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Background   Ulmus lamellosa  (one of the ancient species of  Ulmus ) is an endemic and endangered plant that has undergone climatic oscillations and geographical changes. The elucidation of its demographic history and genetic differentiation is critical for understanding the evolutionary process and ecological adaption to forests in Northern China.    Results  Polymorphic haplotypes were detected in most populations of  U. lamellosa  via DNA sequencing. All haplotypes were divided into three phylogeographic clades fundamentally corresponding to their geographical distribution, namely THM (Taihang Mountains), YM (Yinshan Mountains), and YSM (Yanshan Mountains) groups. The YSM group, which is regarded as ancestral, possessed higher genetic diversity and significant genetic variability in contrast to the YSM and YM groups. Meanwhile, the divergence time of intraspecies haplotypes occurred during the Miocene-Pliocene, which was associated with major Tertiary geological and/or climatic events. Different degrees of gene exchanges were identified between the three groups. During glaciation, the YSM and THM regions might have served as refugia for  U. lamellosa . Based on ITS data, range expansion was not expected through evolutionary processes, except for the THM group. A series of mountain uplifts (e.g., Yanshan Mountains and Taihang Mountains) following the Miocene-Pliocene, and subsequently quaternary climatic oscillations in Northern China, further promoted divergence between  U. lamellosa  populations.    Conclusions  Geographical topology and climate change in Northern China played a critical role in establishing the current phylogeographic structural patterns of  U. lamellosa . These results provide important data and clues that facilitate the demographic study of tree species in Northern China.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-020-02723-7.

Demographic history and genetic differentiation of an endemic and endangered Ulmus lamellosa (Ulmus)