An approach to analysis of colonization dynamics in community functioning of protozoa for bioassessment of marine pollution

Biological trait analysis is a powerful tool to summarize the spatial/temporal patterns of community functioning and ecosystem process at taxon-free resolutions. To identify the optimal colonization period with high homogeneity in functional patterns of protozoa for bioassessment, 1-month baseline colonization survey was conducted in coastal waters of the Yellow Sea. A fuzzy-coding functional trait system was used to summarize the functional structure of protozoan communities during the colonization process. The functional patterns showed a low homogeneity during the early stage (3–7 days), followed by a stable stage (10–14 days) with high homogeneity, and the last stage (21–28 days) with high heterogeneity. The functional richness showed a low variability, while the functional evenness and divergence generally showed a decreasing trend during the whole colonization process. Furthermore, the functional dispersion and RaoQ indices generally leveled off only during the stable stage. These results suggest that it is necessary to determine the optimal exposure time period with high homogeneity of community functioning for bioassessment using protozoan colonization in marine ecosystems.     

Optimizing ecosystem function by manipulating pasture community composition

The ability to design plant communities to optimize particular ecosystem functions and thus more effectively provide ecosystem services would improve all types of ecosystem management, including agriculture. We propose a novel quantitative multi-step method for selecting mixtures of plant species to meet ecosystem objectives: collecting trait data; identifying suites of traits related to relevant community processes; relating those processes to the ecosystem functions of interest; optimizing the planted mixture; and evaluating trade-offs. This approach was tested using planted mixtures of 14 grassland species common in managed pastures of the northeastern United States. Ordination of trait data from greenhouse and small plot studies was used to relate species traits to community processes, followed by generalized additive modeling to relate community-weighted mean process scores to field estimates of biomass production and resistance to invasion. Multi-criteria optimization identified seed mixtures that maximized or minimized selected ecosystem functions, facilitating quantification of trade-offs in processual ability within species and between ecosystem functions at the community level. In this study, predicted seasonal and annual biomass values were within expected ranges, but the optimal mixtures differed from forage mixtures traditionally planted in the northeastern United States. Perennial ryegrass was the most commonly-selected grass. Legumes were represented less than expected, possibly due to attributes such as longevity and forage quality that are important in pastures but were not directly included in the optimization. Ecosystem function was not linearly related to species richness. While further research on quantitatively relating species traits and community processes is needed, multi-criteria optimization offers a new path for linking ecosystem function to ecosystem management.     

Interactions between stochastic and deterministic processes in stream fish community assembly

Synopsis Numerous studies have attempted to determine whether stream fish communities are structured primarily by deterministic or stochastic processes. Previous work has assumed that stream fish communities will show either persistence about an equilibrium because of strong density-dependent processes or random variation in structure as a result of environmental stochasticity. In a 10-year study of a California stream, fish community structure changed under the influence of storm-induced high discharge events that impacted recruitment. Species' relative abundances were altered as pre-recruitment stream discharges differentially influenced year-class strength among species with contrasting life histories. Simulation of stream fish community assembly under flow-driven recruitment variation indicates that community structure will vary depending on how particular high-flow events affect species' relative abundances and ongoing density-dependent processes, including competition and predation. Results suggest that stream fish communities are likely to show alternate states rather than a single persistent equilibrium. However, community assembly will not be random but will depend on situation-specific interactions between density-independent and density-dependent processes.     

Quantifying relationships between traits and explicitly measured gradients of stress and disturbance in early successional plant communities

Questions: How can one explicitly quantify, and separately measure, stress and disturbance gradients? How do these gradients affect functional composition in early successional plant communities and to what extent? Can we accurately predict trait composition from knowledge of these gradients? Location: Southern Quebec, Canada. Methods: Using eight environmental variables measured in 48 early successional plant communities, we estimated stress and disturbance gradients through structural equation modelling. We then measured 10 functional traits on the most abundant species of these 48 communities and calculated their community‐level mean and variance weighted by the relative abundance of each species. Finally, we related these community‐weighted means and variances to the estimated stress and disturbance gradients using general linear models or generalized additive models. Results: We obtained a well‐fitting measurement model of the stress and disturbance gradients existing in our sites. Of the 10 studied traits, only average plant reproductive height was strongly correlated with the stress (r²=0.464) and disturbance (r²=0.543) gradients. Leaf traits were not significantly related to either the stress or disturbance gradients. Conclusions: The well‐fitting measurement model of the stress and disturbance gradients, combined with the generally weak trait–environment linkages, suggests that community assembly in these early successional plant communities is driven primarily by stochastic processes linked to the history of arrival of propagules and not to trait‐based environmental filtering.     

