Genetic diversity of endangered Santalum album Linn. populations in the natural habitat in East Nusa Tenggara, Indonesia

Santalum album Linn. (sandalwood) is a commercially important species due to the essential oils derived from its heartwood. This species has been currently threatened by overharvesting and habitat fragmentation. Therefore, this study aims to assess genetic diversity and population structure of seven Indonesian sandalwood populations using eight nuclear simple sequence repeat (nSSR) markers. The samples comprised 202 individuals from one ex-situ conservation population (artificially established) in Gunungkidul (GK), Java, four natural populations in East Nusa Tenggara (ENT) from three islands: Flores (ED), Sumba (SB), and Timor (TU, TS), along with one rehabilitation site (FT) and one seed production area (SPA, analogous to a seed orchard) on Timor Island. The results showed moderate genetic diversity among the populations. Expected heterozygosity (He) and observed heterozygosity (Ho) ranged from 0.174 to 0.522 and 0.188 to 0.5171, respectively, with mean values of 0.331 and 0.303. The Ende (ED) population showed the highest allelic richness (AR [28] = 4.01), while GK had the lowest (2.30). Significant inbreeding coefficients (FIS) were detected in all ENT populations except ED, alongside a nonsignificant value in GK. Bayesian analysis determined the optimal genetic cluster number to be K = 5, separating the populations into ED, SB, GK, and two clusters within the Timor Island populations (TU and a group comprising TS, FT, and SPA). Principal Coordinate Analysis (PCoA) confirmed the genetic distinction of the GK ex-situ population from the ENT groups. Furthermore, the Analysis of Molecular Variance (AMOVA) revealed that 8% of the total genetic variation occurred among regions, while 3% was found among populations within regions. The absence of significant recent population bottlenecks across all populations suggests demographic resilience, potentially supported by rehabilitation programs. The critically low genetic diversity of the GK population underscores the necessity for urgent, targeted conservation strategies, such as assisted gene flow, to preserve the species’ adaptive potential. These results highlight the importance of conserving natural populations and implementing genetic management for ex-situ and managed stands.