Enriching the ant tree of life: enhanced UCE bait set for genome‐scale phylogenetics of ants and other Hymenoptera

Ecological diversification preceded geographical expansion during the evolutionary radiation of Cataglyphis desert ants

Biological diversity often arises as organisms adapt to new ecological conditions (i.e., ecological opportunities) or colonize suitable areas (i.e., spatial opportunities). Cases of geographical expansion followed by local ecological divergence are well described; they result in clades comprising ecologically heterogeneous subclades. Here, we show that the desert ant genus Cataglyphis likely originated in open grassland habitats in the Middle East ∼18 million years ago and became a taxon of diverse species specializing in prey of different masses. The genus then colonized the Mediterranean Basin around 9 million years ago. The result was the rapid accumulation of species, and the appearance of local assemblages containing species from different lineages that still displayed ancestral foraging specialties. These findings highlight that, in Cataglyphis, ecological diversification preceded geographical expansion, resulting in a clade composed of ecologically homogeneous subclades.

Machine learning approaches delimit cryptic taxa in a previously intractable species complex

Cryptic species are not diagnosable via morphological criteria, but can be detected through analysis of DNA sequences. A number of methods have been developed for identifying species based on genetic data; however, these methods are prone to over-splitting taxa with extreme population structure, such as dispersal-limited organisms. Machine learning methodologies have the potential to overcome this challenge. Here, we apply such approaches, using a large dataset generated through hybrid target enrichment of ultraconserved elements (UCEs). Our study taxon is the Aoraki denticulata species complex, a lineage of extremely low-dispersal arachnids endemic to the South Island of Aotearoa New Zealand. This group of mite harvesters has been the subject of previous species delimitation studies using smaller datasets generated through Sanger sequencing and analytical approaches that rely on multispecies coalescent models and barcoding gap discovery. Those analyses yielded a number of putative cryptic species that seems unrealistic and extreme, based on what we know about species' geographic ranges and genetic diversity in non-cryptic mite harvesters. We find that machine learning approaches, on the other hand, identify cryptic species with geographic ranges that are similar to those seen in other morphologically diagnosable mite harvesters in Aotearoa New Zealand's South Island. We performed both unsupervised and supervised machine learning analyses, the latter with training data drawn either from animals broadly (vagile and non-vagile) or from a custom training dataset from dispersal-limited harvesters. We conclude that applying machine learning approaches to the analysis of UCE-derived genetic data is an effective method for delimiting species in complexes of low-vagility cryptic species, and that the incorporation of training data from biologically relevant analogues can be critically informative.

Mitogenome architecture supports the non-monophyly of the cosmopolitan parasitoid wasp subfamily Doryctinae (Hymenoptera: Braconidae) recovered by nuclear and mitochondrial phylogenomics

Mitochondrial DNA gene organisation is an important source of phylogenetic information for various metazoan taxa at different evolutionary timescales, though this has not been broadly tested for all insect groups nor within a phylogenetic context. The cosmopolitan subfamily Doryctinae is a highly diverse group of braconid wasps mainly represented by ectoparasitoids of xylophagous beetle larvae. Previous molecular studies based on Sanger and genome-wide (ultraconserved elements, UCE; and mitochondrial genomes) sequence data have recovered a non-monophyletic Doryctinae, though the relationships involved have always been weakly supported. We characterised doryctine mitogenomes and conducted separate phylogenetic analyses based on mitogenome and UCE sequence data of ~100 representative doryctine genera to assess the monophyly and higher-level classification of the subfamily. We identified rearrangements of mitochondrial transfer RNAs (tRNAs) that support a non-monophyletic Doryctinae consisting of two separate non-related clades with strong geographic structure ('New World' and 'Old World' clades). This geographic structure was also consistently supported by the phylogenetic analyses preformed with mitogenome and UCE sequence data. These results highlight the utility of the mitogenome gene rearrangements as a potential source of phylogenetic information at different evolutionary timescales.

Phylogenomics of the geometrid tribe Palyadini (Lepidoptera: Geometridae) reveals contrasting patterns of phylogenetic signal in wing colour characters

Next generation sequencing techniques currently represent a practical and efficient way to infer robust evolutionary hypotheses. Palyadini is a small Neotropical tribe of geometrid moths composed of six genera that feature strikingly colourful wings. Here, we investigated patterns of evolution and amount of phylogenetic signal contained in various colour characters featured in the wings of members of this tribe by (i) inferring a robust phylogenetic hypothesis using ultraconserved elements (UCEs), and afterwards, (ii) mapping the morphological characters onto the molecular topology under a parsimonious ancestral character optimization. Our matrix, obtained with 60% completeness, includes 754 UCE loci and 73 taxa (64 ingroup, nine outgroup). Maximum likelihood and parsimony generated largely identical topologies with strongly supported nodes, except for one node inside the genus Opisthoxia. According to our topology, most wing colour characters are reconstructed as homoplastic, particularly at the tribe level, but five of the seven provide evidence supporting common ancestry at the genus level. Our results emphasize, once again, that no character system is infallible, and that more research is necessary to take our understanding of the evolution of wing colour in moths to a level comparable with the knowledge we have for butterflies.

Out of the desert: Paleoclimatic changes drove the diversification of arid-adapted Ocymyrmex ants in southern Africa

A highly endemic ant fauna is found in the arid regions of southern Africa, including species in the genus Ocymyrmex. This genus of ants has higher species richness in the western arid regions of southern Africa compared to tropical and subtropical parts of the continent. The processes that have produced these patterns of diversity and distribution of arid adapted ants in southern Africa have never been investigated. The diversification of many other taxa in the region has been associated with past climate fluctuations that occurred during the Miocene epoch. In this study, the nature and timing of historical processes that may have led to the diversification within Ocymyrmex were assessed. We hypothesized that past climate oscillations, characterized by long periods of aridification, have driven the current distribution of Ocymyrmex species that resulted in the highest species richness of the genus in the Deserts & xeric shrublands biome in southern Africa. Ninety-four Ocymyrmex worker specimens from Botswana, Kenya, Namibia, South Africa, Tanzania and Zimbabwe, representing 21 currently described species and six morphospecies, were included in a phylogenomic analysis. Phylogenies for the genus, based on next generation sequencing data from ultraconserved elements, were inferred using Maximum Likelihood, and a dating analysis was performed using secondary age estimates as calibration points. A distribution database of Ocymyrmex records was used to assign species ranges, which were then coded according to major biomes in southern Africa and used as input for biogeographical analysis. We explored the phylogenomic relationships of Ocymyrmex and analysed these within a biogeographical and paleoclimatic framework to disentangle the potential processes responsible for diversification in this group. Dating analyses estimated that the crown age of Ocymyrmex dates to the Oligocene, around 32 Ma. Diversification within this group occurred between the mid-Miocene (∼12.5 Ma) and Pleistocene (∼2 Ma). Our biogeographic analyses suggest that Ocymyrmex species originated in the south-western region of southern Africa, which is now part of the Deserts & xeric shrublands biome and diversified into eastern subtropical areas during the Pliocene. Paleoclimatic changes resulting in increased aridity during the Miocene likely drove the diversification of the genus Ocymyrmex. It is most likely that the diversification of grasslands, because of historical climate change, facilitated the diversification of these ants to the eastern parts of southern Africa when open grasslands replaced forests during the early Miocene.

