Hyb-Seq data of 27 species of the plant genus Lachemilla (Rosaceae) and three species from closely related genera Targeted loci

Hybridization, incomplete lineage sorting (ILS) and phylogenetic error produce similar incongruence patterns representing a great challenge for phylogenetic reconstruction. Here we use sequence capture data and multiple species tree and species network approaches to resolve the backbone phylogeny of the Neotropical genus Lachemilla, while distinguish the sources of incongruence. We used 396 nuclear loci and complete chloroplast sequences from 27 species to clarify the relationships among the major groups of Lachemilla, and explored multiple sources of conflict between gene tree and species tree inferred with a plurality of approaches. All phylogenetic methods recovered the four major groups previously proposed for Lachemilla, but species tree methods recovered different topologies for relationships between these four clades. Species network analyses revealed that one major clade, Orbiculate, is of ancient hybrid origin and the main sources of the incongruence among the species trees. Additionally, we found evidence for a whole genome duplication event shared by Lachemilla and allied genera. Lachemilla shows clear evidence of ancient and recent hybridization throughout the evolutionary history of the group. Also, it is clear that it is necessary to use phylogenetic approaches that can simultaneously accommodate ILS and hybridization when studying groups that show patterns of reticulation.