Current patterns of plant diversity and phylogenetic structure on the Kunlun Mountains

Large-scale patterns of biodiversity and the underlying mechanisms that regulate these patterns are central topics in biogeography and macroecology.The Qinghai-Tibet Plateau serves as a natural laboratory for studying these issues.However,most previous studies have focused on the entire Qinghai-Tibet Plateau,leaving independent physical geographic subunits in the region less well understood.We studied the current plant diversity of the Kunlun Mountains,an independent physical geographic subunit located in northwestern China on the northern edge of the Qinghai-Tibet Plateau.We integrated measures of species distribution,geological history,and phylogeography,and analyzed the taxonomic richness,phylogenetic diversity,and community phylogenetic structure of the current plant diversity in the area.The distribution patterns of 1911 seed plants showed that species were distributed mainly in the eastern regions of the Kunlun Mountains.The taxonomic richness,phylogenetic diversity,and genera richness showed that the eastern regions of the Kunlun Mountains should be the priority area of biodiversity conservation,particularly the southeastern regions.The proportion of Chinese endemic species inhabiting the Kunlun Mountains and their floristic similarity may indicate that the current patterns of species diversity were favored via species colonization.The Hengduan Mountains,a biodiversity hotspot,is likely the largest source of species colonization of the Kunlun Mountains after the Quaternary.The net relatedness index indicated that 20 of the 28 communities examined were phylo-genetically dispersed,while the remaining communities were phylogenetically clustered.The nearest taxon index indicated that 27 of the 28 communities were phylogenetically clustered.These results suggest that species colonization and habitat filtering may have contributed to the current plant diversity of the Kunlun Mountains via ecological and evolutionary processes,and habitat filtering may play an important role in this ecological process.

Latitudinal and elevational patterns of phylogenetic structure in forest communities in China’s mountains

The phylogenetic structure incorporates both ecological and evolutionary processes to explain assembly of a local community.The "phylogenetic niche conservatism"(PNC) hypothesis suggests that distributions of species along environmental gradients reflect both ancestral traits and ecological fitness of individual species. The temperature is generally regarded to change in similar ways along both latitudinal and elevational gradients but with different historical contingence. Therefore, comparing the latitudinal and elevational patterns of phylogenetic structure of communities is of help to depict the effects of ecological and evolutionary processes in shaping the community assembly. In this study, we explored the latitudinal, elevational and climatic patterns of phylogenetic structure of 569 angiosperm tree communities from 38 mountains across China. We found a larger mean abundance-weighted net relatedness index(NRI) than the presence/absence-based NRI;and the NRI decreased when the species pool downscaled from the full pool to county-level pool. The mean family age and phylogenetic species evenness decreased with latitude, and increased with temperature of the coldest month and precipitation;whilst NRI increased with latitude, and decreased with mean temperature of the coldest month. In most mountains, NRI, mean family age and phylogenetic species evenness showed non-significant trends along the elevational gradient. Our results support the main predictions of PNC for the latitudinal gradient, i.e., species tend to be more phylogenetically related to each other and clades are younger in temperate environments,compared to those in tropical environments. We suggested that independent species pools and abundance should be incorporated in analysis to fully represent the phylogenetic structure of communities.

Precipitation is the dominant driver for bird species richness,phylogenetic and functional structure in university campuses in northern China

Background:Although urbanization is threatening biodiversity worldwide,the increasing green urban spaces could harbor relatively high biodiversity.Therefore,how to maintain the biodiversity in urban ecosystem is crucial for sustainable urban planning and management,especially in arid and semiarid regions with relatively fragile environment and low biodiversity.Here,for the first time we linked species richness,phylogenetic and functional structure of bird assemblages in university campuses in northern China with plant species richness,glacial-interglacial climate change,contemporary climate,and anthropogenic factors to compare their relative roles in shaping urban bird diversity.Methods:Bird surveys were conducted in 20 university campuses across Inner Mongolia,China.Ordinary least squares models and simultaneous autoregressive models were used to assess the relationships between bird species richness,phylogenetic and functional structure with environmental factors.Structural equation models were used to capture the direct and indirect effects of these factors on the three components of bird diversity.Results:Single-variable simultaneous autoregressive models showed that mean annual precipitation was consistently a significant driver for bird species richness,phylogenetic and functional structure.Meanwhile,mean annual temperature and plant species richness were also significant predictors for bird species richness.Conclusions:This study suggests that campuses with warmer and wetter climate as well as more woody plant species could harbor more bird species.In addition,wetter campuses tended to sustain over-dispersed phylogenetic and functional structure.Our findings emphasize the dominant effect of precipitation on bird diversity distribution in this arid and semiarid region,even in the urban ecosystem.

