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We investigated how the phylogenetic structure of Amazonian plant communities varies along an edaphic gradient within the non‐inundated forests. Forty localities were sampled on three terrain types representing two kinds of soil: clayey soils of a high base cation concentration derived from the Solimões formation, and loamy soils with lower base cation concentration derived from the Içá formation and alluvial terraces. Phylogenetic community metrics were calculated for each locality for ferns and palms both with ferns as one group and for each of three fern clades with a crown group age comparable to that of palms. Palm and fern communities showed significant and contrasting phylogenetic signals along the soil gradient. Fern species richness increased but standard effect size of mean pairwise distance (SES.MPD) and variation of pairwise distances (VPD) decreased with increasing soil base cation concentration. In contrast, palm communities were more species rich on less cation‐rich soils and their SES.MPD increased with soil base cation concentration. Species turnover between the communities reflected the soil gradient slightly better when based on species occurrences than when phylogenetic distances between the species were considered. Each of the three fern subclades behaved differently from each other and from the entire fern clade. The fern clade whose phylogenetic patterns were most similar to those of palms also resembled palms in being most species‐rich on cation‐poor soils. The phylogenetic structuring of local plant communities varies along a soil base cation concentration gradient within non‐inundated Amazonian rain forests. Lineages can show either similar or different phylogenetic community structure patterns and evolutionary trajectories, and we suggest this to be linked to their environmental adaptations. Consequently, geological heterogeneity can be expected to translate into a potentially highly diverse set of evolutionarily distinct community assembly pathways in Amazonia and elsewhere., We investigated the phylogenetic structure of Amazonian fern and palm communities on edaphically distinct sites. We show that phylogenetic community structure varies along a soil base cation concentration gradient within non‐inundated Amazonian rain forests. Our results suggest that geological heterogeneity can translate into a potentially highly diverse set of evolutionarily distinct community assembly pathways in Amazonia.

1. Topography affects abiotic conditions which can influence the structure, function and dynamics of ecological communities. An increasing number of studies have demonstrated biological consequences of fine-scale topographic heterogeneity but we have a limited understanding of how these effects depend on the climate context. 2. We merged high-resolution (1 m2) data on topography and canopy height derived from airborne lidar with ground-based data from 15 forest plots in Puerto Rico distributed along a precipitation gradient spanning c. 800?3,500 mm/year. Ground-based data included species composition, estimated above-ground biomass (AGB), and two key functional traits (wood density and leaf mass per area, LMA) that reflect resource-use strategies and a trade-off between hydraulic safety and hydraulic efficiency. We used hierarchical Bayesian models to evaluate how the interaction between topography ? climate is related to metrics of forest structure (i.e. canopy height and AGB), as well as taxonomic and functional alpha- and beta-diversity. 3. Fine-scale topography (characterized with the topographic wetness index, TWI) significantly affected forest structure and the strength (and in some cases direction) of these effects varied across the precipitation gradient. In all plots, canopy height increased with topographic wetness but the effect was much stronger in dry compared to wet forest plots. In dry forest plots, topographically wetter microsites also had higher levels of AGB but in wet forest plots, topographically drier microsites had higher AGB. 4. Fine-scale topography influenced functional composition but had only weak or non-significant effects on taxonomic and functional alpha- and beta-diversity. For instance, community-weighted wood density followed a similar pattern to AGB across plots. We also found a marginally significant association between variation of wood density and topographic heterogeneity that depended on climate context. 5. Synthesis. The effects of fine-scale topographic heterogeneity on tropical forest structure and composition depend on the climate context. Our study demonstrates how a stronger integration of topographic heterogeneity across precipitation gradients could improve estimates of forest structure and biomass, and may provide insight to the ways that topography might mediate species responses to drought and climate change.

Tropical forests are converted at an alarming rate for agricultural use and pastureland, but also regrow naturally through secondary succession. For successful forest restoration, it is essential to understand the mechanisms of secondary succession. These mechanisms may vary across forest types, but analyses across broad spatial scales are lacking. Here, we analyse forest recovery using 1,403 plots that differ in age since agricultural abandonment from 50 sites across the Neotropics. We analyse changes in community composition using species-specific stem wood density (WD), which is a key trait for plant growth, survival and forest carbon storage. In wet forest, succession proceeds from low towards high community WD (acquisitive towards conservative trait values), in line with standard successional theory. However, in dry forest, succession proceeds from high towards low community WD (conservative towards acquisitive trait values), probably because high WD reflects drought tolerance in harsh early successional environments. Dry season intensity drives WD recovery by influencing the start and trajectory of succession, resulting in convergence of the community WD over time as vegetation cover builds up. These ecological insights can be used to improve species selection for reforestation. Reforestation species selected to establish a first protective canopy layer should, among other criteria, ideally have a similar WD to the early successional communities that dominate under the prevailing macroclimatic conditions.

