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Evolutionary History of the Hymenoptera
Abstract
Hymenoptera (sawflies, wasps, ants, and bees) are one of four mega-diverse insect orders, comprising more than 153,000 described and possibly up to one million undescribed extant species. As parasitoids, predators, and pollinators, Hymenoptera play a fundamental role in virtually all terrestrial ecosystems and are of substantial economic importance. To understand the diversification and key evolutionary transitions of Hymenoptera, most notably from phytophagy to parasitoidism and predation (and vice versa) and from solitary to eusocial life, we inferred the phylogeny and divergence times of all major lineages of Hymenoptera by analyzing 3,256 protein-coding genes in 173 insect species. Our analyses suggest that extant Hymenoptera started to diversify around 281 million years ago (mya). The primarily ectophytophagous sawflies are found to be monophyletic. The species-rich lineages of parasitoid wasps constitute a monophyletic group as well. The little-known, species-poor Trigonaloidea are identified as the sister group of the stinging wasps (Aculeata). Finally, we located the evolutionary root of bees within the apoid wasp family "Crabronidae." Our results reveal that the extant sawfly diversity is largely the result of a previously unrecognized major radiation of phytophagous Hymenoptera that did not lead to wood-dwelling and parasitoidism. They also confirm that all primarily parasitoid wasps are descendants of a single endophytic parasitoid ancestor that lived around 247 mya. Our findings provide the basis for a natural classification of Hymenoptera and allow for future comparative analyses of Hymenoptera, including their genomes, morphology, venoms, and parasitoid and eusocial life styles.
... Genome-scale data (transcriptomes) have proven particularly frustrating, presumably because of the lack of signal associated with an old, rapid radiation and the increasing probability of observing conflicting signals between markers Zhang et al., 2020). When chalcid wasps are included in studies of the Hymenopteran treeof-life, conflicts or lack of signal that are reflected in poor statistical support of (some) nodes are highlighted in all datasets: Branstetter et al. (2017) 854 ultraconserved elements (UCEs), nine species of Chalcidoidea in nine families and nine genera; Peters et al. (2017) 3256 protein coding genes, six species in six families and six genera; and Tang et al. (2019) mitochondrial genomes, seven species in six families and seven genera. Blaimer et al. (2023) with 1100 UCEs addressed the largest sampling of Chalcidoidea for genomic data with 148 species in 23 families and 142 genera, but the results within Chalcidoidea were still poorly resolved, with several families not monophyletic. ...
... Our outgroups include a diverse array of Proctotrupomorpha, including Platygastroidea (two genera), Cynipoidea (five genera), Proctotrupoidea (two genera), Diaprioidea (five genera) and Mymarommatoidea (two genera). These outgroups form a grade in which the monophyletic Chalcidoidea was embedded in all recent analyses of Hymenoptera relationships Klopfstein et al., 2013;Branstetter et al., 2017;Peters et al., 2017;Blaimer et al., 2023). ...
... An important result of our study is a revision of the temporal scale over which Chalcidoidea have evolved and dispersed throughout the world (Figs 5 and S4; Table S3). Likely because our taxonomic sampling is one or two orders of magnitude higher than most previous phylogenomic studies (Branstetter et al., 2017;Peters et al., 2017Peters et al., , 2018Tang et al., 2019), we infer an older crown age for Chalcidoidea: 162.2 (154.0-170.0) Ma. ...
Chalcidoidea are mostly parasitoid wasps that include as many as 500 000 estimated species. Capturing phylogenetic signal from such a massive radiation can be daunting. Chalcidoidea is an excellent example of a hyperdiverse group that has remained recalcitrant to phylogenetic resolution. We combined 1007 exons obtained with Anchored Hybrid Enrichment with 1048 ultra-conserved elements (UCEs) for 433 taxa including all extant families, >95% of all subfamilies, and 356 genera chosen to represent the vast diversity of the superfamily. Going back and forth between the molecular results and our collective knowledge of morphology and biology, we detected bias in the analyses that was driven by the saturation of nucleotide data. Our final results are based on a concatenated analysis of the least saturated exons and UCE datasets (2054 loci, 284 106 sites). Our analyses support an expected sister relationship with Mymarommatoidea. Seven previously recognized families were not monophy-letic, so support for a new classification is discussed. Natural history in some cases would appear to be more informative than morphology, as illustrated by the elucidation of a clade of plant gall associates and a clade of taxa with planidial first-instar lar-vae. The phylogeny suggests a transition from smaller soft-bodied wasps to larger and more heavily sclerotized wasps, with egg parasitism as potentially ancestral for the entire superfamily. Deep divergences in Chalcidoidea coincide with an increase in insect families in the fossil record, and an early shift to phytophagy corresponds with the beginning of the "Angiosperm Terrestrial Revolution". Our dating analyses suggest a middle Jurassic origin of 174 Ma (167.3-180.5 Ma) and a crown age of 162.2 Ma (153.9-169.8 Ma) for Chalcidoidea. During the Cretaceous, Chalcidoidea may have undergone a rapid radiation in southern Gondwana with subsequent dispersals to the Northern Hemisphere. This scenario is discussed with regard to knowledge about the host taxa of chalcid wasps, their fossil record and Earth's palaeogeographic history.
... Novel, and further undescribed peptides and proteins are shown in grey. The hymenopteran groups are based on the recent phylogeny according to Peters et al. [33]. Please note that three melittin sequences from wasps are falsely annotated in UniProt as wasp melittins (marked by a black X). ...
... Our analyses clearly show that genes encoding peptides highly similar to honey bee melittin are not present in wasps, see also von Reumont et al. [22]. The phylogeny is pruned to the groups for which data is available based on Peters et al. [33] a multidimensional "protein space" similar to the concept of a "configuration space" in physics, or an "arbitrary space" in multi-scale cognition [35]. Our protein space incorporates data concerning the structure and function of mature proteins to generate a multidimensional model of protein relations. ...
... Our results suggest that the most prevalent venom genes present in bees today were already present in the early Triassic in ancestors of the symphytan lineage, predating the radiation of apocritans starting more than 200 million years ago (Fig. 8) [33]. The restricted waist of apocritans is needed to manoeuvre the ovipositor in such a way that allows its use for predation, parasitism or defense, and only in aculeate hymenopterans (ants, bees and wasps) is the retractable ovipositor modified into a stinger used exclusively for venom injection. ...
Background
Venoms, which have evolved numerous times in animals, are ideal models of convergent trait evolution. However, detailed genomic studies of toxin-encoding genes exist for only a few animal groups. The hyper-diverse hymenopteran insects are the most speciose venomous clade, but investigation of the origin of their venom genes has been largely neglected.
Results
Utilizing a combination of genomic and proteo-transcriptomic data, we investigated the origin of 11 toxin genes in 29 published and 3 new hymenopteran genomes and compiled an up-to-date list of prevalent bee venom proteins. Observed patterns indicate that bee venom genes predominantly originate through single gene co-option with gene duplication contributing to subsequent diversification.
Conclusions
Most Hymenoptera venom genes are shared by all members of the clade and only melittin and the new venom protein family anthophilin1 appear unique to the bee lineage. Most venom proteins thus predate the mega-radiation of hymenopterans and the evolution of the aculeate stinger.
... Two recent simultaneously published studies [2,7], independent of each other, presented analyses of extensive genetic data across the Hymenoptera, although with some emphasis on the Aculeata. One of these [7] analyzed 3256 protein-coding genes derived from sequencing whole-body transcriptomes of 168 hymenopterans, 112 of them aculeates (6 chrysidoids, 82 apoids of which 41 were bees, but only 24 "vespoids" of which 3 were ants and 6 vespids). ...
... Two recent simultaneously published studies [2,7], independent of each other, presented analyses of extensive genetic data across the Hymenoptera, although with some emphasis on the Aculeata. One of these [7] analyzed 3256 protein-coding genes derived from sequencing whole-body transcriptomes of 168 hymenopterans, 112 of them aculeates (6 chrysidoids, 82 apoids of which 41 were bees, but only 24 "vespoids" of which 3 were ants and 6 vespids). They again found the Aculeata to be monophyletic. ...
... They also found the aculeates to be monophyletic (Fig. 2a). However, the chrysidoids came out as paraphyletic, forming two clades, the second (comprising taxa missing from Ref. [7] being sister to the remaining aculeates. The vespoids were again paraphyletic, forming three sequentially diverging clades: (i) a monophyletic group comprising most of the vespoids sister to the vespids plus rhopalosomatids (not in Ref. [7]); (ii) the true bradynobaenids (not included in Ref. [7]) and scoliids; and (iii) the ants which were again Aculeate Hymenoptera: Phylogeny and Classification, Fig. 2 Phylogenies of families of Aculeata based on two different types of analysis. ...
... 32,33 In attempting to align the bioinformatics and molecular results with the evolutionary history, we have contrasted DNMT-related innovations with a recent and most detailed phylogenetic tree of Hymenoptera. 34 This analysis suggests that DNMT losses, or duplications occurred independently in several lineages, whereas the loss of introns in DNMT3 is found in parasitic wasps, and in one species of willow-galling sawflies, Euura lappo (Tenthredinidae). The DNMT-related changes are most frequent in parasitic wasps. ...
... Our analyses reveal a remarkable variability of the epigenetic proteome in Hymenoptera with great disparities in gene number encoding DNMTs. Although previous studies already uncovered a pool of distinct DNA methylation toolkits in insects, 16,21,34 finding such diversity in one order is surprising. Several unique features of the epigenetic toolkit in such a vastly diverse order make this level of regulation particularly interesting from the mechanistic perspective and the potential for driving evolutionary innovations. ...
... Our understanding of the phylogenetic relationships among all major lineages of Hymenoptera has been improved by a study in which 3,256 protein-coding genes in 173 species were used to explore the early history of these insects, as well as the origins and radiation of parasitoids, stinging wasps, and bees. 34 At this stage only broad inferences can be made to link the diversity of the epigenetic machinery with the evolutionary history of this insect order. Hymenoptera are easily distinguishable from other insects, by two pairs of membranous wings (except for some castes that are wingless), the ''wasp waist'' (except for sawflies), the larger forewings, that are kept together by hooks, and females with hardened ovipositor. ...
DNMT3 in Hymenoptera has a unique duplication of the essential PWWP domain. Using GST-tagged PWWP fusion proteins and histone arrays we show that these domains have gained new properties and represent the first case of PWWP domains binding to H3K27 chromatin modifications, including H3K27me3, a key modification that is important during development. Phylogenetic analyses of 107 genomes indicate that the duplicated PWWP domains separated into two sister clades, and their distinct binding capacities are supported by 3D modeling. Other features of this unique DNA methylation system include variable copies, losses, and duplications of DNMT1 and DNMT3, and combinatorial generations of DNMT3 isoforms including variants missing the catalytic domain. Some of these losses and duplications of are found only in parasitic wasps. We discuss our findings in the context of the crosstalk between DNA methylation and histone methylation, and the expanded potential of epigenomic modifications in Hymenoptera to drive evolutionary novelties.
... The evolution of parasitoidism in Hymenoptera has led to one of the largest species radiations in insects [1][2][3][4][5]. A large proportion of parasitoids belong to the Chalcidoidea, an extremely diverse and ecologically important group (nearly 27,000 species described, over 500,000 species estimated) of mainly minute wasps (average body size range from 1-2 mm) that are omnipresent in almost all terrestrial habitats [6][7][8][9][10][11]. ...
... This species exhibits extensive terebra movements during the assessment of a potential host and eventual subsequent egg placement [45,47]. We aimed (1) to analyse the oviposition process in vivo, (2) to describe the ovipositor of L. distinguendus, including all inherent cuticular elements and muscles, (3) to examine the mechanics and mode of function of the musculoskeletal system, including the actuation of the various ovipositor movements, (4) to investigate the underlying working mechanisms of the terebra steering movements and (5) to discuss their eco-evolutionary significance. ...
... The improved manoeuvrability of the metasoma of the Apocrita, which is essential in the female wasp's probing behaviour when searching or assessing a potential host, is attributed to the evolution of the wasp waist (a construction between the 1st and 2nd abdominal segment). The presence of a waist was a major innovation in the evolution of Hymenoptera and presumably contributed to the rapid diversification of Apocrita, since it allowed the successful attack of a variety of new hosts [3][4][5]. However, some chalcidoid wasps, e.g. ...
Various chalcidoid wasps can actively steer their terebra (= ovipositor shaft) in diverse directions, despite the lack of terebral intrinsic musculature. To investigate the mechanisms of these bending and rotational movements, we combined microscopical and microtomographical techniques, together with videography, to analyse the musculoskeletal ovipositor system of the ectoparasitoid pteromalid wasp Lariophagus distinguendus (Förster, 1841) and the employment of its terebra during oviposition. The ovipositor consists of three pairs of valvulae, two pairs of valvifers and the female T9 (9th abdominal tergum). The paired 1st and the 2nd valvulae are interlocked via the olistheter system, which allows the three parts to slide longitudinally relative to each other, and form the terebra. The various ovipositor movements are actuated by a set of nine paired muscles, three of which (i.e. 1st valvifer-genital membrane muscle, ventral 2nd valvifer-venom gland reservoir muscle, T9-genital membrane muscle) are described here for the first time in chalcidoids. The anterior and posterior 2nd valvifer-2nd valvula muscles are adapted in function. (1) In the active probing position, they enable the wasps to pull the base of each of the longitudinally split and asymmetrically overlapping halves of the 2nd valvula that are fused at the apex dorsally, thus enabling lateral bending of the terebra. Concurrently, the 1st valvulae can be pro- and retracted regardless of this bending. (2) These muscles can also rotate the 2nd valvula and therefore the whole terebra at the basal articulation, allowing bending in various directions. The position of the terebra is anchored at the puncture site in hard substrates (in which drilling is extremely energy- and time-consuming). A freely steerable terebra increases the chance of contacting a potential host within a concealed cavity. The evolution of the ability actively to steer the terebra can be considered a key innovation that has putatively contributed to the acquisition of new hosts to a parasitoid’s host range. Such shifts in host exploitation, each followed by rapid radiations, have probably aided the evolutionary success of Chalcidoidea (with more than 500,000 species estimated).