Global patterns of taxonomic and phylogenetic diversity of flowering plants: Biodiversity hotspots and coldspots

Species diversity of angiosperms(flowering plants) varies greatly among regions.Geographic patterns of variation in species diversity are shaped by the interplay of ecological and evolutionary processes.Here,using a comprehensive data set for regional angiosperm floras across the world,we show geographic patterns of taxonomic(species) diversity,phylogenetic diversity,phylogenetic dispersion,and phylogenetic deviation(i.e.,phylogenetic diversity after accounting for taxonomic diversity) across the world.Phylogenetic diversity is strongly and positively correlated with taxonomic diversity;as a result,geographic patterns of taxonomic and phylogenetic diversity across the world are highly similar.Areas with high taxonomic and phylogenetic diversity are located in tropical regions whereas areas with low taxonomic and phylogenetic diversity are located in temperate regions,particularly in Eurasia and North America,and in northern Africa.Similarly,phylogenetic dispersion is,in general,higher in tropical regions and lower in temperate regions.However,the geographic pattern of phylogenetic deviation differs substantially from those of taxonomic and phylogenetic diversity and phylogenetic dispersion.As a result,hotspots and coldspots of angiosperm diversity identified based on taxonomic and phylogenetic diversity and phylogenetic dispersion are incongruent with those identified based on phylogenetic deviations.Each of these metrics may be considered when selecting areas to be protected for their biodiversity.

Phylogenetic and functional structures of succession in plant communities on mounds of Marmota himalayana in alpine regions on the northeast edge of the QinghaieTibet Plateau

Few studies have examined the succession of plant communities in the alpine zone.Studying the succession of plant communities is helpful to understand how species diversity is formed and maintained.In this study,we used species inventories,a molecular phylogeny,and trait data to detect patterns of phylogenetic and functional community structure in successional plant communities growing on the mounds of Himalayan marmots(Marmota himalayana)on the southeast edge of the Qinghai-Tibet Plateau.We found that phylogenetic and functional diversities of plant communities on marmot mounds tended to cluster during the early to medium stages of succession,then trended toward overdispersion from medium to late stages.Alpine species in early and late stages of succession were phylogenetically and functionally overdispersed,suggesting that such communities were assembled mainly through species interactions,especially competition.At the medium and late stages of succession,alpine communities growing on marmot mounds were phylogenetically and functionally clustered,implying that the communities were primarily structured by environmental filtering.During the medium and late stages of succession the phylogenetic and functional structures of plant communities on marmot mounds differed significantly from those on neighboring sites.Our results indicate that environmental filtering and species interactions can change plant community composition at different successional stages.Assembly of plant communities on marmot mounds was promoted by a combination of traits that may provide advantages for survival and adaptation during periods of environmental change.

Multi-scale phylogenetic structure in coastal dune plant communities across the globe

Aims Studies integrating phylogenetic history and large-scale community assembly are few,and many questions remain unanswered.Here,we use a global coastal dune plant data set to uncover the important factors in community assembly across scales from the local filtering processes to the global long-term diversification and dispersal dynamics.Coastal dune plant communities occur worldwide under a wide range of climatic and geologic conditions as well as in all biogeographic regions.However,global patterns in the phylogenetic composition of coastal dune plant communities have not previously been studied.Methods The data set comprised vegetation data from 18463 plots in New Zealand,South Africa,South America,North America and Europe.The phylogenetic tree comprised 2241 plant species from 149 families.We calculated phylogenetic clustering(Net Relatedness Index,NRI,and Nearest Taxon Index,NTI)of regional dune floras to estimate the amount of in situ diversification relative to the global dune species pool and evaluated the relative importance of land and climate barriers for these diversification patterns by geographic analyses of phylogenetic similarity.We then tested whether dune plant communities exhibit similar patterns of phylogenetic structure within regions.Finally,we calculated NRI for local communities relative to the regional species pool and tested for an association with functional traits(plant height and seed mass)thought to vary along sea–inland gradients.Important Findings Regional species pools were phylogenetically clustered relative to the global pool,indicating regional diversification.NTI showed stronger clustering than NRI pointing to the importance of especially recent diversifications within regions.The species pools grouped phylogenetically into two clusters on either side of the tropics suggesting greater dispersal rates within hemispheres than between hemispheres.Local NRI plot values confirmed that most communities were also phylogenetically clustered within regions.NRI values decreased with increasing plant height and seed mass,indicating greater phylogenetic clustering in communities with short maximum height and good dispersers prone to wind and tidal disturbance as well as salt spray,consistent with environmental filtering along sea–inland gradients.Height and seed mass both showed significant phylogenetic signal,and NRI tended to correlate negatively with both at the plot level.Low NRI plots tended to represent coastal scrub and forest,whereas high NRI plots tended to represent herb-dominated vegetation.We conclude that regional diversification processes play a role in dune plant community assembly,with convergence in local phylogenetic community structure and local variation in community structure probably reflecting consistent coastal-inland gradients.Our study contributes to a better understanding of the globally distributed dynamic coastal ecosystems and the structuring factors working on dune plant communities across spatial scales and regions.

