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Plant species can show considerable morphological and functional variation along environmental gradients. This intraspecific trait variation (ITV) can have important consequences for community assembly, biotic interactions, ecosystem functions and responses to global change. However, directly measuring ITV across many species and wide geographic areas is often infeasible. Thus, a method to predict spatial variation in a species’ functional traits could be valuable. We measured specific leaf area (SLA), height and leaf area (LA) of grasses across California, covering 59 species at 230 sampling locations. We asked how these traits change along climate gradients within each species and used machine learning to predict local trait values for any species at any location based on phylogenetic position, local climate and that species’ mean traits. We then examined how much these local predictions alter patterns of assemblage-level trait variation across the state. Most species exhibited higher SLA and grew taller at higher temperatures and produced larger leaves in drier conditions. The random forests predicted spatial variation in functional traits very accurately, with correlations up to 0.97. Because trait records were spatially biased towards warmer areas, and these areas tend to have higher SLA individuals within each species, species means of SLA were upwardly biased. As a result, using species means over-estimates SLA in the cooler regions of the state. Our results also suggest that height may be substantially under-predicted in the warmest areas. Synthesis. Using only species mean traits to characterize the functional composition of communities risks introducing substantial error into trait-based estimates of ecosystem properties including decomposition rates or NPP. The high performance of random forests in predicting local trait values provides a way forward for estimating high-resolution patterns of ITV without a massive data collection effort.

Aim: Here we examine the functional profile of regional tree species pools across the latitudinal distribution of Neotropical moist forests, and test trait–climate relationships among local communities. We expected opportunistic strategies (acquisitive traits, small seeds) to be overrepresented in species pools further from the equator, but also in terms of abundance in local communities in currently wetter, warmer and more seasonal climates. Location: Neotropics. Time period: Recent. Major taxa studied: Trees. Methods: We obtained abundance data from 471 plots across nine Neotropical regions, including c. 100,000 trees of 3,417 species, in addition to six functional traits. We compared occurrence-based trait distributions among regional species pools, and evaluated single trait–climate relationships across local communities using community abundance-weighted means (CWMs). Multivariate trait–climate relationships were assessed by a double-constrained correspondence analysis that tests both how CWMs relate to climate and how species distributions, parameterized by niche centroids in climate space, relate to their traits. Results: Regional species pools were undistinguished in functional terms, but opportunistic strategies dominated local communities further from the equator, particularly in the Northern Hemisphere. Climate explained up to 57% of the variation in CWM traits, with increasing prevalence of lower-statured, light-wooded and softer-leaved species bearing smaller seeds in more seasonal, wetter and warmer climates. Species distributions were significantly but weakly related to functional traits. Main conclusions: Neotropical moist forest regions share similar sets of functional strategies, from which local assembly processes, driven by current climatic conditions, select for species with different functional strategies. We can thus expect functional responses to climate change driven by changes in relative abundances of species already present regionally. Particularly, equatorial forests holding the most conservative traits and large seeds are likely to experience the most severe changes if climate change triggers the proliferation of opportunistic tree species.

Glycans are ubiquitous and play important biological roles, yet chemical methods for probing their structure and function within cells remain limited. Strategies for studying other biomacromolecules, such as proteins, often exploit chemoselective reactions for covalent modification, capture, or imaging. Unlike amino acids that constitute proteins, glycan building blocks lack distinguishing reactivity because they are composed primarily of polyol isomers. Moreover, encoding glycan variants through genetic manipulation is complex. Therefore, we formulated a new, generalizable strategy for chemoselective glycan modification that directly takes advantage of cellular glycosyltransferases. Many of these enzymes are selective for the products they generate yet promiscuous in their donor preferences. Thus, we designed reagents with bioorthogonal handles that function as glycosyltransferase substrate surrogates. We validated the feasibility of this approach by synthesizing and testing probes of d-arabinofuranose (d-Araf), a monosaccharide found in bacteria and an essential component of the cell wall that protects mycobacteria, including Mycobacterium tuberculosis. The result is the first probe capable of selectively labeling arabinofuranose-containing glycans. Our studies serve as a platform for developing new chemoselective labeling agents for other privileged monosaccharides. This probe revealed an asymmetric distribution of d-Araf residues during mycobacterial cell growth and could be used to detect mycobacteria in THP1-derived macrophages.

Latitudinal and elevational richness gradients have received much attention from ecologists but there is little consensus on underlying causes. One possible proximate cause is increased levels of species turnover, or β diversity, in the tropics compared to temperate regions. Here, we leverage a large botanical dataset to map taxonomic and phylogenetic β diversity, as mean turnover between neighboring 100 × 100 km cells, across the Americas and determine key climatic drivers. We find taxonomic and tip-weighted phylogenetic β diversity is higher in the tropics, but that basal-weighted phylogenetic β diversity is highest in temperate regions. Supporting Janzen's ‘mountain passes’ hypothesis, tropical mountainous regions had higher β diversity than temperate regions for taxonomic and tip-weighted metrics. The strongest climatic predictors of turnover were average temperature and temperature seasonality. Taken together, these results suggest β diversity is coupled to latitudinal richness gradients and that temperature is a major driver of plant community composition and change.

Glycans are ubiquitous and play important biological roles, yet chemical methods for probing their structure and function within cells remain limited. Strategies for studying other biomacromolecules, such as proteins, often exploit chemoselective reactions for covalent modification, capture, or imaging. Unlike amino acids that constitute proteins, glycan building blocks lack distinguishing reactivity because they are composed primarily of polyol isomers. Moreover, encoding glycan variants through genetic manipulation is complex. Therefore, we formulated a new, generalizable strategy for chemoselective glycan modification that directly takes advantage of cellular glycosyltransferases. Many of these enzymes are selective for the products they generate yet promiscuous in their donor preferences. Thus, we designed reagents with bioorthogonal handles that function as glycosyltransferase substrate surrogates. We validated the feasibility of this approach by synthesizing and testing probes of D-arabinofuranose (D-Araf), a monosaccharide found in bacteria and an essential component of the cell wall that protects mycobacteria, including Mycobacterium tuberculosis. The result is the first probe capable of selectively labeling arabinofuranose-containing glycans. Our studies serve as a platform for developing new chemoselective labeling agents for other privileged monosaccharides. This probe revealed an asymmetric distribution of D-Araf residues during mycobacterial cell growth and could be used to detect mycobacteria in THP1-derived macrophages.

Soil microorganisms influence a variety of processes in plant communities. Many theoretical and empirical studies have shown that dynamic feedbacks between plants and soil microbes can stabilize plant coexistence by generating negative frequency-dependent plant population dynamics. However, inferring the net effects of soil microbes on plant coexistence requires also quantifying the degree to which they provide one species an average fitness advantage, an effect that has received little empirical attention. We conducted a greenhouse study to quantify microbially mediated stabilization and fitness differences among 15 pairs of annual plants that co-occur in southern California grasslands. We found that although soil microbes frequently generate negative frequency-dependent dynamics that stabilize plant interactions, they simultaneously generate large average fitness differences between species. The net result is that if the plant species are otherwise competitively equivalent, the impact of plant-soil feedbacks is to often favor species exclusion over coexistence, a result that becomes evident only by quantifying the microbially mediated fitness difference. Our work highlights that comparing the stabilizing effects of plant-soil feedbacks to the fitness difference they generate is essential for understanding the influence of soil microbes on plant diversity.

Turnover in species composition and community-wide functional traits across environmental gradients is a ubiquitous pattern in ecology, and is generally assumed to reflect shifts in trait optima across these gradients. However, the demographic processes that give rise to these trait turnover patterns at the community level remain unclear.We asked whether shifts in the community-weighted means of three key functional traits across an environmental gradient in a southern California grassland reflect variation in the trait-performance relationship across the landscape.We planted seeds of 17 annual plant species in cleared patches with no competitors, and quantified the lifetime seed production of 1360 individuals. We then asked whether models that included trait-environment interactions help explain interspecific variation in demographic responses to the environment. This allowed us to evaluate whether observed shifts in community-weighted mean traits matched the direction of any trait-environment interactions detected in the plant performance experiment.Our results indicate that commonly-measured plant functional traits help explain variation in species responses to the environment – for example, high-SLA species had a demographic advantage in soils with high soil Ca:Mg levels, while low-SLA species had an advantage in low Ca:Mg soils. We also found that shifts in community-weighted mean traits often reflect the direction of these trait-environment interactions, though not all trait-environment relationships at the community level reflect interactive effects of traits and environment on species performance.Our results support the value of plant functional traits for predicting species responses to environmental variation, and highlight a need for more detailed evaluation of how trait-performance relationships change across environments to improve such predictions.

