Paine CET, M Stenflo, C Philipson, P Saner, R Bagchi, RC Ong and A Hector. In review. Growth responses of ten Bornean species of dipterocarps to shading and defoliation. Journal of Tropical Ecology.

Mouillot D, DR Bellwood, C Baraloto, J Chave, R Galzin, M Harmelin-Vivien, M Kulbicki, S Lavergne, S Lavorel, N Mouquet, CET Paine, J Renaud & W Thuiller. In review. Rare species support vulnerable functions in high-diversity ecosystems. Science.

Baraloto C, B Hérault, CET Paine, H Massot, L Blanc, D Bonal, J-F Molino, EA Nicolini, D Sabatier. In review. Contrasting taxonomic and functional responses of a tropical tree community to selective logging. Journal of Applied Ecology.

Paine CET, TR Marthews, DR Vogt, D Purves, M Rees, A Hector and LA Turnbull. In press. How to fit nonlinear plant growth models and calculate growth rates: an update for ecologists. Methods in Ecology and Evolution. doi: 10.1111/j.2041-210X.2011.00155.x abstract pdf appendices

1) Plant growth is a fundamental ecological process, integrating across scales from physiology to community dynamics and ecosystem properties. Recent improvements in plant growth modeling have allowed deeper understanding and more accurate predictions for a wide range of ecological issues, including competition among plants, plant-herbivore interactions and ecosystem functioning.
2) One challenge in modeling plant growth is that, for a variety of reasons, relative growth rate (RGR) almost universally decreases with increasing size, though traditional calculations assume that RGR is constant. Nonlinear growth models are flexible enough to account for varying growth rates.
3) We demonstrate a variety of nonlinear models that are appropriate for modeling plant growth and, for each, show how to calculate function-derived growth rates, which allow unbiased comparisons among species at a common time or size. We show how to propagate uncertainty in estimated parameters to express uncertainty in growth rates. Fitting nonlinear models can be challenging, so we present extensive worked examples and practical recommendations, all implemented in R.
4) The use of nonlinear models coupled with function-derived growth rates can facilitate the testing of novel hypotheses in population and community ecology. For example, the use of such techniques has allowed better understanding of the components of RGR, the costs of rapid growth, and the linkage between host and parasite growth rates. We hope this contribution will demystify nonlinear modeling and persuade more ecologists to use these techniques.

Baraloto C, O Hardy, CET Paine, KG Dexter, C Cruaud, L Dunning, M-A Gonzalez, J-F Molino, D Sabatier, V Savolainen and J Chave. In review. Integrating functional traits and phylogenetic trees to examine the assembly of tropical tree communities. Journal of Ecology.

Shipley B, CET Paine and C Baraloto. In press. Quantifying the importance of local niche-based and stochastic processes to tropical tree community assembly. Ecology. doi: 10.1890/11-0944.1 abstract pdf

Although niche-based and stochastic processes, including dispersal limitation and demographic stochasticity, can each contribute to community assembly, it is difficult to quantify the relative importance of each process in natural vegetation. Here, we extend Shipley’s maxent model (Community Assembly by Trait Selection, CATS) for the prediction of relative abundances to incorporate both trait-based filtering and dispersal limitation from the larger landscape and develop a statistical decomposition of the proportions of the total information content of relative abundances in local communities that are attributable to trait-based filtering, dispersal limitation and demographic stochasticity. We apply the method to tree communities in a mature, species-rich, tropical forest in French Guiana at 1, 0.25 and 0.04 ha scales. Trait data consisted of species’ means of 17 functional traits measured over both the entire meta-community and separately in each of nine 1-ha plots. Trait means calculated separately for each site always gave better predictions. There was clear evidence of trait-based filtering at all spatial scales. Trait-based filtering was the most important process at the 1-ha scale (34%), whereas demographic stochasticity was the most important at smaller scales (37 - 53%). Dispersal limitation from the meta-community was less important and approximately constant across scales (~9%), and there was also an unresolved association between site-specific traits and meta-community relative abundances. Our method allows one to quantify the relative importance of local niche-based and meta-community processes and demographic stochasticity during community assembly across spatial and temporal scales.