... Honey bees and social wasps represent independent origins of both eusociality and comb building [8]. In both groups, workers build hexagonal cells, though honey bees (Apis) build a double-sided array out of wax, whereas wasps typically build a single-sided array out of paper [4,6,9,10]. ...
... Here, we investigate hexagonal lattices built by 5 species of honey bees and 5 species of social wasps, representing at least 4 transitions between hexagonal cell size monomorphism and dimorphism in lineages separated by 179 million years [8] (Fig 1). Workers build reproductive cells when colonies reach a critical colony size, time of year, or colony condition, but the 2 cell sizes are constructed within the same hexagonal lattice [18][19][20][21][22][23]. ...
... First, we created a phylogenetic tree of our species using divergence dates (in millions of years ago) from key nodes in [8] (split between Vespidae and Apidae; split between Vespinae and Polistinae) and [35] (splits between species of Apis). We could not find a time-calibrated tree containing our species of Vespula. ...
The hexagonal cells built by honey bees and social wasps are an example of adaptive architecture; hexagons minimize material use, while maximizing storage space and structural stability. Hexagon building evolved independently in the bees and wasps, but in some species of both groups, the hexagonal cells are size dimorphic-small worker cells and large reproductive cells-which forces the builders to join differently sized hexagons together. This inherent tiling problem creates a unique opportunity to investigate how similar architectural challenges are solved across independent evolutionary origins. We investigated how 5 honey bee and 5 wasp species solved this problem by extracting per-cell metrics from 22,745 cells. Here, we show that all species used the same building techniques: intermediate-sized cells and pairs of non-hexagonal cells, which increase in frequency with increasing size dimorphism. We then derive a simple geometric model that explains and predicts the observed pairing of non-hexagonal cells and their rate of occurrence. Our results show that despite different building materials, comb configurations, and 179 million years of independent evolution, honey bees and social wasps have converged on the same solutions for the same architectural problems, thereby revealing fundamental building properties and evolutionary convergence in construction behavior.
... Therefore, reconstructing phylogenetic relationships with USCOs and/or UCEs has been successfully applied to a range of species, such as springtails, bees, rodents, and monocots [26][27][28][29]. At present, although systematic phylogenetic analysis of all major lineages of Hymenoptera based on protein-coding genes has been conducted [30], phylogenetic studies of the subfamily Eumeninae based on nuclear data are still poorly. In this paper, we aim to investigate the phylogenetic relationships of Rhynchium and its related genera in the subfamily Eumeninae using low-coverage whole genome sequencing with USCOs and UCEs, which could also serve as new molecular markers for the subfamily Eumeninae. ...
... The Rhynchium genera group is distributed in the Old World only, including the Australian, Ethiopian, Oriental, and Palearctic regions. The most recent common ancestor (MRCA) of the Rhynchium genera group was inferred in the Cretaceous (95.74 Ma), which is consistent with the results of the evolutionary history of the Hymenoptera [30]. The Rhynchium genera group might have spread in various plates according to the migration history of the Old World. ...
Simple Summary
The eumenine wasps of the genus Rhynchium Spinola, 1806; Allorhynchium van der Vecht, 1963; Anterhynchium de Saussure, 1863; and Pararrhynchium de Saussure, 1855 are related and sometimes hard to tell apart from each other. In this study, we first reconstructed the phylogenetic relationships of these genera based on universal single-copy orthologs and ultraconserved elements extracted from 10 newly sequenced low-coverage whole genomes. The results showed that Allorhynchium and Lissodynerus are distinct from the other four taxa. The genus Rhynchium was recovered as monophyletic, whereas Anterhynchium was recovered as paraphyletic, with Anterhynchium (Dirhynchium) as a sister to Rhynchium and hence deserving a separate genus Dirhynchium; and within the genus Pararrhynchium, P. septemfasciatus feanus and P. venkataramani were separated, not clustered on a branch. It is suggested that the genus Lissodynerus should be restituted as a valid genus, not a synonym of the Pararrhynchium. The results are consistent with previous eumenine mitochondrial genome phylogenetic analyses. This paper confirms the feasibility of low-coverage whole genome eumenine wasp phylogenetics and provides a reference for subsequent research in Eumeninae.
Abstract
The subfamily Eumeninae is a large group of fierce predatory insects that prey mainly on the larvae of Lepidoptera pests. Because of the highly similar morphologies of the genus Rhynchium and its related genera in the subfamily, including Rhynchium Spinola, Allorhynchium van der Vecht, Anterhynchium de Saussure, Pararrhynchium de Saussure, it is essential to delineate their relationships. A previous phylogenetic analysis based on mitochondrial genomes suggested the inconsistent relationships of these genera under traditional classification based on morphological characters. In this study, we first used single-copy orthologs [USCO] and ultraconserved elements [UCE] extracted from 10 newly sequenced low-coverage whole genomes to resolve the phylogenetic relationships of the above genera. The newly sequenced genomes are 152.99 Mb to 211.49 Mb in size with high completeness (BUSCO complete: 91.5–95.6%) and G + C content (36.31–38.76%). Based on extracted 5811 USCOs and 2312 UCEs, the phylogenetic relationships of Rhynchium and its related genera were: ((Allorhynchium + Lissodynerus) + (Pararrhynchium + (Anterhynchium + (Dirhynchium + Rhynchium)))), which was consistent with the mitochondrial genome results. The results supported the genus Rhynchium as monophyletic, whereas Anterhynchium was recovered as paraphyletic, with Anterhynchium (Dirhynchium) as a sister to Rhynchium and hence deserving generic status; In addition, in the genus Pararrhynchium, P. septemfasciatus feanus and P. venkataramani were separated, not clustered on a branch, just as P. septemfasciatus feanus was not together with P. striatum based on mitochondrial genomes. Since Lissodynerus septemfasciatus, the type species of the genus Lissodynerus, was transferred to Pararrhynchium, it is considered that the genus Lissodynerus should be restituted as a valid genus, not a synonym of Pararrhynchium.
... Vilhemsen (1997) asserted that the superfamily Stephanoidea, comprising the sole extant family Stephanidae, was the most basal group of Apocrita (Hymenoptera). Recent molecular analyses, however, have indicated that Stephanoidea + Evanioidea form a sister clade to the Trigonalyoidea + Aculeata clade (Branstetter et al., 2017;Peters et al., 2017). ...
... The comparatively high diversity of basal lineages implies that the diversification of Stephanidae occurred between the early and mid-Cretaceous. Based on our dating using the morphological clock, the origin of stem-Stephanidae is dated back to the Late Jurassic, which is much later than estimated by molecular clock based on genomic data: the divergence of Stephanoidea and Evanioidea was estimated to occurr in the Late Triassic (Peters et al., 2017). ...
The family Stephanidae (Hymenoptera) constitutes a unique group within the Apocrita, playing a pivotal role in the evolution of parasitoid wasps. Although the phylogeny of Stephanidae has been previously inferred, it remains at a low resolution when considering both extinct and extant genera, as well as the enigmatic extinct genus † Electrostephanus . Here, we undertake a revision of Stephanidae extinct, presenting descriptions of new specimens from late Cretaceous Burmese amber and early Eocene Baltic amber. Combining all extant and extinct genera, the phylogeny of Stephanidae was analyzed, incorporating 57 species within 21 genera based on 64 morphological characters. We apply both under maximum parsimony with equal weighting and implied weighting methods, with four species representing early Apocrita as outgroups. Divergence times are estimated by utilizing extinct taxa as calibration points. A new basal subfamily of stephanid wasp, †Lagenostephaninae subf. nov. was established, encompassing † Lagenostephanus and the newly described genera † Tumidistephanus gen. nov and † Neurastephanus gen. nov . The genus † Electrostephanus is redefined, with two species assigned under distinct genera, † Neurastephanus gen. nov. and † Aphanostephanus gen. nov. . We discuss some of the putative morphological synapomorphies of evolutionary significance within the phylogenetic framework. Our results complement several characteristics of great taxonomic importance for Stephanidae and provide new insights into the early evolution of the family.
... Here, we use this approach to examine NGS datasets from 18 bee genera spanning 100 million years of divergence (Figure 1, Bossert et al., 2019;Jack, 2021;Gibbs et al., 2012;Husemann et al., 2021;Kapheim et al., 2019;Lu et al., 2021;Peters et al., 2017) that vary in their social structure, ranging from solitary to obligately eusocial. ...
... Potentially, then, this core microbiome shared between Apini, Bombini and Meliponini may be as ancient as their last common ancestor (LCA) and was composed after the split between the orchid bees and other corbiculates. It could therefore be argued that this LCA would have likely been obligately eusocial, allowing these bacterial communities to establish stably enough to be passed on to three different lineages through ∼55 million years of host diversification (Peters et al., 2017). ...
Microbiomes are increasingly recognised as critical for the health of an organism. In eusocial insect societies, frequent social interactions allow for high‐fidelity transmission of microbes across generations, leading to closer host–microbe coevolution. The microbial communities of bees with other social lifestyles are less studied, and few comparisons have been made between taxa that vary in social structure. To address this gap, we leveraged a cloud‐computing resource and publicly available transcriptomic data to conduct a survey of microbial diversity in bee samples from a variety of social lifestyles and taxa. We consistently recover the core microbes of well‐studied corbiculate bees, supporting this method's ability to accurately characterise microbial communities. We find that the bacterial communities of bees are influenced by host location, phylogeny and social lifestyle, although no clear effect was found for fungal or viral microbial communities. Bee genera with more complex societies tend to harbour more diverse microbes, with Wolbachia detected more commonly in solitary tribes. We present a description of the microbiota of Euglossine bees and find that they do not share the “corbiculate core” microbiome. Notably, we find that bacteria with known anti‐pathogenic properties are present across social bee genera, suggesting that symbioses that enhance host immunity are important with higher sociality. Our approach provides an inexpensive means of exploring microbiomes of a given taxa and identifying avenues for further research. These findings contribute to our understanding of the relationships between bees and their associated microbial communities, highlighting the importance of considering microbiome dynamics in investigations of bee health.
... It has generally been assumed that the phytophagous forms constitute a monophyletic lineage, the family Cynipidae, although it has been surprisingly difficult to find morphological characters supporting their monophyly (Liljeblad & Ronquist, 1998;Ronquist, 1999;Ronquist et al., 2015). The Cynipidae are deeply nested within the insect-parasitic Apocrita (Blaimer et al., 2023;Heraty et al., 2011;Klopfstein et al., 2013;Peters et al., 2017;Ronquist, 1995Ronquist, , 1999Sharkey et al., 2011), and all other members of the superfamily Cynipoidea are insect parasitoids, so it has long been clear that the phytophagous gall inducers and inquilines must have evolved from insect-parasitic ancestors. Except for the Cynipidae, the superfamily Cynipoidea comprises the families Austrocynipidae, Ibaliidae, Liopteridae and Figitidae (Ronquist, 1995(Ronquist, , 1999. ...
... Parnipinae have appeared in previous analyses as the sister group of the remaining Figitidae, or even as the sister group of the Cynipidae (Blaimer et al., 2020;Buffington et al., 2007;Ronquist, 1999;Ronquist et al., 2015). We also included three more Klopfstein et al., 2013;Peters et al., 2017;Sharkey et al., 2011) and was used for rooting the trees generated in our analyses. ...
Gall wasps (Hymenoptera: Cynipidae) comprise 13 distinct tribes whose interrelationships remain incompletely understood. Recent analyses of ultra‐conserved elements (UCEs) represent the first attempt at resolving these relationships using phylogenomics. Here, we present the first analysis based on protein‐coding sequences from genome and transcriptome assemblies. Unlike UCEs, these data allow more sophisticated substitution models, which can potentially resolve issues with long‐branch attraction. We include data for 37 cynipoid species, including two tribes missing in the UCE analysis: Aylacini (s. str.) and Qwaqwaiini. Our results confirm the UCE result that Cynipidae are not monophyletic. Specifically, the Paraulacini and Diplolepidini + Pediaspidini fall outside a core clade (Cynipidae s. str.), which is more closely related to the insect‐parasitic Figitidae, and this result is robust to the exclusion of long‐branch taxa that could mislead the analysis. Given this, we here divide the Cynipidae into three families: the Paraulacidae stat. prom., Diplolepididae stat. prom. and Cynipidae (s. str.). Our results suggest that the Eschatocerini are the sister group of the remaining Cynipidae (s. str.). Within the Cynipidae (s. str.), the Aylacini (s. str.) are more closely related to oak gall wasps (Cynipini) and some of their inquilines (Ceroptresini) than to other herb gallers (Aulacideini and Phanacidini), and the Qwaqwaiini likely form a clade together with Synergini (s. str.) and Rhoophilini. Several alternative scenarios for the evolution of cynipid life histories are compatible with the relationships suggested by our analysis, but all are complex and require multiple shifts among parasitoids, inquilines and gall inducers.
... To further validate the co-loss of CDCA7 and DNMT1/DNMT3 in insects, we focused on the Hymenoptera clade (including M. demolitor), for which genome synteny has been reported (Li et al., 2021). Indeed, a striking synteny is observed in the genome region surrounding CDCA7 among the parasitic wood wasp (Orussus abietinus) and Aculeata species (bees Bombus terrestris and Habropoda laborlosa, and the eusocial wasp Polistes canadensis), which diverged ~250 MYA (Li et al., 2021;Peters et al., 2017; Figure 7 and Figure 7-source data 1). In these species, CDCA7 is located between Methyltransferase-like protein 25 homolog (MET25, E) and Ornithine aminotransferase homolog (OAT, F). ...
... Presence and absence of 5mC, CDCA7, HELLS, DNMT1, DNMT3, and UHRF1 in each genome is indicated by filled and open boxes, respectively. Absence of 5mC in Aphidus gifuensis (marked with an asterisk) is deduced from the study in Aphidius ervi (Bewick et al., 2017b), which has an identical presence/absence pattern of the listed genes (Figure 7-source data 2).The phylogenetic tree is drawn based on published analysis (Li et al., 2021;Peters et al., 2017) and TimeTree. ...