A bivariate quantitative genetic model for a threshold trait and a survival trait

Many of the functional traits considered in animal breeding can be analyzed as threshold traits or survival traits with examples including disease traits, conformation scores, calving difficulty and longevity. In this paper we derive and implement a bivariate quantitative genetic model for a threshold character and a survival trait that are genetically and environmentally correlated. For the survival trait, we considered the Weibull log-normal animal frailty model. A Bayesian approach using Gibbs sampling was adopted in which model parameters were augmented with unobserved liabilities associated with the threshold trait. The fully conditional posterior distributions associated with parameters of the threshold trait reduced to well known distributions. For the survival trait the two baseline Weibull parameters were updated jointly by a Metropolis-Hastings step. The remaining model parameters with non-normalized fully conditional distributions were updated univariately using adaptive rejection sampling. The Gibbs sampler was tested in a simulation study and illustrated in a joint analysis of calving difficulty and longevity of dairy cattle. The simulation study showed that the estimated marginal posterior distributions covered well and placed high density to the true values used in the simulation of data. The data analysis of calving difficulty and longevity showed that genetic variation exists for both traits. The additive genetic correlation was moderately favorable with marginal posterior mean equal to 0.37 and 95% central posterior credibility interval ranging between 0.11 and 0.61. Therefore, this study suggests that selection for improving one of the two traits will be beneficial for the other trait as well.     

A stochastic metapopulation model accounting for habitat dynamics

A stochastic metapopulation model accounting for habitat dynamics is presented. This is the stochastic SIS logistic model with the novel aspect that it incorporates varying carrying capacity. We present results of Kurtz and Barbour, that provide deterministic and diffusion approximations for a wide class of stochastic models, in a form that most easily allows their direct application to population models. These results are used to show that a suitably scaled version of the metapopulation model converges, uniformly in probability over finite time intervals, to a deterministic model previously studied in the ecological literature. Additionally, they allow us to establish a bivariate normal approximation to the quasi-stationary distribution of the process. This allows us to consider the effects of habitat dynamics on metapopulation modelling through a comparison with the stochastic SIS logistic model and provides an effective means for modelling metapopulations inhabiting dynamic landscapes.     

Phylogeny, traits, environment, and space in cerrado plant communities at Emas National Park (Brazil)

Soil, drought, and fire are abiotic factors that may act as environmental filters in the cerrado, the Brazilian savanna. We used a framework to analyze environmental filtering in geographic and phylogenetic context, sampling woody species in one of the largest cerrado reserves. In 100 quadrats, we measured 10 functional traits on each woody individual. We also measured several soil variables, altitude and slope as a rough surrogate of water availability, interval between fires, and time since last fire. Almost all environmental variables were spatially auto-correlated. We found an overall trait clustering, but not an overall phylogenetic clustering. Nevertheless, we found a phylogenetic signal for some traits. Linking phylogeny, traits, environment, and space, we were able to detect a major dichotomy between two geomorphological units. The flat tableland was positively related with altitude, fire frequency, and nutrient-richer soil. Environmental filtering caused by water availability and fire lead to trait clustering, with smaller shrubs and trees that presented thicker barks, denser woods, sclerophyllous leaves, highlighted by the prevalance of Myrtaceae. The other geomorphological unit, hilly terrain, was positively related with slope, low fire frequency, and nutrient-poorer soil. Environmental filtering was caused especially by nutrient-poor soil that lead to trait clustering, assembling taller trees, with thinner barks, lighter woods, and compound, large, tender, nutrient-richer leaves, distributed across many lineages, including Fabaceae. Hence, the high environmental variability in space with different environmental filters assembled different combination of plant traits and lineages, increasing the overall diversity in cerrado.     

Functional diversity analysis helps to identify filters affecting community assembly after fen restoration by top-soil removal and hay transfer

