The Phylogenomic Framework and Infrageneric Classification of Temperate Asian Caraganeae (Leguminosae, Papilionoideae)

The legume tribe Caraganeae, consisting of the genera <i>Caragana</i>, <i>Calophaca</i>, and <i>Halimodendron</i>, is a mid-sized, shrubby clade mainly found in temperate Central and Eastern Asia. Within this tribe, <i>Caragana</i> is the largest genus comprising 63-74 species, and it is recognized for its taxonomic complexity. However, the phylogenetic framework of Caraganeae and the infrageneric delimitations in <i>Caragana</i> remain inadequately resolved. In this study, fifty-four species of Caraganeae were sampled, including 51 <i>Caragana</i> species representing all sections in previous taxonomical treatments. By using the genome skimming approach, we reconstructed the phylogenetic framework, inferred the infrageneric delimitations, and explored the historical diversification of the tribe. Our results demonstrated that Caraganeae is monophyletic, yet significant phylogenetic discordance in tree topology between the complete chloroplast genome and nuclear ribosomal DNA datasets was observed at both deep and shallow nodes. Within Caraganeae, the cp genome tree resolved nine highly supported lineages, with <i>Calophaca</i> and <i>Halimodendron</i> nested within <i>Caragana</i>. Molecular dating estimates suggest that Caraganeae originated during the Oligocene (stem age, 27.47 Ma, 95% HPD: 16.48-38.44 Ma), and diversified during the mid-Miocene (crown age, 16.79 Ma, 95% HPD: 7-30.13 Ma). These findings provide important insights for clarifying the phylogenetic relationships in Caraganeae. The observed cytonuclear discordance may result from hybridization and/or incomplete lineage sorting. Furthermore, climatic and geological changes since the Eocene-Oligocene Transition-including global cooling, progressive aridity, and the rapid uplift of the Qinghai-Tibetan Plateau-likely played essential roles in driving radiative diversification of Caraganeae.