Hong Qian
email: hqian@museum.state.il.us

Robert E Ricklefs

Wilfried Thuiller

Evolutionary assembly of flowering plants into sky islands

Although they experience cold climates, particularly in temperate mountains during winter, alpine floras (plants in the vegetation belts above the climatic treelines) are generally species-rich. Yet, whether these floras represent evolutionarily independent, but convergent, assemblages drawn from their regional floras, or they originated from particular clades pre-adapted to harsh conditions, has not been determined. Here, we analyze the evolutionary relationships of angiosperm (flowering plant) species in 63 alpine floras worldwide (~7,000 species) in comparison with their regional floras (~94,000 species) and to the entire global flora. We find that each of the alpine floras represents an assemblage of more closely related species in comparison to their respective regional floras. The degree of phylogenetic clustering of species in alpine floras in tropical mountains exceeds that in temperate mountains. However, in relation to the global flora, temperate alpine floras are phylogenetically closely-related subsets of floras that colonized cold temperate areas during inter-glacial periods. We conclude that alpine floras include a few dominant families that have evolved tolerance to low temperature, and that evolutionary niche conservatism explains their phylogenetic clustering, compared to species in their regional species pools. The local assembly of species from a pool of regionally available species (i.e., the regional species pool) reflects an interplay between evolutionary and ecological processes 1-2 . Under strong environmental filtering, the tendency of lineages to retain ancestral ecological traits over time (phylogenetic niche conservatism 3 ) will leave a signature in the phylogenetic structure of local assemblages 4 .

 . Elevational gradients also occupy smaller geographical areas than latitudinal gradients, and thus may structure local floras. Altogether, changes in species assemblages across elevational gradients, and notably their phylogenetic structure, might thus differ from variation across latitudinal gradients. Understanding those differences is essential to gather a better understanding of the history of plant assembly.

Several studies (e.g., refs. 14-15) have shown that the phylogenetic relatedness of high-elevation tree species decreases with elevation, which contrasts with the increase in phylogenetic relatedness within tree assemblages with increasing latitude [16][17] . This pattern suggests that niche convergence, rather than niche conservatism, has characterized the assembly of tree species along tropical elevational gradients 18 . Whether niche convergence is restricted to tropical mountains, and whether it characterizes assemblages of both lowland and alpine vegetation (i.e., the entire regional flora), and for both woody and herbaceous plants, remain open questions.

).

Results and Discussion

We constructed a phylogeny for the 94,161 species of angiosperms (more than one quarter of all angiosperm species) occurring in the regional floras utilized in this study. We did so by using an updated version of the largest dated phylogeny of seed plants 19 as a backbone and V.PhyloMaker 20 as a tool to attach additional species to the backbone phylogeny (see Methods). To capture the phylogenetic structure of the floras, we used two complementary metrics 21 , namely phylogenetic diversity (PD) and mean pairwise distance (MPD). PD represents the sum of the branch lengths of the phylogenetic tree linking all species of a particular assemblage. MPD represents the mean phylogenetic distance between all pairs of species in an assemblage, the phylogenetic distance between a pair of species being defined as the total branch length of the shortest path between the two species. A species assemblage with a large PD or MPD represents an assemblage with species from different clades far apart in the phylogeny. In contrast, a species assemblage with low PD or MPD might represent an assemblage from a single clade, or a few clades that recently diversified. However, because these metrics are influenced by species richness, they need to be standardized to be comparable between sites. Each

metric was thus standardized using a set of null models to compare the phylogenetic structure of each alpine flora with its regional flora, with significant differences indicating elevational gradient effects. Expanding the breadth of the compared flora, up to the global flora, allows comparison of the phylogenetic structure of each alpine flora with that of the global pool of species. By varying the scale of the pool of species considered in null models, one can test hypotheses about mechanisms that have generated the phylogenetic structure of alpine assemblages 22 .

Once corrected by these tailor-made null models (Methods), the resulting standardized effect size (ses) metrics quantify the relative excess (e.g., several clades far apart in the phylogeny, old and unique species) or a deficit (e.g., a single highly diversified clade) in phylogenetic diversity for a given assemblage relative to the overall species pool. More specifically, the standardized effect size of PD (PDses) reveals the phylogenetic structure that predominates at the tips of the phylogenetic tree (recent divergences), while standardized effect size of MPD (MPDses) reflects deep-branching (i.e., ancient) divergences 21 . We used these two complementary metrics because different processes may act over different evolutionary time scales, which would not be detectable using a single metric 21 .

