Using phylogeny and functional traits for assessing community assembly along environmental gradients: A deterministic process driven by elevation

Tibetan terrestrial and aquatic ecosystems collapsed with cryosphere loss inferred from sedimentary ancient metagenomics

Glacier and permafrost shrinkage and land-use intensification threaten mountain wildlife and affect nature conservation strategies. Here, we present paleometagenomic records of terrestrial and aquatic taxa from the southeastern Tibetan Plateau covering the last 18,000 years to help understand the complex alpine ecosystem dynamics. We infer that steppe-meadow became woodland at 14 ka (cal BP) controlled by cryosphere loss, further driving a herbivore change from wild yak to deer. These findings weaken the hypothesis of top-down control by large herbivores in the terrestrial ecosystem. We find a turnover in the aquatic communities at 14 ka, transitioning from glacier-related (blue-green) algae to abundant nonglacier-preferring picocyanobacteria, macrophytes, fish, and otters. There is no evidence for substantial effects of livestock herding in either ecosystem. Using network analysis, we assess the stress-gradient hypothesis and reveal that root hemiparasitic and cushion plants are keystone taxa. With ongoing cryosphere loss, the protection of their habitats is likely to be of conservation benefit on the Tibetan Plateau.

Variations and driving factors of leaf functional traits in the dominant desert plant species along an environmental gradient in the drylands of China

Leaf functional traits (LFTs) of desert plants are responsive, adaptable and highly plastic to their environment. However, the macroscale variation in LFTs and driving factors underlying this variation remain unclear, especially for desert plants. Here, we measured eight LFTs, including leaf carbon concentration (LCC), leaf nitrogen concentration (LNC), leaf phosphorus concentration (LPC), specific leaf area (SLA), leaf dry matter content (LDMC), leaf mass per area (LMA), leaf thickness (LTH) and leaf tissue density (LTD) across 114 sites along environmental gradient in the drylands of China and in Guazhou Common Garden and evaluated the effect of environment and phylogeny on the LFTs. We noted that for all species, the mean values of LCC, LNC, LPC, SLA, LDMC, LMA, LTH and LTD were 384.62 mg g-1, 19.91 mg g-1, 1.12 mg g-1, 79.62 cm2 g-1, 0.74 g g-1, 237.39 g m-2, 0.38 mm and 0.91 g cm-3, respectively. LFTs exhibited significant geographical variations and the LNC, LMA and LTH in the plants of Guazhou Common Garden were significantly higher than the field sites in the drylands of China. LDMC and LTD of plants in Guazhou Common Garden were, however, considerably lower than those in the drylands of China. LCC, LPC, LTH and LTD differed significantly among different plant lifeforms, while LNC, SLA, LDMC and LMA didn't show significant variations. We found that the environmental variables explained higher spatial variations (3.6-66.3 %) in LFTs than the phylogeny (1.8-54.2 %). The LCC significantly increased, while LDMC and LTD decreased with increased temperature and reduced precipitation. LPC, LDMC, LMA, and LTD significantly increased, while SLA and LTH decreased with increased aridity. However, leaf elements were not significantly correlated with soil nutrients. The mean annual precipitation was a key factor controlling variations in LFTs at the macroscale in the drylands of China. These findings will provide new insights to better understand the response of LFTs and plants adaptation along environmental gradient in drylands, and will serve as a reference for studying biogeographic patterns of leaf traits.

A network-based approach to identifying correlations between phylogeny, morphological traits and occurrence of fish species in US river basins

The complex network framework has been successfully used to model interactions between entities in Complex Systems in the Biological Sciences such as Proteomics, Genomics, Neuroscience, and Ecology. Networks of organisms at different spatial scales and in different ecosystems have provided insights into community assembly patterns and emergent properties of ecological systems. In the present work, we investigate two questions pertaining to fish species assembly rules in US river basins, a) if morphologically similar fish species also tend to be phylogenetically closer, and b) to what extent are co-occurring species that are phylogenetically close also morphologically similar? For the first question, we construct a network of Hydrologic Unit Code 8 (HUC8) regions as nodes with interaction strengths (edges) governed by the number of common species. For each of the modules of this network, which are found to be geographically separated, there is differential yet significant evidence that phylogenetic distance predicts morphological distance. For the second question, we construct and analyze nearest neighbor directed networks of species based on their morphological distances and phylogenetic distances. Through module detection on these networks and comparing the module-level mean phylogenetic distance and mean morphological distance with the number of basins of common occurrence of species in modules, we find that both phylogeny and morphology of species have significant roles in governing species co-occurrence, i.e. phylogenetically and morphologically distant species tend to co-exist more. In addition, between the two quantities (morphological distance and phylogentic distance), we find that morphological distance is a stronger determinant of species co-occurrences.

Spatial Patterns of Species Diversity of Amphibians in a Nature Reserve in Eastern China

Elevational gradients provide an excellent opportunity to assess biodiversity patterns and community structure. Previous studies mainly focus on higher elevations or are limited to small areas in mountainous regions. Little information can be found on amphibian biodiversity in middle- and low-elevational areas, hence our study was devoted to filling up the current gaps in these research areas. To understand the variability of biodiversity of amphibian species in the Fujian Junzifeng National Nature Reserve in eastern China, our study included taxonomic and phylogenetic components to describe the various patterns of regional and elevational distribution. The results showed that (1) most of the taxonomic and phylogenetic diversity metrics were correlated; with regard to the surveyed area, Faith’s phylogenetic diversity index (PD) and net relatedness index (NRI) were positively correlated with the Shannon–Wiener index (H’), Margalef index (DMG), and species richness (S), while negatively with the Pielou index; whereas for elevation, only the Pielou index was positively correlated with the nearest taxon index (NTI), but negatively with other indices; (2) taxonomic and phylogenetic diversities did not differ among the three survey locations but differed significantly along the elevational gradient; Simpson index, H’, S, and DMG had a hump-shaped relationship with elevations, and PD decreased gradually with the increase in elevation, whereas NRI and NTI sharply increased at the elevation above 900 m; (3) the species range size and the corresponding midpoint of amphibians were affected by a strong phylogenetic signal, which supports the elevational Rapoport’s rule upon removal of Pachytriton brevipes and Boulenophrys sanmingensis from the study.