Habitat specialization and phylogenetic structure of tree species in a coastal Brazilian white-sand forest

Aims The coastal Brazilian rainforest on white-sand(restinga)ranks among the most fragmented forest types in the tropics,owing to both the patchy distribution of sandy soils and widespread coastal development activities.Here we study the environmental and evolutionary determinants of a forest tree assemblage at a single restinga forest in Southeastern Brazil.We also explore the ability of competing hypotheses to explain the maintenance of species diversity in this forest type,which includes contrasting extremes of edaphic conditions associated with flooding stress.Methods The study was conducted in a white-sand forest permanent plot of 10.24 ha on the coastal plain of Southeastern Brazil.This plot was divided into 256 quadrats of 20×20 m,which were classified into two main edaphic habitats(flooded and drained).Trees with a diameter≥1 cm at breast height were identified.We assembled DNA sequence data for each of the 116 morphospecies recognized using two chloroplast markers(rbcL and matK).A phylogenetic tree was obtained using the maximum likelihood method,and a phylogenetic distance matrix was produced from an ultrametric tree.We analyzed similarity in floristic composition and structure between habitats and related them to cross-plot distances using permutation procedures.Null model torus shift simulations were performed to obtain a statistical significance level for habitat association for each species.The phylogenetic structure for the two habitats and for each 20×20 m quadrat was calculated using the mean phylogenetic distance weighted by species abundance and checked for significance using the standardized effect size generated by 5000 randomizations of phylogenetic tip labels.Important Findings Our results indicate that partitioning among edaphic habitats is important for explaining species distributions and coexistence in restinga forests.Species distributions within the plot were found to be non-random:there was greater floristic similarity within than between habitats,and>40%of the more abundant species were positively or negatively associated with at least one habitat.Patterns of habitat association were not independent of phylogenetic relatedness:the community was overdispersed with respect to space and habitat type.Closely related species tended to occur in different habitats,while neighboring trees tended to belong to more distantly related species.We conclude that habitat specialization is important for the coexistence of species in restinga forests and that habitat heterogeneity is therefore an essential factor in explaining the maintenance of diversity of this unique but fragile and threatened type of forest.

Phylogenetic Analysis of Chirality of Twining Plants

Phylogenetic relations of twining chirality of Dioscorea sp.in China were analyzed based on the genes matK,rbcL and trnL;phylogenetic character of higher-level phylogeny of twining plants was analyzed at a high taxon level based on matK gene.A significant phylogenetic framework of chirality was found:(i)based on matK analysis,right-handed Dioscorea species in China congregate completely to form a monophyly;(ii)rbcL and trnL data sets also supported Chinese right-handed Dioscorea a monophyly,although with ex...

Phylogenetic patterns of shrub communities along the longitudinal and latitudinal gradients on the northeastern Qinghai–Tibetan Plateau

Biodiversity distribution patterns are a basic and long-standing but crucial aspect of ecology research.These patterns form the primary source of data used to develop biodiversity protection practices,especially in mountain ecosystems.Shrubs comprise one of the main types of vegetation on the Qinghai–Tibetan Plateau,where they serve vital ecological functions.In this study,we used a community phylogenetic approach to examine the distribution patterns of shrub communities along the longitudinal and latitudinal gradients on the northeastern Qinghai–Tibetan Plateau.We observed significant latitudinal trends in both the phylogenetic diversity(PD)and net relatedness index(NRI)values of shrub communities,such that the former decreased and the latter increased with increasing latitude.However,no significant PD,NRI and nearest taxon index(NTI)distribution patterns were observed along a longitudinal gradient.A further analysis revealed that the combination of temperature-related and precipitation-related climate variables most strongly affected the PD,NRI and NTI values of shrub communities,indicating that the latitudinal patterns in the PD,NRI and NTI of a shrub community may be determined mainly by interactions with these climate factors.

