A population genomic approach was employed to investigate the diversity within species to create a more robust, lineage-specific conservation strategy for an endangered orchid. Pleione formosana is a species native to southeastern China and Taiwan, where it is distributed at an altitude range of 1,200–2,500 m the foggy mountain area and grows in mosses on half-shaded rocks or tree trunks. To identify whether the level of genetic diversity in the species, we used genotyping by sequencing (GBS) to analysis the sub-populations of the species. Fifty-eight individuals of P. formosana were sampled from a total of nine populations within continental island Taiwan and three populations in China as outgroup. Treatment of all samples involved five major steps: sample preparation, library assembly, sequencing, SNP calling and diversity analysis. GBS markers confirmed the China outgroup as distinct, and provided resolution of two clusters of population genetic structure in Taiwan. Outliers provide higher genetic differentiation, and some GBS tags associated with climatic factor were found. Genomic diversity identified among the three clusters suggests that conservation of this species will be best served by considering them as three evolutionary significant units (ESUs). This approach will maximize evolutionary potential among all species during increased isolation and environmental change. According to the genetic consequences, restoration strategies should be carried out in all populations to preserve genetic diversity and evolutionary potential for different environmental factors.
