Phylogeography of Semenovia malcolmii, an endemic species on the Qinghai-Tibet Plateau

Early orogeny and historical climate change strongly influenced the evolution and geological distribution of flora. To further understand the effects of the uplift of the Qinghai-Tibet Plateau (QTP) and Quaternary climatic oscillations on the evolution of modern alpine plants, we conducted a phylogeographic study on Semenovia malcolmii , which is distributed on the QTP and in adjacent areas. We sampled a total of 337 individuals from 45 populations and used a combination of two nuclear fragments ( ITS and ETS ) and three chloroplast fragments ( rps 16, trn L- trn T, and ndh F- rpl 32) to analyze the genetic diversity and differentiation of the species and evaluated the impact of early climatic and geological events on the genetic structure of the populations. Thirty-four nuclear rDNA haplotypes and 33 plastid haplotypes were identified and they formed three branches in the phylogenetic tree. This important phylogenetic structure suggested that S. malcolmii may have experienced long periods of geographic isolation. Based on molecular clock analysis, two divergence events occurred within the species, at approximately 3.34 Ma and 2.57 Ma, leading to the formation of the three major lineages. The populations of S. malcolmii exhibited relatively high genetic diversity and haplotype diversity throughout its entire distribution range. Therefore, we propose that S. malcolmii had multiple refugia across the QTP during the Quaternary glaciation.