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C. E. Timothy Paine
Lecturer
Biological and Environmental Sciences
University of Stirling
Stirling FK9 4LA
United Kingdom
office +44 (0)1786 467785
email [email protected] or [email protected]
URL guianaplants, stir.ac.uk or scholar.google.com
skype cetimothypaine
Research Interests
Species coexistence, community structure, functional traits, plant growth
I am happy to share any of my data with other researchers.
Please contact me to request a dataset or a copy of the any articles listed below.
Peer-reviewed Publications
38
Pellegrini AFA, WRL Anderegg, CET Paine, WA Hoffmann, T Kartzinel, SS Rabin, D Sheil,
AC Franco, SW Pacala. 2017. Convergence of bark investment according to fire and climate
structures ecosystem vulnerability to future change. Ecology Letters. doi: 10.1111/ele.12725
abstract.
Fire regimes in savannas and forests are changing over much of the world. Anticipating the
impact of these changes requires understanding how plants are adapted to fire. Here we test
whether fire imposes a broad selective force on a key fire-tolerance trait, bark thickness, across
572 tree species distributed worldwide. We show that investment in thick bark is a pervasive
adaptation in frequently burned areas across savannas and forests in both temperate and tropical
regions where surface fires occur. Geographic variability in bark thickness is largely explained
by annual burned area and precipitation seasonality. Combining environmental and species
distribution data allowed us to assess the vulnerability to future climate and fire conditions:
tropical rainforests are especially vulnerable, whereas seasonal forests and savannas are more
robust. The strong link between fire and bark thickness provides an avenue for assessing the
vulnerability of tree communities to fire and demands inclusion in global models.
37
Chamagne, J, M Tanadini, D Frank, R Matula, CET Paine, CD Philipson, M Svátek, LA
Turnbull, D Volařík, A Hector. 2017. Forest diversity promotes individual tree growth in central
European forest stands. Journal of Applied Ecology. 54:71-79. abstract.
1. Most experimental evidence on the relationship between biodiversity and ecosystem
functioning comes from ecosystems with fast-growing plants, such as grasslands. Although
forests provide essential ecological services, they have been less well investigated.
2. We used dendrochronology to compare the tree radial growth rates of four important timber
species in replicated, spatially mapped stands that differed in tree composition and diversity
within a central European managed forest. 3. Growth rates differed among species but were
largely unaffected by the density of neighbouring trees..
4. Increasing stand diversity enhanced individual growth rates, after accounting for the effects of
tree density and size. These increases were statistically indistinguishable among the four species.
In contrast, the effects of stand and neighbourhood species composition on growth rates were
non-significant..
5. Policy implications. Our study of long-established central European forest stands revealed
levels of tree diversity can be increased in managed forests, with the potential for modest
increases in tree growth rates. These results suggest that in addition to the biodiversity and risk
mitigation benefits associated with shifting practices away from monoculture management,
increased carbon sequestration and yields in mature forests are likely to be realized. Our results
suggest that it is possible to increase forest diversity with little or no costs to production and even
with the potential for modest increases in tree growth rates.
36
Paine, CET, H Beck, J Terborgh. 2016. How mammalian predation contributes to tropical tree
community structure. Ecology. 97:3326-3336.abstract.
The recruitment of seedlings from seeds is the key demographic transition for rain forest trees.
Though tropical forest mammals are known to consume many seeds, their effects on tree
community structure remain little known. To evaluate their effects, we monitored 8000 seeds of
24 tree species using exclosure cages that were selectively permeable to three size-classes of
mammals for up to 4.4 years. Small and medium-bodied mammals removed many more seeds
than did large mammals, and they alone generated beta diversity and negative density
dependence, whereas all mammals reduced diversity and shaped local species composition.
Thus, small and medium-bodied mammals more strongly contributed to community structure and
promoted species coexistence than did large mammals. Given that seedling recruitment is seedlimited for most species, alterations to the composition of the community of mammalian seed
predators is expected to have long-term consequences for tree community structure in tropical
forests.
35
Fox C, CET Paine, B Sauterey. 2016. Citations increase with manuscript length, author number
and references cited in ecology journals. Ecology and Evolution. 6:7717-7726. abstract.
Commentary on Retractionwatch
Most top impact factor ecology journals indicate a preference or requirement for short
manuscripts; some state clearly defined word limits whereas others indicate a preference for
more concise papers. Yet evidence from a variety of academic fields indicates that, within
journals, longer papers are both more positively reviewed by referees and more highly cited. We
examine the relationship between citations received and manuscript length, number of authors,
and number of references cited for papers published in 32 ecology journals between 2009 and
2012. We find that longer papers, those with more authors, and those that cite more references
are cited more. Though paper length, author count and references cited all positively covary, an
increase in each independently predicts an increase in citations received, with estimated
relationships positive for all the journals we examined. That all three variables covary positively
with citations suggests that papers presenting more and a greater diversity of data and ideas are
more impactful. We suggest that the imposition of arbitrary manuscript length limits discourages
the publication of more impactful studies. We propose that journals abolish arbitrary word or
page limits, avoid declining papers (or requiring shortening) on the basis of length alone
(irrespective of content), and adopt the philosophy that papers should be as long as they need to
be.
