## 3 Discussion
### Historical Biogeography of Sect. Tubulose in the Sino-Japanese Floristic Region  
The diversification of _Clematis_ has been found to begin in the late Miocene, although its causal factors still remain uncertain [43]. The majority of major lineages of _Clematis_, including sect. _Tubulose_ emerged during the Pliocene. Since the Miocene epoch, the establishment of the monsoon system caused by the uplift of the Himalayas and the Qinghai-Tibetan Plateau led to notable changes or substitutions of vegetation types in the SJFR, and frequent glacial and interglacial periods [20]. From the late Miocene through the Pliocene to the Pleistocene, the global temperatures dropped gradually with fluctuations, and seasonality in rainfall and temperature increased, which may have contributed to the disappearance of forests and the expansion of praaries and savannas [74]. In Pliocene, rainfall decreased significantly in Asia, and the climate became cooler and drier, probably forced by global temperature change [75]. On the other hand, the uplifting of the Himalayas and the Tibetan Plateau from the late Palaeocene to the early Pleistocene brought a large amount of rainfall to East Asia by forming a monsoon system [76]. This is the palaeoclimatic background for evolving the erect herbaceous or subshrub group of sect. _Tubulose_ in East Asia from _Clematis_, a genus of climbers. Species of sect. _Tubulose_ are mostly mesophytic and cold-adapted [46]. In northern China, plants of sect. _Tubulose_ are found in mountain areas of low and medium elevation (often lower than 1400 m). In Taiwan island, plants of sect. _Tubulose_ can be found as high as 3600 m in elevation. [PERSON] et al. [46] conducted ecological niche modeling for C. _heraclejolia_ and _C. tubulosa_ and found that BIO18 (Precipitation of Warmest Quarter) is the most important determining factor for the distribution of the two species. This indicated that sect. _Tubulosa_ may have adapted well to the East Asian Monsoon climate. All these lines of evidence suggested that the origin of sect. _Tubulosa_ may have been correlated to the intensification of the Asian monsoon during the Pliocene. Our molecular dating results showed that all the current species of sect. _Tubulose_ diversified during the Pleistocene epoch (Figure 3). The Pleistocene climate was marked by repeated glacial cycles in the Northern Hemisphere but with global effects [77]. According to palaeofloristic studies, from the late Pliocene to the middle Pleistocene, the floristic element change succeeded stepwise in Northern Hemisphere. Humid thermophilous Tertiary floristic elements gradually became extinct and modern elements, including temperate to subarctic elements, emerged instead [78; 79; 80]. This climate change and the vegetation succession may have facilitated the expansion and species diversification of the sect. _Tubulose_. Our phylogenomic analysis using SNPs data generated a phylogeny with strong geographic patterns. When only one sample for each taxon was kept for dating and biogeographic analysis, all the island species formed a clade sister to one of the continental taxa, _C. tubulosa_, from mainland China (Figures 3 and 4). Within this clade, Korean species diverged first, and then taxa from the Japanese archipelago and Taiwan island formed two subclades, respectively. Our results indicated that sect. _Tubulosa_ diverged from its sister clade, most likely in mainland China, and the current species of sect. _Tubulosa_ diverged into two lineages also, possibly in mainland China. The island species clade evolved in about 1.61 Mya (95% HPD: 1.06-2.31 Mya, SNPs) or 1.86 Mya (95% HPD: 1.30-2.53 Mya, plastome) in the Pleistocene. Preceding this period, sect. _Tubulosa_ from mainland China quickly dispersed through the Korean peninsula via the Japanese archipelago to Taiwan island by two successive dispersal events (Figure 4). Within island species, Korean, Japanese, and Taiwanese island species diverged by vicariance events during the Calabrian (1.80-0.77 Mya in the early Pleistocene).