Population Demographic History of a Rare and Endangered Tree Magnolia sprengeri Pamp. in East Asia Revealed by Molecular Data and Ecological Niche Analysis

Quaternary climate and environment oscillations have profoundly shaped the population dynamic history and geographic distributions of current plants. However, how the endangered and rare tree species respond to the climatic and environmental fluctuations in the subtropical regions of China in East Asia still needs elucidation. In this study, we collected 36 natural populations of an endangered and rare tree species Magnolia sprengeri Pamp. in subtropical China to determine the demographic history, and modeled the changes of geographic distributions of this species in East Asia based on the MaxEnt ecological niche analyses. In addition, we sequenced three maternally inherited chloroplast DNA fragments (matK, trnH-psbA, and rbcL) for all the natural populations which covered the whole geographic distributions of M. sprengeri. Population genetic analysis showed that the endangered tree species have a low level of chloroplast DNA diversity. However, the genetic variation contribution within populations was greater than that among populations (FST = 0.276), which demonstrated a high level of genetic differentiation. Interestingly, some unique chloroplast DNA haplotypes and higher genetic variations were identified in the Qinling-Daba Mountains, Central China, and Tianmu Mountains of Zhejiang province, East of China in East Asia. Combining with the species distribution modeling, we speculated that these areas might be the potential glacial refugia for the endangered plant M. sprengeri. Phylogeographic analysis demonstrated that the geographic factors (e.g., mountains, rivers, and other isolation barriers) had little effect on the genetic divergence among populations. Ecological niche modeling further revealed that the natural populations of M. sprengeri did not experience significant geographic distribution changes from the last glacial maximum to the present time. These findings are in line with the analysis results of the multimodal mismatch patterns of the chloroplast DNA variations. To protect the endangered species M. sprengeri, in situ and ex situ conservation strategies should be formulated for the natural populations with higher genetic variations.