34
Li X, B Schmid, W Fang, CET Paine. 2016. Net assimilation rate determines the growth rates of
14 species of subtropical forest trees. PLoS ONE. 11:e0150644 abstract.
Growth rates are of fundamental importance for plants, as individual size affects myriad
ecological processes. We determined the factors that generate variation in RGR among 14
species of trees and shrubs that are abundant in subtropical Chinese forests. We grew seedlings
for two years at four light levels in a shade-house experiment. We monitored the growth of every
juvenile plant every two weeks. After one and two years, we destructively harvested individuals
and measured their functional traits and gas-exchange rates. After calculating individual biomass
trajectories, we estimated relative growth rates using nonlinear growth functions. We
decomposed the variance in log(RGR) to evaluate the relationships of RGR with its components:
specific leaf area (SLA), net assimilation rate (NAR) and leaf mass ratio (LMR). We found that
variation in NAR was the primary determinant of variation in RGR at all light levels, whereas
SLA and LMR made smaller contributions. Furthermore, NAR was strongly and positively
associated with area-based photosynthetic rate and leaf nitrogen content. Photosynthetic rate and
leaf nitrogen concentration can, therefore, be good predictors of growth in woody species.
33
Fortunel C, CET Paine, PVA Fine, I Mesones, J-Y Goret, B Burban, J Cazal, C Baraloto. 2016.
There’s no place like home: seedling mortality contributes to the habitat specialisation of tree
species across Amazonia. Ecology Letters. 19:1256-1266. abstract.
Understanding the mechanisms generating species distributions remains a challenge, especially
in hyperdiverse tropical forests. We evaluated the role of rainfall variation, soil gradients and
herbivory on seedling mortality, and how variation in seedling performance along these gradients
contributes to habitat specialization. In a four-year experiment, replicated at the two extremes of
the Amazon basin, we reciprocally transplanted 4638 tree seedlings of 41 habitat-specialist
species from seven phylogenetic lineages among the three most important forest habitats of
lowland Amazonia. Rainfall variation, flooding and soil gradients strongly influenced seedling
mortality, whereas herbivory had negligible impact. Seedling mortality varied strongly among
habitats, consistent with predictions for habitat specialists in most lineages. This suggests that
seedling performance is a primary determinant of the habitat associations of adult trees across
Amazonia. It further suggests that tree diversity, currently mostly harbored in terra firme forests,
may be strongly impacted by the predicted climate changes in Amazonia.
32
Chamagne J, CET Paine, R Stejskal, D Volařík, J Šebesta, F Trnka, T Koutecký, P Švarc, M
Svátek, A Hector, R Matula. 2016. Do the rich get richer? Varying effects of tree species identity
and diversity on the richness of understory taxa. Ecology. 97:2364-2373 abstract.
Understory herbs and soil invertebrates play key roles in soil formation and nutrient cycling in
forests. Studies suggest that diversity in the canopy and in the understory are positively
associated, but they often confound the effects of tree diversity with those of tree species identity
and abiotic conditions. We combined extensive field sampling with structural equation modeling
to evaluate the simultaneous effects of tree diversity on the species diversity of understory herbs,
beetles, and earthworms. The diversity of earthworms and saproxylic beetles was directly and
positively associated with tree diversity, presumably because species of both these taxa
specialize on certain species of trees. Tree identity also strongly affected diversity in the
understory, especially for herbs, likely as a result of interspecific differences in canopy light
transmittance or litter decomposition rates. Our results suggest that changes in forest
management will disproportionately affect certain understory taxa. For instance, changing
canopy diversity will affect the diversity of earthworms and saproxylic beetles more than
changes in tree species composition, whereas the converse would be expected for understory
herbs and detritivorous beetles. We conclude that the effects of tree diversity on understory taxa
can vary from positive to neutral and may affect biogeochemical cycling in temperate forests.
We recommend to maintain high tree diversity, thereby promoting the diversity of multiple
understory taxa, and to reduce the abundance of tree species that may reduce understory
diversity.
31
Courtois EA, KG Dexter, CET Paine, D Stien, J Engel, C Baraloto, J Chave. 2016. Evolutionary
patterns of volatile terpene emissions across 202 tropical tree species. Ecology and Evolution. 6:
2854-2864. abstract.