Understanding variation in leaf functional traits-including rates of photosynthesis and respiration and concentrations of nitrogen and phosphorus-is a fundamental challenge in plant ecophysiology. When expressed per unit leaf area, these traits typically increase with leaf mass per area (LMA) within species but are roughly independent of LMA across the global flora. LMA is determined by mass components with different biological functions, including photosynthetic mass that largely determines metabolic rates and contains most nitrogen and phosphorus, and structural mass that affects toughness and leaf lifespan (LL). A possible explanation for the contrasting trait relationships is that most LMA variation within species is associated with variation in photosynthetic mass, whereas most LMA variation across the global flora is associated with variation in structural mass. This hypothesis leads to the predictions that (i) gas exchange rates and nutrient concentrations per unit leaf area should increase strongly with LMA across species assemblages with low LL variance but should increase weakly with LMA across species assemblages with high LL variance and that (ii) controlling for LL variation should increase the strength of the above LMA relationships. We present analyses of intra- and interspecific trait variation from three tropical forest sites and interspecific analyses within functional groups in a global dataset that are consistent with the above predictions. Our analysis suggests that the qualitatively different trait relationships exhibited by different leaf assemblages can be understood by considering the degree to which photosynthetic and structural mass components contribute to LMA variation in a given assemblage.

The functional composition of plant communities in montane regions has been studied for decades, and most recent analyses find that environmentally favourable landscapes at lower altitudes tend to be dominated by species with resource-acquisitive traits, while more resource-conservative taxa dominate higher-altitude communities. However, it is unclear the extent to which this pattern is driven by co-gradient variation within clades or changes in clade representation across the gradient. To test for co-gradient variation, species composition, phylogenetic structure and functional traits were quantified for 97 species within the plant family Melastomataceae at five locations across a 2500- m altitudinal gradient along Volcán Barva in Costa Rica. Average melastome leaf force to punch, specific leaf area and leaf size vary with altitude, while four other functional traits do not. Taxonomic dissimilarity between communities was correlated with altitudinal difference, while phylogenetic dissimilarity was correlated with altitudinal dissimilarity only when measured with a metric that emphasizes shallow turnover of the tips of the phylogeny. These results highlight how species turnover may be more pronounced than functional or phylogenetic variation along altitudinal gradients. In addition, these results highlight the conservation value of lowland tropical forests, which here harbour a disproportionate amount of phylogenetic and functional diversity La composición funcional de las comunidades de plantas en las regiones montañosas se ha estudiado durante décadas, y los análisis más recientes encuentran que los paisajes ambientalmente favorables en altitudes más bajas tienden a estar dominados por especies con características de adquisición de recursos, mientras que los taxones más conservadores de recursos dominan las comunidades de altitudes más altas. . Sin embargo, no está claro hasta qué punto este patrón es impulsado por la variación del cogradiente dentro de los clados o los cambios en la representación de los clados a lo largo del gradiente. Para evaluar la variación del cogradiente, se cuantificaron la composición de especies, la estructura filogenética y los rasgos funcionales de 97 especies dentro de la familia de plantas Melastomataceae en cinco lugares a lo largo de un gradiente altitudinal de 2500 m a lo largo del Volcán Barva en Costa Rica. La fuerza promedio de la hoja de melastoma para perforar, el área foliar específica y el tamaño de la hoja varían con la altitud, mientras que otros cuatro rasgos funcionales no lo hacen. La disimilitud taxonómica entre comunidades se correlacionó con la diferencia altitudinal, mientras que la disimilitud filogenética se correlacionó con la disimilitud altitudinal solo cuando se midió con una métrica que enfatiza la rotación superficial de las puntas de la filogenia. Estos resultados resaltan cómo el recambio de especies puede ser más pronunciado que la variación funcional o filogenética a lo largo de los gradientes altitudinales. Además, estos resultados resaltan el valor de conservación de los bosques tropicales de tierras bajas, que aquí albergan una cantidad desproporcionada de diversidad filogenética y funcional. Universidad Nacional, Costa Rica Escuela de Ciencias Biológicas

Spatial processes underlie major species coexistence mechanisms. A range of spatial analysis techniques are increasingly applied to data of fully mapped communities to quantify spatial structures in species and phylogenetic and functional diversity at some given spatial scale with the goal of gaining insights into processes of community assembly and dynamics. We review these techniques, including spatial point pattern analysis, quadrat-based analyses, and individual-based neighborhood models, and provide a practical roadmap for ecologists in the analysis of local spatial structures in species and phylogenetic and functional diversity. We show how scale-dependent metrics of spatial diversity can be used in concert with ecological null models, statistical models, and dynamic community simulation models to detect spatial patterns, reveal the influence of the biotic neighborhood on plant performance, and quantify the relative contribution of species interactions, habitat heterogeneity, and stochastic processes to community assembly across scale. Future works should integrate these approaches into a dynamic spatiotemporal framework.

Soil microorganisms influence a variety of processes in plant communities. Many the-oretical and empirical studies have shown that dynamic feedbacks between plants and soil microbes can stabilize plant coexistence by generating negative frequency-dependent plant population dynamics. However, inferring the net effects of soil microbes on plant coexistence requires also quantifying the degree to which they provide one species an average fitness advantage, an effect that has received little empirical attention. We conducted a greenhouse study to quantify microbially mediated stabilization and fitness differences among fifteen pairs of annual plants that co-occur in southern California grasslands. We found that although soil microbes frequently generate negative frequency-dependent dynamics that stabilize plant interactions, they simultaneously mediate large average fitness differences between species. The net result is that if the plant species are otherwise competitively equivalent, the impact of plant-soil feedbacks is often to favor species exclusion over coexistence, a result that only becomes evident by quantifying the microbially mediated fitness difference. Our work highlights that comparing the stabilizing effects of plant-soil feedbacks to the fitness difference they generate is essential for understanding the influence of soil microbes on plant diversity.

[Aim] Intraspecific trait variation (ITV) within natural plant communities can be large, influencing local ecological processes and dynamics. Here, we shed light on how ITV in vegetative and floral traits responds to large‐scale abiotic and biotic gradients (i.e., climate and species richness). Specifically, we tested whether associations of ITV with temperature, precipitation and species richness were consistent with any of four hypotheses relating to stress tolerance and competition. Furthermore, we estimated the degree of correlation between ITV in vegetative and floral traits and how they vary along the gradients., [Location] Global., [Time period] 1975–2016., [Major taxa studied] Herbaceous and woody plants., [Methods] We compiled a dataset of 18,401 measurements of the absolute extent of ITV (measured as the coefficient of variation) in nine vegetative and seven floral traits from 2,822 herbaceous and woody species at 2,372 locations., [Results] Large‐scale associations between ITV and climate were trait specific and more prominent for vegetative traits, especially leaf morphology, than for floral traits. The ITV showed pronounced associations with climate, with lower ITV values in colder areas and higher values in drier areas. The associations of ITV with species richness were inconsistent across traits. Species‐specific associations across gradients were often idiosyncratic, and covariation in ITV was weaker between vegetative and floral traits than within the two trait groups. [Main conclusions] Our results show that, depending on the traits considered, ITV either increased or decreased with climate stress and species richness, suggesting that both factors can constrain or enhance ITV, which might foster plant‐population persistence in stressful conditions. Given the species‐specific responses and covariation in ITV, associations can be hard to predict for traits and species not yet studied. We conclude that consideration of ITV can improve our understanding of how plants cope with stressful conditions and environmental change across spatial and biological scales., Open Access funding was provided by Ulm University under the DEAL‐agreement.

