Demographic history, spatiotemporal genetic structure and climate vulnerability of Shorea robusta: a keystone species of moist deciduous forest in India.

UNLABELLED: Shorea robusta, a dominant tree species of tropical moist deciduous forests, is of considerable ecological and economic importance but is increasingly threatened by habitat fragmentation, poor regeneration, land-use change, and climate change, and is consequently classified as "Near Threatened" in the International Union for Conservation of Nature (IUCN) Red List (2025). However, comprehensive information on its genetic diversity, population structure, demographic history, and historical distribution remains limited across its broad natural range. The present study assessed population genetic diversity and structure using 10 species-specific genomic simple sequence repeat markers in 507 individuals representing 18 populations distributed across the Shivalik hills, Terai, Bundelkhand, and Vindhyan regions of India. The populations exhibited high genetic diversity, with mean expected and observed heterozygosity of 0.761 and 0.585, respectively. Moderate genetic differentiation (FST = 0.116) coupled with relatively high gene flow (Nm = 1.906), indicated substantial genetic connectivity among populations. Bayesian STRUCTURE analysis identified two major genetic clusters, which were also supported by the Unweighted Pair Group Method with Arithmetic Mean and Principal Coordinate Analysis. Discriminant Analysis of Principal Components further revealed higher-order genetic structuring, suggesting finer-scale differentiation within the two genetic clusters. Mantel and partial Mantel analyses indicated that geographic distance, rather than environmental heterogeneity, was the principal determinant of contemporary genetic structure. Bottleneck analysis suggested recent demographic expansion in most populations, whereas a recent bottleneck was detected only in the GIR population. Ecological niche modelling identified mean temperature of the wettest quarter and precipitation of the driest quarter as the principal bioclimatic determinants of S. robusta distribution. The predicted distribution map indicated a marked northward and upslope contraction of suitable habitat, potentially increasing the vulnerability of populations in the northern plains. In contrast, the Terai region and Shivalik hills along north and northeastern India showed relatively stable climatic suitability from the Last Glacial Maximum to the present, highlighting their possible role as climatic refugia. Overall, S. robusta has retained substantial genetic diversity and connectivity despite historical climatic fluctuations and contemporary habitat fragmentation. Conservation should therefore prioritize both major genetic clusters and climatically stable refugial populations. Integration of landscape genomics, genotype-environment association analyses, and niche modelling will further facilitate identification of climate-adaptive variation and development of climate-resilient conservation strategies.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at https://doi.org/10.1007/s12298-026-01822-3.