Genetic diversity and structure of Eusideroxylon zwageri (Teijsm. & Binn.) in Indonesia revealed by nuclear microsatellite markers

Eusideroxylon zwageri (Teijsm. & Binn.) or ironwood, a durable and long-lived timber species native to Indonesia, is classified as vulnerable due to overexploitation and habitat fragmentation. This study evaluated genetic diversity and population structure of ironwood across nine populations in Kalimantan (Gunung Palung, Kapuas Hulu, Bukit Suharto, Kutai, Kintap, Berau, Busang) and Sumatra (Jambi, Musi Rawas) using 11 nuclear microsatellite markers. The results indicated moderate genetic diversity (HO: 0.511–0.623). Most Kalimantan populations exhibited significant heterozygosity deficiencies, as reflected by positive inbreeding coefficient (FIS) values (FIS: 0.091–0.224); in contrast, Sumatra populations showed no significant deviations (FIS: 0.055–171). Population genetic analyses revealed a significant bottleneck in all studied populations according to the Infinite Allele Model (IAM), while no significant bottleneck was detected under the Stepwise Mutation Model (SMM), Two-Phase Model (TPM), and model shift analysis. A dendrogram analysis, Principal Coordinate Analysis (PCoA), and STRUCTURE analysis grouped the populations into three distinct clusters, revealing regional genetic structuring. Analysis of Molecular Variance (AMOVA) demonstrated significant genetic differentiation among regions (15%, p < 0.001). The Approximate Bayesian Computation (ABC) analysis definitively identifies the hierarchical simple split model as the more biologically probable representation of ironwood’s evolutionary history compared to the traditional invasion model. This study concluded that ironwood populations in Indonesia exhibit moderate genetic diversity and are grouped into western Kalimantan, eastern Kalimantan, and Musi Rawas. Eastern Kalimantan, with its higher genetic richness and broader distribution, serves as a key gene pool for the species. Future research should focus on understanding ironwood’s adaptability to climate change and the role of gene flow in maintaining genetic diversity, particularly for the vulnerable Musi Rawas population.