Phylogenetic Relationships and Ecological Adaptability Diversity of Twelve Caragana Species in China

Background The spatial replacement distribution pattern observed among Caragana species makes this genus an ideal model for investigating plant ecological adaptation and biodiversity maintenance mechanisms. However, the molecular basis underlying these adaptive strategies remains unclear. Results We generated a full-length transcriptome of C. korshinskii and second-generation transcriptomes for 12 Caragana species collected from Inner Mongolia, Xinjiang, and Tibet. Based on the identified single-copy and one-to-one orthologous genes, we performed comparative transcriptomic analyses to reconstruct a robust phylogenetic tree, thereby elucidating the evolutionary relationships among these Caragana species—particularly the three small-leaved taxa ( C. intermedia , C. korshinskii , and C. microphylla ). Evolutionary analyses identified positively selected genes and rapidly evolving genes associated with divergent adaptive strategies, including flowering phenology modulation, root system optimization, and reactive oxygen species scavenging. In addition, cuticular wax and cutin biosynthesis pathways were identified as conserved xeromorphic traits shared among multiple species. Furthermore, convergent evolution was observed in species occupying similar altitudinal and hydrothermal niches, as evidenced by parallel amino acid substitutions in C2H2, C3H, NAC, and mTERF transcription factor families, suggesting their key roles in ecological convergence. Conclusions This study not only resolves phylogenetic uncertainties within twelve Caragana species but also elucidates the molecular evolutionary mechanisms underlying their ecological adaptations. Our findings reveal how closely related species achieve ecological divergence through both adaptive and convergent evolution, offering new insights into plant adaptation under spatial replacement dynamics.