Calophyllum inophyllum L. belongs to the genus Calophyllum (Clusiaceae) which is widely distributed in Southeast Asia, India, Okinawa (Japan), Australia, and the Pacific Islands. Taiwan is located at the edge of the species’ distribution area, and the species is mainly distributed on the Hengchun Peninsula and Lanyu. C. inophyllum is one of the coastal windbreak trees, and is seed oil can be extracted and used for cosmetics and medicinal purposes and also developed into biomass energy; so, it possesses high value for landscping and economics. In this study, genetic variations and the population genetic structure of 79 individuals sampled from 8 populations in Taiwan,
Lanyu, the Pratas Island, and Okinawa (Japan), were examined using inter-simple sequence repeat (ISSR) markers. For a total, 14 primers were used and 159 polymorphic sites were detected. A POPGENE analysis revealed that the total gene diversity (H) was 0.2021, the genetic differentiation index (Gst) was 0.6385, and the gene flow index (Nm) was 0.2832. An analysis of molecular variance (AMOVA) revealed that the variance component between population regions was 47.87% (p < 0.001), that of populations within regions was 14.53% (p < 0.001), and the among individuals within populations was 37.60 (p < 0.001). The results indicated significant genetic differentiation among islands and among population within island. In addition, the Mantel test showed that there was no significant relation between the genetic distance and geographic distance (r = 0.78, p = 0.99),pointing to a random distribution among populations. In conclusion, the gene flow among populations was relatively restricted, and populations on different islands showed significant genetic differentiation.
Based on results of the UPGMA cluster analysis, the clustering of populations proved significant genetic differentiation among islands. It wasspeculated that geographic segmentation may be a significant factor in the genetic differentiation among the 4 regions. In addition, the genetic diversity of C. inophyllum is relatively low compared to those of other coastal plants. Based on the above findings, both in-situ and ex-situ conservation approaches are necessary for this species.