Aim Palms are an iconic, diverse and often abundant component of tropical ecosystems that provide many ecosystem services. Being monocots, tree palms are evolutionarily, morphologically and physiologically distinct from other trees, and these differences have important consequences for ecosystem services (e.g., carbon sequestration and storage) and in terms of responses to climate change. We quantified global patterns of tree palm relative abundance to help improve understanding of tropical forests and reduce uncertainty about these ecosystems under climate change. Location Tropical and subtropical moist forests. Time period Current. Major taxa studied Palms (Arecaceae). Methods We assembled a pantropical dataset of 2,548 forest plots (covering 1,191ha) and quantified tree palm (i.e., ≥10cm diameter at breast height) abundance relative to co‐occurring non‐palm trees. We compared the relative abundance of tree palms across biogeographical realms and tested for associations with palaeoclimate stability, current climate, edaphic conditions and metrics of forest structure. Results On average, the relative abundance of tree palms was more than five times larger between Neotropical locations and other biogeographical realms. Tree palms were absent in most locations outside the Neotropics but present in >80% of Neotropical locations. The relative abundance of tree palms was more strongly associated with local conditions (e.g., higher mean annual precipitation, lower soil fertility, shallower water table and lower plot mean wood density) than metrics of long‐term climate stability. Life‐form diversity also influenced the patterns; palm assemblages outside the Neotropics comprise many non‐tree (e.g., climbing) palms. Finally, we show that tree palms can influence estimates of above‐ground biomass, but the magnitude and direction of the effect require additional work. Conclusions Tree palms are not only quintessentially tropical, but they are also overwhelmingly Neotropical. Future work to understand the contributions of tree palms to biomass estimates and carbon cycling will be particularly crucial in Neotropical forests.

While calls for interdisciplinary research in environmental contexts are common, it often remains a struggle to integrate humanities/qualitative social sciences insights with those of bio-physical approaches. We propose that cross-disciplinary historical perspectives can open new avenues for collaboration among social and natural scientists while expanding visions of possible future environments and management scenarios. We make these arguments through attention to woodlands, which are under pressure from complex socio-ecological stressors that can best be understood from interdisciplinary perspectives. By combining deep ecological and shallower social historical approaches, we show how history can both enrich our understandings of woodland pasts and provide a ground for better combining the case-based insights of humanistic history with those of deep-time ecological history. We conclude that such interdisciplinary historical approaches are important not only for research, but also for management (especially rewilding and scenario-building), as the surprisingly large range of past changes reminds us that future conditions can be more varied than typically acknowledged. This Perspective proposes that cross-disciplinary historical approaches can assist in improving collaborations among social and natural scientists and in expanding environmental management imaginaries. Through the example of woodlands, we illustrate how combining natural science insights on deep-time changes with social science research on histories of commercialization and industrialization can generate better understandings of socio-ecological dynamics. We emphasize that qualitative historical case studies have a place alongside other approaches in broadening visions of woodland futures via attention to pasts.

Predicting drought responses of individual trees in tropical forests remains challenging, in part because trees experience drought differently depending on their position in spatially heterogeneous environments. Specifically, topography and the competitive environment can influence the severity of water stress experienced by individual trees, leading to individual-level variation in drought impacts. A drought in 2015 in Puerto Rico provided the opportunity to assess how drought response varies with topography and neighborhood crowding in a tropical forest. In this study, we integrated 3 years of annual census data from the El Yunque Chronosequence plots with measurements of functional traits and LiDAR-derived metrics of microsite topography. We fit hierarchical Bayesian models to examine how drought, microtopography, and neighborhood crowding influence individual tree growth and survival, and the role functional traits play in mediating species’ responses to these drivers. We found that while growth was lower during the drought year, drought had no effect on survival, suggesting that these forests are fairly resilient to a single-year drought. However, growth response to drought, as well as average growth and survival, varied with topography: tree growth in valley-like microsites was more negatively affected by drought, and survival was lower on steeper slopes while growth was higher in valleys. Neighborhood crowding reduced growth and increased survival, but these effects did not vary between drought/non-drought years. Functional traits provided some insight into mechanisms by which drought and topography affected growth and survival. For example, trees with high specific leaf area grew more slowly on steeper slopes, and high wood density trees were less sensitive to drought. However, the relationships between functional traits and response to drought and topography were weak overall. Species sorting across microtopography may drive observed relationships between average performance, drought response, and topography. Our results suggest that understanding species’ responses to drought requires consideration of the microenvironments in which they grow. Complex interactions between regional climate, topography, and traits underlie individual and species variation in drought response.

Projected increases in cyclonic storm intensity under a warming climate will have profound effects on forests, potentially changing these ecosystems from carbon sinks to sources. Forecasting storm impacts on these ecosystems requires consideration of risk factors associated with storm meteorology, landscape structure, and forest attributes. Here we evaluate risk factors associated with damage severity caused by Hurricanes María and Irma across Puerto Rican forests. Using field and remote sensing data, total forest aboveground biomass (AGB) lost to the storms was estimated at 10.44 (±2.33) Tg, ca. 23% of island-wide pre-hurricane forest AGB. Storm-related rainfall was a stronger predictor of forest damage than maximum wind speeds. Soil water storage capacity was also an important risk factor, corroborating the influence of rainfall on forest damage. Expected increases of 20% in hurricane-associated rainfall in the North Atlantic highlight the need to consider how such shifts, together with high speed winds, will affect terrestrial ecosystems.

