of Dnmt3 within hornets (genus: Vespa).

Do the different life history strategies of ants and honeybees determine fat body morphology?

The separation of two sister groups such as ants and bees in the Cretaceous involved the development of distinctive characteristics to occupy separate ecological niches. From the point of view of biology and ecology, it is important to see how different life history strategies affect the physiology of these insects. The fat body is the most metabolically important tissue in the organism of each insect. Therefore, we conducted a comparative analysis of the morphological image of the subcuticular fat body in different localisation/segments in Formica (Seviformica) cinerea and Apis mellifera mellifera foragers, because of the similarity of their functions in colonies. We observed that the fat bodies of ants and bees were composed of the same cell types: trophocytes and oenocytes. However, in each of the segments, the fat body cells in ants were bigger and there were fewer of them in comparison with bees. The dorsal part of the fat body of ants had a bilayer structure, where the outer layer was formed by binucleated oenocytes. Binucleated oenocytes were also found in the inner layer near the heart and tracheole. In bees, the fat body was unilayered and the trophocytes and oenocytes were present side by side. The similarities and, in particular, the differences in the structure of the fat body are the adaptation of these sister groups to life in a diverse environment.

Evidence for the evolution of eusociality in stem ants and a systematic revision of †Gerontoformica (Hymenoptera: Formicidae)

It is generally assumed that Cretaceous stem ants were obligately eusocial, because of the presence of wingless adult females, yet the available evidence is ambiguous. Here, we report the syninclusion of a pupa and adult of a stem ant species from Mid-Cretaceous amber. As brood are immobile, the pupa was likely to have been transported by an adult. Therefore, the fossil substantiates the hypothesis that wingless females were cooperators, thus these were true ‘workers’. Re-examination of all described Cretaceous ant species reveals that winged–wingless diphenism – hence a variable dispersal capacity – may have been ancestral to the total clade of the ants, and that highly specialized worker-specific phenotypes evolved in parallel between the stem and crown groups. The soft-tissue preservation of the fossil is exceptional, demonstrating the possibility of analysing the development of the internal anatomy in stem ants. Based on the highest-resolution µ-CT scans of stem ants to date, we describe †Gerontoformica sternorhabda sp. nov., redescribe †G. gracilis, redefine the species group classification of †Gerontoformica, and provide a key to the species of the genus. Our work clarifies the species boundaries of †Gerontoformica and renders fossils relevant to the discussion of eusocial evolution in a way that has heretofore been intractable.

Anatomy and evolution of the head of Dorylus helvolus (Formicidae: Dorylinae): Patterns of sex- and caste-limited traits in the sausagefly and the driver ant

Ants are highly polyphenic Hymenoptera, with at least three distinct adult forms in the vast majority of species. Their sexual dimorphism, however, is overlooked to the point of being a nearly forgotten phenomenon. Using a multimodal approach, we interrogate the near total head microanatomy of the male of Dorylus helvolus, the "sausagefly," and compare it with the conspecific or near-conspecific female castes, the "driver ants." We found that no specific features were shared uniquely between the workers and males to the exclusion of the queens, indicating independence of male and worker development; males and queens, however, uniquely shared several features. Certain previous generalizations about ant sexual dimorphism are confirmed, while we also discover discrete muscular presences and absences, for which reason we provide a coarse characterization of functional morphology. Based on the unexpected retention of a medial carinate line on the structurally simplified mandible of the male, we postulate a series of developmental processes to explain the patterning of ant mandibles. We invoke functional and anatomical principles to classify sensilla. Critically, we observe an inversion of the expected pattern of male-queen mandible development: male Dorylus mandibles are extremely large while queen mandibles are poorly developed. To explain this, we posit that the reproductive-limited mandible phenotype is canalized in Dorylus, thus partially decoupling the queen and worker castes. We discuss alternative hypotheses and provide further comparisons to understand mandibular evolution in army ants. Furthermore, we hypothesize that the expression of the falcate phenotype in the queen is coincidental, that is, a "spandrel," and that the form of male mandibles is also generally coincidental across the ants. We conclude that the theory of ant development and evolution is incomplete without consideration of the male system, and we call for focused study of male anatomy and morphogenesis, and of trait limitation across all castes.

Is Phylotranscriptomics as Reliable as Phylogenomics?