Plant responses to natural enemies include formation of secondary metabolites acting as direct or
indirect defences. Volatile terpenes represent one of the most diverse groups of secondary
metabolites. We aimed to explore evolutionary patterns of volatile terpene emission. We
measured the composition of damage-induced volatile terpenes from 202 Amazonian tree
species, spanning the angiosperm phylogeny. Volatile terpenes were extracted with Solid Phase
Micro Extraction and desorbed in a Gas Chromatography-Mass Spectrometry for compound
identification. The chemical diversity of the terpene blend showed a strong phylogenetic signal
as closely related species emitted a similar number of compounds. Closely related species also
tended to have compositionally similar blends, although this relationship was weak. Meanwhile,
the ability to emit a given compound showed no significant phylogenetic signal for 200 of 286
compounds, indicating a high rate of diversification in terpene synthesis and/or great variability
in their expression. Three lineages (Magnoliales, Laurales, Sapindales), showed exceptionally
high rates of terpene diversification. Of the 70 compounds found in >10% of their species, 69
displayed significant correlated evolution with at least one other compound. These results
provide insights into the complex evolutionary history of volatile terpenes in angiosperms, while
highlighting the need for further research into this important class of compounds.
30
Paine CET, C Baraloto, S Diaz. 2015. Optimal strategies for sampling functional traits in
species-rich forests. Functional Ecology 29:1325-1331. abstract Lay summary
Functional traits provide insight into a variety of ecological questions, yet the optimal sampling
method to estimate the community-level distribution of plant functional trait values remains a
subject of debate, especially in species-rich forests. We present a simulation analysis of the trait
distribution of a set of nine completely sampled permanent plots in the lowland rain forests of
French Guiana. Increased sampling intensity consistently improved accuracy in estimating
community-weighted means and variances of functional trait values, whereas there was
substantial variation among functional traits, and minor differences among sampling strategies.
Thus, investment in intensified sampling yields a greater improvement in the accuracy of
estimation than does an equivalent investment in sampling design complication. Notably, ‘taxonfree’ strategies frequently had greater accuracy than did abundance-based strategies, which had
the additional cost of requiring botanical surveys. We conclude that there is no substitute for
extensive field sampling to accurately characterize the distribution of functional trait values in
species-rich forests.
29
Velazquez E, CET Paine, F May, T Wiegand. 2015. Linking trait similarity to interspecific
spatial associations in a moist tropical forest. Journal of Vegetation Science 26:1068-1079.
abstract.
Aim: Community assembly theory predicts that niche differentiation promotes the spatial
clustering of functionally dissimilar species, whereas habitat filtering has the converse effect. We
used these predictions to assess the relative effects of habitat filtering and niche differentiation
on recruit community assembly over spatial (5- and 30-m neighborhoods) and temporal (20-yr)
scales in the forest dynamics plot at Barro Colorado Island, Panama.
Methods: We integrated data on the spatial patterns of ≥1 cm DBH (diameter at 1.3 m above
ground) recruits with data on seven functional traits for 64 species. First we quantified the
interspecific association patterns of all species pairs i and j using the K-function Kij(r) and the
nearest neighbor distribution function Dij(r). Second, for those pairs with significant spatial
associations, we calculated an index of interspecific spatial association using the results of these
two summary statistics. Finally, we examined the relationship between interspecific spatial
association and trait similarity using simple and partial Mantel tests.
Results: In all censuses, almost one-half of species pairs had no spatial associations, but for pairs
that were significantly spatially associated, positive relationships between trait similarity and
spatial association occurred in 5-m and 30-m neighborhoods, whereas significant negative
relationships only appeared in 5-m neighborhoods. This suggests that habitat filtering was more
important than niche differentiation in assembling recruit communities at 5- and 30-m scales.
Habitat filtering mainly acted upon traits related to topographic habitat preferences and dispersal
mode, whereas spatial association was inversely related to similarity in terms of wood specific
gravity and shade-tolerance.
Conclusions: Our findings suggest that both stochastic and deterministic processes operate in
species-rich ecological communities, but the role of habitat filtering and niche differentiation as
determinants of community assembly vary over spatial and temporal scales. Species cooccurrence was driven by habitat filtering at small and large scales, but also by a combination of
niche differentiation and weaker-competitor exclusion effects at smaller scales. Temporal
variations in the importance of habitat filtering and niche differentiation could be related to the
occurrence of disturbances such as tree-falls. Our results emphasize the role of trait-based
processes in plant community assembly.
28
Gagnon PR, HA Passmore, M Slocum, JA Myers, KE Harms, WJ Platt, CET Paine. 2015. Fuels
and fires influence vegetation via above- and below-ground pathways in a high-diversity plant
community. Journal of Ecology 4:1009-1019. abstract.
1. Fire strongly influences plant populations and communities around the world, making it an
important agent of plant evolution. Fire influences vegetation through multiple pathways, both
above- and belowground. Few studies have yet attempted to tie these pathways together in a
mechanistic way through soil heating even though the importance of soil heating for plants in
fire-prone ecosystems is increasingly recognized.
2. Here we combine an experimental approach with structural equation modeling (SEM) to
simultaneously examine multiple pathways through which fire might influence herbaceous
vegetation. In a high-diversity longleaf pine groundcover community in Louisiana, USA, we
manipulated fine-fuel biomass and monitored the resulting fires with high-resolution
thermocouples placed in vertical profile above- and belowground.