BACKGROUND AND AIMS: Identifying the processes that generate and maintain biodiversity requires understanding of how evolutionary processes interact with abiotic conditions to structure communities. Edaphic gradients are strongly associated with floristic patterns but, compared with climatic gradients, have received relatively little attention. We asked (1) How does the phylogenetic composition of palm communities vary along edaphic gradients within major habitat types? and (2) To what extent are phylogenetic patterns determined by (a) habitat specialists, (b) small versus large palms, and (c) hyperdiverse genera? METHODS: We paired data on palm community composition from 501 transects of 0.25 ha located in two main habitat types (non-inundated uplands and seasonally inundated floodplains) in western Amazonian rain forests with information on soil chemistry, climate, phylogeny and metrics of plant size. We focused on exchangeable base concentration (cmol+ kg-1) as a metric of soil fertility and a floristic index of inundation intensity. We used a null model approach to quantify the standard effect size of mean phylogenetic distance for each transect (a metric of phylogenetic community composition) and related this value to edaphic variables using generalized linear mixed models, including a term for spatial autocorrelation. KEY RESULTS: Overall, we recorded 112 008 individuals belonging to 110 species. Palm communities in non-inundated upland transects (but not floodplain transects) were more phylogenetically clustered in areas of low soil fertility, measured as exchangeable base concentration. In contrast, floodplain transects with more severe flood regimes (as inferred from floristic structure) tended to be phylogenetically clustered. Nearly half of the species recorded (44 %) were upland specialists while 18 % were floodplain specialists. In both habitat types, phylogenetic clustering was largely due to the co-occurrence of small-sized habitat specialists belonging to two hyperdiverse genera (Bactris and Geonoma). CONCLUSIONS: Edaphic conditions are associated with the phylogenetic community structure of palms across western Amazonia, and different factors (specifically, soil fertility and inundation intensity) appear to underlie diversity patterns in non-inundated upland versus floodplain habitats. By linking edaphic gradients with palm community phylogenetic structure, our study reinforces the need to integrate edaphic conditions in eco-evolutionary studies in order to better understand the processes that generate and maintain tropical forest diversity. Our results suggest a role for edaphic niche conservatism in the evolution and distribution of Amazonian palms, a finding with potential relevance for other clades.

Abtract 1.Scientific research increasingly calls for open-source software that is flexible, interactive, and expandable, while providing methodological guidance and reproducibility. Currently, many analyses in ecology are implemented with “black box” graphical user interfaces that lack flexibility or command-line interfaces that are infrequently used by non-specialists. 2.To help remedy this situation in the context of species distribution modeling, we created Wallace, an open and modular application with a richly documented graphical user interface to underlying R scripts that is flexible and highly interactive. 3.Wallace guides users from acquiring and processing data to building models and examining predictions. Additionally, it is designed to grow via community contributions of new modules to expand functionality. All results are downloadable, along with code to reproduce the analysis. 4.Wallace provides an example of an innovative platform to increase access to cutting-edge methods and encourage plurality in science and collaboration in software development. This article is protected by copyright. All rights reserved.

Host-parasite coevolution can maintain high levels of genetic diversity in traits involved in species interactions. In many systems, host traits exploited by parasites are constrained by use in other functions, leading to complex selective pressures across space and time. Here, we study genome-wide variation in the staple crop Sorghum bicolor (L.) Moench and its association with the parasitic weed Striga hermonthica (Delile) Benth., a major constraint to food security in Africa. We hypothesize that geographic selection mosaics across gradients of parasite occurrence maintain genetic diversity in sorghum landrace resistance. Suggesting a role in local adaptation to parasite pressure, multiple independent loss-of-function alleles at sorghum LOW GERMINATION STIMULANT 1 (LGS1) are broadly distributed among African landraces and geographically associated with S. hermonthica occurrence. However, low frequency of these alleles within S. hermonthica-prone regions and their absence elsewhere implicate potential tradeoffs restricting their fixation. LGS1 is thought to cause resistance by changing stereochemistry of strigolactones, hormones that control plant architecture and belowground signaling to mycorrhizae and are required to stimulate parasite germination. Consistent with tradeoffs, we find signatures of balancing selection surrounding LGS1 and other candidates from analysis of genome-wide associations with parasite distribution. Experiments with CRISPR-Cas9 edited sorghum further indicate the benefit of LGS1-mediated resistance strongly depends on parasite genotype and abiotic environment and comes at the cost of reduced photosystem gene expression. Our study demonstrates long-term maintenance of diversity in host resistance genes across smallholder agroecosystems, providing a valuable comparison to both industrial farming systems and natural communities.SIGNIFICANCE STATEMENTUnderstanding co-evolution in crop-parasite systems is critical to management of myriad pests and pathogens confronting modern agriculture. In contrast to wild plant communities, parasites in agricultural ecosystems are usually expected to gain the upper hand in co-evolutionary ‘arms races’ due to limited genetic diversity of host crops in cultivation. Here, we develop a framework to characterize associations between genome variants in global landraces (traditional varieties) of the staple crop sorghum with the distribution of the devastating parasitic weed Striga hermonthica. We find long-term maintenance of diversity in genes related to parasite resistance, highlighting an important role of host adaptation for co-evolutionary dynamics in smallholder agroecosystems.

Western Amazonia is a global biodiversity hotspot that encompasses extensive variation in geologic, climatic, and biotic features. Palms (Arecaceae) are among the most diverse and iconic groups of plants in the region with more than 150 species that exhibit extraordinary variation of geographical distributions, regional abundance patterns, and life history strategies and growth forms, and provide myriad ecosystem services. Understanding the ecological and evolutionary drivers that underpin palm distribution and abundance patterns may shed light on the evolution and ecology of the tropical forest biomes more generally. Edaphic conditions, in particular, are increasingly recognized as critical drivers of tropical plant diversity and distributions but data deficiencies inhibit our understanding of plant–soil relationships at broad scales, especially in the tropics. We present data from 546, 0.25‐ha (5 × 500 m) georeferenced transects located throughout western Amazonia where all individual palms were identified, counted, and assigned to a life‐history stage. Several environmental covariates were recorded along each transect and surface soil samples were collected from multiple points in N = 464 of transects. Altogether, the transects include 532,602 individuals belonging to 135 species. Variation among transects in terms of palm species richness and abundance is associated with major habitat types and soil properties. The soil properties including pH, acidity, all macronutrients for all samples, and texture, carbon, nitrogen, and micronutrients for some transects vary substantially across the study area, providing insight to broad‐scale variation of tropical surface soils. The data provided here will help advance our understanding of plant distributions and abundance patterns, and associations with soil conditions. No copyright restrictions are associated with this data set but please cite this paper if data are used for publication.

