Ultraconserved elements resolve the phylogeny and corroborate patterns of molecular rate variation in herons (Aves: Ardeidae)

Lay Summary center dot We use genetic data from across the genome and produce a robust family tree for herons, which clarifies the relationships among subfamilies and genera. center dot A comprehensive phylogeny of herons is lacking. As a result, their taxonomy is unstable and their evolutionary history is poorly known. center dot Several species were found to be incorrectly classified, and we recommend appropriate taxonomic revisions. center dot Comparisons of molecular evolution support previous studies. Bitterns have evolved comparatively faster, with some tiger herons and the Boat-billed Heron having evolved comparatively slower. Thoroughly sampled and well-supported phylogenetic trees are essential to taxonomy and to guide studies of evolution and ecology. Despite extensive prior inquiry, a comprehensive tree of heron relationships (Aves: Ardeidae) has not yet been published. As a result, the classification of this family remains unstable, and their evolutionary history remains poorly studied. Here, we sample genome-wide ultraconserved elements (UCEs) and mitochondrial DNA sequences (mtDNA) of >90% of extant species to estimate heron phylogeny using a combination of maximum likelihood, coalescent, and Bayesian inference methods. The UCE and mtDNA trees are mostly concordant with one another, providing a topology that resolves relationships among the 5 heron subfamilies and indicates that the genera Gorsachius, Botaurus, Ardea, and Ixobrychus are not monophyletic. We also present the first genetic data from the Forest Bittern Zonerodius heliosylus, an enigmatic species of New Guinea; our results suggest that it is a member of the genus Ardeola and not the Tigrisomatinae (tiger herons), as previously thought. Finally, we compare molecular rates between heron clades in the UCE tree with those in previously constructed mtDNA and DNA-DNA hybridization trees. We show that rate variation in the UCE tree corroborates rate patterns in the previously constructed trees-that bitterns (Ixobrychus and Botaurus) evolved comparatively faster, and some tiger herons (Tigrisoma) and the Boat-billed Heron (Cochlearius) more slowly, than other heron taxa.