1 Introduction
The Qinghai-Tibet Plateau (QTP), as the ”roof of the world”, has fostered a variety of plateau organisms, and the Himalayan-Hengduan Mountains (HHM) on ITS margin represent two distinct biodiversity hotspots (Deng, Ding, & Deng, 2015; Favre et al., 2015; H. H. Meng et al., 2017). As key features of the biodiversity hotspots of East and South Asia, Himalaya Mountains define the southern edge of the QTP, whereas the Hengduan Mountains of Southwest China form the southeastern frontier of the plateau(Marchese, 2015; Y. L. Zhang, Li, & Zheng, 2002). Both regions have impressive animal and plant diversity, with alpine plant diversity being an important contributor to the hotspot (D. Z. Li, 2008; J. Li et al., 2020; C. Xie et al., 2019). Previous studies have suggested that the Himalayas were formed by the collision of the Indo-Australian plate with Eurasian plate, accompanied by continuous and prolonged uplifts(Aitchison & Ali, 2008; Dupont-Nivet, Lippert, Hinsbergen, Meijers, & Kapp, 2010; H. B. Zheng, Powell, An, Zhou, & Dong, 2000). The collision of the Indian plate and Eurasia resulted in the consequent rise of the Himalayas and QTP. This collision also created folded mountains and faulted basins that formed the present-day HHM(Chatterjee, Goswami, & Scotese, 2013; Dupont-Nivet et al., 2010). Most studies suggest that the collision began in the Eocene, around 55-50 Mya, followed by a continuous uplift of the Himalayas. parts of the region, such as Thakkhola, Gyirong and Zhada, reached an average elevation of about 4000 to 6000 m during the Miocene (Chatterjee et al., 2013; Dupont-Nivet et al., 2010; Saylor et al., 2009; Q. Zhang & Willems, 2012). During the Late Miocene and the Pliocene, the QTP experienced further uplift. The uplift of the HHM on the southeastern edge of the QTP was particularly pronounced and reached ITS peak elevation rapidly before the Late Pliocene(Mulch & Chamberlain, 2006; Xiong et al., 2022; H. B. Zheng et al., 2000).
The formation and uplift of the QTP have had a profound impact on the local area and ITS surrounding regions. This has resulted in a series of topographic and climatic changes, which has especially shaped the unusually rugged and complex topography of the HHM and the special East Asian monsoon climate of this region(Cao, Shi, Zhang, & Wang, 2009; Huntington, Blythe, & Hodges, 2006; X. Sun & Wang, 2005; P. Z. Zhang et al., 2004). Since the Quaternary period, climatic fluctuations have had significant effects on the distribution and history of plants populations in the Northern Hemisphere, causing their range-wide migration or extinction and possibly driving local adaptation(J. M. Chen, Zhi-Yuan, Yuan, & Wang, 2014; G. M. Hewitt, 2004; Hickerson et al., 2010). Previous studies have shown that there were four major ice ages and three interglacials that occurred during the Pleistocene, with each ice period being separated by interglacial period. The repeated alternation of ice ages and interglacials caused oscillations of warm and cold climates, which profoundly affected the genetic diversity and spatial distribution patterns of biological taxa found on the QTP and adjacent areas(Borns, 1994; G. Hewitt, 2000; Keller & Seehausen, 2012; Z. Zhang & Sun, 2011). And the repeated alternating cycles of population contraction during the ice age and expansion after the ice age became the dominant pattern for many plants in the Northern Hemisphere, enabling their survival throughout the Quaternary ice age(Godfrey M. Hewitt, 1996). On the QTP and ITS adjacent areas, the HHM region in the southeastern part of the QTP may have served as an important refuge for endemic species during the ice age, thanks toITS distinctive mountainous topography(Q. B. Gao et al., 2012; J. Q. Liu, Duan, Hao, Xue㎎Un, & Sun, 2014; Qiu, Fu, & Comes, 2011). This region is characterized by north-south peaks separated by valley bottoms(Song et al., 2016). From valleys situated approximately 1,000 m above sea level to the peakof Minya Konka at 7,556 m, the huge drop in altitude can form “sky islands”(Kai & Jiang, 2014; Qian, Ricklefs, & Thuiller, 2021). During the Quaternary, these low elevation valley areas on the edge of the ice age impact may have provided shelter for certain local plants to survive the ice age(Q. B. Gao et al., 2012; J. Q. Liu et al., 2014). In addition, many studies have suggested that during the Ice Age, plant species from the QTP region may have survived in invisible refuges at high altitudes(J. Q. Liu, Sun, Ge, Gao, & Qiu, 2012; Luo, Yue, & Sun, 2016). These different habitat zones and ecosystems, such as the refuges found in different elevation zones and sky islands, have also resulted in speciation and radiation(J. Q. Liu et al., 2014; Qiu et al., 2011; H. Wang et al., 2010; Xu et al., 2010). Thus, the climatic and specific topographic changes caused by the uplift of the QTP have played a key role in the origin, speciation and evolution of several plant taxa throughout the HHM and adjacent areas.
