Abstract: The Himalayas represent a complex mountain system housing some of the world's richest floras along with a high level of endemism. Among them, Lysionotus (Gesneriaceae) stands out as a small genus (~34 species) that is unexpectedly distributed across southern to eastern Asia. Within this genus, the mountain forests of the south Pan-Himalaya region emerge as a hotspot of diversity, hosting most epiphytic and endemic Lysionotus species. To explore the origin, evolutionary history and development of the current distribution pattern of Lysionotus, we inferred a highly resolved phylogenetic framework using 649 nuclear genes sourced from transcriptomes for 27 species. We revealed three major clades within Lysionotus with strong support, corresponding to the genus's classification into three sections (sects. Didymocarpoides, Lysionotus, and Cyathocalyx) based on morphological characters. Molecular dating suggests that Lysionotus is likely to have originated in the karst regions of northern Vietnam to southwestern China during the middle Oligocene (28.18 Ma), and then migrated westward to the southern Himalaya regions during the Miocene. The speciation rates of Lysionotus were likely to be positively linked to changes in East Asian monsoons and past temperatures. Notably, epiphytic species of sect. Lysionotus began colonizing the tropical and subtropical forests of the Pan-Himalaya around the mid-Miocene Climatic Optimum, coinciding with the transition to long seed appendages. Our findings support that the formation and development of forests in the southern Himalaya, along with paleo-climate changes and morphological innovations, which probably facilitated the evolution and expansion of the spatial distribution of Lysionotus.

Key words: biogeography, Lysionotus, morphology, phylogenomics, transcriptome.