Advances in forest carbon mapping have the potential to greatly reduce uncertainties in the global carbon budget and to facilitate effective emissions mitigation strategies such as REDD+ (Reducing Emissions from Deforestation and Forest Degradation). Though broad-scale mapping is based primarily on remote sensing data, the accuracy of resulting forest carbon stock estimates depends critically on the quality of field measurements and calibration procedures. The mismatch in spatial scales between field inventory plots and larger pixels of current and planned remote sensing products for forest biomass mapping is of particular concern, as it has the potential to introduce errors, especially if forest biomass shows strong local spatial variation. Here, we used 30 large (8–50 ha) globally distributed permanent forest plots to quantify the spatial variability in aboveground biomass density (AGBD in Mg ha–1) at spatial scales ranging from 5 to 250 m (0.025–6.25 ha), and to evaluate the implications of this variability for calibrating remote sensing products using simulated remote sensing footprints. We found that local spatial variability in AGBD is large for standard plot sizes, averaging 46.3% for replicate 0.1 ha subplots within a single large plot, and 16.6% for 1 ha subplots. AGBD showed weak spatial autocorrelation at distances of 20–400 m, with autocorrelation higher in sites with higher topographic variability and statistically significant in half of the sites. We further show that when field calibration plots are smaller than the remote sensing pixels, the high local spatial variability in AGBD leads to a substantial "dilution" bias in calibration parameters, a bias that cannot be removed with standard statistical methods. Our results suggest that topography should be explicitly accounted for in future sampling strategies and that much care must be taken in designing calibration schemes if remote sensing of forest carbon is to achieve its promise.

© 2018 The Author(s). The nutrient demands of regrowing tropical forests are partly satisfied by nitrogen-fixing legume trees, but our understanding of the abundance of those species is biased towards wet tropical regions. Here we show how the abundance of Leguminosae is affected by both recovery from disturbance and large-scale rainfall gradients through a synthesis of forest inventory plots from a network of 42 Neotropical forest chronosequences. During the first three decades of natural forest regeneration, legume basal area is twice as high in dry compared with wet secondary forests. The tremendous ecological success of legumes in recently disturbed, water-limited forests is likely to be related to both their reduced leaflet size and ability to fix N2, which together enhance legume drought tolerance and water-use efficiency. Earth system models should incorporate these large-scale successional and climatic patterns of legume dominance to provide more accurate estimates of the maximum potential for natural nitrogen fixation across tropical forests.

Models of species ecological niches and geographic distributions now represent a widely used tool in ecology, evolution, and biogeography. However, the very common situation of species with few available occurrence localities presents major challenges for such modeling techniques, in particular regarding model complexity and evaluation. Here, we summarize the state of the field regarding these issues and provide a worked example using the technique Maxent for a small mammal endemic to Madagascar (the nesomyine rodent Eliurus majori). Two relevant model-selection approaches exist in the literature (information criteria, specifically AICc; and performance predicting withheld data, via a jackknife), but AICc is not strictly applicable to machine-learning algorithms like Maxent. We compare models chosen under each selection approach with those corresponding to Maxent default settings, both with and without spatial filtering of occurrence records to reduce the effects of sampling bias. Both selection approaches chose simpler models than those made using default settings. Furthermore, the approaches converged on a similar answer when sampling bias was taken into account, but differed markedly with the unfiltered occurrence data. Specifically, for that dataset, the models selected by AICc had substantially fewer parameters than those identified by performance on withheld data. Based on our knowledge of the study species, models chosen under both AICc and withheld-data-selection showed higher ecological plausibility when combined with spatial filtering. The results for this species intimate that AICc may consistently select models with fewer parameters and be more robust to sampling bias. To test these hypotheses and reach general conclusions, comprehensive research should be undertaken with a wide variety of real and simulated species. Meanwhile, we recommend that researchers assess the critical yet underappreciated issue of model complexity both via information criteria and performance on withheld data, comparing the results between the two approaches and taking into account ecological plausibility. This article is protected by copyright. All rights reserved.

Land-use change occurs nowhere more rapidly than in the tropics, where the imbalance between deforestation and forest regrowth has large consequences for the global carbon cycle(1). However, considerable uncertainty remains about the rate of biomass recovery in secondary forests, and how these rates are influenced by climate, landscape, and prior land use(2-4). Here we analyse aboveground biomass recovery during secondary succession in 45 forest sites and about 1,500 forest plots covering the major environmental gradients in the Neotropics. The studied secondary forests are highly productive and resilient. Aboveground biomass recovery after 20 years was on average 122 megagrams per hectare (Mg ha(-1)), corresponding to a net carbon uptake of 3.05 Mg C ha(-1) yr(-1), 11 times the uptake rate of old-growth forests. Aboveground biomass stocks took a median time of 66 years to recover to 90% of old-growth values. Aboveground biomass recovery after 20 years varied 11.3-fold ( from 20 to 225 Mg ha(-1)) across sites, and this recovery increased with water availability (higher local rainfall and lower climatic water deficit). We present a biomass recovery map of Latin America, which illustrates geographical and climatic variation in carbon sequestration potential during forest regrowth. The map will support policies to minimize forest loss in areas where biomass resilience is naturally low (such as seasonally dry forest regions) and promote forest regeneration and restoration in humid tropical lowland areas with high biomass resilience.

