The Tianshan Mountains as a biogeographic barrier driving North-South divergence and local adaptation in Typha...

The Tianshan Mountains constitute a major biogeographic barrier in Arid Central Asia, yet their impact on plant genomic divergence and adaptation remains poorly understood. Using Typha laxmannii, a wetland species distributed across this range, we generated a chromosome-scale genome and performed integrated population genomic and environmental analyses of 126 individuals from 31 sites. Our results revealed a clear north-south genetic split demarcated by the Tianshan Mountains, with gene flow restricted since divergence approximately 88.1 thousand years ago (Kya), a pattern further reinforced by post-Pleistocene demographic contraction. Northern and southern populations evolved distinct adaptive signatures in response to their local environments, including differentiation in genes associated with stress response, transcriptional regulation, and flowering time. Beyond single loci, adaptation also acts on large genomic blocks: a ∼2.5 Mb parallel sweep (∼91 Kya) contains a linked block of stress-response genes shared across the species, suggesting a range-wide response to intensified continentality and repeated glacial-interglacial aridification following population decline (∼100 Kya) but preceding the north-south split. In contrast, a ∼3 Mb divergent sweep (∼85 Kya) harbours northern-specific alleles related to glutathione metabolism, zeatin biosynthesis, and transcriptional regulation, likely enhancing tolerance to extreme winter cooling and freeze-thaw cycles under a strengthened Siberian High after divergence. Together, our findings establish a "spatio-temporal environmental sorting" model of biodiversity, providing a critical framework for understanding how the topography and climate of the Arid Central Asian mountains promote evolutionary novelty and safeguard genetic resilience in the face of ongoing global climate change.