Aim: Plant trait databases often contain traits that are correlated, but for whom direct (undirected statistical dependency) and indirect (mediated by other traits) connections may be confounded. The confounding of correlation and connection hinders our understanding of plant strategies, and how these vary among growth forms and climate zones. We identified the direct and indirect connections across plant traits relevant to competition, resource acquisition and reproductive strategies using a global database and explored whether connections within and between traits from different tissue types vary across climates and growth forms. Location: Global. Major taxa studied: Plants. Time period: Present. Methods: We used probabilistic graphical models and a database of 10 plant traits (leaf area, specific leaf area, mass- and area-based leaf nitrogen and phosphorous content, leaf life span, plant height, stem specific density and seed mass) with 16,281 records to describe direct and indirect connections across woody and non-woody plants across tropical, temperate, arid, cold and polar regions. Results: Trait networks based on direct connections are sparser than those based on correlations. Land plants had high connectivity across traits within and between tissue types; leaf life span and stem specific density shared direct connections with all other traits. For both growth forms, two groups of traits form modules of more highly connected traits; one related to resource acquisition, the other to plant architecture and reproduction. Woody species had higher trait network modularity in polar compared to temperate and tropical climates, while non-woody species did not show significant differences in modularity across climate regions. Main conclusions: Plant traits are highly connected both within and across tissue types, yet traits segregate into persistent modules of traits. Variation in the modularity of trait networks suggests that trait connectivity is shaped by prevailing environmental conditions and demonstrates that plants of different growth forms use alternative strategies to cope with local conditions. © 2019 John Wiley and Sons Ltd

Despite the ubiquity and importance of glycans in biology, methods to probe their structures in cells are limited. Mammalian glycans can be modulated using metabolic incorporation, a process in which non-natural sugars are taken up by cells, converted to nucleotide-sugar intermediates, and incorporated into glycans via biosynthetic pathways. These studies have revealed examples in which glycan intermediates can be shunted through multiple pathways, and this complexity can be heightened in bacteria, as they can catabolize diverse glycans. We sought to develop a strategy that probes structures recalcitrant to metabolic incorporation and that complements approaches focused on nucleotide sugars. We reasoned lipid-linked glycans, which are intermediates directly used in glycan biosynthesis, would offer an alternative. We generated synthetic arabinofuranosyl phospholipids to test this strategy in Corynebacterium glutamicum and Mycobacterium smegmatis, organisms that serve as models of Mycobacterium tuberculosis. Using a C. glutamicum mutant that lacks arabinan, we identified synthetic glycosyl donors whose addition restores cell wall arabinan, demonstrating that non-natural glycolipids can serve as biosynthetic intermediates and function in chemical complementation. The addition of an isotopically labeled glycan substrate facilitated cell wall characterization by NMR. Structural analysis revealed that all the five known arabinofuranosyl transferases could process the exogenous lipid-linked sugar donor allowing for the full recovery of the cell envelope. The lipid-based probe could also rescue wild type cells treated with an inhibitor of cell wall biosynthesis. Our data indicate that surrogates of natural lipid-linked glycans can intervene in the cell’s traditional workflow, indicating biosynthetic incorporation is a powerful strategy to probe glycan structure and function.

Drought events are increasing globally, and reports of consequent forest mortality are widespread. However, due to a lack of a quantitative global synthesis, it is still not clear whether drought-induced mortality rates differ among global biomes and whether functional traits influence the risk of drought-induced mortality. To address these uncertainties, we performed a global meta-analysis of 58 studies of drought-induced forest mortality. Mortality rates were modelled as a function of drought, temperature, biomes, phylogenetic and functional groups and functional traits. We identified a consistent global-scale response, where mortality increased with drought severity [log mortality (trees trees−1 year−1) increased 0.46 (95% CI = 0.2–0.7) with one SPEI unit drought intensity]. We found no significant differences in the magnitude of the response depending on forest biomes or between angiosperms and gymnosperms or evergreen and deciduous tree species. Functional traits explained some of the variation in drought responses between species (i.e. increased from 30 to 37% when wood density and specific leaf area were included). Tree species with denser wood and lower specific leaf area showed lower mortality responses. Our results illustrate the value of functional traits for understanding patterns of drought-induced tree mortality and suggest that mortality could become increasingly widespread in the future. Fil: Greenwood, Sarah. University Of Stirling; Reino Unido Fil: Ruiz Benito, Paloma. Universidad de Alcalá; España. University Of Stirling; Reino Unido Fil: Martínez Vilalta, Jordi. Consejo Superior de Investigaciones Científicas. Centre de Recerca Ecológica I Aplicacions Forestals; España. Universitat Autònoma de Barcelona; España Fil: Lloret, Francisco. Universitat Autònoma de Barcelona; España. Consejo Superior de Investigaciones Científicas. Centre de Recerca Ecológica I Aplicacions Forestals; España Fil: Kitzberger, Thomas. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto de Investigaciones en Biodiversidad y Medioambiente. Universidad Nacional del Comahue. Centro Regional Universidad Bariloche. Instituto de Investigaciones en Biodiversidad y Medioambiente; Argentina Fil: Allen, Craig D.. United States Geological Survey; Estados Unidos Fil: Fensham, Rod. The University Of Queensland; Australia. Queensland Herbarium; Australia. University of Queensland; Australia Fil: Laughlin, Daniel C.. University Of Waikato; Nueva Zelanda Fil: Kattge, Jens. German Centre for Integrative Biodiversity Research; Alemania. Max Planck Institut Fur Biogeochemie Jena; Alemania Fil: Bönisch, Gerhard. Max Planck Institut Fur Biogeochemie Jena; Alemania Fil: Kraft, Nathan J. B.. University of California at Los Angeles; Estados Unidos Fil: Jump, Alistair S.. University Of Stirling; Reino Unido. Consejo Superior de Investigaciones Científicas. Centre de Recerca Ecológica I Aplicacions Forestals; España

International audience; Many plant species exhibit strong association with topographic habitats at local scales. However, the historical biogeographic and physiological drivers of habitat specialization are still poorly understood, and there is a need for relatively easy-to-measure predictors of species habitat niche breadth. Here, we explore whether species geographic range, climatic envelope, or intraspecific variability in leaf traits is related to the degree of habitat specialization in a hyperdiverse tropical tree community in Amazonian Ecuador. Contrary to our expectations, we find no effect of the size of species geographic ranges, the diversity of climate a species experiences across its range, or intraspecific variability in leaf traits in predicting topographic habitat association in the ~300 most common tropical tree species in a 25-ha tropical forest plot. In addition, there was no phylogenetic signal to habitat specialization. We conclude that species geographic range size, climatic niche breadth, and intraspecific variability in leaf traits fail to capture the habitat specialization patterns observed in this highly diverse tropical forest.

Environmental filtering and dispersal limitation can both maintain diversity in plant communities by aggregating conspecifics, but parsing the contribution of each process has proven difficult empirically. Here, we assess the contribution of filtering and dispersal limitation to the spatial aggregation patterns of 456 tree species in a hyperdiverse Amazonian forest and find distinct functional trait correlates of interspecific variation in these processes. Spatial point process model analysis revealed that both mechanisms are important drivers of intraspecific aggregation for the majority of species. Leaf drought tolerance was correlated with species topographic distributions in this aseasonal rainforest, showing that future increases in drought severity could significantly impact community structure. In addition, seed mass was associated with the spatial scale and density of dispersal-related aggregation. Taken together, these results suggest environmental filtering and dispersal limitation act in concert to influence the spatial and functional structure of diverse forest communities.

Plant functional group dominance has been linked to climate, topography and anthropogenic factors. Here, we assess existing theory linking functional group dominance patterns to their drivers by quantifying the spatial distribution of plant functional groups at a 100-km grid scale. We use a standardized plant species occurrence dataset of unprecedented size covering the entire New World. Functional group distributions were estimated from 3 648 533 standardized occurrence records for a total of 83 854 vascular plant species, extracted from the Botanical Information and Ecology Network (BIEN) database. Seven plant functional groups were considered, describing major differences in structure and function: epiphytes; climbers; ferns; herbs; shrubs; coniferous trees; and angiosperm trees. Two measures of dominance (relative number of occurrences and relative species richness) were analysed against a range of hypothesized predictors. The functional groups showed distinct geographical patterns of dominance across the New World. Temperature seasonality and annual precipitation were most frequently selected, supporting existing hypotheses for the geographical dominance of each functional group. Human influence and topography were secondarily important. Our results support the prediction that future climate change and anthropogenic pressures could shift geographical patterns in dominance of plant functional groups, with probable consequences for ecosystem functioning Plant functional group dominance has been linked to climate, topography and anthropogenic factors. Here, we assess existing theory linking functional group dominance patterns to their drivers by quantifying the spatial distribution of plant functional groups at a 100-km grid scale. We use a standardized plant species occurrence dataset of unprecedented size covering the entire New World. Functional group distributions were estimated from 3 648 533 standardized occurrence records for a total of 83 854 vascular plant species, extracted from the Botanical Information and Ecology Network (BIEN) database. Seven plant functional groups were considered, describing major differences in structure and function: epiphytes; climbers; ferns; herbs; shrubs; coniferous trees; and angiosperm trees. Two measures of dominance (relative number of occurrences and relative species richness) were analysed against a range of hypothesized predictors. The functional groups showed distinct geographical patterns of dominance across the New World. Temperature seasonality and annual precipitation were most frequently selected, supporting existing hypotheses for the geographical dominance of each functional group. Human influence and topography were secondarily important. Our results support the prediction that future climate change and anthropogenic pressures could shift geographical patterns in dominance of plant functional groups, with probable consequences for ecosystem functioning.

