Premise Understanding relationships among orchid species and populations is of critical importance for orchid conservation. Target sequence capture has become a standard method for extracting hundreds of orthologous loci for phylogenomics. Up-front cost and time associated with design of bait sets makes this method prohibitively expensive for many researchers. Therefore, we designed a target capture kit to reliably sequence hundreds of orthologous loci across orchid lineages. Methods We designed an Orchidaceae target capture bait set for 963 single-copy genes identified in published orchid genome sequences. The bait set was tested on 28 orchid species, with representatives of the subfamilies Cypripedioideae, Orchidoideae, and Epidendroideae. Results Between 1,518,041 and 87,946,590 paired-end 150-base reads were generated for target-enriched genomic libraries. We assembled an average of 812 genes per library for Epidendroideae species and a mean of 501 genes for species in the subfamilies Orchidoideae and Cypripedioideae. Furthermore, libraries had on average 107 of the 254 genes that are included in the Angiosperms353 bait set, allowing for direct comparison of studies using either bait set. Discussion The Orchidaceae963 kit will enable greater accessibility and utility of next-generation sequencing for orchid systematics, population genetics, and identification in the illegal orchid trade.

Premise Researchers adopting target-enrichment approaches often struggle with the decision of whether to use universal or lineage-specific probe sets. To circumvent this quandary, we investigate the efficacy of a simultaneous enrichment by combining universal probes and lineage-specific probes in a single hybridization reaction, to benefit from the qualities of both probe sets with little added cost or effort. Methods and Results Using 26 Brassicaceae libraries and standard enrichment protocols, we compare results from three independent data sets. A large average fraction of reads mapping to the Angiosperms353 (24–31%) and Brassicaceae (35–59%) targets resulted in a sizable reconstruction of loci for each target set (x̄ ≥ 70%). Conclusions High levels of enrichment and locus reconstruction for the two target sets demonstrate that the sampling of genomic regions can be easily extended through the combination of probe sets in single enrichment reactions. We hope that these findings will facilitate the production of expanded data sets that answer individual research questions and simultaneously allow wider applications by the research community as a whole.

The long-term impact of viruses residing in the human bone marrow (BM) remains unexplored. However, chronic inflammatory processes driven by single or multiple viruses could significantly alter hematopoiesis and immune function. We performed a systematic analysis of the DNAs of 38 viruses in the BM. We detected, by quantitative PCRs and next-generation sequencing, viral DNA in 88.9% of the samples, up to five viruses in one individual. Included were, among others, several herpesviruses, hepatitis B virus, Merkel cell polyomavirus and, unprecedentedly, human papillomavirus 31. Given the reactivation and/or oncogenic potential of these viruses, their repercussion on hematopoietic and malignant disorders calls for careful examination. Furthermore, the implications of persistent infections on the engraftment, regenerative capacity, and outcomes of bone marrow transplantation deserve in-depth evaluation.

Robber or assassin flies (Asilidae) are a diverse family of venomous predators. The most recent classification organizes Asilidae into 14 subfamilies based on a morphological phylogeny, but many of these are not supported by molecular data. To test the monophyly of various clades in Asilidae, we used the recently developed Diptera-wide ultraconserved element bait set to compile seven datasets comprising 151 robber flies and 145–2496 loci. We also compared the performance of various nodal support metrics. Our Maximum Likelihood phylogeny was fully resolved and well supported, but partially incongruent with the coalescent phylogeny. Further examination of datasets suggested that GC bias had influenced gene tree inference and subsequent species tree analyses. The subfamilies Brachyrhopalinae, Dasypogoninae, Dioctriinae, Stenopogoninae, Tillobromatinae, Trigonomiminae and Willistonininae were not recovered as monophyletic. The inter-subfamily relationships are summarized as follows: Laphriinae and Dioctriinae (in part) successively sister to the remaining subfamilies, which form two clades: the first consists of a grade of Stenopogoninae (in part), Willistonininae (in part), Bathypogoninae+Phellinae, Stichopogoninae, Leptogastrinae, Ommatiinae and Asilinae; the second clade consists of a paraphyletic assemblage of genera from Dioctriinae (in part), Trigonomiminae, Stenopogoninae (in part), Tillobromatinae, Brachyrhopalinae and Dasypogoninae. This phylogeny demonstrates that the higher classification of Asilidae is far from settled, but does provide a much-needed foundation for a thorough revision of the subfamily classification.

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 resolve the phylogeny of Osmia s.s. and show strong support that Nearctic Osmia ribifloris is the sister group to the rest of the subgenus. Biogeographic analyses indicate that the group originated during the Late Miocene in the West Nearctic plus East Palearctic region following dispersal from the East Palearctic to the West Nearctic across the Bering land bridge prior to its closure 5.5–4.8 Ma. The mitochondrial DNA results reveal potential taxonomic synonymies involving Osmia yanbianensis and Osmia opima, and Osmia rufina, Osmia rufinoides and Osmia taurus.