Paine CET, N Norden, J Chave, P-M Forget, C Fortunel, KG Dexter and C Baraloto. 2012. Environmental filtering and phylogenetically correlated functional traits predict seedling mortality in a tropical forest. Ecology Letters 15: 34-41. abstract pdf appendices R scripts

Negative density dependence (NDD) and environmental filtering (EF) shape community assembly, but their relative importance is poorly understood. Recent studies have shown that seedling’s mortality risk is positively related to the phylogenetic relatedness of neighbors. However, natural enemies, whose depredations often cause NDD, respond to functional traits of hosts rather than phylogenetic relatedness per se. To understand the roles of NDD and EF in community assembly, we assessed the effects on seedling mortality of functional similarity, phylogenetic relatedness and stem density of neighboring seedlings and adults in a species-rich tropical forest. Mortality risks increased for common species when their functional traits departed substantially from the neighborhood mean, and for all species when surrounded by close relatives. This indicates that NDD affects community assembly more broadly than does EF, and leads to the tentative conclusion that natural enemies respond to phylogenetically correlated traits. Our results affirm the prominence of NDD in structuring species-rich communities.

Paine CET, C Baraloto, J Chave and B Hérault. 2011. Functional traits of individual trees reveal ecological constraints on community assembly in tropical rain forests. Oikos 120: 720-727. abstract pdf

Niche differentiation and ecological filtering are primary ecological processes that shape community assembly, but their relative importance remains poorly understood. Analyses of the distributions of functional traits can provide insight into the community structure generated by these processes. We predicted the trait distributions expected under the ecological processes of niche differentiation and environmental filtering, then tested these predictions with a dataset of 4672 trees located in nine 1-ha plots of tropical rain forest in French Guiana. Five traits related to leaf function (foliar N concentration, chlorophyll content, toughness, tissue density and specific leaf area), and three traits related to stem function (trunk sapwood density, branch sapwood density, and trunk bark thickness), as well as laminar surface area, were measured on every individual tree. There was far more evidence for environmental filtering than for niche differentiation in these forests. Furthermore, we contrasted results from species-mean and individual-level trait values. Analyses that took within-species trait variation into account were far more sensitive indicators of niche differentiation and ecological filtering. Species-mean analyses, by contrast, may underestimate the effects of ecological processes on community assembly. Environmental filtering appeared somewhat more intense on leaf traits than on stem traits, whereas niche differentiation affected neither strongly. By accounting for within-species trait variation, we were able to more properly consider the ecological interactions among individual trees and between individual trees and their environment. In so doing, our results suggest that the ecological processes of niche differentiation and environmental filtering may be more pervasive than previously believed.

Hérault B, B Bachelot, L Poorter, V Rossi, F Bongers, J Chave, CET Paine, F Wagner and C Baraloto. 2011. Functional traits shape ontogenetic growth trajectories of rain forest tree species. Journal of Ecology 99: 1431-1440. abstract pdf appendices

1. Functional traits are posited to explain interspecific differences in performance, but these relationships are difficult to describe for long-lived organisms such as trees, which exhibit strong ontogenetic changes in demographic rates. Here, we use a size-dependent model of tree growth to test the extent to which of 17 functional traits related to leaf and stem economics, adult stature and seed size predict the ontogenetic trajectory of tree growth.
2. We used a Bayesian modelling framework to parameterize and contrast three size-dependent diameter growth models using 16 years of census data from 5524 individuals of 50 rainforest tree species: a size-dependent model, a size-dependent model with species-specific parameters, and a size-dependent model based on functional traits.
3. Most species showed clear hump-shaped ontogenetic growth trajectories and, across species, maximum growth rate varied nearly ten-fold, from 0.58 to 5.51 mm year^-1. Most species attained their maximum growth at 60% of their maximum size, whereas the magnitude of ontogenetic changes in growth rate varied widely among species.
4. The trait model provided the best compromise between explained variance and model parsimony, and needed considerably fewer parameters than the model with species terms.
5. Stem economics and adult stature largely explained interspecific differences in growth strategy. Maximum absolute diameter growth rates increased with increasing adult stature and leaf δ¹³C and decreased with increasing wood density. Species with light wood had the greatest potential to modulate their growth, resulting in hump-shaped ontogenetic growth curves. Seed size and leaf economics, generally thought to be of paramount importance for plant performance, had no significant relationships with the growth parameters.
6. Synthesis. Our modelling approach offers a promising way to link demographic parameters to their functional determinants and, hence, to predict growth trajectories in species-rich communities with little parameter inflation, bridging the gap between functional ecology and population demography.

