Conflicting phylogenomic signals unveil reticulate evolution in Uraria and allies (Leguminosae: Desmodieae)

The tribe Desmodieae represents one of the most taxonomically challenging lineages within Leguminosae, characterized by high morphological diversity and phylogenetic incongruence that have long hindered generic delimitation. Here, we addressed this taxonomic problem using Uraria and its allied genera as a case study. We integrated genome-scale nuclear and plastid datasets generated from transcriptome sequencing and whole-genome resequencing to reconstruct the evolutionary history of this lineage. Our phylogenomic reconstructions, based on 1,079 single- or low-copy nuclear genes and complete plastomes, recovered Urariopsis brevissima as a strongly supported, early-diverging lineage and showed that Uraria and Christia are non-monophyletic. We observed gene-tree discordance in the relationships of Uraria and Christia, both among individual gene trees and between nuclear and plastid phylogenies. Using complementary phylogenomic approaches, we evaluated the sources of the observed gene-tree discordance, and found that gene-tree estimation error had the largest relative explanatory contribution overall, and gene flow had a greater explanatory contribution than ILS among the biological factors evaluated. Analyses of incomplete lineage sorting (ILS) and gene flow, together with network inference, yielded patterns consistent with a putative reticulation scenario between Uraria and Christia. On the basis of these phylogenomic findings, we proposed taxonomic treatments that recognize Urariopsis as a distinct genus and transfer Christia campanulata to Uraria. Our results not only clarify the taxonomy of Uraria and its allied genera but also offer a phylogenomic framework for reassessing generic delimitation in Desmodieae.