3. We predicted that vegetation response to burning would be inversely related to fuel load
owing to relationships among fuels, fire temperature, duration, and soil heating.
4. We found that fuel manipulations altered fire properties and vegetation responses, of which
soil heating proved to be a highly accurate predictor. Fire duration acting through soil heating
was important for vegetation response in our SEMs, whereas fire temperature was not. 5. Our
results indicate that in this herbaceous plant community, fire duration is a good predictor of soil
heating, and therefore, of vegetation response to fire. Soil heating may be the key determinant of
vegetation response to fire in ecosystems wherein plants persist by resprouting or reseeding from
soil-stored propagules.
6. Synthesis. Our SEMs demonstrate how the complex pathways through which fires influence
plant community structure and dynamics can be examined simultaneously. Comparative studies
of these pathways across different communities will provide important insights into the ecology,
evolution, and conservation of fire-prone ecosystems.
27
Paine CET, Amissah L, Auge H, Baraloto C, Baruffol M, Bourland N, Bruelheide H, Daînou K,
de Gouvenain R, Doucet J-L, Doust S, Fine P, Fortunel C, Haase J, Holl K, Jactel H, Li X,
Kitajima K, Koricheva J, Martínez-Garza C, Messier C, Paquette A, Philipson C, Piotto D,
Poorter L, Posada J, Potvin C, Rainio K, Russo SE, Ruiz-Jaen M, Scherer-Lorenzen M, Webb
CO, Wright SJ, Zahawi R, Hector A. 2015. Globally, functional traits are weak predictors of
juvenile tree growth, and we do not know why. Journal of Ecology 4: 978-989. abstract
1. Plant functional traits, in particular specific leaf area (SLA), wood density and seed mass, are
often good predictors of individual tree growth rates within communities. Individuals and species
with high SLA, low wood density and small seeds tend to have faster growth rates.
2. If community-level relationships between traits and growth have general predictive value, then
similar relationships should also be observed in analyses that integrate across taxa,
biogeographic regions, and environments. Such global consistency would imply that traits could
serve as valuable proxies for the complex suite of factors that determine growth rate, and,
therefore, could underpin a new generation of robust dynamic vegetation models. Alternatively,
growth rates may depend more strongly on the local environment or growth-trait relationships
may vary along environmental gradients.
3. We tested these alternative hypotheses using data on 27,352 juvenile trees, representing 278
species from 27 sites on all forested continents, and extensive functional-trait data, 38% of which
were obtained at the same sites at which growth was assessed. Data on potential
evapotranspiration (PET), which summarises the joint ecological effects of temperature and
precipitation, were obtained from a global database.
4. We estimated size-standardized relative height growth rates (SGR) for all species, then related
them to functional traits and PET using mixed-effect models for the fastest-growing species and
for all species together.
5. Both the mean and 95th percentile SGR were more strongly associated with functional traits
than with PET. PET was unrelated to SGR at the global scale. SGR increased with increasing
SLA and decreased with increasing wood density and seed mass, but these traits explained only
3.1% of the variation in SGR. SGR-trait relationships were consistently weak across families and
biogeographic zones, and over a range of tree statures. Thus, the most widely studied functional
traits in plant ecology were poor predictors of tree growth over large scales.
6. Synthesis. We conclude that these functional traits alone may be unsuitable for predicting
growth of trees over broad scales. Determining the functional traits that predict vital rates under
specific environmental conditions may generate more insight than a monolithic global
relationship can offer.
26
Fortunel C, CET Paine, PVA Fine, NJB Kraft, C Baraloto. 2014. Environmental factors predict
community functional composition in Amazonian forests. Journal of Ecology. 102:145-155.
abstract
1. The consequences of biodiversity loss for ecosystem services largely depend on the functional
identities of extirpated species. However, poor descriptions of spatial patterns of community
functional composition across landscapes hamper the making of accurate predictidiv
class="abs"ons, particularly in highly diverse tropical regions. Therefore understanding how
community functional composition varies across environmental gradients remains an important
challenge.
2. We sampled 15 functional traits in 800 Neotropical tree species across 13 forest plots
representative of the broad climatic and soil gradients encompassed by three widespread lowland
forest habitats (terra firme forests on clay-rich soils, seasonally flooded forests, and white-sand
forests) at opposite ends of Amazonia (Peru and French Guiana). We combined univariate and
multivariate approaches to test the magnitude and predictability of environmental filtering on
community leaf and wood functional composition.
3. Directional shifts in community functional composition correlated with environmental
changes across the 13 plots, with denser leaves, stems and roots in forests occurring in
environments with limited water and soil-nutrient availability. Critically, these relationships
allowed us to accurately predict the functional composition of 61 additional forest plots from
environmental data alone.
4. Synthesis: Environmental filtering consistently shapes the functional composition of highly
diverse tropical forests at large scales across the terra firme, seasonally flooded and white-sand
forests of lowland Amazonia. Environmental factors drive and allow the prediction of variation
in community functional composition among habitat types in Amazonian forests.
