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ABSTRACT AimInsect brood parasites (i.e., cleptoparasites), like cuckoo bees, typically attack hosts within specific lineages, but seem to be less constrained by the biogeographical movements of their hosts compared to obligate parasites. Cuckoo bees depend on stable host populations, being particularly sensitive to environmental changes and thus valuable bioindicators of the bee community health. We here test the congruence between the biogeographical history of cuckoo oil bees and their oil bee hosts. LocationThe Americas. TaxonBees (Hymenoptera, Apidae). MethodsUsing phylogenomic and Sanger sequence data, we present new time‐calibrated phylogenies for cuckoo oil bees in the ericrocidine line and their oil bee hosts,CentrisandEpicharis.We estimate their ancestral ranges using six historical biogeographical models on a set of 100 trees, randomly sampled from the posterior distribution of phylogenies in each group, thus accounting for uncertainties in divergence time estimates and model selection. ResultsThe origin of the hosts stem in the Cretaceous precedes the origin of their cleptoparasite's stem in the Palaeocene. Cleptoparasite and host crown origins were synchronous in the Eocene, and both took place in tropical South America. While the pair Rhathymini‐Epicharisremained mostly associated within this region,Centrisand their cleptoparasites expanded their distribution to other parts of Neotropical and Nearctic regions in independent range expansions events. In all cases, host range shifts preceded the cleptoparasite shifts. Main ConclusionThe biogeographical history of cleptoparasitic oil bees and oil‐collecting hosts is generally congruent in time and space. Events of range expansion mainly occurred in the more species‐rich lineages of cleptoparasites. Range shifts in cleptoparasites followed the distribution of their hosts and coincided with the distribution of oil‐producing plants visited by the host bees. Our results broaden our understanding of the complex biogeography of interacting partners and on how changes in host distributions may impact cleptoparasitic bees. 

Abstract The apid subfamily Nomadinae is the oldest and most diverse clade of brood parasitic bees. Through the incorporation of data from a variety of sources, we generated the most detailed and taxonomically complete phylogeny of this group to date. Despite differing amounts of genetic data available for different species, the tree topology largely matched with expected relationships based on previous findings, with 95% of barcode-only taxa placed in taxonomically consistent positions and all tribes recovered as monophyletic. We further carried out divergence time estimation to investigate the evolutionary history of Nomadinae and place the phylogeny along the geological time scale, recovering an estimated age of 99 Ma for the group. Testing for the effect of barcode-only taxa on estimated dates indicated that ages for deep nodes were robust, though the inclusion of such taxa with limited sequence data tended to push shallower nodes towards older dates. Though this approach may not be appropriate for all applications, the potential for integration of cytochrome oxidase DNA barcode sequences with modern phylogenomic (ultraconserved element) sequence data is an encouraging indication that the wealth of previously published data available through sequence repositories retains the capacity to be informative to future phylogenetic studies. 

Abstract Accurate species delimitation is critical to identifying the conservation status of species. Molecular species delimitation methods have revealed previously unrecognized cryptic species across the taxonomic spectrum. However, studies vary in the molecular markers selected, analytical approaches used, and taxon sampling, which sometimes results in conflicting conclusions. One example of such a conflict is seen in the species delimitation analyses of the western bumble bee,Bombus occidentalis. This species was once an abundant insect pollinator in western North America but has declined severely since the mid 1990s and is predicted to continue to diminish under even optimistic future climate scenarios. Complicating this conservation crisis, the species status ofB. occidentalishas varied over time, with most recent studies recognizing one or two species. Previous studies that used molecular methods to address this question focused on a Bayesian phylogeny of the mitochondrialcytochrome oxidase I(COI) gene. Phylogenetic studies that focus on a single gene are criticized for misrepresenting the evolutionary history of species because nuclear and mitochondrial genomes, and even some genes within them, may have different evolutionary patterns. We tested a two species hypothesis of theB. occidentaliscomplex using nuclear (ultraconserved elements) and mitochondrial (COI) markers to infer maximum likelihood and Bayesian phylogenies for the taxa. We present our results and conclusions from eight species delimitation methods. Based on the genomic, morphological and geographic differences between the taxa we find support for the two species hypothesis, withB. occidentalisandB. mckayias separate species. We discuss the strengths and limitations of each genetic dataset and delimitation method, make recommendations for best practices, and highlight opportunities for equitable knowledge and technology development for phylogenomics in conservation biology. 