Using these metrics, we test whether angiosperm species in alpine floras are phylogenetically clustered (as predicted by the niche conservatism hypothesis) or phylogenetically over-dispersed (as predicted by the niche convergence hypothesis) in comparison to their respective regional species pools (including species in alpine belts and below). We also investigate whether this phylogenetic structure differs between continents and climate regions of the world. Finally, we test whether the phylogenetic clustering of alpine floras differs across latitude (and thus temperature) gradients and in relation to the species pool considered.

All 63 alpine floras analyzed here comprise groups of phylogenetically more closely related species (i.e., MPDses and PDses < 0), compared to groups of species randomly drawn from their regional species pools (Supplementary Figure 1). This result was significant for 50 (79%) and 59 (94%) of the 63 alpine floras for MPDses and PDses, respectively (i.e., MPDses and PDses < -1.96) (Figure 1, Supplementary Figure 2). Thus, most alpine floras represent specific phylogenetic subsets of the regional floras of the mountain systems in which they occur. Interestingly, clustering due to shallow-branching divergences (i.e., PDses) near the tips of the phylogenetic tree was stronger than clustering due to deep-time divergences (i.e., MPDses, Supplementary Figure 2), with the exception of the alpine floras in South America (Supplementary Figure 2). Thus, phylogenetic clustering is rather recent for most alpine floras and characterizes shallow-branching divergences within the regional phylogenies. Conversely, evolutionary divergence between alpine and lowland floras in South America involves primarily deep-time splits within the regional floras. This pattern might originate from ancient mountain uplifts in South America that early on induced deep-time divergence of floras. We tested whether phylogenetic clustering holds even when alpine floras and their respective regional species pools are aggregated at continental scales. Here again, alpine floras represented closely-related assemblages compared to their respective continental species pools, irrespective of the metric used (Figure 2). This result was confirmed when the combinations of species in all alpine floras were compared to the combinations of the species in all regional species pools. In this case, values for MPDses and PDses were extremely negative (MPDses = -38.6 and PDses = -35.0), demonstrating very strong phylogenetic clustering for the global alpine flora examined in this study.

Strikingly, the strength of phylogenetic clustering of each alpine flora varies with latitude (Figure 1, Figure 3), irrespective of the metric used. When each alpine flora was compared to its regional flora, clustering was stronger at low latitudes than at high latitudes (Figure 3a). Thus, the alpine floras of tropical mountains form distinct phylogenetic groupings of species, compared to their regional floras. In contrast, species in alpine floras at high latitudes, such as those in North America and Europe, are only loosely clustered assemblages of species drawn from their regional floras (Figure 3a). This difference might reflect the fact that high latitude floras are already a non-random set of the global flora, primarily with clades adapted to cold conditions [START_REF] Wu | Scientific Survey of Gansu Baishui River Nature Reserve[END_REF] , with an arcticalpine affiliation. To test this hypothesis, we first compared each alpine flora to a global pool of the 313,855 angiosperm species in the combination of our regional floras and The Plant List (see Methods), and then compared each associated regional flora (alpine and lowland species combined) to the same global angiosperm species pool. Interestingly, high latitude alpine floras were still less clustered than low latitude ones when extending the species pool of each alpine flora to the global species pool of angiosperms (Figure 3b). However, in agreement with the hypothesis that high latitude regional floras (i.e., the species in alpine belts plus lowlands) are already clustered phylogenetically compared to low latitude floras, the strength of the phylogenetic clustering is strongly linked to latitude but with a negative slope (Figure 3d). This clustering of the entire regional mountain floras at high latitudes partly explains the lower phylogenetic clustering of their individual alpine floras in contrast to that in low latitude alpine floras. When each alpine flora was compared to the combination of all angiosperm species in the 63 alpine floras, species in alpine floras at low latitudes tended to be more strongly clustered than those at high latitudes (Figure 3c). This implies that species in each of the alpine floras at high latitudes are more phylogenetically related to each other than those at low latitudes when species in each alpine flora are compared to the species pool that included all species of the 63 alpine floras. When latitude was substituted with growing degree days in these analyses, the results were generally consistent with those based on latitude (Supplementary Figure 3).