25
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. 2013. Rare species
support vulnerable functions in high-diversity ecosystems. PLoS Biology 11:e1001569 abstract
Background
Around the world, the human-induced collapse of populations and species has triggered a sixth
mass extinction crisis, with rare species being the first to disappear. Although the role of species
diversity in the maintenance of ecosystem processes has been widely investigated, the role of
rare species remains controversial. A critical issue is whether common species insure against the
loss of functions supported by rare species. This issue is even more critical in species-rich
ecosystems where high functional redundancy among species is likely and where it is thus often
assumed that ecosystem functioning is buffered against species loss.
Methodology/Principal Findings
Here, using extensive datasets of species occurrences and functional traits from three highly
diverse ecosystems (coral reef fishes, alpine plants and tropical trees), we demonstrate that the
most distinct combinations of traits are supported predominantly by rare species at both local
abundance and regional scales. Moreover, species that have low functional redundancy and are
likely to support the most vulnerable functions, are rarer than expected by chance in all three
ecosystems. For instance, 63% and 98% of fish species that are likely to support highly
vulnerable functions in coral reef ecosystems are locally and regionally rare, respectively. For
alpine plants, 32% and 89% of such species are locally and regionally rare, respectively.
Remarkably, 47% of fish species and 55% of tropical tree species which are likely to support
highly vulnerable functions have only one individual per sample on average.
Conclusions/Significance
Our results emphasize the importance of rare species conservation, even in highly diverse
ecosystems, which are thought to exhibit high functional redundancy. Rare species have value
beyond that of aesthetics or taxonomic diversity; they disproportionately increase the breadth of
functions provided by ecosystems. As such, they are likely to insure against future uncertainty
arising from climate change and the ever-increasing anthropogenic pressures on ecosystems at a
range of scales. Our results call for a more detailed understanding of the role of rarity and
functional vulnerability in ecosystem functioning. close
24
Paine CET, N Norden, J Chave, P-M Forget, C Fortunel, KG Dexter, C Baraloto. 2012.
Phylogenetic density dependence and environmental filtering predict seedling mortality in a
tropical forest. Ecology Letters 15:34-41. abstract 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.
23
Paine CET, TR Marthews, DR Vogt, D Purves, M Rees, A Hector, LA Turnbull. 2012. How to
fit nonlinear plant growth models and calculate growth rates: an update for ecologists. Methods
in Ecology and Evolution. 3:245-256. abstract 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.
22
Paine CET, M Stenflo, C Philipson, P Saner, R Bagchi, RC Ong, A Hector. 2012. Differential
growth responses in seedlings of ten species of Dipterocarpaceae to experimental shading and
defoliation. Journal of Tropical Ecology. 28:377-384. abstract
The responses of plants to shade and foliar herbivory jointly affect growth rates and community
assembly. We grew 600 seedlings of ten species of the economically important Dipterocarpaceae
in experimental gradients of shading (0.3–47.0% of full sunlight) and defoliation (0, 25%, 50%
or 75% of leaf area removed). We assessed stem diameters initially, after 2 and 4 mo, and
calculated relative growth rates (RGR) with a linear model. Shading interacted with defoliation,
reducing RGR by 21.6% in shaded conditions and 8.9% in well-lit conditions. We tested three
hypotheses for interspecific trade-offs in growth responses to shading and defoliation. They
could be positively related, because both reduce a plant’s access to carbon, or inversely related
because of trade-offs between herbivore resistance and tolerance. We observed, however, that
species varied in their response to shading, but not defoliation, precluding an interspecific tradeoff and suggesting that plants tolerate shade and herbivorywith differing strategies. Shading most
strongly reduced the growth of species with less-dense wood and larger seeds. The strong and
variable growth responses to shade, contrasted with the weak and uniform responses to
defoliation, suggest that variation in light availabilitymore strongly affects the growth of tropical
tree seedlings, and thus community assembly, than does variation in herbivory.
21
Baraloto C, OJ Hardy, CET Paine, KG Dexter, C Cruaud, LT Dunning, M-A Gonzalez, J-F
Molino, D Sabatier, V Savolainen, J Chave. 2012. Using functional traits and phylogenetic trees
to examine the assembly of tropical tree communities. Journal of Ecology. 100:690-701. abstract
1. Niche theory proposes that species differences underlie both coexistence within
communities and the differentiation in species composition among communities via limiting
similarity and envi- ronmental filtering. However, it has been difficult to extend niche theory to
species-rich communities because of the empirical challenge of quantifying niches for many
species. This has motivated the development of functional and phylogeny-based approaches in
community ecology, which represent two different means of approximating niche attributes.
2. Here, we assess the utility of plant functional traits and phylogenetic relationships in
predicting community assembly processes using the largest trait and phylogenetic data base to
date for any set of species-rich communities.