Spatial and phylogenetic structure of Alpine stonefly assemblages across seven habitats using DNA-species

Stream ecosystems are spatially heterogeneous, with many different habitat patches distributed within a small area. The influence of this heterogeneity on the biodiversity of benthic insect communities is well documented; however, studies of the role of habitat heterogeneity in species coexistence and assembly remain limited. Here, we investigated how habitat heterogeneity influences spatial structure (beta biodiversity) and phylogenetic structure (evolutionary processes) of benthic stonefly (Plecoptera, Insecta) communities. We sampled 20 sites along two Alpine rivers, including seven habitats in four different reaches (headwaters, meandering, bar-braided floodplain, and lowland spring-fed). We identified 21 morphological species and delineated 52 DNA-species based on sequences from mitochondrial cox1 and nuclear ITS markers. Using DNA-species, we first analysed the patterns of variation in richness, diversity, and assemblage composition by quantifing the contribution of each reach and habitat to the overall DNA-species diversity using an additive partition analysis and distance-based redundancy analysis. Using gene-tree phylogenies, we assessed whether environmental filtering could lead to the co-occurrence of DNA-species using a two-step analysis to detect a phylogenetic signal. All four reaches significantly contributed to DNA-species richness, with the meandering reach having the highest contribution. Habitats had an effect on DNA-species diversity, where glide, riffle and, pool influenced the spatial structure of stonefly assemblage possibly due to the high habitat heterogeneity. Among the habitats, the pool showed significant phylogenetic clustering, suggesting high levels of evolutionary adaptation and strong habitat filtering. This assemblage structure may be caused by long-term stability of the habitat and the similar requirements for co-occurring species. Our study shows the importance of different habitats for the spatial and phylogenetic structure of stonefly assemblage and sheds light on the habitat-specific diversity that may help improve conservation practices.

Human Disturbance and Geometric Constraints Drive Small Mammal Diversity and Community Structure along an Elevational Gradient in Eastern China

Simple Summary

Biodiversity patterns and mechanisms along elevational gradients have long been the focus of conservation research. However, few studies have been conducted in mountainous areas of eastern China, especially for small mammals. In this study, we used a standard sampling method to survey small mammals along the gradient of Qingliang Mountain in eastern China and analyzed the patterns and mechanisms of diversity and community structure. We found inconsistencies between different diversity dimensions. Functional and phylogenetic structures were mainly clustered but showed opposite elevation patterns. Human disturbance and MDE were the main drivers of the diversity patterns, but with contrasting effects on different dimensions. These findings emphasize the importance of a multiple dimensions approach to biodiversity conservation and call for increased conservation efforts in the low and middle elevation regions.

Abstract

Understanding the mechanisms influencing patterns and processes of biological diversity is critical to protecting biodiversity, particularly in species-rich ecosystems such as mountains. Even so, there is limited knowledge of biodiversity patterns and processes in the mountains of eastern China, especially about small mammals. In this study, we examined the taxonomic, functional, and phylogenetic diversity of small mammal distribution and community structure along the elevational gradient of Qingliang Mountain, eastern China. We then evaluated how they are influenced by space (area and mid-domain effect (MDE)), environment (temperature, precipitation, and normalized difference vegetation index (NDVI)), and human disturbance. The results showed hump-shaped patterns of taxonomic and phylogenetic diversity along elevation gradients, peaking at 1000 m, unlike functional diversity, which peaked at lower elevations (600 m). The mean pairwise distance and mean nearest taxon distance of functional and phylogenetic variance (MFD and MPD, respectively) were also incongruent. The MFD and MPD showed hump-shaped patterns along elevations; however, unlike MFD, which peaked at lower elevations (600 m), MPD peaked at higher elevations (1200 m). The mean nearest functional taxon distance (MNFD) decreased, while the mean nearest phylogenetic taxon distance (MNTD) increased along the elevation gradient. The higher elevations were functionally more clustered, while the lower elevations were phylogenetically more clustered, suggesting that environmental filtering for traits was stronger at higher elevations. In comparison, phylogenetic conservatism of ecological niches had a stronger influence at lower elevations. The diversity and community structure indices were inconsistently explained, with human disturbance and MDE accounting for the biggest proportions of the model-explained variances. Overall, the results confirm that environmental filtering and human disturbance significantly influence small mammals’ diversity and community structure. These findings also emphasize the need for increased conservation efforts in the middle and lower elevation regions of Qingliang Mountain.

The thermal niche and phylogenetic assembly of evergreen tree metacommunities in a mid-to-upper tropical montane zone

Frost and freezing temperatures have posed an obstacle to tropical woody evergreen plants over evolutionary time scales. Thus, along tropical elevation gradients, frost may influence woody plant community structure by filtering out lowland tropical clades and allowing extra-tropical lineages to establish at higher elevations. Here we assess the extent to which frost and freezing temperatures influence the taxonomic and phylogenetic structure of naturally patchy evergreen forests (locally known as shola) along a mid-upper montane elevation gradient in the Western Ghats, India. Specifically, we examine the role of large-scale macroclimate and factors affecting local microclimates, including shola patch size and distance from shola edge, in driving shola metacommunity structure. We find that the shola metacommunity shows phylogenetic overdispersion with elevation, with greater representation of extra-tropical lineages above 2000 m, and marked turnover in taxonomic composition of shola woody communities near the frost-affected forest edge above 2000 m, from those below 2000 m. Both minimum winter temperature and patch size were equally important in determining metacommunity structure, with plots inside very large sholas dominated by older tropical lineages, with many endemics. Phylogenetic overdispersion in the upper montane shola metacommunity thus resulted from tropical lineages persisting in the interiors of large closed frost-free sholas, where their regeneration niche has been preserved over time.