Question Understanding how the relative importance of different community assembly processes changes during secondary succession of diverse systems remains elusive. Functional and phylogenetic approaches that place species along continuous axes of niche differentiation and evolutionary relatedness, however, are deepening our understanding of the mechanisms that drive successional dynamics. We ask whether successional shifts in the functional and phylogenetic composition of post-agricultural tropical forests provide evidence for niche partitioning or competitive dominance hierarchies as drivers of successional change. Location Subtropical wet forests, Puerto Rico. Methods We combined data on four functional traits [leaf dry mass per area (LMA), wood density (WD), maximum height (Hmax), seed dry mass] and a well-resolved molecular phylogeny to characterize taxonomic, functional and phylogenetic composition of sapling and adult tree communities along a regionally replicated chronosequence. We used a null model approach to assess how functional and phylogenetic diversity change with forest age. Results Corresponding increases of community-weighted mean LMA, Hmax and seed mass with forest age reflected a shift in dominance of species with acquisitive resource-use strategies and small seeds towards species with more conservative resource use and larger seeds. A negative relationship between forest age and local diversity of Hmax and seed mass suggested increased importance of competitive hierarchies for light capture and shade-tolerant regeneration in older forests. In contrast, the colonization of palms in older forest plots led to a positive relationship between forest age and local phylogenetic diversity, suggesting functional convergence of distantly related lineages on traits that confer competitive dominance under low resource conditions. Conclusions We linked both functional and phylogenetic dimensions of community diversity with successional trajectories of post-agricultural tropical forests. Contrasting patterns of these dimensions of diversity shed light on the underlying community assembly processes. We argue that integrating traits and phylogeny with specific hypotheses about physiological and historical mechanisms is essential for advancing our understanding of the drivers of community change during succession.

Predicting the fate of tropical forests under a changing climate requires understanding species responses to climatic variability and extremes. Seedlings may be particularly vulnerable to climatic stress given low stored resources and undeveloped roots; they also portend the potential effects of climate change on future forest composition. Here we use data for ca. 50,000 tropical seedlings representing 25 woody species to assess (i) the effects of interannual variation in rainfall and solar radiation between 2007 and 2016 on seedling survival over 9 years in a subtropical forest; and (ii) how spatial heterogeneity in three environmental factors-soil moisture, understory light, and conspecific neighborhood density-modulate these responses. Community-wide seedling survival was not sensitive to interannual rainfall variability but interspecific variation in these responses was large, overwhelming the average community response. In contrast, community-wide responses to solar radiation were predominantly positive. Spatial heterogeneity in soil moisture and conspecific density were the predominant and most consistent drivers of seedling survival, with the majority of species exhibiting greater survival at low conspecific densities and positive or nonlinear responses to soil moisture. This environmental heterogeneity modulated impacts of rainfall and solar radiation. Negative conspecific effects were amplified during rainy years and at dry sites, whereas the positive effects of radiation on survival were more pronounced for seedlings existing at high understory light levels. These results demonstrate that environmental heterogeneity is not only the main driver of seedling survival in this forest but also plays a central role in buffering or exacerbating impacts of climate fluctuations on forest regeneration. Since seedlings represent a key bottleneck in the demographic cycle of trees, efforts to predict the long-term effects of a changing climate on tropical forests must take into account this environmental heterogeneity and how its effects on regeneration dynamics play out in long-term stand dynamics.

In the southwestern USA, recent large‐scale die‐offs of conifers raise the question of their resilience and mortality under droughts. To date, little is known about the interannual structural response to droughts. We hypothesized that piñon pines (Pinus edulis) respond to drought by reducing the drop of leaf water potential in branches from year to year through needle morphological adjustments. We tested our hypothesis using a 7‐year experiment in central New Mexico with three watering treatments (irrigated, normal, and rain exclusion). We analyzed how variation in “evaporative structure” (needle length, stomatal diameter, stomatal density, stomatal conductance) responded to watering treatment and interannual climate variability. We further analyzed annual functional adjustments by comparing yearly addition of needle area (LA) with yearly addition of sapwood area (SA) and distance to tip (d), defining the yearly ratios SA:LA and SA:LA/d. Needle length (l) increased with increasing winter and monsoon water supply, and showed more interannual variability when the soil was drier. Stomatal density increased with dryness, while stomatal diameter was reduced. As a result, anatomical maximal stomatal conductance was relatively invariant across treatments. SA:LA and SA:LA/d showed significant differences across treatments and contrary to our expectation were lower with reduced water input. Within average precipitation ranges, the response of these ratios to soil moisture was similar across treatments. However, when extreme soil drought was combined with high VPD, needle length, SA:LA and SA:LA/d became highly nonlinear, emphasizing the existence of a response threshold of combined high VPD and dry soil conditions. In new branch tissues, the response of annual functional ratios to water stress was immediate (same year) and does not attempt to reduce the drop of water potential. We suggest that unfavorable evaporative structural response to drought is compensated by dynamic stomatal control to maximize photosynthesis rates. ISSN:2045-7758

