Phylogenetic and Population Genetic Analysis Decipher the Taxonomic Consistency on Cryptic Betula costata Trautv. (Betulaceae) Populations in Japan and the Process on Its Divergence and Isolation

East Asia is rich in physiographical heterogeneity, which has resulted in greater species diversity and the persistence of relict species, potentially concealing undiscovered tree populations. Betula costata is an ideal species for studying the persistence of relict plants in this region; notably, cryptic populations of this species have been reported in central Japan in recent years. In contrast, given the taxonomic complexity of the genus Betula , which exhibits high levels of intraspecific variation and interspecific hybridization, molecular evidence is essential for clear species delineation. This study is the first to estimate the phylogenetic position of putative B. costata populations in Japan and evaluate their history of divergence and isolation using restriction site‐associated DNA sequencing (RAD‐seq), a method well‐suited for deciphering complex phylogenetic relationships within Betula . Both maximum likelihood and neighbor‐joining trees placed the putative Japanese B. costata individuals in the same cluster as B. costata from China. Leaf morphology (e.g., leaf length, width, and the number of veins) and ploidy levels estimated via flow cytometry (which confirmed a diploid state) also supported the classification of the Japanese individuals as B. costata . Population genetic analysis revealed low genetic distinctness between populations, as well as evidence of a past bottleneck and population size decline. Our findings suggest that B. costata in Japan diverged from continental populations and has persisted in isolated enclaves with benign environmental conditions since the Last Glacial Maximum.