Phylogenomics, the study of phylogenetic relationships among taxa based on their genome sequences, has emerged as the preferred phylogenetic method because of the wealth of phylogenetic information contained in genome sequences. Genome sequencing, however, can be prohibitively expensive, especially for taxa with huge genomes and when many taxa need sequencing. Consequently, the less costly phylotranscriptomics has seen an increased use in recent years. Phylotranscriptomics reconstructs phylogenies using DNA sequences derived from transcriptomes, which are often orders of magnitude smaller than genomes. However, in the absence of corresponding genome sequences, comparative analyses of transcriptomes can be challenging and it is unclear whether phylotranscriptomics is as reliable as phylogenomics. Here, we respectively compare the phylogenomic and phylotranscriptomic trees of 22 mammals and 15 plants that have both sequenced nuclear genomes and publicly available RNA sequencing data from multiple tissues. We found that phylotranscriptomic analysis can be sensitive to orthologous gene identification. When a rigorous method for identifying orthologs is employed, phylogenomic and phylotranscriptomic trees are virtually identical to each other, regardless of the tissue of origin of the transcriptomes and whether the same tissue is used across species. These findings validate phylotranscriptomics, brighten its prospect, and illustrate the criticality of reliable ortholog detection in such practices.

Comparative mitogenomics and phylogenetics of the stinging wasps (Hymenoptera: Aculeata)

The stinging wasps (Hymenoptera: Aculeata) include diverse groups such as vespid wasps, ants and bees. Phylogenetic relationships among major lineages of stinging wasps have been inferred from molecular and morphological data. However, the genomic features of the mitochondrial genomes and their phylogenetic utility remain to be explored. In this study, we determined 23 mitochondrial genomes from the Aculeata. Four Mutillidae species showed relatively low A + T content compared to other species of the Aculeata (69.7%-77.4%). Eleven out of 44 species, mainly from the Chrysididae and the Pompilidae, showed reversals of GC skews. Gene rearrangements occurred across the species. Patterns of tRNA rearrangement were conserved in some groups, including the Chrysididae, Bethylidae, Pompilidae, Scolioidea and Vespoidea. Rearrangement of protein-coding genes were found in 12 out of 44 species of the Aculeata, including all four species from the Chrysididae, both species from the Bethylidae, one species from the Dryinidae, all three Scolioidea species and two Apoidea species. Phylogenetic inference showed a long branch in species with unusual genomic features, such as in the Mutillidae and Bethylidae. By excluding these species, we found paraphyly of the Chrysidoidea and a sister group relationship between the Formicoidea and Vespoidea. These results improve our understanding of the evolution of mitochondrial genomes in the Aculeata and, in general, the evolution across this subclade.

The origin of wing polyphenism in ants: An eco-evo-devo perspective

The evolution of eusociality, where solitary individuals integrate into a single colony, is a major transition in individuality. In ants, the origin of eusociality coincided with the origin of a wing polyphenism approximately 160 million years ago, giving rise to colonies with winged queens and wingless workers. As a consequence, both eusociality and wing polyphenism are nearly universal features of all ants. Here, we synthesize fossil, ecological, developmental, and evolutionary data in an attempt to understand the factors that contributed to the origin of wing polyphenism in ants. We propose multiple models and hypotheses to explain how wing polyphenism is orchestrated at multiple levels, from environmental cues to gene networks. Furthermore, we argue that the origin of wing polyphenism enabled the subsequent evolution of morphological diversity across the ants. We finally conclude by outlining several outstanding questions for future work.

† Camelosphecia gen. nov., lost ant-wasp intermediates from the mid-Cretaceous (Hymenoptera, Formicoidea)

Fossils provide primary material evidence for the pattern and timing of evolution. The newly discovered "beast ants" from mid-Cretaceous Burmite, †Camelosphecia gen. nov., display an exceptional combination of plesiomorphies, including absence of the metapleural gland, and a series of unique apomorphies. Females and males, represented by †C. fossor sp. nov. and †C. venator sp. nov., differ in a number of features which suggest distinct sexual biologies. Combined-evidence phylogenetic analysis recovers †Camelosphecia and †Camelomecia as a clade which forms the extinct sister group of the Formicidae. Notably, these genera are only known from alate males and females; workers, if present, have yet to be recovered. Based on ongoing study of the total Aculeata informed by the beast ant genera, we provide a brief diagnosis of the Formicoidea. We also provide the first comprehensive key to the major groupings of Mesozoic Formicoidea, alongside a synoptic classification in which †Zigrasimeciinaestat. nov. and †Myanmyrma maraudera comb. nov. are recognized. Finally, a brief diagnosis of the Formicoidea is outlined.

