Intraspecific alternative phenotypes contribute to variation in species' strategies for growth

Ecologists have historically sought to identify the mechanisms underlying the maintenance of local species diversity. High-dimensional trait-based relationships, such as alternative phenotypes, have been hypothesized as important for maintaining species diversity such that phenotypically dissimilar individuals compete less for resources but have similar performance in a given environment. The presence of alternative phenotypes has primarily been investigated at the community level, despite the importance of intraspecific variation to diversity maintenance. The aims of this research are to (1) determine the presence or absence of intraspecific alternative phenotypes in three species of tropical tree seedlings, (2) investigate if these different species use the same alternative phenotypes for growth success, and (3) evaluate how findings align with species co-occurrence patterns. We model species-specific relative growth rate with individual-level measurements of leaf mass per area (LMA) and root mass fraction (RMF), environmental data, and their interactions. We find that two of the three species have intraspecific alternative phenotypes, with individuals within species having different functional forms leading to similar growth. Interestingly, individuals within these species use the same trait combinations, high LMA × low RMF and low LMA × high RMF, in high soil nutrient environments to acquire resources for higher growth. This similarity among species in intraspecific alternative phenotypes and variables that contribute most to growth may lead to their negative spatial co-occurrence. Overall, we find that multiple traits or interactions between traits and the environment drive species-specific strategies for growth, but that individuals within species leverage this multi-dimensionality in different ways for growth success.

Leaf gene expression trajectories during the growing season are consistent between sites and years in American beech

Transcriptomics provides a versatile tool for ecological monitoring. Here, through genome-guided profiling of transcripts mapping to 33 042 gene models, expression differences can be discerned among multi-year and seasonal leaf samples collected from American beech trees at two latitudinally separated sites. Despite a bottleneck due to post-Columbian deforestation, the single nucleotide polymorphism-based population genetic background analysis has yielded sufficient variation to account for differences between populations and among individuals. Our expression analyses during spring-summer and summer-autumn transitions for two consecutive years involved 4197 differentially expressed protein coding genes. Using Populus orthologues we reconstructed a protein-protein interactome representing leaf physiological states of trees during the seasonal transitions. Gene set enrichment analysis revealed gene ontology terms that highlight molecular functions and biological processes possibly influenced by abiotic forcings such as recovery from drought and response to excess precipitation. Further, based on 324 co-regulated transcripts, we focused on a subset of GO terms that could be putatively attributed to late spring phenological shifts. Our conservative results indicate that extended transcriptome-based monitoring of forests can capture diverse ranges of responses including air quality, chronic disease, as well as herbivore outbreaks that require activation and/or downregulation of genes collectively tuning reaction norms maintaining the survival of long living trees such as the American beech.

On functional groups and forest dynamics

Functional trait variation measured on continuous scales has helped ecologists to unravel important ecological processes. However, forest ecologists have recently moved back toward using functional groups. There are pragmatic and biological rationales for focusing on functional groups. Both of these approaches have inherent limitations including binning clearly continuous distributions, poor trait-group matching, and narrow conceptual frameworks for why groups exist and how they evolved. We believe the pragmatic use of functional groups due to data deficiencies will eventually erode. Conversely, we argue that existing conceptual frameworks for why a limited number of tree functional groups may exist is a useful, but flawed, starting point for modeling forests that can be improved through the consideration of unmeasured axes of functional variation.

Comparative transcriptomics reveals divergence in pathogen response gene families amongst 20 forest tree species

Forest trees provide critical ecosystem services for humanity that are under threat due to ongoing global change. Measuring and characterizing genetic diversity are key to understanding adaptive potential and developing strategies to mitigate negative consequences arising from climate change. In the area of forest genetic diversity, genetic divergence caused by large-scale changes at the chromosomal level has been largely understudied. In this study, we used the RNA-seq data of 20 co-occurring forest trees species from genera including Acer, Alnus, Amelanchier, Betula, Cornus, Corylus, Dirca, Fraxinus, Ostrya, Populus, Prunus, Quercus, Ribes, Tilia, and Ulmus sampled from Upper Peninsula of Michigan. These data were used to infer the origin and maintenance of gene family variation, species divergence time, as well as gene family expansion and contraction. We identified a signal of common whole genome duplication events shared by core eudicots. We also found rapid evolution, namely fast expansion or fast contraction of gene families, in plant-pathogen interaction genes amongst the studied diploid species. Finally, the results lay the foundation for further research on the genetic diversity and adaptive capacity of forest trees, which will inform forest management and conservation policies.