Ant backbone phylogeny resolved by modelling compositional heterogeneity among sites in genomic data

Ants are the most ubiquitous and ecologically dominant arthropods on Earth, and understanding their phylogeny is crucial for deciphering their character evolution, species diversification, and biogeography. Although recent genomic data have shown promise in clarifying intrafamilial relationships across the tree of ants, inconsistencies between molecular datasets have also emerged. Here I re-examine the most comprehensive published Sanger-sequencing and genome-scale datasets of ants using model comparison methods that model among-site compositional heterogeneity to understand the sources of conflict in phylogenetic studies. My results under the best-fitting model, selected on the basis of Bayesian cross-validation and posterior predictive model checking, identify contentious nodes in ant phylogeny whose resolution is modelling-dependent. I show that the Bayesian infinite mixture CAT model outperforms empirical finite mixture models (C20, C40 and C60) and that, under the best-fitting CAT-GTR + G4 model, the enigmatic Martialis heureka is sister to all ants except Leptanillinae, rejecting the more popular hypothesis supported under worse-fitting models, that place it as sister to Leptanillinae. These analyses resolve a lasting controversy in ant phylogeny and highlight the significance of model comparison and adequate modelling of among-site compositional heterogeneity in reconstructing the deep phylogeny of insects.

Systematic revision of the ant subfamily Leptanillinae (Hymenoptera, Formicidae)

The genus-level taxonomy of the ant subfamily Leptanillinae (Hymenoptera: Formicidae) is here revised, with the aim of delimiting genus-level taxa that are reciprocally monophyletic and readily diagnosable based upon all adult forms. This new classification reflects molecular phylogenetics and is informed by joint consideration of both male and worker morphology. Three valid genera are recognized in the Leptanillinae: Opamyrma, Leptanilla (= Scyphodonsyn. nov., Phaulomyrma, Leptomesites, Noonillasyn. nov., Yavnellasyn. nov.), and Protanilla (= Anomalomyrmasyn. nov., Furcotanilla). Leptanilla and Protanilla are further divided into informal, monophyletic species groups. Synoptic diagnoses are provided for all genera and informal supraspecific groupings. In addition, worker-based keys to all described species within the Leptanillinae for which the worker caste is known are provided; and male-based keys to all species for which males are known, plus undescribed male morphospecies for which molecular data are published. The following species are described as new: Protanillawallaceisp. nov., Leptanillaacherontiasp. nov., Leptanillabelantansp. nov., Leptanillabethyloidessp. nov., and Leptanillanajaphallasp. nov.

The rediscovery of the putative ant social parasite Manica parasitica syn. nov. (Hymenoptera: Formicidae) reveals an unexpected endoparasite syndrome

Parasitism is ubiquitous across the tree of life, and parasites comprise approximately half of all animal species. Social insect colonies attract many pathogens, endo- and ectoparasites, and are exploited by social parasites, which usurp the social environment of their hosts for survival and reproduction. Exploitation by parasites and pathogens versus social parasites may cause similar behavioural and morphological modifications of the host. Ants possess two overlapping syndromes: the endo- and social parasite syndromes. We rediscovered two populations of the putative social parasite Manica parasitica in the Sierra Nevada, and tested the hypothesis that M. parasitica is an independently evolving social parasite. We evaluated traits used to discriminate M. parasitica from its host Manica bradleyi, and examined the morphology of M. parasitica in the context of ant parasitic syndromes. We find that M. parasitica is not a social parasite. Instead, M. parasitica represents cestode-infected M. bradleyi. We propose that M. parasitica should be regarded as a junior synonym of M. bradleyi. Our results emphasize that an integrative approach is essential for unravelling the complex life histories of social insects and their symbionts.

Novel tRNA Gene Rearrangements in the Mitochondrial Genomes of Poneroid Ants and Phylogenetic Implication of Paraponerinae (Hymenoptera: Formicidae)

Ants (Formicidae) are the most diverse eusocial insects in Hymenoptera, distributed across 17 extant subfamilies grouped into 3 major clades, the Formicoid, Leptanilloid, and Poneroid. While the mitogenomes of Formicoid ants have been well studied, there is a lack of published data on the mitogenomes of Poneroid ants, which requires further characterization. In this study, we first present three complete mitogenomes of Poneroid ants: Paraponera clavata, the only extant species from the subfamily Paraponerinae, and two species (Harpegnathos venator and Buniapone amblyops) from the Ponerinae subfamily. Notable novel gene rearrangements were observed in the new mitogenomes, located in the gene blocks CR-trnM-trnI-trnQ-ND2, COX1-trnK-trnD-ATP8, and ND3-trnA-trnR-trnN-trnS1-trnE-trnF-ND5. We reported the duplication of tRNA genes for the first time in Formicidae. An extra trnQ gene was identified in H. venator. These gene rearrangements could be explained by the tandem duplication/random loss (TDRL) model and the slipped-strand mispairing model. Additionally, one large duplicated region containing tandem repeats was identified in the control region of P. clavata. Phylogenetic analyses based on protein-coding genes and rRNA genes via maximum likelihood and Bayes methods supported the monophyly of the Poneroid clade and the sister group relationship between the subfamilies Paraponerinae and Amblyoponinae. However, caution is advised in interpreting the positions of Paraponerinae due to the potential artifact of long-branch attraction.

An Opiliones-specific ultraconserved element probe set with a near-complete family-level phylogeny

Sequence capture of ultraconserved elements (UCEs) has transformed molecular systematics across many taxa, with arachnids being no exception. The probe set available for Arachnida has been repeatedly used across multiple arachnid lineages and taxonomic levels, however more specific probe sets for spiders have demonstrated that more UCEs can be recovered with higher probe specificity. In this study, we develop an Opiliones-specific UCE probe set targeting 1915 UCEs using a combination of probes designed from genomes and transcriptomes, as well as the most useful probes from the Arachnida probe set. We demonstrate the effectiveness of this probe set across Opiliones with the most complete family-level phylogeny made to date, including representatives from 61 of 63 currently described families. We also test UCE recovery from historical specimens with degraded DNA, examine population-level data sets, and assess "backwards compatibility" with samples hybridized with the Arachnida probe set. The resulting phylogenies - which include specimens hybridized using both the Opiliones and Arachnida probe sets, historical specimens, and transcriptomes - are largely congruent with previous multi-locus and phylogenomic analyses. The probe set is also "backwards compatible", increasing the number of loci obtained in samples previously hybridized with the Arachnida probe set, and shows high utility down to shallow population-level divergences. This probe set has the potential to further transform Opiliones molecular systematics, resolving many long-standing taxonomic issues plaguing this lineage.

Phylogeny of Rhynchium and Its Related Genera (Hymenoptera: Eumeninae) Based on Universal Single-Copy Orthologs and Ultraconserved Elements

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.

The evolutionary history of bees in time and space

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.

Phylogeny of the carpenter bees (Apidae: Xylocopinae) highlights repeated evolution of sociality

Many groups of animals have evolved social behaviours in different forms, from intimate familial associations to the complex eusocial colonies of some insects. The subfamily Xylocopinae, including carpenter bees and their relatives, is a diverse clade exhibiting a wide range of social behaviours, from solitary to obligate eusociality with distinct morphological castes, making them ideal focal taxa in studying the evolution of sociality. We used ultraconserved element data to generate a broadly sampled phylogeny of the Xylocopinae, including several newly sequenced species. We then conducted ancestral state reconstructions on the evolutionary history of sociality in this group under multiple coding models. Our results indicate solitary origins for the Xylocopinae with multiple transitions to sociality across the tree and subsequent reversals to solitary life, demonstrating the lability and dynamic nature of social evolution in carpenter bees. Ultimately, this work clarifies the evolutionary history of the Xylocopinae, and expands our understanding of independent origins and gains and losses of social complexity.