Community assembly, functional traits, and phylogeny in Himalayan river birds

Heterogeneity in riverine habitats acts as a template for species evolution that influences river communities at different spatio‐temporal scales. Although birds are conspicuous elements of these communities, the roles of phylogeny, functional traits, and habitat character in their niche use or species' assembly have seldom been investigated. We explored these themes by surveying multiple headwaters over 3000 m of elevation in the Himalayan Mountains of India where the specialist birds of montane rivers reach their greatest diversity on Earth. After ordinating community composition, species traits, and habitat character, we investigated whether river bird traits varied with elevation in ways that were constrained or independent of phylogeny, hypothesizing that trait patterns reflect environmental filtering. Community composition and trait representation varied strongly with increasing elevation and river naturalness as species that foraged in the river/riparian ecotone gave way to small insectivores with direct trophic dependence on the river or its immediate channel. These trends were influenced strongly by phylogeny as communities became more clustered by functional traits at a higher elevation. Phylogenetic signals varied among traits, however, and were reflected in body mass, bill size, and tarsus length more than in body size, tail length, and breeding strategy. These variations imply that community assembly in high‐altitude river birds reflects a blend of phylogenetic constraint and habitat filtering coupled with some proximate niche‐based moulding of trait character. We suggest that the regional co‐existence of river birds in the Himalaya is facilitated by this same array of factors that together reflect the highly heterogeneous template of river habitats provided by these mountain headwaters.

Phylogenetic independence in the variations in leaf functional traits among different plant life forms in an arid environment

Leaf traits of global plants reveal the fundamental trade-offs in plant resource acquisition to conservation strategies. However, which leaf traits are consistent, converged, or diverged among herbs, shrubs, and subshrubs in an arid environment remains unclear. In the present study, we evaluated the trade-offs in six leaf functional traits (LFTs): leaf fresh mass (LFM), leaf dry mass (LDM), leaf dry matter content (LDMC), leaf area (LA), specific leaf area (SLA), and leaf thickness (LTh) of 37 desert plant species. LFTs differed between different plant life forms; LFM, LDM, and LA were slightly higher in herbs, LDMC and LTh in shrubs, and SLA in subshrubs. Conversely, the correlations among LFTs were inconsistent in different life forms, which may indicate their different adaptation strategies in an arid environment. Legumes and C₃ plants exhibited slightly higher LDMC, LA, and SLA than non-legumes and C₄ plants, whereas non-legumes and C₄ plants showed higher (nonsignificant) LFM, LDM, and LTh than legumes and C₃ plants. A significant phylogenetic signal (PS) and maximum K-value were found for SLA (K = 0.32). LFTs exhibited convergent and divergent variations among different life forms. However, these variations in LFTs were not influenced by phylogeny. Together, these findings increase our understanding of the variations in ecological adaptations of desert plants as well as adaption strategies of different life forms in an arid environment.

Community assembly during vegetation succession after metal mining is driven by multiple processes with temporal variation

The mechanisms governing community assembly is fundamental to ecological restoration and clarification of the assembly processes associated with severe disturbances (characterized by no biological legacy and serious environmental problems) is essential. However, a systematic understanding of community assembly in the context of severe anthropogenic disturbance remains lacking. Here, we explored community assembly processes after metal mining, which is considered to be a highly destructive activity to provide insight into the assembly rules associated with severe anthropogenic disturbance. Using a chronosequence approach, we selected vegetation patches representing different successional stages and collected data on eight plant functional traits from each stage. The traits were classified as establishment and regenerative traits. Based on these traits, null models were constructed to identify the processes driving assembly at various successional stages. Comparison of our observations with the null models indicated that establishment and regenerative traits converged in the primary stage of succession. As succession progressed, establishment traits shifted to neutral assembly, whereas regeneration traits alternately converged and diverged. The observed establishment traits were equal to expected values, whereas regenerative traits diverged significantly after more than 20 years of succession. Furthermore, the available Cr content was linked strongly to species' ecological strategies. In the initial stages of vegetation succession in an abandoned metal mine, the plant community was mainly affected by the available metal content and dispersal limitation. It was probably further affected by strong interspecific interaction after the environmental conditions had improved, and stochastic processes became dominant during the stage with a successional age of more than 20 years.

Comparing Elevational Patterns of Taxonomic, Phylogenetic, and Functional Diversity of Woody Plants Reveal the Asymmetry of Community Assembly Mechanisms on a Mountain in the Hengduan Mountains Region

