Evolutionary history and population dynamics of a rare and endangered medicinal plant Bergenia scopulosa (Saxifragaceae): Evidences from chloroplast genomes and ecological niche analysis

Geological and climatic events have long been considered to profoundly affect population evolution and demographic history of species, but the population evolutionary history of the rare and endangered herbaceous plants in East Asia remains less well understood. In this study, chloroplast genomes, environmental variables and geographical distribution information were integrated to determine the evolutionary history and population dynamics of Bergenia scopulosa T.P.Wang, an endangered medicinal herb endemic in central China (Qinling Mountains). Population genomic analysis based on chloroplast genomes indicated a significant degree of intraspecific differentiation within B. scopulosa, where two separate genetic lineages were identified in the eastern and western groups in the Qinling Mountains, respectively. The two groups were found to have a low level of nucleotide diversity. Meanwhile, ecological niche analysis revealed that the two groups had obvious ecological divergence. Species distribution modeling illustrated that B. scopulosa had experienced a prominent population contraction from the interglacial periods to the present, while the suitable habitat was predicted to shift to higher elevations in response to global warming in future scenarios. These findings suggested that the geological and environmental factors together affected the intraspecific divergence and population dynamics of B. scopulosa in the Qinling Mountains in East Asia. In particular, geographic isolation appeared to play a greater role in genetic differentiation within B. scopulosa. Therefore, the evolutionary conservation units of eastern and western groups should be correspondingly established for this endangered medicinal herb B. scopulosa.