Evolutionary events in Lilium (including Nomocharis, Liliaceae) are temporally correlated with orogenies of the Q-T plateau and the Hengduan Mountains

The Hengduan Mountains (H-D Mountains) in China flank the eastern edge of the Qinghai-Tibet Plateau (Q-T Plateau) and are a center of great temperate plant diversity. The geological history and complex topography of these mountains may have prompted the in situ evolution of many diverse and narrowly endemic species. Despite the importance of the H-D Mountains to biodiversity, many uncertainties remain regarding the timing and tempo of their uplift. One hypothesis is that the Q-T Plateau underwent a final, rapid phase of uplift 8-7 million years ago (Mya) and that the H-D Mountains orogeny was a separate event occurring 4-3 Mya. To evaluate this hypothesis, we performed phylogenetic, biogeographic, divergence time dating, and diversification rate analyses of the horticulturally important genus Lilium, including Nomocharis. The Lilium-Nomocharis complex is distributed throughout the temperate Northern Hemisphere but is most diverse within the H-D Mountains and Q-T Plateau. Our matK and ITS phylogenies support previous studies showing that Nomocharis is nested within Lilium. However, we detected incongruence between the two gene trees which may result from hybridization. Dating analyses performed using the ITS dataset showed that the evolution of major lineages within Lilium-Nomocharis may be temporally coincident with Q-T Plateau uplift occurring 8-7 Mya and H-D Mountains uplift approximately 4-3 Mya. Our analyses of diversification times and rates among Lilium-Nomocharis clades are less conclusive. However, these do suggest high extinction rates among H-D Mountains lineages.