Novel evidence from Taxus fuana forests for niche-neutral process assembling community

Background:Understanding the mechanisms underlying community assembly is helpful for conservation and restoration of communities, particularly those that contain rare and endangered species like Taxus fuana, which are endemic to the Western Himalayas. The niche (limiting similarity) vs. neutral (randomness) assembly of the T.fuana forest community in Gyirong County, Tibet, China, was investigated. The net relatedness index (NRI) was calculated using a phylogenetic tree. The phylogenetic characteristics of the community and its relationships with environment were analyzed.Results:The value of the mean NRI at the community level was less than-1.96, indicating that the phylogenetic structure was overdispersed;whereas majority of the NRIs at the tree, shrub, and herb layers were within-1.96 to1.96, indicating random dispersion. Environmental factors accounted for 44.38%, 46.52%, 24.04%, and 14.07%of the variation at the community level, tree, shrub, and herb layer, respectively. The phylogenetic structure at the community level and tree layer were significantly influenced by both topographic and soil factors, while shrub and herb layers tended to be affected by a single environmental factor.Conclusions:Community assembly of the T. fuana forest was simultaneously affected by niche and neutral processes, and their variations were closely related to the environment. Neutral process dominated community assembly in the shrub and herb layers. However, the interaction of limiting similarity and randomness played a dominant role at the community level and tree layer;and contributed to maintenance of biodiversity stability. The synergy of multiple environmental factors had a more obvious influence on community assembly than individual environmental factors, especially at the community level. These findings would help to understand the conservation of rare and endangered tree species, such as T. fuana, in the native community;and highlight the importance of random and non-random processes in assembly and biodiversity maintenance of alpine plant communities.

Diversity patterns of cushion plants on the Qinghai-Tibet Plateau:A basic study for future conservation efforts on alpine ecosystems

The Qinghai-Tibet Plateau(QTP)is an important cushion plant hotspot.However,the distribution of cushion plants on the QTP is unknown,as are the factors that drive cushion plant distribution,limiting our understanding of the evolution of cushion species in the region.In this study,we assessed spatial patterns of total cushion plant diversity(including taxonomic and phylogenetic)over the entire QTP and compared patterns of diversity of cushion plants with different typologies(i.e.,compact vs.loose).We also examined how these patterns were related to climatic features.Our results indicate that the southern QTP hosts the highest total cushion plant richness,especially in the south-central Hengduan Mountains subregion.The total number of cushion species declines from south to north and from southeast to northwest.Compact cushion plants exhibit similar patterns as the total cushion plant richness,whereas loose cushion plants show random distribution.Cushion plant phylogenetic diversity showed a similar pattern as that of the total cushion plant richness.In addition,cushion plant phylogenetic community structure was clustered in the eastern and southwestern QTP,whereas random or overdispersed in other areas.Climatic features represented by annual energy and water trends,seasonality and extreme environmental factors,had significant effects on cushion plant diversity patterns but limited effects on the phylogenetic community structure,suggesting that climatic features indeed promote the formation of cushion plants.Because cushion plants play vital roles in alpine ecosystems,our findings not only promote our understanding of the evolution and formation of alpine cushion plant diversity but also provide an indispensable foundation for future studies on cushion plant functions and thus alpine ecosystem sustainability in the entire QTP region.

Climatic correlates of phylogenetic relatedness of woody angiosperms in forest communities along a tropical elevational gradient in South America

Aims This study assesses the relationship between phylogenetic relat-edness of angiosperm tree species and climatic variables in local forests distributed along a tropical elevational gradient in South America.In particular,this paper addresses two questions:Is phylo-genetic relatedness of plant species in communities related to tem-perature variables more strongly than to water variables for tropical elevational gradients?Is phylogenetic relatedness of plant species in communities driven by extreme climatic conditions(e.g.minimum temperature(MT)and water deficit)more strongly than by climatic seasonal variability(e.g.temperature seasonality and precipitation seasonality)?Methods I used a set of 34 angiosperm woody plant assemblages along an elevational gradient in the Andes within less than 5 degrees of the equator.Phylogenetic relatedness was quantified as net relatedness index(NRI)and nearest taxon index(NTI)and was related to major climatic variables.Correlation analysis and structure equation modeling approach were used to assess the relationships between phylogenetic relatedness and climatic variables.Important Findings Phylogenetic relatedness of angiosperm woody species in the local forest communities is more strongly associated with temperature-related variables than with water-related variables,is positively cor-related with mean annual temperature(MAT)and MT,and is related with extreme cold temperature more strongly than with seasonal temperature variability.NTI was related with elevation,MAT and MT more strongly than was NRI.Niche convergence,rather than niche conservatism,has played a primary role in driving community assem-bly in local forests along the tropical elevational gradient examined.Negative correlations of phylogenetic relatedness with elevation and higher correlations of phylogenetic relatedness with elevation and temperature for NTI than for NRI indicate that evolution of cold toler-ance at high elevations in tropical regions primarily occurred at recent(terminal)phylogenetic nodes widely distributed among major clades.