5-Methylcytosine (5mC) and DNA methyltransferases (DNMTs) are broadly conserved in eukaryotes but are also frequently lost during evolution. The mammalian SNF2 family ATPase HELLS and its plant ortholog DDM1 are critical for maintaining 5mC. Mutations in HELLS, its activator CDCA7, and the de novo DNA methyltransferase DNMT3B, cause immunodeficiency-centromeric instability-facial anomalies (ICF) syndrome, a genetic disorder associated with the loss of DNA methylation. We here examine the coevolution of CDCA7, HELLS and DNMTs. While DNMT3, the maintenance DNA methyltransferase DNMT1, HELLS, and CDCA7 are all highly conserved in vertebrates and green plants, they are frequently co-lost in other evolutionary clades. The presence-absence patterns of these genes are not random; almost all CDCA7 harboring eukaryote species also have HELLS and DNMT1 (or another maintenance methyltransferase, DNMT5). Coevolution of presence-absence patterns (CoPAP) analysis in Ecdysozoa further indicates coevolutionary linkages among CDCA7, HELLS, DNMT1 and its activator UHRF1. We hypothesize that CDCA7 becomes dispensable in species that lost HELLS or DNA methylation, and/or the loss of CDCA7 triggers the replacement of DNA methylation by other chromatin regulation mechanisms. Our study suggests that a unique specialized role of CDCA7 in HELLS-dependent DNA methylation maintenance is broadly inherited from the last eukaryotic common ancestor.
... The clade Aculeata, the group containing stinging wasps, ants and bees, was characterized by the dominance of 11 nucleotide motifs. The motif (Cameron et al., 2007;Peters et al., 2017;Sann et al., 2018Sann et al., , 2021Blaimer et al., 2023). Telomeric motifs for Cephidae, Orussidae, Braconidae, Scelionidae, Platygastridae, Cynipoidea, Mymaroidea, Chalcidoidea and Colletidae are taken from Fajkus et al. (2023). ...
... Both clades, Ditrysia in Lepidoptera and (Pemphredonidae + Philanthidae) to Apidae in Hymenoptera, have an evolutionary age of about 150 Myr (Peters et al., 2017;Sann et al., 2018Sann et al., , 2021Kawahara et al., 2019). Probably, during this time, in the course of evolution, there has been a loss of similarity in the primary structure of the telomerase gene. ...
The telomerase mechanism and telomeric motifs are vital for maintaining chromosome integrity. Their functions are conserved in eukaryotic organisms; therefore, it is not surprising that the structure of telomeric motifs is stable. For example, the TTAGG motif persists for hundreds of millions of years in most insects and other arthropods. Here we describe bursts of high diversity of telomeric motifs that have evolved independently in pentatomomorphic bugs (Hemiptera, Pentatomomorpha) and several lineages of parasitic and stinging wasps and bees (Hymenoptera, Apocrita). We show that in most insects, the telomeric DNA sequence is not just a collection of short repeats, but a very long array consisting of (TTAGG)n (or other motifs such as TTGGG, TCAGG, TCTGGG, TTAGGGATGG, TTAGGGGTGG, TTAGGGTGGT, TTAGGTCTGGG, TTAGGTTGGGG, TTAGGTTTGGG and TTGGGTCTGGG), regularly and specifically interrupted by the insertion of non-long terminal repeat (non-LTR) retrotransposons of the TRAS and SART families. Long (173–381 bp) repeats were found at chromosome ends in flies of the families Syrphidae and Tachinidae (Diptera). We hypothesize that the balance of telomerase-dependent machinery and telomerase-independent mechanisms (such as SART and TRAS transpositions) maintains telomeres in many insects. We also discuss how shifting this balance can lead to an increased variability of telomeric motifs and to their complete disappearance.
... Source data • Source Data sets, 28,[30][31][32][33][34][35][36][37][38][39][40][41][42][43][44][45][46] and their analysis within GeneSortR 19 were used to assess the efficacy of Scoutknife. All files used to assess the efficacy of Scoutknife can be found reproduced in our underlying data link (below). ...
... Further information on the Source datasets can also be found in the supplemental data for Koch et al. (2021). 19 Underlying data • Both our real and simulated data analyses are available at DataDryad, along with copies of individual gene fasta files from Source Data sets 28,[30][31][32][33][34][35][36][37][38][39][40][41][42][43][44][45][46] ...
Background: The phylogenetic bootstrap, first proposed by Felsenstein in 1985, is a critically important statistical method in assessing the robusticity of phylogenetic datasets. Core to its concept was the use of pseudo sampling - assessing the data by generating new replicates derived from the initial dataset that was used to generate the phylogeny. In this way, phylogenetic support metrics could overcome the lack of perfect, infinite data. With infinite data, however, it is possible to sample smaller replicates directly from the data to obtain both the phylogeny and its statistical robusticity in the same analysis. Due to the growth of whole genome sequencing, the depth and breadth of our datasets have greatly expanded and are set to only expand further. With genome-scale datasets comprising thousands of genes, we can now obtain a proxy for infinite data. Accordingly, we can potentially abandon the notion of pseudo sampling and instead randomly sample small subsets of genes from the thousands of genes in our analyses.
Methods: We introduce Scoutknife, a jackknife-style subsampling implementation that generates 100 datasets by randomly sampling a small number of genes from an initial large-gene dataset to jointly establish both a phylogenetic hypothesis and assess its robusticity. We assess its effectiveness by using 18 previously published datasets and 100 simulation studies.
Results: We show that Scoutknife is conservative and informative as to conflicts and incongruence across the whole genome, without the need for subsampling based on traditional model selection criteria.
Conclusions: Scoutknife reliably achieves comparable results to selecting the best genes on both real and simulation datasets, while being resistant to the potential biases caused by selecting for model fit. As the amount of genome data grows, it becomes an even more exciting option to assess the robusticity of phylogenetic hypotheses.
... Following the processes of alignment, trimming, and filtering, the matrix of 1,176,406 amino acid sites derived from 1,951 single-copy genes was used for phylogeny inference and divergence time estimation. The phylogenetic relationships obtained the highest statistical support (100/100), coinciding with the results of previous studies (Peters et al. 2017;Sharanowski et al. 2021;Jasso-Martinez et al. 2022). The divergence time analysis revealed the emergence of the common ancestor of three microgastrine species that appeared during the Eocene epoch ( (Weisman et al. 2022). ...
... The divergence times were calculated using the MCMCTree plugin of PAML v4.9j (Yang 2007). A total of six fossil calibration points were selected to estimate the divergence time based on the PDBD database (https:// paleobiodb.org/) and two published articles (Misof et al. 2014;Peters et al. 2017). Additional detailed descriptions are available in supplementary table S18, Supplementary Material online. ...
Parasitoid wasps are invaluable natural enemies extensively used to control coleopteran, dipteran, and lepidopteran pests in agriculture and forestry owing to their killing and reproductive actions on the hosts. The important larval endoparasitoid wasp Microplitis manilae, which belongs to the Microgastrinae subfamily, parasitizes the larval stages of Spodoptera spp., such as Spodoptera litura and Spodoptera frugiperda. The absence of a genomic resource of M. manilae has impeded studies on chemosensory- and detoxification-related genes. This study presents a chromosome-level genome assembly of M. manilae with a genome size of 293.18 Mb, which includes 222 contigs (N50 size, 7.58 Mb) and 134 scaffolds (N50 size, 27.33 Mb). A major proportion of the genome (284.76Mb; 97.13%) was anchored to 11 pseudo-chromosomes with a single-copy BUSCO score of 98.4%. Furthermore, 14,316 protein-coding genes, 165.14 Mb (57.99%) repetitive elements, and 871 noncoding RNAs were annotated and identified. Additionally, a manual annotation of 399 genes associated with chemosensation and 168 genes involved in detoxification was conducted. This study provides a valuable and high-quality genomic resource to facilitate further functional genomics research on parasitoid wasps.
... Analyses of gene synteny confirms the conserved genomic landscape of the CYP9 cluster across bee families but highlights a loss in a Megachilidae species Syntenic analyses offer a useful augmentation of sequencebased phylogenetics. Recent molecular studies now place the Melittidae as a sister group to the other bee families and so the inclusion of the M. europea genome(Falk et al., 2022) in our analyses allows us to resolve the ancestral genomic architecture of the CYP9 locus(Branstetter et al., 2017;Peters et al., 2017).Eight good-quality bee genomes were used alongside that of M.europea, comprising 2 Apidae, 3 Megachilidae, 1 Halictidae, 1 Andrenidae and 1 Colletidae species. Scaffolds containing the CYP9 locus from each assembly were examined for evidence of microsynteny (Figure 2). ...
Recent work has demonstrated that many bee species have specific cytochrome P450 enzymes (P450s) that can efficiently detoxify certain insecticides. The presence of these P450s, belonging or closely related to the CYP9Q subfamily (CYP9Q‐related), is generally well conserved across the diversity of bees. However, the alfalfa leafcutter bee, Megachile rotundata, lacks CYP9Q‐related P450s and is 170–2500 times more sensitive to certain insecticides than bee pollinators with these P450s. The extent to which these findings apply to other Megachilidae bee species remains uncertain. To address this knowledge gap, we sequenced the transcriptomes of four Megachile species and leveraged the data obtained, in combination with publicly available genomic data, to investigate the evolution and function of P450s in the Megachilidae. Our analyses reveal that several Megachilidae species, belonging to the Lithurgini, Megachilini and Anthidini tribes, including all species of the Megachile genus investigated, lack CYP9Q‐related genes. In place of these genes Megachile species have evolved phylogenetically distinct CYP9 genes, the CYP9DM lineage. Functional expression of these P450s from M. rotundata reveal they lack the capacity to metabolize the neonicotinoid insecticides thiacloprid and imidacloprid. In contrast, species from the Osmiini and Dioxyini tribes of Megachilidae have CYP9Q‐related P450s belonging to the CYP9BU subfamily that are able to detoxify thiacloprid. These findings provide new insight into the evolution of P450s that act as key determinants of insecticide sensitivity in bees and have important applied implications for pesticide risk assessment.
... A comparative study of Hymenoptera, the most widely studied example of mushroom body elaboration, shows that, there, the expansion coincided with the emergence of parasitoidism, suggesting it may have been driven by the cognitive demands of spatial memory of host locations, rather than social cognition (Farris and Schulmeister 2011). However, this expansion event likely occurred approximately 250 million years ago (Farris and Schulmeister 2011;Peters et al. 2017) and this large phylogenetic distance, and accompanying ecological and life history differences, makes it difficult to directly test hypothesised links between cognitive ecology and mushroom body expansion through comparative behavioural experiments due to the potential confounding factors resulting from comparing such distantly related taxa. ...
The evolutionary relationships between ecology, cognition, and neurobiology remain elusive, despite important contributions from functional studies and comparative analyses. Recently, Heliconius butterflies and their Heliconiini allies have emerged as a promising system for investigating the evolution and ecology of cognition. In Heliconius, regions of the brain involved in learning and memory, called the mushroom bodies, have quadrupled in size and contain up to 8 times more neurons than closely related genera. This expansion, largely driven by increased dedication to processing visual input, occurred relatively recently (~12–18 Ma) and coincides with the evolution of a novel foraging behaviour — trapline foraging between pollen resources, which provide an adult source of amino acids. Behavioural experiments show that, relative to other Heliconiini, Heliconius exhibit superior visual long-term memory and non-elemental learning, behaviours which have putative relevance for visual learning during traplining, while exhibiting no differences in shape learning or reversal learning. These cognitive differences are also associated with changes in the plastic response of the mushroom body to learning and experience. Heliconius thus constitute a clear example of a suite of neural adaptations that coincides with a novel behaviour reliant on distinct cognitive shifts. We highlight the Heliconiini as a well-positioned, developing case study in cognitive ecology and evolution, where there is the possibility of synthesising comparative neuroanatomical, developmental and behavioural data with extensive genomic resources. This would provide a rich dataset linking genes, brains, behaviour, and ecology, and offer key insights into the mechanisms and selective pressures shaping the evolution of interspecific cognitive variation.
... The supra-generic classification is currently debated and the subject of studies that attempt to delineate the relationships between the various evolutionary lines of the family, as recent studies based on molecular data (Schmitz & Moritz 1998;Hines et al. 2007;Bank et al. 2017;Peters et al. 2017;Piekarski et al. 2018) are largely incongruent with those based on morphological and behavioral traits (e.g., Carpenter 1982Carpenter , 1987Carpenter , 1988aCarpenter , 1988bCarpenter , 1991Carpenter , 1993Carpenter , 1996Carpenter & Cumming 1985;Carpenter & Rasnitsyn 1990;Vernier 1997;Gess 1998;Krenn et al. 2002;Carpenter & Perera 2006;Hermes et al. 2013;Perrard et al. 2017). In particular, some authors separate two groups from the subfamily Eumeninae, the so-called "Zethini" and "Raphiglossini", sometimes as a single subfamily (Zethinae) and others as two separate lineages (Zethinae and Raphiglossinae) (Bank et al. 2017;Piekarski et al. 2018). ...
An illustrated key for the identification of genera and subgenera, and a checklist of Italian Vespidae (Hymenoptera) are presented.
... As mentioned above, one group of insects that generally escapes from threats by flying and therefore could benefit from flushing bars is the insect order Hymenoptera. It is one of the most species-rich insect order in the world (Forbes et al., 2018), comprising ants, bees, sawflies and wasps (Peters et al., 2017). While their importance for pollination is well-known to the public (Klein et al., 2007;Potts et al., 2016), their function as natural control agents for pest species is rarely mentioned in the public discussion (but see Fornoff et al., 2023). ...
The worldwide decline of insects is one of the major challenges for humankind. One of its main drivers is intensive farming, which reduces habitats and food resources for insect populations and causes direct mortality by pesticides. In addition, mowing of grassland poses another threat to insects, especially when it is done frequently, such as in roadside verges. Roadside verges comprise large areas worldwide and can serve as habitats for animals and plants and as corridors to connect populations when they are maintained ecologically, for example when mowing is done arthropod-friendly and with low frequency. Microhymenoptera are highly diverse, mostly show a parasitoid lifestyle and occur in large numbers in meadows and grasslands. Although they have an important ecological function in regulating their arthropod host populations, they were mostly neglected in studies on the influence of mowing on insects. Therefore, we assessed which families of microhymenoptera occur in roadside verges and meadows , examined if they are affected by the mowing process with a conventional mulch-ing mower, and studied which groups benefit from arthropod-friendly mowing, using the mowing head Eco 1200 plus from MULAG, and a flushing bar made of track tarpaulin. In our experimental grassland plots, we found specimens of 18 families from the six microhymenoptera superfamilies Chalcidoidea, Ceraphronoidea, Diaprioidea, Ichneumonoidea, Platygastroidea and Proctotrupoidea. Mowing with a conventional mulching mower caused a significant loss of up to 64% for parasitoid Hymenoptera. The Eco 1200 plus showed an arthropod-friendly effect only on the number of individuals of Chalcidoidea, saving 38% of individuals compared with the conventional mower. The flushing bar showed a significant effect on total number of individuals with a reduction only on Chalcidoidea and a tendency for Ichneumonoidea with 30% and 47%, respectively. Our study demonstrates the detrimental effect of mowing with a conventional mulching mower on microhymenoptera and shows that this effect can be partly reversed for Chalcidoidea and Ichneumonoidea through the arthropod-friendly mower and a flushing bar. Our study highlights the importance to consider microhymenoptera in the context of insect decline.