Eastman J, CET Paine and O Hardy. 2011. spacodiR: structuring of phylogenetic diversity in ecological communities. Bioinformatics 27: 2437-2438. abstract R package pdf

Motivation: spacodiR is a cross-platform package, written for the R environment, for studying partitioning of diversity among natural communities in space and time. Complementing and extending existing software, spacodiR allows for hypothesis testing and parameter estimation in studying spatial structuring of species-, phylogenetic-, and trait-diversities.
Availability: Integrated with other software in the R environment and with well-documented and demonstrated functions, spacodiR is an open-source package and available at http://cran.r-project.org

Zalamea P-C, P Heuret, F Munoz, CET Paine, C Sarmiento, D Sabatier and PR Stevenson. 2011. Continental-scale patterns of Cecropia phenology: Evidence from herbarium specimens. Proceedings of the Royal Society B 278: 2437-2445. abstract pdf appendix

Plant phenology is concerned with the timing of recurring biological events. Though phenology has traditionally been studied using intensive surveys of a local flora, results from such surveys are difficult to generalize to broader spatial scales. In this study, contrastingly, we assembled a continental-scale dataset of herbarium specimens for the emblematic genus of neotropical pioneer trees, Cecropia, and applied Fourier spectral and cospectral analyses to investigate the reproductive phenology of 35 species. We detected significant annual, sub-annual and continuous patterns, and discuss the variation in patterns within and among climatic regions. Although previous studies have suggested that pioneer species generally produce flowers continually throughout the year, we found that at least one third of Cecropia species are characterized by clear annual flowering behavior. In previous studies, we found that it is possible to estimate the age of C. obtusa and C. sciadophylla individuals by observing their morphology and the annual periodicity of flowering events. With the assumption that the age of pioneer trees reflects the age of the secondary forest, our findings suggest that at least 21 Cecropia species could be used as chronometers to date secondary forests. We verified our results against field survey data gathered from the literature. Our findings indicate that herbarium material is a reliable resource for use in the investigation of large-scale patterns in plant phenology, offering a promising complement to local intensive field studies.

Sarmiento C, S Patiño, CET Paine, J Beauchêne, A Thibaut and C Baraloto. 2011. Within-individual variation in tropical tree wood density. American Journal of Botany 98:140-149 abstract pdf

• Premise of the study: Wood density correlates with mechanical and physiological strategies of trees and is important for esti- mating global carbon stocks. Nonetheless, the relationship between branch and trunk xylem density has been poorly explored in neotropical trees. Here, we examine this relationship in trees from French Guiana and its variation among different families and sites, to improve the understanding of wood density in neotropical forests.
• Methods: Trunk and branch xylem densities were measured for 1909 trees in seven sites across French Guiana. A major-axis fit was performed to explore their general allometric relationship and its variation among different families and sites.
• Key results: Trunk xylem and branch xylem densities were significantly positively correlated, and their relationship explained 47% of the total variance. Trunk xylem was on average 9% denser than branch xylem. Family-level differences and interactions between family and site accounted for more than 40% of the total variance, whereas differences among sites explained little variation.
• Conclusions: Variation in xylem density within individual trees can be substantial, and the relationship between branch xylem and trunk xylem densities varies considerably among families and sites. As such, whole-tree biomass estimates based on non- destructive branch sampling should correct for both taxonomic and environmental factors. Furthermore, detailed estimates of the vertical distribution of wood density within individual trees are needed to determine the extent to which relying solely upon measures of trunk wood density may cause carbon stocks in tropical forests to be overestimated.

Paine CET, C Stahl, E Courtois, S Patiño, C Sarmiento and C Baraloto. 2010. Functional explanations for variation in bark thickness in tropical rain forest trees. Functional Ecology 24:1202-1210 abstract pdf appendices R script

1. The complex structure of tree bark reflects its many functions, which include structural support as well as defense against fire, pests and pathogens. Thick bark, however, might limit respiration by the living tissues of the trunk. Nevertheless, little research has addressed community-level variation in bark thickness, and to the best of our knowledge, no one has tested multiple hypotheses to explain variation in bark thickness.
2. We conducted an extensive survey of bark thickness within and among species of trees in the tropical rain forests of French Guiana. Trunk bark thickness increased by 1.2 mm per 10 cm increase in stem diameter, and varied widely at all taxonomic levels. Mean trunk bark thickness was 4.5 mm (range: 0.5 – 29 mm), which was less that found in two Amazonian rain forests in previous studies. This survey of bark thickness should be of use for forest management since tree survival through fire is strongly predicted by bark thickness.
3. We combined the survey data with multiple datasets to test several functional hypotheses proposed to explain variation in bark thickness. We found bark to provide an average of 10% of the flexural rigidity of tree stems, which was substantially less than that found in the only other study of bark stiffness. Bark thickness was uncorrelated with species’ association with fire-prone habitats, suggesting that the influence of fire on bark thickness does not extend into moist-forest habitats. There was also little evidence that bark thickness is affected by its function as a defense against herbivory. Nor was there evidence that thick bark limits trunk respiration.
4. A re-analysis of previously collected anatomical data indicated that variation in rhytidome (non-conducting outer bark) thickness explains much of the variation in overall bark thickness. Since rhytidome is primarily involved in protecting the living tissues of the trunk, we suggest that bark thickness is driven mostly by its defensive function.
5. Functional explanations for the variation in bark thickness were not clear-cut. Nevertheless, this study provides a foundation for further investigation of the functional bases of bark in tropical trees.

