Effects of mountain uplift and climate change on phylogeography and species divergence of East Asia Morella

Mountain uplift and Quaternary climate oscillations have profoundly influenced plant species' distribution and diversification, yet their impacts on demographic history and biogeographic patterns remain unclear. This study investigates the effects of habitat fragmentation and climatic shifts on genetic diversity and phylogeographic distribution of four East Asian Morella species. Using chloroplast DNA (cpDNA) sequences and simple sequence repeats (SSR) were used to study the species divergence and genetic structure of Morella from 477 individuals of 63 populations. The whole-genome resequencing was also applied to ensure the accuracy of the estimation of species differentiation time and phylogenetic relationship. We identified species-specific haplotypes, only H2 haplotype was shared by M. rubra and M. adenophora , and H3 was shared by M. esculenta and M. rubra in cpDNA sequence. Phylogenetic analysis revealed a topology of M. esculenta + ( M. nana ( M. rubra + M. adenophora )), with significant gene flow among species. Its divergence occurring between 5.02 and 12.72 Ma was completed before the Quaternary period. Results suggest Late Miocene-Pliocene geological and climatic shifts drove speciation, while Quaternary climate fluctuations shaped their geographic distribution, with potential refugia maintaining genetic diversity. Our findings highlight the roles of orogeny and paleoclimate in speciation and range dynamics, providing insights into East Asia's history of lineage differentiation.