3. We measured 17 functional traits for all 4672 individuals of 668 tree species co-occurring in
nine tropical rain forest plots in French Guiana. Trait variation was summarized into two
ordination axes that reflect species niche overlap.
4. We also generated a dated molecular phylogenetic tree based on DNA sequencing of two
plastid loci (rbcL and matK) comprising 97% of the individuals and 91% of the species in the
plots.
5. We found that, on average, co-occurring species had greater functional and, to a lesser extent,
phylogenetic similarity than expected by chance.
6. We also found that functional traits and their ordination loadings showed significant, albeit
weak, phylogenetic signal, suggesting that phylogenetic distance provides pertinent information
on niche overlap in tropical tree communities.
7. Synthesis. We provide the most comprehensive examination to date of the relative importance
of environmental filtering and limiting similarity in structuring tropical tree communities. Our
results confirm that environmental filtering is the overriding influence on community assembly
in these species-rich systems.
20
Baraloto C, B Hérault, CET Paine, H Massot, L Blanc, D Bonal, J-F Molino, EA Nicolini, D
Sabatier. 2012. Contrasting taxonomic and functional responses of a tropical tree community to
selective logging. Journal of Applied Ecology. 49:861-870. abstract
1. Considerable debate surrounds the extent to which tropical forests can be managed for
resource extraction while conserving biodiversity and ecosystem properties, which depend on
functional composition. Here we evaluate the compatibility of these aims by examining the
effects of logging on taxonomic and functional diversity and composition in a tropical forest.
2. Twenty years after selective logging, we inventoried 4140 stems regenerating in logging gaps
and adjacent undisturbed areas, and we integrated a database of 13 functional traits describing
leaf and wood economics of tropical trees.
3. We found no differences in taxonomic and functional richness among habitats, but logging
gaps had significantly higher taxonomic evenness and especially functional evenness.
4. Logging also effected striking, long-term changes in both species and functional composition.
In particular, the xylem density of recruits in logging gaps was 6% less than in unlogged forests,
and leaves were 11% less tough, and had 6 - 13% greater mineral nutrient concentrations.
5. Synthesis and applications. Our results suggest that managers of tropical forests should limit
overall surface area converted to logging gaps by creating fewer, larger gaps during selective
logging, to reduce impacts on the taxonomic and functional composition of the regenerating
stand.
19
Courtois EA, C Baraloto, CET Paine, P Petronelli, P-A Blandinieres, D Stien, E Höuel, J-M
Bessière, J Chave. 2012. Differences in volatile terpene composition between the bark and leaves
of tropical tree species. Phytochemistry 82:81-88. abstract
Volatile terpenes are among the most diverse class of defensive compounds in plants, and they
are implicated in both direct and indirect defense against herbivores. In terpenes, both the
quantity and the diversity of compounds appear to increase the efficiency of defense as a diverse
blend of compounds provides a more efficient protection against a broader range of herbivores
and limits the chances that an enemy evolves resistance. Theory predicts that plant defensive
compounds should be allocated differentially among tissues according to the value of the tissue,
its cost of construction and the herbivore pressure on it. We collected volatile terpenes from bark
and leaves of 178 individual tree belonging to 55 angiosperm species in French Guiana and
compare the kind, amount, and diversity of compounds in these tissues. We hypothesized that in
woody plants, the outermost part of the trunk should hold a more diverse blend of volatile
terpenes. Additionally, as herbivore communities associated with the leaves is different to the
one associated with the bark, we also hypothesized that terpene blends should be distinct in the
bark vs. the leaves of a given species. We found that the mixture of volatile terpenes released by
bark is different and more diverse than that released by leaves, both in monoterpenes and
sesquiterpenes. This supports our hypothesis and further suggests that the emission of terpenes
by the bark should be more important for trunk defense than previously thought.
18
Shipley B, CET Paine, C Baraloto. 2012. Quantifying the importance of local niche-based and
stochastic processes to tropical tree community assembly. Ecology. 93:760-769. abstract
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, speciesrich, 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. Traitbased 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.
17
Paine CET, C Baraloto, J Chave, B Hérault. 2011. Functional traits of individual trees reveal
ecological constraints on community assembly in tropical rain forests. Oikos 120:720-727.
abstract
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.
16
Hérault B, B Bachelot, L Poorter, V Rossi, F Bongers, J Chave, CET Paine, F Wagner, C
Baraloto. 2011. Functional traits shape ontogenetic growth trajectories of rain forest tree species.
Journal of Ecology 99:1431-1440. abstract 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.
15
Eastman J, CET Paine, O Hardy. 2011. SPACODIR: structuring of phylogenetic diversity in
ecological communities. Bioinformatics 27:2437-2438. abstract R package
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.rproject.org
14
Zalamea P-C, P Heuret, F Munoz, CET Paine, C Sarmiento, D Sabatier, PR Stevenson. 2011.
Continental-scale patterns of Cecropia phenology: Evidence from herbarium specimens.
Proceedings of the Royal Society B 278:2437-2445. abstract 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.
