The typical owl family (Strigidae) comprises 194 species in 28 genera, 14 of which are monotypic. Relationships within and among genera in the typical owls have been challenging to discern because mitochondrial data have produced equivocal results and because many monotypic genera have been omitted from previous molecular analyses. Here, we collect and analyze ultraconserved elements (UCEs) from 43 species of typical owls to produce concatenated and multispecies coalescent-based phylogenetic hypotheses for all but one genus in the typical owl family. Our results reveal extensive paraphyly of different taxonomic groups across phylogenies inferred using different analytical approaches. For example, we resolved a clade comprising Glaucidium brodiei and the monotypic genera Micrathene and Xenoglaux that excluded other Glaucidium species; we resolved Pyrroglaux podargina nested in a clade consisting of other Otus species; all analyses suggested Nesasio solomonensis and Pseudoscops grammicus belonged in a clade consisting of other Asio species; and Scotopelia peli and Ketupa ketupu were nested in a clade comprising other Bubo species. Secondary analyses of protein coding mitochondrial genes harvested from UCE assemblies and downloaded from GenBank generally support the extent of paraphyly we observed, while there are some disagreements at higher taxonomic levels between our nuclear and mitochondrial results. In sum, our results suggest the genera Athene, Otus, Asio, Megascops, Bubo, and Strix are paraphyletic, while Ninox and Glaucidium are polyphyletic, reiterating the importance of taxon sampling for understanding and describing evolutionary relationships and suggesting the need for additional sampling, study, and taxonomic revision of this fascinating avian group.
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