The contributions and interaction of biotic and abiotic processes in community assembly are crucial for understanding the elevational patterns of biodiversity. The combined analyses of taxonomic, phylogenetic, and functional diversity are necessary to resolve this issue. By investigating vegetation in 24 transects sampled on Hongla Snow Mountain, in the central Hengduan Mountain Ranges in Southwest China, we delineated the elevational vegetation spectrum on the eastern and western slopes, analyzed the elevational variation in taxonomic, phylogenetic, and functional diversity of woody plant species, and compared the community structure of phylogeny and function in the low-elevational shrublands, mid-elevational forests, and alpine shrubs and meadows. The species richness, phylogenetic diversity, and functional diversity of woody plants showed nonstandard hump-shaped patterns with two peaks along the elevational gradient. The community structure of phylogeny and function (including tree height, leaf area, specific leaf area, leaf thickness, bark thickness, and wood density) clustered in the low-elevation shrub communities, being random and over-dispersed in mid-elevational forests. The phylogenic structure was over-dispersed in alpine communities, whereas the functional structure was clustered. Elevational patterns in taxonomic, phylogenetic, and functional diversity, together with the mean and variation in woody plant functional traits, suggested drought stress and freeze stress as environmental filters dominating the assembly of low and high elevation non-forest communities, and a conspicuous effect of biotic facilitation was also suggested for alpine habitats. By contrast, interspecific competition dominated the community assembly of forests at mid-elevations. The difference in biodiversity indices between the west and east slopes reflected the effects of the Indian Monsoon on the geomorphic patterns of ecosystem structure. These results increased our understanding of biodiversity patterns and underlying mechanisms in the Hengduan Mountains of Southwest China and highlighted the priorities for biodiversity conservation in this region.

Specific Rhizobacteria Responsible in the Rhizosheath System of Kengyilia hirsuta

The rhizosheath is a critical interface supporting the exchange of resources between plants and their associated environment of soil. Favorable microenvironment of rhizosphere soil provides the rhizosheath formed and then promotes desert plant survival. However, it remains unclear how rhizosheath benefits the colonization of pioneer plants in alpine desert under changing environment. In this study, we investigated the effect of different soil moisture and sterilization treatments (three moisture levels and unsterilized or sterilized soil) on rhizosheath forming process of Kengyilia hirsuta (K. hirsuta), a sand-inhabiting and drought-resistant pioneer plant of the Tibetan Plateau desert. The results showed that in both unsterilized and sterilized soil, increasing soil moisture first increased and then decreased rhizosheath weight, with the highest value is 25%. During rhizosheath formation, developing rhizosheaths were selectively enriched in the bacterial genera Massilia and Arthrobacter. These suggest the existence of a highly specialized signal recognition system during rhizosheath formation that involves the accumulation of bacteria. These bacterial species exhibited different roles in the process of rhizosheath formation and is an advantageous strategy for K. hirsuta.

Nutrient cycling drives plant community trait assembly and ecosystem functioning in a tropical mountain biodiversity hotspot

Community trait assembly in highly diverse tropical rainforests is still poorly understood. Based on more than a decade of field measurements in a biodiversity hotspot of southern Ecuador, we implemented plant trait variation and improved soil organic matter dynamics in a widely used dynamic vegetation model (the Lund-Potsdam-Jena General Ecosystem Simulator, LPJ-GUESS) to explore the main drivers of community assembly along an elevational gradient. In the model used here (LPJ-GUESS-NTD, where NTD stands for nutrient-trait dynamics), each plant individual can possess different trait combinations, and the community trait composition emerges via ecological sorting. Further model developments include plant growth limitation by phosphorous (P) and mycorrhizal nutrient uptake. The new model version reproduced the main observed community trait shift and related vegetation processes along the elevational gradient, but only if nutrient limitations to plant growth were activated. In turn, when traits were fixed, low productivity communities emerged due to reduced nutrient-use efficiency. Mycorrhizal nutrient uptake, when deactivated, reduced net primary production (NPP) by 61-72% along the gradient. Our results strongly suggest that the elevational temperature gradient drives community assembly and ecosystem functioning indirectly through its effect on soil nutrient dynamics and vegetation traits. This illustrates the importance of considering these processes to yield realistic model predictions.

Spatial Scale Dependence of Ecological Factors That Regulate Functional and Phylogenetic Assembly in a Mediterranean High Mountain Grassland

Understanding how functional and phylogenetic patterns vary among scales and along ecological gradients within a given species pool is critical for inferring community assembly processes. However, we lack a clear understanding of these patterns in stressful habitats such as Mediterranean high mountains where ongoing global warming is expected to affect species fitness and species interactions, and subsequently species turnover. In this study, we investigated 39 grasslands with the same type of plant community and very little species turnover across an elevation gradient above the treeline at Sierra de Guadarrama National Park in central Spain. In particular, we assessed functional and phylogenetic patterns, including functional heterogeneity, using a multi-scale approach (cells, subplots, and plots) and determined the relevance of key ecological factors (i.e., elevation, potential solar radiation, pH, soil organic carbon, species richness, and functional heterogeneity) that affect functional and phylogenetic patterns at each spatial scale. Overall, at the plot scale, coexisting species tended to be more functionally and phylogenetically similar. By contrast, at the subplot and cell scales, species tended to be more functionally different but phylogenetically similar. Functional heterogeneity at the cell scale was comparable to the variation across plots along the gradient. The relevance of ecological factors that regulate diversity patterns varied among spatial scales. An increase in elevation resulted in functional clustering at larger scales and phylogenetic overdispersion at a smaller scale. The soil pH and organic carbon levels exhibited complex functional patterns, especially at small spatial scales, where an increase in pH led to clustering patterns for the traits related to the leaf economic spectrum (i.e., foliar thickness, specific leaf area, and leaf dry matter content). Our findings confirm the presence of primary environmental filters (coldness and summer drought at our study sites) that constrain the regional species pool, suggesting the presence of additional assembly mechanisms that act at the smallest scale (e.g., micro-environmental gradients and/or species interactions). Functional and phylogenetic relatedness should be determined using a multi-scale approach to help interpret community assembly processes and understand the initial community responses to environmental changes, including ongoing global warming.