Predicting biotic responses to environmental change requires understanding the joint effects of abiotic conditions and biotic interactions on community dynamics. One major challenge is to separate the potentially confounding effects of abiotic environmental variation and local biotic interactions on individual performance. The stress gradient hypothesis (SGH) addresses this issue directly by predicting that the effects of biotic interactions on performance become more positive as the abiotic environment becomes more stressful. It is unclear, however, how the predictions of the SGH apply to plants of differing functional strategies in diverse communities. We asked (1) how the effect of crowding on performance (growth and survival) of trees varies across a precipitation gradient, and (2) how functional strategies (as measured by two key traits: wood density and leaf mass per area, LMA) mediate average demographic rates and responses to crowding across the gradient. We built trait-based neighborhood models of growth and survival across a regional precipitation gradient where increasing precipitation is associated with reduced abiotic stress. In total, our dataset comprised ~170,000 individual trees belonging to 252 species. The effect of crowding on tree performance varied across the gradient; crowding negatively affected growth across plots and positively affected survival in the wettest plot. Functional traits mediated average demographic rates across the gradient, but we did not find clear evidence that the strength of these responses depends on species’ traits. Our study lends support to the SGH and demonstrates how a trait-based perspective can advance these concepts by linking the diversity of species interactions with functional variation across abiotic gradients.

Arbuscular mycorrhizal (AM) fungi in the soil may influence tropical tree dynamics and forest succession. The mechanisms are poorly understood, because the functional characteristics and abundances of tree species and AM fungi are likely to be codependent. We used generalized joint attribute modeling to evaluate if AM fungi are associated with three forest community metrics for a sub-tropical montane forest in Puerto Rico. The metrics chosen to reflect changes during forest succession are the abundance of seedlings of different successional status, the amount of foliar damage on seedlings of different successional status, and community-weighted mean functional trait values (adult specific leaf area [SLA], adult wood density, and seed mass). We used high-throughput DNA sequencing to identify fungal operational taxonomic units (OTUs) in the soil. Model predictions showed that seedlings of mid- and late-successional species had less leaf damage when the 12 most common AM fungi were abundant compared to when these fungi were absent. We also found that seedlings of mid-successional species were predicted to be more abundant when the 12 most common AM fungi were abundant compared to when these fungi were absent. In contrast, early-successional tree seedlings were predicted to be less abundant when the 12 most common AM fungi were abundant compared to when these fungi were absent. Finally, we showed that, among the 12 most common AM fungi, different AM fungi were correlated with functional trait characteristics of early- or late-successional species. Together, these results suggest that early-successional species might not rely as much as mid- and late-successional species on AM fungi, and AM fungi might accelerate forest succession.

Invasive allergenic plant species may have severe health-related impacts. In this study we aim to predict the effects of climate change on the distribution of three allergenic ragweed species (Ambrosiaspp.) in Europe and discuss the potential associated health impact. We built species distribution models based on presence-only data for three ragweed species, using MAXENT software. Future climatic habitat suitability was modeled under two IPCC climate change scenarios (RCP 6.0 and RCP 8.5). We quantify the extent of the increase in ‘high allergy risk’ (HAR) areas, i.e., parts of Europe with climatic conditions corresponding to the highest quartile (25%) of present day habitat suitability for each of the three species. We estimate that by year 2100, the distribution range of all three ragweed species increases towards Northern and Eastern Europe under all climate scenarios. HAR areas will expand in Europe by 27–100%, depending on species and climate scenario. Novel HAR areas will occur mostly in Denmark, France, Germany, Russia and the Baltic countries, and overlap with densely populated cities such as Paris and St. Petersburg. We conclude that areas in Europe affected by severe ragweed associated allergy problems are likely to increase substantially by year 2100, affecting millions of people. To avoid this, management strategies must be developed that restrict ragweed dispersal and establishment of new populations. Precautionary efforts should limit the spread of ragweed seeds and reduce existing populations. Only by applying cross-countries management plans can managers mitigate future health risks and economical consequences of a ragweed expansion in Europe.

Mechanisms of community assembly and ecosystem function are often analyzed using community-weighted mean trait values (CWMs). We present a novel conceptual framework to quantify the contribution of demographic processes (i.e., growth, recruitment, and mortality) to temporal changes in CWMs. We used this framework to analyze mechanisms of secondary succession in wet tropical forests in Mexico. Seed size increased over time, reflecting a trade-off between colonization by small seeds early in succession, to establishment by large seeds later in succession. Specific leaf area (SLA) and leaf phosphorus content decreased over time, reflecting a trade-off between fast growth early in succession vs. high survival late in succession. On average, CWM shifts were driven mainly (70%) by growth of surviving trees that comprise the bulk of standing biomass, then mortality (25%), and weakly by recruitment (5%). Trait shifts of growing and recruiting trees mirrored the CWM trait shifts, and traits of dying trees did not change during succession, indicating that these traits are important for recruitment and growth, but not for mortality, during the first 30 yr of succession. Identifying the demographic drivers of functional composition change links population dynamics to community change, and enhances insights into mechanisms of succession.

The distributions of arbuscular mycorrhizal (AM) fungal communities are driven by climate, soil nutrients, and plant community composition. However, these distributions are estimated at the community level and AM fungal taxa will respond to selection pressure of global change at the species level. Thus, ecological niche models of individual AM fungal taxa may be an informative approach to predict AM fungal composition and function under future climates at the global scale. Here we present the first attempt to model AM fungal distributions with ecological niche models for the widespread AM fungal taxon Rhizophagus irregularis (formerly Glomus intraradices). We show that despite varying the definition of the operational taxonomic unit (OTU) for R. irregularis, the predicted distributions of this species complex are consistently affected by a positive association with soil moisture. The spatial extent of ecological niche models affected the predicted distribution of R. irregularis, with climatic drivers and resources affecting its distribution more strongly in the northern and southern hemispheres, respectively. Given that AM fungi are not dispersal limited and coexist at the landscape scale relevant for ecological niche model predictions, this widely distributed fungal clade provides a robust case study to apply hypothesis-driven distributional models to predict the biogeography of microorganisms.

