Aim: East Asia exhibits complex geomorphological and climatic characteristics. The aim of this study was to test whether the so-called three-step landforms of China, together with the East China Sea (ECS), have acted to shape specific phylogeographic patterns and affected the biogeographic history of the species belonging to the East Asian Flora (EAF).

Location: China and Japan

Taxon: Kerria japonica (L.) DC

Methods: Three chloroplast DNA (cpDNA) regions and 15 nuclear microsatellite (nSSR) loci were sequenced and genotyped in 576/450 individuals of K. japonica. Phylogeographical analyses were performed to assess the genetic structure, historical gene flow, and demographic history of these individuals, and climatic factors were examined to determine their effects on phylogeographical breaks. Furthermore, time-calibrated phylogenetic trees and ancestral range reconstruction were used to infer the biogeographic history of K. japonica. Potential habitats at present and during the last glacial maximum (LGM) were identified using ecological niche modelling (ENM).

Results: Distinct phylogeographical breaks were found across the ECS and along the boundary of the three-step landforms of China. Low historical gene flow and significant climatic differences were detected in each pair of adjacent regions. The results of molecular dating and ancestral range reconstruction indicated that K. japonica originated in North America during the mid-Miocene (14.76 Ma), and intra-specific diversification began in the late Miocene (7.78 Ma). Compared to the relatively stable distribution range of Chinese populations, Japanese populations experienced range expansion after the LGM in response to Quaternary climate change.

Main conclusions: Kerria japonica has a complex biogeographic history, with a mid-Miocene origin in North America and subsequent migration into East Asia via the Bering land bridge. The onset of intra-specific diversification was probably associated with Asian monsoon intensifications, while exposure to the ECS floor facilitated the formation of the Japanese lineage in the late Miocene. The spatiotemporal population differentiation on the Chinese mainland demonstrates the significant role of biogeographic divides delineated by the three-step landforms of China and provides clues to understand the floristic regionalization and evolutionary history of plant diversity in East Asia, especially with respect to the Hengduan Mountains, Central China, and East China.