Population genome-wide analysis reveals historical divergence and adaptive signals in Rubroshorea leprosula (Dipterocarpaceae), a near-threatened tropical forest tree

Abstract Background Lowland dipterocarp forests in Southeast Asia represent one of the world’s most significant biodiversity hotspots, yet they have experienced extensive fragmentation by rapid land-use change. Rubroshorea leprosula , a near-threatened and economically important dipterocarp, occurs widely across Peninsular Malaysia, Sumatra and Borneo, yet its evolutionary history and adaptive potential remain poorly understood. Understanding how and why genetic variation is structured across this geographic range is essential for predicting the resilience of tropical tree species, particularly where geographical isolation and heterogeneous environments may drive localized adaptation. Results Whole-genome resequencing of 194 individuals from 37 natural populations revealed moderate genome-wide diversity, with notable regional contrasts. Populations from Peninsular Malaysia and Sumatra exhibited higher heterozygosity and shared ancestral variation, while Bornean populations showed signals of recent demographic expansion. Population structure analyses identified two major genetic clusters corresponding to Western (Peninsular Malaysia + Sumatra) and Eastern (Borneo) lineages, with a small number of admixed individuals in northern Peninsular Malaysia suggesting historical gene flow. Demographic modelling supports divergence during the Mid- to Late-Pleistocene followed by low, asymmetric post-divergence gene flow, consistent with secondary contact during post-glacial forest reconnection across Sundaland. Integration of outlier detection ( F ST and pcadapt) with environmental association analyses (RDA and LFMM2) identified candidate loci associated with stress response, signalling and metabolic pathways, suggesting that environmental heterogeneity across the species’ range has contributed to adaptive genomic differentiation. Conclusions This study reveals strong west-east genetic divergence in R. leprosula and identifies climate-associated loci linked to adaptation across temperature, elevation and precipitation gradients. These genome-wide patterns clarify evolutionary processes and provide a foundation for climate-informed conservation management of threatened dipterocarp forests.