Phytochemical diversity impacts herbivory in a tropical rainforest tree community

Metabolomics provides an unprecedented window into diverse plant secondary metabolites that represent a potentially critical niche dimension in tropical forests underlying species coexistence. Here, we used untargeted metabolomics to evaluate chemical composition of 358 tree species and its relationship with phylogeny and variation in light environment, soil nutrients, and insect herbivore leaf damage in a tropical rainforest plot. We report no phylogenetic signal in most compound classes, indicating rapid diversification in tree metabolomes. We found that locally co-occurring species were more chemically dissimilar than random and that local chemical dispersion and metabolite diversity were associated with lower herbivory, especially that of specialist insect herbivores. Our results highlight the role of secondary metabolites in mediating plant-herbivore interactions and their potential to facilitate niche differentiation in a manner that contributes to species coexistence. Furthermore, our findings suggest that specialist herbivore pressure is an important mechanism promoting phytochemical diversity in tropical forests.

Demographic trade-offs and functional shifts in a hurricane-impacted tropical forest

BACKGROUND AND AIMS

Understanding shifts in the demographic and functional composition of forests after major natural disturbances has become increasingly relevant given the accelerating rates of climate change and elevated frequency of natural disturbances. Although plant demographic strategies are often described across a slow-fast continuum, severe and frequent disturbance events influencing demographic processes may alter the demographic trade-offs and the functional composition of forests. We examined demographic trade-offs and the shifts in functional traits in a hurricane-disturbed forest using long-term data from the Luquillo Forest Dynamics Plot (LFPD) in Puerto Rico.

METHODS

We analysed information on growth, survival, seed rain and seedling recruitment for 30 woody species in the LFDP. In addition, we compiled data on leaf, seed and wood functional traits that capture the main ecological strategies for plants. We used this information to identify the main axes of demographic variation for this forest community and evaluate shifts in community-weighted means for traits from 2000 to 2016.

KEY RESULTS

The previously identified growth-survival trade-off was not observed. Instead, we identified a fecundity-growth trade-off and an axis representing seedling-to-adult survival. Both axes formed dimensions independent of resprouting ability. Also, changes in tree species composition during the post-hurricane period reflected a directional shift from seedling and tree communities dominated by acquisitive towards conservative leaf economics traits and large seed mass. Wood specific gravity, however, did not show significant directional changes over time.

CONCLUSIONS

Our study demonstrates that tree demographic strategies coping with frequent storms and hurricane disturbances deviate from strategies typically observed in undisturbed forests, yet the shifts in functional composition still conform to the expected changes from acquisitive to conservative resource-uptake strategies expected over succession. In the face of increased rates of natural and anthropogenic disturbance in tropical regions, our results anticipate shifts in species demographic trade-offs and different functional dimensions.

Biogeographic context is related to local scale tree demography, co-occurrence and functional differentiation

Identifying the drivers of community structure and dynamics is a major pursuit in ecology. Emphasis is typically placed on the importance of local scale interactions when attempting to explain these fundamental ecological patterns. However, regional scale phenomena are also important predictors. The importance of regional scale context should be more evident in assemblages where multiple species are close to their range margins. Here, we test the importance of regional scale context using data from a temperate forest plot that contains two species groups - one near its northern range limit and one near its southern range limit. We show the proximity of species to their southern or northern range margins is linked to local scale co-occurrence, similarity in gene expression responses to a key environmental driver, demographic performance and inter-specific variation in conspecific negative density dependence. In sum, many of the key local scale patterns and processes of interest to community ecologists are linked to biogeographic context that is frequently ignored.

Height and crown allometries and their relationship with functional traits: An example from a subtropical wet forest

Forest tree communities are largely structured by interactions between phenotypes and their environments. Functional traits have been popularized as providing key insights into plant functional tradeoffs. Similarly, tree crown-stem diameter and tree height-stem diameter allometric relationships are likely to be strongly coordinated with functional trait tradeoff axes. Specifically, species with functional traits indicative of conservative strategies (i.e., dense wood, heavy seeds) should be related to tree architectures that have lower heights and wider crowns for a given stem diameter. For example, shade-tolerant species in tropical forests are typically characterized as having dense wood, large seeds, and relatively broad crowns at early ontogenetic stages. Here, we focus on 14 dominant dicot tree species in a tropical forest. We utilized hierarchical Bayesian models to characterize species-specific height and crown size allometric parameters. We sampled from the posterior distributions for these parameters and correlated them with six functional traits. We also characterize the expected height and crown size for a series of reference stem diameters to quantify the relationship between traits and tree architecture across size classes. We find little interspecific variation in allometric slopes, but clear variation in allometric intercepts. Allometeric height intercepts were negatively correlated with wood density and crown size intercepts were positively related to wood density and seed mass and negatively related to leaf percent phosphorus. Thus, interspecific variation in tree architecture is generated by interspecific variation in allometric intercepts and not slopes. These intercepts could be predicted using a handful of functional traits where conservative traits were indicative of trees that are relatively short and have larger crown sizes. This demonstrates a coordination of tropical tree life histories that can be characterized simultaneously with functional traits and tree allometries.