Top-soil removal followed by species introduction through hay transfer has appeared as a method to restore drained fens. This method addresses abiotic constraints by restoring hydrology and nutrient status, and biotic constraints by removing an unwanted seed bank and counteracting dispersal-limitation. Restoration works by altering environmental filters. Knowledge about the restoration actions effect on functional traits is necessary to understand which types of species may establish. In this study we analyse which factors in top-soil removal followed by hay transfer influence selection and composition of functional traits. Top-soil removal followed by hay transfer from reference sites was conducted at two sites in the Całowanie fen, 33 km SE of Warsaw, Poland. Species and abundance data were recorded for three consecutive years. These data, combined with data on functional traits were used to analyse the effect of the restoration actions on four functional diversity-indices and the community weighted mean of functional traits. Our results reveal a strong habitat filter in the restoration site that follows an elevation gradient. At low elevation this filter selects low values of autochory and specific leaf area and high values of clonal lateral spread, Ellenberg moisture values, and dispersal through hydrochory. The transferred hay differs in trait characteristics compared to the reference site vegetation by having species of higher specific leaf area, lower Ellenberg moisture value and lower dispersal by autochory and hydrochory. The result presented here has three important implications for fen restoration. First, the difference in trait-characteristics between the transferred hay and the reference site it was harvested from limits the restoration potential. Second, since for several fen species important functional traits are filtered along an elevation-gradient, careful planning regarding depth of top-soil removal is needed. Finally the results illustrate how a functional analysis can be used to detect environmental filters acting during ecological restoration.     

A conceptual model of the dynamics of the Syamozero Lake community

We present a conceptual mathematical model of the dynamics of a spatially heterogeneous population system whose prototype is the fish community of Lake Syamozero. Analysis of the solutions of this model is used to demonstrate that interactions between the predator and prey populations in two neighboring biotopes (the pelagic and coastal zones) may result in either undamped oscillations or steady states of the population sizes. The model population densities are of the same order of magnitude as the values obtained in long-term observations of the Syamozero biota. It is also demonstrated that the transition to steady states may be accompanied by long-term (dozens or hundreds of years) damped oscillations of the prey and predator population densities. Under natural conditions, long transitional periods may prevent fish communities from reaching stationary modes.     

Modelling environmentally mediated spread of livestock-associated methicillin-resistant Staphylococcus aureus in a pig herd

Infectious disease models are a useful tool to support within-herd disease control strategies. This study presents a stochastic compartment model with environmentally mediated transmission to represent the spread of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) in a farrow-to-finish pig herd. The aims of the study were to (1) construct a model of the spread of LA-MRSA that included spread of LA-MRSA through the environment; (2) parameterise the model to fit previously published observational data in order to obtain realistic LA-MRSA transmission rates; (3) and to investigate how changes in the mixing of animals in the farrowing and finishing units may affect the prevalence of LA-MRSA in a herd. The results showed that indirect transmission allowed LA-MRSA to persist in the herd without the assumption of persistently shedding individuals. Reducing the mixing of pigs upon entry to the finishing unit was also shown to lower the LA-MRSA prevalence in the unit if the initial LA-MRSA level in the unit was low, but at high prevalence, no effect of mixing was identified. In the farrowing unit, changing the proportion of piglets that were cross-fostered did not affect the within-herd LA-MRSA prevalence. The study demonstrates that there are several important knowledge gaps regarding the shedding and transmission of LA-MRSA in different animal age groups and further experimental studies are needed. This work also provides a new, robust and flexible model framework for the investigation of control and mitigation strategies for LA-MRSA and other infections in a pig herd.     

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.     

Functional characters combined with null models reveal inconsistency in mechanisms of species turnover in lacustrine fish communities

Functional characters have the potential to act as indicators of species turnover between local communities. Null models provide a powerful statistical approach to test for patterns using functional character information. A combined null model/functional character approach provides the ability to distinguish between the effect of competition and environmental filtering on species turnover. We measured 13 functional characters relating directly to resource use for the fish species found in French lakes. We combined this functional character data with a null model approach to test whether co-occurring species overlapped more or less than expected at random for four primary niche axes. We used an environmentally constrained null model approach to determine if the same mechanisms were responsible for species turnover at different sections of the altitudinal gradient. Functional diversity indices were used to examine the variation in functional character diversity with altitude, as a test of the hypothesis that competitive intensity decreases with increasing environmental adversity. The unconstrained null model showed that environmental filtering was the dominant influence on species turnover between lakes. In the constrained null model, there was much less evidence for environmental filtering, emphasising the strong effect of altitude on turnover in functional character values between local communities. Different results were obtained for low-altitude and high-altitude lake subsets, with more evidence for the effect of environmental filtering being found in the high-altitude lakes. This demonstrates that different processes may influence species turnover throughout an environmental gradient. Functional diversity values showed a slight decrease with altitude, indicating that there was only weak evidence that competitive intensity decreased with increasing altitude. Variation resource availability and environmental stress probably cause the observed turnover in functional characters along the altitudinal gradient, though the effects of dispersal limitation and species introductions in high-altitude lakes cannot be ruled out.