Experimental tests of trophic dynamics: taking a closer look

The relative importance of bottom-up versus top-down forces, and the effect of productivity on community dynamics continue to be of much interest to ecologists. Trophic dynamic theories are difficult to test, as they require explicit knowledge of the many organisms involved, as well as the nature of the interactions between them. The Oksanen-Fretwell (OF) theory, which suggests that the relative roles of top-down and bottom-up factors vary with primary productivity, is well known in the literature, but is difficult to test rigorously. Recently, two experimental studies have tried to test OF theory. In this paper we discuss methodological problems associated with these studies that may weaken the conclusions drawn by the authors. Received: 21 April 1998 / Accepted: 30 July 1998     

杭州湾南岸大桥建设区域潮间带大型底栖动物功能群及营养等级的季节动态

2006年5月至2007年1月在杭州湾南岸跨海大桥附近潮滩共采集到32种大型底栖动物,根据其食性类型划分为5种功能群。用功能群方法对这些物种生境变化的关系进行了分析,结果表明:大型底栖动物各多样性指数在潮带间差异显著,季节间则只有Margalef种类丰度(S)和Shannon-Wiener指数(H′)存在显著性差异;各功能群密度在季节间均不存在显著性差异,而在潮带间除了浮游生物食者外,其它类群均存在显著性差异;肉食者的种类数在潮带间不存在显著性差异,而在季节间存在显著性差异,其它功能群刚好相反。滩涂大型底栖动物群落主要包括4个营养级别,各营养级的构成密度在季节间差异不显著,在潮带间则差异显著;各营养级种类数是处于第四级的肉食者季节间差异显著,潮带间变化不显著,处于第二、三营养等级的功能群则正好相反。底栖动物功能群多样性综合反映了杭州湾南岸大桥建设区域潮间带大型底栖动物群落变化情况。     

The role of biodiversity for element cycling and trophic interactions: an experimental approach in a grassland community

The focus of a new experiment, set up in Jena in spring 2002, are the effects of biodiversity on element cycles and the interaction of plant diversity with herbivores and soil fauna. The experimental design explicitly addresses criticisms provoked by previous biodiversity experiments. In particular, the choice of functional groups, the statistical separation of sampling versus complementarity effects, and testing for the effects of particular functional groups differ from previous experiments. Based on a species pool of 60 plant species common to the Central European Arrhenatherion grasslands, mixtures of one to 16 (60) species and of one to four plant functional groups were established on 90 plots (20 m × 20 m) with nested experiments. In order to test specific hypotheses 390 additional small-area plots (3.5 m × 3.5 m) were set-up. Exact replicates of all species mixtures serve to assess the variability in ecosystem responses. In a dominance experiment, the effects of interactions among nine selected highly productive species are studied. Each species is grown as monoculture replicated once.Effekte der Biodiversität auf Elementkreisläufe und Wechselwirkungen der pflanzlichen Artenvielfalt mit Bodenfauna und Herbivoren stehen im Mitttelpunkt eines neuen Experiments, das im Frühjahr 2002 in Jena eingerichtet wurde. Das Versuchsdesign berücksichtigt ausdrücklich die Kritik, die an den Aufbau früherer Biodiversitätsversuche gerichtet wurde. Die Auswahl funktioneller Gruppen von Pflanzenarten, die statistischen Möglichkeiten, die Effekte des “Sampling” gegen Komplementarität zu trennen sowie den Einfluß funktioneller Gruppen zu überprüfen, unterscheiden dieses Experiment von früheren Versuchen. Sechzig typische Pflanzenarten der zentraleuropäischen Frischwiesen (Arrhenatherion) bilden den Artenpool für den Versuch. Auf 90 Flächen wurden Artenmischungen etabliert, die 1 bis 16 (60) Arten und 1 bis 4 funktionelle Gruppen dieser Pflanzenarten enthalten. Die Versuchsparzellen haben eine Größe von 20 m × 20 m, auf denen in genesteter Anordnung verschiedene Teilexperimente durchgeführt werden. Zusätzlich wurden 390 kleine Parzellen (3.5 m × 3.5 m) angelegt, um spezifische Hypothesen zu überprüfen. Alle Arten werden hier mit je einer Wiederholung als Monokulturen kultiviert. Identische Wiederholungen aller Artenmischungen sollen deren Variabilität untersuchen. In einem Dominanz-Versuch werden die Effekte der Wechselwirkungen zwischen 9 ausgewählten hochproduktiven Arten untersucht.     