One of the main goals of conservation biology is to understand the factors shaping variation in biodiversity across the planet. This understanding is critical for conservation planners to be able to develop effective conservation strategies. Although many studies have focused on species richness and the protection of rare and endemic species, less attention has been paid to the protection of the phylogenetic dimension of biodiversity. We explored how phylogenetic diversity, species richness, and phylogenetic community structure vary in seed plant communities along an elevational gradient in a relatively understudied high mountain region, the Dulong Valley, in southeastern Tibet, China. As expected, phylogenetic diversity was well correlated with species richness among the elevational bands and among communities. At the community level, evergreen broad-leaved forests had the highest levels of species richness and phylogenetic diversity. Using null model analyses, we found evidence of nonrandom phylogenetic structure across the region. Evergreen broad-leaved forests were phylogenetically overdispersed, whereas other vegetation types tended to be phylogenetically clustered. We suggest that communities with high species richness or overdispersed phylogenetic structure should be a focus for biodiversity conservation within the Dulong Valley because these areas may help maximize the potential of this flora to respond to future global change. In biodiversity hotspots worldwide, we suggest that the phylogenetic structure of a community may serve as a useful measure of phylogenetic diversity in the context of conservation planning.

Extensive glycan microarray and structural analyses reveal that human intelectin-1 interacts selectively with microbial glycan epitopes through recognition of a terminal 1,2-diol group, an interaction that would be blocked in human glycans such as α-Neu5Ac. The glycans displayed on mammalian cells can differ markedly from those on microbes. Such differences could, in principle, be 'read' by carbohydrate-binding proteins, or lectins. We used glycan microarrays to show that human intelectin-1 (hIntL-1) does not bind known human glycan epitopes but does interact with multiple glycan epitopes found exclusively on microbes: β-linked D-galactofuranose (β-Galf), D-phosphoglycerol–modified glycans, heptoses, D-glycero- D-talo-oct-2-ulosonic acid (KO) and 3-deoxy-D- manno-oct-2-ulosonic acid (KDO). The 1.6-A-resolution crystal structure of hIntL-1 complexed with β-Galf revealed that hIntL-1 uses a bound calcium ion to coordinate terminal exocyclic 1,2-diols. N-acetylneuraminic acid (Neu5Ac), a sialic acid widespread in human glycans, has an exocyclic 1,2-diol but does not bind hIntL-1, probably owing to unfavorable steric and electronic effects. hIntL-1 marks only Streptococcus pneumoniae serotypes that display surface glycans with terminal 1,2-diol groups. This ligand selectivity suggests that hIntL-1 functions in microbial surveillance.

AimDespite several recent efforts to map plant traits and to identify their climatic drivers, there are still major gaps. Global trait patterns for major functional groups, in particular, the differences between woody and herbaceous plants, have yet to be identified. Here, we take advantage of big data efforts to compile plant species occurrence and trait data to analyse the spatial patterns of assemblage means and variances of key plant traits. We tested whether these patterns and their climatic drivers are similar for woody and herbaceous plants. LocationNew World (North and South America). MethodsUsing the largest currently available database of plant occurrences, we provide maps of 200 × 200 km grid‐cell trait means and variances for both woody and herbaceous species and identify environmental drivers related to these patterns. We focus on six plant traits: maximum plant height, specific leaf area, seed mass, wood density, leaf nitrogen concentration and leaf phosphorus concentration. ResultsFor woody assemblages, we found a strong climate signal for both means and variances of most of the studied traits, consistent with strong environmental filtering. In contrast, for herbaceous assemblages, spatial patterns of trait means and variances were more variable, the climate signal on trait means was often different and weaker. Main conclusionTrait variations for woody versus herbaceous assemblages appear to reflect alternative strategies and differing environmental constraints. Given that most large‐scale trait studies are based on woody species, the strikingly different biogeographic patterns of herbaceous traits suggest that a more synthetic framework is needed that addresses how suites of traits within and across broad functional groups respond to climate.

1. There is an urgent need for large-scale botanical data to improve our understanding of community assembly, coexistence, biogeography, evolution, and many other fundamental biological processes. Understanding these processes is critical for predicting and handling human-biodiversity interactions and global change dynamics such as food and energy security, ecosystem services, climate change, and species invasions.2. The Botanical Information and Ecology Network (BIEN) database comprises an unprecedented wealth of cleaned and standardised botanical data, containing roughly 81 million occurrence records from c. 375,000 species, c. 915,000 trait observations across 28 traits from c. 93,000 species, and co-occurrence records from 110,000 ecological plots globally, as well as 100,000 range maps and 100 replicated phylogenies (each containing 81,274 species) for New World species. Here, we describe an R package that provides easy access to these data.3. The BIEN R package allows users to access the multiple types of data in the BIEN database. Functions in this package query the BIEN database by turning user inputs into optimised PostgreSQL functions. Function names follow a convention designed to make it easy to understand what each function does. We have also developed a protocol for providing customised citations and herbarium acknowledgements for data downloaded through the BIEN R package.4. The development of the BIEN database represents a significant achievement in biological data integration, cleaning and standardization. Likewise, the BIEN R package represents an important tool for open science that makes the BIEN database freely and easily accessible to everyone.

International audience; The concept of the biome has a long history dating back to Carl Ludwig Willdenow and Alexander von Humboldt. However, while the association between climate and the structure and diversity of vegetation has a long history, scientists have only recently begun to develop a more synthetic understanding of biomes based on the evolution of plant diversity, function, and community assembly. At the broadest scales, climate filters species based on their functional attributes, and the resulting functional differences in dominant vegetation among biomes are important to modeling the global carbon cycle and the functioning of the Earth system. Nevertheless, across biomes, plant species have been shown to occupy a common set of global functional “spectra”, reflecting variation in overall plant size, leaf economics, and hydraulics. Still, comprehensive measures of functional diversity and assessments of functional similarity have not been compared across biomes at continental to global scales. Here, we examine distributions of functional diversity of plant species across the biomes of North and South America, based on distributional information for > 80,000 vascular plant species and functional trait data for ca. 8,000 of those species. First, we show that despite progress in data integration and synthesis, significant knowledge shortfalls persist that limit our ability to quantify the functional biodiversity of biomes. Second, our analyses of the available data show that all the biomes in North and South America share a common pattern–most geographically common, widespread species in any biome tend to be functionally similar whereas the most functionally distinctive species are restricted in their distribution. Third, when only the widespread and functionally similar species in each biome are considered, biomes can be more readily distinguished functionally, and patterns of dissimilarity between biomes appear to reflect a correspondence between climate and functional niche space. Taken together, our results suggest that while the study of the functional diversity of biomes is still in its formative stages, further development of the field will yield insights linking evolution, biogeography, community assembly, and ecosystem function.