The First Complete Mitochondrial Genome of the Genus Pachycondyla (Formicidae, Ponerinae) and Insights into the Phylogeny of Ants

Ants are the standout group among eusocial insects in terms of their exceptional species richness and ecological dominance. The phylogenetic relationships among the group remain elusive. Mitochondrial genome sequences, as a kind of molecular marker, have been widely utilized in the phylogenetic analysis of insects. However, the number of ant mitogenomes published is still very limited. In this study, we utilized next-generation sequencing to determine the complete mitogenome of Pachycondyla annamita (Formicidae, Ponerinae). This is the first mitogenome from the genus Pachycondyla. Two gene rearrangements were identified in the mitogenome, the transposition of trnQ and trnM and the transposition of trnV and rrnS. The secondary structures of tRNAs were predicted. The tRNA genes trnR and trnS1 lacked the dihydrouridine (DHU) arm, and the trnE lacked the TΨC (T) arm. Phylogenetic analyses of the mitochondrial protein-coding genes under maximum likelihood (ML) and Bayesian inference (BI) criteria resulted in conflicting hypotheses. BI analysis using amino acid data with the site-heterogeneous mixture model produced a tree topology congruent with previous studies. The Formicidae was subdivided into two main clades, namely the "poneroid" clade and the "formicoid" clade. A sister group relationship between Myrmicinae and Formicinae was recovered within the "formicoid" clade.

Low hybridization temperatures improve target capture success of invertebrate loci: a case study of leaf-footed bugs (Hemiptera: Coreoidea)

Target capture is widely used in phylogenomic, ecological and functional genomic studies. Bait sets that allow capture from a diversity of species can be advantageous, but high-sequence divergence from baits can limit yields. Currently, only four experimental comparisons of a critical target capture parameter, hybridization temperature, have been published. These have been in vertebrates, where bait divergences are typically low, and none include invertebrates where bait-target divergences may be higher. Most invertebrate capture studies use a fixed, high hybridization temperature to maximize the proportion of on-target data, but many report low locus recovery. Using leaf-footed bugs (Hemiptera: Coreoidea), we investigate the effect of hybridization temperature on capture success of ultraconserved elements targeted by (i) baits developed from divergent hemipteran genomes and (ii) baits developed from less divergent coreoid transcriptomes. Lower temperatures generally resulted in more contigs and improved recovery of targets despite a lower proportion of on-target reads, lower read depth and more putative paralogues. Hybridization temperatures had less of an effect when using transcriptome-derived baits, which is probably due to lower bait-target divergences and greater bait tiling density. Thus, accommodating low hybridization temperatures during target capture can provide a cost-effective, widely applicable solution to improve invertebrate locus recovery.

Biogeography and evolution of social parasitism in Australian Myrmecia bulldog ants revealed by phylogenomics

Studying the historical biogeography and life history transitions from eusocial colony life to social parasitism contributes to our understanding of the evolutionary mechanisms generating biodiversity in eusocial insects. The ants in the genus Myrmecia are a well-suited system for testing evolutionary hypotheses about how their species diversity was assembled through time because the genus is endemic to Australia with the single exception of the species M. apicalis inhabiting the Pacific Island of New Caledonia, and because at least one social parasite species exists in the genus. However, the evolutionary mechanisms underlying the disjunct biogeographic distribution of M. apicalis and the life history transition(s) to social parasitism remain unexplored. To study the biogeographic origin of the isolated, oceanic species M. apicalis and to reveal the origin and evolution of social parasitism in the genus, we reconstructed a comprehensive phylogeny of the ant subfamily Myrmeciinae. We utilized Ultra Conserved Elements (UCEs) as molecular markers to generate a comprehensive molecular genetic dataset consisting of 2,287 loci per taxon on average for 66 out of the 93 known Myrmecia species as well as for the sister lineage Nothomyrmecia macrops and selected outgroups. Our time-calibrated phylogeny inferred that: (i) stem Myrmeciinae originated during the Paleocene ∼58 Ma ago; (ii) the current disjunct biogeographic distribution of M. apicalis was driven by long-distance dispersal from Australia to New Caledonia during the Miocene ∼14 Ma ago; (iii) the single social parasite species, M. inquilina, evolved directly from one of the two known host species, M. nigriceps, in sympatry via the intraspecific route of social parasite evolution; and (iv) 5 of the 9 previously established taxonomic species groups are non-monophyletic. We suggest minor changes to reconcile the molecular phylogenetic results with the taxonomic classification. Our study enhances our understanding of the evolution and biogeography of Australian bulldog ants, contributes to our knowledge about the evolution of social parasitism in ants, and provides a solid phylogenetic foundation for future inquiries into the biology, taxonomy, and classification of Myrmeciinae.

Ant venoms contain vertebrate-selective pain-causing sodium channel toxins

Stings of certain ant species (Hymenoptera: Formicidae) can cause intense, long-lasting nociception. Here we show that the major contributors to these symptoms are venom peptides that modulate the activity of voltage-gated sodium (Na_V) channels, reducing their voltage threshold for activation and inhibiting channel inactivation. These peptide toxins are likely vertebrate-selective, consistent with a primarily defensive function. They emerged early in the Formicidae lineage and may have been a pivotal factor in the expansion of ants.

A novel probe set for the phylogenomics and evolution of RTA spiders

Spiders are important models for evolutionary studies of web building, sexual selection and adaptive radiation. The recent development of probes for UCE (ultra-conserved element)-based phylogenomic studies has shed light on the phylogeny and evolution of spiders. However, the two available UCE probe sets for spider phylogenomics (Spider and Arachnida probe sets) have relatively low capture efficiency within spiders, and are not optimized for the retrolateral tibial apophysis (RTA) clade, a hyperdiverse lineage that is key to understanding the evolution and diversification of spiders. In this study, we sequenced 15 genomes of species in the RTA clade, and using eight reference genomes, we developed a new UCE probe set (41 845 probes targeting 3802 loci, labelled as the RTA probe set). The performance of the RTA probes in resolving the phylogeny of the RTA clade was compared with the Spider and Arachnida probes through an in-silico test on 19 genomes. We also tested the new probe set empirically on 28 spider species of major spider lineages. The results showed that the RTA probes recovered twice and four times as many loci as the other two probe sets, and the phylogeny from the RTA UCEs provided higher support for certain relationships. This newly developed UCE probe set shows higher capture efficiency empirically and is particularly advantageous for phylogenomic and evolutionary studies of RTA clade and jumping spiders.

Target enrichment of long open reading frames and ultraconserved elements to link microevolution and macroevolution in non-model organisms

Despite the increasing accessibility of high-throughput sequencing, obtaining high-quality genomic data on non-model organisms without proximate well-assembled and annotated genomes remains challenging. Here, we describe a workflow that takes advantage of distant genomic resources and ingroup transcriptomes to select and jointly enrich long open reading frames (ORFs) and ultraconserved elements (UCEs) from genomic samples for integrative studies of microevolutionary and macroevolutionary dynamics. This workflow is applied to samples of the African unionid bivalve tribe Coelaturini (Parreysiinae) at basin and continent-wide scales. Our results indicate that ORFs are efficiently captured without prior identification of intron-exon boundaries. The enrichment of UCEs was less successful, but nevertheless produced substantial data sets. Exploratory continent-wide phylogenetic analyses with ORF supercontigs (>515,000 parsimony informative sites) resulted in a fully resolved phylogeny, the backbone of which was also retrieved with UCEs (>11,000 informative sites). Variant calling on ORFs and UCEs of Coelaturini from the Malawi Basin produced ~2000 SNPs per population pair. Estimates of nucleotide diversity and population differentiation were similar for ORFs and UCEs. They were low compared to previous estimates in molluscs, but comparable to those in recently diversifying Malawi cichlids and other taxa at an early stage of speciation. Skimming off-target sequence data from the same enriched libraries of Coelaturini from the Malawi Basin, we reconstructed the maternally-inherited mitogenome, which displays the gene order inferred for the most recent common ancestor of Unionidae. Overall, our workflow and results provide exciting perspectives for integrative genomic studies of microevolutionary and macroevolutionary dynamics in non-model organisms.