Cascading extinctions, functional complementarity, and selection in two-trophic-level model communities: A trait-based mechanistic approach

The influence of diversity on ecosystem functioning and ecosystem services is now well established. Yet predictive mechanistic models that link species traits and community-level processes remain scarce, particularly for multitrophic systems. Here we revisit MacArthur's classical consumer resource model and develop a trait-based approach to predict the effects of consumer diversity on cascading extinctions and aggregated ecosystem processes in a two-trophic-level system. We show that functionally redundant efficient consumers generate top-down cascading extinctions. This counterintuitive result reveals the limits of the functional redundancy concept to predict the consequences of species deletion. Our model also predicts that the biodiversity-ecosystem functioning relationship is different for different ecosystem processes and depends on the range of variation of consumer traits in the regional species pool, which determines the sign of selection effects. Lastly, competition among resources and consumer generalism both weaken complementarity effects, which suggests that selection effects may prevail at higher trophic levels. Our work emphasizes the potential of trait-based approaches for transforming biodiversity and ecosystem functioning research into a more predictive science.     

Phylogenetic tests of distribution patterns in South Asia: towards an integrative approach

The last four decades have seen an increasing integration of phylogenetics and biogeography. However, a dearth of phylogenetic studies has precluded such biogeographic analyses in South Asia until recently. Noting the increase in phylogenetic research and interest in phylogenetic biogeography in the region, we outline an integrative framework for studying taxon distribution patterns. While doing so, we pay particular attention to challenges posed by the complex geological and ecological history of the region, and the differences in distribution across taxonomic groups. We outline and compare three widely used phylogenetic biogeographic approaches: topology-based methods (TBMs), pattern-based methods (PBMs) and event-based methods (EBMs). TBMs lack a quantitative framework and utilize only part of the available phylogenetic information. Hence, they are mainly suited for preliminary enquiries. Both PBMs and EBMs have a quantitative framework, but we consider the latter to be particularly suited to the South Asian context since they consider multiple biogeographic processes explicitly, and can accommodate a reticulated history of areas. As an illustration, we present a biogeographic analysis of endemic Sri Lankan agamid lizards. The results provide insights into the relative importance of multiple processes and specific zones in the radiation of two speciose lizard clades.     

Experimental validation of molecular dynamics simulations of lipid bilayers: a new approach

A novel protocol has been developed for comparing the structural properties of lipid bilayers determined by simulation with those determined by diffraction experiments, which makes it possible to test critically the ability of molecular dynamics simulations to reproduce experimental data. This model-independent method consists of analyzing data from molecular dynamics bilayer simulations in the same way as experimental data by determining the structure factors of the system and, via Fourier reconstruction, the overall transbilayer scattering-density profiles. Multi-nanosecond molecular dynamics simulations of a dioleoylphosphatidylcholine bilayer at 66% RH (5.4 waters/lipid) were performed in the constant pressure and temperature ensemble using the united-atom GROMACS and the all-atom CHARMM22/27 force fields with the GROMACS and NAMD software packages, respectively. The quality of the simulated bilayer structures was evaluated by comparing simulation with experimental results for bilayer thickness, area/lipid, individual molecular-component distributions, continuous and discrete structure factors, and overall scattering-density profiles. Neither the GROMACS nor the CHARMM22/27 simulations reproduced experimental data within experimental error. The widths of the simulated terminal methyl distributions showed a particularly strong disagreement with the experimentally observed distributions. A comparison of the older CHARMM22 with the newer CHARMM27 force fields shows that significant progress is being made in the development of atomic force fields for describing lipid bilayer systems empirically.     

Marine ecosystem dynamics: Comparison of scales

When marine and terrestrial ecological systems are compared at the same time scales, there are very great differences in their relations with their physical environments. Similarities arise when comparisons are made at different time scales. There are significant consequences for management.     