International audience; Abiotic constraints and biotic interactions act simultaneously to shape communities. However, these community assembly mechanisms are often studied independently, which can limit understanding of how they interact to affect species dynamics and distributions. We develop a hierarchical Bayesian neighborhood modeling approach to quantify the simultaneous effects of topography and crowding by neighbors on the growth of 124,704 individual stems 1cm DBH for 1,047 tropical tree species in a 25-ha mapped rainforest plot in Amazonian Ecuador. We build multi-level regression models to evaluate how four key functional traits (specific leaf area, maximum tree size, wood specific gravity and seed mass) mediate tree growth response to topography and neighborhood crowding. Tree growth is faster in valleys than on ridges and is reduced by neighborhood crowding. Topography and crowding interact to influence tree growth in similar to 10% of the species. Specific leaf area, maximum tree size and seed mass are associated with growth responses to topography, but not with responses to neighborhood crowding or with the interaction between topography and crowding. In sum, our study reveals that topography and neighborhood crowding each influence tree growth in tropical forests, but act largely independently in shaping species distributions. While traits were associated with species response to topography, their role in species response to neighborhood crowding was less clear, which suggests that trait effects on neighborhood dynamics may depend on the direction (negative/positive) and degree of symmetry of biotic interactions. Our study emphasizes the importance of simultaneously assessing the individual and interactive role of multiple mechanisms in shaping species dynamics in high diversity tropical systems.

International audience

17 páginas.-- 9 figuras.-- 55 referencias.-- Additional supporting information may be found online at: http://onlinelibrary.wiley.com/doi/10.1002/ecm.1263/full486 SERGUEI SAAVEDRA ET AL. Ecological Monographs Vol. 87, No. 3 .-- "Copyright by the Ecological Society of America", Although observations of species-rich communities have long served as a primary motivation for research on the coexistence of competitors, the majority of our empirical and theoretical understanding comes from two-species systems. How much of the coexistence observed in species-rich communities results from indirect effects among competitors that only emerge in diverse systems remains poorly understood. Resolving this issue requires simple, scalable, and intuitive metrics for quantifying the conditions for coexistence in multispecies systems, and how these conditions differ from those expected based solely on pairwise interactions. To achieve these aims, we develop a structural approach for studying the set of parameter values compatible with n-species coexistence given the geometric constraints imposed by the matrix of competition coefficients. We derive novel mathematical metrics analogous to stabilizing niche differences and fitness differences that measure the range of conditions compatible with multispecies coexistence, incorporating the effects of indirect interactions emerging in diverse systems. We show how our measures can be used to quantify the extent to which the conditions for coexistence in multispecies systems differ from those that allow pairwise coexistence, and apply the method to a field system of annual plants. We conclude by presenting new challenges and empirical opportunities emerging from our structural metrics of multispecies coexistence., We thank the Plant Ecology Group at ETH Zurich for stimulating discussions that improved this manuscript, and Jacob Usinowicz for valuable comments on the paper. Funding was provided by the 2016 MIT Research Committee Funds (S. Saavedra), the European Research Council through an Advanced Grant (J. Bascompte), NSF 1644641 (N. J. B. Kraft and J. M. Levine), ETH Zurich (J. M. Levine), and postdoctoral financial support provided by the Spanish Ministry of Economy and Competitiveness JCI-2012-12061 (O. Godoy). The authors declare no competing financial interests. S. Saavedra and R. P. Rohr performed the study and contributed equally to the work. S Saavedra, R. P. Rohr, J. Bascompte, and J. M. Levine contributed to the design of the study; O. Godoy, N. J. B. Kraft, and J. M. Levine provided the empirical data; S. Saavedra, R. P. Rohr, and J. M. Levine wrote the first draft of the manuscript; all authors contributed to revisions.

8 páginas.-- 2 figuras.-- 41 referencias.-- 3 Additional supporting information may be found in the online version of this article at http://onlinelibrary.wiley.com/doi/10.1002/ecy.1782/suppinfo, Intransitive competition is often projected to be a widespread mechanism of species coexistence in ecological communities. However, it is unknown how much of the coexistence we observe in nature results from this mechanism when species interactions are also stabilized by pairwise niche differences. We combined field-parameterized models of competition among 18 annual plant species with tools from network theory to quantify the prevalence of intransitive competitive relationships. We then analyzed the predicted outcome of competitive interactions with and without pairwise niche differences. Intransitive competition was found for just 15–19% of the 816 possible triplets, and this mechanism was never sufficient to stabilize the coexistence of the triplet when the pair-wise niche differences between competitors were removed. Of the transitive and intransitive triplets, only four were predicted to coexist and these were more similar in multidimensional trait space defined by 11 functional traits than non-coexisting triplets. Our results argue that intransitive competition may be less frequent than recently posed, and that even when it does operate, pairwise niche differences may be key to possible coexistence., Postdoctoral financial support provided by the Spanish Ministry for Education and Science (Juan de la Cierva, JCI- 2012- 12061). D. B. Stouffer acknowledges support from the Royal Society of New Zealand (via Marsden Fast- Start UOC- 1101 and a Rutherford Discovery Fellowship). N. J. B. Kraft and J. M. Levine were supported by NSF DEB 1644641

8 páginas.-- 2 figuras.-- 45 referencias.-- Data accessibility The list of all papers reviewed here is included in the supplementary material and Appendix S1. Literature review details., Especial Feature COMMUNITY PHYLOGENETICS AND ECOSYSTEM FUNCTIONING, Summary One of the most pervasive concepts in the study of community assembly is the metaphor of the environmental filter, which refers to abiotic factors that prevent the establishment or persistence of species in a particular location. The metaphor has its origins in the study of community change during succession and in plant community dynamics, although it has gained considerable attention recently as part of a surge of interest in functional trait and phylogenetic-based approaches to the study of communities. While the filtering metaphor has clear utility in some circumstances, it has been challenging to reconcile the environmental filtering concept with recent developments in ecological theory related to species coexistence. These advances suggest that the evidence used in many studies to assess environmental filtering is insufficient to distinguish filtering from the outcome of biotic interactions. We re-examine the environmental filtering metaphor from the perspective of coexistence theory. In an effort to move the discussion forward, we present a simple framework for considering the role of the environment in shaping community membership, review the literature to document the evidence typically used in environmental filtering studies and highlight research challenges to address in coming years. The current usage of the environmental filtering term in empirical studies likely overstates the role abiotic tolerances play in shaping community structure. We recommend that the term `environmental filtering¿ only be used to refer to cases where the abiotic environment prevents establishment or persistence in the absence of biotic interactions, although only 15% of the studies in our review presented such evidence. Finally, we urge community ecologists to consider additional mechanisms aside from environmental filtering by which the abiotic environment can shape community pattern.

A central current debate in community ecology concerns the relative importance of deterministic versus stochastic processes underlying community structure. However, the concept of stochasticity presents several profound philosophical, theoretical and empirical challenges, which we address here. The philosophical argument that nothing in nature is truly stochastic can be met with the following operational concept of neutral stochasticity in community ecology: change in the composition of a community (i.e. community dynamics) is neutrally stochastic to the degree that individual demographic events – birth, death, immigration, emigration – which cause such changes occur at random with respect to species identities. Empirical methods for identifying the stochastic component of community dynamics or structure include null models and multivariate statistics on observational species-by-site data (with or without environmental or trait data), and experimental manipulations of ‘stochastic’ species colonization order or relative densities and frequencies of competing species. We identify the fundamental limitations of each method with respect to its ability to allow inferences about stochastic community processes. Critical future needs include greater precision in articulating the link between results and ecological inferences, a comprehensive theoretical assessment of the interpretation of statistical analyses of observational data, and experiments focusing on community size and on natural variation in species colonization order. Synthesis Community structure and dynamics have often been described as being underlain by ‘stochastic’ or ‘neutral’ processes, but there is great confusion as to what exactly this means. We attempt to provide conceptual clarity by specifying precisely what focal ecological variable (e.g. species distributions, community composition, demography) is considered to be stochastic with respect to what other variables (e.g. other species' distributions, traits, environment) when using different empirical methods. We clarify what inferences can be drawn by different observational and experimental approaches, and we suggest future avenues of research to better understand the role of neutral stochasticity in community ecology.

