Ultraconserved element phylogenomics and biogeography of the agriculturally important mason bee subgenus Osmia (Osmia)

One of the most important non‐Apis groups of bees for agriculture is the mason bee subgenus Osmia Panzer (Osmia), or Osmia s.s. (Hymenoptera: Megachilidae). Out of the 29 known species, four have been developed as managed pollinators of orchards. In addition, the group is important as a source of non‐native pollinators, given that several species have been introduced into new areas. Osmia s.s. occurs naturally throughout the northern temperate zone with greatest species richness in Europe and Asia. Here, we integrate phylogenomic data from ultraconserved elements (UCEs), near complete taxon sampling, and a diversity of analytical approaches to infer the phylogeny, divergence times, and biogeographic history of Osmia s.s. We also demonstrate how mitochondrial sequence data can be extracted from ultraconserved element data and combined with sequences from public repositories in order to test the phylogeny, examine species boundaries and identify specimen‐associated, non‐bee DNA. We resolv..., See accompanying paper for more details. 
UCE Molecular Data Generation
To generate a genome-scale dataset of Osmia s.s we used ultra-conserved element (UCE) phylogenomics (Branstetter et al., 2017; Faircloth et al., 2012), an approach that combines the targeted enrichment of thousands of nuclear, UCE loci with multiplexed next-generation sequencing. Enrichment was performed using a recently published bait set that targets loci shared across all Hymenoptera (“hym-v2-bee-ant-specific”; Grab et al., 2019). This bait set is a subset of the principal Hymenoptera bait set (Branstetter et al., 2017) and includes probes synthesized from one ant and one bee genome only. It includes 9,068 unique baits targeting 2,545 UCE loci, plus an additional 264 baits targeting 12 exons from 7 “legacy” markers (ArgK, CAD, EF1aF1 and F2, LwRh, NaK, PolD1, and TopI) that have been used extensively in Sanger sequencing-based studies. The bait set is currently available for purchase from Arbor Biosciences as a c..., , # Data from: Ultraconserved element phylogenomics and biogeography of the agriculturally important mason bee subgenus Osmia (Osmia)

[https://doi.org/10.5061/dryad.7d7wm37t4](https://doi.org/10.5061/dryad.7d7wm37t4)

UCE phylogenomics and biogeography of the agriculturally important mason bee subgenus Osmia (Osmia)

Michael G. Branstetter1, Andreas Müller2, Terry L. Griswold1, Michael C. Orr3, Chao-Dong Zhu3

1U.S. Department of Agriculture, Agricultural Research Service, Pollinating Insects Research Unit, 5310 Old Main Hill, Utah State University, Logan, UT 84322, USA; ORCID-iD: [https://orcid.org/0000-0002-3734-6166](https://orcid.org/0000-0002-3734-6166)

2ETH Zurich, Institute of Agricultural Sciences, Biocommunication and Entomology, Schmelzbergstrasse 9/LFO, 8092 Zurich, Switzerland

3Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, P. R. China.

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