Baraloto C, CET Paine, L Poorter, J Beauchene, D Bonal, J Chave, A-M Domenach, B Hérault, S Patino and J-C Roggy. 2010. Decoupled leaf and stem economics in rain forest trees. Ecology Letters 13: 1338-1347 abstract pdf appendices

Cross-species analyses of plant functional traits have shed light on factors contributing to differences in performance and distribution, but to date most studies have focused on either leaves or stems. We extend these tissue-specific analyses of functional strategy toward a whole-plant approach by integrating data on functional traits for 13,448 leaves and wood tissues from 4,672 trees representing 668 species of Neotropical trees. Strong correlations among traits previously defined as the leaf economics spectrum reflect a tradeoff between investments in productive leaves with rapid turnover versus costly physical leaf structure with a long revenue stream. A second axis of variation, the "stem economics spectrum", defines a similar trade-off at the stem level: dense wood versus high wood water content and thick bark. Most importantly, these two axes are orthogonal, suggesting that tradeoffs operate independently at the leaf and at the stem levels. By simplifying the multivariate ecological strategies of tropical trees into positions along these two spectra, our results provide a basis to improve global vegetation models predicting responses of tropical forests to global change.

Gagnon PR, HA Passmore, WJ Platt, JA Myers, CET Paine and KE Harms. 2010. Does pyrogenicity protect burning plants? Ecology 91:3481-3486. (Cover article) abstract pdf

Pyrogenic plants dominate many fire-prone ecosystems. Their prevalence suggests some advantage to their enhanced flammability, but researchers have had difficulty tying pyrogenicity to individual-level advantages. Based on our review, we propose that enhanced flammability in fire-prone ecosystems should protect the belowground organs and nearby propagules of certain individual plants during fires. We base this hypothesis on five points: 1) organs and propagules by which many fire-adapted plants survive fires are vulnerable to elevated soil temperatures during fires; 2) the degree to which burning plant fuels heat the soil depends mainly on residence times of fires and on fuel location relative to the soil; 3) fires and fire effects are locally heterogeneous, meaning that individual plants can affect local soil heating via their fuels; 4) how a plant burns can thus affect its fitness; 5) in many cases, natural selection in fire-prone habitats should therefore favor plants that burn rapidly and retain fuels off the ground. We predict an advantage of enhanced flammability for plants whose fuels influence local fire characteristics and whose regenerative tissues or propagules are affected by local variation in fires. Our “pyrogenicity as protection” hypothesis has the potential to apply to a range of life histories. We discuss implications for ecological and evolutionary theory and suggest considerations for testing the hypothesis.

Gonzalez M, A Roger E Courtois, F Jabot, N Norden, CET Paine, C Baraloto, C Thébaud and J Chave. 2010. Shifts in species and phylogenetic diversity between sapling and tree communities indicate negative density-dependence in a lowland rain forest. Journal of Ecology 98: 137-146. abstract pdf appendices

