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To understand the origin and evolutionary history, and the geographical and historical causes for the formation of the current distribution pattern of Lquidambar formosana Hance, we investigated the phylogeography by using chloroplasts DNA (cpDNA) non-coding sequences and species distribution models (SDM). Four cpDNA intergenic spacer regions were amplified and sequenced for 251 individuals from 25 populations covering most of its geographical range in China. A total of 20 haplotypes were recovered. The species had a high level of chloroplast genetic variation (Ht = 0.909 ± 0.0192) and a significant phylogeographical structure (genetic differentiation takes into account distances among haplotypes (Nst) = 0.730 &gt; population differentiation that does not consider distances among haplotypes (Gst) = 0.645; p &lt; 0.05), whereas the genetic variation within populations (Hs = 0.323 ± 0.0553) was low. The variation of haplotype mainly occurred among populations (genetic differentiation coefficient (Fst) = 0.73012). The low genetic diversity within populations may be attributed to the restricted gene flow (Nm = 0.18). The time of the most recent common ancestor for clade V mostly distributed in Southwestern China, Central China, Qinling and Dabieshan mountains was 10.30 Ma (95% Highest posterior density (HPD): 9.74–15.28) dating back to the middle Miocene, which revealed the genetic structure of L. formosana was of ancient origin. These results indicated that dramatic changes since the Miocene may have driven the ancestors of L. formosana to retreat from the high latitudes of the Northern Hemisphere to subtropical China in which the establishment and initial intensification of the Asian monsoon provided conditions for their ecological requirements. This scenario was confirmed by the fossil record. SDM results indicated there were no contraction–expansion dynamics, and there was a stable range since the last interglacial period (LIG, 130 kya). Compared with the population expansion detected by Fu’s Fs value and the mismatch distribution, we speculated the expansion time may happen before the interglacial period. Evidence supporting L. formosana was the ancient origin and table range since the last interglacial period.

Phylogeographical Structure of Liquidambar formosana Hance Revealed by Chloroplast Phylogeography and Species Distribution Models