Taxonomic status and spatial genetic pattern of Taxus in northern and central China: insights from integrative taxonomy, ecology and phylogeography

Abstract Background Phenotypic, ecological, and genetic differences are crucial for species delimitation and understanding speciation. However, the defining the distribution boundaries and mechanisms driving lineage differentiation of Taxus species in northern and central China remain unclear. This study combines three molecular markers (trnL-trnF, rbcL, ITS), leaf morphological, and ecological data, integrating multiple taxonomy, ecology, and phylogeography approaches to systematically investigate the taxonomic status and spatial genetic patterns of Taxus species in these regions. Results A total of 177 samples from 27 populations, representing the natural distribution of Taxus in central and northern China, were collected. T. chinensis (TC) mainly occurs from 1000–2400 m in the south of Qinling Mountains, T. mairei (TM) from 100–1000 m in the south of Daba Mountains, and T. qinlingensis (TQ) from 900–1800 m in the north of Qinling Mountains. The three species overlap in the central Qinling, eastern Daba, and Wushan Mountains at elevations of 900–1800 m. Seventeen haplotypes and 21 ribotypes were identified, forming three clusters corresponding to TC, TM, and TQ. Both cpDNA and nDNA data reveals distinct phylogeographic structures, significant genetic differentiation, and smaller bidirectional gene flow among species. Genetic and niche play a more prominent role in species divergence than morphological traits. Effective population sizes and genetic diversity are higher in TC and TM than in TQ. Suitable habitats expanded southwestward after the Last Glacial Maximum (LGM) and are projected to shift northwestward and contract under future warming scenarios. Conclusion Geologic movement (rapid uplift of the Qinling and surrounding mountains), climate fluctuations (cold-drying effect, and glacial-interglacial cycles), and habitat heterogeneity (gradients in geography and elevation) together shaped interspecific adaptive differentiation and shifts in population dynamics of the three Taxus species. The Qinling-Daba-Wushan mountain range likely played a key role in the independent evolution of these species in local glacial refugia and their post-glacial recontact at the intersection of these mountain ranges. This study provides new insights into the taxonomic status and genetic variation pattern of Taxus species in central and northern China.