Data from: Divergent genomic trajectories and future dynamics of boreal and Qinghai-Tibet plateau (QTP) larches under global change

The Arctic and Qinghai–Tibet Plateau (QTP), two of the coldest regions on Earth, have undergone significant faster rates of climate warming than the global average. Cold-tolerant coniferous forests play a crucial role in both regions and are much more sensitive to global warming. Understanding how closely related lineages evolved and adapted to the two extreme environments in a comparative framework is particularly crucial for predicting their future dynamics. Larches (Larix Mill.) are keystone trees across both boreal and QTP subalpine forests, offering a model system to address the question. Here, we used population transcriptomics, two chloroplast genes (ycf1 and trnS-trnfM) and two mitochondrial genes (rps19F-rps3_R2 and nad4) to compare the evolutionary trajectories and genetic diversity patterns of boreal and QTP larches. Landscape genomics analysis was used to detect environment-associated genomic variants and to predict genomic offset under future climates. Our results revealed contrasting evolutionary paths and genetic variation patterns between boreal and QTP larches, which have been shaped primarily by distinct climatic and geological histories. Local adaptation in QTP larches was driven predominantly by annual temperature variation and winter UV-B radiation, whereas adaptation in boreal larches was strongly associated with temperature seasonality and photoperiod. Genomic offset predicted that QTP larches will be more vulnerable to future climate warming than their boreal counterparts. This study highlights the distinct responses between boreal and QTP larches to global changes and provides critical insights into developing region-specific conservation and forest management strategies in a warming world.