Functional trait space and redundancy of plant communities decrease toward cold temperature at high altitudes in Southwest China

Plant communities in mountainous areas shift gradually as climatic conditions change with altitude. How trait structure in multivariate space adapts to these varying climates in natural forest stands is unclear. Studying the multivariate functional trait structure and redundancy of tree communities along altitude gradients is crucial to understanding how temperature change affects natural forest stands. In this study, the leaf area, specific leaf area, leaf carbon, nitrogen, and phosphorous content from 1,590 trees were collected and used to construct the functional trait space of 12 plant communities at altitudes ranging from 800 m to 3,800 m across three mountains. Hypervolume overlap was calculated to quantify species trait redundancy per community. First, hypervolumes of species exclusion and full species set were calculated, respectively. Second, the overlap between these two volumes was calculated to obtain hypervolume overlap. Results showed that the functional trait space significantly increased with mean annual temperature toward lower altitudes within and across three mountains, whereas species trait redundancy had different patterns between mountains. Thus, warming can widen functional trait space and alter the redundancy in plant communities. The inconsistent patterns of redundancy between mountains suggest that warming exerts varying influences on different ecosystems. Identification of climate-vulnerable ecosystems is important in the face of global warming.

Differential impacts of adult trees on offspring and non-offspring recruits in a subtropical forest

An important mechanism promoting species coexistence is conspecific negative density dependence (CNDD), which inhibits conspecific neighbors by accumulating host-specific enemies near adult trees. Natural enemies may be genotype-specific and regulate offspring dynamics more strongly than non-offspring, which is often neglected due to the difficulty in ascertaining genetic relatedness. Here, we investigated whether offspring and non-offspring of a dominant species, Castanopsis eyrei, suffered from different strength of CNDD based on parentage assignment in a subtropical forest. We found decreased recruitment efficiency (proxy of survival probability) of offspring compared with non-offspring near adult trees during the seedling-sapling transition, suggesting genotype-dependent interactions drive tree demographic dynamics. Furthermore, the genetic similarity between individuals of same cohort decreased in late life history stages, indicating genetic-relatedness-dependent tree mortality throughout ontogeny. Our results demonstrate that within-species genetic relatedness significantly affects the strength of CNDD, implying genotype-specific natural enemies may contribute to population dynamics in natural forests.

Comparative transcriptomics of tropical woody plants supports fast and furious strategy along the leaf economics spectrum in lianas

Lianas, climbing woody plants, influence the structure and function of tropical forests. Climbing traits have evolved multiple times, including ancestral groups such as gymnosperms and pteridophytes, but the genetic basis of the liana strategy is largely unknown. Here, we use a comparative transcriptomic approach for 47 tropical plant species, including ten lianas of diverse taxonomic origins, to identify genes that are consistently expressed or downregulated only in lianas. Our comparative analysis of full-length transcripts enabled the identification of a core interactomic network common to lianas. Sets of transcripts identified from our analysis reveal features related to functional traits pertinent to leaf economics spectrum in lianas, include upregulation of genes controlling epidermal cuticular properties, cell wall remodeling, carbon concentrating mechanism, cell cycle progression, DNA repair and a large suit of downregulated transcription factors and enzymes involved in ABA-mediated stress response as well as lignin and suberin synthesis. All together, these genes are known to be significant in shaping plant morphologies through responses such as gravitropism, phyllotaxy and shade avoidance.

Summary: The full-length fraction of liana transcriptomes mapped on a protein–protein interactome revealed the nature of their convergence through distinct sets of expressed and downregulated genes not observed in free-standing plants.

Analyses of three-dimensional species associations reveal departures from neutrality in a tropical forest

The study of community spatial structure is central to understanding diversity patterns over space and species co-occurrence at local scales. While most analytical approaches consider horizontal and vertical dimensions separately, in this study we introduce a three-dimensional spatial analysis that simultaneously includes horizontal and vertical species associations. Using tree census data (2000 to 2016) and allometries from the Luquillo forest plot in Puerto Rico, we show that spatial organization becomes less random over time as the forest recovered from land-use legacy effects and hurricane disturbance. Tree species vertical segregation is predominant in the forest with almost all species that co-occur in the horizontal plane avoiding each other in the vertical dimension. Horizontal segregation is less common than vertical, while three-dimensional aggregation (a proxy for direct tree competition) is the least frequent type of spatial association. Furthermore, dominant species are involved in more non-random spatial associations, implying that species co-occurrence is facilitated by species segregation in space. This novel three-dimensional analysis allowed us to identify and quantify tree species spatial distributions, how interspecific competition was reduced through forest structure, and how it changed over time after disturbance, in ways not detectable from two-dimensional analyses alone.