Functional leaf traits indicate phylogenetic signals in forests across an elevational gradient in the central Himalaya

Traits are the primary attributes that distinguish a species niche. Species and higher taxa are part of a structured phylogeny, and variation in plant traits depends on lineage as well as on environmental conditions. Therefore, it is crucial to investigate linkages between taxonomic identity, shared ancestry, and environment for understanding the variation in leaf traits. We investigated the evolutionary relationships, based on multiple gene sequences among 26 plant species sampled along an elevational gradient from 650 to 3600 m a.s.l. in the central Himalaya. We tested for the phylogenetic signal based on three different measures in 10 leaf traits having a significant association with the resource acquisition-conservation trade-offs axis and influencing plant growth, development, and ecological performance. We further assessed the role of elevation and growth forms as the potential drivers of leaf traits variation while controlling for phylogeny. 5 out of 10 leaf traits showed significant phylogenetic signal. Plant species clustered more often by growth forms at the tips of the phylogeny indicating multiple instances of independent evolution. Evergreen taxa showed niche separation with deciduous and incorporated larger trait variation. Trait variations were guided by both growth forms and elevation when accounted for phylogeny. Growth form has a higher contribution to trait variation compared to elevation. Trade-offs were detected between resource conservation and resource acquisition machinery traits (that would maximise carbon gain), differing between growth forms and along elevation.

Phylogenetic and Functional Traits Verify the Combined Effect of Deterministic and Stochastic Processes in the Community Assembly of Temperate Forests along an Elevational Gradient

Explaining community assembly mechanisms along elevational gradients dominated by deterministic processes or stochastic processes is a pressing challenge. Many studies suggest that phylogenetic and functional diversity are significant indicators of the process. In this study, we analyzed the structure and beta diversity of phylogenetic and functional traits along an elevational gradient and discussed the effects of environmental and spatial factors. We found that the phylogenetic and functional traits showed inconsistent changes, and their variations were closely related to the abiotic environment. The results suggested that the community assembly of woody plants was obviously affected by the combined effect of deterministic processes and the stochastic hypothesis (primarily by the latter). Phylogenetic and functional traits had a certain relationship but changed according to different rules. These results enhance our understanding of the assembly mechanism of forest communities by considering both phylogenetic and functional traits.

Identifying the patterns of changes in α- and β-diversity across Dacrydium pectinatum communities in Hainan Island, China

Exploring vegetation distribution spatial patterns facilitates understanding how biodiversity addresses the potential threat of future climate variability, especially for highly diverse and threatened tropical plant communities, but few empirical studies have been performed. Dacrydium pectinatum is a constructive and endangered species in the tropical mountain forests of Hainan Island, China. In this study, sixty-eight 30 m × 30 m permanent plots of D. pectinatum were investigated, and species-based and phylogenetic-based methods were used to analyze the α- and β-diversity pattern variation and its key drivers. Our study showed that species and phylogenetic α-diversity patterns are different on a local scale. However, on a regional scale, the variations in the two α-diversity patterns tend to converge, and they decrease with increasing elevation. The phylogenetic structure changes from overdispersion to convergence with increasing elevation. Soil (SOM, TP, AP), topography (EL, SL), and stand (CD) factors and α-diversity showed close correlations. Species and phylogenetic β-diversity have significant positive correlations with changing environmental distance and geographical distance; however, as a representative form of habitat heterogeneity, elevation distance has a greater impact on β-diversity changes than geographical distance. In conclusion, the α- and β-diversity patterns of the D. pectinatum community are mainly related to habitat filtering, especially in high-elevation areas, and the colonization history of various regions also affects the formation of diversity patterns. Species-based and phylogenetic-based methods robustly demonstrated the key role of the habitat filtering hypothesis in community assembly. We believe that more plant diversity patterns need to be explored to understand the biodiversity formation mechanisms in tropical forests. We also recommend strengthening the construction and management of nature reserves to help address the biodiversity loss crisis in endangered tropical plant communities.

Linkage between species traits and plant phenology in an alpine meadow

Plant phenology differs largely among coexisting species within communities that share similar habitat conditions. However, the factors explaining such phenological diversity of plants have not been fully investigated. We hypothesize that species traits, including leaf mass per area (LMA), seed mass, stem tissue mass density (STD), maximum plant height (H_max), and relative growth rate in height (RGR_H), explain variation in plant phenology, and tested this hypothesis in an alpine meadow. Results showed that both LMA and STD were positively correlated with the onset (i.e., beginning) and offset (i.e., ending) times of the four life history events including two reproductive events (flowering and fruiting) and two vegetative events (leafing and senescing). In contrast, RGR_H was negatively correlated with the four life phenological events. Moreover, H_max was positively correlated with reproductive events but not with vegetative events. However, none of the eight phenological events was associated with seed size. In addition, the combination of LMA and STD accounted for 50% of the variation in plant phenologies. Phylogenetic generalized least squares analysis showed plant phylogeny weakened the relationships between species traits vs. phenologies. Phylogeny significantly regulated the variation in the ending but not the beginning of phenologies. Our results indicate that species traits are robust indicators for plant phenologies and can be used to explain the diversity of plant phenologies among co-occurring herbaceous species in grasslands. The findings highlight the important role of the combination of and trade-offs between functional traits in determing plant phenology diversity in the alpine meadow.