Abstract The New World army ants (Hymenoptera: Formicidae) comprise the 5 genera of the Eciton species group, and together they are important keystone predators in tropical and subtropical environments. Generic boundaries in the group have been considered solid and stable for nearly 100 years. Workers of the widespread and diverse genus Neivamyrmex are readily separable from the other 4 genera by lacking a subapical tooth on the tarsal claw, while males can be separated with genitalic characters. The genus Labidus is also widespread and is often abundant, with several species that are conspicuous surface foragers. The least known species of Labidus is L. mars, the workers of which have the tarsal tooth but otherwise share many traits with some Neivamyrmex, being completely eyeless and subterranean. This led us to question its generic placement. Here, we used ultraconserved element (UCE) phylogenomics to show that Labidus mars belongs to the genus Neivamyrmex. All phylogenies, inferred using multiple partitioning schemes and a species tree analysis, recovered the same topology, placing Labidus mars workers within Neivamyrmex. Sequenced males of L. mars were found to be within Labidus and thus incorrectly associated with L. mars. Based on these results and review of key specimens, including types, the following taxonomic changes are made: Neivamyrmex mars (Forel 1912) is a new combination; Labidus nero (Santschi 1930) (rev. stat.) is a male-based taxon revived from synonymy under L. mars; and L. denticulatus (Borgmeier 1955) (new stat.), a male-based taxon and former subspecies of L. mars, is raised to species. 

Abstract The recent advances in sequencing technologies, phylogenomics and divergence dating methods call for an integrative review of the current state of Hymenoptera systematics. We here explore the impact of these latest developments on the Hymenoptera phylogeny and our understanding of the timing of Hymenoptera evolution, while identifying the current methodological constraints and persistent knowledge gaps that warrant further investigation. Our review highlights the lack of consensus among the backbone phylogeny of Hymenoptera between key phylogenomic studies, as the higher level phylogeny remains unresolved in key nodes such as the relationships among Eusymphyta, the relationships within the Infraorder Proctotrupomorpha and the placements of the superfamilies Ichneumonoidea, Ceraphronoidea and Vespoidea. Furthermore, we underline the huge variation in divergence age estimates for Hymenoptera and detect several major gaps and/or disagreements between the fossil record and available age estimates, either due to the poorly studied fossil record or problematic age estimates, or both. To better understand the timing of Hymenoptera evolution and the role of key diversification factors, we will need continuous efforts to (i) reconcile conflicts among morphological and molecular phylogenies, by improving taxon sampling of underrepresented lineages, applying novel techniques to study morphology, making use of genome‐scale data and critically assessing incongruences in genetic markers; (ii) improve the Hymenoptera fossil record, by exercising integrative taxonomy and bringing together paleontologists and neontologists; and (iii) reconcile age estimates, by relying on tip dating approaches to bridge fossils, morphology and genomes across time. 

Abstract AimAn antitropical pattern is characterized by the occurrence of closely related taxa south and north of the tropics but absent or uncommonly represented closer to the equator, in contrast to most taxa, which tend to have their highest diversity in the tropical regions. We investigate the antitropical distribution of eucerine bees with the aim of contributing to the characterization and understanding of this pattern. LocationAll continents except Antarctica and Australia. TaxonEucerine bees (Hymenoptera: Apidae: Eucerinae). MethodsWe carried out phylogenomic dating under two different clock models and used multiple strategies to vary matrix composition, evaluating the overlapping of divergence times estimated across models using Bhattacharyya coefficients. Lastly, we reconstructed the biogeographic history of eucerine bees using a Bayesian implementation of the DEC model. ResultsEucerinae is estimated to have started diversifying during the Palaeocene, with all its tribes originating during the Palaeocene/Eocene transition in southern South America. At least two range expansions happened into North America before the full closure of the Isthmus of Panama. We show that divergence between closely related groups with disjunct distributions would have happened in periods when the climate favoured the expansion of open habitats and became isolated when the forests were re‐established. Main conclusionsWe describe the early diversification of eucerine bees, revealing an intimate association with southern South America. Events of range evolution of Eucerinae were likely affected by periods of global cooling and aridification, and palaeoclimatic and vegetational conditions probably have been more relevant to the formation of the antitropical distribution of Eucerinae than the consolidation of the Isthmus of Panama connecting the Americas. We also demonstrate that most uncertainty in divergence time estimation is not due to the amount of molecular data being used, but more likely other factors like fossil calibrations and violations of clock models. 

Abstract Sequence data assembly is a foundational step in high‐throughput sequencing, with untold consequences for downstream analyses. Despite this, few studies have interrogated the many methods for assembling phylogenomic UCE data for their comparative efficacy, or for how outputs may be impacted. We study this by comparing the most commonly used assembly methods for UCEs in the under‐studied bee lineage Nomiinae and a representative sampling of relatives. Data for 63 UCE‐only and 75 mixed taxa were assembled with five methods, including ABySS, HybPiper, SPAdes, Trinity and Velvet, and then benchmarked for their relative performance in terms of locus capture parameters and phylogenetic reconstruction. Unexpectedly, Trinity and Velvet trailed the other methods in terms of locus capture and DNA matrix density, whereas SPAdes performed favourably in most assessed metrics. In comparison with SPAdes, the guided‐assembly approach HybPiper generally recovered the highest quality loci but in lower numbers. Based on our results, we formally moveClavinomiato Dieunomiini and renderEpinomiaonce more a subgenus ofDieunomia. We strongly advise that future studies more closely examine the influence of assembly approach on their results, or, minimally, use better‐performing assembly methods such as SPAdes or HybPiper. In this way, we can move forward with phylogenomic studies in a more standardized, comparable manner. 