Overall, our analyses, based on two complementary metrics and tailored definitions of the species pool, confirmed that alpine floras represent phylogenetically closely-related species assemblages and that the origin of this clustering varies with latitude. These observations do not reflect sampling bias since our study includes the majority (~70%) of all alpine angiosperm species in the world (based on the global estimate reported in ref. 23). Instead, the phylogenetic clustering appears to reflect strong environmental filtering in combination with phylogenetic niche conservatism. That is, owing to shared evolutionary adaptations to low temperature, species in alpine environments are likely more closely related to each other, on average, than are species in lowlands.

Biotic interactions may further increase this pattern 11 . For instance, both asymmetric competition 24 and facilitation between similar species 25 can increase phylogenetic clustering. However, these processes probably do not drive the observed pattern for alpine plants because competitive interactions are usually reduced, and plantplant interactions are thought to be more positive due to facilitation (mutual benefits of shelter) in alpine environments 26 . For example, plant species with a cushion habit (e.g., an androsace, or rock jasmine) can facilitate the establishment of individuals of species that would otherwise be less successful at such locations 27 . Such a mechanism should lead to phylogenetic overdispersion (androsace and grass are far apart on the phylogeny of angiosperms), rather than phylogenetic clustering. It is also unlikely that, within each mountain system, dispersal limitation has caused phylogenetic clustering of alpine species compared to the whole flora of the mountain system. This is because geographical distances across elevational gradients are relatively small, and major dispersal barriers are unlikely across such small geographical extents 28 . However, dispersal limitation might explain, to some degree, the stronger phylogenetic clustering observed when an alpine flora is compared to the global species pool. This is because defining the global species pool to include species from different biogeographic realms, i.e., on different continents, would likely over-extend the breadth of the phylogenetic tree used to standardize the phylogenetic metrics of a given alpine flora. In other words, the global species pool includes some lineages (e.g., families or even orders) that are absent from the biogeographic realm of any particular focal alpine flora, which tend to 'artificially' increase the relative phylogenetic clustering of the alpine flora, compared to the global species pool. This is supported by our major result, i.e., the average MPDses of the 63 alpine floras was less negative when their respective regional floras were used as species pools, compared to that when the global species pool was used as species pools for each alpine flora (-4.76 and -5.91, respectively). In other words, the larger the reference species pool, the more deficient in phylogenetic diversity the alpine flora becomes. This pattern reflects the dominance of few clades in the alpine flora of the world compared to the global angiosperm flora.

Interestingly, while the phylogenetic clustering of alpine floras presents a general pattern, its strength varies with latitude, with temperate alpine floras less clustered than tropical alpine floras compared to their respective lowland regional floras. This difference might result, at least in part, from the fact that ecological gradients (particularly temperature) are shorter in high latitude mountains with fewer altitudinal life belts than in low latitude mountains 28 (e.g., a tropical mountain has a tropical vegetation belt at low elevations, but this belt is lacking in temperate mountains). However, this general pattern is reversed when the overall angiosperm flora of a mountain area (including both alpine and lowland elevations) is compared to the global species pool of angiosperms. This simply confirms that species in temperate floras are already a clustered, rather than random, subset of the entire angiosperm flora of the world [START_REF] Wu | Scientific Survey of Gansu Baishui River Nature Reserve[END_REF] . In other words, tropical alpine floras represent primarily clades that have diverged early in flowering plant evolution, while temperate alpine floras are recent clustered assemblages of temperate floras (i.e., mostly herbaceous species), which are particular, closely-related species groups of the global angiosperm flora.

Nonetheless, these relationships cannot fully explain the overall patterns. Indeed, when comparing each alpine flora to the angiosperm flora of the world, low latitude alpine floras remained more clustered than high latitude ones (Figure 3b). A complementary hypothesis is that ecological gradients are shorter in high latitude mountains with fewer life belts than in low latitude mountains, as noted above. Because genera and families are generally similar among all alpine floras of the world (e.g., 88% of angiosperm families in tropical-latitude alpine floras examined in this study also occur in temperate-latitude alpine floras), including more tropical taxa (families, genera, and species) in regional species pools of low latitude regions would necessarily cause stronger phylogenetic clustering for their alpine floras, compared to their regional species pools.

