Phylotranscriptomics reveals the evolutionary history of subtropical East Asian white pines: further insights into gymnosperm diversification

(A) Geographic distributions and seed morphological traits of the subtropical East Asian white pines. Orange dash line demarcates the major geographical distribution of evergreen broad-leaved forests (EBLFs) in East Asia. The lowercase letters (a-g) shown in the seed pictures on the bottom-right correspond to the cone photos from same species. Bars, 1 cm. (B) Phylogeny of the subtropical East Asian white pines inferred from 2, 606 OGs. Numbers attached to the branches show the bootstrap supports (* for 100%). [Display omitted] •Phylotranscriptomics resolves the evolutionary history of subtropical East Asian white pines.•Both biotic and abiotic factors shaped the diversification of subtropical Eastern Asian white pines.•Two Taiwan species experienced independent migrations and regional extinction.•Phylotranscriptomics sheds new light on species delimitation and conservation of white pines. Floristic composition within a geographic area is driven by a wide array of factors from local biotic interactions to biogeographical processes. Subtropical East Asia is a key biodiversity hotspot of the world, and harbors the most families of extant gymnosperms and a large number of endemic genera with ancient origins, but rare phylogenetic studies explored whether it served as a diversification center for gymnosperms. Here, we investigated the evolutionary and biogeographical history of subtropical East Asian white pines using an integrative approach that combines phylotranscriptomic and ecological analyses. Using 2,606 orthologous nuclear genes, we reconstructed a fully resolved and dated phylogeny of these species. Two main clades first diverged in the early Miocene, and by the late Miocene, all species appeared. Two white pines endemic to Taiwan Island experienced independent colonization events and regional extinction, which resulted in the present disjunctive distribution from mainland China. Ecological and biogeographical analyses indicate that the monsoon-driven assembly of evergreen broadleaved forests (EBLFs) might have significantly affected the diversification of subtropical East Asian white pines. Our study highlights the interactions of biotic and abiotic forces in the diversification and speciation of subtropical East Asian white pines. These findings indicate that subtropical East Asia is not only a floristic museum, but also a diversification center for gymnosperms. Our study also demonstrates the importance of phylotranscriptomics on species delimitatio