Population Genetic Differentiation and Evolutionary History in Liriodendron Revealed by Stress‐Related Single‐Copy Genes

Liriodendron was widely distributed across the Northern Hemisphere during the early to middle Miocene, but now is confined to East Asia and North America. As a relic plant of environmental shifts, Liriodendron provides valuable insights into the adaptation of temperate trees to changing environments. To investigate the genetic differentiation and evolutionary history of Liriodendron , 8667 single‐copy orthologs were identified as ideal markers owing to their slow mutation rate and generational stability. Their most enriched functions, specifically in energy metabolism, photosynthetic efficiency, and stress resilience, underpinned Liriodendron' s survival in harsh conditions. Three single‐copy genes ( LtDHN2 , LtDHN3 , and LtTLP11 ) associated with abiotic stress tolerance were cloned and sequenced in 20 Liriodendron populations. LtDHN2 , LtDHN3 , and LtTLP11 exhibited high SNP density (1/15.80–1/19.45 bp) and significant interspecific differentiation ( F st = 0.71–0.94), whereas intraspecific variation was minimal, suggesting recent expansion. Both L. tulipifera and the eastern and western populations of L. chinense served as ancestral populations, exhibiting asymmetric historical gene flow among these populations. Divergence events were driven by disrupted trans‐Beringian gene flow (11.4–13.4 Ma) and Quaternary glaciations (2.19–2.23 Ma). The effective population size of L. chinense underwent rapid expansion during the Early Last Glacial and the Last Interglacial, while L. tulipifera exhibited recolonization during the warmer MIS 3 interstadial resilience phase, the fluctuating substages of the Last Interglacial, and the late Penultimate Glacial Maximum warming phase. These findings highlight how paleogeographic constraints, climatic oscillations, and locus‐specific selection have shaped the evolutionary trajectory and current disjunct distribution of Liriodendron .