... Parasitoid wasps, which unlike traditional parasites would have killed their prey (e.g. Olmi et al. 2022), also underwent major radiation between the mid-Jurassic and Early Cretaceous (Peters et al. 2017;Wang et al. 2022) and are well represented in Cretaceous amber, indicating a shift from bottom-up to top-down regulation of terrestrial food webs (Zhang and Harzhauser 2022). ...
Amber first became relatively abundant and widespread in the geological record during the Cretaceous period. It originated often as copious resin production by a variety of incompletely understood coniferous trees, generally under humid climates, but not excluding seasonal aridity. Study of insect and other organic inclusions only commenced in the twentieth century, but has expanded considerably since then, with several thousand taxa now described. Cretaceous amber insects can be exquisitely preserved in three dimensions, although tend to be biased towards smaller individuals that lived in the local forest environment. They are therefore complemented by the Cretaceous rock record, which sampled larger insects and other habitats. As well as the fine morphological detail exhibited by the amber insect inclusions, various behaviours and interactions unlikely to be otherwise preserved can be found frozen in time, such as brooding behaviour and the entrapment of insects in spiders' webs. Insects in amber also provide important information about evolutionary changes over the course of the Cretaceous, including the rise of eusociality and angiosperm pollination.
... The resulting transcripts or isoforms were manually inspected, and the expression and usage of each transcript (or isoform) in each tissue sample were estimated using the methods described above. Finally, we mapped this information to the phylogeny obtained from (Peters et al. 2017;Ye et al. 2022) for comprehensive evolutionary analyses. ...
Animal venom systems have emerged as valuable models for investigating how novel polygenic phenotypes may arise from gene evolution by varying molecular mechanisms. However, a significant portion of venom genes produce alternative mRNA isoforms that have not been extensively characterized, hindering a comprehensive understanding of venom biology. In this study, we present a full-length isoform-level profiling workflow integrating multiple RNA sequencing technologies, allowing us to reconstruct a high-resolution transcriptome landscape of venom genes in the parasitoid wasp Pteromalus puparum . Our findings demonstrate that more than half of the venom genes generate multiple isoforms within the venom gland. Through mass spectrometry analysis, we confirm that alternative splicing contributes to the diversity of venom proteins, acting as a mechanism for expanding the venom repertoire. Notably, we identified seven venom genes that exhibit distinct isoform usages between the venom gland and other tissues. Furthermore, evolutionary analyses of venom serpin3 and orcokinin further reveal that the co-option of an ancient isoform and a newly evolved isoform, respectively, contributes to venom recruitment, providing valuable insights into the genetic mechanisms driving venom evolution in parasitoid wasps. Overall, our study presents a comprehensive investigation of venom genes at the isoform level, significantly advancing our understanding of alternative isoforms in venom diversity and evolution and setting the stage for further in-depth research on venoms.
... Among the extant families of Chysidoidea s.s., the grouping of Chrysididae and Scolebythidae is further supported by the loss of four muscles (M8-M11) associated with the sting apparatus (Barbosa et al. 2021). The phylogenetic relationships obtained for extant chrysidoid families are also congruent with recent phylogenomic analyses, which recovered a sistergroup relationship between Bethylidae and Plumariidae, with Chrysididae forming the sister-group of this clade (Branstetter et al. 2017, Peters et al. 2017, Pauli et al. 2021. As aforementioned, scolebythids have not been included as terminals in any phylogenomic study to date. ...
Scolebythidae constitute the smallest family of Aculeata in number of extant species, but with a considerable diversity of extinct lineages. Twenty Cretaceous species are attributed to the family coming from deposits in Canada, Lebanon, Myanmar, New Jersey, and Spain. However, several of these taxa lack characters of the family groundplan. Although phylogenetic investigations have been conducted for the family based on a relatively small set of morphological characters, the substantial diversity of species from Burmese amber have not yet been accounted for in a phylogenetic perspective. In the present work, we reconstruct the phylogenetic relationships of Scolebythidae using a new morphological matrix and explore it through parsimony and Bayesian model evaluation. In Bayesian analyses, homoplasy-based partitioning outperformed anatomy-based partitioning and the unpartitioned models. Our phylogenetic results support the relocation of a few taxa previously attributed to Scolebythidae to the families Bethylidae and Chrysididae. We also describe †Chrysopsenellidae fam. nov., a new family of Chrysidoidea, based on an inclusion in Burmese amber. In all analyses the new family is recovered as closely related to Scolebythidae, with the whole clade being sister-group to Chrysididae + †Chrysobythidae. Finally, we discuss the origin of the Burmese amber biota distinctiveness.
... Mariana Marchi Santoni mmsantoni@gmail.com as they are associated with the origin of Anthophila, which is the clade that includes bee species (Ohl and Bleidorn 2005;Peters et al. 2017;Sann et al. 2018). Among crabronid wasps, the genus Trypoxylon Latreille, 1796 is one of the seven genera in the cosmopolitan tribe Trypoxylini and is characterized by its slender body, medium tibia with an apical spur, elongated, pedunculated metasomal segment 1, distinctly marginalized inner eye sockets, and forewings with a submarginal cell (Bohart and Menke 1976;Jeong and Kim 2020). ...
Studying the nesting biology of wasp and bee species provides valuable insights into the ecology and evolution of these insects, shedding light on their ecological significance and aiding in their conservation efforts. Trypoxylon Latreille, 1796 is a genus of spider-hunting wasps that provisions their brood with paralyzed preys. This study focuses on aspects of nesting biology of Trypoxylon (Trypargilum) species such as sex ratio, sexual dimorphism, and morphometric variation at both inter- and intraspecific levels. The secondary sex ratio (SR) exhibited variation among species and populations. Males predominantly emerged from the first brood cells and from trap nests with smaller diameters. In comparison, females showed significantly larger body mass and linear wing measurements than males. Procrustes ANOVA values for centroid size (CS) and wing shape (SH) indicated significant differences in both wing size and shape among the five analyzed Trypoxylon species. Sexual dimorphism indices (SDI) derived from centroid size were found to be similar to those obtained from linear measurements, while SDI values based on body mass were significantly higher. Nests containing a greater number of cells tended to produce a larger number of higher-quality males and females. This observation, along with the lower coefficient of variation for female body size and high heritability, suggests that this trait may be subject to natural selection. Further studies that estimate the size of parents and their respective offspring are necessary to confirm the fitness advantage associated with larger female sizes in Trypoxylon species.
... The genus Megischus Brullé, 1846, is the second species-rich genus of the crown wasps family Stephanidae Leach, 1815 which is a clade with the superfamily Evanioidea sister to all other groups of the aculeate Hymenoptera (Branstetter et al. 2017;Peters et al. 2017). The genus Megischus consists of 89 extant species up to date, with a worldwide distribution but mainly found in the Oriental regions (Aguiar 2004;Hong et al. 2011;Binoy et al. 2020;Ge et al. 2021aGe et al. , 2021bGe et al. , 2022. ...
A new crown wasp species, Megischus shixiangi Ge & Tan, sp. nov. from Vietnam (Hymenoptera: Stephanidae), is described and illustrated. In addition, M. kuafu Ge & Tan is first recorded in Vietnam. A distribution map of the Vietnamese species is provided.
... Hymenopterans are not known from sediments below Middle-Upper Triassic boundary, including Anisian 'Grès à Voltzia' Formation (Vosges Mts., France, 242-247 Ma), the second richest fossil insect fauna of Triassic (Gall and Grauvogel-Stamm 2005). On the other hand, molecular dating suggests that Hymenoptera diversification began as early as the Late Paleozoic-Middle Triassic (329-239 Ma according to Peters et al. 2017). It can be assumed that the most ancient hymenopterans successfully avoided entering the fossil record for millions of years. ...
One new genus and three new species of Archexyelinae (Xyelidae) are described from the Middle–Late Triassic Madygen Formation of Kyrgyzstan, including Xyelinus scherbachov sp. nov., Triassoxyela sharovi sp. nov., and Microxyela minuta gen. et sp. nov. Xyelidae is the most ancient hymenopteran family in fossil records and the only one known from the Triassic. Triassic xyelids are known from five localities throughout the whole Pangaea. The most diverse and abundant Triassic xyelid fauna comes from Madygen, with 16 genera and 34 species in the two subfamilies Archexyelinae and Madygellinae.
... Juvenile hormone (JH) is one compound involved in bumble bee queen reproduction that is regulated by the social environment in incipient nests ). In honey bees, which share a common origin of eusociality with bumble bees (Peters, 2017), juvenile hormone titer is associated with division of labor and specifically brood care and foraging behaviors (Robinson 1987). The observed changes in bumble bee maternal care behavior (i.e., brood feeding and food collection) in Chapter 3 occurred around the same point that JH rose in Chapter 1. Future work should investigate whether this compound may play a direct role in regulating maternal care behaviors in bumble bees, in addition to its observed impact on queen reproduction, across the ontogeny of eusociality. ...
This dissertation presents a deep dive into the behavior and physiology of spring
queen bumble bees. Bumble bee queens emerge from diapause and initiate new nests
independently in spring. As they lay eggs and subsequently rear offspring to adulthood, queens undergo a dramatic transition from a solitary, to subsocial, to eusocial lifestyle, which presents a unique opportunity to investigate phenotypic plasticity and life history transitions. This colony founding stage of their life cycle may also represent a particularly important demographic for bumble bee populations, many of which are experiencing dramatic declines. An improved understanding of this life stage may help inform conservation strategies and predict bumble bee responses to a changing world.
In this dissertation, I investigate behavioral and physiological plasticity in bumble
bee queens across the spring colony founding stage. In Chapter One, I show that queen ovary development and nest searching and occupation occur simultaneously, which may enable rapid nest initiation. In Chapter Two, I show that the emergence of workers in incipient nests increases queen survival and reproduction, suggesting that the timing of early worker emergence in the nest likely impacts queen fitness, colony developmental trajectories, and ultimately nesting success. In Chapter Three, I show that queens respond to the emergence of workers in young nests by performing fewer brood care and food collection tasks, suggesting that queen maternal care behavior is tightly regulated by the number of helpers in the nest. And finally, in Chapter Four, I show that wild queens spend most of each day foraging via short, frequent trips, which highlights the heightened demands placed on early season queens.
Collectively, this work has yielded three major insights into spring queen bumble
bee biology. First, it suggests that queens are highly plastic in the incipient stages of
colony founding and have the capacity to change dynamically in response to social and environmental fluctuations. Second, it suggests that starting nests earlier in the season may be advantageous for bumble bees. Lastly, it underlines the importance of
conservation interventions that support the early nesting period and facilitate the
production and maintenance of workers in incipient nests
... These peptide databases were used toproduce an ultrametric species tree from. The previously determined divergence of Acromyrmex echinatior and Camponotus floridanus is 62 MYA [85], which with the sum of branch lengths between these two species of 0.1101, gives a scaling factor of 563.12. This factor was used to scale the ultrametric Orthofinder species tree in Figtree, resulting in a phylogenetic tree with inferred divergence estimates, allowing for the divergence between M. hyperodae and M. aethiopoides to be estimated. ...
Background
Biocontrol is a key technology for the control of pest species. Microctonus parasitoid wasps (Hymenoptera: Braconidae) have been released in Aotearoa New Zealand as biocontrol agents, targeting three different pest weevil species. Despite their value as biocontrol agents, no genome assemblies are currently available for these Microctonus wasps, limiting investigations into key biological differences between the different species and strains.
Methods and findings
Here we present high-quality genomes for Microctonus hyperodae and Microctonus aethiopoides , assembled with short read sequencing and Hi-C scaffolding. These assemblies have total lengths of 106.7 Mb for M. hyperodae and 129.2 Mb for M. aethiopoides , with scaffold N50 values of 9 Mb and 23 Mb respectively. With these assemblies we investigated differences in reproductive mechanisms, and association with viruses between Microctonus wasps. Meiosis-specific genes are conserved in asexual Microctonus , with in-situ hybridisation validating expression of one of these genes in the ovaries of asexual Microctonus aethiopoides . This implies asexual reproduction in these Microctonus wasps involves meiosis, with the potential for sexual reproduction maintained. Investigation of viral gene content revealed candidate genes that may be involved in virus-like particle production in M. aethiopoides , as well as a novel virus infecting M. hyperodae , for which a complete genome was assembled.
Conclusion and significance
These are the first published genomes for Microctonus wasps which have been deployed as biocontrol agents, in Aotearoa New Zealand. These assemblies will be valuable resources for continued investigation and monitoring of these biocontrol systems. Understanding the biology underpinning Microctonus biocontrol is crucial if we are to maintain its efficacy, or in the case of M. hyperodae to understand what may have influenced the significant decline of biocontrol efficacy. The potential for sexual reproduction in asexual Microctonus is significant given that empirical modelling suggests this asexual reproduction is likely to have contributed to biocontrol decline. Furthermore the identification of a novel virus in M. hyperodae highlights a previously unknown aspect of this biocontrol system, which may contribute to premature mortality of the host pest. These findings have potential to be exploited in future in attempt to increase the effectiveness of M. hyperodae biocontrol.
... The gut microbiomes of a total of 861 individuals across 34 insect pollinator species (belonging to three orders: Hymenoptera, Lepidoptera, and Diptera) and two outgroup comparison species (Hemiptera: Aphis craccivora and Halyomorpha halys) were analyzed (Table S1; Fig. S1). Species were identified by morphology and by cytochrome c oxidase subunit I (COI) gene barcoding, and unless specific phylogenetic distances based on COI sequences were calculated for analyses, phylogenetic relatedness refers to previous studies (35)(36)(37)(38)(39)(40)(41). Amplicon sequencing of the hypervariable V3-V4 region of the bacterial 16S rRNA was performed on individual whole-gut samples. ...