Maximum Likelihood Estimation of Species Trees from Gene Trees in the Presence of Ancestral Population Structure

Though large multilocus genomic data sets have led to overall improvements in phylogenetic inference, they have posed the new challenge of addressing conflicting signals across the genome. In particular, ancestral population structure, which has been uncovered in a number of diverse species, can skew gene tree frequencies, thereby hindering the performance of species tree estimators. Here we develop a novel maximum likelihood method, termed TASTI (Taxa with Ancestral structure Species Tree Inference), that can infer phylogenies under such scenarios, and find that it has increasing accuracy with increasing numbers of input gene trees, contrasting with the relatively poor performances of methods not tailored for ancestral structure. Moreover, we propose a supertree approach that allows TASTI to scale computationally with increasing numbers of input taxa. We use genetic simulations to assess TASTI's performance in the three- and four-taxon settings and demonstrate the application of TASTI on a six-species Afrotropical mosquito data set. Finally, we have implemented TASTI in an open-source software package for ease of use by the scientific community.

Phylogenomics of Ichneumonoidea (Hymenoptera) and implications for evolution of mode of parasitism and viral endogenization

Ichneumonoidea is one of the most diverse lineages of animals on the planet with >48,000 described species and many more undescribed. Parasitoid wasps of this superfamily are mostly beneficial insects that attack and kill other arthropods and are important for understanding diversification and the evolution of life history strategies related to parasitoidism. Further, some lineages of parasitoids within Ichneumonoidea have acquired endogenous virus elements (EVEs) that are permanently a part of the wasp's genome and benefit the wasp through host immune disruption and behavioral control. Unfortunately, understanding the evolution of viral acquisition, parasitism strategies, diversification, and host immune disruption mechanisms, is deeply limited by the lack of a robust phylogenetic framework for Ichneumonoidea. Here we design probes targeting 541 genes across 91 taxa to test phylogenetic relationships, the evolution of parasitoid strategies, and the utility of probes to capture polydnavirus genes across a diverse array of taxa. Phylogenetic relationships among Ichneumonoidea were largely well resolved with most higher-level relationships maximally supported. We noted codon use biases between the outgroups, Braconidae, and Ichneumonidae and within Pimplinae, which were largely solved through analyses of amino acids rather than nucleotide data. These biases may impact phylogenetic reconstruction and caution for outgroup selection is recommended. Ancestral state reconstructions were variable for Braconidae across analyses, but consistent for reconstruction of idiobiosis/koinobiosis in Ichneumonidae. The data suggest many transitions between parasitoid life history traits across the whole superfamily. The two subfamilies within Ichneumonidae that have polydnaviruses are supported as distantly related, providing strong evidence for two independent acquisitions of ichnoviruses. Polydnavirus capture using our designed probes was only partially successful and suggests that more targeted approaches would be needed for this strategy to be effective for surveying taxa for these viral genes. In total, these data provide a robust framework for the evolution of Ichneumonoidea.

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

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

Distal leg structures of the Aculeata (Hymenoptera): A comparative evolutionary study of Sceliphron (Sphecidae) and Formica (Formicidae)

The distal parts of the legs of Sceliphron caementarium (Sphecidae) and Formica rufa (Formicidae) are documented and discussed with respect to phylogenetic and functional aspects. The prolegs of Hymenoptera offer an array of evolutionary novelties, mainly linked with two functional syndromes, walking efficiently on different substrates and cleaning the body surface. The protibial-probasitarsomeral cleaning device is almost always well-developed. A complex evolutionary innovation is a triple set of tarsal and pretarsal attachment devices, including tarsal plantulae, probasitarsomeral spatulate setae, and an arolium with an internal spring-like arcus, a dorsal manubrium, and a ventral planta. The probasitarsal adhesive sole and a complex arolium are almost always preserved, whereas the plantulae are often missing. Sceliphron has retained most hymenopteran ground plan features of the legs, and also Formica, even though the adhesive apparatus of Formicidae shows some modifications, likely linked to ground-oriented habits of most ants. Plantulae are always absent in extant ants, and the arolium is often reduced in size, and sometimes vestigial. The arolium contains resilin in both examined species. Additionally, resilin enriched regions are also present in the antenna cleaners of both species, although they differ in which of the involved structures is more flexible, the calcar in Sceliphron and the basitarsal comb in Formica. Functionally, the hymenopteran distal leg combines (a) interlocking mechanisms (claws, spine-like setae) and (b) adhesion mechanisms (plantulae, arolium). On rough substrate, claws and spine-like setae interlock with asperities and secure a firm grip, whereas the unfolding arolium generates adhesive contact on smooth surfaces. Differences of the folded arolium of Sceliphron and Formica probably correlate with differences in the mechanism of folding/unfolding.

Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta)

Diatoms (Bacillariophyta) are a species-rich group of eukaryotic microbes diverse in morphology, ecology, and metabolism. Previous reconstructions of the diatom phylogeny based on one or a few genes have resulted in inconsistent resolution or low support for critical nodes. We applied phylogenetic paralog pruning techniques to a data set of 94 diatom genomes and transcriptomes to infer perennially difficult species relationships, using concatenation and summary-coalescent methods to reconstruct species trees from data sets spanning a wide range of thresholds for taxon and column occupancy in gene alignments. Conflicts between gene and species trees decreased with both increasing taxon occupancy and bootstrap cutoffs applied to gene trees. Concordance between gene and species trees was lowest for short internodes and increased logarithmically with increasing edge length, suggesting that incomplete lineage sorting disproportionately affects species tree inference at short internodes, which are a common feature of the diatom phylogeny. Although species tree topologies were largely consistent across many data treatments, concatenation methods appeared to outperform summary-coalescent methods for sparse alignments. Our results underscore that approaches to species-tree inference based on few loci are likely to be misled by unrepresentative sampling of gene histories, particularly in lineages that may have diversified rapidly. In addition, phylogenomic studies of diatoms, and potentially other hyperdiverse groups, should maximize the number of gene trees with high taxon occupancy, though there is clearly a limit to how many of these genes will be available.

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.

Hydrocarbons mediate seed dispersal: a new mechanism of vespicochory

Vespicochory, seed dispersal by hornets, is an uncommon seed dispersal pattern in angiosperms. To date, this phenomenon has been recorded in only four families. Because of its rarity, the causes and consequences of vespicochory remain unclear. Hence, this seed dispersal syndrome is often regarded as anecdotal. Through field investigations, chemical analyses, electrophysiological tests, identification of chemosensory proteins from the antennae of hornets, and behavioral assays, we investigated whether olfactory and/or visual cues of the diaspores of Stemona tuberosa mediate the behavior of the social hornets and maintain their mutualism. This study demonstrated that the elaiosome of S. tuberosa emits hydrocarbons, which are attractive to hornets. However, these compounds, which induce responses in the antennae of naive hornets, are ubiquitous substances on insect cuticle surfaces. Innate preference and experienced foraging behavior of hornets can increase their seed dispersal efficiency. This is the first example in which hydrocarbons have been identified as a diaspore odour involved in the attraction of hornets. Given that the ubiquity of hornets, and the communication function of hydrocarbons in insects, we predict that this rare seed dispersal mechanism may be an overlooked mechanism of insect-plant mutualism.

Kenyon Cell Subtypes/Populations in the Honeybee Mushroom Bodies: Possible Function Based on Their Gene Expression Profiles, Differentiation, Possible Evolution, and Application of Genome Editing

Mushroom bodies (MBs), a higher-order center in the honeybee brain, comprise some subtypes/populations of interneurons termed as Kenyon cells (KCs), which are distinguished by their cell body size and location in the MBs, as well as their gene expression profiles. Although the role of MBs in learning ability has been studied extensively in the honeybee, the roles of each KC subtype and their evolution in hymenopteran insects remain mostly unknown. This mini-review describes recent progress in the analysis of gene/protein expression profiles and possible functions of KC subtypes/populations in the honeybee. Especially, the discovery of novel KC subtypes/populations, the “middle-type KCs” and “KC population expressing FoxP,” necessitated a redefinition of the KC subtype/population. Analysis of the effects of inhibiting gene function in a KC subtype-preferential manner revealed the function of the gene product as well as of the KC subtype where it is expressed. Genes expressed in a KC subtype/population-preferential manner can be used to trace the differentiation of KC subtypes during the honeybee ontogeny and the possible evolution of KC subtypes in hymenopteran insects. Current findings suggest that the three KC subtypes are unique characteristics to the aculeate hymenopteran insects. Finally, prospects regarding future application of genome editing for the study of KC subtype functions in the honeybee are described. Genes expressed in a KC subtype-preferential manner can be good candidate target genes for genome editing, because they are likely related to highly advanced brain functions and some of them are dispensable for normal development and sexual maturation in honeybees.

Current Advances in Immunological Studies on the Vespidae Venom Antigen 5: Therapeutic and Prophylaxis to Hypersensitivity Responses

Although systemic reactions caused by allergenic proteins present in venoms affect a small part of the world population, Hymenoptera stings are among the main causes of immediate hypersensitivity responses, with risk of anaphylactic shock. In the attempt to obtain therapeutic treatments and prophylaxis to hypersensitivity responses, interest in the molecular characterization of these allergens has grown in the scientific community due to the promising results obtained in immunological and clinical studies. The present review provides an update on the knowledge regarding the immune response and the therapeutic potential of Antigen 5 derived from Hymenoptera venom. The results confirm that the identification and topology of epitopes, associated with molecular regions that interact with antibodies, are crucial to the improvement of hypersensitivity diagnostic methods.