Functional trait-based approaches have seen rapid development in community ecology and biogeography in recent years, as they promise to offer a better mechanistic and predictive understanding of community structure. However, several key challenges remain. First, while many studies have explored connections between functional traits and abiotic gradients, far fewer have directly tested the common assumption that functional trait differences influence interspecific interactions. Second, empirical studies often ignore intraspecific trait variation within communities, even though intraspecific variation has been known to have substantial impacts on community dynamics. Here we present an experiment designed to assess the role of functional trait differences in predicting the outcome of interspecific species interactions among a suite of California vernal pool annual plants. Eight species were grown in pairwise combinations in two levels of inundation in a greenhouse and functional traits were measured on all individuals. Nested models predicting focal plant performance were fit to the data. For seven of the eight species in the experiment, the best model included a functional trait difference term that was consistent with a competitive hierarchy, indicating that focal species tended to do better when they had larger leaf size, lower specific leaf area, and greater investment in lateral canopy spread than their neighbors. Models that included individually measured trait values generally performed better than models using species trait averages. We tested if the same trait measurements predicted tolerance of inundation (a feature of vernal pool habitats), and species depth distributions from extensive field surveys, though we did not find strong relationships. Our results suggest that functional traits can be used to make inferences about the outcome of interspecific interactions, and that greater predictive power can come from considering intraspecific variation in functional traits, particularly in low diversity communities.

Recent hypotheses argue that phylogenetic relatedness should predict both the niche differences that stabilise coexistence and the average fitness differences that drive competitive dominance. These still largely untested predictions complicate Darwin's hypothesis that more closely related species less easily coexist, and challenge the use of community phylogenetic patterns to infer competition. We field parameterised models of competitor dynamics with pairs of 18 California annual plant species, and then related species' niche and fitness differences to their phylogenetic distance. Stabilising niche differences were unrelated to phylogenetic distance, while species' average fitness showed phylogenetic structure. This meant that more distant relatives had greater competitive asymmetry, which should favour the coexistence of close relatives. Nonetheless, coexistence proved unrelated to phylogeny, due in part to increasing variance in fitness differences with phylogenetic distance, a previously overlooked property of such relationships. Together, these findings question the expectation that distant relatives should more readily coexist.

Summary 1. A key issue in plant/herbivore interaction research is to understand which plant traits drive differ- ences in herbivore damage. Variation in chemical, physical or phenological traits of plants may all modulate the degree of herbivore damage among species and individuals, yet the relative importance of these factors is still subject to debate, particularly in species-rich systems such as tropical rain forests. 2. To address this issue, we quantified leaf herbivore damage in 28 common tree species of the Yasun! i forest dynamic plot (YFDP) in the Ecuadorian Amazon over 11 months. Census data from the YFDP allowed us to quantify several aspects of tree ecology potentially affecting herbivory including leaf turnover and spatial distribution patterns. We measured six chemical, eight physical and four ecological traits of the focal species. Using a combination of multivariate analyses and phy- logenetic generalized linear regression model (PGLS), we assessed trade-offs between physical and chemical traits and the relative effect of all these traits on leaf herbivore damage. 3. Herbivore damage was highly variable among species and individuals, with leaves on average displaying damage over 13.4% (2.5-29.5%) of their area. We found no significant trade-off between physical and chemical defences for the 28 studied tree species. Overall, leaf size, shearing resistance, cellulose, ash content and leaf size 9 ash were the best predictors of herbivore damage. Surpris- ingly, condensed tannins and latex did not significantly correlate with herbivore damage. In addition, we found no relationships between herbivory and local tree density. However, we did find a weak effect of tree clustering and strong effect of tree leaf turnover rates on herbivore damage. 4. Synthesis. In the western Amazon, leaves are defended against herbivores through a combination of physical (toughness), chemical (toughness-related elements), and phenological (rapid leaf replace- ment) characteristics that do not appear to be subject to obvious trade-offs. Conventional strategies, such as condensed tannins or latex, do not seem to be strongly involved as a defence against herbi- vores in this community.

Phenotypic traits mediate organisms' interactions with the environment and determine how they affect and are affected by their biotic and abiotic milieu. Thus, dispersion of trait values, or functional diversity (FD) of a community can offer insights into processes driving community assembly. For example, underdispersion of FD suggests that habitat "filtering" of species with unfavorable trait values restricts the species that can exist in a particular habitat, while even spacing of FD suggests that interspecific competition, or biotic "sorting," discourages the coexistence of species with similar trait values. Since assembly processes are expected to vary as a function of spatial scale, we should also expect patterns of FD to reflect scale dependence in filtering and biotic sorting. Here we present the concept of the functional-diversity-area relationship (FAR), which is similar to the species-area relationship but plots a measure of phenotypic trait diversity as a function of spatial scale. We develop a set of null model tests that discriminate between FARs generated predominantly by filtering or biotic sorting and indicate the scales at which these effects are pronounced. The utility of the FAR for addressing long-standing issues in ecology is illustrated with several examples. A multi-scale examination of FD and its pattern relative to null expectations provides an important tool for ecologists interested in understanding the scale dependence of community assembly processes.

Recent theory predicts that stochastic dilution effects may result in species-rich communities with statistically independent species spatial distributions, even if the underlying ecological processes structuring the community are driven by deterministic niche differences. Stochastic dilution is a consequence of the stochastic geometry of biodiversity where the identities of the nearest neighbors of individuals of a given species are largely unpredictable. Under such circumstances, the outcome of deterministic species interactions may vary greatly among individuals of a given species. Consequently, nonrandom patterns in the biotic neighborhoods of species, which might be expected from coexistence or community assembly theory (e.g., individuals of a given species are neighbored by phylogenetically similar species), are weakened or do not emerge, resulting in statistical independence of species spatial distributions. We used data on phylogenetic and functional similarity of tree species in five large forest dynamics plots located across a gradient of species richness to test predictions of the stochastic dilution hypothesis. To quantify the biotic neighborhood of a focal species we used the mean phylogenetic (or functional) dissimilarity of the individuals of the focal species to all species within a local neighborhood. We then compared the biotic neighborhood of species to predictions from stochastic null models to test if a focal species was surrounded by more or less similar species than expected by chance. The proportions of focal species that showed spatial independence with respect to their biotic neighborhoods increased with total species richness. Locally dominant, high-abundance species were more likely to be surrounded by species that were statistically more similar or more dissimilar than expected by chance. Our results suggest that stochasticity may play a stronger role in shaping the spatial structure of species rich tropical forest communities than it does in species poorer forests. These findings represent an important step towards understanding the factors that govern the spatial configuration of local biotic communities. The stochastic dilution effect is a simple geometric mechanism that can explain why species' spatial distributions in species-rich communities approximate independence from their biotic neighborhood, even if deterministic niche processes are in effect.

Aim A long-standing challenge in ecology is to identify the suite of factors that lead to turnover in species composition in both space and time.These factors might be stochastic (e.g. sampling and priority effects) or deterministic (e.g. competition and environmental filtering).While numerous studies have examined the relationship between turnover and individual drivers of interest (e.g.primary productivity, habitat heterogeneity,or regional ‐‘gamma’‐ diversity),few studies have disentangled the simultaneous influences of multiple stochastic and deterministic processes on both temporal and spatial turnover. If turnover is governed primarily by stochastic sampling processes, removing the sampling effects of gamma diversity should result in non-significant relationships between turnover and environmental variables.Conversely,if deterministicprocessesgovernturnoverpatterns,removing sampling effects will have little influence on turnover gradients. Here, we test these predictions. Location The United States. Methods Continental-scale,multidecadal data were used to quantify spatial and temporal turnover in avian community composition within 295 survey routes. A series of regression and structural equation models were coupled with a null model to construct statistical models describing turnover patterns. Results Examining explanatory variables alone or in combination showed that spatial and temporal turnover increased together, decreased with primary productivity and increased with habitat heterogeneity.The relationships between turnover and all variables became weaker when sampling effects were removed,but relationships with primary productivity and habitat heterogeneity remained relatively strong. In addition, spatial turnover increased strongly with spatial gamma diversity after sampling effects were removed.