Strategies of tolerance reflected in two North American maple genomes

The first chromosome‐scale assemblies for North American members of the Acer genus, sugar maple (Acer saccharum) and boxelder (Acer negundo), as well as transcriptomic evaluation of the abiotic stress response in A. saccharum are reported. This integrated study describes in‐depth aspects contributing to each species' approach to tolerance and applies current knowledge in many areas of plant genome biology with Acer physiology to help convey the genomic complexities underlying tolerance in broadleaf tree species.

Relating leaf traits to seedling performance in a tropical forest: building a hierarchical functional framework

Trait-based approaches have been extensively used in community ecology to provide a mechanistic understanding of the drivers of community assembly. However, a foundational assumption of the trait framework, traits relate to performance, has been mainly examined through univariate relationships that simplify the complex phenotypic integration of organisms. We evaluate a conceptual framework in which traits are organized hierarchically combining trait information at the individual- and species-level from biomass allocation and organ-level traits. We focus on photosynthetic traits and predict that the positive effects of increasing plant leaf mass on growth depend on species-level leaf traits. We modeled growth data on more than 1,500 seedlings from 97 seedling species from a tropical forest in China. We found that seedling growth increases with allocation to leaves (high leaf area ratio and leaf mass fraction) and this effect is accentuated for species with high specific leaf area and leaf area. Also, we found that light has a significant effect on growth, and this effect is additive with leaf allocation traits. Our work offers an approach to gain further understanding of the effects of traits on the whole plant-level growth via a hierarchical framework including organ-level and biomass allocation traits at species and individual levels.

On the modelling of tropical tree growth: the importance of intra-specific trait variation, non-linear functions and phenotypic integration

BACKGROUND AND AIMS

The composition and dynamics of plant communities arise from individual-level demographic outcomes, which are driven by interactions between phenotypes and the environment. Functional traits that can be measured across plants are frequently used to model plant growth and survival. Perhaps surprisingly, species average trait values are often used in these studies and, in some cases, these trait values come from other regions or averages calculated from global databases. This data aggregation potentially results in a large loss of valuable information that probably results in models of plant performance that are weak or even misleading.

METHODS

We present individual-level trait and fine-scale growth data from >500 co-occurring individual trees from 20 species in a Chinese tropical rain forest. We construct Bayesian models of growth informed by theory and construct hierarchical Bayesian models that utilize both individual- and species-level trait data, and compare these models with models only using individual-level data.

KEY RESULTS

We show that trait-growth relationships measured at the individual level vary across species, are often weak using commonly measured traits and do not align with the results of analyses conducted at the species level. However, when we construct individual-level models of growth using leaf area ratio approximations and integrated phenotypes, we generated strong predictive models of tree growth.

CONCLUSIONS

Here, we have shown that individual-level models of tree growth that are built using integrative traits always outperform individual-level models of tree growth that use commonly measured traits. Furthermore, individual-level models, generally, do not support the findings of trait-growth relationships quantified at the species level. This indicates that aggregating trait and growth data to the species level results in poorer and probably misleading models of how traits are related to tree performance.

Tree seedling trait optimization and growth in response to local-scale soil and light variability

At local scales, it has been suggested that high levels of resources lead to increased tree growth via trait optimization (highly peaked trait distribution). However, this contrasts with (1) theories that suggest that trait optimization and high growth occur in the most common resource level and (2) empirical evidence showing that high trait optimization can be also found at low resource levels. This raises the question of how are traits and growth optimized in highly diverse plant communities. Here, we propose a series of hypotheses about how traits and growth are expected to be maximized under different resource levels (low, the most common, and high) in tree seedling communities from a subtropical forest in Puerto Rico, USA. We studied the variation in the distribution of biomass allocation and leaf traits and seedlings growth rate along four resource gradients: light availability (canopy openness) and soil K, Mg, and N content. Our analyses consisted of comparing trait kurtosis (a measurement of trait optimization), community trait means, and relative growth rates at three resource levels (low, common, and high). Trait optimization varied across the three resource levels depending on the type of resource and trait, with leaf traits being optimized under high N and in the most common K and Mg conditions, but not at any of the light levels. Also, seedling growth increased at high-light conditions and high N and K but was not related to trait kurtosis. Our results indicate that local-scale variability of soil fertility and understory light conditions result in shifts in species ecological strategies that increase growth despite a weak trait optimization, suggesting the existence of alternative phenotypes that achieve similar high performance. Uncovering the links between abiotic factors, functional trait diversity and performance is necessary to better predict tree responses to future changes in abiotic conditions.

