Phylogeography and ecological niche modelling implicate multiple micro-refugia of Swertia tetraptera during Quaternary glaciations

Background: Climate fluctuations during the Pleistocene and mountain uplift are vital driving powers affecting the geographic distribution and population dynamics history of organisms. However, how did an annual plant react to Pleistocene glaciations was little to know. Methods In this study, we analyzed the population demographic history of the endemic QTP annual herb plant Swertia tetraptera Maxim (Gentianaceae). Phylogeographic analysis with species distribution modeling were combined to detect the genetic variations in S.tetraptera . In total, 301 individuals from 35 populations of S.tetraptera were analyzed based on two maternally inherited chloroplast fragments ( trn L- trn F and trnS - trnG ). Results The genetic diversity of S.tetraptera was high, which was caused by wide natural range, high proportion of endemic haplotypes and evolutionary history. Fifty-four haplotypes were identified in S.tetraptera . Only a few haplotypes were widespread (H4, H1, H3) which were dispersed throughout the present geographical range of S.tetraptera , while a lot of haplotypes were confined to single populations. The cpDNA dataset showed that the phylogeographic structure was lack across the distribution range of S.tetraptera . Meanwhile, analyses of molecular variance showed that most of genetic variation was found within populations (70.51%). In addition, the relationships of the haplotypes were almost completely not resolved by phylogenetic reconstruction. Both mismatch distribution analysis and neutrality tests showed a recent expansion across the distribution range of S. tetraptera . The MAXENT analysis showed S.tetraptera had a wider distribution range during the last glacial maximum and a narrower distribution range during the current, with predictions into the future showing the distribution range of S.tetraptera shrinking. Conclusion Our study implies current geographic and genetic distribution of S.tetraptera is likely to have been shaped by both QTP uplift and Quaternary periods. Multiple micro-refugia of S.tetraptera were existed during Quaternary glaciations. Rapid intraspecific diversification and hybridization and/or introgression may have played a vital role in shaping current distribution patterns of S.tetraptera. The distribution range of S.tetraptera appeared to have experienced expansion during the LGM; in the future, when the global climate becomes warmer with rising carbon dioxide, the distribution of S.tetraptera will expansion and migration to higher altitude.