13
Sarmiento C, S Patiño, CET Paine, J Beauchêne, A Thibaut, C Baraloto. 2011. Withinindividual variation in tropical tree wood density. American Journal of Botany 98:140-149
abstract
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.
12
Paine CET, C Stahl, E Courtois, S Patiño, C Sarmiento, C Baraloto. 2010. Functional
explanations for variation in bark thickness in tropical rain forest trees. Functional Ecology
24:1202-1210 abstract 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.
11
Baraloto C, CET Paine, L Poorter, J Beauchene, D Bonal, J Chave, A-M Domenach, B Hérault,
S Patino, J-C Roggy. 2010. Decoupled leaf and stem economics in rain forest trees. Ecology
Letters 13:1338-1347 abstract 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 wholeplant 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.
10
Gagnon PR, HA Passmore, WJ Platt, JA Myers, CET Paine, KE Harms. 2010. Does
pyrogenicity protect burning plants? Ecology 91:3481-3486. (Cover article) abstract
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.
9
Gonzalez M, A Roger E Courtois, F Jabot, N Norden, CET Paine, C Baraloto, C Thébaud, 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 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.
8
Baraloto C, CET Paine, S Patiño, D. Bonal, B. Hérault, J. Chave. 2010. Functional trait
variation and sampling strategies in species-rich communities. Functional Ecology 24:208-216.
abstract 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 values 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 relative performance of designs was strongly positively correlated with relative financial cost, suggesting 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.
7
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.
6
Paine CET, KE Harms. 2009. Quantifying the effects of seed arrival and environmental
conditions on tropical seedling community structure. Oecologia 160:139-150 abstract
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.
5
Paine CET, KE Harms, J Ramos. 2009. Supplemental irrigation increases seedling performance
and diversity in a tropical forest. Journal of Tropical Ecology 25:171-180. abstract
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 lowlandassociated 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.
4
Paine CET, KE Harms, SA Schnitzer, 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
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 ambientdensity 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.
Photo credit:
CET Paine
3
Terborgh J, G Nuñez, N Pitman, F Cornejo, P Alvarez, V Swamy, B Pringle, CET Paine. 2008.
Tree recruitment in an "empty" forest. Ecology 89:1757-1768. (Cover article) abstract
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 largeseeded 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.
2
Paine CET, H Beck. 2007. Seed predation by Neotropical rainforest mammals increases
diversity in seedling recruitment. Ecology 88:3076-3087. abstract
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
Harms, KE, CET Paine. 2003. Regeneración de árboles tropicales e implicaciones para el
manejo de bosques naturales. Ecosistemas 2003/3. abstract
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.
Book
Paine CET 2007. Seedling Recruitment in a Tropical Rain Forest: Ecological factors that
maintain diversity and shape community structure. 80 pp. AV Akademikerverlag. ISBN: 978-3639-41885-9 Available at Morebooks
Book Chapter
Paine, CET, Alvarez-Loayza, P 2013 Estructura y dinámica de la comunidad de plántulas de la
Estación Biológica Cocha Cashu. Reporte Manu 2013. pp. 34–43. abstract pdf
The seedling community at Estación Biologica Cocha Cashu has been monitored since 2003. We
followed the fates of 5,149 individual tree seedlings over the course of seven years. Here, we
relate baseline data on the structure and dynamics of the seedling community. The seedlings
belonged to 265 taxa representing 61 families of plants. Many species were very rare: 28% of the
total species richness occurred at a density of less than 1 individual per 100m2. The list of mostcommon seedlings was largely concordant with that of adult trees, at least at the genus level,
though interesting discrepancies occur. More-common species were more strongly spatially
clumped, probably because they tend to generate high- density ‘seedling carpets’. This report
illustrates the diversity and dynamism of the seedling layer of this extraordinary forest. Longterm observational studies are essential for detecting patterns among rare species, which may not
be detectable in smaller-scale studies. Thus, the value of our monitoring program at EBCC
should continue to grow.
Website
Paine CET and P Alvarez, Manuplants.org. Photos detailing the flowers, fruit, seeds, and
seedlings of plants from Southeastern Peru. http://manuplants.org
Theses
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.
Education & Professional Experience
Lecturer
2012–now
Biological and Environmental Sciences
University of Stirling
Stirling, UK
Postdoctoral Institute of Evolutionary Biology and Environmental Studies
2010–2012 researcher University of Zurich
Zurich, Switzerland
Postdoctoral ENGREF-UMR EcoFoG
2008–2010
researcher Kourou, French Guiana
Ph.D.
Department of Biological Sciences
2002–2007
Louisiana State University
Baton Rouge, Louisiana USA
2005
Likelihood Methods in Forest Ecology
Cary Institute for Ecosystem Studies
Millbrook, New York USA
B.A.