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

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

Linking patterns and processes of tree community assembly across spatial scales in tropical montane forests

Many studies have tried to assess the role of both deterministic and stochastic processes in community assembly, yet a lack of consensus exists on which processes are more prevalent and at which spatial scales they operate. To shed light on this issue, we tested two nonmutually exclusive, scale-dependent hypotheses: (1) that competitive exclusion dominates at small spatial scales; and (2) that environmental filtering does so at larger ones. To accomplish this, we studied the functional patterns of tropical montane forest communities along two altitudinal gradients, in Ecuador and Peru, using floristic and functional data from 60 plots of 0.1 ha. We found no evidence of either functional overdispersion or clustering at small spatial scales, but we did find functional clustering at larger ones. The observed pattern of clustering, consistent with an environmental filtering process, was more evident when maximizing the environmental differences among any pair of plots. To strengthen the link between the observed community functional pattern and the underlying process of environmental filtering, we explored differences in the climatic preferences of the most abundant species found at lower and higher elevations and examined whether their abundances shifted along the elevation gradient. We found (1) that greater community functional differences (observed between lower and upper tropical montane forest assemblies) were mostly the result of strong climatic preferences, maintained across the Neotropics; and (2) that the abundances of such species shifted along the elevational gradient. Our findings support the conclusion that, at large spatial scales, environmental filtering is the overriding mechanism for community assembly, because the pattern of functional clustering was linked to species' similarities in their climatic preferences, which ultimately resulted in shifts in species abundances along the gradient. However, there was no evidence of competitive exclusion at more homogeneous, smaller spatial scales, where plant species effectively compete for resources.

Differential soil fungus accumulation and density dependence of trees in a subtropical forest

The mechanisms underlying interspecific variation in conspecific negative density dependence (CNDD) are poorly understood. Using a multilevel modeling approach, we combined long-term seedling demographic data from a subtropical forest plot with soil fungal community data by means of DNA sequencing to address the feedback of various guilds of soil fungi on the density dependence of trees. We show that mycorrhizal type mediates tree neighborhood interactions at the community level, and much of the interspecific variation in CNDD is explained by how tree species differ in their fungal density accumulation rates as they grow. Species with higher accumulation rates of pathogenic fungi suffered more from CNDD, whereas species with lower CNDD had higher accumulation rates of ectomycorrhizal fungi, suggesting that mutualistic and pathogenic fungi play important but opposing roles.

Alternative designs and tropical tree seedling growth performance landscapes

The functional trait values that constitute a whole-plant phenotype interact with the environment to determine demographic rates. Current approaches often fail to explicitly consider trait × trait and trait × environment interactions, which may lead to missed information that is valuable for understanding and predicting the drivers of demographic rates and functional diversity. Here, we consider these interactions by modeling growth performance landscapes that span multidimensional trait spaces along environmental gradients. We utilize individual-level leaf, stem, and root trait data combined with growth data from tree seedlings along soil nutrient and light gradients in a hyper-diverse tropical rainforest. We find that multiple trait combinations in phenotypic space (i.e., alternative designs) lead to multiple growth performance peaks that shift along light and soil axes such that no single or set of interacting traits consistently results in peak growth performance. Evidence from these growth performance peaks also generally indicates frequent independence of above- and belowground resource acquisition strategies. These results help explain how functional diversity is maintained in ecological communities and question the practice of utilizing a single trait or environmental variable, in isolation, to predict the growth performance of individual trees.

Intraspecific variation in traits and tree growth along an elevational gradient in a subtropical forest

A conspicuous feature of natural communities is that individuals within species exhibit broad variation in their phenotype. While the phenotypic differences among species are prominent and have received considerable attention in earlier studies, recent findings suggest that about 40% of the trait variation is found within species. How this intraspecific variation is related to underlying environmental gradients and ultimately linked to performance is an outstanding question in ecology and evolution. Here, we study six broadly distributed species across an elevational gradient in a subtropical forest. We focused on five functional traits reflecting plant functional differentiation in stem transport, leaf architecture, and leaf resource acquisition. We found that leaf thickness, leaf toughness, and specific leaf area generally varied with elevation, while wood density and leaf area exhibited constrained variation. Results on multivariate trait axes also showed mixed evidence with the PC1 values (positively related to leaf toughness and negatively related to specific leaf area) shifting with elevation, while PC2 values (negatively related to wood density) did not change with elevation. We also found that, despite the important variation in some traits along the gradient, growth performance did not follow this same trend. This suggests that strong directional changes in traits along the gradient may result in similar levels of demographic performance. The results, therefore, challenge the simple expectation that a trait will correlate with a demographic rate. More nuanced approaches and additional mechanisms must be considered to advance understanding of the performance-trait relationships.