Topological support and data quality can only be assessed through multiple tests in reviewing Blattodea phylogeny

Assessing support for molecular phylogenies is difficult because the data is heterogeneous in quality and overwhelming in quantity. Traditionally, node support values (bootstrap frequency, Bayesian posterior probability) are used to assess confidence in tree topologies. Other analyses to assess the quality of phylogenetic data (e.g. Lento plots, saturation plots, trait consistency) and the resulting phylogenetic trees (e.g. internode certainty, parameter permutation tests, topological tests) exist but are rarely applied. Here we argue that a single qualitative analysis is insufficient to assess support of a phylogenetic hypothesis and relate data quality to tree quality. We use six molecular markers to infer the phylogeny of Blattodea and apply various tests to assess relationship support, locus quality, and the relationship between the two. We use internode-certainty calculations in conjunction with bootstrap scores, alignment permutations, and an approximately unbiased (AU) test to assess if the molecular data unambiguously support the phylogenetic relationships found. Our results show higher support for the position of Lamproblattidae, high support for the termite phylogeny, and low support for the position of Anaplectidae, Corydioidea and phylogeny of Blaberoidea. We use Lento plots in conjunction with mutation-saturation plots, calculations of locus homoplasy to assess locus quality, identify long branch attraction, and decide if the tree's relationships are the result of data biases. We conclude that multiple tests and metrics need to be taken into account to assess tree support and data robustness.

Phylogenomic analysis of Apoidea sheds new light on the sister group of bees

Background

Apoid wasps and bees (Apoidea) are an ecologically and morphologically diverse group of Hymenoptera, with some species of bees having evolved eusocial societies. Major problems for our understanding of the evolutionary history of Apoidea have been the difficulty to trace the phylogenetic origin and to reliably estimate the geological age of bees. To address these issues, we compiled a comprehensive phylogenomic dataset by simultaneously analyzing target DNA enrichment and transcriptomic sequence data, comprising 195 single-copy protein-coding genes and covering all major lineages of apoid wasps and bee families.

Results

Our compiled data matrix comprised 284,607 nucleotide sites that we phylogenetically analyzed by applying a combination of domain- and codon-based partitioning schemes. The inferred results confirm the polyphyletic status of the former family “Crabronidae”, which comprises nine major monophyletic lineages. We found the former subfamily Pemphredoninae to be polyphyletic, comprising three distantly related clades. One of them, Ammoplanina, constituted the sister group of bees in all our analyses. We estimate the origin of bees to be in the Early Cretaceous (ca. 128 million years ago), a time period during which angiosperms rapidly radiated. Finally, our phylogenetic analyses revealed that within the Apoidea, (eu)social societies evolved exclusively in a single clade that comprises pemphredonine and philanthine wasps as well as bees.

Conclusion

By combining transcriptomic sequences with those obtained via target DNA enrichment, we were able to include an unprecedented large number of apoid wasps in a phylogenetic study for tracing the phylogenetic origin of bees. Our results confirm the polyphyletic nature of the former wasp family Crabonidae, which we here suggest splitting into eight families. Of these, the family Ammoplanidae possibly represents the extant sister lineage of bees. Species of Ammoplanidae are known to hunt thrips, of which some aggregate on flowers and feed on pollen. The specific biology of Ammoplanidae as predators indicates how the transition from a predatory to pollen-collecting life style could have taken place in the evolution of bees. This insight plus the finding that (eu)social societies evolved exclusively in a single subordinated lineage of apoid wasps provides new perspectives for future comparative studies.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1155-8) contains supplementary material, which is available to authorized users.

So many genes, so little time: A practical approach to divergence-time estimation in the genomic era

Phylogenomic datasets have been successfully used to address questions involving evolutionary relationships, patterns of genome structure, signatures of selection, and gene and genome duplications. However, despite the recent explosion in genomic and transcriptomic data, the utility of these data sources for efficient divergence-time inference remains unexamined. Phylogenomic datasets pose two distinct problems for divergence-time estimation: (i) the volume of data makes inference of the entire dataset intractable, and (ii) the extent of underlying topological and rate heterogeneity across genes makes model mis-specification a real concern. “Gene shopping”, wherein a phylogenomic dataset is winnowed to a set of genes with desirable properties, represents an alternative approach that holds promise in alleviating these issues. We implemented an approach for phylogenomic datasets (available in SortaDate) that filters genes by three criteria: (i) clock-likeness, (ii) reasonable tree length (i.e., discernible information content), and (iii) least topological conflict with a focal species tree (presumed to have already been inferred). Such a winnowing procedure ensures that errors associated with model (both clock and topology) mis-specification are minimized, therefore reducing error in divergence-time estimation. We demonstrated the efficacy of this approach through simulation and applied it to published animal (Aves, Diplopoda, and Hymenoptera) and plant (carnivorous Caryophyllales, broad Caryophyllales, and Vitales) phylogenomic datasets. By quantifying rate heterogeneity across both genes and lineages we found that every empirical dataset examined included genes with clock-like, or nearly clock-like, behavior. Moreover, many datasets had genes that were clock-like, exhibited reasonable evolutionary rates, and were mostly compatible with the species tree. We identified overlap in age estimates when analyzing these filtered genes under strict clock and uncorrelated lognormal (UCLN) models. However, this overlap was often due to imprecise estimates from the UCLN model. We find that “gene shopping” can be an efficient approach to divergence-time inference for phylogenomic datasets that may otherwise be characterized by extensive gene tree heterogeneity.

