Genomic insights into gene flow and local adaptation among three Taxus species

Local adaptation refers to the evolutionary process whereby organisms become better suited to their local environmental conditions, resulting in higher fitness. However, patterns of gene flow among Taxus species and their capacity for local adaptation across current and future climatic landscapes remains unclear. Here, we analyzed dd-RAD sequencing data from 252 individuals from three Taxus species to identify their genetic structure and gene flow patterns, identify climate-associated single-nucleotide polymorphisms (SNPs) across the genome, and predict their spatio-temporal shifts under future climate change. Our study demonstrated that T. qinlingensis harbors the highest genetic diversity and represents a relatively ancient lineage, whereas T. chinensis and T. mairei are closely related. Demographic history analyses indicated that population contractions of the three species were triggered by the Younger Dryas Event (12.8-11.5 ka) and the 4.2-kiloyear Event. Interspecific gene flow were relatively scarce, with the exception of the LYW and LWT populations, where gene flow was from T. mairei to T. chinensis. Furthermore, 26 common climate-associated SNPs were identified across the three species, primarily associated with metabolic and functional categories, highlighting the role of genetic variation in stress-responsive pathways and climate adaptation. Gradient Forest analysis revealed substantial distributional overlap among the species across the Sichuan Basin and adjacent regions. Notably, the higher predicted genomic offset along the southern, southeastern and northeastern margins of the basin indicate a greater vulnerability to future climatic changes, relative to the northern and western regions. Collectively, these findings reveal the key constraints on the evolutionary potential of three Taxus species and provide an important foundation for their conservation strategies.