1. As trees in a given cohort progress through ontogeny, many individuals die. This risk of mortalty is unevenly distributed across species because of many processes such as habitat filtering, inter-specific competition and negative density dependence. Here, we predict and test the patterns that such ecological processes should inscribe on both species and phylogenetic diversity as plants recruit from saplings to the canopy.
2. We compared species and phylogenetic diversity of sapling and tree communities at two sites in French Guiana. We surveyed 2084 adult trees in four 1-ha tree plots and 943 saplings in sixteen 16-m2 subplots nested within the tree plots. Species diversity was measured using Fisher’s alpha (species richness) and Simpson’s index (species evenness). Phylogenetic diversity was measured using Faith’s phylogenetic diversity (phylogenetic richness) and Rao’s quadratic entropy index (phylogenetic evenness). The phylogenetic diversity indices were inferred using four phylogenetic hypotheses: two based on rbcLa plastid DNA sequences obtained from the inventoried individuals with different branch lengths, a global phylogeny available from the Angiosperm Phylogeny Group, and a combination of both.
3. Taxonomic identification of the saplings was performed by combining morphological and DNA barcoding techniques using three plant DNA barcodes (psbA-trnH, rpoC1 and rbcLa). DNA barcoding enabled us to increase species assignment and to assign unidentified saplings to molecular operational taxonomic units.
4. Species richness was similar between saplings and trees, but in about half of our comparisons, species evenness was higher in trees than in saplings. This suggests that negative density dependence plays an important role during the sapling-to-tree transition.
5. Phylogenetic richness increased between saplings and trees in about half of the comparisons. Phylogenetic evenness increased significantly between saplings and trees in a few cases (4 out of 16) and only with the most resolved phylogeny. These results suggest that negative density dependence operates largely independently of the phylogenetic structure of communities.
6. Synthesis. By contrasting species richness and evenness across size classes, we suggest that nega- tive density dependence drives shifts in composition during the sapling-to-tree transition. In addition, we found little evidence for a change in phylogenetic diversity across age classes, suggesting that the observed patterns are not phylogenetically constrained.

Baraloto C, CET Paine, S Patiño, D. Bonal, B. Hérault and J. Chave. 2010. Functional trait variation and sampling strategies in species-rich communities. Functional Ecology 24: 208-216. abstract pdf appendices

1. Despite considerable interest in the application of plant functional traits to questions of community assembly and ecosystem structure and function, there is no consensus on the appropriateness of sampling designs to obtain plot-level estimates in diverse plant communities.
2. We measured 10 plant functional traits describing leaf and stem morphology and ecophysiology for all trees in nine 1-ha plots in terra firme lowland tropical rain forests of French Guiana (N = 4709).
3. We calculated, by simulation, the mean and variance in trait values for each plot and each trait expected under seven sampling methods and a range of sampling intensities. Simulated sampling methods included a variety of spatial designs, as well as the application of existing data base val- ues to all individuals of a given species.
4. For each trait in each plot, we defined a performance index for each sampling design as the proportion of resampling events that resulted in observed means within 5% of the true plot mean, and observed variance within 20% of the true plot variance.
5. The relative performance of sampling designs was consistent for estimations of means and variances. Data base use had consistently poor performance for most traits across all plots, whereas sampling one individual per species per plot resulted in relatively high performance. We found few differences among different spatial sampling strategies; however, for a given strategy, increased intensity of sampling resulted in markedly improved accuracy in estimates of trait mean and variance.
6. We also calculated the financial cost of each sampling design based on data from our ‘every individual per plot’ strategy and estimated the sampling and botanical effort required. The rela- tive performance of designs was strongly positively correlated with relative financial cost, sug- gesting that sampling investment returns are relatively constant.
7. Our results suggest that trait sampling for many objectives in species-rich plant communities may require the considerable effort of sampling at least one individual of each species in each plot, and that investment in complete sampling, though great, may be worthwhile for at least some traits.

Courtois E, CET Paine, P-A Blandinières, D. Stein, J-M Bessière, E Houël, C Baraloto, J Chave. 2009. Diversity of the volatile organic compounds emitted by 55 species of tropical trees: A survey in French Guiana. Journal of Chemical Ecology 35: 1349-1362. abstract

Volatile organic compounds (VOCs) are pro- duced by a broad range of organisms, from bacteria to mammals, and they represent a vast chemical diversity. In plants, one of the preeminent roles of VOCs is their repellent or cytotoxic activity, which helps the plant deter its predators. Most studies on VOCs emitted by vegetative parts have been conducted in model plant species, and little is known about patterns of VOC emissions in diverse plant communities. We conducted a survey of the VOCs released immediately after mechanical damage of the bark and the leaves of 195 individual trees belonging to 55 tropical tree species in a lowland rainforest of French Guiana. We discovered a remarkably high chemical diversity, with 264 distinct VOCs and a mean of 37 compounds per species. Two monoterpenes (α-pinene and limonene) and two sesquiterpenes (β-caryophyllene and α-copaene), which are known to have cytotoxic and deterrent effects, were the most frequent compounds in the sampled species. As has been established for floral scents, the blend of VOCs is largely species-specific and could be used to discriminate among 43 of the 55 sampled species. The species with the most diverse blends were found in the Sapindales, Laurales, and Magnoliales, indicating that VOC diversity is not uniformly distributed among tropical species. Interspecific variation in chemical diversity was caused mostly by variation in sesquiterpenes. This study emphasizes three aspects of VOC emission by tropical tree species: the species-specificity of the mixtures, the importance of sesquiterpenes, and the wide-ranging complexity of the mixtures.