Departments of Biology and Earth Sciences
1995–1999
Dartmouth College
Hanover, New Hampshire USA
Dartmouth Field Course in Tropical Ecology
1999
Costa Rica and Jamaica
Grants and Awards
2013
2009
2008
2007
2004
2003
2002–
2006
1999
LabEx CEBA €11,000
Biotropica Award for Excellence in Tropical Biology and Conservation
CNRS Amazonie grant, Co-PI with Chris Baraloto €9,000
CNRS Amazonie grant, Co-PI with Natalia Norden €5,660
Daisy and William Luke Botany Teaching Assistant Award $500
OAS LASPAU Fellowship $2,500
Sigma Xi Grant-in-Aid of Research $1,000
LSU Board of Regents Graduate Fellowship and enhancement $23,000 per year for
four years
Undergraduate Thesis with Honors ‘Holocene water quality and climate fluctuations
in the New World District, Montana’
Teaching
2013Now
Community Ecology, Coordinator, Stirling BIOU9CE
Tropical Ecology, Coordinator, Stirling BIOU9TE
Environmental Geography Field Course, Coordinator, Stirling SCIU3FC
Introduction to Ecology, Contributor, Stirling ENVU3EC
Population Ecology, Contributor, Stirling BIOU9PO
Plant Ecology, Contributor, Stirling BIOU9PE
Biology Field Course, Contributor, Stirling BIOU7FC
Ecology Field Course, Contributor, Stirling SCIU3LO
Statistics Using R, Contributor, Stirling SCIU7SR
2011
Ecological Field Skills, Contributor, Stirling SCIU2FS
Tropical Forest Ecology Lectures
2007
2006
Analysing plant growth: Nonlinear regression and mixed-effect models Lecture 1
Lecture 2
Plant Taxonomy (LSU Biology 4041)
Mycology (LSU Biology 4054)
Presentations
BES Annual Symposium, Cambridge UK. ‘Rooting mechanistic growth models in
physiology & traits to enhance generality’
ATBC Annual Meeting, Arusha Tanzania. ‘The effects of resource competition and
climate on the growth of Cecropia’
Universidad de los Andes, Bogotá, Colombia. ‘Algunos factores que afectan la diversidad
2010
de los bosques tropicales’ Invited presentation. pdf
ESA Annual Meeting, Pittsburgh, Pennsylvania. ‘A bestiary of non-linear functions for
growth analysis’ pdf
ATBC Annual Meeting, Bali, Indonesia. ‘Functional explanations for variation in bark
thickness in tropical rain forest trees’ pdf
5th International Symposium-Workshop on Frugivores and Seed Dispersal, Montpellier,
France. ‘A general, community-level test of the Janzen-Connell hypothesis’ pdf
Universität Zürich, Zurich, Switzerland. ‘Rain forest diversity, and the factors that affect
it’ powerpoint keynote
ESA Annual Meeting. Milwaukee, Wisconsin. ‘Quantifying habitat filtering in the forests
2008
of French Guiana using functional traits’
ATBC Annual Meeting. Paramaribo, Suriname. ‘Water availability, seedling performance,
and diversity in a tropical forest’ powerpoint keynote
ESA Annual Meeting. San Jose, California. ‘What shapes tropical seedling community
2007
structure? Seed dispersal versus environmental conditions’ powerpoint keynote
ESA Annual Meeting. Memphis, Tennessee. ‘Predation, more than water availability,
2006
limits seedling recruitment’
2011
2005
ESA Annual Meeting. Montreal, Quebec. ‘Restricted zones of influence limit competition
among seedlings of a tropical tree’
Museum of Natural Science, Louisiana State University. Baton Rouge, Louisiana.
‘Mammals, not competition, affect seedling recruitment’
Professional Activities
Biotropica
Subject Editor
Functional Ecology
Reviewer
Professional
Memberships
Languages
Photographs
published in
Basic & Applied Ecology; Biotropica (3); Colombia Forestal; Ecology;
Ecology Letters (2); Functional Ecology (2); Journal of Applied Vegetation
Science (2); Journal of Biogeography; Journal of Ecology (2); Journal of
Tropical Ecology; Journal of Vegetation Science (3); US National Science
Foundation; Oecologia; PLoS ONE and Proceedings of the Royal Society B
(since 2012)
British Ecological Society, Ecological Society of America, Association for
Tropical Biology and Conservation
Native: English. Fluent: French, Spanish, R, HTML, PHP, MySQL.
Conversant: C++. Studying: German.
Books: The Encyclopedia of Snake Species. Amazonie: Une aventure
scientifique et humaine. An illustrated guide to the orchids of French Guiana
(Cover photo). Newspapers: La Nacion (Costa Rica). Websites: Encyclopedia
of Life: Iriartea deltoidea, Paris polyphylla, Roridula gorgonias, Aristolochia
tricaudata, Pseudomalmea diclina, Randia ruiziana, Polygala scleroxylon,
Phytelephas macrocarpa, and many other taxa. Carnegie Museum of Natural
History. Schildpadden.net: Podocnemis unifilis & Chelonoidis denticulata.
Testudines.org. Heterotrophic Plants. Antark.net. Oblog. Touristlink