A Phylogenomic Analysis of <i>Genipa</i> (Rubiaceae) Using Target Sequence Capture Data

Abstract— The genus Genipa is a widespread, lowland, Neotropical lineage of trees in the coffee family, Rubiaceae. There is long-standing disagreement on the delimitation of species in the genus and how broadly Genipa is circumscribed. Here, we use genomic data to resolve the classification within Genipa . Using target sequence capture we generated a high-resolution 245-locus dataset to produce a comprehensive species phylogeny under the multi-species coalescent model. The phylogenomic results strongly support Genipa spruceana, often synonymised with Genipa americana , as a distinct monophyletic species. Similarly, the monophyly of Genipa infundibuliformis , a recently recognized species, is also strongly supported. The phylogeny also shows three distinct, well-supported clades within the widespread species, Genipa americana . These clades are interpreted as three independently evolving lineages in contrast to the two varieties most commonly recognized in G. americana based on previous morphological studies.