Background

Ongoing climate change poses major threats to species worldwide, making it essential to understand local adaptations and vulnerabilities to both climatic and anthropogenic pressures when developing conservation strategies. This study integrated transcriptome-guided SNP of 54 individuals with ecological and environmental analyses to investigate the biogeographic patterns, genetic divergence, demographic trajectories, and climate and anthropogenic threats of the endangered orchid Cypripedium palangshanense.

Results

We identified four distinct lineages, three confined to the Min Mountains and one to the Daba Mountains in China. Climatic fluctuations strongly influenced demographic history and genetic structure, with evidence of a severe recent bottleneck that may reduce adaptive potential and compromise long-term viability. Higher ancestral diversity and/or limited gene flow during prolonged divergence prevented sharp increases in genetic differentiation (FST) but allowed the accumulation of absolute divergence (DXY).

Conclusions

Overall, we detected pressures under climate and anthropogenic activity and identified vulnerability hotspots (JZG2, SP1, SP2 and DB) requiring conservation priority. Alternatively, ecological niche modeling combined with RONA analysis suggests that the marginal population (CK and PW) is likely to have the highest risk of maladaptation in the future. Our findings highlight how population genomics, ecological and environmental data can be integrated to inform targeted conservation.