Miocene diversification of a golden-thread nanmu tree species (Phoebe zhennan, Lauraceae) around the Sichuan Basin shaped by the East Asian monsoon

Understanding the role of climate changes and geography as drivers of population divergence and speciation is a long-standing goal of evolutionary biology and can inform conservation. In this study, we used restriction site-associated DNA sequencing (RAD-seq) to evaluate genetic diversity, population structure, and infer demographic history of the endangered tree,Phoebe zhennanwhich is distributed around the Sichuan Basin. Genomic patterns revealed two distinct clusters, each largely confined to the West and East. Despite sympatry of the two genomic clusters at some sites, individuals show little or no evidence of genomic introgression. Demographic modeling supported an initial divergence time between the West and East lineages at similar to 15.08 Ma with further diversification within the West lineage at similar to 7.12 Ma. These times largely coincide with the two independent intensifications of the East Asian monsoon that were initiated during the middle (Langhian) and late Miocene (Messinian), respectively. These results suggest that the Miocene intensification phases of the East Asian monsoon played a pivotal role in shaping the current landscape-level patterns of genetic diversity withinP. zhennan, as has been found for the interspecific divergence of other subtropical Chinese plants. Based on isolation-by-distance and species distribution modeling, we hypothesize thatP. zhennanfollowed a ring diversification which was facilitated by the Sichuan Basin acting as barrier to gene flow. In situ and ex situ conservation management plans should consider the results obtained in this study to help secure the future of this beautiful and culturally significant endangered tree.