After Coptis diverged from Xanthorhiza, a subsequent dispersal from Japan to southern East Asia occurred in the early late Miocene (9.55 Ma, 95% HPD: 6.66–12.92; node 2). This time is markedly later than the time of the opening of the Japan Sea (23–15 Ma), which separated the Japanese Islands from the Northeast Asian margins [54–56]. However, during the early late Miocene, a marked drop of sea level occurred (Fig. 3) , which might have resulted in East China Sea seafloor exposure between the Eurasian mainland and the Japanese Archipelago. Hence, Coptis could have migrated westward into continental Asia via this land bridge. Subsequent sea-level rise might have resulted in the interruption of population exchange of the genus between the Asian mainland and the Japanese Islands. Accordingly, Coptis diverged into two clades (I and II).