Does trait variation within broadly distributed species mirror patterns across species? A case study in Puerto Rico

Although populations are phenotypically diverse, the majority of trait-based studies have focused on examining differences among species. The justification for this broadly applied approach is based on the assumption that differences among species are always greater than within species. This is likely true for local communities, but species are often broadly distributed across a wide range of environments and patterns of intraspecific variation might surpass differences among species. Therefore, an appropriate interpretation of the functional diversity requires an assessment of patterns of trait variation across different ecological scales. In this study, we examine and characterize patterns of leaf trait variation for species that are broadly distributed along an elevational gradient. We focus on seven leaf traits that represent a main axis of functional differentiation in plants reflecting the balance between photosynthetic efficiency, display, and stomatal conductance. We evaluated patterns of trait variance across ecological scales (elevation, species, populations, and individuals) and examined trait covariance at both within species and across species levels, along the elevation gradient. Our results show three key patterns: (1) intraspecific leaf trait variation for broadly distributed species is comparable to the interspecific trait variation, (2) the trait variance structure is highly variable across species, and (3) trait coordination between pairs of leaf traits is evident across species along the gradient, but not always within species. Combined, our results show that trait coordination and covariance are highly idiosyncratic across broadly distributed and co-occurring species, indicating that species may achieve similar functional roles even when exhibiting different phenotypes. This result challenges the traditional paradigm of functional ecology that assumes single trait values as optimal solutions for environments. In conclusion, patterns of trait variation both across and within species should be considered in future studies that assess trade-offs among traits over environmental gradients.

Contrasting outcomes of species- and community-level analyses of the temporal consistency of functional composition

Multiple anthropogenic drivers affect every natural community, and there is broad interest in using functional traits to understand and predict the consequences for future biodiversity. There is, however, no consensus regarding the choice of analytical methods. We contrast species- and community-level analyses of change in the functional composition for four traits related to drought tolerance using three decades of repeat censuses of trees in the 50-ha Forest Dynamics Plot on Barro Colorado Island, Panama. Community trait distributions shifted significantly through time, which may indicate a shift toward more drought tolerant species. However, at the species level, changes in abundance were unrelated to trait values. To reconcile these seemingly contrasting results, we evaluated species-specific contributions to the directional shifts observed at the community level. Abundance changes of just one to six of 312 species were responsible for the community-level shifts observed for each trait. Our results demonstrate that directional changes in community-level functional composition can result from idiosyncratic change in a few species rather than widespread community-wide changes associated with functional traits. Future analyses of directional change in natural communities should combine community-, species-, and possibly individual-level analyses to uncover relationships with function that can improve understanding and enable prediction.

Linking individual-level functional traits to tree growth in a subtropical forest

Forging strong links between traits and performance is essential for understanding and predicting community assembly and dynamics. Functional trait analyses of trees that have correlated single-trait values with measures of performance such as growth and mortality have generally found weak relationships. A reason for these weak relationships is the failure to use individual-level trait data while simultaneously putting that data into the context of the abiotic setting, neighborhood composition, and the remaining axes constituting the overall phenotype. Here, utilizing detailed growth and trait data for 59 species of trees in a subtropical forest, we demonstrate that the individual-level functional trait values are strongly related to individual growth rates, and that the strength of these relationships critically depends on the context of that individual. We argue that our understanding of trait-performance relationships can be greatly improved with individual-level data so long as that data is put into the proper context.

Associations among arbuscular mycorrhizal fungi and seedlings are predicted to change with tree successional status

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.

Tree co-occurrence and transcriptomic response to drought

The distribution and co-occurrence of species are partly the outcome of their interactions with environmental drivers. Drought is a key driver related to the distribution of plant species. Drought events continue to increase in frequency and severity and identifying those aspects of plant function that are related to drought is critical. Here, we perform a community-level analysis of gene expression in relation to experimental drought and relate the similarity in gene set enrichment across species to their natural co-occurrence. Species with similar gene set enrichment in response to experimental drought tend to non-randomly co-occur in a natural stand. We demonstrate that similarity in the transcriptomic response of species to drought is a significantly better indicator of natural co-occurrence than measures of functional trait similarity and phylogenetic relatedness and that transcriptomics has the capacity to greatly enhance ecological investigations of species distributions and community structure.

