Ecological factors affecting the diversity of tropical tree seedlings

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 xii 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

A bestiary of non-linear functions for growth analysis

Plant growth is an essential ecological process, integrating across scales from physiology to community dynamics. Predicting the growth of plants is essential to understand a wide range of ecological issues, including competition, plant-herbivore interactions and ecosystem functioning.
A challenge in modeling plant growth is that growth rates almost universally decrease with increasing size, for a variety of reasons. Traditional analyses of growth are hampered by the need to remain within the structures of linear models, which handle this slowing poorly. We demonstrate the implementation of a variety of non-linear models that are more appropriate for modeling plant growth than are the traditional, linear, models.
Ecological inference is frequently based on growth rates, rather than model parameters. Traditional calculations of absolute and relative growth rates assume that they are invariant with respect to time or biomass, which is almost never valid. We advocate and demonstrate the calculation of function-derived growth rates, which highlight the time- and biomass-varying nature of growth. We further show how uncertainty in estimated parameter values can be propagated to express uncertainty in absolute and relative growth rates. 
The use of non-linear models and function-derived growth rates can facilitate testing novel hypotheses in population and community ecology. Even so, we acknowledge that fitting non-linear models can be tricky. To foster the spread of these methods, we make many recommendations for ecologists to follow when their hypotheses lead them into the subject of plant growth. 
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Optimal strategies for sampling functional traits in species-rich forests

1. 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. 2. 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. 3. 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. 4. Thus, investment in intensified sampling yields a greater improvement in the accuracy of estimation than does an equivalent investment in sampling design complication. 5. Notably, ‘taxon-free' strategies frequently had greater accuracy than did abundance-based strategies, which had the additional cost of requiring botanical surveys. 6. We conclude that there is no substitute for extensive field sampling to accurately characterize the distribution of functional trait values in species-rich forests

Towards the general mechanistic prediction of community dynamics

”What controls the distribution and abundance of organisms”? This question, at the heart of the dynamics of ecological communities, would have been familiar to the earliest ecologists. Having lain effectively abandoned for many years, community dynamics today is a vibrant research topic of great conceptual interest with practical import for conservation, ecological management, ecosystem services and the responses of ecological communities to climate change.  We describe how modern coexistence theory can be applied to predict community dynamics through the use of demography. We explore the challenges that limit the deployment of this demographic framework, and the tools from phylogenetic and functional ecology that have been used to surmount them.  Finding existing tools not altogether sufficient, we propose the use of ‘hard’ functional traits and physiological tolerances of environmental conditions and low resource availability to extend the demographic framework so that the dynamics of a broader range of ecological communities can be accurately predicted.  We illustrate these new approaches with two case studies. Given the urgent need to accurately forecast the dynamics of ecological communities, we hope that many ecologists will adopt these tools

spacodiR: structuring of phylogenetic diversity in ecological communities

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. Contact: [email protected]; [email protected]

Initial test results on bolometers for the Planck high frequency instrument

We summarize the fabrication, flight qualification, and dark performance of bolometers completed at the Jet Propulsion Laboratory for the High Frequency Instrument (HFI) of the joint ESA/NASA Herschel/Planck mission to be launched in 2009. The HFI is a multicolor focal plane which consists of 52 bolometers operated at 100 mK. Each bolometer is mounted to a feedhorn-filter assembly which defines one of six frequency bands centered between 100-857 GHz. Four detectors in each of five bands from 143-857 GHz are coupled to both linear polarizations and thus measure the total intensity. In addition, eight detectors in each of four bands (100, 143, 217, and 353 GHz) couple only to a single linear polarization and thus provide measurements of the Stokes parameters, Q and U, as well as the total intensity. The measured noise equivalent power (NEP) of all detectors is at or below the background limit for the telescope and time constants are a few ms, short enough to resolve point sources as the 5 to 9 arc min beams move across the sky at 1 rpm

An exploratory case study of interactive simulation for teaching Ecology

This paper explores the effectiveness of interactive simulation for teaching a selected complex subject, Ecology, in higher education. Specifically, we carry out a lab intervention using interactive agent based simulation, to teach the complex concept of spatially-explicit predator prey interaction to undergraduate students of an advanced module: BIOU9CE (Community Ecology & Conservation Applications) at the University of Stirling. We propose use of Netlogo, an interactive agent-based simulation tool, and evaluate its effectiveness for learning and teaching of interactive simulation developed specifically for the classroom, compared with an existing, less interactive, simulation tool (R)

Within-individual variation of trunk and branch xylem density in tropical trees

Premise of the study: Wood density correlates with mechanical and physiological strategies of trees and is important for estimating 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

Differential growth responses in seedlings of ten species of Dipterocarpaceae to experimental shading and defoliation

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 trade-off and suggesting that plants tolerate shade and herbivory with 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 availability more strongly affects the growth of tropical tree seedlings, and thus community assembly, than does variation in herbivor

Defective phagocyte association during infection of Galleria mellonella with Yersinia pseudotuberculosis is detrimental to both insect host and microbe

Adhesins facilitate bacterial colonization and invasion of host tissues and are considered virulence factors, but their impact on immune-mediated damage as a driver of pathogenesis remains unclear. Yersinia pseudotuberculosis encodes for a multivalent adhesion molecule (MAM), a mammalian cell entry (MCE) family protein and adhesin. MAMs are widespread in Gram-negative bacteria and enable enteric bacteria to colonize epithelial tissues. Their role in bacterial interactions with the host innate immune system and contribution to pathogenicity remains unclear. Here, we investigated how Y. pseudotuberculosis MAM contributes to pathogenesis during infection of the Galleria mellonella insect model. We show that Y. pseudotuberculosis MAM is required for efficient bacterial binding and uptake by hemocytes, the host phagocytes. Y. pseudotuberculosis interactions with insect and mammalian phagocytes are determined by bacterial and host factors. Loss of MAM, and deficient microbe–phagocyte interaction, increased pathogenesis in G. mellonella. Diminished phagocyte association also led to increased bacterial clearance. Furthermore, Y. pseudotuberculosis that failed to engage phagocytes hyperactivated humoral immune responses, most notably melanin production. Despite clearing the pathogen, excessive melanization also increased phagocyte death and host mortality. Our findings provide a basis for further studies investigating how microbe- and host-factors integrate to drive pathogenesis in a tractable experimental system