The diverse topography and mild monsoon climate in East Asia are considered to be important drivers for the long-term ecological success of the Tertiary relict ‘living fossil’ plants during the glacial/interglacial cycles. Here we investigated the phylogeographic pattern and demographic history of a hamamelidaceous Tertiary relict ‘living fossil’ tree (Parrotia subaequalis) endemic to the subtropical forests of eastern China, employing molecular data and ecological niche modeling. In the long evolutionary history, P. subaequalis has accumulated a high haplotype diversity. Weak gene flow by seeds, geographical isolation, and heterogeneous habitats have led to a relatively high level of genetic differentiation in this species. The divergence time of two cpDNA lineages of P. subaequalis was dated to the late Miocene of the Tertiary period, and the diversification of haplotypes occurred in the Quaternary period. Paleo-distribution modeling suggested that P. subaequalis followed the pattern of ‘glacial expansion-interglacial compression’. The Dabie Mountain and Yellow Mountain in Anhui Province and the Tianmu Mountain and Simin Mountain in Zhejiang Province were inferred to be multiple glacial refugia of P. subaequalis in East Asia and have been proposed to be protected as ‘Management Units’. Collectively, our study offers insights into the plant evolution and adaptation of P. subaequalis and other Tertiary relict ‘living fossil’ trees endemic to East Asia refugia.

In the traditional classification system of the Lauraceae family based on morphology and anatomy, the phylogenetic position of the genus Sassafras has long been controversial. Chloroplast (cp) evolution of Sassafras has not yet been illuminated. In this study, we first sequenced and assembled the complete cp genomes of Sassafras, and conducted the comparative cp genomics, phylogenomics, and divergence time estimation of this ecological and economic important genus. The whole length of cp genomes of the 10 Sassafras ranged from 151,970 bp to 154,011 bp with typical quadripartite structure, conserved gene arrangements and contents. Variations in length of cp were observed in the inverted repeat regions (IRs) and a relatively high usage frequency of codons ending with T/A was detected. Four hypervariable intergenic regions (ccsA-ndhD, trnH-psbA, rps15-ycf1, and petA-psbJ) and 672 cp microsatellites were identified for Sassafras. Phylogenetic analysis based on 106 cp genomes from 30 genera within the Lauraceae family demonstrated that Sassafras constituted a monophyletic clade and grouped a sister branch with the Cinnamomum sect. Camphora within the tribe Cinnamomeae. Divergence time between S. albidum and its East Asian siblings was estimated at the Middle Miocene (16.98 Mya), S. tzumu diverged from S. randaiense at the Pleistocene epoch (3.63 Mya). Combined with fossil evidence, our results further revealed the crucial role of the Bering Land Bridge and glacial refugia in the speciation and differentiation of Sassafras. Overall, our study clarified the evolution pattern of Sassafras cp genomes and elucidated the phylogenetic position and divergence time framework of Sassafras.