Phylogeny of a cosmopolitan family of morphologically conserved trapdoor spiders (Mygalomorphae, Ctenizidae) using Anchored Hybrid Enrichment, with a description of the family, Halonoproctidae Pocock 1901

The mygalomorph family Ctenizidae has a world-wide distribution and currently contains nine genera and 135 species. However, the monophyly of this group has long been questioned on both morphological and molecular grounds. Here, we use Anchored Hybrid Enrichment (AHE) to gather hundreds of loci from across the genome for reconstructing the phylogenetic relationships among the nine genera and test the monophyly of the family. We also reconstruct the possible ancestral ranges of the most inclusive clade recovered. Using AHE, we generate a supermatrix of 565 loci and 115,209 bp for 27 individuals. For the first time, analyses using all nine genera produce results definitively establishing the non-monophyly of Ctenizidae. A lineage formed exclusively by representatives of South African Stasimopus was placed as the sister group to the remaining taxa in the tree, and the Mediterranean Cteniza and Cyrtocarenum were recovered with high support as sister to exemplars of Euctenizidae, Migidae, and Idiopidae. All the remaining genera-Bothriocyrtum, Conothele, Cyclocosmia, Hebestatis, Latouchia, and Ummidia-share a common ancestor. Based on these results, we formally elevate this clade to the level of family. Our results definitively establish both the non-monophyly of the Ctenizidae and non-validity of the subfamilies Ummidiinae and Ctenizinae. In order to establish the placement of the remaining three ctenizid genera, Cteniza, Cyrtocarenum, and Stasimopus, thorough analyses within the context of a complete mygalomorph phylogenetic framework are needed. We formally describe the family Halonoproctidae Pocock 1901 and infer that the family's most recent common ancestor was likely distributed in western North America and Asia.

FoxP in bees: A comparative study on the developmental and adult expression pattern in three bee species considering isoforms and circuitry

Mutations in the transcription factors FOXP1, FOXP2, and FOXP4 affect human cognition, including language. The FoxP gene locus is evolutionarily ancient and highly conserved in its DNA-binding domain. In Drosophila melanogaster FoxP has been implicated in courtship behavior, decision making, and specific types of motor-learning. Because honeybees (Apis mellifera, Am) excel at navigation and symbolic dance communication, they are a particularly suitable insect species to investigate a potential link between neural FoxP expression and cognition. We characterized two AmFoxP isoforms and mapped their expression in the brain during development and in adult foragers. Using a custom-made antiserum and in situ hybridization, we describe 11 AmFoxP expressing neuron populations. FoxP was expressed in equivalent patterns in two other representatives of Apidae; a closely related dwarf bee and a bumblebee species. Neural tracing revealed that the largest FoxP expressing neuron cluster in honeybees projects into a posterior tract that connects the optic lobe to the posterior lateral protocerebrum, predicting a function in visual processing. Our data provide an entry point for future experiments assessing the function of FoxP in eusocial Hymenoptera.

HiMAP: Robust phylogenomics from highly multiplexed amplicon sequencing

High-throughput sequencing has fundamentally changed how molecular phylogenetic data sets are assembled, and phylogenomic data sets commonly contain 50- to 100-fold more loci than those generated using traditional Sanger sequencing-based approaches. Here, we demonstrate a new approach for building phylogenomic data sets using single-tube, highly multiplexed amplicon sequencing, which we name HiMAP (highly multiplexed amplicon-based phylogenomics) and present bioinformatic pipelines for locus selection based on genomic and transcriptomic data resources and postsequencing consensus calling and alignment. This method is inexpensive and amenable to sequencing a large number (hundreds) of taxa simultaneously and requires minimal hands-on time at the bench (<1/2 day), and data analysis can be accomplished without the need for read mapping or assembly. We demonstrate this approach by sequencing 878 amplicons in single reactions for 82 species of tephritid fruit flies across seven genera (384 individuals), including some of the most economically important agricultural insect pests. The resulting filtered data set (>150,000-bp concatenated alignment, ~20% missing character sites across all individuals and amplicons) contained >40,000 phylogenetically informative characters, and although some discordance was observed between analyses, it provided unparalleled resolution of many phylogenetic relationships in this group. Most notably, we found high support for the generic status of Zeugodacus and the sister relationship between Dacus and Zeugodacus. We discuss HiMAP, with regard to its molecular and bioinformatic strengths, and the insight the resulting data set provides into relationships of this diverse insect group.

