Sample size re‐estimation in clinical trials

Adaptive clinical trials are becoming very popular because of their flexibility in allowing mid‐stream changes of sample size, endpoints, populations, etc. At the same time, they have been regarded with mistrust because they can produce bizarre results in very extreme settings. Understanding the advantages and disadvantages of these rapidly developing methods is a must. This paper reviews flexible methods for sample size re‐estimation when the outcome is continuous.     

Assessing the ecological integrity of a grassland ecosystem: the applicability and rapidity of the SAGraSS method

The Grassland Biome is currently one of the most threatened biomes in South Africa and is in dire need of a biomonitoring protocol. The components of ecological integrity in these ecosystems are, however, too diverse and time-consuming to measure scrupulously. It is therefore necessary to develop a set of grassland indicators that are efficient and rapid in their assessment of grassland ecosystem integrity. The South African Grassland Scoring System (SAGraSS), based on the grassland insect community, is such a suggested indicator. The present study is the first to investigate the applicability and rapidity of this proposed method. Although SAGraSS scores correlated significantly with Ecological Index values (the most commonly used index by which veld condition is evaluated in central South Africa), the method proved to be tedious and the identification of insects taxing. We offer a number of changes to make the SAGraSS method a more rapid method of assessment.     

Evolutionary dynamics of ecological niche in three Rhinogobio fishes from the upper Yangtze River inferred from morphological traits

In the past decades, it has been debated whether ecological niche should be conserved among closely related species (phylogenetic niche conservatism, PNC) or largely divergent (traditional ecological niche theory and ecological speciation) and whether niche specialist and generalist might remain in equilibrium or niche generalist could not appear. In this study, we employed morphological traits to describe ecological niche and test whether different niche dimensions exhibit disparate evolutionary patterns. We conducted our analysis on three Rhinogobio fish species (R. typus, R. cylindricus, and R. ventralis) from the upper Yangtze River, China. Among the 32 measured morphological traits except body length, PCA extracted the first four principal components with their loading scores >1.000. To find the PNC among species, Mantel tests were conducted with the Euclidean distances calculated from the four principal components (representing different niche dimensions) against the pairwise distances calculated from mitochondrial cytochrome b sequence variations. The results showed that the second and the third niche dimension, both related to swimming ability and behavior, exhibited phylogenetic conservatism. Further comparison on niche breadth among these three species revealed that the fourth dimension of R. typus showed the greatest width, indicating that this dimension exhibited niche generalism. In conclusion, our results suggested that different niche dimensions could show different evolutionary dynamic patterns: they may exhibit PNC or not, and some dimensions may evolve generalism.     

The neglected tool in the Bayesian ecologist's shed: a case study testing informative priors' effect on model accuracy

Despite benefits for precision, ecologists rarely use informative priors. One reason that ecologists may prefer vague priors is the perception that informative priors reduce accuracy. To date, no ecological study has empirically evaluated data‐derived informative priors' effects on precision and accuracy. To determine the impacts of priors, we evaluated mortality models for tree species using data from a forest dynamics plot in Thailand. Half the models used vague priors, and the remaining half had informative priors. We found precision was greater when using informative priors, but effects on accuracy were more variable. In some cases, prior information improved accuracy, while in others, it was reduced. On average, models with informative priors were no more or less accurate than models without. Our analyses provide a detailed case study on the simultaneous effect of prior information on precision and accuracy and demonstrate that when priors are specified appropriately, they lead to greater precision without systematically reducing model accuracy.     

WIDESPREAD HOST‐DEPENDENT HYBRID UNFITNESS IN THE PEA APHID SPECIES COMPLEX

Linking adaptive divergence to hybrid unfitness is necessary to understand the ecological factors contributing to reproductive isolation and speciation. To date, this link has been demonstrated in few model systems, most of which encompass ecotypes that occupy relatively early stages in the speciation process. Here we extend these studies by assessing how host‐plant adaptation conditions hybrid fitness in the pea aphid, Acyrthosiphon pisum. We made crosses between and within five pea aphid biotypes adapted to different host plants and representing various stages of divergence within the complex. Performance of F1 hybrids and nonhybrids was assessed on a “universal” host that is favorable to all pea aphid biotypes in laboratory conditions. Although hybrids performed equally well as nonhybrids on the universal host, their performance was much lower than nonhybrids on the natural hosts of their parental populations. Hence, hybrids, rather than being intrinsically deficient, are maladapted to their parents’ hosts. Interestingly, the impact of this maladaptation was stronger in certain hybrids from crosses involving the most divergent biotype, suggesting that host‐dependent postzygotic isolation has continued to evolve late in divergence. Even though host‐independent deficiencies are not excluded, hybrid maladaptation to parental hosts supports the hypothesis of ecological speciation in this complex.     