Determining how the relative strength of community assembly processes varies along resource gradients is critical for understanding community responses to environmental change. A key challenge for addressing this issue at regional scales is that environmental gradients typically encompass multiple coupled resource gradients (e.g. water, light, soils), which can complicate hypotheses about the drivers of community variation. We used data on functional traits and phylogenetic relatedness to infer assembly processes of tree communities across regional environmental gradients in Puerto Rico. We censused trees in 24, 0.25-ha mature plots located along a precipitation gradient and on soils derived from two parent materials (limestone and volcanic). In each plot, we quantified abiotic conditions in terms of mean annual precipitation, canopy openness, and soil nutrients. We used three functional traits with relevance for drought tolerance and resource acquisition strategies (wood density [WD], leaf mass per area [LMA], and maximum height [Hmax]), and a molecular phylogeny, to characterize tree community composition in terms of (i) community-weighted mean trait values (i.e., plot average trait values, weighted by relative basal area), (ii) functional diversity, and (iii) phylogenetic diversity. Mean annual precipitation was negatively correlated with understory light availability (for plots on both soil types), and soil fertility (among plots on limestone soils). Soil fertility varied substantially between plots on each parent material, and was generally higher among plots on limestone-derived soils. Among the limestone soil plots, which occur on the drier half of the precipitation gradient, increasing mean annual precipitation was associated with lower community-weighted mean WD and LMA, and taller Hmax. Additionally, functional diversity (of WD and Hmax) and phylogenetic diversity increased with precipitation among limestone soil plots, suggesting an important role for abiotic filtering in driving functional and phylogenetic convergence in arid conditions. In contrast, we did not find significant relationships between environmental conditions and community-weighted mean traits or diversity metrics among plots on volcanic-derived soils, which occur along the wetter half of the precipitation gradient. Together, our results suggest that drought tolerance is the dominant assembly mechanism controlling tree composition in dry forests. In wetter forests, functional diversity appears to be maintained by a combination of hierarchical competition for light and niche partitioning. Overall, our results exhibit geographic variation in the mechanisms governing composition of tropical forests across regional environmental gradients, and highlight the importance of considering complex environmental gradients at large spatial scales.

Interspecific variation in phenology is a key axis of functional diversity, potentially mediating how communities respond to climate change. The diverse drivers of phenology act across multiple temporal scales. For example, abiotic constraints favor synchronous reproduction (positive covariance among species), while biotic interactions can favor synchrony or compensatory dynamics (negative covariance). We used wavelet analyses to examine phenology of community flower and seed production for 45 tree species across multiple temporal scales in a tropical dry forest in Puerto Rico with marked rainfall seasonality. Weasked three questions: (1) do species exhibit synchronous or compensatory temporal dynamics in reproduction, (2) do interspecific differences in phenology reflect variable responses to rainfall, and (3) is interspecific variation in phenology and response to a major drought associated with functional traits that mediate responses to moisture? Community-level flowering was synchronized at seasonal scales (similar to 5-6mo) and at short scales (similar to 1 mo, following rainfall). However, seed rain exhibited significant compensatory dynamics at intraseasonal scales (similar to 3 mo), suggesting interspecific variation in temporal niches. Species with large leaves (associated with sensitivity to water deficit) peaked in reproduction synchronously with the peak of seasonal rainfall (similar to 5mo scale). By contrast, species with high wood specific gravity (associated with drought resistance) tended to flower in drier periods. Flowering of tall species and those with large leaves was most tightly linked to intraseasonal (similar to 2mo scale) rainfall fluctuations. Although the 2015 drought dramatically reduced community-wide reproduction, functional traits were not associated with the magnitude of species-specific declines. Our results suggest opposing drivers of synchronous versus compensatory dynamics at different temporal scales. Phenology associations with functional traits indicated that distinct strategies for coping with seasonality underlie phenological diversity. Observed drought responses highlight the importance of non-linear community responses to climate. Community phenology exhibits scale-specific patterns highlighting the need for multi-scale approaches to community dynamics.

The notion that relationships between community-weighted mean (CWM) traits (i.e. plot-level trait values weighted by species abundances) and environmental conditions reflect selection towards locally optimal phenotypes is challenged by the large amount of interspecific trait variation typically found within ecological communities. Reconciling these contrasting patterns is a key to advancing predictive theories of functional community ecology. We combined data on geographical distributions and three traits (wood density, leaf mass per area and maximum height) of 173 tree species in Puerto Rico. We tested the hypothesis that species are more likely to occur where their trait values are more similar to the local CWM trait values (the ‘ CWM-optimality’ hypothesis) by comparing species occurrence patterns (as a proxy for fitness) with the functional composition of forest plots across a precipitation gradient. While 70% of the species supported CWM-optimality for at least one trait, nearly 25% significantly opposed it for at least one trait, thereby contributing to local functional diversity. The majority (85%) of species that opposed CWM-optimality did so only for one trait and few species opposed CWM-optimality in multivariate trait space. Our study suggests that constraints to local functional variation act more strongly on multivariate phenotypes than on univariate traits.

