Power matters in closing the phenotyping gap

Much of our understanding of physiology and metabolism is derived from investigating mouse mutants and transgenic mice, and open-access platforms for standardized mouse phenotyping such as the German Mouse Clinic (GMC) are currently viewed as one powerful tool for identifying novel gene-function relationships. Phenotyping or phenotypic screening involves the comparison of wild-type control mice with their mutant or transgenic littermates. In our study, we explored the extent to which standardized phenotyping will succeed in detecting biologically relevant phenotypic differences in mice generated and provided by different collaborators. We analyzed quantitative metabolic data (body mass, energy intake, and energy metabolized) collected at the GMC under the current workflow, and used them for statistical power considerations. Our results demonstrate that there is substantial variability in these parameters among lines of wild-type C57BL/6 (B6) mice from different sources. Given this variable background noise in mice that serve as controls, subtle phenotypes in mutant or transgenic littermates may be overlooked. Furthermore, a phenotype observed in one cohort of a mutant line may not be reproducible (to the same extent) in mice coming from a different environment or supplier. In the light of these constraints, we encourage researchers to incorporate information on intrastrain variability into future study planning, or to perform advanced hierarchical analyses. Both will ultimately improve the detectability of novel phenotypes by phenotypic screening. Carola W. Meyer and Ralf Elvert contributed equally to this work.     

Human appropriation of net primary production as determinant of avifauna diversity in Austria

The relationship between land-use induced changes in production ecology and avifauna diversity was analysed using a GIS land cover dataset on a 0.25 km × 0.25 km grid covering Austria's national territory. Considering only aboveground processes, the “human appropriation of net primary production” (HANPP = potential NPP − NPP_t), actual NPP (NPP_act), harvest (NPP_h) and NPP_t (= NPP_act − harvest) were recalculated based on existing datasets. Elevation as well as indicators of land cover heterogeneity and landscape heterogeneity were also considered. Correlation analyses were performed between these potential determinants of avifauna diversity and breeding bird species richness data as well as the percentage of endangered breeding birds included in the Austrian red list. Four spatial scales—0.25 km × 0.25 km, 1 km × 1 km, 4 km × 4 km and 16 × 16 km, were analysed. It was shown that breeding bird species richness was more strongly correlated with production ecological indicators and elevation than with heterogeneity indicators. A residual analysis in which the effect of elevation (a proxy for climate) on species richness and its potential determinants was removed confirmed the importance of the availability of trophic energy (NPP) for bird diversity patterns. The results support the species-energy hypothesis, thus confirming the notion that HANPP could be a useful pressure indicator for biodiversity loss.     

Effects of grazer richness and composition on algal biomass in a closed and open marine system

Most natural local systems exchange organisms with a regional pool of species through migration and dispersal. Such metacommunity processes of interconnected multispecies assemblages are likely to affect local dynamics of both species and processes. We present results from an artificial marine outdoor rock pool system in which we investigated the factors of (1) local grazer richness and composition, and (2) connectivity of local patches to a regional species pool, and their effects on algal biomass. Local species richness of six grazers was manipulated in both open and closed pools, which were embedded in a regional species pool containing all six grazers. Grazer richness showed significant net biodiversity effects on grazing in the closed, but not in the open, system. Grazer composition, on the other hand, showed significant effects on grazing in both open and closed systems, depending on which species were initially present. The two most efficient grazers were able to compensate for less efficient grazers in species mixtures, hence ensuring the function of grazing. The efficiency of top-down control of algal biomass in open systems thus depends on which particular species are lost. Further, differences in grazing between the open and closed system changed over time due to temporal dynamics in grazer composition. The results emphasize the importance of including system connectivity in experimental designs to allow an extrapolation of biodiversity ecosystem-functioning relationships to natural systems.     

A general approach to the analysis of habitat selection

The investigation of animal habitat selection aims at the detection of selective usage of habitat types and the identification of covariates influencing their selection. The results not only allow for a better understanding of the habitat selection process but are also intended to help improve the conservation of animals. Usually, habitat selection by larger animals is assessed by radio-tracking or visual observation studies, where the chosen habitat is determined for some animals at a set of specific points in time. Hence the resulting data often have the following structure: a categorical variable indicating the habitat type selected by an animal at a specific point in time is repeatedly observed and will be explained by covariates. These may either describe properties of the habitat types currently available and/or properties of the animal. In this paper, we present a general approach to the analysis of such data in a categorical regression setup. The proposed model generalizes and improves upon several of the approaches previously discussed in the literature. In particular, it accounts for changing habitat availability due to the movement of animals within the observation area. It incorporates both habitat- and animal-specific covariates, and includes individual-specific random effects to account for correlations introduced by the repeated measurements on single animals. Furthermore, the assumption that the effects are linear can be dropped by including the effects in nonparametric manner based on a penalized spline approach. The methodology is implemented in a freely available software package. We demonstrate the general applicability and the potential of the proposed approach in two case studies: The analysis of a songbird community in South-America and a study on brown bears in Central Europe.     