Interestingly, when each alpine flora is compared to the species pool that includes only the species of the 63 alpine floras, species in low latitude alpine floras remain more strongly clustered than those in high latitude alpine floras (Figure 3c). The following hypothesis might account for this pattern. Angiosperms originated in, and spread from, the tropics 29 . Some early tropical lineages became adapted to tropical montane climates, forming clustered assemblages compared to lowland tropical floras. While species in tropical alpine belts, as a whole, might be clustered compared to the global species pool, species adapted to tropical alpine belts within different continents or major mountain systems might belong to different major lineages, and thus might be further clustered, because dispersal among mountains within and between continents is particularly limited within tropical latitudes 30 . This would cause 'double-clustering' for tropical alpine floras. In contrast, although species in temperate alpine floras are also clustered compared to the global species pool, glacial-interglacial cycles during the Pleistocene repeatedly mixed species of alpine floras at low elevation among different regions and continents, particularly in the Northern Hemisphere. This would have tended to homogenize alpine floras across continental regions. Overall, these processes would have resulted in stronger phylogenetic clustering in tropical than in temperate alpine floras, in comparison with the global alpine species pool.

Methods Alpine belt

We defined the alpine belt in a mountain system as the area located above the natural climatic limit of trees (alpine treeline). Because alpine belts of different mountains are commonly separated by extensive forested or rangeland areas below alpine treelines, alpine belts are often considered as 'sky islands' [31][32] . Alpine vegetation represents the only terrestrial biogeographic unit that occurs at all latitudes worldwide 23 , a remarkable fact first documented by Alexander von Humbolt 33 . Vegetation above the alpine (elevational) treeline resembles that north of the arctic (latitudinal) treeline 23,34 . Although the total area of alpine vegetation represents only 2.6 % of the Earth's terrestrial surface outside Antarctica 23,35 , and only half as much area as arctic vegetation (c. 5% of the land area), global species diversity of vascular plants in alpine vegetation is ca. six-fold higher than that in arctic vegetation (ca. 10,000 species in alpine vegetation; vs. ca. 1,500 arctic species; ref. 36). Alpine belts present severe environmental challenges to plant life, including low temperatures and high ultraviolet radiation 21 .

Floras

The latitudinal range of this study was confined between 50°N and 50°S. We did not include higher latitudes because elevational gradients below alpine treelines at these latitudes are generally short, with few vegetation belts, which would have weakened comparisons with other alpine belts. We assembled 63 alpine floras worldwide (Figure 1). Of these 63 alpine floras, 62 are typical alpine floras located above climate treelines. No true alpine flora exists in southeastern North America; to represent this broad region in our study, we included one plant assemblage from the highest mountain peaks for this region (maximum elevation 2037 m) (we call it an "alpine" flora for convenience of discussion). The 63 alpine floras represent the major mountain systems across the world, including Mount Kenya and the Drakensberg Escarpment in Africa, the Himalayas in Asia, the Andes in South America, the Rocky Mountains in North America, and the European Alps. We assigned each of the 63 alpine floras to either temperate or tropical latitudes, using 23.5°N and 23.5°S as the temperate-tropical boundaries.

We then assembled a regional species pool for each alpine flora. These regional species pools included all angiosperm species along the entire elevational gradient (from the lowest to highest elevations) within the region. For example, the regional species pool for the alpine flora of Nepal included all angiosperm species recorded in Nepal from 59 to 6,400 m in elevation (i.e., the entire elevation range of Nepal over which angiosperms are distributed). Details about each alpine flora and its regional species pool are available in Supplementary Table 1. The species of the alpine floras included in this study are restricted to non-tree species. Botanical nomenclature was standardized according to The Plant List (version 1.1, www.theplantlist.org). Infraspecific taxa were combined with their respective species. Non-native species in each flora were excluded. In total, the regional species pools of the 63 alpine floras included 94,161 species in 369 families of angiosperms (more than one quarter of angiosperm species in the world). Of these, 6,918 species in 140 families) comprised the 63 alpine floras. Each species was assigned to a family recognized in APG IV 37 , based on information on the relationships between genera and families provided by the Angiosperm Phylogeny Website (http://www.mobot.org/MOBOT/research/APweb/).