Pollination services provided by wild insect pollinators are critical to natural ecosystems and crops around the world. There is an increasing appreciation that the gut microbiota of these insects influences their health and consequently their services. However, pollinator gut microbiota studies have focused on well-described social bees, but rarely include other, more phylogenetically divergent insect pollinators. To expand our understanding, we explored the insect pollinator microbiomes across three insect orders through two DNA sequencing approaches. First, in an exploratory 16S amplicon sequencing analysis of taxonomic community assemblages, we found lineage-specific divergences of dominant microbial genera and microbiota community composition across divergent insect pollinator genera. However, we found no evidence for a strong broad-scale phylogenetic signal, which we see for community relatedness at finer scales. Subsequently, we utilized metagenomic shotgun sequencing to obtain metagenome-assembled genomes and assess the functionality of the microbiota from pollinating flies and social wasps. We uncover a novel gut microbe from pollinating flies in the family Orbaceae that is closely related to Gilliamella spp. from social bees but with divergent functions. We propose this novel species be named Candidatus Gilliamella eristali . Further metagenomes of dominant fly and wasp microbiome members suggest that they are largely not host-insect adapted and instead may be environmentally derived. Overall, this study suggests selective processes involving ecology or physiology, or neutral processes determining microbe colonization may predominate in the turnover of lineages in insect pollinators broadly, while evolution with hosts may occur only under certain circumstances and on smaller phylogenetic scales.
IMPORTANCE
Wild insect pollinators provide many key ecosystem services, and the microbes associated with these insect pollinators may influence their health. Therefore, understanding the diversity in microbiota structure and function, along with the potential mechanisms shaping the microbiota across diverse insect pollinators, is critical. Our study expands beyond existing knowledge of well-studied social bees, like honey bees, including members from other bee, wasp, butterfly, and fly pollinators. We infer ecological and evolutionary factors that may influence microbiome structure across diverse insect pollinator hosts and the functions that microbiota members may play. We highlight significant differentiation of microbiomes among diverse pollinators. Closer analysis suggests that dominant members may show varying levels of host association and functions, even in a comparison of closely related microbes found in bees and flies. This work suggests varied importance of ecological, physiological, and non-evolutionary filters in determining structure and function across largely divergent wild insect pollinator microbiomes.
... Furthermore, it is the first taxonomic study on this group and region since 1999 when the last five species of Megaspilidae were described, which totals 65 described Afrotropical mainland species of Ceraphronoidea (Dessart 1999). Considering that Ceraphronoidea is a superfamily separated from its closest relatives presumably for more than 200 Ma (Peters et al. 2017), it is one of the most abundant hymenopteran lineages in the understorey of tropical forests (Querino et al. 2011;Silva & Feitosa 2017) and the fourth most commonly collected hymenopteran superfamily (Martínez de Murgía et al. 2001;Schmitt 2004) this is highly astonishing, if not disturbing. Even without any further insights into Ceraphronoidea diversity this already directly implies that they are grotesquely understudied and that the currently described diversity will not reflect true species diversity. ...
The number of currently described species of Afrotropical parasitoid wasps does not reflect the true species diversity. One of the most severely understudied parasitoid wasp groups is Ceraphronoidea. In this first study on Afrotropical mainland Ceraphronoidea in more than 20 years, which is also the first ever taxonomic monograph focusing on Ceraphronidae, we describe 88 new species of Ceraphronidae (85 new species) and Megaspilidae (3 new species) from Kakamega Forest (Kenya), Mt. Kilimanjaro (Tanzania) and Ivindo NP (Gabon): Aphanogmus abaluhya sp. nov., A. ashitakai sp. nov., A. idakho sp. nov., A. ikhongamurwi sp. nov., A. isiukhu sp. nov., A. kakamegaensis sp. nov., A. lateritorum sp. nov., A. mangimelii sp. nov., A. mariae sp. nov., A. mashariki sp. nov., A. nehbergi sp. nov., A. njia sp. nov., A. vestrii sp. nov., A. yala sp. nov. (all clavicornis species group), A. dimidiatus sp. nov., A. fraterculus sp. nov., A. guenteri sp. nov., A. kakakili sp. nov., A. kisiwa sp. nov., A. maua sp. nov., A. morriconei sp. nov., A. ndefu sp. nov., A. ngai sp. nov., A. nikii sp. nov., A. pilosicoxa sp. nov., A. rafikii sp. nov., A. robustus sp. nov., A. simbai sp. nov., A. taji sp. nov., A. ukanda sp. nov. (all fumipennis species group), A. campanula sp. nov., A. kikuyu sp. nov., A. pagoda sp. nov. (all tenuicornis species group), Ceraphron banda sp. nov., C. brashi sp. nov., C. breviharpis sp. nov., C. breviscapus sp. nov., C. buyangu sp. nov., C. chemositi sp. nov., C. cingulum sp. nov., C. clavatumeris sp. nov., C. digiti sp. nov., C. eaerendili sp. nov., C. ekero sp. nov., C. ellae sp. nov., C. eulbergi sp. nov., C. herreni sp. nov., C. hitagarciai sp. nov., C. insolitus sp. nov., C. isecheno sp. nov., C. isukha sp. nov., C. ivindoensis sp. nov., C. kaharabu sp. nov., C. kaimosiensis sp. nov., C. kakamegaensis sp. nov., C. kidole sp. nov., C. kimathii sp. nov., C. lirhanda sp. nov., C. longiharpis sp. nov., C. longisetae sp. nov., C. longumerunus sp. nov., C. maathaiae sp. nov., C. malava sp. nov., C. mamamutere sp. nov., C. metapleuralis sp. nov., C. mikoi sp. nov., C. mwekaensis sp. nov., C. nandi sp. nov., C. nzoia sp. nov., C. onesimusi sp. nov., C. pilosiharpis sp. nov., C. pleurosulcus sp. nov., C. reinholdi sp. nov., C. salazar sp. nov., C. sataoi sp. nov., C. semira sp. nov., C. sungura sp. nov., C. tenuimeris sp. nov., C. tiriki sp. nov., C. trietschae sp. nov., Cyoceraphron dhahabudorsalis sp. nov., C. harpe sp. nov., C. invisibilis sp. nov., C. kahawia sp. nov., C. njano sp. nov. (all Ceraphronidae), Conostigmus kijiko sp. nov., C. koleo sp. nov., and Dendrocerus wachagga sp. nov. (all Megaspilidae). In addition, we describe four species of Aphanogmus and five species of Ceraphron without formal naming. A neotype is designated for Dendrocerus anneckei Dessart, 1985 (Megaspilidae). With these new species we more than double the number described from the Afrotropical mainland (65 vs 153). The species numbers found allow us to estimate the real worldwide species number of Ceraphronoidea as being roughly 12 000–21 000, i.e., 16–29 times the number of the currently described species (~730, including the species described herein). This study is meant to highlight that it is necessary and also possible to study the parasitoid wasps of tropical regions and provide momentum for exploring the diversity of small and diverse insect groups in the Afrotropics and elsewhere while also providing the basic knowledge that is much needed for protecting biodiversity and understanding evolution and the networks of life on earth. All described species are diagnosed and illustrated, with focus on the male genitalia. Furthermore, we provide an identification key to males of Afrotropical Ceraphronidae.
... Com grande representatividade dentro do grupo dos insetos, encontra-se a Ordem Hymenoptera, incluindo cerca de 150.000 espécies, popularmente conhecida pelas espécies de formigas, vespas e abelhas (GILLOT, 2005;PETERS et al., 2017). Os representantes himenópteros mais conhecidos pela população em geral são os caracterizados por possuírem um ferrão originado da modificação da estrutura do ovipositor (SHARKEY, 2007). ...
A etnozoologia pode ser compreendida como uma área científica que busca estabelecer relações entre as comunidades tradicionais, os animais e o ambiente. Assim, o objetivo deste trabalho foi avaliar a construção de conceitos associados a insetos e vespas em uma comunidade rural em Biriricas, Domingos Martins, no interior do Espírito Santo. Para isso, compartilhamos um questionário com os moradores dessa comunidade, em que continham seis perguntas relacionadas aos insetos e vespas especificamente, bem como suas relações com o ambiente. Percebemos que a etnotaxonomia da região possui falhas na identificação entomológica, pois os domínios etnozoológicos “inseto” e “vespa” foram confundidos com outros animais, como aranha, minhoca, lombriga e cobra. Além disso, os serviços ecossistêmicos dos insetos, de forma geral, e das vespas também não foram reconhecidos pela comunidade entrevistada. Dessa forma, sugerimos que ações educativas sejam estabelecidas na região, visando o aprofundamento nos conhecimentos biológicos, já que se tratando de uma comunidade rural, esses conhecimentos poderiam auxiliar nas atividades da agricultura familiar, como polinização e controle de pragas.
... This is probably because most dipteran larvae develop in moist or aquatic environments that are particularly suitable habitats for nematodes (Poinar, 2011). It is evident that Holometabola are the most important hosts of extant mermithids as well as all invertebrate-parasitizing nematodes (Poinar, 1975) and this hexapod subgroup dominated the insect fauna during the Cretaceous (Labandeira and Sepkoski, 1993;Labandeira, 2005;Sohn et al., 2015;Peters et al., 2017;Zhang et al., 2018;Thomas et al., 2020;Wang et al., 2022). Our study suggests that, except for Diptera, nematodes had not completely exploited Holometabola as hosts in the mid-Cretaceous. ...
Mermithid nematodes are obligate invertebrate parasites dating back to the Early Cretaceous. Their fossil record is sparse, especially before the Cenozoic, thus little is known about their early host associations. This study reports 16 new mermithids associated with their insect hosts from mid-Cretaceous Kachin amber, 12 of which include previously unknown hosts. These fossils indicate that mermithid parasitism of invertebrates was already widespread and played an important role in the mid-Cretaceous terrestrial ecosystem. Remarkably, three hosts (bristletails, barklice, and perforissid planthoppers) were previously unknown to be parasitized by mermithids both past and present. Furthermore, our study shows that in contrast to their Cenozoic counterparts, Cretaceous nematodes including mermithids are more abundant in non-holometabolous insects. This result suggests that nematodes had not completely exploited the dominant Holometabola as their hosts until the Cenozoic. This study reveals what appears to be a vanished history of nematodes that parasitized Cretaceous insects.
... This is probably because most dipteran larvae develop in moist or aquatic environments that are particularly suitable habitats for nematodes (Poinar, 2011). It is evident that Holometabola are the most important hosts of extant mermithids as well as all invertebrate-parasitizing nematodes (Poinar, 1975) and this hexapod subgroup dominated the insect fauna during the Cretaceous (Labandeira and Sepkoski, 1993;Labandeira, 2005;Sohn et al., 2015;Peters et al., 2017;Zhang et al., 2018;Thomas et al., 2020;Wang et al., 2022). Our study suggests that, except for Diptera, nematodes had not completely exploited Holometabola as hosts in the mid-Cretaceous. ...
Mermithid nematodes are obligate invertebrate parasites dating back to the Early Cretaceous. Their fossil record is sparse, especially before the Cenozoic, thus little is known about their early host associations. This study reports 16 new mermithids associated with their insect hosts from mid-Cretaceous Kachin amber, 12 of which include previously unknown hosts. These fossils indicate that mermithid parasitism of invertebrates was already widespread and played an important role in the mid-Cretaceous terrestrial ecosystem. Remarkably, three hosts (bristletails, barklice, and perforissid planthoppers) were previously unknown to be parasitized by mermithids both past and present. Furthermore, our study shows that in contrast to their Cenozoic counterparts, Cretaceous nematodes including mermithids are more abundant in non-holometabolous insects. This result suggests that nematodes had not completely exploited the dominant Holometabola as their hosts until the Cenozoic. This study reveals what appears to be a vanished history of nematodes that parasitized Cretaceous insects.
... This is probably because most dipteran larvae develop in moist or aquatic environments that are particularly suitable habitats for nematodes (Poinar, 2011). It is evident that Holometabola are the most important hosts of extant mermithids as well as all invertebrate-parasitizing nematodes (Poinar, 1975) and this hexapod subgroup dominated the insect fauna during the Cretaceous (Labandeira and Sepkoski, 1993;Labandeira, 2005;Sohn et al., 2015;Peters et al., 2017;Zhang et al., 2018;Thomas et al., 2020;Wang et al., 2022). Our study suggests that, except for Diptera, nematodes had not completely exploited Holometabola as hosts in the mid-Cretaceous. ...
Mermithid nematodes are obligate invertebrate parasites dating back to the Early Cretaceous. Their fossil record is sparse, especially before the Cenozoic, thus little is known about their early host associations. This study reports 16 new mermithids associated with their insect hosts from mid-Cretaceous Kachin amber, 12 of which include previously unknown hosts. These fossils indicate that mermithid parasitism of invertebrates was already widespread and played an important role in the mid-Cretaceous terrestrial ecosystem. Remarkably, three hosts (bristletails, barklice, and perforissid planthoppers) were previously unknown to be parasitized by mermithids both past and present. Furthermore, our study shows that in contrast to their Cenozoic counterparts, Cretaceous nematodes including mermithids are more abundant in non-holometabolous insects. This result suggests that nematodes had not completely exploited the dominant Holometabola as their hosts until the Cenozoic. This study reveals what appears to be a vanished history of nematodes that parasitized Cretaceous insects.