Key innovations and the diversification of Hymenoptera

The order Hymenoptera (wasps, ants, sawflies, and bees) represents one of the most diverse animal lineages, but whether specific key innovations have contributed to its diversification is still unknown. We assembled the largest time-calibrated phylogeny of Hymenoptera to date and investigated the origin and possible correlation of particular morphological and behavioral innovations with diversification in the order: the wasp waist of Apocrita; the stinger of Aculeata; parasitoidism, a specialized form of carnivory; and secondary phytophagy, a reversal to plant-feeding. Here, we show that parasitoidism has been the dominant strategy since the Late Triassic in Hymenoptera, but was not an immediate driver of diversification. Instead, transitions to secondary phytophagy (from parasitoidism) had a major influence on diversification rate in Hymenoptera. Support for the stinger and the wasp waist as key innovations remains equivocal, but these traits may have laid the anatomical and behavioral foundations for adaptations more directly associated with diversification.

Pollinator and host sharing lead to hybridization and introgression in Panamanian free-standing figs, but not in their pollinator wasps

Obligate pollination mutualisms, in which plant and pollinator lineages depend on each other for reproduction, often exhibit high levels of species specificity. However, cases in which two or more pollinator species share a single host species (host sharing), or two or more host species share a single pollinator species (pollinator sharing), are known to occur in current ecological time. Further, evidence for host switching in evolutionary time is increasingly being recognized in these systems. The degree to which departures from strict specificity differentially affect the potential for hybridization and introgression in the associated host or pollinator is unclear. We addressed this question using genome-wide sequence data from five sympatric Panamanian free-standing fig species (Ficus subgenus Pharmacosycea, section Pharmacosycea) and their six associated fig-pollinator wasp species (Tetrapus). Two of the five fig species, F. glabrata and F. maxima, were found to regularly share pollinators. In these species, ongoing hybridization was demonstrated by the detection of several first-generation (F1) hybrid individuals, and historical introgression was indicated by phylogenetic network analysis. By contrast, although two of the pollinator species regularly share hosts, all six species were genetically distinct and deeply divergent, with no evidence for either hybridization or introgression. This pattern is consistent with results from other obligate pollination mutualisms, suggesting that, in contrast to their host plants, pollinators appear to be reproductively isolated, even when different species of pollinators mate in shared hosts.

Testing the systematic status of Homalictus and Rostrohalictus with weakened cross-vein groups within Halictini (Hymenoptera: Halictidae) using low-coverage whole-genome sequencing

The halictid genus Lasioglossum, as one of the most species-rich bee groups with persistently contentious subgeneric boundaries, is one of the most challenging bee groups from a systematic standpoint. An enduring question is the relationship of Lasioglossum and Homalictus, whether all halictine bees with weakened distal wing venation comprise one or multiple genera. Here, we analyzed the phylogenetic relationships among the subgroups within Lasioglossum s.l. based on thousands of single-copy orthologs and ultraconserved elements, which were extracted from 23 newly sequenced low-coverage whole genomes alongside a published genome (22 ingroups plus 2 outgroups). Both marker sets provided consistent results across maximum likelihood and coalescent-based species tree approaches. The phylogenetic and topology test results show that the Lasioglossum and Hemihalictus series are reciprocally monophyletic and Homalictus and Rostrohalictus are valid subgenera of Lasioglossum. Consequently, we lower Homalictus to subgenus status within Lasioglossum again, and we also raise Rostrohalictus to subgenus status from its prior synonymy with subgenus Hemihalictus. Lasioglossum przewalskyi is also transferred to the subgenus Hemihalictus. Ultimately, we redefine Lasioglossum to include all halictine bees with weakened distal wing venation.

Species and genetic diversity relationships in benthic macroinvertebrate communities along a salinity gradient

BACKGROUND

Species- and genetic diversity can change in parallel, resulting in a species-genetic diversity correlation (SGDC) and raising the question if the same drivers influence both biological levels of diversity. The SGDC can be either positive or negative, depending on whether the species diversity and the genetic diversity of the measured species respond in the same or opposite way to drivers. Using a traditional species diversity approach together with ultra-conserved elements and high throughput sequencing, we evaluated the SGDCs in benthic macrofauna communities in the Baltic Sea, a geologically young brackish water sea characterised by its steep salinity gradient and low species richness. Assessing SGDCs from six focal marine invertebrate species from different taxonomic groups and with differing life histories and ecological functions on both a spatial and temporal scale gives a more comprehensive insight into the community dynamics of this young ecosystem and the extrinsic factors that might drive the SGDCs.

RESULTS

No significant correlations between species diversity and genetic diversity were found for any of the focal species. However, both negative and positive trends of SGDCs for the individual focal species were observed. When examining the environmental drivers, no common trends between the species were found, even when restricting the analysis to specific taxonomic classes. Additionally, there were no common environmental factors driving the diversity relationships for species sharing the same SGDC trend (positive or negative). Local population dynamics, together with the invasion history of the individual species and their unique adaptation to the distinctive environment of the Baltic Sea, are expected to be of major influence on the outcome of the SGDCs.

CONCLUSIONS

The present results highlight the importance of assessing SGDCs using multiple species, not just a single indicator species. This emphasises a need to pay attention to the ecology and life history of the focal species. This study also provides insight into the large differences in both patterns and drivers of genetic diversity, which is important when including genetic biodiversity in conservation plans. We conclude that the effects of environmental and biological factors and processes that affects diversity patterns at both the community and genetic levels are likely species dependent, even in an environment such as the Baltic Sea with strong environmental gradients.

Phylogenetic resolution of the fly superfamily Ephydroidea-Molecular systematics of the enigmatic and diverse relatives of Drosophilidae

The schizophoran superfamily Ephydroidea (Diptera: Cyclorrhapha) includes eight families, ranging from the well-known vinegar flies (Drosophilidae) and shore flies (Ephydridae), to several small, relatively unusual groups, the phylogenetic placement of which has been particularly challenging for systematists. An extraordinary diversity in life histories, feeding habits and morphology are a hallmark of fly biology, and the Ephydroidea are no exception. Extreme specialization can lead to "orphaned" taxa with no clear evidence for their phylogenetic position. To resolve relationships among a diverse sample of Ephydroidea, including the highly modified flies in the families Braulidae and Mormotomyiidae, we conducted phylogenomic sampling. Using exon capture from Anchored Hybrid Enrichment and transcriptomics to obtain 320 orthologous nuclear genes sampled for 32 species of Ephydroidea and 11 outgroups, we evaluate a new phylogenetic hypothesis for representatives of the superfamily. These data strongly support monophyly of Ephydroidea with Ephydridae as an early branching radiation and the placement of Mormotomyiidae as a family-level lineage sister to all remaining families. We confirm placement of Cryptochetidae as sister taxon to a large clade containing both Drosophilidae and Braulidae-the latter a family of honeybee ectoparasites. Our results reaffirm that sampling of both taxa and characters is critical in hyperdiverse clades and that these factors have a major influence on phylogenomic reconstruction of the history of the schizophoran fly radiation.

