Genetic diversity and population structure of Shorea macrophylla using genome-wide single-nucleotide polymorphisms and microsatellite markers in Indonesia for conservation

In the tropical forests of Southeast Asia, the dipterocarp species stands out as the most significant tree group in terms of ecosystem stability and forestry management. Shorea macrophylla, found on Borneo Island, is particularly noteworthy for its rapid growth, high oil content nut production, and versatile timber characteristics, making it a prime candidate for plantation material in rehabilitating degraded forests. We collected population samples of S. macrophylla in Kalimantan Island and evaluated parameters such as genetic diversity, genetic structure, and estimated divergence times of the populations using SSR (simple sequence repeat) markers and SNPs (single-nucleotide polymorphisms). Interestingly, the estimated divergence time of genetic groups was similar between the two markers, with SNP markers likely offering a more accurate estimation owing to their higher marker count. Although SNP markers generally offer advantages over SSR markers in genetic studies, the latter remains valuable for assessing genetic diversity due to its high polymorphism. We conclude that SSR markers are still useful for identifying hotspot areas in terms of genetic diversity. Our study revealed that both DNA markers identified the Northeast Kalimantan population as the most genetically distinct population of S. macrophylla, which is important for the conservation of this species. By using multiple DNA markers with different characteristics, the history and features of the population can be more clearly explored. The result of species distribution modeling suggests that the habitat of this species may expand on Kalimantan Island due to future global warming. © 2025 The Author(s). Ecological Research published by John Wiley & Sons Australia, Ltd on behalf of The Ecological Society of Japan.