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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.

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.

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.

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.

The family Mutillidae (Hymenoptera) is a species‐rich group of aculeate wasps that occur worldwide. The higher‐level classification of the family has historically been controversial due, in part, to the extreme sexual dimorphism exhibited by these insects and their morphological similarity to other wasp taxa that also have apterous females. Modern hypotheses on the internal higher classification of Mutillidae have been exclusively based on morphology and, further, they include Myrmosinae as a mutillid subfamily. In contrast, several molecular‐based family‐level studies of Aculeata recovered Myrmosinae as a nonmutillid taxon. To test the validity of these morphology‐based classifications and the phylogenetic placement of the controversial taxon Myrmosinae, a phylogenomic study of Mutillidae was conducted using ultraconserved elements (UCEs). All currently recognized subfamilies and tribes of Mutillidae were represented in this study using 140 ingroup taxa. The maximum likelihood criterion (ML) and the maximum parsimony criterion (MP) were used to infer the phylogenetic relationships within the family and related taxa using an aligned data set of 238,764 characters; the topologies of these respective analyses were largely congruent. The modern higher classification of Mutillidae, based on morphology, is largely congruent with the phylogenomic results of this study at the subfamily level, whereas the tribal classification is poorly supported. The subfamily Myrmosinae was recovered as sister to Sapygidae in the ML analysis and sister to Sapygidae + Pompilidae in the MP analysis; it is consequently raised to the family level, Myrmosidae,stat.nov.The two constituent tribes of Myrmosidae are raised to the subfamily level, Kudakrumiinae,stat.nov., and Myrmosinae,stat.nov.All four recognized tribes of Mutillinae were found to be non‐monophyletic; three additional mutilline clades were recovered in addition to Ctenotillini, Mutillini, Smicromyrmini, and Trogaspidiini sensu stricto. Three new tribes are erected for members of these clades: Pristomutillini Waldren,trib.nov., Psammothermini Waldren,trib.nov., and Zeugomutillini Waldren,trib.nov.All three recognized tribes of Sphaeropthalminae were found to be non‐monophyletic; six additional sphaeropthalmine clades were recovered in addition to Dasymutillini, Pseudomethocini, and Sphaeropthalmini sensu stricto. The subtribe Ephutina of Mutillinae: Mutillini was found to be polyphyletic, with theEphutagenus‐group recovered within Sphaeropthalminae and theOdontomutillagenus‐group recovered as sister to Myrmillinae + Mutillinae. Consequently, the subtribe Ephutina is transferred from Mutillinae: Mutillini and is raised to a tribe within Sphaeropthalminae, Ephutini,stat.nov.Further, the taxon Odontomutillinae,stat.nov., is raised from a synonym of Ephutina to the subfamily level. The sphaeropthalmine tribe Pseudomethocini was found to be polyphyletic, with the subtribe Euspinoliina recovered as a separate clade in Sphaeropthalminae; consequently, Euspinoliina is raised to a tribe, Euspinoliini,stat.nov., in Sphaeropthalminae. The dasylabrine tribe Apteromutillini was recovered within Dasylabrini and is proposed as a new synonym of Dasylabrinae. Finally, dating analyses were conducted to infer the ages of the Pompiloidea families (Mutillidae, Myrmosidae, Pompilidae, and Sapygidae) and the ages of the Mutillidae subfamilies and tribes.