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Abstract PremiseThe genusCalceolaria(Calceolariaceae) is emblematic of the Andes, is hypothesized to have originated as a recent, rapid radiation, and has important taxonomic needs. Additionally, the genus is a model for the study of specialized pollination systems, as its flowers are nectarless and many offer floral oils as a pollination reward collected by specialist bees. Despite their evolutionary and ecological significance, obtaining a resolved phylogeny for the group has proved difficult. To address this challenge, we present a new bait set for targeted sequencing of nuclear loci in Calceolariaceae and close relatives. MethodsWe developed a bioinformatic workflow to use incomplete, low‐coverage genomes of 10Calceolariaspecies to identify single‐copy loci suitable for phylogenetic studies and design baits for targeted sequencing. ResultsOur approach resulted in the identification of 809 single‐copy loci (733 noncoding and 76 coding regions) and the development of 39,937 baits, which we validated in silico (10 specimens) and in vitro (29 Calceolariaceae and six outgroups). In both cases, the data allowed us to recover robust phylogenetic estimates. DiscussionOur results demonstrate the appropriateness of the bait set for sequencing recent and historic specimens of Calceolariaceae and close relatives, and open new doors for further investigation of the evolutionary history of this hyperdiverse genus. 

Abstract Calceolaria (Calceolariaceae) is an emblematic and diverse genus in the Americas. Despite being one of the most easily recognized genera in the region and a system with great potential to improve our understanding of different drivers of species diversification in the Andes, its intrageneric evolutionary relationships are still poorly understood. Responding to the need for additional molecular markers to resolve the phylogenetic relationships of the group, we perform plastome analyses and resolve the backbone of the genus. Specifically, using low-coverage genomes for 14 species, we assembled plastomes, estimated and dated phylogenetic hypotheses and evaluated evolutionary trends in the group. Our approach allowed us to resolve the backbone of the genus, identify two main clades and estimate a timing of diversification contemporaneous to major climatic and orogenic events. Our biogeographic reconstructions suggest an independent colonization of the whole range of the genus by both clades. Finally, our evaluations of floral morphology reveal future avenues for investigating the relationship between the pollination biology and diversification of the group.