Data from: Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae)

Hybridization, incomplete lineage sorting, 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
distinguishing among sources of incongruence. We used 396 nuclear loci and
nearly complete plastome sequences from 27 species to clarify the
relationships among the major groups of Lachemilla, and explored multiple
sources of conflict between gene trees and species trees 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 likely of ancient hybrid origin, representing one of the
main sources of incongruence among the species trees. Additionally, we
found evidence for a potential 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, we show the necessity to use phylogenetic network approaches that
can simultaneously accommodate incomplete lineage sorting and gene flow
when studying groups that show patterns of reticulation.