Fragmented habitat drives significant genetic divergence in the Chinese endemic plant, Urophysa henryi (Ranuculaceae)

•The first based on ISSR data to investigate the genetic diversity of Urophysa henryi.•Finding a high level of genetic diversity at the species level.•Detecting a high level of genetic differentiation among populations.•Fragmented habitat plays important role in its modern distribution pattern.•Strategies for the conservation of U. henryi were suggested.

Urophysa henryi (Oliv.) Ulbr., endemic to China with small populations, is known as a medicinal plant. In this study, ISSR markers were used to assess the genetic diversity and population structure throughout its entire distribution areas. Twelve primers revealed high genetic diversity at the species level (PPB = 95.6%; H = 0.3441; I = 0.5111), as well as high level of genetic differentiation (FST = 0.659, p < 0.001; GST = 0.677) and restricted gene flow (Nm = 0.239) among populations. According to the UPGMA and PCoA analysis, the 9 populations were clustered into three main groups, which were roughly in accordance with their geographical regions. In addition, a significant correlation between the genetic difference and geographic distances among populations was detected from the IBD analysis (r = 0.516, p = 0.003). These results indicated that the habitat heterogeneity and physical barriers play important roles in the modern distribution pattern and population divergence of U. henryi. However, human activities have posed serious threat to its living environment and continued survival. It is necessary to adopt some measures to restrict anthropogenic disturbances and preserve the existing populations.