2 | MATERIALS AND METHODS
| Study area
The Kunlun Mountains are an independent physical geographic unit, located in northwest China on the northern edge of the QTP. Geographically, they border the Pamirs plateau to the west, southeast Qinghai to the east, the Qaidam and Tarim Basins to the north, and northwest Tibet Autonomous Region to the south. The Kunlun Mountains range is oriented east-west, located between 34°N–40°N and 75°E–100°E, with an average altitude >4,000 meters. The range extends for a total length of ~2,500 km and width of 130–200 km. The mountain range is narrower in the west compared to the east and covers a total area of more than 500,000 km2(Zheng, 1999; Wu, 2012–2015; Figure 1).
The elevation of the mountain range increases from the east to the west, and ranges between 3,000 m and 7,719 m. The area has an annual precipitation that varies from ~100 to 500 mm and an average annual temperature of < 0℃. The annual precipitation and temperatures show an obvious decrease from the east to the west. The climate on the slopes of the mountain range varies greatly and the steep climate gradient results in a dramatic change in vegetation cover. From east to west, the vegetation types are alpine scrub, alpine meadow, and alpine steppe. In addition, there are a few coniferous forests in the east and west of the Kunlun Mountains (Zheng, 1999; Wu, 2012–2015).
The formation of the Kunlun Mountains coincided with the Himalayan movement. According to numerous studies, extensive uplifts of the QTP occurred ca. 15–13 Ma and ca. 8–7 Ma, and the last abrupt and rapid uplift took place 3.6–1.2 Ma (Harrison, Copeland, Kidd, & Yin, 1992; Li, Shi, & Li, 1995; Shi, Li, & Li, 1998; Sun & Zheng, 1998; Spicer et al., 2003). Recent studies have demonstrated that the current QTP ecosystem began in the early Miocene (Deng, Wu, Wang, Su, & Zhou, 2019), and that the Kunlun Mountains reached their present height over the last 17 million years (Pan, 2000; Sun et al., 2015). After the early Miocene, the Kunlun Mountains experienced the Kunhuang movement (Cui et al., 1998) and numerous glacial events (Su, 1998).
To accurately reveal the current plant community, the study region was divided into 28 county-level geographical units. Geographically, the Kunlun Mountains are divided into three parts: east, west, and middle. The western part consists of 6 counties; the middle part consists of 14 counties, with 6 counties on the southern slope and 8 counties on the northern slope; and the eastern part consists of 8 counties.
| Distribution data
The basic distribution data were obtained fromFlora Kunlunica published in four volumes by Wu and his colleagues (Wu, 2012–2015), with reference to published monographs and other literature, includingFlora of Xinjiang (Shen, 1993–2011),Flora of Qinghai (Liu, 1996–1999),Flora of Tibet Autonomous Region (Wu, 1983–1987), andThe Vascular Plants and Their Eco-geographical Distribution of the Qinghai-Tibet Plateau (Wu, 2008). Based on these sources, and using the order of families from the Angiosperm Phylogeny Group Ⅳ (APGⅣ, 2016), species were classified into genera and families according to A Dictionary of the Families and Genera of Chinese Vascular Plants(Li, Chen, Wang, & Lu, 2018),http://www.catalogueoflife.org/annual-checklist/2019/, andhttp://www.theplantlist.org. Genera and species that were not native to the Kunlun Mountains were excluded, and the infraspecific taxa were preserved.
The information presented a comprehensive checklist of the seed plant species in the Kunlun Mountains. To analyze the spatial patterns, these species were divided into 28 county-level geographical units based on species distribution data.
| Similarity of taxa
To determine the origin of the Kunlun Mountains flora (KMF), the species were compared with the flora in nearby biodiversity hotspots. Three biodiversity hotspots exist around the Kunlun Mountains, including the Mountains of Central Asia, the Eastern Himalayas, and the Mountains of Southwest China, which are located to the north, south, and southeast of the Kunlun Mountains, respectively (Myers, Mittermeier, Mittermeier, da Fonseca, & Kent, 2000; Zachos & Habel, 2011). The Mountains of Southwest China host the highest number of plant species among these three biodiversity hotspots, and the Hengduan Mountains are representative of the Mountains of Southwest China. Therefore, the Hengduan Mountains form an important biodiversity hotspot, and harbor one of the richest temperate floras in the world, with ~12,000 vascular plants (Boufford, 2014). We evaluated the species-level, genus-level, and family-level similarities between the KMF and the Hengduan Mountains flora (HMF). The plant species richness in the Kunlun Mountains was approximately one sixth of that in the Hengduan Mountains. The taxa similarity (TS) between the KMF and the HMF was calculated as follows:
\begin{equation} \text{TS}=\frac{\text{SR}}{\text{TR}}\times 100\%\nonumber \\ \end{equation}
where SR represents the number of shared taxa between a KMF sample and the HMF, TR represents the number of taxa in the KMF sample (taxa represent families, genera, or species), and TS is the similarity of taxa between the KMF sample and the HMF.
| Phylogenetic diversity and structure
We calculated the species level phylogenetic diversity (PD), standard effect size phylogenetic diversity (SES-PD), net relatedness index (NRI), and nearest taxon index (NTI) in each county.
