Silas Bossert

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 move Clavinomia to Dieunomiini and render Epinomia once more a subgenus of Dieunomia . 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.