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The Neotropical Gesneriaceae is a lineage known for its colorful and diverse flowers, as well as an extensive history of intra‐ and intergeneric hybridization, particularly among Achimenes (the magic flowers) and other members of subtribe Gloxiniinae. Despite numerous studies seeking to elucidate the evolutionary relationships of these lineages, relatively few have sought to infer specific patterns of gene flow despite evidence of widespread hybridization.

To explore the utility of phylogenomic data for reassessing phylogenetic relationships and inferring patterns of gene flow among species of Achimenes, we sequenced 12 transcriptomes. We used a variety of methods to infer the species tree, examine gene tree discordance, and infer patterns of gene flow.

Phylogenomic analyses resolve clade relationships at the crown of the lineage with strong support. In contrast to …