In the Northern Hemisphere, East Asia is a pivotal biogeographic region as it presents high levels of plant species diversity and endemism [14, 15]. Based on Takhtajan’s  floristic system, southern East Asia belongs to the Paleotropical Kingdom, whereas northern East Asia is part of the Holarctic Kingdom (Fig. 1). Recent molecular phylogenetic studies also indicate that the Tertiary relict floras within East Asia could be subdivided into two distinct southern and northern regions [17, 18]. The former consists of southern and southeastern China with extending to the Himalayas, while the latter contains Japan, Korea, and northeastern China. Besides, as a continental island adjacent to southeastern mainland China, the Ryukyus Islands, and Philippines, the floristic source of Taiwan is not clear [19–21]. To date, biogeographic relationships among southern East Asia, northern East Asia and Taiwan are far from understood.Fig. 1Geographic range of Coptis species. Doted lines in bold demarcate boundaries of the Holarctic and Paleotropical kingdoms according to Takhtajan 