Abstract We reconstruct the phylogeny of the most speciose genus of cuckoo bees, genus Nomada Scopoli, 1770, using 221 species from throughout its distribution, yet with a strong emphasis on the West Palearctic. For phylogenetic reconstruction, we sequenced ultraconserved elements, allowing robust phylogenetic estimates with both concatenation and coalescent-based methods. By integrating extensive information on Nomada host records, we study macroevolutionary patterns of host associations, transitions, and phylogenetic conservatism. Using Bayesian divergence time estimates, we assess the historical biogeography of the genus, focusing on the West Palearctic. Our results show that Nomada likely originated in the Eastern Mediterranean and Near Eastern region, and likely expanded its range to a near-global distribution from there. We recovered long-standing phylogenetic conservatism in the host usage of Nomada and provided strong statistical evidence for an ancestral host association with Andrena and its most recent common ancestor. However, host transitions occurred multiple times independently in the natural history of Nomada, and species of the genus are brood parasites in at least 5 genera and 4 different families of bees in the Old World. At last, we systematically revise the taxonomy of the Old World Nomada by integrating morphological study with our well-supported phylogenetic estimates. We re-establish the genus Acanthonomada Schwarz, 1966, stat. res., as a distinct, second genus in the tribe Nomadini. We recognize 13 subgenera for Nomada, 9 of which are described as new: Afronomada Straka and Bossert, subgen. nov., Colliculla Straka, subgen. nov., Gestamen Straka, subgen. nov., Hungias Straka, subgen. nov., Mininomada Straka, subgen. nov., Nomacolla Straka, subgen. nov., Nomonosa Straka, subgen. nov., Plumada Straka, subgen. nov., and Profuga Straka, subgen. nov. Aside from the subgenus Nomada s.s., we reinstitute 3 previously synonymized subgenera: Heminomada Cockerell, 1902, stat. res., Holonomada Robertson, 1903, stat. res., and Hypochrotaenia Holmberg, 1886 stat. res. A total of 15 subgeneric names are formally synonymized with the newly established subgeneric concepts. 

Abstract Species occurrence data are foundational for research, conservation, and science communication, but the limited availability and accessibility of reliable data represents a major obstacle, particularly for insects, which face mounting pressures. We presentBeeBDC, a newRpackage, and a global bee occurrence dataset to address this issue. We combined >18.3 million bee occurrence records from multiple public repositories (GBIF, SCAN, iDigBio, USGS, ALA) and smaller datasets, then standardised, flagged, deduplicated, and cleaned the data using the reproducibleBeeBDC R-workflow. Specifically, we harmonised species names (following established global taxonomy), country names, and collection dates and, we added record-level flags for a series of potential quality issues. These data are provided in two formats, “cleaned” and “flagged-but-uncleaned”. TheBeeBDCpackage with online documentation provides end users the ability to modify filtering parameters to address their research questions. By publishing reproducibleRworkflows and globally cleaned datasets, we can increase the accessibility and reliability of downstream analyses. This workflow can be implemented for other taxa to support research and conservation. 

Abstract Despite recent advances in phylogenomics, the early evolution of the largest bee family, Apidae, remains uncertain, hindering efforts to understand the history of Apidae and establish a robust comparative framework. Confirming the position of Anthophorinae—a diverse, globally distributed lineage of apid bees—has been particularly problematic, with the subfamily recovered in various conflicting positions, including as sister to all other Apidae or to the cleptoparasitic Nomadinae. We aimed to resolve relationships in Apidae and Anthophorinae by combining dense taxon sampling, with rigorous phylogenomic analysis of a dataset consisting of ultraconserved elements (UCEs) acquired from multiple sources, including low-coverage genomes. Across a diverse set of analyses, including both concatenation and species tree approaches, and numerous permutations designed to account for systematic biases, Anthophorinae was consistently recovered as the sister group to all remaining Apidae, with Nomadinae sister to (Apinae, [Xylocopinae, Eucerinae]). However, several alternative support metrics (concordance factors, quartet sampling, and gene genealogy interrogation) indicate that this result should be treated with caution. Within Anthophorinae, all genera were recovered as monophyletic, following synonymization of Varthemapistra with Habrophorula. Our results demonstrate the value of dense taxon sampling in bee phylogenomics research and how implementing diverse analytical strategies is important for fully evaluating results at difficult nodes.