Taxon-specific ultraconserved element probe design for phylogenetic analyses of scale insects (Hemiptera: Sternorrhyncha: Coccoidea)

Scale insects (Coccoidea) are morphologically specialized members of the order Hemiptera, with 56 families recognized to date. However, the phylogenetic relationships within and among families are poorly resolved. In this study, to further characterize the phylogenetic relationships among scale insects, an ultraconserved element (UCE) probe set was designed specifically for Coccoidea based on three low-coverage whole genome sequences along with three publicly available genomes. An in silico test including eight additional genomes was performed to evaluate the effectiveness of the probe set. Most scale insect lineages were recovered by the phylogenetic analysis. This study recovered the monophyly of neococcoids. The newly developed UCE probe set has the potential to reshape and improve our understanding of the phylogenetic relationships within and among families of scale insects at the genome level.

Genomic-Phenomic Reciprocal Illumination: Desyopone hereon gen. et sp. nov., an Exceptional Aneuretine-like Fossil Ant from Ethiopian Amber (Hymenoptera: Formicidae: Ponerinae)

Fossils are critical for understanding the evolutionary diversification, turnover, and morphological disparification of extant lineages. While fossils cannot be sequenced, phenome-scale data may be generated using micro-computed tomography (µ-CT), thus revealing hidden structures and internal anatomy, when preserved. Here, we adduce the male caste of a new fossil ant species from Miocene Ethiopian amber that resembles members of the Aneuretinae, matching the operational definition of the subfamily. Through the use of synchrotron radiation for µ-CT, we critically test the aneuretine-identity hypothesis. Our results indicate that the new fossils do not belong to the Aneuretinae, but rather the Ponerini (Ponerinae). Informed by recent phylogenomic studies, we were able to place the fossils close to the extant genus Cryptopone based on logical character analysis, with the two uniquely sharing absence of the subpetiolar process among all ponerine genera. Consequently, we: (1) revise the male-based key to the global ant subfamilies; (2) revise the definitions of Aneuretinae, Ponerinae, Platythyreini, and Ponerini; (3) discuss the evolution of ant mandibles; and (4) describe the fossils as †Desyopone hereon gen. et sp. nov. Our study highlights the value of males for ant systematics and the tremendous potential of phenomic imaging technologies for the study of ant evolution.

Speciation in Nearctic oak gall wasps is frequently correlated with changes in host plant, host organ, or both

Quantifying the frequency of shifts to new host plants within diverse clades of specialist herbivorous insects is critically important to understand whether and how host shifts contribute to the origin of species. Oak gall wasps (Hymenoptera: Cynipidae: Cynipini) comprise a tribe of ∼1000 species of phytophagous insects that induce gall formation on various organs of trees in the family Fagacae-primarily the oaks (genus Quercus; ∼435 sp.). The association of oak gall wasps with oaks is ancient (∼50 my), and most oak species are galled by one or more gall wasp species. Despite the diversity of both gall wasp species and their plant associations, previous phylogenetic work has not identified the strong signal of host plant shifting among oak gall wasps that has been found in other phytophagous insect systems. However, most emphasis has been on the Western Palearctic and not the Nearctic where both oaks and oak gall wasps are considerably more species rich. We collected 86 species of Nearctic oak gall wasps from most of the major clades of Nearctic oaks and sequenced >1000 Ultraconserved Elements (UCEs) and flanking sequences to infer wasp phylogenies. We assessed the relationships of Nearctic gall wasps to one another and, by leveraging previously published UCE data, to the Palearctic fauna. We then used phylogenies to infer historical patterns of shifts among host tree species and tree organs. Our results indicate that oak gall wasps have moved between the Palearctic and Nearctic at least four times, that some Palearctic wasp clades have their proximate origin in the Nearctic, and that gall wasps have shifted within and between oak tree sections, subsections, and organs considerably more often than previous data have suggested. Given that host shifts have been demonstrated to drive reproductive isolation between host-associated populations in other phytophagous insects, our analyses of Nearctic gall wasps suggest that host shifts are key drivers of speciation in this clade, especially in hotspots of oak diversity. Although formal assessment of this hypothesis requires further study, two putatively oligophagous gall wasp species in our dataset show signals of host-associated genetic differentiation unconfounded by geographic distance, suggestive of barriers to gene flow associated with the use of alternative host plants.

Phylogeography and population genetics of a widespread cold-adapted ant, Prenolepis imparis

As species arise, evolve, and diverge, they are shaped by forces that unfold across short and long time scales and at both local and vast geographic scales. It is rare, however, to be able document this history across broad sweeps of time and space in a single species. Here, we report the results of a continental-scale phylogenomic analysis across the entire range of a widespread species. We analyzed sequences of 1,402 orthologous Ultraconserved Element (UCE) loci from 75 individuals to identify population genetic structure and historical demographic patterns across the continent-wide range of a cold-adapted ant, the winter ant, Prenolepis imparis. We recovered five well-supported, genetically isolated clades representing lineages that diverged from 8.2-2.2 million years ago. These include: 1) an early diverging lineage located in Florida, 2) a lineage that spans the southern United States, 3) populations that extend across the midwestern and northeastern United States, 4) populations from the western United States, and 5) populations in southwestern Arizona and Mexico. Population genetic analyses revealed little or no gene flow among these lineages, but patterns consistent with more recent gene flow among populations within lineages, and localized structure with migration in the western United States. High support for five major geographic lineages and lack of evidence of contemporary gene flow indicate in situ diversification across the species' range, producing relatively ancient lineages that persisted through subsequent climate change and glaciation during the Quaternary.

A phylogenomic backbone for gastropod molluscs

Gastropods have survived several mass extinctions during their evolutionary history resulting in extraordinary diversity in morphology, ecology, and developmental modes, which complicate the reconstruction of a robust phylogeny. Currently, gastropods are divided into six subclasses: Caenogastropoda, Heterobranchia, Neomphaliones, Neritimorpha, Patellogastropoda, and Vetigastropoda. Phylogenetic relationships among these taxa historically lack consensus, despite numerous efforts using morphological and molecular information. We generated sequence data for transcriptomes derived from twelve taxa belonging to clades with little or no prior representation in previous studies in order to infer the deeper cladogenetic events within Gastropoda and, for the first time, infer the position of the deep-sea Neomphaliones using a phylogenomic approach. We explored the impact of missing data, homoplasy, and compositional heterogeneity on the inferred phylogenetic hypotheses. We recovered a highly supported backbone for gastropod relationships that is congruent with morphological and mitogenomic evidence, in which Patellogastropoda, true limpets, are the sister lineage to all other gastropods (Orthogastropoda) which are divided into two main clades (i) Vetigastropoda s.l. (including Pleurotomariida + Neomphaliones) and (ii) Neritimorpha + (Caenogastropoda + Heterobranchia). As such, our results support the recognition of five subclasses (or infraclasses) in Gastropoda: Patellogastropoda, Vetigastropoda, Neritimorpha, Caenogastropoda and Heterobranchia.

A single-cell transcriptomic atlas tracking the neural basis of division of labour in an ant superorganism

Ant colonies with permanent division of labour between castes and highly distinct roles of the sexes have been conceptualized to be superorganisms, but the cellular and molecular mechanisms that mediate caste/sex-specific behavioural specialization have remained obscure. Here we characterized the brain cell repertoire of queens, gynes (virgin queens), workers and males of Monomorium pharaonis by obtaining 206,367 single-nucleus transcriptomes. In contrast to Drosophila, the mushroom body Kenyon cells are abundant in ants and display a high diversity with most subtypes being enriched in worker brains, the evolutionarily derived caste. Male brains are as specialized as worker brains but with opposite trends in cell composition with higher abundances of all optic lobe neuronal subtypes, while the composition of gyne and queen brains remained generalized, reminiscent of solitary ancestors. Role differentiation from virgin gynes to inseminated queens induces abundance changes in roughly 35% of cell types, indicating active neurogenesis and/or programmed cell death during this transition. We also identified insemination-induced cell changes probably associated with the longevity and fecundity of the reproductive caste, including increases of ensheathing glia and a population of dopamine-regulated Dh31-expressing neurons. We conclude that permanent caste differentiation and extreme sex-differentiation induced major changes in the neural circuitry of ants.