The seed-to-seedling transition constitutes a critical bottleneck in the life history of plants and represents a major determinant of species composition and abundance. However, we have surprisingly little knowledge regarding the forces driving this ontogenetic transition. Here we utilize information regarding organismal function to investigate the strength of intra-and interspecific negative density dependence during the seed-to-seedling transition in Puerto Rican tree species. Our analyses were implemented at individual sites and across an entire 16-ha forest plot, spanning 6 years. The functional richness of seedling assemblages was significantly lower than expected given the seed assemblages, but the functional evenness was significantly higher than expected, indicating the simultaneous importance of constraints on the overall phenotypic space and trait differences for successful transitions from seed to seedling. The results were consistent across years. Within species, we also found evidence for strong intraspecific negative density dependence, where the probability of transition was proportionally lower when in a site with high conspecific density. These results suggest that filtering of similar phenotypes across species and strong negative density dependence within and among species are simultaneously driving the structure and dynamics of tropical tree assemblages during this critical life-history transition.

Biodiversity is inherently multidimensional, encompassing taxonomic, functional, phylogenetic, genetic, landscape and many other elements of variability of life on the Earth. However, this fundamental principle of multidimensionality is rarely applied in research aimed at understanding biodiversity's value to ecosystem functions and the services they provide. This oversight means that our current understanding of the ecological and environmental consequences of biodiversity loss is limited primarily to what unidimensional studies have revealed. To address this issue, we review the literature, develop a conceptual framework for multidimensional biodiversity research based on this review and provide a case study to explore the framework. Our case study specifically examines how herbivory by whitetail deer ( Odocoileus virginianus ) alters the multidimensional influence of biodiversity on understory plant cover at Black Rock Forest, New York. Using three biodiversity dimensions (taxonomic, functional and phylogenetic diversity) to explore our framework, we found that herbivory alters biodiversity's multidimensional influence on plant cover; an effect not observable through a unidimensional approach. Although our review, framework and case study illustrate the advantages of multidimensional over unidimensional approaches, they also illustrate the statistical and empirical challenges such work entails. Meeting these challenges, however, where data and resources permit, will be important if we are to better understand and manage the consequences we face as biodiversity continues to decline in the foreseeable future.

Models reveal the high carbon mitigation potential of tropical forest regeneration., Regrowth of tropical secondary forests following complete or nearly complete removal of forest vegetation actively stores carbon in aboveground biomass, partially counterbalancing carbon emissions from deforestation, forest degradation, burning of fossil fuels, and other anthropogenic sources. We estimate the age and spatial extent of lowland second-growth forests in the Latin American tropics and model their potential aboveground carbon accumulation over four decades. Our model shows that, in 2008, second-growth forests (1 to 60 years old) covered 2.4 million km2 of land (28.1% of the total study area). Over 40 years, these lands can potentially accumulate a total aboveground carbon stock of 8.48 Pg C (petagrams of carbon) in aboveground biomass via low-cost natural regeneration or assisted regeneration, corresponding to a total CO2 sequestration of 31.09 Pg CO2. This total is equivalent to carbon emissions from fossil fuel use and industrial processes in all of Latin America and the Caribbean from 1993 to 2014. Ten countries account for 95% of this carbon storage potential, led by Brazil, Colombia, Mexico, and Venezuela. We model future land-use scenarios to guide national carbon mitigation policies. Permitting natural regeneration on 40% of lowland pastures potentially stores an additional 2.0 Pg C over 40 years. Our study provides information and maps to guide national-level forest-based carbon mitigation plans on the basis of estimated rates of natural regeneration and pasture abandonment. Coupled with avoided deforestation and sustainable forest management, natural regeneration of second-growth forests provides a low-cost mechanism that yields a high carbon sequestration potential with multiple benefits for biodiversity and ecosystem services.

Background The use of phylogenetic information in community ecology and conservation has grown in recent years. Two key issues for community phylogenetics studies, however, are (i) low terminal phylogenetic resolution and (ii) arbitrarily defined species pools. Methodology/principal findings We used three DNA barcodes (plastid DNA regions rbcL, matK, and trnH-psbA) to infer a phylogeny for 527 native and naturalized trees of Puerto Rico, representing the vast majority of the entire tree flora of the island (89%). We used a maximum likelihood (ML) approach with and without a constraint tree that enforced monophyly of recognized plant orders. Based on 50% consensus trees, the ML analyses improved phylogenetic resolution relative to a comparable phylogeny generated with Phylomatic (proportion of internal nodes resolved: constrained ML = 74%, unconstrained ML = 68%, Phylomatic = 52%). We quantified the phylogenetic composition of 15 protected forests in Puerto Rico using the constrained ML and Phylomatic phylogenies. We found some evidence that tree communities in areas of high water stress were relatively phylogenetically clustered. Reducing the scale at which the species pool was defined (from island to soil types) changed some of our results depending on which phylogeny (ML vs. Phylomatic) was used. Overall, the increased terminal resolution provided by the ML phylogeny revealed additional patterns that were not observed with a less-resolved phylogeny. Conclusions/significance With the DNA barcode phylogeny presented here (based on an island-wide species pool), we show that a more fully resolved phylogeny increases power to detect nonrandom patterns of community composition in several Puerto Rican tree communities. Especially if combined with additional information on species functional traits and geographic distributions, this phylogeny will (i) facilitate stronger inferences about the role of historical processes in governing the assembly and composition of Puerto Rican forests, (ii) provide insight into Caribbean biogeography, and (iii) aid in incorporating evolutionary history into conservation planning.