Ciliates as bioindicators of water quality: A case study in the neotropical region and evidence of phylogenetic signals (18S-rDNA)

The aim of our study was to evaluate the water quality of an urban stream in southeastern Brazil by analyzing epibenthic ciliates, and to investigate the existence of phylogenetic signal for saprobity in ciliates. However, before conducting this type of phylogenetic study, it is necessary to evaluate if the saprobic classification used frequently in the northern Hemisphere is suitable for neotropical ecosystems. Sediment samples were collected from five sampling stations: two in rural areas and three in urban areas. During the one-year study, with monthly collections, 39 ciliates species were found, of which 32 are included in the saprobic system. Physical, chemical and biological parameters of water confirm the spatial heterogeneity of the sampling stations, with a clear influence of organic pollution on the composition and structure of ciliates taxocenosis. The saprobic index and the saprobic valence index were used to evaluate the water quality of the sampling stations and demonstrated clear heterogeneity between the stations and high degree of pollution of the urban area. These sampling stations were dominated by ciliates indicators of polysaprobric environments. Since we were able to successfully use the saprobic index in a limnic ecosystem in Brazil, we applied the phylogenetic signal validation as a tool for saprobity prediction of the limnic ciliate species not yet analyzed. A phylogenetic tree containing only 18S-rDNA nominal sequences of freshwater ciliates was estimated and used to explore the existence of the phylogenetic signal, which showed that the sensitivity/tolerance of ciliates to organic pollution reflected evolutionary divergence. The results confirm the existence of phylogenetic signal for the saprobrity in Ciliophora. Also, our results suggest that evolutionary analysis is a potential method to predict lineages of ciliates not yet classified for saprobity.

Global functional and phylogenetic structure of avian assemblages across elevation and latitude

Mountain systems are exceptionally species rich, yet the associated elevational gradients in functional and phylogenetic diversity and their consistency across latitude remain little understood. Here, we document how avian functional and phylogenetic diversity and structure vary along all major elevational gradients worldwide and uncover strong latitudinal differences. Assemblages in warm tropical lowlands and cold temperate highlands are marked by high functional overdispersion and distinctiveness, whereas tropical highlands and temperate lowlands appear strongly functionally clustered and redundant. We additionally find strong geographic variation in the interplay of phylogenetic and functional structure, with strongest deviations between the two in temperate highlands. This latitudinal and elevational variation in assemblage functional structure is underpinned by nuanced shifts in the position, shape and composition of multivariate trait space. We find that, independent of latitude, high-elevation assemblages emerge as exceptionally susceptible to functional change.

A phylogenetic and trait-based analysis of community assembly in a subtropical forest in central China

Despite several decades of study in community ecology, the relative importance of the ecological processes that determine species co-occurrence across spatial scales remains uncertain. Some of this uncertainty may be reduced by studying the scale dependency of community assembly in the light of environmental variation. Phylogenetic information and functional trait information are often used to provide potentially valuable insights into the drivers of community assembly. Here, we combined phylogenetic and trait-based tests to gain insights into community processes at four spatial scales in a large stem-mapped subtropical forest dynamics plot in central China. We found that all of the six leaf economic traits measured in this study had weak, but significant, phylogenetic signal. Nonrandom phylogenetic and trait-based patterns associated with topographic variables indicate that deterministic processes tend to dominate community assembly in this plot. Specifically, we found that, on average, co-occurring species were more phylogenetically and functionally similar than expected throughout the plot at most spatial scales and assemblages of less similar than expected species could only be found on finer spatial scales. In sum, our results suggest that the trait-based effects on community assembly change with spatial scale in a predictable manner and the association of these patterns with topographic variables, indicates the importance of deterministic processes in community assembly relatively to random processes.

The role of environmental vs. biotic filtering in the structure of European ant communities: A matter of trait type and spatial scale

Functional trait-based approaches are increasingly used for studying the processes underlying community assembly. The relative influence of different assembly rules might depend on the spatial scale of analysis, the environmental context and the type of functional traits considered. By using a functional trait-based approach, we aim to disentangle the relative role of environmental filtering and interspecific competition on the structure of European ant communities according to the spatial scale and the type of trait considered. We used a large database on ant species composition that encompasses 361 ant communities distributed across the five biogeographic regions of Europe; these communities were composed of 155 ant species, which were characterized by 6 functional traits. We then analysed the relationship between functional divergence and co-occurrence between species pairs across different spatial scales (European, biogeographic region and local) and considering different types of traits (ecological tolerance and niche traits). Three different patterns emerged: negative, positive and non-significant regression coefficients suggest that environmental filtering, competition and neutrality are at work, respectively. We found that environmental filtering is important for structuring European ant communities at large spatial scales, particularly at the scale of Europe and most biogeographic regions. Competition could play a certain role at intermediate spatial scales where temperatures are more favourable for ant productivity (i.e. the Mediterranean region), while neutrality might be especially relevant in spatially discontinuous regions (i.e. the Alpine region). We found that no ecological mechanism (environmental filtering or competition) prevails at the local scale. The type of trait is especially important when looking for different assembly rules, and multi-trait grouping works well for traits associated with environmental responses (tolerance traits), but not for traits related to resource exploitation (niche traits). The spatial scale of analysis, the environmental context and the chosen traits merit special attention in trait-based analyses of community assembly mechanisms.

Differentiation of Environmental Conditions Promotes Variation of Two Quercus wutaishanica Community Assembly Patterns

Two contradictory niche-based processes, environmental filtering and competitive exclusion, are important ecological processes in community assembly. Quercus wutaishanica forests are the climax communities in the Qinling Mountains and the Loess Plateau, China. Since these areas are characterized by different climate and evolutionary histories, these forests could be a suitable study system to test the phylogenetic niche conservatism hypothesis. We compared variation in community assembly of two distinct Q. wutaishanica forest communities and analyzed how the variations are formed. Quercus wutaishanica forest communities had significantly different species pool, phylogenetic structure and phylogenetic diversity between the two regions that were driven by inconsistency in environment conditions and evolutionary history at the local scale. Soil ammonium nitrogen, soil water content, and nitrate nitrogen play a major role in phylogenetic beta diversity patterns. The effect of environmental filtering on community assembly was more significant on the Loess Plateau than in the Qinling Mountains. Our study also found that local environment is important in mediating the patterns of phylogenetic structure. These findings provide insights into the mechanisms of local community assembly.