Overyielding and the role of complementary use of nitrogen in wetland plant communities

Biodiversity and ecosystem functioning experiments have demonstrated that plant biomass of species grown in mixtures is often greater than plant biomass of monocultures (i.e., mixtures over yield). While we understand that plant species utilize resources differently, how a combination of species increases resource use and productivity is not well known, especially in wetland ecosystems. Here, we used a mesocosm experiment to explore diversity effects on plant biomass production and to examine the role of N partitioning as a mechanism for overyielding in wetland ecosystems. Plant functional groups (FGs) represented the unit of diversity, and we included five levels of diversity (0-4 FGs). To test for N partitioning, we used a stable isotope technique to determine niche breadth and proportion similarity of inorganic N use (NO₃⁻ and NH₄⁺) for individual FGs as well as mixtures containing 3 and 4 FGs. We found that total plant biomass increased in the first season from an average of 290 ± 60 SE g ash-free dry mass (AFDM) m⁻² at the 1 FG level to 490 ± 70 g AFDM m⁻² at the 4 FG level and in the second season from an average of 560 ± 80 g AFDM m⁻² at the 1 FG level to 1000 ± 90 g AFDM m⁻² at the 4 FG level indicating overyielding. Plant species comprising the majority of mesocosm biomass demonstrated preferential uptake of ¹⁵NO₃⁻, while species with relatively less biomass (e.g., Acorus calamus and Carex crinita) preferred ¹⁵NH₄⁺. Concentrations of ¹⁵N in biomass increased with FG richness, but only in the ¹⁵NO₃⁻ treatment. Niche breadth did not vary among levels of FG richness. We observed a greater niche overlap with an increase of FGs, with species taking up greater proportion of ¹⁵NO₃⁻ than ¹⁵NH₄⁺. Our results indicate that plant overyielding in wetland mesocosms is not the result of niche partitioning of N chemical forms, but is associated with greater uptake of NO₃.     

Characterizing the role benthos plays in large coastal seas and estuaries: A modular approach

Ecologists studying coastal and estuarine benthic communities have long taken a macroecological view, by relating benthic community patterns to environmental factors across several spatial scales. Although many general ecological patterns have been established, often a significant amount of the spatial and temporal variation in soft-sediment communities within and among systems remains unexplained. Here we propose a framework that may aid in unraveling the complex influence of environmental factors associated with the different components of coastal systems (i.e. the terrestrial and benthic landscapes, and the hydrological seascape) on benthic communities, and use this information to assess the role played by benthos in coastal ecosystems. A primary component of the approach is the recognition of system modules (e.g. marshes, dendritic systems, tidal rivers, enclosed basins, open bays, lagoons). The modules may differentially interact with key forcing functions (e.g. temperature, salinity, currents) that influence system processes and in turn benthic responses and functions. Modules may also constrain benthic characteristics and related processes within certain ecological boundaries and help explain their overall spatio-temporal variation. We present an example of how benthic community characteristics are related to the modular structure of 14 coastal seas and estuaries, and show that benthic functional group composition is significantly related to the modular structure of these systems. We also propose a framework for exploring the role of benthic communities in coastal systems using this modular approach and offer predictions of how benthic communities may vary depending on the modular composition and characteristics of a coastal system.     

Species diversity and functional assessment of macroinvertebrate communities in Austrian rivers

We applied an extensive data set from 211 locations along Austrian rivers to assess community structure and the ratios of functional feeding groups of benthic macroinvertebrates. A total of 569 taxa have been identified. At the catchment scale, the Enns, Salzach, and Traun Rivers exhibited the highest taxa richness whereas the Inn River showed the lowest richness. Beta-diversity was highest along the impounded and fragmented Enns and Drau Rivers. Consequently, high corridor diversity corresponded to a low degree of nestedness. Overall, scrapers and gathering-collectors dominated the benthic community. Further, the relationship between habitat conditions and metrics based on functional feeding groups were statistically analyzed to validate the potential of these metrics as indicators of ecosystem attributes. We examined four major ecosystem attributes: species diversity, material cycling, longitudinal material transport, and lateral material input. Multiple regression analyses for midorder rivers demonstrated that metrics were significantly related to habitat conditions. For example, the metric set indicating primary production was positively correlated with periphyton cover, dissolved oxygen, dominant sediment size, and average annual discharge. Overall, most metrics exhibited unique responses to habitat conditions, implying that they are useful proxies of ecosystem attributes. Thus, a function-based approach based on macroinvertebrates has the potential to become an effective tool for the assessment of river ecosystems.     

Immediate shift towards source dynamics: The pioneer species Conyza canadensis in an initial ecosystem

The aim of this study was to detect a potential temporal shift from sink to source dynamics of pioneer plants during primary succession. The study was done in an initial ecosystem, namely an artificially constructed catchment on Pleistocene sands in eastern Germany. The import and export of seeds (including soil seed bank and seed rain), the development of vegetation cover and the population size of all pioneer species were recorded in 2005-2009. The interplay between the spatial distribution of seed rain and the prevailing wind direction provide evidence that seeds of Conyza canadensis (Asteraceae) first and to a considerable amount left the developing ecosystem. A change from a sink to source dynamics was detected already in the first year of both the existence of the site and occurrence of C. canadensis individuals within the site. Population patterns at the landscape unit scale demonstrated extensive auto-correlations in the coverage of this invasive plant at first. Our results underline the pioneer traits of C. canadensis as a prolific seeder and excellent wind disperser, which enables this species to become rapidly dominant over relatively large areas.     