The HHM region has a special climatic environment, complex geological landscape, and bioecological diversity, making it an ideal and captivating location for studying species diversification and adaptive evolution. Previous studies have mostly focused on how species in the HHM adapt to climatic oscillations brought by uplift of the plateau(Luo et al., 2016; Shahzad, Jia, Chen, Zeb, & Li, 2017; Xu et al., 2010; J. Yang, Zhou, Huang, & He, 2018). The refuge pattern of species in the QTP region during the ice age, as well as their migration out of the plateau, is also a topic of current research (Q. Li et al., 2020; H. R. Liu et al., 2022; M. L. Liu, He, López-Pujol, Jia, & Li, 2019; Shahzad et al., 2017). Available phylogenetic and biogeographic studies have suggested that population differentiation and demography within species have also been strongly influenced by the uplift of the QTP and the consequent climate oscillations during the Quaternary ice age in the region(H. R. Liu et al., 2022; Y. Sun et al., 2014; H. Wang et al., 2010; F. S. Yang, Qin, Li, & Wang, 2012). In recent years, while most studies continue to focus on population differentiation and biogeography within species, very few researchers have focused on an entire endemic genus in the HHM region(H. Y. Zheng, Guo, Price, He, & Zhou, 2021). Therefore, we expect to investigate the origins, diversification, and population response of species to climatic oscillations since the Pleistocene by studying the distribution and population history of plant taxa that are mainly distributed in the HHM and QTP region.
Notholirion is a genus of Liliaceae and is mainly distributed in the HHM and QTP region, where it grows in alpine meadows and shrublands(M. Yang, Zhou, Xingjin, & Peng, 2016).Notholirion species are distinguished from other genera of Liliaceae by the presence of racemes and numerous small bulbs surrounding their bulbs. According to the records of Notholirionin the Flora of China and Li et al. (2021), four morphologically distinct species are accepted, and three species occur in the HHM and QTP region, except for N. koeiei , which are found in Iran and Iraq in the West Asia region(J. Li et al., 2022; J. Q. Liu et al., 2014). Particularly, the two species with distribution in China (N. macrophyllum and N. bulbuliferum ) both live at altitudes above 2800 m and are typical plants of the QTP(M. Yang et al., 2016). N. bulbuliferum exhibITS the widest distribution in China, ranging from the Qinling Mountains in Shaanxi to Western Sichuan, northwestern Yunnan, and eastern Tibet. N. macrophyllum is restricted to specific areas such as Jilong in Tibet and Daocheng in Sichuan(J. Li et al., 2022). Additionally, we were fortunate to acquire a population of N. thomsonianum from Nepal. N. thomsonianum does not occur naturally in China, but to maximize the representation of Notholirion species, we included the only available population from Nepal in our analysis. As for N. koeiei , there are only five recorded specimens from Iraq and Iran in western Asia, and unfortunately, we did not have access to any samples of this species. Based on the descriptions in the Flora of China and our own field observations, we have noted several distinct characteristics among the Notholirion species. Mature plants of N. macrophyllum typically have a height of less than 40 cm, and their racemes typically bear 3-7 flowers. On the other hand, N. bulbuliferum and N. thomsonianum generally grow taller than 40 cm, and their racemes typically bear a larger number of flowers. Furthermore, N. bulbuliferum lacks any stripes at the base of the tepals and typically flowers from July to August, whereas N. thomsonianum exhibITS longitudinal dark stripes consisting of spots at the base of the tepals and flowers from March to May(S. C. Chen, Liang, Xu, & Minoru, 2000; J. Li et al., 2022). The recent phylogenetic study indicated that N. bulbuliferum and N. macrophyllum are sister taxa, and they form a sister clade together with N. thomsonianum . The three Notholirion species form a distinct monophyletic clade. Therefore, this genus is an ideal taxon to investigate the evolution and diversification of alpine plants in the HHM and QTP region(J. Li et al., 2022).
In this study, we reconstructed the phylogenetic tree ofNotholirion based on data from 31 populations of three species that distributed in the HHM and QTP regions. We used biogeographical and population genetics approaches to identify the mechanism of origin, genetic structure, and lineage evolutionary history in the genusNotholirion . Our aims were to: (i) reconstruct the phylogenetic relationships within the genus Notholirion using materials from 31 populations; (ii) investigate the origin and species diversification of Notholirion in the HHM and QTP regions; (iii) explore the geological and climatic changes that influenced distribution shifts and genetic diversity of Notholirion . We hope that this study will provide some clues to explore the evolutionary patterns of species in the HHM region.