HiMAP: Robust phylogenomics from highly multiplexed amplicon sequencing

High-throughput sequencing has fundamentally changed how molecular phylogenetic data sets are assembled, and phylogenomic data sets commonly contain 50- to 100-fold more loci than those generated using traditional Sanger sequencing-based approaches. Here, we demonstrate a new approach for building phylogenomic data sets using single-tube, highly multiplexed amplicon sequencing, which we name HiMAP (highly multiplexed amplicon-based phylogenomics) and present bioinformatic pipelines for locus selection based on genomic and transcriptomic data resources and postsequencing consensus calling and alignment. This method is inexpensive and amenable to sequencing a large number (hundreds) of taxa simultaneously and requires minimal hands-on time at the bench (<1/2 day), and data analysis can be accomplished without the need for read mapping or assembly. We demonstrate this approach by sequencing 878 amplicons in single reactions for 82 species of tephritid fruit flies across seven genera (384 individuals), including some of the most economically important agricultural insect pests. The resulting filtered data set (>150,000-bp concatenated alignment, ~20% missing character sites across all individuals and amplicons) contained >40,000 phylogenetically informative characters, and although some discordance was observed between analyses, it provided unparalleled resolution of many phylogenetic relationships in this group. Most notably, we found high support for the generic status of Zeugodacus and the sister relationship between Dacus and Zeugodacus. We discuss HiMAP, with regard to its molecular and bioinformatic strengths, and the insight the resulting data set provides into relationships of this diverse insect group.

Polistes metricus queens exhibit personality variation and behavioral syndromes

Consistent differences in behavior between individuals, otherwise known as animal personalities, have become a staple in behavioral ecology due to their ability to explain a wide range of phenomena. Social organisms are especially serviceable to animal personality techniques because they can be used to explore behavioral variation at both the individual and group level. Despite the success of personality research in social organisms generally, and social Hymenoptera in particular, social wasps (Vespidae) have received little to no attention in the personality literature. In the present study, we test Polistes metricus (Vespidae; Polistinae) paper wasp queens for the presence of repeatable variation in, and correlations ("behavioral syndromes") between, several commonly used personality metrics: boldness, aggressiveness, exploration, and activity. Our results indicate that P. metricus queens exhibit personalities for all measured traits and correlations between different behavioral measures. Given that paper wasps have served as a model organism for a wide range of phenomena such as kin selection, dominance hierarchies, mate choice, facial recognition, social parasitism, and chemical recognition, we hope that our results will motivate researchers to explore whether, or to what degree, queen personality is important in their research programs.

Genomes of the Hymenoptera

Hymenoptera is the second-most sequenced arthropod order, with 52 publically archived genomes (71 with ants, reviewed elsewhere), however these genomes do not capture the breadth of this very diverse order (Figure 1, Table 1). These sequenced genomes represent only 15 of the 97 extant families. Although at least 55 other genomes are in progress in an additional 11 families (see Table 2), stinging wasps represent 35 (67%) of the available and 42 (76%) of the in progress genomes. A more comprehensive catalog of hymenopteran genomes is needed for research into the evolutionary processes underlying the expansive diversity in terms of ecology, behavior, and physiological traits within this group. Additional sequencing is needed to generate an assembly for even 0.05% of the estimated 1 million hymenopteran species, and we recommend premier level assemblies for at least 0.1% of the >150,000 named species dispersed across the order. Given the haplodiploid sex determination in Hymenoptera, haploid male sequencing will help minimize genome assembly issues to enable higher quality genome assemblies.