What pair formation can do to the battle of the sexes: towards more realistic game dynamics

In the various dynamic models of Dawkin's Battle of the Sexes, payoff matrices serve as the basic ingredients for the specification of a game-dynamic model. Here I model the sex war mechanistically, by expressing the costs of raising the offspring and performing a prolonged courtship via a time delay for the corresponding individuals, instead of via payoff matrices. During such a time delay an individual is not able to have new matings. Only after the delay has occurred, an individual (and its offspring) appears on the mating market again. From these assumptions I derive a pair-formation submodel, and a system of delay-differential equations describing the dynamics of the game. By a time-scale argument, I obtain an approximation of this system by means of a much simpler system of ordinary differential equations. Analysis of this simplified system shows that the model can give rise to two non-trivial asymptotically stable equilibrium points: an interior equilibrium where both female strategies and both male strategies are present, and a boundary equilibrium where only one of the female strategies and both male strategies are present. This behaviour is qualitatively different from that of models of the battle of the sexes formulated in the traditional framework of game-dynamic equations. In other words, the addition of a most elementary further assumption about individual life history fundamentally changes the model predictions. These results show that in analysing evolutionary games one should pay careful attention to the specific mechanisms involved in the conflict. In general, I advocate deriving simple models for evolutionary games, starting from more complex, mechanistic building blocks. The wide-spread method of modelling games at a high phenomenological level, through payoff matrices, can be misleading.     

Cluster analysis of short-term tests: a new methodological approach

A totally data-based approach to the evaluation of short-term tests is proposed. The performances of 22 tests over a range of 42 chemicals (data from literature) were studied by cluster analysis. The comparison between them was performed only on the basis of their responses to the chemicals. Two different clustering methods produced a coincident classification, pointing to a clear resolution of all tests into 3 groups with common characteristics. With respect to carcinogen discrimination, cluster 1 showed the highest sensitivity and the lowest specificity. Cluster 3 had opposite characteristics. The tests of cluster 2 showed intermediate features. As far as the membership to clusters is concerned, the literature data about the responses to chemicals indicated a strong test system specificity. This apparently overcame both phylogeny and end-point community. A major characteristic of the present approach is the ability to elicit underlying patterns, the knowledge of which can contribute both to hypothesis formulation and be useful for practical purposes.     

Conformational study of valinomycin: a molecular dynamics approach

Valinomycin is a highly flexible cyclic dodecadepsipeptide that transports ions across membranes. Such a flexibility in the conformation is required for its biological function since it has to encounter a variety of environments and liganding state. Exploration of conformational space of this molecule is therefore important and is one of the objectives of the present study that has been carried out by means of high temperature Molecular Dynamics. Further, the stability of the known bracelet-like structure of the uncomplexed valinomycin and the inherent flexibility around this structure has been investigated. The uncomplexed form of valinomycin has been simulated at 75-100 K for 1 ns in order to elucidate the average conformational properties. An alanine-analog of valinomycin has been simulated under identical conditions in order to evaluate the effect of sidechain on the conformational properties, The studies confirm the effect of sidechain on conformational equilibrium.     

Effects of large herbivore browsing on the functional groups of woody plants in a southern African savanna

This study examined the effect of different large herbivore species and stocking rates in savanna ecosystems of Zimbabwe on the richness and abundances of woody plant functional groups and woody plant functional attributes. Seven fence-lines with different herbivore species and stocking rates on either side of the fence were sampled. Plots were placed on both sides of each fence at each of 18 randomly selected positions. The size and species of each woody plant was recorded for each plot. It was found that the number of species with different functional attributes of spinescence, leaf longevity, fruit type and dispersal mechanism and in the functional groups of palatability were not different on the different sides of the fence. However, there were differences in plant abundances for 26 out of the 35 tests carried out on plant abundances with different functional attributes and functional groups. It was hypothesised that the time needed to change woody plant species richness is hundreds of years in these systems, whereas the time needed to change woody plant abundances is decades.