An assessment of macrophyte community metrics in the determination of the ecological condition and total phosphorus concentration of Mediterranean ponds

The macrophyte vegetation of 51 ponds situated in the Duero river basin on the Northern Iberian Plateau was studied with the aim of selecting metrics that responded clearly to perturbation and that should be included in a multimetric index for assessing the ecological condition (expression of the quality of the structure and functioning of aquatic ecosystems associated with surface waters) of Mediterranean ponds. Furthermore, the specific response of metrics to the total phosphorus (TP) concentration was also investigated because of agricultural activities, which usually increase the concentration of nutrients in aquatic systems, are one of the principal types of impairment affecting ponds in the Duero basin.A total of 19 metrics representing several aspects of the structure of macrophyte communities (cover, richness, diversity) were selected as potential metrics.The strong overlap which was observed for macrophyte metrics between classes of ecological conditions (bad, poor, moderate, good, best available) and TP concentrations (>600, 600-300, 300-100, 100-50, <50 μg L⁻¹ TP) constitutes a major problem in defining and separating these classes. For this reason, Mann-Whitney U-test and discrimination efficiency were carried out to determine which of the measures best discriminated between slightly impaired sites (ponds in good or best available condition) and perturbed ponds (ponds in moderate, poor or bad condition). Most of the metrics showed significant differences (p < 0.05) between slightly impaired and perturbed ponds. However, only total cover and hydrophyte richness, which had the highest discrimination efficiency (>78%), showed no inter-quartile overlap (25th-75th percentile) between the two ecological classes. For these reasons, both total cover and hydrophyte richness were selected for the implementation of a multimetric index able to discriminate between slightly impaired and degraded Mediterranean flatland ponds.Currently, eutrophication is considered the main pressure on lakes. However, macrophyte metrics were far less sensitive to TP concentration than to ecological condition changes. This shows that other pressures are also of considerable importance. Thus, the definition of the ecological condition of lakes using macrophytes should not be based only on responses to eutrophication pressure, as has been done in some European countries.     

Mutations within a human IgG2 antibody form distinct and homogeneous disulfide isomers but do not affect Fc gamma receptor or C1q binding

Human IgG2 antibodies may exist in at least three distinct structural isomers due to disulfide shuffling within the upper hinge region. Antibody interactions with Fc gamma receptors and the complement component C1q contribute to immune effector functions. These interactions could be impacted by the accessibility and structure of the hinge region. To examine the role structural isomers may have on effector functions, a series of cysteine to serine mutations were made on a human IgG2 backbone. We observed structural homogeneity with these mutants and mapped the locations of their disulfide bonds. Importantly, there was no observed difference in binding to any of the Fc gamma receptors or C1q between the mutants and the wild‐type IgG2. However, differences were seen in the apparent binding affinity of these antibodies that were dependent on the selection of the secondary detection antibody used.     

Grazing with Galloway cattle for floodplain restoration in the Syr Valley, Luxembourg

Three years after a river restoration scheme in the Syr Valley (Luxembourg) we investigated habitat development and habitat use of Galloway cattle deployed in a low-intensity grazing system on a permanent floodplain pasture. Habitats were delimited with a mobile GPS/GIS mapping system and their spatial development was assessed over three consecutive years. During these three years, the patches of the six habitats decreased to 40% of mean initial size, and a rapid net area expansion of wetland habitats (large sedge swamps: +100%, marsh and tall forb grasslands: +43%) was observed. The behavioural patterns and grazing preferences of the cattle were observed directly during the vegetation period in June, August and November. These observations were complemented by a transect analysis of cattle impact indicators in June and November. The cattle grazed the different habitats very selectively, as they preferred the mesophilic, and ruderal grasslands 1.6, and 5.6 times more than expected respectively. During the growing season, the grazing niche breadth declined (3.92 in June to 2.68 in November), and less preferred forage habitats like large sedge swamps were grazed primarily in the autumn. We used bite and step rates to investigate grazing intensity by habitat type. During summer, grazing intensity correlated with forage quality in the different habitat patches, whereas in autumn it was obviously influenced by the effort required to access the desired forage plants in a given habitat. The impact indicators revealed a matter transfer from riparian areas to the valley edge. Here, we give a first insight into habitat development and habitat use of Galloway cattle in a recently restored floodplain area and derive recommendations for the adaptive management of future projects.     

Functional indicators of stream health: a river‐basin approach

1. The efficacy of leaf‐litter decomposition, sediment respiration, biofilm biomass, growth, chlorophyll a concentration and the autotrophic index (biofilm ash‐free dry mass/chlorophyll a) and fungal biomass for detecting human‐induced change was evaluated using 24 references and 15 disturbed stream sites located in central Portugal. 2. Decomposition rates of alder (Alnus glutinosa) and oak (Quercus robur) leaves and sediment respiration rates were effective in discriminating impairment. Decomposition was negatively correlated with abiotic factors, such as ammonium and nitrite concentrations, connectivity and alterations in the hydrological regime, and positively correlated with nitrate concentration and oxygen concentration. Sediment respiration rates were correlated with organic contamination, land use and morphological changes. 3. Growth rates of biofilm, concentration of chlorophyll a and the autotrophic index, although 41–73% higher at disturbed compared to reference sites, were not significantly different. These three variables were significantly correlated with total organic carbon, oxygen concentration, pH, nitrite and the presence of dams. Fungal biomass on leaves and biofilm biomass on natural substrata did not differ between reference and disturbed sites. 4. Our findings lend support to the use of functional variables like decomposition and sediment respiration in monitoring and when used together with structural variables should give a more holistic measure of stream health.