Data for: Phylogenetic resolution and conflict in the species-rich flowering plant family Leguminosae

The Tree of Life is central to evolutionary biology, yet resolving deep,
recalcitrant phylogenetic relationships remains challenging due to complex
processes such as incomplete lineage sorting (ILS), hybridization, and
polyploidization. Although previous phylogenetic studies have advanced our
understanding of Leguminosae (Fabaceae), a species-rich and ecologically
diverse family, many deep relationships at the tribal and higher levels
remain unresolved. Integrating newly generated genome skimming data for
231 species with previously issued plastid genomic, mitochondrial genomic
and transcriptomic data, we reconstructed a phylogeny of the family using
whole plastome, 39 mitochondrial genes, and 1559 low-copy nuclear genes,
achieving dense taxonomic sampling across almost all recognized tribes and
major unplaced lineages. Our results supported the monophyly of the six
subfamilies and 49 recognized tribes, resolved ten clades worthy of
recognition as new tribes in subfamily Papilionoideae, and clarified many
contentious relationships. However, nuclear-nuclear and cytonuclear
conflicts persists at multiple nodes among trees inferred from different
datasets and analytical methods. We propose the most probable resolution
for 22 contentious nodes by applying nuclear gene-tree quartet analysis
and corroboration from support of nuclear Maximum Likelihood (ML) and
ASTRAL trees. Our results indicate ILS significantly contributes to
observed phylogenetic conflicts, while gene flow represents an additional
and previously underappreciated factor that mainly contributes to
cytonuclear conflicts, particularly along the branches of the
Angylocalyceae + Dipterygeae + Amburaneae (ADA) clade and Wisterieae. Both
processes likely underlie recalcitrant phylogenetic relationships, such as
those within the 50-kb inversion clade of Papilionoideae. Our study uses
multiple data partitions and analytical methods to resolve contentious
phylogenetic relationships in Leguminosae, resulting in a robust
phylogenomic framework to guide further investigations in this
economically important and exceptionally diverse family.