Paine CET and KE Harms. 2009. Quantifying the effects of seed arrival and environmental conditions on tropical seedling community structure. Oecologia 160: 139-150 abstract pdf

Though it is recognized that both stochastic and deterministic processes structure all communities, empirical assessments of their relative importance are rare, particularly within any single community. In this paper, we quantify the dynamic effects of dispersal assembly and niche assembly on the seedling layer in a diverse Neotropical rain forest. The two theories make divergent predictions regarding the roles of seed arrival and environmental heterogeneity in generating community structure. Put simply, dispersal assembly posits that the stochasticity inherent to seed arrival structures communities, whereas niche assembly suggests that heterogeneity in post-dispersal environmental conditions is more important. We experimentally sowed 15,132 seeds of eight tree species at varying levels of density and diversity. Every six months we censused the seedlings that germinated and assessed the abiotic and biotic conditions of each plot. We assessed the density, diversity, and species composition of three nested subsets of the seedling layer: seedlings germinated from sown seeds, all seedlings germinated between July 2003 and 2004, and all woody seedlings. We partitioned the variance in density and diversity of each subset of the seedling layer into components representing seed-addition treatments and environmental conditions at 6- to 12-month intervals. Seed additions initially explained more variance in the density and diversity than did environmental heterogeneity for seven of eight sown species, but explained little variance in the density or diversity of the entire seedling layer. Species composition was better explained by seed-addition treatments than by environmental heterogeneity for all three subsets and in all time periods. Nevertheless, the variance in community structure explained by seed-addition treatments declined over the twoyears following germination, presaging shifts in the relative importance of dispersal assembly and niche assembly. Our study quantifies how dispersal assembly and niche assembly may vary among the components of an ecological community and shift dynamically through time.

Paine CET, KE Harms and J Ramos. 2009. Water availability increases seedling performance and diversity in a tropical forest. Journal of Tropical Ecology 25: 171-180. abstract pdf

Diversity is positively correlated with water availability at global, continental and regional scales. With the objective of better understanding the mechanisms that drive these relationships, we investigated the degree to which variation in water availability affects the performance (recruitment, growth and survival) of juvenile trees. Precipitation was supplemented throughout two dry seasons in a seasonal moist forest in south-eastern Peru. Supplementing precipitation by 160 mm mo^-1 , we increased soil moisture by 17%. To generate seedling communities of known species composition, we sowed 3840 seeds of 12 species. We monitored the fates of the 554 seedlings recruited from the sown seeds, as well as 1856 older non-sown seedlings (10 cm < height < 50 cm), and 2353 saplings (> 1 m tall). Watering significantly enhanced young seedling growth and survival, increasing stem density and diversity. Watering diminished the recruitment of species associated with upland forests, but increased the survival of both upland- and lowland-associated species. Though supplemental watering increased the growth of older seedlings, their density and diversity were unaffected. Sapling performance was insensitive to watering. We infer that variation in dry-season water availability may affect seedling community structure by differentially affecting recruitment and increasing overall survival. These results suggest that differential seedling recruitment and survival may contribute to the observed relationships between water availability, habitat associations and patterns of tree species richness.

Paine CET, KE Harms, SA Schnitzer and WP Carson. 2008. Weak competition among tropical tree seedlings: implications for species coexistence. Biotropica 40: 432-440. This paper was selected for the 2009 Biotropica Award for Excellence in Tropical Biology and Conservation abstract pdf citation