TUGAI: An Integrated Simulation Tool for Ecological Assessment of Alternative Water Management Strategies in a Degraded River Delta

The development of ecologically sound water allocation strategies that account for the needs of riverine ecosystems is a pressing issue, especially in semiarid river basins. In the Aral Sea Basin, a search for strategies to mitigate ecological and socioeconomic deterioration has been in process since the early 1990s. The Geographic Information System–based simulation tool TUGAI has been developed to support the policy determination process by providing a simple, problem-oriented method to assess ecological effects of alternative water management strategies for the Amudarya River. It combines a multiobjective water allocation model with simple, spatially explicit statistical and rule-based models of landscape dynamics. Changes in environmental conditions are evaluated by a fuzzy habitat suitability index for Populus euphratica, which is the dominant species of the characteristic riverine Tugai forests. Water management scenarios can be developed by altering spatiotemporal water distribution in the delta area or the amount of water inflow into the delta. Outcomes of scenario analysis are qualitative comparisons of the ecological effects of different options for a time period of up to 28 years. The given approach utilizes different types of knowledge, from quantitative hydrological data to qualitative local expert knowledge. The main purpose of the tool is to integrate the knowledge in a comprehensive way to make it available for discussions on alternative policies in moderated workshops with stakeholders. In this article, the modules of the tool, their integration, and three hypothetical scenarios are presented. Based on the experience gained when developing the TUGAI tool, we propose that the general framework can be transferred to other areas where tradeoffs in water allocation between the environment and other water users are of major concern. The potential for a simulation tool to structure and inform a complex resource management situation by involving local experts and stakeholders in the development of possible future scenarios will become increasingly valuable for transparent and participatory resource management.     

Contribution of tobacco smoke to environmental benzene exposure in Germany

The concentrations of environmental tobacco smoke (ETS) constituents including benzene were measured in the living rooms of 10 nonsmoking households and 20 households with at least one smoker situated in the city and suburbs of Munich. In the city, the median benzene levels during the evening, when all household members were at home, were 8.1 and 10.4 μg/m³ in nonsmoking and smoking homes, respectively. The corresponding levels of 3.5 and 4.6 μg/m³ were considerably lower in the suburbs. Median time-integrated 1-week benzene concentrations in the city were 10.6 μg/m³ in nonsmoking homes and 13.1 μg/m³ in smoking homes. In the suburbs, the corresponding values were 3.2 and 5.6 μg/m³. While the benzene concentrations in nonsmoking homes located in the city were significantly higher (p < 0.05) than in suburban nonsmoking households, no difference was found between smoking and nonsmoking households located either in the city or in the suburbs. Individual exposures to benzene and to specific markers for tobacco smoke of all household members (82 nonsmokers and 32 smokers) were determined by questionnaire, personal monitoring, and biomonitoring. Within the city, the benzene exposure determined by personal samplers was 11.8 μg/m³ for nonsmokers living in nonsmoking homes and 13.3 μg/m³ for nonsmokers in smoking homes. The corresponding values for nonsmokers living in the suburbs were 5.9 and 6.9 μg/m³, respectively. Neither difference was statistically significant. Nonsmokers living in nonsmoking households in the city had significantly higher exposure to benzene compared to their counterparts living in the suburbs (personal samplers: 11.8 vs 5.9 μg/m³, p < 0.001; benzene in exhalate: 2.4 vs. 1.1 μg/m³, p < 0.05; trans,trans-muconic acid excretion in urine: 92 vs. 54 μg/g creatinine, p < 0.05). Nonsmokers from all households with smokers were significantly more exposed to benzene than nonsmokers living in the nonsmoking households (personal samplers: 13.2 vs. 7.0 μg/m³, p < 0.05; benzene in exhalate: 2.6 vs. 1.8 μg/m³, p < 0.01; trans,trans-muconic acid excretion in urine: 73 vs. 62 μg/g creatinine), but the contribution of ETS to the total benzene exposure was relatively low compared to that from other sources. Analysis of variance showed that at most 15% of the benzene exposure of nonsmokers living in smoking homes was attributable to ETS. For nonsmokers living in nonsmoking households benzene exposure from ETS was insignificant.