Construction of a Species-Level Tree of Life for the Insects and Utility in Taxonomic Profiling

Although comprehensive phylogenies have proven an invaluable tool in ecology and evolution, their construction is made increasingly challenging both by the scale and structure of publically available sequences. The distinct partition between gene-rich (genomic) and species-rich (DNA barcode) data is a feature of data that has been largely overlooked, yet presents a key obstacle to scaling supermatrix analysis. I present a phyloinformatics framework for draft construction of a species-level phylogeny of insects (Class Insecta). Matrix-building requires separately optimized pipelines for nuclear transcriptomic, mitochondrial genomic, and species-rich markers, whereas tree-building requires hierarchical inference in order to capture species-breadth while retaining deep-level resolution. The phylogeny of insects contains 49,358 species, 13,865 genera, 760 families. Deep-level splits largely reflected previous findings for sections of the tree that are data rich or unambiguous, such as inter-ordinal Endopterygota and Dictyoptera, the recently evolved and relatively homogeneous Lepidoptera, Hymenoptera, Brachycera (Diptera), and Cucujiformia (Coleoptera). However, analysis of bias, matrix construction and gene-tree variation suggests confidence in some relationships (such as in Polyneoptera) is less than has been indicated by the matrix bootstrap method. To assess the utility of the insect tree as a tool in query profiling several tree-based taxonomic assignment methods are compared. Using test data sets with existing taxonomic annotations, a tendency is observed for greater accuracy of species-level assignments where using a fixed comprehensive tree of life in contrast to methods generating smaller de novo reference trees. Described herein is a solution to the discrepancy in the way data are fit into supermatrices. The resulting tree facilitates wider studies of insect diversification and application of advanced descriptions of diversity in community studies, among other presumed applications. [Data integration; data mining; insects; phylogenomics; phyloinformatics; tree of life.].

Entomological Collections in the Age of Big Data

With a million described species and more than half a billion preserved specimens, the large scale of insect collections is unequaled by those of any other group. Advances in genomics, collection digitization, and imaging have begun to more fully harness the power that such large data stores can provide. These new approaches and technologies have transformed how entomological collections are managed and utilized. While genomic research has fundamentally changed the way many specimens are collected and curated, advances in technology have shown promise for extracting sequence data from the vast holdings already in museums. Efforts to mainstream specimen digitization have taken root and have accelerated traditional taxonomic studies as well as distribution modeling and global change research. Emerging imaging technologies such as microcomputed tomography and confocal laser scanning microscopy are changing how morphology can be investigated. This review provides an overview of how the realization of big data has transformed our field and what may lie in store.

Increased complexity of mushroom body Kenyon cell subtypes in the brain is associated with behavioral evolution in hymenopteran insects

In insect brains, the mushroom bodies (MBs) are a higher-order center for sensory integration and memory. Honeybee (Apis mellifera L.) MBs comprise four Kenyon cell (KC) subtypes: class I large-, middle-, and small-type, and class II KCs, which are distinguished by the size and location of somata, and gene expression profiles. Although these subtypes have only been reported in the honeybee, the time of their acquisition during evolution remains unknown. Here we performed in situ hybridization of tachykinin-related peptide, which is differentially expressed among KC subtypes in the honeybee MBs, in four hymenopteran species to analyze whether the complexity of KC subtypes is associated with their behavioral traits. Three class I KC subtypes were detected in the MBs of the eusocial hornet Vespa mandarinia and the nidificating scoliid wasp Campsomeris prismatica, like in A. mellifera, whereas only two class I KC subtypes were detected in the parasitic wasp Ascogaster reticulata. In contrast, we were unable to detect class I KC subtype in the primitive and phytophagous sawfly Arge similis. Our findings suggest that the number of class I KC subtypes increased at least twice - first with the evolution of the parasitic lifestyle and then with the evolution of nidification.

Hornets Have It: A Conserved Olfactory Subsystem for Social Recognition in Hymenoptera?

Eusocial Hymenoptera colonies are characterized by the presence of altruistic individuals, which rear their siblings instead of their own offspring. In the course of evolution, such sterile castes are thought to have emerged through the process of kin selection, altruistic traits being transmitted to following generation if they benefit relatives. By allowing kinship recognition, the detection of cuticular hydrocarbons (CHCs) might be instrumental for kin selection. In carpenter ants, a female-specific olfactory subsystem processes CHC information through antennal detection by basiconic sensilla. It is still unclear if other families of eusocial Hymenoptera use the same subsystem for sensing CHCs. Here, we examined the existence of such a subsystem in Vespidae (using the hornet Vespa velutina), a family in which eusociality emerged independently of ants. The antennae of both males and female hornets contain large basiconic sensilla. Sensory neurons from the large basiconic sensilla exclusively project to a conspicuous cluster of small glomeruli in the antennal lobe, with anatomical and immunoreactive features that are strikingly similar to those of the ant CHC-sensitive subsystem. Extracellular electrophysiological recordings further show that sensory neurons within hornet basiconic sensilla preferentially respond to CHCs. Although this subsystem is not female-specific in hornets, the observed similarities with the olfactory system of ants are striking. They suggest that the basiconic sensilla subsystem could be an ancestral trait, which may have played a key role in the advent of eusociality in these hymenopteran families by allowing kin recognition and the production of altruistic behaviors toward relatives.