The intensity of competition among forest tree seedlings is poorly understood, but has important ramifications for their recruitment and for the maintenance of species diversity. Intense competition among seedlings could allow competitively dominant species to exclude subordinate species. Alternatively, the low density and small stature of forest tree seedlings could preclude intense interseedling competition. In this case, other processes, such as size-asymmetric competition with adults, interactions with consumers, or neutral dynamics would prevail as those structuring the forest understory. We tested the intensity of, and potential for, intraspecific competition among tree seedlings of three species (Brosimum alicastrum, Matisia cordata, and Pouteria reticulata) in two Neotropical rain forests. We reduced stem densities by up to 90 percent and monitored individual growth and survival rates for up to 24 mo. Individual growth and survival rates were generally unrelated to stem density. Contrary to the predicted behavior of intensely competing plant populations, the distribution of individual heights did not become more left-skewed with time for any species, regardless of plot density; i.e., excesses of short, suppressed individuals did not accumulate in high-density plots. We further measured the overlap of zones of influence (ZOIs) to assess the potential for resource competition. Seedling ZOIs overlapped only slightly in extremely dense monodominant plots, and even less in ambient-density plots of mixed composition. Our results thus suggest that interseedling competition was weak. Given the low density of tree seedlings in Neotropical forests, we infer that resource competition among seedlings may be irrelevant to their recruitment.

Terborgh J, G Nuñez, N Pitman, F Cornejo, P Alvarez, V Swamy, B Pringle and CET Paine. 2008. Tree recruitment in an "empty" forest. Ecology 89: 1757-1768. (Cover article) abstract pdf

To assess how the decimation of large vertebrates by hunting alters recruitment processes in a tropical forest, we compared the sapling cohorts of two structurally and compositionally similar forests in the Rio Manu floodplain in southeastern Peru. Large vertebrates were severely depleted at one site, Boca Manu (BM), whereas the other, Cocha Cashu Biological Station (CC), supported an intact fauna. At both sites we sampled small (>1 m tall, <1 cm dbh) and large (>1 cm and <10 cm dbh) saplings in the central portion of 4-ha plots within which all trees >10 cm dbh were mapped and identified. This design ensured that all conspecific adults within at least 50 m (BM) or 55 m (CC) of any sapling would have known locations.
We used the Janzen-Connell model to make five predictions about the sapling cohorts at BM with respect to CC: (1) reduced overall sapling recruitment, (2) increased recruitment of species dispersed by abiotic means, (3) altered relative abundances of species, (4) prominence of large-seeded species among those showing depressed recruitment, and (5) little or no tendency for saplings to cluster closer to adults at BM. Our results affirmed each of these predictions.
Interpreted at face value, the evidence suggests that few species are demographically stable at BM and that up to 28% are increasing and 72% decreasing. Loss of dispersal function allows species dispersed abiotically and by small birds and mammals to substitute for those dispersed by large birds and mammals. Although we regard these conclusions as preliminary, over the long run, the observed type of directional change in tree composition is likely to result in biodiversity loss and negative feedbacks on both the animal and plant communities. Our results suggest that the best, and perhaps only, way to prevent compositional change and probable loss of diversity in tropical tree communities is to prohibit hunting. (Photo credit: CET Paine)

Paine CET and H Beck. 2007. Seed predation by Neotropical rainforest mammals increases diversity in seedling recruitment. Ecology 88: 3076-3087. abstract pdf

Seed dispersal and seedling recruitment (the transition of seeds to seedlings) set the spatiotemporal distribution of new individuals in plant communities. Many terrestrial rain forest mammals consume post-dispersal seeds and seedlings, often inflicting density-dependent mortality. In part because of density-dependent mortality, diversity often increases during seedling recruitment, making it a critical stage for species coexistence. We determined how mammalian predators, adult tree abundance, and seed mass interact to affect seedling recruitment in a western Amazonian rain forest. We used exclosures that were selectively permeable to three size classes of mammals: mice and spiny rats (weighing <1 kg), medium-sized rodents (1-12 kg), and large mammals (20-200 kg). Into each exclosure, we placed seeds of 13 tree species and one canopy liana, which varied by an order of magnitude in adult abundance and seed mass. We followed the fates of the seeds and resulting seedlings for at least 17 months. We assessed the effect of each mammalian size class on seed survival, seedling survival and growth, and the density and diversity of the seedlings that survived to the end of the experiment. Surprisingly, large mammals had no detectable effect at any stage of seedling recruitment. In contrast, small- and medium-sized mammals significantly reduced seed survival, seedling survival, and seedling density. Furthermore, predation by small mammals increased species richness on a per-stem basis. This increase in diversity resulted from their disproportionately intense predation on common species and large-seeded species. Small mammals thereby generated a rare-species advantage in seedling recruitment, the critical ingredient for frequency dependence. Predation by small (and to a lesser extent, medium-sized) mammals on seeds and seedlings significantly increases tree species diversity in tropical forests. This is the first long-term study to dissect the effects of various mammalian predators on the recruitment of a diverse set of tree species.