Local neighbourhood and regional climatic contexts interact to explain tree performance

Tree neighbourhood modelling has significantly contributed to our understanding of the mechanisms structuring communities. Investigations into the impact of neighbouring crowding on tree performance have generally been conducted at local scales, missing important regional-scale context such as the suitability of the climate for each species. Favourable climates may enhance tree performance, but this may come at the cost of increased neighbourhood crowding and competition negatively impacting survival and growth. Through the synthesis of continental-scale forest inventory and trait datasets from the northeast USA and Puerto Rico we present an analytical approach that elucidates the important interactions between local competitive and regional climatic contexts. Our results show strong asymmetries in competitive interactions and significant niche differences that are dependent on habitat suitability. The strong interaction between local neighbourhood and regional climate highlights the need for models that consider the interaction between these two processes that have been previously ignored.

A core-transient framework for trait-based community ecology: an example from a tropical tree seedling community

Trait-based studies in community ecology have generally focused on the community as a unit where all species occur due to stochasticity, determinism or some mixture of the two. However, the processes governing population dynamics may vary greatly among species. We propose a core-transient framework for trait-based community studies where a core group of species has a strong link to the local environment while transient species have weaker responses to the environment. Consistent with the expectations of the framework, we found that common species exhibit clear linkages between performance and their environment and traits while rare species tend to have weaker or non-significant relationships. Ultimately, trait-based ecology should move beyond applying a set of processes to a community as a whole and towards quantifying inter-specific variation in the drivers of population dynamics that ultimately scale up to determine community structure.

Lack of phylogenetic signals within environmental niches of tropical tree species across life stages

The lasting imprint of phylogenetic history on current day ecological patterns has long intrigued biologists. Over the past decade ecologists have increasingly sought to quantify phylogenetic signals in environmental niche preferences and, especially, traits to help uncover the mechanisms driving plant community assembly. However, relatively little is known about how phylogenetic patterns in environmental niches and traits compare, leaving significant uncertainty about the ecological implications of trait-based analyses. We examined phylogenetic signals within known environmental niches of 64 species, at seedling and adult life stages, in a Chinese tropical forest, to test whether local environmental niches had consistent relationships with phylogenies. Our analyses show that local environmental niches are highly phylogenetically labile for both seedlings and adult trees, with closely related species occupying niches that are no more similar than expected by random chance. These findings contrast with previous trait-based studies in the same forest, suggesting that phylogenetic signals in traits might not a reliable guide to niche preferences or, therefore, to community assembly processes in some ecosystems, like the tropical seasonal rainforest in this study.

Stochastic assembly in a subtropical forest chronosequence: evidence from contrasting changes of species, phylogenetic and functional dissimilarity over succession

Deterministic and stochastic processes jointly determine the community dynamics of forest succession. However, it has been widely held in previous studies that deterministic processes dominate forest succession. Furthermore, inference of mechanisms for community assembly may be misleading if based on a single axis of diversity alone. In this study, we evaluated the relative roles of deterministic and stochastic processes along a disturbance gradient by integrating species, functional, and phylogenetic beta diversity in a subtropical forest chronosequence in Southeastern China. We found a general pattern of increasing species turnover, but little-to-no change in phylogenetic and functional turnover over succession at two spatial scales. Meanwhile, the phylogenetic and functional beta diversity were not significantly different from random expectation. This result suggested a dominance of stochastic assembly, contrary to the general expectation that deterministic processes dominate forest succession. On the other hand, we found significant interactions of environment and disturbance and limited evidence for significant deviations of phylogenetic or functional turnover from random expectations for different size classes. This result provided weak evidence of deterministic processes over succession. Stochastic assembly of forest succession suggests that post-disturbance restoration may be largely unpredictable and difficult to control in subtropical forests.

Linking leaf veins to growth and mortality rates: an example from a subtropical tree community

A fundamental goal in ecology is to link variation in species function to performance, but functional trait-performance investigations have had mixed success. This indicates that less commonly measured functional traits may more clearly elucidate trait-performance relationships. Despite the potential importance of leaf vein traits, which are expected to be related to resource delivery rates and photosynthetic capacity, there are few studies, which examine associations between these traits and demographic performance in communities. Here, we examined the associations between species traits including leaf venation traits and demographic rates (Relative Growth Rate, RGR and mortality) as well as the spatial distributions of traits along soil environment for 54 co-occurring species in a subtropical forest. Size-related changes in demographic rates were estimated using a hierarchical Bayesian approach. Next, Kendall's rank correlations were quantified between traits and estimated demographic rates at a given size and between traits and species-average soil environment. Species with denser venation, smaller areoles, less succulent, or thinner leaves showed higher RGR for a wide range of size classes. Species with leaves of denser veins, larger area, cheaper construction costs or thinner, or low-density wood were associated with high mortality rates only in small size classes. Lastly, contrary to our expectations, acquisitive traits were not related to resource-rich edaphic conditions. This study shows that leaf vein traits are weakly, but significantly related to tree demographic performance together with other species traits. Because leaf traits associated with an acquisitive strategy such as denser venation, less succulence, and thinner leaves showed higher growth rate, but similar leaf traits were not associated with mortality, different pathways may shape species growth and survival. This study suggests that we are still not measuring some of key traits related to resource-use strategies, which dictate the demography and distributions of species.

