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’ distributions and diversification, yet their impacts on plant biogeography and population demographic history often remain unclear. In this study, the effects of habitat fragmentation and historical climatic shifts on the genetic diversity and phylogeography of four East Asian Morella species were investigated. Chloroplast DNA (cpDNA) sequences and simple sequence repeats (SSRs) were used to assess population genetic structure and phylogenetic relationships within Morella based on 477 individuals from 63 populations. Whole-genome resequencing was also utilized to ensure the accuracy of divergence time estimates and reconstructed phylogenetic relationships. Most cpDNA haplotypes were species-specific, with only two haplotypes shared among species: H2 was shared by M. adenophora and M. rubra, while H3 was shared by M. esculenta and M. rubra. Phylogenetic reconstruction supported the following relationships: M. esculenta + (M. nana (M. rubra + M. adenophora)). There was also evidence of significant gene flow among species. The four study species diverged between 5.02 and 12.72 Ma, before the Quaternary period. Late Miocene-Pliocene geologic and climatic shifts likely drove speciation, while Quaternary climate fluctuations shaped species’ geographic ranges, with potential refugia maintaining genetic diversity through the Last Glacial Maximum. These findings highlight the roles of orogeny and paleoclimatic events in driving speciation and range dynamics, providing insights into East Asia’s history of plant species diversification.