For the 63 alpine floras, on average, each regional species pool included 3,867 (± 4,709 SD) angiosperm species, and each alpine flora included 171 (± 124) angiosperm species; on average, 9.1% of species in a regional species pool were present in its alpine flora. When the 63 sites were considered together, 7.3% of the 94,161 species in the regional species pools occurred in the 63 alpine floras.

Phylogeny reconstruction

We used a recently generated time-calibrated megatree for vascular plants, GBOTB_extended.tre 20 , as a backbone to generate a phylogeny for the 94,161 species. The megatree included an updated version of the phylogeny for pteridophytes (ref. 8) and an updated version of GBOTB for seed plants (ref. 19). The megatree includes all families of vascular plants worldwide, including families that are absent from the phylogenies of refs. 8 and 19. Of the 8,341 genera in our data set, 80% (6,673) were present in the megatree. We added the genera and species in our data set that were absent from the megatree to their respective families and genera using the Phylomatic and BLADJ approaches 38 implemented in the V.PhyloMaker software 20 . V.PhyloMaker sets branch lengths of added taxa in a family by placing the nodes evenly between dated nodes and terminals within the family and placing a missing species at the mid-point of the branch length of its genus (e.g., ref. 14). A recent study (ref. 39) showed that for the two phylogenetic metrics used in our present study (see below), values of a phylogenetic metric derived from a phylogenetic tree resolved only at the genus level are nearly perfectly correlated to those derived from a phylogenetic tree resolved fully at the species level (Pearson's correlation coefficient is 1.000 for one phylogenetic metric and 0.992 for the other phylogenetic metric), suggesting that patterns of phylogenetic structure measured with the two phylogenetic metrics would be similar or identical regardless of whether a phylogenetic tree resolved at the species or genus level is used to calculate these phylogenetic metrics. Finally, we pruned the megatree to generate a phylogenetic tree for each of the regional species pools, retaining only the species present in the regional species pool.

We also used V.PhyloMaker, and the approach described above, to build a phylogeny for angiosperm species worldwide, which included all angiosperm species in the regional floras included in this study, plus angiosperm species in The Plant List that can be directly assigned to the families of APG IV. We considered the 313,855 species in this phylogeny as a global species pool of angiosperms for the analyses in this study.

Phylogenetic structure metrics

We analyzed the phylogenetic structure of the alpine floras using two complementary metrics, namely phylogenetic diversity (PD; ref. 40) and mean pairwise distance (MPD). Because PD and MPD are positively correlated with species richness, in order to make them comparable between sites, it is necessary to standardize their values by accounting for species richness. This is commonly done with the use of a null model that keeps species richness constant while randomizing the phylogenetic relationships between species. Using this null model, the standardized effect size, which gives the relative position of an observed value with respect to the null distribution, can be calculated as:

Metricses = [Metricobsmean(Metricnull)]/sd(Metricnull), where Metricses is the standardized effect size of PD or MPD (i.e., PDses or MPDses, respectively), Metricobs is the observed phylogenetic structure metric in a given alpine flora, and Metricnull is the same metric calculated n times with n randomized assemblages drawn from a species pool (see below for the definition of the species pool). Both PDses and MPDses quantify the relative excess (overdispersion) or deficit (clustering) in phylogenetic structure for a given alpine flora relatively to the species pool. In other words, a negative PDses or MPDses reflects relative phylogenetic clustering of species while a positive PDses or MPDses reflects relative phylogenetic overdispersion of species.

PDses and MPDses measure the phylogenetic structure of assemblages at different evolutionary depths: MPDses is linked to the more basal structure of the phylogenetic tree, whereas PDses describes the more terminal structure of the phylogenetic tree 41 . It is important to use metrics that can assess phylogenetic structure at both basal and shallow depths of evolutionary history across a phylogeny because some processes produce basal clustering while others create terminal overdispersion, generating 'clusters of overdispersion' 21 .

The two metrics were calculated using computationally efficient algorithms 42-43 based on exact solutions given a particular phylogenetic tree and species richness (rather than being based on a resampling approximation of the mean and variance), using a null model that considers all possible combinations of S species from the species pool (where S is the number of species in a sample under investigation) to be equally likely 44 . To determine whether MPDses and PDses values for a particular alpine flora were significantly smaller (i.e., more clustering and lower phylogenetic diversity) or larger (i.e., more overdispersion and higher phylogenetic diversity) compared to null assemblages randomly drawn from its species pool, we generated 999 null assemblages from the given species pool with the number of species in each null assemblage being equal to the number of species in the alpine flora. The position of the observed value relative to the null distribution was computed as the proportion of null values that are lower or higher than the observed value, which corresponds to a p-value. For normally distributed data, significance at p-value < 0.05 is equivalent to a standardized effect size > 1.96 (or < -1.96).