Using single-cell transcriptomics, the authors generate a brain cell atlas for the pharaoh ant including individuals of different sexes and castes and show changes in cell composition underlying division of labour and reproductive specialization.

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

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

Mitochondrial phylogenomics and mitogenome organization in the parasitoid wasp family Braconidae (Hymenoptera: Ichneumonoidea)

Background

Mitochondrial (mt) nucleotide sequence data has been by far the most common tool employed to investigate evolutionary relationships. While often considered to be more useful for shallow evolutionary scales, mt genomes have been increasingly shown also to contain valuable phylogenetic information about deep relationships. Further, mt genome organization provides another important source of phylogenetic information and gene reorganizations which are known to be relatively frequent within the insect order Hymenoptera. Here we used a dense taxon sampling comprising 148 mt genomes (132 newly generated) collectively representing members of most of the currently recognised subfamilies of the parasitoid wasp family Braconidae, which is one of the largest radiations of hymenopterans. We employed this data to investigate the evolutionary relationships within the family and to assess the phylogenetic informativeness of previously known and newly discovered mt gene rearrangements.

Results

Most subfamilial relationships and their composition obtained were similar to those recovered in a previous phylogenomic study, such as the restoration of Trachypetinae and the recognition of Apozyginae and Proteropinae as valid braconid subfamilies. We confirmed and detected phylogenetic signal in previously known as well as novel mt gene rearrangements, including mt rearrangements within the cyclostome subfamilies Doryctinae and Rogadinae.

Conclusions

Our results showed that both the mt genome DNA sequence data and gene organization contain valuable phylogenetic signal to elucidate the evolution within Braconidae at different taxonomic levels. This study serves as a basis for further investigation of mt gene rearrangements at different taxonomic scales within the family.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-01983-1.

Detection of F1 hybrids from single-genome data reveals frequent hybridization in Hymenoptera and particularly ants

Hybridization occupies a central role in many fundamental evolutionary processes, such as speciation or adaptation. Yet, despite its pivotal importance in evolution, little is known about the actual prevalence and distribution of current hybridization across the tree of life. Here we develop and implement a new statistical method enabling the detection of F1 hybrids from single-individual genome sequencing data. Using simulations and sequencing data from known hybrid systems, we first demonstrate the specificity of the method, and identify its statistical limits. Next, we showcase the method by applying it to available sequencing data from more than 1,500 species of Arthropods, including Hymenoptera, Hemiptera, Coleoptera, Diptera, and Archnida. Among these taxa, we find Hymenoptera, and especially ants, to display the highest number of candidate F1 hybrids, suggesting higher rates of recent hybridization between previously isolated gene pools in these groups. The prevalence of F1 hybrids was heterogeneously distributed across ants, with taxa including many candidates tending to harbor specific ecological and life-history traits. This work shows how large-scale genomic comparative studies of recent hybridization can be implemented, uncovering the determinants of first-generation hybridization across whole taxa.

Phylogenomics and historical biogeography of the cleptoparasitic bee genus Nomada (Hymenoptera: Apidae) using ultraconserved elements

The genus Nomada Scopoli (Hymenoptera: Apidae) is the largest genus of brood parasitic bees with nearly 800 species found across the globe and in nearly all biogeographic realms except Antarctica. There is no previous molecular phylogeny focused on Nomada despite their high species abundance nor is there an existing comprehensive biogeography for the genus. Using ultraconserved element (UCE) phylogenomic data, we constructed the first molecular phylogeny for the genus Nomada and tested the monophyly of 16 morphologically established species groups. We also estimated divergence dates using fossil calibration points and inferred the origin and of this genus around the globe. Our phylogeny recovered 14 of the 16 previously established species groups as monophyletic. The superba and ruficornis groups, however, were recovered as non-monophyletic and need to be re-evaluated using morphology. Divergence dating and historic biogeographic analyses performed on the phylogenetic reconstruction indicates that Nomada most likely originated in the Holarctic ∼65 Mya. Geodispersal into the southern hemisphere occurred three times; once during the Eocene into the Afrotropics, once during the Oligocene into the Neotropics, and once during the Miocene into Australasia. Geodispersal across the Holarctic was most frequent and occurred repeatedly throughout the Cenozoic era, using the De Geer, Thulean, and the Bering Land Bridges. This is the first instance of a bee using both the Thulean and De Geer land bridges and has implications of how early bee species dispersed throughout the Palearctic in the late Cretaceous and early Paleogene.

Genome-wide sequence data show no evidence of hybridization and introgression among pollinator wasps associated with a community of Panamanian strangler figs

The specificity of pollinator host choice influences opportunities for reproductive isolation in their host plants. Similarly, host plants can influence opportunities for reproductive isolation in their pollinators. For example, in the fig and fig wasp mutualism, offspring of fig pollinator wasps mate inside the inflorescence that the mothers pollinate. Although often host specific, multiple fig pollinator species are sometimes associated with the same fig species, potentially enabling hybridization between wasp species. Here, we study the 19 pollinator species (Pegoscapus spp.) associated with an entire community of 16 Panamanian strangler fig species (Ficus subgenus Urostigma, section Americanae) to determine whether the previously documented history of pollinator host switching and current host sharing predicts genetic admixture among the pollinator species, as has been observed in their host figs. Specifically, we use genome‐wide ultraconserved element (UCE) loci to estimate phylogenetic relationships and test for hybridization and introgression among the pollinator species. In all cases, we recover well‐delimited pollinator species that contain high interspecific divergence. Even among pairs of pollinator species that currently reproduce within syconia of shared host fig species, we found no evidence of hybridization or introgression. This is in contrast to their host figs, where hybridization and introgression have been detected within this community, and more generally, within figs worldwide. Consistent with general patterns recovered among other obligate pollination mutualisms (e.g. yucca moths and yuccas), our results suggest that while hybridization and introgression are processes operating within the host plants, these processes are relatively unimportant within their associated insect pollinators.

UCEasy: A software package for automating and simplifying the analysis of ultraconserved elements (UCEs)

Background

The use of Ultraconserved Elements (UCEs) as genetic markers in phylogenomics has become popular and has provided promising results. Although UCE data can be easily obtained from targeted enriched sequencing, the protocol for in silico analysis of UCEs consist of the execution of heterogeneous and complex tools, a challenge for scientists without training in bioinformatics. Developing tools with the adoption of best practices in research software can lessen this problem by improving the execution of computational experiments, thus promoting better reproducibility.

New information

We present UCEasy, an easy-to-install and easy-to-use software package with a simple command line interface that facilitates the computational analysis of UCEs from sequencing samples, following the best practices of research software. UCEasy is a wrapper that standardises, automates and simplifies the quality control of raw reads, assembly and extraction and alignment of UCEs, generating at the end a data matrix with different levels of completeness that can be used to infer phylogenetic trees. We demonstrate the functionalities of UCEasy by reproducing the published results of phylogenomic studies of the bird genus Turdus (Aves) and of Adephaga families (Coleoptera) containing genomic datasets to efficiently extract UCEs.