Exposure to insecticides may contribute to global insect declines due to sublethal insecticide effects on non-target species. Thus far, much research on non-target insecticide effects has focused on neonicotinoids in a few bee species. Much less is known about effects on other insect taxa or newer insecticides, such as sulfoxaflor. Here, we studied the effects of an acute insecticide exposure on both olfactory and visual learning in free-moving Polistes fuscatus paper wasps. Wasps were exposed to a single, field realistic oral dose of either low dose imidacloprid, high dose imidacloprid, or sulfoxaflor. Then, visual and olfactory learning and short-term memory were assessed. We found that acute insecticide exposure influenced performance, as sulfoxaflor and high dose imidacloprid exposed wasps made fewer correct choices than control wasps. Notably, both visual and olfactory performance were similarly impaired. Wasps treated with high dose imidacloprid were also less likely to complete the learning assay than wasps from other treatment groups. Instead, wasps remained stationary and unmoving in the testing area, consistent with imidacloprid interfering with motor control. Finally, wasps treated with sulfoxaflor were more likely to die in the week after treatment than wasps in the other treatment groups. Our findings demonstrate that sublethal, field-realistic dosages of both neonicotinoid and sulfoximine-based insecticides impair wasp learning and short-term memory may have additional effects on survival and motor functioning. Insecticides have broadly detrimental effects on diverse non-target insects that may influence foraging effectiveness, pollination services, and ecosystem function.
Identification of bees and wasps in trap nests - An identification key for Germany
A central goal in evolutionary biology is to determine the predictability of adaptive genetic changes. Despite many documented cases of convergent evolution at individual loci, little is known about the repeatability of gene family expansions and contractions. To address this void, we examined gene family evolution in the redheaded pine sawfly Neodiprion lecontei , a noneusocial hymenopteran and exemplar of a pine‐specialized lineage evolved from angiosperm‐feeding ancestors. After assembling and annotating a draft genome, we manually annotated multiple gene families with chemosensory, detoxification, or immunity functions before characterizing their genomic distributions and molecular evolution. We find evidence of recent expansions of bitter gustatory receptor, clan 3 cytochrome P450, olfactory receptor, and antimicrobial peptide subfamilies, with strong evidence of positive selection among paralogs in a clade of gustatory receptors possibly involved in the detection of bitter compounds. In contrast, these gene families had little evidence of recent contraction via pseudogenization. Overall, our results are consistent with the hypothesis that in response to novel selection pressures, gene families that mediate ecological interactions may expand and contract predictably. Testing this hypothesis will require the comparative analysis of high‐quality annotation data from phylogenetically and ecologically diverse insect species and functionally diverse gene families. To this end, increasing sampling in under‐sampled hymenopteran lineages and environmentally responsive gene families and standardizing manual annotation methods should be prioritized.
Esta pesquisa teve como objetivo identificar os visitantes florais em seis espécies arbóreas em uma savana amazônica na localidade de Itapuá no município de Vigia de Nazaré, estado do Pará, Foram identificados e numerados dez indivíduos de Byrsonima crassifolia (L.) Kunth (Malpighiaceae), Curatella americana L. (Dilleniaceae), Himatanthus articulatus (Vahl) Woodson (Apocynaceae), Myrcia cuprea (O.Berg) Kiaersk. (Myrtaceae), Myrcia sylvatica (G.Mey) DC. (Myrtaceae) e Ouratea microdonta (Dalzell) Engl. (Ochnaceae). As observações de campo ocorreram quinzenalmente de outubro/2021 a setembro/2022 com a coleta diurna de visitantes florais no período mais chuvoso e menos chuvoso. A identificação ocorreu no Laboratório de Entomologia do Museu Paraense Emilio Goeldi. Foram coletados 1.687 indivíduos pertencentes a nove ordens, quatorze famílias, trinta gêneros e trinta e cinco espécies. Hymenoptera obteve o maior número de espécies (16) seguida por Coleoptera (12) que juntas representaram 80% do total de espécies. Formicidae (11), Curculionidae (5) e Apidae (4) obtiveram o maior número de espécies. Nove famílias registraram apenas uma espécie. Formicidae obteve 60% dos indivíduos coletados (1.013) e distribuídos em onze espécies onde Camponotus crassus e Cephalotes pusillus obtiveram o maior número de indivíduos; Curculionidae registrou cinco espécies e Andranthobius bondari o maior número de indivíduos e Apidae obteve quatro espécies e Trigona spinipes com mais indivíduos. As ordens Hymenoptera e Coleoptera são comuns em áreas de savanas e Camponotus crassus, Cephalotes pusillus, Andranthobius bondari e Trigona spinipes formaram o grupo de possíveis polinizadores como também evidenciaram a presença dessas espécies como indicadoras de degradação por atividades antrópicas. As condições climáticas influenciaram na dinâmica dos visitantes florais, demonstrando que o período chuvoso reduz o número de visitantes florais.
Hymenoptera is an order accounting for a large proportion of species in Insecta, among which Chalcidoidea contains many parasitoid species of biocontrol significance. Currently, some species genomes in Chalcidoidea have been assembled, but the chromosome-level genomes of Aphelinidae are not yet available. Using Illumina, PacBio HiFi and Hi-C technologies, we assembled a genome assembly of Eretmocerus hayati (Aphelinidae, Hymenoptera), a worldwide biocontrol agent of whiteflies, at the chromosome level. The assembled genome size is 692.1 Mb with a contig N50 of 7.96 Mb. After Hi-C scaffolding, the contigs was assembled onto four chromosomes with a mapping rate of > 98%. The scaffold N50 length is 192.5 Mb, and Benchmarking Universal Single-Copy Orthologues (BUSCO) value is 95.9%. The genome contains 370.8 Mb repeat sequences and total of 24471 protein coding genes. P450 gene families were identified and analyzed. In conclusion, our chromosome-level genome assembly provides valuable support for future research on the evolution of parasitoid wasps and the interaction between hosts and parasitoid wasps.
Insects are the most diverse living beings and their ancestors moved from the sea and colonized the land long before the chordates. Phylogenetic and fossil data were combined to detail the patterns of insect evolution. Insects able to flex their wings over the back (Neoptera) correspond to most of the insects and evolved along the major lineages: Polyneoptera, Condylognatha, and Holometabola. Polyneoptera includes Dictyoptera – cockroaches and termites that are omnivorous or wood feeders and the carnivorous mantids – and Orthoptera – the omnivorous crickets and grass-feeding grasshoppers. Condylognatha includes Hemiptera which are the only insects able to live entirely on plant sap such as aphids, cicadas, and spittlebugs; and others like bugs adapted to different diets. Holometabola is the most successful lineage with 86% of the insect species, have complete metamorphosis (larva, pupa, and adult) and comprises the major insect orders: Coleoptera (beetles); Hymenoptera (wasps, ants, and bees); Diptera (mosquitoes and flies); and Lepidoptera (butterflies and moths). Insects of these orders explore the most diverse food sources like other insects, stems, leaves and wood, seeds, keratin (like woolen carpets), pollen, nectar, fungi, and vertebrate blood. The major selective pressures affecting insect guts identified were: (a) adaptations to deal with large amounts of dilute fluid food, (b) adaptations to digesting plant and fungal cells as a result of horizontal transfer of genes from microorganisms and recruitment of lysosomal proteins as digestive enzymes, (c) adaptations to avoiding plant inhibitors by gene expansion and new functionalization, (d) and adaptations to avoiding prolonged exposure to natural enemies and to living in short-lived media by reduction of life span permitted by more efficient midguts.
Recent advancements in next-generation sequencing (NGS) technology and bioinformatics tools have revealed a vast array of viral diversity in insects, particularly RNA viruses. However, our current understanding of insect RNA viruses has primarily focused on hematophagous insects due to their medical importance, while research on the viromes of agriculturally relevant insects remains limited. This comprehensive review aims to address the gap by providing an overview of the diversity of RNA viruses in agricultural pests and beneficial insects within the agricultural ecosystem. Based on the NCBI Virus Database, over eight hundred RNA viruses belonging to 39 viral families have been reported in more than three hundred agricultural insect species. These viruses are predominantly found in the insect orders of Hymenoptera, Hemiptera, Thysanoptera, Lepidoptera, Diptera, Coleoptera, and Orthoptera. These findings have significantly enriched our understanding of RNA viral diversity in agricultural insects. While further virome investigations are necessary to expand our knowledge to more insect species, it is crucial to explore the biological roles of these identified RNA viruses within insects in future studies. This review also highlights the limitations and challenges for the effective virus discovery through NGS and their potential solutions, which might facilitate for the development of innovative bioinformatic tools in the future.
Where and when bees originated and how they dispersed and diversified across ancient continents has remained ambiguous. A new study that combines phylogenetics with fossil data reconstructs the origin and diversification of bees across geological time and space.
In evolutionary terms, life is about reproduction. Yet, in some species, individuals forgo their own reproduction to support the reproductive efforts of others. Social insect colonies for example, can contain up to a million workers that actively cooperate in tasks such as foraging, brood care and nest defence, but do not produce offspring. In such societies the division of labour is pronounced, and reproduction is restricted to just one or a few individuals, most notably the queen(s). This extreme eusocial organisation exists in only a few mammals, crustaceans and insects, but strikingly, it evolved independently up to nine times in the order Hymenoptera (including ants, bees and wasps). Transitions from a solitary lifestyle to an organised society can occur through natural selection when helpers obtain a fitness benefit from cooperating with kin, owing to the indirect transmission of genes through siblings. However, this process, called kin selection, is vulnerable to parasitism and opportunistic behaviours from unrelated individuals. An ability to distinguish kin from non-kin, and to respond accordingly, could therefore critically facilitate the evolution of eusociality and the maintenance of non-reproductive workers. The question of how the hymenop-teran brain has adapted to support this function is therefore a fundamental issue in evolutionary neuroethology. Early neu-roanatomical investigations proposed that social Hymenoptera have expanded integrative brain areas due to selection for increased cognitive capabilities in the context of processing social information. Later studies challenged this assumption and instead pointed to an intimate link between higher social organisation and the existence of developed sensory structures involved in recognition and communication. In particular, chemical signalling of social identity, known to be mediated through cuticular hydrocarbons (CHCs), may have evolved hand in hand with a specialised chemosensory system in Hymenoptera. Here, we compile the current knowledge on this recognition system, from emitted identity signals, to the molecular and neuronal basis of chemical detection, with particular emphasis on its evolutionary history. Finally, we ask whether the evolution of social behaviour in Hymenoptera could have driven the expansion of their complex olfactory system, or whether the early origin and conservation of an olfactory subsystem dedicated to social recognition could explain the abundance of eusocial species in this insect order. Answering this question will require further comparative studies to provide a comprehensive view on lineage-specific adaptations in the olfactory pathway of Hymenoptera.
Bees are the most significant pollinators of flowering plants. This partnership began ca. 120 million years ago, but the uncertainty of how and when bees spread across the planet has greatly obscured investigations of this key mutualism. We present a novel analysis of bee biogeography using extensive new genomic and fossil data to demonstrate that bees originated in Western Gondwana (Africa and South America). Bees likely originated in the Early Cretaceous, shortly before the breakup of Western Gondwana, and the early evolution of any major bee lineage is associated with either the South American or African land masses. Subsequently, bees colonized northern continents via a complex history of vicariance and dispersal. The notable early absences from large landmasses, particularly in Australia and India, have important implications for understanding the assembly of local floras and diverse modes of pollination. How bees spread around the world from their hypothesized Southern Hemisphere origin parallels the histories of numerous flowering plant clades, providing an essential step to studying the evolution of angiosperm pollination syndromes in space and time.
Chouioia cunea Yang 1989 is a parasitic wasp of many lepidopteran insects during their pupal stage, and has been successfully used to control pests such as the fall webworm Hyphantria cunea. Here we reported the chromosome-level genome of C. cunea by using short (MGI-SEQ), long (Oxford Nanopore), chromatin-linked (Hi-C) sequencing reads and transcriptomic data, representing the first chromosome-level genome of parasitic wasps of the family Eulophidae. The total assembly length is 171.99 Mb, containing 6 pesudo-chromosomes with a GC content of 36.89% and the scaffold/contig N50 length of 31.70/26.52 Mb. The BUSCO completeness of the assembly was estimated to be 98.7%. A total of 12,258 protein-coding genes (PCGs), 10,547 3′-UTRs, and 10,671 5′-UTRs were annotated. This high-quality genome is an important step toward a better understanding of the genomes of the Eulophidae (Chalcidoidea), and will serve as a valuable resource for analyses of phylogenetic relationships and the evolution of Hymenoptera.
Mermithid nematodes are obligate invertebrate parasites dating back to the Early Cretaceous. Their fossil record is sparse, especially before the Cenozoic, thus little is known about their early host associations. This study reports 16 new mermithids associated with their insect hosts from mid-Cretaceous Kachin amber, 12 of which include previously unknown hosts. These fossils indicate that mermithid parasitism of invertebrates was already widespread and played an important role in the mid-Cretaceous terrestrial ecosystem. Remarkably, three hosts (bristletails, barklice, and perforissid planthoppers) were previously unknown to be parasitized by mermithids both past and present. Furthermore, our study shows that in contrast to their Cenozoic counterparts, Cretaceous nematodes including mermithids are more abundant in non-holometabolous insects. This result suggests that nematodes had not completely exploited the dominant Holometabola as their hosts until the Cenozoic. This study reveals what appears to be a vanished history of nematodes that parasitized Cretaceous insects.
A review of hexapod systematics in Italian language.
Scarab beetles (Scarabaeidae) are a diverse and ecologically important group of angiosperm-associated insects. As conventionally understood, scarab beetles comprise two major lineages: dung beetles and the phytophagous Pleurosticti. However, previous phylogenetic analyses have not been able to convincingly answer the question whether or not the two lineages form a monophyletic group. Here, we report our results from phylogenetic analyses of more than 4000 genes mined from transcriptomes of more than 50 species of Scarabaeidae and other Scarabaeoidea. Our results provide convincing support for the monophyly of Scarabaeidae, confirming the debated sister group relationship of dung beetles and phytophagous pleurostict scarabs. Supermatrix-based maximum likelihood and multispecies coalescent phylogenetic analyses strongly imply the subfamily Melolonthinae as currently understood being paraphyletic. We consequently suggest various changes in the systematics of Melolonthinae: Sericinae Kirby, 1837 stat. rest. and sensu n. to include the tribes Ablaberini, Diphucephalini and Sericini, and Sericoidinae Erichson, 1847 stat. rest. and sensu n. to include the tribes Automoliini, Heteronychini, Liparetrini, Maechidiini, Phylloto-cini, Scitalini, and Sericoidini. Both subfamilies appear to consistently form a monophyletic sister group to all remaining subfamilies so far included within pleurostict scarabs except Orphninae. Our results represent a major step towards understanding the diversification history of one of the largest angiosperm-associated radiations of beetles.
