Population genetic structure and conservation of small fragmented locations of Dactylorhiza hatagirea in Ladakh region of India

•Dactylorhiza hatagirea (D. Don) is an endangered orchid possessing high medicinal value.•NJ and Bayesian clustering analysis indicated that two clusters were gathered.•Habitat fragmentation from human pressure is the main threats for this species.•A proper conservation strategy is proposed for this endangered species.

Analysis of molecular variance (AMOVA) of ISSR analysis revealed a moderate level of genetic differentiation among populations (60% of the total variance components, P < 0.001), with gene differentiation coefficients (Gst = 0.258, Fst = 0.135) and moderate gene flow (Nm = 1.432). Both Principal coordinate's analysis (PCoA) and Neighbor-Joining (NJ) cluster analysis supported the grouping of all 96 sample sizes of nine locations into two collection groups. The present level and pattern of genetic diversity and structure of Dactylorhiza hatagirea were assumed to result largely from its habitat fragmentation, its unique biological traits and evolutionary history. The genetic structure could be attributed to an earlier period of more pronounced gene flow when the species had a more continuous distribution. A Mantel test revealed no significant positive correlation between genetic distances and geographic distances (R2 = 0.0165, P = 0.290).