Historical Climatic Fluctuations and Geographic Isolation Shaped the Phylogeographic Patterns of a Mycoheterotrophic Species in Subtropical China

ABSTRACT Subtropical China, dominated by evergreen broad‐leaved forests, harbors exceptionally rich and highly endemic plant diversity, yet the evolutionary history of its understory herbs remains poorly understood. Here, we investigated Burmannia nepalensis , a fully mycoheterotrophic herb endemic to these forests, to uncover the evolutionary and demographic processes shaping understory biodiversity. Using plastome sequences and nuclear microsatellite loci, we examined spatial patterns of genetic variation across 20 populations. The species exhibited low within‐population genetic diversity but pronounced genetic differentiation among populations. Geographic isolation and historical climatic fluctuations emerged as the main drivers of population divergence. Concordant phylogeographic patterns from plastid and nuclear markers, together with species distribution modeling, suggest that B . nepalensis persisted in multiple glacial refugia during the Last Glacial Maximum (LGM), particularly in the Nanling Mountains, Wuyi Mountains, and southwestern karst regions. Demographic reconstructions indicate population expansion after the LGM, followed by a decline in effective population size approximately 3000 years before present (BP), likely driven by human‐induced habitat fragmentation. Our findings highlight the combined roles of geography and climatic history in structuring genetic diversity in fully mycoheterotrophic plants, provide evidence for multiple northern refugia, and underscore the vulnerability of forest‐dependent understory herbs in subtropical China.