Phylogenetic relationships and the evolution of host preferences in the largest clade of brood parasitic bees (Apidae: Nomadinae)

Brood parasites (also known as cleptoparasites) represent a substantial fraction of global bee diversity. Rather than constructing their own nests, these species instead invade those of host bees to lay their eggs. Larvae then hatch and consume the food provisions intended for the host's offspring. While this life history strategy has evolved numerous times across the phylogeny of bees, the oldest and most speciose parasitic clade is the subfamily Nomadinae (Apidae). However, the phylogenetic relationships among brood parasitic apids both within and outside the Nomadinae have not been fully resolved. Here, we present new findings on the phylogeny of this diverse group of brood parasites based on ultraconserved element (UCE) sequence data and extensive taxon sampling with 114 nomadine species representing all tribes. We suggest a broader definition of the subfamily Nomadinae to describe a clade that includes almost all parasitic members of the family Apidae. The tribe Melectini forms the sister group to all other Nomadinae, while the remainder of the subfamily is composed of two sister clades: a "nomadine line" representing the former Nomadinae sensu stricto, and an "ericrocidine line" that unites several mostly Neotropical lineages. We find the tribe Osirini Handlirsch to be polyphyletic, and divide it into three lineages, including the newly described Parepeolini trib. nov. In addition to our taxonomic findings, we use our phylogeny to explore the evolution of different modes of parasitism, detecting two independent transitions from closed-cell to open-cell parasitism. Finally, we examine how nomadine host-parasite associations have evolved over time. In support of Emery's rule, which suggests close relationships between hosts and parasites, we confirm that the earliest nomadines were parasites of their close free-living relatives within the family Apidae, but that over time their host range broadened to include more distantly related hosts spanning the diversity of bees. This expanded breadth of host taxa may also be associated with the transition to open-cell parasitism.

A phylogenomic perspective on the evolutionary history of the stonefly genus Suwallia (Plecoptera: Chloroperlidae) revealed by ultraconserved genomic elements

Evolutionary biologists have long sought to disentangle phylogenetic relationships among taxa spanning the tree of life, an increasingly important task as anthropogenic influences accelerate population declines and species extinctions, particularly in insects. Phylogenetic analyses are commonly used to identify unique evolutionary lineages, to clarify taxonomic designations of the focal taxa, and to inform conservation decisions. Advances in DNA sequencing techniques have increasingly facilitated the ability of researchers to apply genomic methods to phylogenetic analyses, even for non-model organisms. Stoneflies are non-model insects that are important bioindicators of the quality of freshwater habitats and landscape disturbance as they spend the immature stages of their life cycles in fresh water, and the adult stages in terrestrial environments. Phylogenetic relationships within the stonefly genus Suwallia (Insecta: Plecoptera: Chloroperlidae) are poorly understood, and have never been assessed using molecular data. We used DNA sequence data from genome-wide ultraconserved element loci to generate the first molecular phylogeny for the group and assess its monophyly. We found that Palearctic and Nearctic Suwallia do not form reciprocally monophyletic clades, and that a biogeographic history including dispersal, vicariance, and founder event speciation via jump dispersal best explains the geographic distribution of this group. Our results also strongly suggest that Neaviperla forcipata (Neave, 1929) is nested within Suwallia, and the concept of the genus Suwallia should be revised to include it. Thus, we formally propose a new taxonomic combination wherein Neaviperla forcipata (Neave, 1929) is reclassified as Suwallia forcipata (Neave, 1929). Moreover, some Suwallia species (e.g., S. amoenacolens, S. kerzhneri, S. marginata, S. pallidula, and S. starki) exhibit pronounced cryptic diversity that is worthy of further investigation. These findings provide a first glimpse into the evolutionary history of Suwallia, improve our understanding of stonefly diversity in the tribe Suwallini, and highlight areas where additional research is needed.

Ultraconserved elements-based systematics reveals evolutionary patterns of host-plant family shifts and phytophagy within the predominantly parasitoid braconid wasp subfamily Doryctinae

Phytophagy has promoted species diversification in many insect groups, including Hymenoptera, one of the most diverse animal orders on Earth. In the predominantly parasitoid family Braconidae, an association with insect-induced, plant galls in angiosperms have been reported in three subfamilies, but in particular in the Doryctinae, where it has been recorded to occur in species of ten genera. Allorhogas Gahan is the most species-rich of these genera, with its species having different phytophagous strategies. Here we conducted a comprehensive phylogenomic study for the doryctine gall-associated genera, with an emphasis on Allorhogas, using ultraconserved elements (UCEs). Based on this estimate of phylogeny we: (1) evaluated their taxonomic composition, (2) estimated the timing of origin of the gall-associated clade and divergence of its main subclades, and (3) performed ancestral state reconstruction analyses for life history traits related to their host-plant association. Our phylogenetic hypothesis confirmed Allorhogas as polyphyletic, with most of its members being nested in a main clade composed of various subclades, each comprising species with a particular host-plant family and herbivorous feeding habit. The origin of gall-association was estimated to have occurred during the late Oligocene to early Miocene, with a subsequent diversification of subclades during the middle to late Miocene and Pliocene. Overlap in divergence timing appears to occur between some taxa and their host-associated plant lineages. Evolution of the feeding strategies in the group shows "inquilinism-feeding" as the likely ancestral state, with gall-formation in different plant organs and seed predation having independently evolved on multiple occasions.

The evolution of social parasitism in Formica ants revealed by a global phylogeny

Studying the behavioral and life history transitions from a cooperative, eusocial life history to exploitative social parasitism allows for deciphering the conditions under which changes in behavior and social organization lead to diversification. The Holarctic ant genus Formica is ideally suited for studying the evolution of social parasitism because half of its 172 species are confirmed or suspected social parasites, which includes all three major classes of social parasitism known in ants. However, the life history transitions associated with the evolution of social parasitism in this genus are largely unexplored. To test competing hypotheses regarding the origins and evolution of social parasitism, we reconstructed a global phylogeny of Formica ants. The genus originated in the Old World ∼30 Ma ago and dispersed multiple times to the New World and back. Within Formica, obligate dependent colony-founding behavior arose once from a facultatively polygynous common ancestor practicing independent and facultative dependent colony foundation. Temporary social parasitism likely preceded or arose concurrently with obligate dependent colony founding, and dulotic social parasitism evolved once within the obligate dependent colony-founding clade. Permanent social parasitism evolved twice from temporary social parasitic ancestors that rarely practiced colony budding, demonstrating that obligate social parasitism can originate from a facultative parasitic background in socially polymorphic organisms. In contrast to permanently socially parasitic ants in other genera, the high parasite diversity in Formica likely originated via allopatric speciation, highlighting the diversity of convergent evolutionary trajectories resulting in nearly identical parasitic life history syndromes.

Ultra-Conserved Elements and morphology reciprocally illuminate conflicting phylogenetic hypotheses in Chalcididae (Hymenoptera, Chalcidoidea)

Recent technical advances combined with novel computational approaches have promised the acceleration of our understanding of the tree of life. However, when it comes to hyperdiverse and poorly known groups of invertebrates, studies are still scarce. As published phylogenies will be rarely challenged by future taxonomists, careful attention must be paid to potential analytical bias. We present the first molecular phylogenetic hypothesis for the family Chalcididae, a group of parasitoid wasps, with a representative sampling (144 ingroups and seven outgroups) that covers all described subfamilies and tribes, and 82% of the known genera. Analyses of 538 Ultra-Conserved Elements (UCEs) with supermatrix (RAxML and IQTREE) and gene tree reconciliation approaches (ASTRAL, ASTRID) resulted in highly supported topologies in overall agreement with morphology but reveal conflicting topologies for some of the deepest nodes. To resolve these conflicts, we explored the phylogenetic tree space with clustering and gene genealogy interrogation methods, analyzed marker and taxon properties that could bias inferences and performed a thorough morphological analysis (130 characters encoded for 40 taxa representative of the diversity). This joint analysis reveals that UCEs enable attainment of resolution between ancestry and convergent/divergent evolution when morphology is not informative enough, but also shows that a systematic exploration of bias with different analytical methods and a careful analysis of morphological features is required to prevent publication of artifactual results. We highlight a GC content bias for maximum-likelihood approaches, an artifactual mid-point rooting of the ASTRAL tree and a deleterious effect of high percentage of missing data (>85% missing UCEs) on gene tree reconciliation methods. Based on the results we propose a new classification of the family into eight subfamilies and ten tribes that lay the foundation for future studies on the evolutionary history of Chalcididae.