Is Phylogeny More Useful than Functional Traits for Assessing Diversity Patterns Under Community Assembly Processes?

Phylogenetic and functional diversities and their relationship are important for understanding community assembly, which relates to forest sustainability. Thus, both diversities have been used in ecological studies evaluating community responses to environmental changes. However, it is unclear whether these diversity measures can uncover the actual community assembly processes. Herein, we examined their utility to assess such assembly processes by analyzing similarities in phylogenetic, functional, and taxonomic α- and β-diversities along an elevational gradient. Additionally, we examined the relationships among environment, phylogeny, and functional traits within the community. Based on our results, we evaluated whether phylogenetic or functional diversity could better reveal the actual community assembly processes. We found that taxonomic, phylogenetic, and functional α-diversities were correlated with one another. Although the functional α-diversity showed a linear correlation with the elevational gradient, taxonomic and phylogenetic α-diversities showed unimodal patterns. Both phylogenetic and functional β-diversities correlated with taxonomic β-diversity, but there was no significant relationship between the former. Overall, our results evidenced that phylogenetic diversity and taxonomic diversity showed similar patterns, whereas functional diversity showed a relatively independent pattern, which may be due to limitations in the functional trait dimensions used in the present study. Although it is difficult to unravel whether the environment shapes phylogeny or functional traits within a community, phylogenetic diversity is a good proxy for assessing the assembly processes, whereas functional diversity may improve knowledge on the community by maximizing information about the functional trait dimensions.

Influence of phylogenetic structure and climate gradients on geographical variation in the morphology of Mexican flycatcher forests assemblages (Aves: Tyrannidae)

Morphological variation is strongly related to variation in the ecological characteristics and evolutionary history of each taxon. To explore how geographical variation in morphology is related to different climatic gradients and phylogenetic structure, we analyzed the variation of morphological traits (body size, bill, and wing) of 64 species of tyrant flycatchers (Tyrannidae) distributed in Mexico. We measured these morphological traits in specimens from biological collections and related them to the climatic and topographic data of each collection locality. We performed the analyses separately at two levels: (1) the regional level and (2) the assemblage level, which was split into (assemblage I) lowland forests and (assemblage II) highland forests and other vegetation types. We also calculated the phylogenetic structure of flycatchers of each locality in order to explore the influence of climatic variables and the phylogenetic structure on the morphological variation of tyrant flycatchers, by means of linear mixed-effects models. We mapped the spatial variation of the relationship between morphological traits and environmental gradients, taking into account the phylogenetic structure. Important climatic variables explaining the morphological variation were those of temperature ranges (seasonality) and the results suggest that the phylogenetic clustering increases towards the highlands of Sierra Madre Oriental and Sierra Madre del Sur, and the lowlands of Balsas Depression. For the regional level, the spatial distribution of body size showed a pattern coincident with Bergmann's rule, with increasing in size from south to north. In the tropical lowland forests assemblage, body size tend to increase in seasonally dry forests (western Mexico) and decrease in the humid ones (eastern Mexico). In the assemblage of highland forests and other types of vegetation, morphological trait values increased northeast to southwest. Phylogenetic structure helped to explain the variation of morphology at the assemblage level but not at the regional level. The patterns of trait variation in the lowland and highland assemblages suggest that parts of morphological variation are explained both by the climatic gradients and by the lineage relatedness of communities. Overall, our results suggest that morphological variation is best explained by a varied set of variables, and that regression models representing this variation, as well as integrating phylogenetic patterns at different community levels, provide a new understanding of the mechanisms underlying the links among biodiversity, its geographical setting, and environmental change.

Distribution and Community Assembly of Trees Along an Andean Elevational Gradient

Highlighting patterns of distribution and assembly of plants involves the use of community phylogenetic analyses and complementary traditional taxonomic metrics. However, these patterns are often unknown or in dispute, particularly along elevational gradients, with studies finding different patterns based on elevation. We investigated how patterns of tree diversity and structure change along an elevation gradient using taxonomic and phylogenetic diversity metrics. We sampled 595 individuals (36 families; 53 genera; 88 species) across 15 plots along an elevational gradient (2440-3330 m) in Ecuador. Seventy species were sequenced for the rbcL and matK gene regions to generate a phylogeny. Species richness, Shannon-Weaver diversity, Simpson's Dominance, Simpson's Evenness, phylogenetic diversity (PD), mean pairwise distance (MPD), and mean nearest taxon distance (MNTD) were evaluated for each plot. Values were correlated with elevation and standardized effect sizes (SES) of MPD and MNTD were generated, including and excluding tree fern species, for comparisons across elevation. Taxonomic and phylogenetic metrics found that species diversity decreases with elevation. We also found that overall the community has a non-random phylogenetic structure, dependent on the presence of tree ferns, with stronger phylogenetic clustering at high elevations. Combined, this evidence supports the ideas that tree ferns have converged with angiosperms to occupy the same habitat and that an increased filtering of clades has led to more closely related angiosperm species at higher elevations.

