Effects of mountain uplift and climatic oscillations on phylogeography and species divergence of Notholirion (Liliaceae)

Investigating geological and climatic shifts in the Himalayan-Hengduan Mountains (HHM) and Qinghai-Tibet Plateau (QTP) is vital for unraveling environmental impacts on biogeography and evolution. We analyzed the evolutionary history of 3 Notholirion species across these regions, studying 254 individuals from 31 populations using 5 chloroplast DNA markers (matK, ndhA, ndhG-ndhI, petB-petD, and petL-petG) and nuclear ITS. A total of 1,145 low-copy nuclear genes (LCGs) and 112 chloroplast genes from 11 representative individuals were further utilized for phylogenetic reconstruction. Divergence timing was estimated with 147 plastomes, including 10 Notholirion populations. Fourteen cpDNA and 27 ITS haplotypes revealed species-specific variation. Phylogenetic analyses confirmed a monophyletic origin for all 3 species, with population-level nested relationships and cytonuclear discordance attributed to incomplete lineage sorting (ILS) and hybridization. Dating and ancestral reconstruction traced Notholirion’s origin to the southern Himalayas during the Late Oligocene (25.05 Ma), with diversification commencing in the Late Pliocene (7.43 Ma). MaxEnt modeling indicated stable species distributions from the Last Interglacial to future projections. The initial split of Notholirion was triggered by climate changes following the uplift of the QTP. Subsequently, dramatic climatic fluctuations during the Pleistocene and the complex topography of the HHM region jointly promoted species dispersal and diversification, ultimately shaping its current biogeographic distribution and phylogenetic structure. High genetic diversity likely stems from prolonged evolutionary history, sexual reproduction, and habitat fragmentation. The high genetic differentiation observed among Notholirion populations may be attributed to pronounced environmental changes across their distribution range, along with limited seed production and dispersal capacity.