Shifting roles of the East China Sea in the phylogeography of red nanmu in East Asia

This dataset contains one README file and two raw data files on the distribution and genetic data described in the paper: Jiang et al. (2021) Shifting roles of the East China Sea in the phylogeography of Machilus thunbergii (Lauraceae) in East Asia. Journal of Biogeography.

Ecological niche modeling was employed to predict the potential distribution of M. thunbergii during the Last Glacial Maximum (LGM) and the last interglacial period. Nuclear microsatellite and chloroplast markers were used to reveal the phylogeographic pattern and infer the population history of 33 M. thunbergii populations.

The ecological niche models suggested that the ECS provided potentially suitable habitats for M. thunbergii during the LGM. A sharp change in cpDNA haplotypes was found along the eastern China coasts, while microsatellites revealed a clinal pattern for genetic composition from eastern China to central Japan. The divergent lineages formed an admixture on the Zhoushan Archipelago of China and Kyushu Island of Japan. The estimated divergent and admixture times were c. 68 kyr and c. 15 kyr, corresponding to the periods where there were rising sea levels after the MIS4 glaciation and falling sea levels during the LGM, respectively. 

Machilus thunbergii probably underwent alternating population isolation during interglacial periods and connection during glacial maxima across the ECS, but such periodicity of isolation and connection seems not to have promoted diversification as suggested by the species pump hypothesis. Incipient divergence has been periodically wiped out due to frequent coalescence, rendering the ECS more like a "species vacuum", particularly for species with relatively long generation lengths.