Genomic insights into the evolutionary history and adaptive capacity of the threatened ornamental Firmiana major in the Jinsha River Basin, China

Firmiana major is a threatened and ornamental tree restricted to the Jinsha River basin in China. Rapid population decline, driven by climate change and human disturbance, led to its designation as a second-class nationally protected plant in 2021. Yet our understanding of its evolutionary history and adaptive potential has been hindered by the absence of genomic resources. We generated a 1 418 Mb chromosome-level genome for F. major and conducted whole-genome re-sequencing of all known wild populations. Population genomic analyses were used to delineate genetic lineages, quantify nucleotide diversity, reconstruct demographic history, estimate inbreeding and mutational load, and project future adaptive capacity under climate-change scenarios. Comparative genomics revealed expansion of gene families involved in biological regulation, which likely facilitates persistence on the nutrient-poor soils of the Jinsha valley. All individuals clustered into four lineages that diverge progressively along the downstream–upstream river gradient; nucleotide diversity increases in the downstream direction. Only central populations (Pudu, Wanbi, Yuanmou and Panzhihua) retain detectable gene flow, whereas upstream and peripheral populations are isolated by geographical barriers and exhibit elevated inbreeding and mutational load. Each lineage has evolved distinct haplotypes associated with its local habitat, but future climate projections indicate heightened risk for all populations. This study provides the genomic framework for the conservation and horticultural exploitation of F. major and offers a model for integrating evolutionary history into the management of other threatened endemic species.