Background: Orthology characterizes genes of different organisms that arose from a single ancestral gene via speciation, in contrast to paralogy, which is assigned to genes that arose via gene duplication. An accurate orthology assignment is a crucial step for comparative genomic studies. Orthologous genes in two organisms can be identified by applying a so-called reciprocal search strategy, given that complete information of the organisms' gene repertoire is available. In many investigations, however, only a fraction of the gene content of the organisms under study is examined (e.g., RNA sequencing). Here, identification of orthologous nucleotide or amino acid sequences can be achieved using a graph-based approach that maps nucleotide sequences to genes of known orthology. Existing implementations of this approach, however, suffer from algorithmic issues that may cause problems in downstream analyses.
Results: We present a new software pipeline, Orthograph, that addresses and solves the above problems and implements useful features for a wide range of comparative genomic and transcriptomic analyses. Orthograph applies a best reciprocal hit search strategy using profile hidden Markov models and maps nucleotide sequences to the globally best matching cluster of orthologous genes, thus enabling researchers to conveniently and reliably delineate orthologs and paralogs from transcriptomic and genomic sequence data. We demonstrate the performance of our approach on de novo-sequenced and assembled transcript libraries of 24 species of apoid wasps (Hymenoptera: Aculeata) as well as on published genomic datasets.
Conclusion: With Orthograph, we implemented a best reciprocal hit approach to reference-based orthology prediction for coding nucleotide sequences such as RNAseq data. Orthograph is flexible, easy to use, open source and freely available at https://mptrsen.github.io/Orthograph. Additionally, we release 24 de novo-sequenced and assembled transcript libraries of apoid wasp species.
The Aculeata comprises some of the best known Hymenoptera. Traditionally, their sister group has been considered to be the Ichneumo-noidea; however, recent phylogenetic analyses contradict this hypothesis. We evaluate three potential candidates for the sister group of aculeate wasps: Ichneumonoidea, Evanioidea and Trigonaloidea. This is addressed by investigating the internal head anatomy of representatives of the relevant taxa, specifically the tentorium, musculature and glands. One species each of the families Braconidae, Evaniidae, Gasteruptiidae, Aulacidae and Trigonalidae, as well as Sphecidae and Sapygidae as representatives of Aculeata, and Ibaliidae as outgroup is examined. 33 head anatomical characters are mapped on the three competing hypotheses. Aculeata + Evanioidea are corroborated by the presence of a secondary bridge, the presence of a subforaminal cup and the presence of one medial sulcus on the ventral head sclerotisation instead of two sublateral ones. Trigonaloidea + (Aculeata + Evanioidea) is corroborated by the presence of a bent cibarium. The presence of a hypopharyngeal gland, the backwards shift of the origin of the antennal muscles, the loss of the connection of the dorsal tentorial arms with the head capsule and the loss of ventral salivarial dilators are retrieved as synapomorphies of Aculeata. Two hitherto unknown glands, a hypopharyngeal salivary gland in Sphecidae and Sapygidae and a hypopharyngeal-maxillary gland in Evaniidae, are described.
Myriapods, including the diverse and familiar centipedes and millipedes, are one of the dominant terrestrial arthropod groups.
Although molecular evidence has shown that Myriapoda is monophyletic, its internal phylogeny remains contentious and understudied,
especially when compared to those of Chelicerata and Hexapoda. Until now, efforts have focused on taxon sampling (e.g., by
including a handful of genes from many species) or on maximizing matrix size (e.g., by including hundreds or thousands of
genes in just a few species), but a phylogeny maximizing sampling at both levels remains elusive. In this study, we analyzed
forty Illumina transcriptomes representing three of the four myriapod classes (Diplopoda, Chilopoda and Symphyla); twenty-five
transcriptomes were newly sequenced to maximize representation at the ordinal level in Diplopoda and at the family level in
Chilopoda. Ten supermatrices were constructed to explore the effect of several potential phylogenetic biases (e.g., rate of
evolution, heterotachy) at three levels of gene occupancy per taxon (50%, 75% and 90%). Analyses based on maximum likelihood
and Bayesian mixture models retrieved monophyly of each myriapod class, and resulted in two alternative phylogenetic positions
for Symphyla, as sister group to Diplopoda + Chilopoda, or closer to Diplopoda, the latter hypothesis having been traditionally
supported by morphology. Within centipedes, all orders were well supported, but two deep nodes remained in conflict in the
different analyses despite dense taxon sampling at the family level. Relationships among centipede orders in all analyses
conducted with the most complete matrix (90% occupancy) are at odds not only with the sparser but more gene-rich supermatrices
(75% and 50% supermatrices) and with the matrices optimizing phylogenetic informativeness or most conserved genes, but also
with previous hypotheses based on morphology, development or other molecular data sets. Our results indicate that a high percentage
of ribosomal proteins in the most complete matrices, in conjunction with distance from the root, can act in concert to compromise
the estimated relationships within the ingroup. We discuss the implications of these findings in the context of the ever more
prevalent quest for completeness in phylogenomic studies.
A new genus and species of basal cyclostome Braconidae is described and figured from a male preserved in mid-Cretaceous amber from northern Myanmar. Rhetinorhyssalus morticinus Engel, new genus and species, is interesting for its combination of primitive features such as a minute apical costal cell and anal stubs in the forewing, while lacking 2Cu in the hind wing, a putatively derived trait. As such, the genus may represent a lineage diverging from the braconid stem subsequent to many protorhyssalines, while remaining basal relative to generalized cyclostome groups such as Rhyssalinae. In addition, the Late Cretaceous Diospilus allani Brues, in Campanian Canadian amber, is transferred to Diorhyssalus Engel, new genus, and its similarity to Rhetinorhyssalus is discussed. This transfer results in the new combination, Diorhyssalus allani (Brues). Both genera are tentatively considered as subfamily incertae sedis.
Spiders (Order Araneae) are massively abundant generalist arthropod predators that are found in nearly every ecosystem on the planet and have persisted for over 380 million years. Spiders have long served as evolutionary models for studying complex mating and web spinning behaviors, key innovation and adaptive radiation hypotheses, and have been inspiration for important theories like sexual selection by female choice. Unfortunately, past major attempts to reconstruct spider phylogeny typically employing the “usual suspect” genes have been unable to produce a well-supported phylogenetic framework for the entire order. To further resolve spider evolutionary relationships we have assembled a transcriptome-based data set comprising 70 ingroup spider taxa. Using maximum likelihood and shortcut coalescence-based approaches, we analyze eight data sets, the largest of which contains 3,398 gene regions and 696,652 amino acid sites forming the largest phylogenomic analysis of spider relationships produced to date. Contrary to long held beliefs that the orb web is the crowning achievement of spider evolution, ancestral state reconstructions of web type support a phylogenetically ancient origin of the orb web, and diversification analyses show that the mostly ground-dwelling, web-less RTA clade diversified faster than orb weavers. Consistent with molecular dating estimates we report herein, this may reflect a major increase in biomass of non-flying insects during the Cretaceous Terrestrial Revolution 125–90 million years ago favoring diversification of spiders that feed on cursorial rather than flying prey. Our results also have major implications for our understanding of spider systematics. Phylogenomic analyses corroborate several well-accepted high level groupings: Opisthothele, Mygalomorphae, Atypoidina, Avicularoidea, Theraphosoidina, Araneomorphae, Entelegynae, Araneoidea, the RTA clade, Dionycha and the Lycosoidea. Alternatively, our results challenge the monophyly of Eresoidea, Orbiculariae, and Deinopoidea. The composition of the major paleocribellate and neocribellate clades, the basal divisions of Araneomorphae, appear to be falsified. Traditional Haplogynae is in need of revision, as our findings appear to support the newly conceived concept of Synspermiata. The sister pairing of filistatids with hypochilids implies that some peculiar features of each family may in fact be synapomorphic for the pair. Leptonetids now are seen as a possible sister group to the Entelegynae, illustrating possible intermediates in the evolution of the more complex entelegyne genitalic condition, spinning organs and respiratory organs.
The following new taxa of the family Sphecidae are described from Upper Cretaceous Burmese amber: Burmastatus triangularis gen. et sp. nov. and Cirrosphex admirabilis gen. et sp. nov., are members of the new subfamilies Burmastatinae and Cirrosphecinae; Apodolichurus sphaecephalus gen. et sp. nov., A. diaphanous sp. nov., Cretampulex gracilis gen. et sp. nov., and Mendampulex monilicularis gen. et sp. nov. are members of the new ampulicine tribes, Apodolichurini, Cretampulicini, and Mendampulicini, respectively; Prolemistus apiformis gen. et sp. nov. and Cretospilomena familiaris gen. et sp. nov., are placed in the tribe Pemphredonini. Trigonalys pervetus Cockerell, 1917, originally described in the family Trigonalyidae, is moved to the new sphecid genus Trigampulex gen. nov., incerta sedis. The principal differences of the evolution of the wing venation between the Upper Cretaceous and recent sphecid wasps are discussed.
As increasingly large molecular data sets are collected for phylogenomics, the conflicting phylogenetic signal among gene trees poses challenges to resolve some difficult nodes of the Tree of Life. Among these nodes, the phylogenetic position of the honeybees (Apini) within the corbiculate bee group remains controversial, despite its considerable importance for understanding the emergence and maintenance of eusociality. Here we show that this controversy stems in part from pervasive phylogenetic conflicts among GC-rich gene trees. GC-rich genes typically have a high nucleotidic heterogeneity among species, which can induce topological conflicts among gene trees. When retaining only the most GC-homogeneous genes or using a non-homogeneous model of sequence evolution, our analyses reveal a monophyletic group of the three lineages with a eusocial lifestyle (honeybees, bumblebees and stingless bees). These phylogenetic relationships strongly suggest a single origin of eusociality in the corbiculate bees, with no reversal to solitary living in this group. To accurately reconstruct other important evolutionary steps across the Tree of Life, we suggest removing GC-rich and GC-heterogeneous genes from large phylogenomic datasets. Interpreted as a consequence of genome-wide variations in recombination rates, this GC-effect can affect all taxa featuring GC-biased gene conversion, which is common in eukaryotes.
An overview of recent advances in our understanding of the higher phylogeny and classification is presented. Molecular and morphological cladistic and pre-cladistic studies are summarized. A superfamily-level classification of the Hymenoptera is offered to reflect recent advances in our understanding of the phylogenetic relationships of the Hymenoptera. It differs from most recent classifications in the recognition of the Diaprioidea, to include Diapriidae, Monomachidae, and Maamingidae.
Phylogenies are increasingly used in all fields of medical and biological research. Because of the next generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. We present ExaML version 3, a dedicated production-level code for inferring phylogenies on whole-transcriptome and whole-genome alignments using supercomputers.
We introduce several improvements and extensions to ExaML: Extensions of substitution models and supported data types, the integration of a novel load balance algorithm as well as a parallel I/O optimization that significantly improve parallel efficiency, and a production-level implementation for Intel MIC-based hardware platforms.
The code is available under GNU GPL at https://github.com/stamatak/ExaML.
Alexandros.Stamatakis@h-its.org.
© The Author(s) 2015. Published by Oxford University Press.
Spider wasps had long been proposed to originate in the mid-Cretaceous based on the Burmese amber fossil Bryopompilus interfector Engel and Grimaldi, 2006. We performed a morphological examination of this fossil and determined it does not belong to Pompilidae or any other described hymenopteran family. Instead, we place it in the new family Bryopompilidae. The oldest verifiable member of the Pompilidae is from Baltic amber, which suggests the family probably originated in the Eocene, not in the mid-Cretaceous as previously proposed. The origin of spider wasps appears to be correlated with an increase in spider familial diversity in the Cenozoic. We also we add two genera to the extinct pompilid fauna: Tainopompilus gen. nov., and Paleogenia gen. nov., and describe three new species of fossil spider wasps: Anoplius planeta sp. nov., from Dominican amber (Burdigalian to Langhian); Paleogenia wahisi sp. nov., from Baltic amber (Lutetian to Priabonian); and Tainopompilus argentum sp. nov, from Dominican amber (Chattian to Langhian).
Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved.
We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences,
with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent
results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician
[~479 million years ago (Ma)], of insect flight to the Early Devonian (~406 Ma), of major extant lineages to the Mississippian
(~345 Ma), and the major diversification of holometabolous insects to the Early Cretaceous. Our phylogenomic study provides
a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects.
Modern sequencing technology now allows biologists to collect the entirety of molecular evidence for reconstructing evolutionary
trees. We introduce a novel, user-friendly software package engineered for conducting state-of-the-art Bayesian tree inferences
on data sets of arbitrary size. Our software introduces a nonblocking parallelization of Metropolis-coupled chains, modifications
for efficient analyses of data sets comprising thousands of partitions and memory saving techniques. We report on first experiences
with Bayesian inferences at the whole-genome level using the SuperMUC supercomputer and simulated data.
Archaeplastida (= Kingdom Plantae) are primary plastid-bearing organisms that evolved via the endosymbiotic association of a heterotrophic eukaryote host cell and a cyanobacterial endosymbiont approximately 1.4 GYA. Here we present analyses of cyanobacterial and plastid genomes that show strongly conflicting phylogenies based on 75 plastid (or nuclear plastid-targeted) protein-coding genes and their direct translations to proteins. The conflict between genes and proteins is largely robust to the use of sophisticated data- and tree-heterogeneous composition models. However, by using nucleotide ambiguity codes to eliminate synonymous substitutions due to codon-degeneracy, we identify a composition bias, and dependent codon-usage bias, resulting from synonymous substitutions at all third codon positions and first codon positions of leucine and arginine, as the main cause for the conflicting phylogenetic signals.We argue that the protein-coding gene data analyses are likely misleading due to artefacts induced by convergent composition biases at first codon positions of leucine and arginine and at all third codon positions. Our analyses corroborate previous studies based on gene sequence analysis that suggest Cyanobacteria evolved by the early paraphyletic splitting of Gloeobacter and a specific Synechococcus strain (JA33Ab), with all other remaining cyanobacterial groups, including both unicellular and filamentous species, forming the sister-group to the Archaeplastida lineage. In addition, our analyses using better-fitting models suggest (but without statistically strong support) an early divergence of Glaucophyta within Archaeplastida, with the Rhodophyta (red algae) and Viridiplantae (green algae and land plants) forming a separate lineage.
