4.3 Origin and Diversification of Notholirion
In the vast timeline of Earth’s evolution, every geological event and climate change has had unprecedented effects on organisms, making it a highly researched topic in the present day. Based on the complete plastid genomic dataset, we estimated the origin of the genusNotholirion and the divergence times of the three species within the genus (Figure 7, 8) . Additionally, we reconstructed their ancestral distribution using the chloroplast fragments (Figure 9) . The results suggest that the ancestral lineage of theNotholirion genus originated in the southern Himalayas during the end of the Tertiary period in the Cenozoic era (25.05 Ma, 95% HPD: 35.56-16.62 Ma). The prevailing theory regarding this period suggests that from 38.0-23.03 Ma, the Earth transitioned from the end of the Eocene epoch through the Oligocene epoch and into the early Miocene epoch. During this time, the climate gradually cooled, resulting in a moderate icehouse climate, and plants and animals evolved and diversified rapidly(O’Brien et al., 2020; Straume, Nummelin, Gaina, & Nisancioglu, 2022). It is during this period that the evolution and spread of modern types of flowering plants primarily took place(Nge, Biffin, Thiele, & Waycott, 2020). Furthermore, during this period, as a result of the gradual collision between the Indian subcontinent and the Eurasian Plate, the Qinghai-Tibetan Plateau continued to uplift both to the south and north. The ongoing uplift of the Qinghai-Tibet Plateau has caused dramatic changes in the topography of the region and has directly contributed to the formation of the monsoon climate(Favre et al., 2015). The significant changes in habitat have also facilitated the formation and differentiation of populations, as seen in Chamaesium ,Cardiocrinum , and Sinopteris (J. Li et al., 2022; L. Wang, Yang, Zhang, Zhang, & Zhang, 2023; H. Y. Zheng et al., 2021). Therefore, we speculate that the origin of the genus Notholirionis closely related to the uplift events that occurred on Tibetan Plateau.
During the early to middle Miocene (23.03-10 Ma), the Earth’s climate experienced significant cooling and entered a period of massive glaciation. The uplift of the Himalayas and surrounding mountains caused aridification of the local climate and a decrease in temperature, limiting plant growth and reproduction and having a profound impact on the evolution of local species, such as Gentiana crassicaulis ,Polygonatum and Allium section Daghestanica (M. J. Li, Yu, Guo, & He, 2021; Ni, Li, Zhao, Gaawe, & Liu, 2022; Xia et al., 2022). By the late Miocene (10-5.33 Ma), the Qinghai-Tibetan Plateau experienced a more significant uplift and expansion, which affected numerous mountain ranges in the plateau’s eastern margin region. Among them, the Himalayas and the Gangdise Mountains run parallel to each other in a northwest-southeast direction, forming a natural barrier. This allows the warm and humid airflow from the Indian Ocean to enter China exclusively through the Hengduan Mountains. This has brought abundant rainfall to the southeastern Tibetan Plateau, significantly impacting species in that region, such as Cardiocrinum ,Chamaesium thalictrifolium , Allium sectionSikkimensia , andRabdosia (J. Li et al., 2022; C. Xie et al., 2019; X. Q. Yu et al., 2014; H. Y. Zheng et al., 2021). Our molecular dating analysis suggested that N. thomsonianum diverged during the late Miocene (7.43 Ma, 95% HPD: 14.86-2.53 Ma). Therefore, we infer that climate change and complex geological activity play important roles in the differentiation and dispersal ofNotholirion species during this period.
During the Pleistocene period (2.588-0.126 Ma), the most far-reaching geological event was the Last Ice Age, a repeated cycle of alternating ice ages and interglacials that caused widespread climatic upheaval with unprecedented effects on the biology of the period(G. M. Hewitt, 2004). During the Ice Age, a continuous ice cap did not form on the Tibetan Plateau and surrounding areas, especially in the Hengduan Mountains located on ITS eastern edge. Intense orogenic movements in the Hengduan Mountains during and after the late Miocene caused the mountains to stretch north and south, resulting in high mountain valleys and diverse topography characterized by folded mountains and faulted basins. While the ice age caused most of the region to become cold and dry, there were still relatively warm and moist areas in the Hengduan Mountains region where organisms could survive. The harsh conditions of the ice age forced organisms to seek refuge in these areas, resulting in natural isolation that may have led to the divergence and formation of new species(Q. Meng et al., 2022). Through BEAST analysis, we discovered that the divergence ofN. macrophyllum and N. bulbuliferum occurred during the Last Glacial Maximum (2.46 Ma, 95% HPD: 4.74-0.81 Ma), indicating that the significant climate fluctuations and natural isolation between different refuges may play a crucial role in the formation and distribution of these species.