Gene tree discordance characterizes shallow evolutionary scales of Tillandsia subgenus Tillandsia (Bromeliaceae, Poales)

Phylogenetic discordance poses significant challenges for reconstructing evolutionary relationships, particularly in recently diversified lineages where incomplete lineage sorting, hybridization, and gene flow may obscure evolutionary history. We employed a Hyb-Seq approach to generate complete plastomes and nuclear data from 295 loci to investigate phylogenetic relationships and discordance in the Tillandsia erubescens species group, a recently radiated lineage endemic to Mexico. Phylogenetic analyses confirmed the monophyly of the T. erubescens species group in both plastid and nuclear datasets. No strongly supported discordance was detected between plastome and coalescence-based nuclear trees within the group, indicating broad agreement between genomic compartments at the species level. In contrast, PhyParts analyses revealed extensive discordance among individual nuclear gene trees, with most loci supporting alternative topologies relative to both the plastome tree and nuclear species tree. Discordance was most pronounced at deeper nodes, whereas shallower relationships showed greater concordance. Low gene concordance and site concordance factor values indicate heterogeneous phylogenetic signal across loci, consistent with rapid diversification. These findings demonstrate the utility of phylogenomic approaches that integrate multiple genomic compartments and accommodate gene-tree heterogeneity when investigating recent evolutionary radiations.