Daniel J. Gates, Diana Pilson, Stacey D. Smith

This paper tests multiple methods for detecting and localizing hybrids in the genus Iochroma (Solanaceae). We created a series of datasets varying in the amount of expected hybridization, and we included both natural hybrids and a positive control (an artificial hybrid). We found that adding hybrids to the dataset markedly increased discordance and decreased tree certainty, as predicted. Nevertheless, our analyses largely failed to correctly identify hybrid taxa and their parental lineages, even for the positive control. We suggest several paths forward for improving the detection and localization of hybridization in phylogenomic datasets.