Partitioning involves estimating independent models of molecular evolution for different subsets of sites in a sequence alignment, and has been shown to improve phylogenetic inference. Current methods for estimating best-fit partitioning schemes, however, are only computationally feasible with datasets of less than 100 loci. This is a problem because datasets with thousands of loci are increasingly common in phylogenetics.
We develop two novel methods for estimating best-fit partitioning schemes on large phylogenomic datasets: strict and relaxed hierarchical clustering. These methods use information from the underlying data to cluster together similar subsets of sites in an alignment, and build on clustering approaches that have been proposed elsewhere.
We compare the performance of our methods to each other, and to existing methods for selecting partitioning schemes. We demonstrate that while strict hierarchical clustering has the best computational efficiency on very large datasets, relaxed hierarchical clustering provides scalable efficiency and returns dramatically better partitioning schemes as assessed by common criteria such as AICc and BIC scores.
These two methods provide the best current approaches to inferring partitioning schemes for very large datasets. We provide free open-source implementations of the methods in the PartitionFinder software. We hope that the use of these methods will help to improve the inferences made from large phylogenomic datasets.
Despite considerable progress in systematics, a comprehensive scenario of the evolution of phenotypic characters in the mega-diverse Holometabola based on a solid phylogenetic hypothesis was still missing. We addressed this issue by de novo sequencing transcriptome libraries of representatives of all orders of holometabolan insects (13 species in total) and by using a previously published extensive morphological dataset. We tested competing phylogenetic hypotheses by analyzing various specifically designed sets of amino acid sequence data, using maximum likelihood (ML) based tree inference and Four-cluster Likelihood Mapping (FcLM). By maximum parsimony-based mapping of the morphological data on the phylogenetic relationships we traced evolutionary transformations at the phenotypic level and reconstructed the groundplan of Holometabola and of selected subgroups.
In our analysis of the amino acid sequence data of 1,343 single-copy orthologous genes, Hymenoptera are placed as sister group to all remaining holometabolan orders, i.e., to a clade Aparaglossata, comprising two monophyletic subunits Mecopterida (Amphiesmenoptera + Antliophora) and Neuropteroidea (Neuropterida + Coleopterida). The monophyly of Coleopterida (Coleoptera and Strepsiptera) remains ambiguous in the analyses of the transcriptome data, but appears likely based on the morphological data. Highly supported relationships within Neuropterida and Antliophora are Raphidioptera + (Neuroptera + monophyletic Megaloptera), and Diptera + (Siphonaptera + Mecoptera). ML tree inference and FcLM yielded largely congruent results. However, FcLM, which was applied here for the first time to large phylogenomic supermatrices, displayed additional signal in the datasets that was not identified in the ML trees.
Our phylogenetic results imply that an orthognathous larva belongs to the groundplan of Holometabola, with compound eyes and well-developed thoracic legs, externally feeding on plants or fungi. Ancestral larvae of Aparaglossata were prognathous, equipped with single larval eyes (stemmata), and possibly agile and predacious. Ancestral holometabolan adults likely resembled in their morphology the groundplan of adult neopteran insects. Within Aparaglossata, the adult's flight apparatus and ovipositor underwent strong modifications. We show that the combination of well-resolved phylogenies obtained by phylogenomic analyses and well-documented extensive morphological datasets is an appropriate basis for reconstructing complex morphological transformations and for the inference of evolutionary histories.
Transcriptome sequencing has long been the favored method for quickly and inexpensively obtaining a large number of gene sequences from an organism with no reference genome. Due to the rapid increase in throughputs and decrease in costs of next generation sequencing, RNA-Seq in particular has become the method of choice. However, the very short reads (e.g. 2 × 90 bp paired ends) from next generation sequencing makes de novo assembly to recover complete or full-length transcript sequences an algorithmic challenge.
Here, we present SOAPdenovo-Trans, a de novo transcriptome assembler designed specifically for RNA-Seq. We evaluated its performance on transcriptome datasets from rice and mouse. Using as our benchmarks the known transcripts from these well-annotated genomes (sequenced a decade ago), we assessed how SOAPdenovo-Trans and two other popular transcriptome assemblers handled such practical issues as alternative splicing and variable expression levels. Our conclusion is that SOAPdenovo-Trans provides higher contiguity, lower redundancy, and faster execution.
Source code and user manual are available at http://sourceforge.net/projects/soapdenovotrans/ CONTACT: xieyl@genomics.cn or bgi-soap@googlegroups.com.
The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome, published in 2006, was noted for its bimodal GC content distribution that affected the quality of the assembly in some regions and for fewer genes in the initial gene set (OGSv1.0) compared to what would be expected based on other sequenced insect genomes.
Here, we report an improved honey bee genome assembly (Amel_4.5) with a new gene annotation set (OGSv3.2), and show that the honey bee genome contains a number of genes similar to that of other insect genomes, contrary to what was suggested in OGSv1.0. The new genome assembly is more contiguous and complete and the new gene set includes ~5000 more protein-coding genes, 50% more than previously reported. About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data.
Lessons learned from this genome upgrade have important implications for future genome sequencing projects. Furthermore, the improvements significantly enhance genomic resources for the honey bee, a key model for social behavior and essential to global ecology through pollination.
Character matrices with extensive missing data are frequently used in phylogenomics with potentially detrimental effects on the accuracy and robustness of tree inference. Therefore, many investigators select taxa and genes with high data coverage. Drawbacks of these selections are their exclusive reliance on data coverage without consideration of actual signal in the data which might, thus, not deliver optimal data matrices in terms of potential phylogenetic signal. In order to circumvent this problem, we have developed a heuristics implemented in a software called mare which (1) assesses information content of genes in supermatrices using a measure of potential signal combined with data coverage and (2) reduces supermatrices with a simple hill climbing procedure to submatrices with high total information content. We conducted simulation studies using matrices of 50 taxa x 50 genes with heterogeneous phylogenetic signal among genes and data coverage between 10 - 30 %.
With matrices of 50 taxa x 50 genes with heterogeneous phylogenetic signal among genes and data coverage between 10 - 30 % Maximum Likelihood (ML) tree reconstructions failed to recover correct trees. A selection of a data subset with the herein proposed approach increased the chance to recover correct partial trees more than 10-fold. The selection of data subsets with the herein proposed simple hill climbing procedure performed well either considering the information content or just a simple presence/absence information of genes. We also applied our approach on an empirical data set, addressing questions of vertebrate systematics. With this empirical dataset selecting a data subset with high information content and supporting a tree with high average boostrap support was most successful if information content of genes was considered.
Our analyses of simulated and empirical data demonstrate that sparse supermatrices can be reduced on a formal basis outperforming the usually used simple selections of taxa and genes with high data coverage.
Phylogenetic relationships of the primarily wingless insects are still considered unresolved. Even the most comprehensive phylogenomic studies that addressed this question did not yield congruent results. In order to get a grip on these problems, we here analyzed the sources of incongruence in these phylogenomic studies using an extended transcriptome dataset.Our analyses showed that unevenly distributed missing data can be severely misleading by inflating node support despite the absence of phylogenetic signal. In consequence, only decisive datasets should be used which exclusively comprise data blocks containing all taxa whose relationships are addressed. Additionally, we employed Four-cluster Likelihood-Mapping (FcLM) to measure the degree of congruence among genes of a dataset, as a measure of support alternative to bootstrap. FcLM showed incongruent signal among genes, which in our case is correlated with neither functional class assignment of these genes, nor with model misspecification due to unpartitioned analyses. The herein analyzed dataset is the currently largest dataset covering primarily wingless insects, but failed to elucidate their interordinal phylogenetic relationships. While this is unsatisfying from a phylogenetic perspective, we try to show that the analyses of structure and signal within phylogenomic data can protect us from biased phylogenetic inferences due to analytical artefacts.
An updated classification of the order Hymenoptera is provided with the current numbers of genera and species described so far specified. The order is composed of 2 suborders, 27 superfamilies, 132 families, 8423 extant genera with an additional 685 extinct genera. Considered one of the most species-rich insects orders a total of 153088 extant species have been described, in addition to 2429 extinct species.
Insects and their arthropod relatives including mites, spiders, and crustaceans play major roles in the world’s terrestrial,
aquatic, and marine ecosystems. Arthropods compete with humans for food and transmit devastating diseases. They also comprise
the most diverse and successful branch of metazoan evolution, with millions of extant species. Here, we describe an international
effort to guide arthropod genomic efforts, from species prioritization to methodology and informatics. The 5000 arthropod
genomes initiative (i5K) community met formally in 2012 to discuss a roadmap for sequencing and analyzing 5000 high-priority
arthropods and is continuing this effort via pilot projects, the development of standard operating procedures, and training
of students and career scientists. With university, governmental, and industry support, the i5K Consortium aspires to deliver
sequences and analytical tools for each of the arthropod branches and each of the species having beneficial and negative effects
on humankind.
Previous molecular analyses of higher hymenopteran relationships have largely been based on subjectively aligned ribosomal sequences (18S and 28S). Here, we reanalyze the 18S and 28S data (unaligned about 4.4 kb) using an objective and a semi-objective alignment approach, based on MAFFT and BAli-Phy, respectively. Furthermore, we present the first analyses of a substantial protein-coding data set (4.6 kb from one mitochondrial and four nuclear genes). Our results indicate that previous studies may have suffered from inflated support values due to subjective alignment of the ribosomal sequences, but apparently not from significant biases. The protein data provide independent confirmation of several earlier results, including the monophyly of non-xyelid hymenopterans, Pamphilioidea + Unicalcarida, Unicalcarida, Vespina, Apocrita, Proctotrupomorpha and core Proctotrupomorpha. The protein data confirm that Aculeata are nested within a paraphyletic Evaniomorpha, but cast doubt on the monophyly of Evanioidea. Combining the available morphological, ribosomal and protein-coding data, we examine the total-evidence signal as well as congruence and conflict among the three data sources. Despite an emerging consensus on many higher-level hymenopteran relationships, several problems remain unresolved or contentious, including rooting of the hymenopteran tree, relationships of the woodwasps, placement of Stephanoidea and Ceraphronoidea, and the sister group of Aculeata.
A new subfamily, a new genus and a new species of Bethylidae are described and illustrated from a single individual in Early Cretaceous amber from central Lebanon. Lancepyrinae subfam. nov. represented by Lancepyris opertus gen. and sp. nov. present a mosaic of features common among several bethylid subfamilies. The new taxon is easily distinguished from related taxa mainly by the forewing venation, which has an unusual combination of closed lanceolate marginal cell, Rs+M tubular and well pigmented and M+RS angled. Phylogenetic analysis including indicates that Lancepyris opertus gen. and sp. nov. is a sister group of all subfamilies that have Coleoptera as hosts. A checklist of the 45 known fossil bethylid species is provided.
Non homogeneous processes and, in particular, base compositional non-stationarity have long been recognized as a critical source of systematic error. But only a small fraction of current molecular systematic studies methodically examine and effectively account for the potentially confounding effect of non-stationarity. The problem is especially overlooked in multi-locus or phylogenomic scale analyses, in part because no efficient tools exist to accommodate base composition heterogeneity in large data sets. We present a detailed analysis of a data set with 20 genes and 214 taxa to study the phylogeny of flatfishes (Pleuronectiformes) and their position among percomorphs. Most genes vary significantly in base composition among taxa and fail to resolve flatfish monophyly and other emblematic groups, suggesting that non-stationarity may be causing systematic error. We show a strong association between base compositional bias and topological discordance among individual gene partitions and their inferred trees. Phylogenetic methods applying non-homogeneous models to accommodate non-stationarity have relatively minor effect to reduce gene tree discordance, suggesting that available computer programs applying these methods do not scale up efficiently to the data set of modest size analyzed in this study. By comparing phylogenetic trees obtained with species-tree (STAR) and concatenation approaches, we show that gene-tree discordance in our data set is most likely due to base compositional biases than to incomplete lineage sorting. Multi-locus analyses suggest that the combined phylogenetic signal from all loci in a concatenated data set overcomes systematic biases induced by non-stationarity at each partition. Finally, relationships among flatfishes and their relatives are discussed in the light of these results. We find support for the monophyly of flatfishes and confirm findings from previous molecular phylogenetic studies suggesting their close affinity with several carangimorph groups (i.e., jack and allies, barracuda, archerfish, billfish and swordfish, threadfin, moonfish, beach salmon, and snook and barramundi).
Reliable estimates on the ages of the major bee clades are needed to further understand the evolutionary history of bees and their close association with flowering plants. Divergence times have been estimated for a few groups of bees, but no study has yet provided estimates for all major bee lineages. To date the origin of bees and their major clades, we first perform a phylogenetic analysis of bees including representatives from every extant family, subfamily and almost all tribes, using sequence data from seven genes. We then use this phylogeny to place 14 time calibration points based on information from the fossil record for an uncorrelated relaxed clock divergence time analysis taking into account uncertainties in phylogenetic relationships and the fossil record. We explore the effect of placing a hard upper age bound near the root of the tree and the effect of different topologies on our divergence time estimates. We estimate that crown bees originated approximately 123 Ma (million years ago) (113-132 Ma), concurrently with the origin or diversification of the eudicots, a group comprising 75 per cent of angiosperm species. All of the major bee clades are estimated to have originated during the Middle to Late Cretaceous, which is when angiosperms became the dominant group of land plants.
We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including
options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained
alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples
to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to
clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
The concept of orthology provides a foundation for formulating hypotheses on gene and genome evolution, and thus forms the cornerstone of comparative genomics, phylogenomics and metagenomics. We present the update of OrthoDB-the hierarchical catalog of orthologs (http://www.orthodb.org). From its conception, OrthoDB promoted delineation of orthologs at varying resolution by explicitly referring to the hierarchy of species radiations, now also adopted by other resources. The current release provides comprehensive coverage of animals and fungi representing 252 eukaryotic species, and is now extended to prokaryotes with the inclusion of 1115 bacteria. Functional annotations of orthologous groups are provided through mapping to InterPro, GO, OMIM and model organism phenotypes, with cross-references to major resources including UniProt, NCBI and FlyBase. Uniquely, OrthoDB provides computed evolutionary traits of orthologs, such as gene duplicability and loss profiles, divergence rates, sibling groups, and now extended with exon-intron architectures, syntenic orthologs and pa