Phylogenetic structure and defined species pools

To depict the evolutionary structure of alpine floras around the world, we considered several ways to define the species pools and associated alpine floras. First, we used three species pools to calculate values of MPDses and PDses for each alpine flora: (1) a species pool that included all angiosperm species in the region within which the focal alpine flora was located (the 'regional species pool', see below for details; Supplementary Table 1), (2) a species pool that included all angiosperm species in the 63 alpine floras, and (3) a global species pool for angiosperms, which included 313,855 species (see above for details). For each alpine flora, the regional species pool was defined as all the species in the published flora of the mountain region (Supplementary Table 1). When several independent regional species pools could be retrieved from the literature, we chose the one that maximized the elevation range while minimizing the area of the region. This strategy provided a good representation of the area while minimizing the effects of dispersal limitation. On average, the geographic distance from the alpine belt of a region to the edge of the region was less than 250 km in our study. Because the distributions of most plant species exceed this distance within a region, we suggest that plant species distributions across different elevation belts within a mountain region are primarily a result of environmental sorting, rather than dispersal limitation.

Second, to test whether the phylogenetic structure of alpine floras varied significantly between climate zones across latitudes (tropical and temperate) and between continents, we combined the 63 alpine floras, and their respective regional species pools, into 12 climato-continental species pools (temperate versus tropical across continents). For each of the 12 species pools, we generated a species list of alpine plants by combining all alpine plant species in the alpine floras belonging to each pool (Supplementary Table 2). These species pools allowed us to strictly compare MPDses and PDses values across continents and climates. We also generated a global alpine flora and a single associated species pool.

Finally, to test whether species in temperate regional floras are more closely related (clustered) than species in tropical regional floras, compared to the global flora of angiosperms, we measured phylogenetic structure for each of the 63 regional floras based on the global angiosperm species pool.

Data availability

The data used in this study have been published and are accessible. Details about data sources are provided in Supplementary Table 1 or cited in the article. The data on which the analyses of this study were based are available at https://github.com/Kifir0411/NATECOLEVOL-200610646.

Figure Legends

Figure 1 Geographic patterns of standardized effect size of mean pairwise distance (MPDses, upper panel) and standardized effect size of phylogenetic diversity (PDses, lower panel) for the 63 alpine floras used in this study. MPDses and PDses of each alpine flora were calculated in regard to its regional flora. Filled symbols are significant (p<0.05). A more negative value represents a stronger degree of phylogenetic clustering among species within an alpine flora compared to its regional flora. Note that the location of a dot represents the location of the mid-point of a region, for which its alpine flora was analyzed in this study, i.e., the center of a regional flora (species pool), not a place where an alpine flora was located. Figure 2. Comparisons of standardized effect size of mean pairwise distance (MPDses, red triangles) and standardized effect size of phylogenetic diversity (PDses, blue triangles) with histograms for distributions of these two phylogenetic metrics derived from null assemblages (see Methods for details) for different climates (temperate versus tropical) and continents, and the globe. Each histogram represents the frequency (Freq.) of MPDses or PDses values derived from 999 null assemblages randomly drawn from the species pool defined at the climato-continental or global scale. A more negative value of MPDses or PDses (indicated by a red or blue triangle) represents a stronger degree of phylogenetic clustering among alpine species compared to the reference species pool. Figure 3. Relationships (Pearson's correlation coefficient, r) between latitude (in absolute terms) and standardized effect size of mean pairwise distance (MPDses) for (a) species in alpine floras with MPDses being calculated using the regional species pool of each of the alpine floras, (b) species in alpine floras with MPDses being calculated using the global species pool of angiosperm species in the combination of our regional floras and The Plant List (Methods), (c) species in alpine floras with MPDses being calculated using all species in the 63 alpine floras as a species pool, and (d) species in the regional floras of the alpine sites with MPDses being calculated using the global species pool of angiosperm species in the combination of our regional floras and The Plant List. Lines are linear least squares best fits; we used them to show linear trends, not for statistical tests.