PD was the sum of the phylogenetic length of the communities in each sample and was measured based on the approach developed by Faith (1992). SES-PD was calculated by dividing the difference between the observed (PDobserved) and expected phylogenetic diversity (PDrandom) by the standard deviation (s.d.) of the null distribution (s.d.[PDrandom]) (Rodrigues et al., 2005), as follows:
\begin{equation} SES-PD=\frac{\text{PD}_{\text{observed}}-\text{PD}_{\text{random}}}{\text{s.d.}\left(\text{PD}_{\text{random}}\right)}\nonumber \\ \end{equation}
The NRI and NTI were calculated to analyze community phylogenetic structure (clustering or overdispersion), and to examine possible ecological and evolutionary processes within communities (Webb, Ackerly, McPeek, & Donoghue, 2002). The NRI was based on the mean phylogenetic distance (MPD), which is an estimate of the average phylogenetic relatedness between all possible pairs of taxa within a sample. The NTI was based on the mean nearest taxon distance (MNTD), which is an estimate of the mean phylogenetic relatedness between each pair of taxa in a sample and its nearest relative in a phylogeny. The NRI and NTI values were calculated as follows:
\begin{equation} NRI=-1\times\frac{\text{MPD}_{\text{observed}}-\text{MPD}_{\text{random}}}{\text{s.d.}\left(\text{MPD}_{\text{random}}\right)}\nonumber \\ \end{equation}\begin{equation} NTI=-1\times\frac{\text{MNTD}_{\text{observed}}-\text{MNTD}_{\text{random}}}{\text{s.d.}\left(\text{MNTD}_{\text{random}}\right)}\nonumber \\ \end{equation}
where, respectively, MPDobserved and MNTDobserved represent the observed MPD and MNTD values; MPDrandom and MNTDrandom represent the mean values of the expected MPD and MNTD of the randomized assemblages (n = 999); s.d.(MPDrandom) and s.d.(MNTDrandom) represent the standard deviations of the MPDrandom and MNTDrandom values for the randomized assemblages. The null distributions of MPD and MNTD were created by randomly selecting the observed number of taxa in each sample 999 times, with all taxa in the phylogeny serving as the sampling pool.
The phylogenetic analyses require a phylogenetic tree of seed plants, the phylogenetic tree was constructed using Phylomatic (http://phylodiversity.net/phylomatic/) with the stored tree in Zanne et al. (2014). The ecological indexes were calculated using R version 3.3.3 (R Core Team, 2017) and picante packages (Kembel et al., 2010).
| Statistical analysis
To examine the community assembly processes in the Kunlun Mountains, two key issues were studied: 1) the patterns of species diversity in the area, and 2) relevant mechanisms relating to community assembly. The HMF has been assembled through recent in situ diversification during its rapid uplift over the last 8 Ma (Xing & Ree, 2017). In the northern hemisphere, it is the largest refuge for species in the glacial age (Liu, Luo, Li, & Gao, 2017), and a center for species diversification for many current plants (Wen, Zhang, Nie, Zhong, & Sun, 2014; Chen, Deng, Zhou, & Sun, 2018), such as Saussurea ,Gentiana , Pedicularis , Salix , Primula ,Saxifraga , Ranunculus , and Corydalis . Endemic species of seed plants account for 32.4% of the total species in the Hengduan Mountains (Zhang, Boufford, Ree, & Sun, 2009). Therefore, the results of the TS revealed the relationship of species migrations between the Kunlun Mountains and the Hengduan Mountains. The analysis of these results, the geological history, and rules of species migration revealed the patterns of species diversity.
PD and SES-PD have been used to determine the floristic histories of communities (Faith, 1992; Rodrigues et al., 2005). Negative SES-PD values imply that the actual PD is lower than the predicted PD, and the community consists of young flora with relatively close phylogenetic relationships among species; whereas positive SES-PD values imply that the actual PD is higher than the predicted PD, and the community consists of ancient flora with more distant phylogenetic relationships among species. The NRI primarily reflects the structure in deeper parts of a phylogeny and is more appropriate for explaining evolutionary processes; whereas the NTI reflects the structure in shallower parts of a phylogeny, and is more appropriate for exploring ecological processes (Webb, Ackerly, McPeek, & Donoghue, 2002). At the community level, positive NRI and NTI values indicate phylogenetic clustering, whereas negative values indicate phylogenetic dispersion. The analysis of NRIs, NTIs, and SES-PDs were used to explain the evolutionary and ecological processes of community assembly.