Harms, KE and CET Paine. 2003. Regeneración de árboles tropicales e implicaciones para el manejo de bosques naturales. Ecosistemas 2003/3. abstract pdf

El reclutamiento exitoso desde semillas en bosques neotropicales implica una secuencia de etapas. La disponibilidad del polen y recursos consumibles por los árboles maternales puede limitar el número de semillas producidas. La dispersión de semillas a un sitio determinado puede ser limitada por la densidad o la dispersión de árboles frutales, o por el agrupamiento impuesto por los procesos de dispersión de semillas. El establecimiento de semillas dispersadas puede ser limitado por la mortalidad debida a enemigos naturales, por ejemplo depredadores de semillas y herbivoros, o por factores abióticos tales como la disponibilidad de agua, nutrientes y luz. Como la limitación impuesta por estas etapas puede verse afectada por la explotación forestal selectiva, es necesario investigar el efecto de las prácticas selvícolas sobre cada etapa en la dinámica del bosque.

Paine CET 2007. Seedling Recruitment in a Tropical Rain Forest: Ecological factors that maintain diversity and shape community structure. 80 pp. VDM Verlag Dr. Müller, Saarbrucken, Germany. ISBN: 978-3-8364-2926-9 Available at Barnes & Noble or Amazon

Paine CET and P Alvarez, Manuplants.org. Photos detailing the flowers, fruit, seeds, and seedlings of plants from Southeastern Peru. http://manuplants.org

Paine CET 2007. Ecological factors affecting the diversity of tropical tree seedlings. 134 pp. Ph.D. Dissertation, Louisiana State University, Baton Rouge, LA. abstract english español

Seed dispersal and seedling establishment - the two stages in seedling recruitment - set the spatiotemporal distribution of new individuals in plant communities. Diversity often increases at the seed to seedling transition, making it critical for species coexistence. Debate continues regarding the effects of each stage on the community structure of diverse forests. Neutral theories postulate a strong role of dispersal, whereas niche-differentiation theories suggest that environmental conditions may be more important. This dissertation tested the effects of dispersal, competition and predation on the structure of the seedling layer in a pristine Amazonian rainforest.
Seed-addition experiments broadly tested the relative importance of dispersal and environmental conditions on seedling community structure. Dispersal treatments explained more variance in community structure than did environmental conditions. This was the first variance-partitioning study to show that dispersal affects not only seedling density, but also diversity and species composition. Two more narrowly focused studies tested the intensity of competition among seedlings, and examined the effects of various mammalian predators on seedling recruitment. Evidence for inter-seedling competition was weak: individual growth and survival rates were generally unrelated to stem density, and seedlings' zones of influence rarely overlapped substantially. As predators, small and medium-sized mammals reduced seedling density, whereas large mammals had no detectable effects. Furthermore, small mammals generated a rare-species advantage, the fundamental element of frequency dependence.
Integrating the three studies, we suggest that dispersal is more important for seedling community structure than are environmental conditions. Given the low density of seedlings in Neotropical forests, we infer that competition among tree seedlings is largely irrelevant to their recruitment. Seed predators operated in a distinctly non-neutral manner, preferentially removing seeds of common and large-seeded species. Despite the powerful effects of predation, dispersal explained more variance in seedling recruitment than did all aspects of environmental variation (including predation). Taken together, the results of these three experiments support a view that, at least for young plants, and at small scales, dispersal may more strongly influence the species composition of tropical trees than environmental conditions, consistent with predictions from neutral models.

Paine CET 1999. Holocene water quality and climate fluctuations in the New World District, Montana. 37 pp. Senior Honors Thesis, Dartmouth College, Hanover, NH. abstract

The question of remediating Fisher Creek to pre-mining conditions assumes importance with the closing of the New World District, Montana (NWD). Fisher Creek, which drains the area, currently has high acidity and metal concentrations. As well, there is a lack of local, temporally detailed descriptions of Holocene climate for the NWD. Both issues are addressed in this study, through the analysis of metal concentrations preserved in four ¹⁴C-dated wetland core profiles. In wetlands downwind of the NWD, metal concentrations, especially Fe, are found to increase with age. This strongly suggests that Fisher Creek has been contaminated throughout the Holocene, and that remediation is neither possible nor necessary for Fisher Creek. The 4,000 yr metal concentration record from a wetland upwind of the NWD suggests that the area was warmer and drier 3,000-1,000 ybp than earlier or later. The agreement of this depositional record with other published climate records for the region suggests that it could serve as an additional paleoclimate proxy.