A taxonomic and phylogenetic perspective on plant community assembly along an elevational gradient in subtropical forests

Aims Biodiversity patterns along elevational gradients have been well documented.Yet,the variations of biodiversity patterns along elevations and their underlying mechanisms are still unclear.Integrating multiple facets of biodiversity provides novel insights into the mechanisms for driving community assembly.In this study,species abundance information was incorporated into taxonomic and phylogenetic diversity to reveal the ecological and evolutionary forces of plant community assembly along an elevational gradient in subtropical forests.Methods We selected 17 woody plant plots along an elevational gradient from 270 to 1470 m in eastern China’s subtropical forests.Both presence-based and abundance-based measures of angiosperm species were used to quantify taxonomic alpha diversity,phylogenetic alpha diversity,phylogenetic relatedness,as well as taxonomic and phylogenetic dissimilarity among these plots.And the relations between these measures and climatic and topographic variables were analyzed.Important Findings For both abundance-weighted and unweighted measures,we observed an overall increasing pattern for taxonomic alpha diversity along elevation,and distance-decay trends of taxonomic and phylogenetic similarity with increased elevational distances.However,there were disparity patterns of phylogenetic alpha diversity between abundance-weighted and unweighted measures.For phylogenetic structure,there was no significant trend along elevation.Both topographical and microclimatic variables were main drivers of diversity patterns and phylogenetic structure.Compared with unweighted measures,abundance-weighted measures were strongly related with the slope and stand basal area.Overall,our results prove that deterministic processes mediated by local species abundance imprint on plant community composition along the elevational gradient.

Species turnover drives grassland community to phylogenetic clustering over long-term grazing disturbance

Aims Grazing exerts profound effects on grassland ecosystem service and functions by regulating species composition and diversity,and structuring community assembly worldwide.However,adaptions of phylogenetic diversity and phylogenetic community structure to long-term grazing disturbance remain poorly studied,especially for ecosystems distributed in extreme environments.Methods Here,we conducted an experiment with multigrazing intensities to explore the impacts of grazing disturbance on plant phylogenetic diversity and community structure in an alpine grassland of the Tibetan Plateau.Important Findings Grazing disturbance enriched plant species richness(SR),and stimulated species turnover from regional species pool,consequently changing community species composition.Under low intensities,grazing exerted no obvious effects on phylogenetic diversity and community structure,whereas communities changed from overdispersion to clustering under high grazing intensity.High grazing intensity resulted in stronger environmental filtering,which consequently selected those species with high resilience to grazing disturbance.The observed clustering structure was associated with the colonizing species which were closely related to resident species,and locally extinct species,and distantly related to residents.At the plant functional trait level,high grazing intensity increased species colonization largely by altering the effect of root depth on species colonization compared to light grazing.Our results highlight that solely utilization of SR and diversity cannot fully represent grassland communities responses to grazing.The effects of species turnover on community phylogenetic diversity and structure are entailed to be explored in the future grazing studies.

Point process models, the dimensions of biodiversity and the importance of small-scale biotic interactions

Aims Recent mechanistic explanations for community assembly focus on the debates surrounding niche-based deterministic and dispersalbased stochastic models.This body of work has emphasized the importance of both habitat filtering and dispersal limitation,and many of these works have utilized the assumption of species spatial independence to simplify the complexity of the spatial modeling in natural communities when given dispersal limitation and/or habitat filtering.One potential drawback of this simplification is that it does not consider species interactions and how they may influence the spatial distribution of species,phylogenetic and functional diversity.Here,we assess the validity of the assumption of species spatial independence using data from a subtropical forest plot in southeastern China.Methods We use the four most commonly employed spatial statistical models—the homogeneous Poisson process representing pure random effect,the heterogeneous Poisson process for the effect of habitat heterogeneity,the homogenous Thomas process for sole dispersal limitation and the heterogeneous Thomas process for joint effect of habitat heterogeneity and dispersal limitation—to investigate the contribution of different mechanisms in shaping the species,phylogenetic and functional structures of communities.Important Findings Our evidence from species,phylogenetic and functional diversity demonstrates that the habitat filtering and/or dispersal-based models perform well and the assumption of species spatial independence is relatively valid at larger scales(50×50 m).Conversely,at local scales(10×10 and 20×20 m),the models often fail to predict the species,phylogenetic and functional diversity,suggesting that the assumption of species spatial independence is invalid and that biotic interactions are increasingly important at these spatial scales.