Relationship between microbial diversity and nitrogenase activity of Stipagrostis pennata rhizosheath

Nitrogen is the key factor for plant survival and growth, especially in the desert. Stipagrostis pennata, a sand born drought-resistant plant, could colonize pioneerly in Gurbantunggut Desert during revegetation. One strategy for their environment adaptation was the rhizosheath formatted by root-hair, mucilaginous exudates, microbial components, and soil particles, for which not only provides a favorable living microenvironment but also supplies essential nutrients. To understand the relationship between microorganisms living in rhizosheaths and the nitrogen nutrition supply, the microbial diversity and nitrogenase activity was estimated during the growth of S. pennata. Five samples of the rhizosheath, which based on the development periods of the plant, regreen, flowering, filling, seed maturating, and withering period, were collected. The nitrogenase activity was estimated by acetylene reduction and the microbial diversity was analyzed by 16S rRNA high-throughput sequencing. The results showed that the nitrogenase activity was increased slowly during regreen to flowering, while reached a peak rapidly at filling sample and then decreased gradually. A total of 274 operational taxonomic units (OTUs) were identified and significant differences in community structure and composition at each growth period. Among them, the main phyla included Actinobacteria and Proteus, which were the most abundant phyla in all periods. In addition, the microbial diversity in the grain filling period was higher than other periods in view of the analysis of alpha diversity and beta diversity. Furthermore, principal component analysis (PCA) analysis showed that the microbial communities in the filling period was low in similarity with other periods. Most importantly, the OTUs associated with nitrogen fixation is the most during the filling period, involving Phagecidae and Fucoraceae. Overall, the study not only revealed the differences in nitrogenase activity among different developmental periods in S. pennata, but also explored the potential bridges between it and community structure and diversity of bacteria.

Community structure and tree diversity in a subtropical forest in southern Brazil

Abstract: Local and regional environmental variations lead to different species composition, creating transitional areas. An example is the Araucaria and Seasonal forest in southern Brazil. Our objectives were (1) to describe the tree community structure and composition of a subtropical forest in southern Brazil and (2) to compare the floristic relationships between two forest typologies (Araucaria and Seasonal forest) in order to characterize the study area and the distribution patterns of tree species. We conducted a survey at Chapecó National Forest (in southern Brazil) in an area of 1.2 ha, where all individuals ≥ 30 cm of circumference at breast height were sampled. Community structure was described using the traditional phytosociological parameters. The floristic relationships were obtained by comparing our results with compiled data from other scientific papers through cluster analyses using an unweighted average linkage method, based on Jaccard similarity coefficient. We sampled 809 individuals belonging to 61 species and 28 families. The richest family was Fabaceae and Coussarea contracta (Walp.) Müll.Arg. was the most abundant species. Taxonomic diversity was 3.06 and the evenness was 0.74. The floristic similarity revealed that species composition of our study area is more similar to Seasonal forest. Species composition is related to environmental factors such as great thermal amplitude and seasonality. This subtropical forest is well structured, highly diverse and extremely important for the local and regional biodiversity conservation.

Shifts in Plant Community Assembly Processes across Growth Forms along a Habitat Severity Gradient: A Test of the Plant Functional Trait Approach

Species respond to changes in their environments. A core goal in ecology is to understand the process of plant community assembly in response to a changing climate. Examining the performance of functional traits and trait-based assembly patterns across species among different growth forms is a useful way to explore the assembly process. In this study, we constructed a habitat severity gradient including several environment factors along a 2300 m wide elevational range at Taibai Mountain, central China. Then we assessed the shift on functional trait values and community assembly patterns along this gradient across species among different growth forms. We found that (1) although habitat-severity values closely covaried with elevation in this study, an examined communities along a habitat severity gradient might reveal community dynamics and species responses under future climate change. (2) the occurrence of trait values along the habitat severity gradient across different growth forms were similar, whereas the assembly pattern of herbaceous species was inconsistent with the community and woody species. (3) the trait-trait relationships of herbaceous species were dissimilar to those of the community and woody species. These results suggest that (1) community would re-assemble along habitat severity gradient through environmental filtering, regardless of any growth forms and that (2) different growth forms' species exhibiting similar trait values' shift but different trait-trait relationship by different trait combinations.

Using phylogeny and functional traits for assessing community assembly along environmental gradients: A deterministic process driven by elevation

Community assembly processes is the primary focus of community ecology. Using phylogenetic‐based and functional trait‐based methods jointly to explore these processes along environmental gradients are useful ways to explain the change of assembly mechanisms under changing world. Our study combined these methods to test assembly processes in wide range gradients of elevation and other habitat environmental factors. We collected our data at 40 plots in Taibai Mountain, China, with more than 2,300 m altitude difference in study area and then measured traits and environmental factors. Variance partitioning was used to distinguish the main environment factors leading to phylogeny and traits change among 40 plots. Principal component analysis (PCA) was applied to colligate other environment factors. Community assembly patterns along environmental gradients based on phylogenetic and functional methods were studied for exploring assembly mechanisms. Phylogenetic signal was calculated for each community along environmental gradients in order to detect the variation of trait performance on phylogeny. Elevation showed a better explanatory power than other environment factors for phylogenetic and most traits’ variance. Phylogenetic and several functional structure clustered at high elevation while some conserved traits overdispersed. Convergent tendency which might be caused by filtering or competition along elevation was detected based on functional traits. Leaf dry matter content (LDMC) and leaf nitrogen content along PCA 1 axis showed conflicting patterns comparing to patterns showed on elevation. LDMC exhibited the strongest phylogenetic signal. Only the phylogenetic signal of maximum plant height showed explicable change along environmental gradients. Synthesis. Elevation is the best environment factors for predicting phylogeny and traits change. Plant's phylogenetic and some functional structures show environmental filtering in alpine region while it shows different assembly processes in middle‐ and low‐altitude region by different trait/phylogeny. The results highlight deterministic processes dominate community assembly in large‐scale environmental gradients. Performance of phylogeny and traits along gradients may be independent with each other. The novel method for calculating functional structure which we used in this study and the focus of phylogenetic signal change along gradients may provide more useful ways to detect community assembly mechanisms.