How does habitat filtering affect the detection of conspecific and phylogenetic density dependence?

Conspecific negative density dependence (CNDD) has been recognized as a key mechanism underlying species coexistence, especially in tropical forests. Recently, some studies have reported that seedling survival is also negatively correlated with the phylogenetic relatedness between neighbors and focal individuals, termed phylogenetic negative density dependence (PNDD). In contrast to CNDD or PNDD, shared habitat requirements between closely related individuals are thought to be a cause of observed positive effects of closely related neighbors, which may affect the strength and detectability of CNDD or PNDD. In order to investigate the relative importance of these mechanisms for tropical tree seedling survival, we used generalized linear mixed models to analyze how the survival of more than 10 000 seedlings of woody plant species related to neighborhood and habitat variables in a tropical rainforest in southwest China. By comparing models with and without habitat variables, we tested how habitat filtering affected the detection of CNDD and PNDD. The best-fitting model suggested that CNDD and habitat filtering played key roles in seedling survival; but that, contrary to our expectations, phylogenetic positive density dependence (PPDD) had a distinct and important effect. While habitat filtering affected the detection of CNDD by decreasing its apparent strength, it did not explain the positive effects of closely related neighbors. Our results demonstrate that a failure to control for habitat variables and phylogenetic relationships may obscure the importance of conspecific and heterospecific neighbor densities for seedling survival.

Stochastic dilution effects weaken deterministic effects of niche-based processes in species rich forests

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.

Carbon sequestration potential of second-growth forest regeneration in the Latin American tropics

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 km(2) 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.

Constancy in Functional Space across a Species Richness Anomaly

The relationship between large-scale gradients in species richness and functional diversity provides important information regarding the mechanisms driving patterns of biodiversity. A classic hypothesis in ecology is that strong interspecific interactions should result in an increase in the functional volume of assemblages as the species richness increases, whereas climatic constraints may result in no change in functional volume. Most research of this kind examines latitudinal gradients in species richness, but the results are likely confounded by underlying gradients in climate and phylogenetic composition. We take an alternative approach that examines functional richness across a tree species richness anomaly where species richness doubles from Europe to eastern North America. The results demonstrate that the functional richness on both continents saturates at a similar point as species richness increases and that the packing of functional space becomes tighter. Further, the species richness anomaly is driven primarily by genera unique to North America, but those genera contribute less than expected functional richness to the region, indicating a high level of redundancy with genera shared between the continents. Taken together, the results indicate that the species richness anomaly is associated with diversification within a climatically constrained trait space. More generally, the work demonstrates the power of utilizing species richness anomalies in biodiversity research, particularly when they are coupled with information regarding organismal function.

Biogeography and evolutionary diversification in one of the most widely distributed and species rich genera of the Pacific

The historical biogeography of many lineages-of both terrestrial and marine ocean habitats-remains poorly investigated even though remote ocean habitat covers approximately 66% of the Earth's surface. One such lineage with poorly understood biogeographic affinities across vast ocean habitat is the genus Coprosma (Rubiaceae) with numerous species, and a widespread and disjunct distribution among the far-flung insular localities of multiple Pacific Islands. Here, the first taxonomically robust phylogeny for Coprosma s.s. was dated using molecular clock techniques and indicated Coprosma s.s. diverged from its sister genus Nertera likely during or shortly after the Oligocene Marine Transgression of New Zealand. Diversification of the five major clades identified occurred in New Zealand during the Miocene, which was then followed by multiple independent dispersals from New Zealand to various localities in many directions. The pattern of Coprosma's distribution in the Pacific appears stochastic both temporally and spatially, but evolution of an orange to red fruit colour prior to nearly all inferred dispersals hints at endozoochory by birds. The number of inferred long-distance dispersals of Coprosma s.s. (>30), and number of repeated dispersals to the same insular locality from unrelated Coprosma s.s. sublineages (>8) is perhaps the most currently known for a remote Pacific-centred genus investigated to date. A New Zealand origin for a Pacific-wide dispersal of taxa is not novel, but the manner in which the temporal and spatial distribution for Coprosma s.s. was achieved contributes to a novel understanding of the historical biogeography of widespread Pacific genera that have origins in the Southern Hemisphere.