Intraguild predation—competition and predation by the same antagonist—is widespread, but its evolutionary consequences are unknown. Intraguild prey may evolve antipredator defenses, superior competitive ability on shared resources, or the ability to use an alternative resource, any of which may alter the structure of the food web. We tested for evolutionary responses by threespine stickleback to a benthic intraguild predator, prickly sculpin. We used a comparative morphometric analysis to show that stickleback sympatric with sculpin are more armored and have more limnetic-like body shapes than allopatric stickleback. To test the ecological implications of this shift, we conducted a mesocosm experiment that varied sculpin presence and stickleback population of origin (from one sympatric and one allopatric lake). Predation by sculpin greatly increased the mortality of allopatric stickleback. In contrast, sculpin presence did not affect the mortality of sympatric stickleback, although they did have lower growth rates suggesting increased nonpredatory effects of sculpin. Consistent with their morphology, sympatric stickleback included more pelagic prey in their diets, leading to depletion of zooplankton in the mesocosms. These findings suggest that intraguild prey evolution has altered food web structure by reducing both predation by the intraguild predator and diet overlap between species

The tendency for more closely related species to share similar traits and ecological strategies can be explained by their longer shared evolutionary histories and represents phylogenetic conservatism. How strongly species traits co-vary with phylogeny can significantly impact how we analyze cross-species data and can influence our interpretation of assembly rules in the rapidly expanding field of community phylogenetics. Phylogenetic conservatism is typically quantified by analyzing the distribution of species values on the phylogenetic tree that connects them. Many phylogenetic approaches, however, assume a completely sampled phylogeny: while we have good estimates of deeper phylogenetic relationships for many species-rich groups, such as birds and flowering plants, we often lack information on more recent interspecific relationships (i.e., within a genus). A common solution has been to represent these relationships as polytomies on trees using taxonomy as a guide. Here we show that such trees can dramatically inflate estimates of phylogenetic conservatism quantified using S. P. Blomberg et al.'s K statistic. Using simulations, we show that even randomly generated traits can appear to be phylogenetically conserved on poorly resolved trees. We provide a simple rarefaction-based solution that can reliably retrieve unbiased estimates of K, and we illustrate our method using data on first flowering times from Thoreau's woods (Concord, Massachusetts, USA).

Aim In recent years evidence has accumulated that plant species are differentially sorted from regional assemblages into local assemblages along local-scale environmental gradients on the basis of their function and abiotic filtering. The favourability hypothesis in biogeography proposes that in climatically difficult regions abiotic filtering should produce a regional assemblage that is less functionally diverse than that expected given the species richness and the global pool of traits. Thus it seems likely that differential filtering of plant traits along local-scale gradients may scale up to explain the distribution, diversity and filtering of plant traits in regional-scale assemblages across continents. The present work aims to address this prediction.

Phorbol 12-myristate 13-acetate (PMA) and bryostatin 1 are both potent protein kinase C (PKC) activators. In LNCaP human prostate cancer cells, PMA induces tumor necrosis factor alpha (TNFα) secretion and inhibits proliferation; bryostatin 1 does not, and indeed blocks the response to PMA. This difference has been attributed to bryostatin 1 not localizing PKCδ to the plasma membrane. Since phorbol ester lipophilicity influences PKCδ localization, we have examined in LNCaP cells a series of phorbol esters and related derivatives spanning some eight logs in lipophilicity (logP) to see if any behave like bryostatin 1. The compounds showed marked differences in their effects on proliferation and TNFα secretion. For example, maximal responses for TNFα secretion relative to PMA ranged from 97 % for octyl-indolactam V to 24 % for phorbol 12,13-dibenzoate. Dose-response curves ranged from monophasic for indolactam V to markedly biphasic for sapintoxin D. The divergent patterns of response, however, correlated neither to lipophilicity, to plasma membrane translocation of PKCδ, nor to the ability to interact with model membranes. In U937 human leukemia cells, a second system in which PMA and bryostatin 1 have divergent effects, viz. PMA but not bryostatin 1 inhibits proliferation and induces attachment, all the compounds acted like PMA for proliferation, but several induced a reduced level or a biphasic dose-response curve for attachment. We conclude that active phorbol esters are not all equivalent. Depending on the system, some might partially resemble bryostatin 1 in their behavior; this encourages the concept that bryostatin-like behavior may be obtained from other structural templates.

A recent increase in studies of β diversity has yielded a confusing array of concepts, measures and methods. Here, we provide a roadmap of the most widely used and ecologically relevant approaches for analysis through a series of mission statements. We distinguish two types of β diversity: directional turnover along a gradient vs. non-directional variation. Different measures emphasize different properties of ecological data. Such properties include the degree of emphasis on presence/absence vs. relative abundance information and the inclusion vs. exclusion of joint absences. Judicious use of multiple measures in concert can uncover the underlying nature of patterns in β diversity for a given dataset. A case study of Indonesian coral assemblages shows the utility of a multi-faceted approach. We advocate careful consideration of relevant questions, matched by appropriate analyses. The rigorous application of null models will also help to reveal potential processes driving observed patterns in β diversity.

Summary • Patterns of precipitation are likely to change significantly in the coming century, with important but poorly understood consequences for plant communities. Experimental and correlative studies may provide insight into expected changes, but little research has addressed the degree of concordance between these approaches. • We synthesized results from four experimental water addition studies with a correlative analysis of community changes across a large natural precipitation gradient in the United States. We investigated whether community composition, summarized with plant functional traits, responded similarly to increasing precipitation among studies and sites. • In field experiments, increased precipitation favored species with small seed size, short leaf life span and high leaf nitrogen (N) concentration. However, with increasing precipitation along the natural gradient, community composition shifted towards species with higher mean seed mass, longer leaf life span and lower leaf N concentrations. • The differences in temporal and spatial scale of experimental manipulations and natural gradients may explain these contrasting results. Our results highlight the complexity of responses to climate change, and suggest that transient dynamics may not reflect long-term shifts in functional diversity and community composition. We propose a model of community change that incorporates these differences between short- and long-term responses to climate change.

Aim Sustaining biological diversity requires the protection of the ecological, evolutionary and landscape-level processes that generate it. Here, we identify areas of high neoendemism in a global diversity hotspot, the California flora, using range size data and molecular-based estimates of taxon age. Location California, USA. Methods We compiled distribution and range size data for all plant taxa endemic to California and internal transcribed spacer (ITS)-based age estimates for 337 putative neoendemics (15% of the endemic flora). This information was combined to identify areas in the state with high proportions of young and restricted-range taxa. We overlaid the distribution of neoendemic hotspots on maps of currently protected lands and also explored correlations between our diversity measures and climate. Results The central coast of California, the Sierra Nevada and the San Bernardino Range contained endemics with the most restricted distributions on average, while areas in the Desert and Great Basin provinces found within the state were composed of the youngest neoendemics on average. Diversity measures that took age and range size into account shifted the estimate of highest endemic diversity in the state towards the Desert and Great Basin regions relative to simple counts of endemic species richness. Our diversity measures were poorly correlated with climate and topographic heterogeneity. Main conclusions Substantial portions of California with high levels of plant neoendemism fall outside of protected lands, indicating that additional action will be needed to preserve the geographic areas apparently associated with high rates of plant diversification. The neoendemic flora of the deserts appears particularly young in our analyses, which may reflect the relatively recent origin of desert environments within the state.

Background Antidepressant response is likely influenced by genetic constitution, but the actual genes involved have yet to be determined. We have carried out a genomewide association study to determine whether common DNA variation influences antidepressant response. Methods Our sample is derived from Level 1 participants in the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study, all treated with citalopram. Association for the response phenotype included 883 responders and 608 nonresponders. For the remission phenotype, 743 subjects that achieved remission were compared with 608 nonresponders. We used a subset of single nucleotide polymorphisms (SNPs; n = 430,198) from the Affymetrix 500K and 5.0 Human SNP Arrays, and association analysis was carried out after correcting for population stratification. Results We identified three SNPs associated with response with p values less than 1 × 10 −5 near the UBE3C gene (rs6966038, p = 4.65 × 10 −7 ), another 100 kb away from BMP7 (rs6127921, p = 3.45 × 10 −6 ), and a third that is intronic in the RORA gene (rs809736, p = 8.19 × 10 −6 ). These same SNPs were also associated with remission. Thirty-nine additional SNPs are of interest with p values ≤ .0001 for the response and remission phenotypes. Conclusions Although the findings reported here do not meet a genomewide threshold for significance, the regions identified from this study provide targets for independent replication and novel pathways to investigate mechanisms of antidepressant response. This study was not placebo controlled, making it possible that we are also observing associations to nonspecific aspects of drug treatment of depression.