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

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

New targets acquired: Improving locus recovery from the Angiosperms353 probe set

PREMISE

Universal target enrichment kits maximize utility across wide evolutionary breadth while minimizing the number of baits required to create a cost-efficient kit. The Angiosperms353 kit has been successfully used to capture loci throughout the angiosperms, but the default target reference file includes sequence information from only 6-18 taxa per locus. Consequently, reads sequenced from on-target DNA molecules may fail to map to references, resulting in fewer on-target reads for assembly, and reducing locus recovery.

METHODS

We expanded the Angiosperms353 target file, incorporating sequences from 566 transcriptomes to produce a 'mega353' target file, with each locus represented by 17-373 taxa. This mega353 file is a drop-in replacement for the original Angiosperms353 file in HybPiper analyses. We provide tools to subsample the file based on user-selected taxon groups, and to incorporate other transcriptome or protein-coding gene data sets.

RESULTS

Compared to the default Angiosperms353 file, the mega353 file increased the percentage of on-target reads by an average of 32%, increased locus recovery at 75% length by 49%, and increased the total length of the concatenated loci by 29%.

DISCUSSION

Increasing the phylogenetic density of the target reference file results in improved recovery of target capture loci. The mega353 file and associated scripts are available at: https://github.com/chrisjackson-pellicle/NewTargets.

Molecular phylogeny, historical biogeography and revised classification of andrenine bees (Hymenoptera: Andrenidae)

The mining bee subfamily Andreninae (Hymenoptera: Andrenidae) is a widely distributed and diverse group of ground-nesting solitary bees, including numerous species known to be important pollinators. Most of the species diversity of Andreninae is concentrated in the mainly Holarctic genus Andrena, comprising ca. 1550 described species. The subfamily and especially the genus have remained relatively neglected by recent molecular phylogenetic studies, with current classifications relying largely on morphological characters. We sampled ultraconserved element (UCE) sequences from 235 taxa, including all andrenine genera and 98 out of 104 currently recognized Andrena subgenera. Using 419,858 aligned nucleotide sites from 1009 UCE loci, we present a comprehensive molecular phylogenetic analysis of the subfamily. Our analysis supports the recognition of seven distinct genera in the Andreninae: Alocandrena, Ancylandrena, Andrena, Cubiandrena, Euherbstia, Megandrena, and Orphana. Within the genus Andrena, present-day subgeneric concepts revealed high degrees of paraphyly and polyphyly, due to strong homoplasy of morphological characters, necessitating a thorough, extensive revision of the higher classification of the genus. Based on our findings, we place the subgenus Calcarandrena in synonymy with Andrena (Lepidandrena); Hyperandrena, Nemandrena, Scoliandrena, Tylandrena and Zonandrena with A. (Melandrena); Distandrena, Fumandrena and Proxiandrena with A. (Micrandrena); Carandrena with A. (Notandrena); Agandrena with A. (Plastandrena); Xiphandrena with A. (Scrapteropsis); and Platygalandrena and Poliandrena with A. (Ulandrena) (new synonymies). We additionally reestablish the groups known as Opandrena and Truncandrena as valid subgenera of Andrena. Our results also show that the MRCA of Andrena+Cubiandrena dispersed from the New World to the Palaearctic probably during the Eocene-early Oligocene, followed by 10-14 Neogene dispersal events from the Palaearctic to the Nearctic and 1-6 Neogene dispersals back into the Palaearctic, all within the genus Andrena.

Partitioned Gene-Tree Analyses and Gene-Based Topology Testing Help Resolve Incongruence in a Phylogenomic Study of Host-Specialist Bees (Apidae: Eucerinae)

Incongruence among phylogenetic results has become a common occurrence in analyses of genome-scale data sets. Incongruence originates from uncertainty in underlying evolutionary processes (e.g., incomplete lineage sorting) and from difficulties in determining the best analytical approaches for each situation. To overcome these difficulties, more studies are needed that identify incongruences and demonstrate practical ways to confidently resolve them. Here, we present results of a phylogenomic study based on the analysis 197 taxa and 2,526 ultraconserved element (UCE) loci. We investigate evolutionary relationships of Eucerinae, a diverse subfamily of apid bees (relatives of honey bees and bumble bees) with >1,200 species. We sampled representatives of all tribes within the group and >80% of genera, including two mysterious South American genera, Chilimalopsis and Teratognatha. Initial analysis of the UCE data revealed two conflicting hypotheses for relationships among tribes. To resolve the incongruence, we tested concatenation and species tree approaches and used a variety of additional strategies including locus filtering, partitioned gene-trees searches, and gene-based topological tests. We show that within-locus partitioning improves gene tree and subsequent species-tree estimation, and that this approach, confidently resolves the incongruence observed in our data set. After exploring our proposed analytical strategy on eucerine bees, we validated its efficacy to resolve hard phylogenetic problems by implementing it on a published UCE data set of Adephaga (Insecta: Coleoptera). Our results provide a robust phylogenetic hypothesis for Eucerinae and demonstrate a practical strategy for resolving incongruence in other phylogenomic data sets.

The basitarsal sulcus gland, a novel exocrine structure in ants

The basitarsus of the mid- and/or hindlegs of several Amblyoponinae ants shows a deep longitudinal groove or sulcus on its anterior face in workers and queens. Histological examination reveals this sulcus is associated with a conspicuous novel epithelial gland, which brings the number of exocrine glands in the legs of ants to 25. The ultrastructural characteristics of the gland show the presence of a well-developed smooth endoplasmic reticulum. This is indicative for the elaboration of a non-proteinaceous and thus possibly pheromonal secretion. Behavioural observations show that this secretion is collected by the tarsomeres and spread onto the brood and nest, suggesting a role in nestmate recognition. A similar basitarsal sulcus gland was also found in Nothomyrmecia, Paraponera and Tetraponera, which represents both a wide phylogenetic and ecological distribution, as it includes arboreal, ground-dwelling as well as subterranean taxa.

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

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

Synonymisation of the male-based ant genus Phaulomyrma (Hymenoptera:Formicidae) with Leptanilla based upon Bayesian total-evidence phylogenetic inference

Although molecular data have proven indispensable in confidently resolving the phylogeny of many clades across the tree of life, these data may be inaccessible for certain taxa. The resolution of taxonomy in the ant subfamily Leptanillinae is made problematic by the absence of DNA sequence data for leptanilline taxa that are known only from male specimens, including the monotypic genus Phaulomyrma Wheeler & Wheeler. Focusing upon the considerable diversity of undescribed male leptanilline morphospecies, the phylogeny of 35 putative morphospecies sampled from across the Leptanillinae, plus an outgroup, is inferred from 11 nuclear loci and 41 discrete male morphological characters using a Bayesian total-evidence framework, with Phaulomyrma represented by morphological data only. Based upon the results of this analysis Phaulomyrma is synonymised with Leptanilla Emery, and male-based diagnoses for Leptanilla that are grounded in phylogeny are provided, under both broad and narrow circumscriptions of that genus. This demonstrates the potential utility of a total-evidence approach in inferring the phylogeny of rare extant taxa for which molecular data are unavailable and begins a long-overdue systematic revision of the Leptanillinae that is focused on male material.