< -8.0 < -6.0, > -8.0 < -4.0, > -6.0 < -2.0, > -4.0 > -2.0 Supplementary Table 1 Alpine floras and their regional species pools used in this study. Supplementary Figure 1 (continued,1).

Supplementary Figure 3. Relationships between growing degree days (GDD) and standardized effect size of mean pairwise distance (MPD ses ) for (a) species in alpine floras with MPD ses being calculated using the regional species pool of each of the alpine floras, (b) species in alpine floras with MPD ses being calculated using the global species pool of angiosperm species in The Plant List (Methods), (c) species in alpine floras with MPD ses being calculated using all species in the 63 alpine floras as a species pool, and (d) species in the regional floras of the alpine floras with MPD ses being calculated using the global species pool of angiosperm species in The Plant List. GDD for each site represents the average value of annual growing degree days above 5°C calculated for an area of nine squares of half-degree latitude and longitude (with the centroid of the focal site being located in the center square of the frame work of 3 by 3 squares) using climate data obtained from IIASA (https://iiasa.ac.at). GDD was standardized to vary from 0 to 1. Lines are linear least squares best fits; we used them to show linear trends, not for statistical tests.

Figure 1 Longitude

 1 Figure 1

  Figure 2 588 589

  Killick, D.J.B.. 1978. The Afro-alpine Region. In: Werger M.J.A. (eds) Biogeography and Ecology of Southern Africa. Monographiae Biologicae, vol 31. Springer, Dordrecht. 4. Beck, E., Scheibe, R. & Senser, M. 1983. The vegetation of the Shira Plateau and the western slopes of Kibo (Mount Kilimanjaro, Tanzania). Phytocoenologia, 11:1 -30. 5. Li, H.-W. 2003. Baima Snow Mountain National Nature Reserve. Yunnan Nationalities Publishing House. 6. Sun, H. and Z. Zhou. 2002. Seed plants of the Big Bend Gorge of Yalu Tsangpo in SE Tibet, E Himalayas. Yunnan Science and Technology Press, Kunming. 7. Qian, H. 1989. Alpine Tundra of Mt. Changbai: Phytotaxonomy, Florology and Phytoecology. Ph.D. dissertation. Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang. 8. Li, H. et al. (eds.). 2000. Flora of Gaoligong Mountains. Science Press, Beijing. 9. Liu, Z.-G. 1985. Vegetation of Gongga Mountains. Sichuan Science and Technology Press. 10. Zhang, L.-S. 2006. Yunnan Jiaozishan Nature Reserve. Yunnan Science and Technology Press.