During the Late Pleistocene and early Holocene 59 species of South American megafauna went extinct. Their extinction potentially triggered population declines of large-seeded tree species dispersed by the large-bodied frugivores with which they co-evolved, a theory first proposed by Janzen and Martin (1982). We tested this hypothesis using species range maps for 257 South American tree species, comparing 63 species thought to be primarily distributed by megafauna with 194 distributed by other animals. We found a highly significant (p 95% following disperser extinction. A numerical gap dynamic simulations suggests that over a 10 000 yr period following the disperser extinctions, the average convex hull range size of large-seeded tree species decreased by ∼ 31%, while the estimated decrease in population size was ∼ 54%, indicating a likely greater decrease in species population size than indicated by the empirical range patterns. Finally, we found a positive correlation between seed size and wood density of animal-dispersed tree species implying that the Late Pleistocene and early Holocene megafaunal extinctions reduced carbon content in the Amazon by ∼ 1.5 ± 0.7%. In conclusion, we 1) provide some empirical evidence that megafauna distributed fruit species have a smaller mean range size than wind, water or other animal-dispersed species, 2) demonstrate mathematically that such range reductions are expected from megafauna extinctions ca 12 000 yr ago, and 3) illustrate that these extinctions may have reduced the Amazon's carbon storage capacity.

Summary Advances in both informatics and mobile technology are providing exciting new opportunities for generating, disseminating, and engaging with information in the biological sciences at unprecedented spatial scales, particularly in disentangling information on the distributions and natural history of hyperdiverse groups of organisms. We describe an application serving as a mobile catalog of all of the plants of the Americas developed using species distribution models estimated from field observations of plant occurrences. The underlying data comprise over 3·5 million standardized observations of over 88 000 plant species. Plant-O-Matic, a free iOS application, combines the species distribution models with the location services built into a mobile device to provide users with a list of all plant species expected to occur in the 100 × 100 km geographic grid cell corresponding to the user's location. The application also provides ancillary information on species’ attributes (when available) including growth form, reproductive mode, flower color, and common name. Results can be searched and conditionally filtered based on these attributes. Links to externally sourced specimen images further aid in identification of species by the user. The application's ability to assemble locally relevant lists of plant species and their attributes on demand for anywhere in the Americas provides a powerful new tool for identifying, exploring, and understanding plant diversity. Mobile applications such as Plant-O-Matic can facilitate dynamic new approaches to science, conservation, and science education.

One of the key hypothesized drivers of gradients in species richness is environmental filtering, where environmental stress limits which species from a larger species pool gain membership in a local community owing to their traits. Whereas most studies focus on small-scale variation in functional traits along environmental gradient, the effect of large-scale environmental filtering is less well understood. Furthermore, it has been rarely tested whether the factors that constrain the niche space limit the total number of coexisting species. We assessed the role of environmental filtering in shaping tree assemblages across North America north of Mexico by testing the hypothesis that colder, drier, or seasonal environments (stressful conditions for most plants) constrain tree trait diversity and thereby limit species richness. We assessed geographic patterns in trait filtering and their relationships to species richness pattern using a comprehensive set of tree range maps. We focused on four key plant functional traits reflecting major life history axes (maximum height, specific leaf area, seed mass, and wood density) and four climatic variables (annual mean and seasonality of temperature and precipitation). We tested for significant spatial shifts in trait means and variances using a null model approach. While we found significant shifts in mean species' trait values at most grid cells, trait variances at most grid cells did not deviate from the null expectation. Measures of environmental harshness (cold, dry, seasonal climates) and lower species richness were weakly associated with a reduction in variance of seed mass and specific leaf area. The pattern in variance of height and wood density was, however, opposite. These findings do not support the hypothesis that more stressful conditions universally limit species and trait diversity in North America. Environmental filtering does, however, structure assemblage composition, by selecting for certain optimum trait values under a given set of conditions.

Traditional attempts to delineate floristic regions typically focus on species distributions, often ignoring the rich context that phylogenetic relationships can provide. In this study, we explore how phylogenetic relatedness, taxonomic composition and regional phylogenetic structure change across a global biodiversity hotspot region, Yunnan, located in southwestern China. We propose a system of floristic regions within Yunnan by combining data on the distributions and phylogenetic relationships of 1,983 genera of native seed plants. We identified eight distinct floristic regions in Yunnan, which were grouped into two larger northern and southern geographical units. Phylogenetic relatedness was well correlated with taxonomic composition between floras in Yunnan. Across the Yunnan region we examined, the central Yunnan region shows the lowest level of spatial turnover in phylogenetic relationships and taxonomic composition of the floristic assemblages. Using null model analyses, we found evidence of nonrandom phylogenetic structure across the region, in which four areas show higher phylogenetic turnover than expected given the underlying taxonomic composition between sites. Our results show that the integration of phylogenetic information can provide valuable insight in floristic assessments and help us to better understand the structure of a global biodiversity hotspot.

We present a framework to measure the strength of environmental filtering and disequilibrium of the species composition of a local community across time, relative to past, current, and future climates. We demonstrate the framework by measuring the impact of climate change on New World forests, integrating data for climate niches of more than 14 000 species, community composition of 471 New World forest plots, and observed climate across the most recent glacial–interglacial interval. We show that a majority of communities have species compositions that are strongly filtered and are more in equilibrium with current climate than random samples from the regional pool. Variation in the level of current community disequilibrium can be predicted from Last Glacial Maximum climate and will increase with near-future climate change.

6 páginas, 3 figuras.-- 3 tablas.-- 41 referencias.-- This article contains supporting information online at http://www.pnas.org/lookup/suppl/doi:10.1073/pnas.1413650112/-/DCSupplemental, Understanding the processes maintaining species diversity is a central problem in ecology, with implications for the conservation and management of ecosystems. Although biologists often assume that trait differences between competitors promote diversity, empirical evidence connecting functional traits to the niche differences that stabilize species coexistence is rare. Obtaining such evidence is critical because traits also underlie the average fitness differences driving competitive exclusion, and this complicates efforts to infer community dynamics from phenotypic patterns. We coupled fieldparameterized mathematical models of competition between 102 pairs of annual plants with detailed sampling of leaf, seed, root, and whole-plant functional traits to relate phenotypic differences to stabilizing niche and average fitness differences. Single functional traits were often well correlated with average fitness differences between species, indicating that competitive dominance was associated with late phenology, deep rooting, and several other traits. In contrast, single functional traits were poorly correlated with the stabilizing niche differences that promote coexistence. Niche differences could only be described by combinations of traits, corresponding to differentiation between species in multiple ecological dimensions. In addition, several traits were associated with both fitness differences and stabilizing niche differences. These complex relationships between phenotypic differences and the dynamics of competing species argue against the simple use of single functional traits to infer community assembly processes but lay the groundwork for a theoretically justified trait-based community ecology., Lindsey Rice provided field assistance in all stages of the project. We thank Janneke HilleRisLambers and Marti Anderson for discussion and statistical advice and Peter Adler, Mark Vellend, and members of the J.M.L. and N.J.B.K. laboratories for comments. Peter Chesson helped us derive the stabilizing niche difference and average fitness difference in our annual plant model. The D’Antonio laboratory at University of California, Santa Barbara and the Dawson laboratory at University of California, Berkeley made the nutrient and isotope analyses possible.

Phenological events - defined points in the life cycle of a plant or animal - have been regarded as highly plastic traits, reflecting flexible responses to various environmental cues. The ability of a species to track, via shifts in phenological events, the abiotic environment through time might dictate its vulnerability to future climate change. Understanding the predictors and drivers of phenological change is therefore critical. Here, we evaluated evidence for phylogenetic conservatism - the tendency for closely related species to share similar ecological and biological attributes - in phenological traits across flowering plants. We aggregated published and unpublished data on timing of first flower and first leaf, encompassing ̃4000 species at 23 sites across the Northern Hemisphere. We reconstructed the phylogeny for the set of included species, first, using the software program Phylomatic, and second, from DNA data. We then quantified phylogenetic conservatism in plant phenology within and across sites. We show that more closely related species tend to flower and leaf at similar times. By contrasting mean flowering times within and across sites, however, we illustrate that it is not the time of year that is conserved, but rather the phenological responses to a common set of abiotic cues. Our findings suggest that species cannot be treated as statistically independent when modelling phenological responses. Synthesis. Closely related species tend to resemble each other in the timing of their life-history events, a likely product of evolutionarily conserved responses to environmental cues. The search for the underlying drivers of phenology must therefore account for species' shared evolutionary histories. Closely related species tend to resemble each other in the timing of their life-history events, a likely product of evolutionarily conserved responses to environmental cues. The search for the underlying drivers of phenology must therefore account for species' shared evolutionary histories. © 2013 British Ecological Society.