	Site
	ID	Continent	Country [region]	Alpine flora	Regional species pool	Data source
	54 55	Africa Africa Africa South America Africa South America	Ethiopia Kenya South Africa and Lesotho Colombia Tanzania Ecuador	Alpine flora of Mt Galama Alpine flora of Parque Alpine flora of Mt. Kenya Flora of Kenya Flora of Ethiopia Nacional Natural Cocuy Flora of Colombia Alpine flora of Drakensberg Mountains Alpine flora of Chisacá Flora of Colombia Flora of KwaZulu-Natal Flora of northwestern Province of South Africa and Lesotho Ecuador (incl. the provinces of Esmeraldas, Alpine flora of Mount Kilimanjaro Flora of Tanzania Alpine flora of Complejo Carch, Imbabura, Volcánico Pichincha Pichincha)	1, 63 46, 2, 63 49, 3, 64, 101 4, 53, 63 46,
	56 57	Asia South America Asia South America	China Ecuador China Ecuador	Alpine flora of Baima Snow Mountains Alpine flora of El Cajas Alpine flora of Big Bend Gorge of Yalu Tsangpo Alpine flora of Parque Nacional Podocarpus	Flora of Baima Snow Mountains Flora of Azuay Province Flora of Big Bend Gorge of Yalu Tsangpo Flora of Loja Province Flora of Pichincha	50, 60, 92 5 46, 6
	58 59	Asia South America Asia Asia South America	China Ecuador China China Ecuador	Alpine flora of Changbai Mountains Alpine flora of Quito Alpine flora of Gaoligong Mountains Alpine flora of Gongga Mountains Alpine flora of Reserva Ecológica Antisana	Province Flora of Changbai Moutains Flora of northwestern Ecuador (incl. the Flora of Gaoligong Mountains provinces of Esmeraldas, Carch, Imbabura, Flora of grid cell #1616 in ref. 66 Pichincha) Flora of northwestern	51, 7, 65 8 46, 9, 66
	60	Asia Asia South America	China China Ecuador	Alpine flora of Jiaozi Mountains Alpine flora of Motianling Alpine flora of Reserva Ecológica El Ángel	Ecuador (incl. the Flora of Jiaozi Mountains provinces of Esmeraldas, Carch, Imbabura, Flora of Baishuijiang Nature Reserve Pichincha)	10, 54 11 46,
	Asia Asia South America Asia South America South America Asia Data sources 61 62 63 1. Hedberg, O. 1971. The high mountain flora of the Galama Mountain in Arussic Province, China Alpine flora of Cordillera Alpine flora of Taibai Mountains Flora of Taibai Mountains de Vilcanota -Laguna de Flora of Cuzco Department China Alpine flora of Wutai Mountains Peru Sibinacocha (Region) Flora of grid cell #990 in ref. 66 Alpine flora of Páramos Flora of Piura Department China Alpine flora of Yulong Snow Mountains Peru de Pacaipampa (Region) Flora of Yulong Snow Mountains Venezuela Alpine flora of Venezuela Flora of Venezuela India Alpine flora of Kashmir Himalaya Flora of Jammu and Kashmir Asia Japan Alpine flora of Hokkaido Flora of Hokkaido Ethiopia. Webbia, 26, 101-128. Asia Nepal Alpine flora of Nepal Flora of Nepal 2. Rehder, H., Beck, E. & Kokwaro, J.O. 1988. The Afroalpine plant communities of Mt. Kenya 12, 67 46, 13, 66 46, 52, 14, 55, 61 15, 68 16, 69 17 Asia [New Guinea] (Kenya). Phytocoenologia 16: 433-463. Alipine flora of New Guinea Flora of New Guinea 18, 56, 70, 96 3.
		Australia	Australia	Alpine flora of Tasmania	Flora of Tasmania	19, 71
		Australia	Australia	Alpine flora of Victoria	Flora of Victoria	20, 71
		Australia Europe Europe Europe South America Europe South America Europe South America South America	New Zealand France France Germany Argentina Spain Bolivia Spain Bolivia Bolivia	Alpine flora of New Zealand Alpine flora of Monumen Alpine flora of Corsica to Natural Abra del Acay Alpine flora of Écrins National Park Alpine flora of Parque Provincial Cumbres Alpine flora of Germany Calchaquíes Alpine flora of Área Natural de Manejo Integrado Apolobamba Alpine flora of Rasón and San Isidro Alpine flora of Parque Nacional Sajama Alpine flora of Sierra Nevada Alpine flora of Parque Alpine flora of Nacional Tuni Condoriri	Flora of New Zealand Flora of Corsica Flora of Salta Province Flora of Écrins National Park Flora of Tucumán Province 46, 91 21, 72 46, 91 22 23 Flora of Baden-Württemberg and Bavaria States 24, 57, 73 Flora of Bolivia 46, 92 Flora of Asturias 25, 74 Flora of Bolivia 46, 92 Flora of Andalusia 26, 74 Flora of Bolivia 46, 92
		Europe	Switzerland	Switzerland	Flora of Switzerland	27, 75

Supplementary Information

Supplementary Table 1. Alpine floras and their regional species pools used in this study. Supplementary Table 2. Alpine floras and their species pools in broad geographical regions.

Supplementary Figure 1. Standardized effect size of mean pairwise distance (MPD ses , red triangles) and standardized effect size of phylogenetic diversity (PD ses , blue triangles) in the 63 alpine floras examined in this study. Supplementary Figure 2. Standardized effect size of mean pairwise distance (MPD ses ) and the standardized effect size of phylogenetic diversity (PD ses ) for the 63 alpine floras examined in this study. Supplementary Figure 3. Relationships between growing degree days and standardized effect size of mean pairwise distance (MPD ses ). Supplementary Table 2 Supplementary Figure 1 (continued,2).

15

N America, site 33 Supplementary Figure 1 (continued,3).

16

S America, site 47 Supplementary Figure 1 (continued,4).

S America, site 60