Mahonia invasions in different habitats: local adaptation or general-purpose genotypes?

Rapid evolutionary adaptations and phenotypic plasticity have been suggested to be two important, but not mutually exclusive, mechanisms contributing to the spread of invasive species. Adaptive evolution in invasive plants has been shown to occur at large spatial scales to different climatic regions, but local adaptation at a smaller scale, e.g. to different habitats within a region, has rarely been studied. Therefore, we performed a case study on invasive Mahonia populations to investigate whether local adaptation may have contributed to their spread. We hypothesized that the invasion success of these populations is promoted by adaptive differentiation in response to local environmental conditions, in particular to the different soils in these habitats. To test this hypothesis, we carried out a reciprocal transplantation experiment in the field using seedlings from five Mahonia populations in Germany that are representative for the range of habitats invaded, and a greenhouse experiment that specifically compared the responses to the different soils of these habitats. We found no evidence for local adaptation of invasive Mahonia populations because seedlings from all populations responded similarly to different habitats and soils. In a second greenhouse experiment we examined genetic variation within populations, but seedlings from different maternal families did not vary in their responses to soil conditions. We therefore suggest that local adaptation of seedlings does not play a major role for the invasion success of Mahonia populations and that phenotypic plasticity, instead, could be an important trait in this stage of the life cycle.     

Commentary: oxidative stress reconsidered

All definitions of the terms ‘oxidative stress’ and ‘antioxidants’ implicate that oxidants are just damaging. However, there is increasing evidence that reactive oxygen species (ROS) are not only toxic but that we need them for healthy life. This change in paradigm has been discussed at the third international symposium on ‘Nutrition, oxygen biology and medicine—micronutrients, exercise, energy and aging disorders’, of the Society for Free Radical Research France and the Oxygen Club of California on April 8–10, 2009 in Paris. The beneficial effect of a low to moderate concentration of oxidants produced during exercise was taken as most discussed example. In this case, ROS are required for normal force production in skeletal muscle, for the development of training-induced adaptation in endurance performance, as well as for the induction of endogenous defense systems. Taking antioxidants during training prevents adaptation. Although substantial progress on the understanding of the physiological functions of ROS was communicated at the meeting, it remained obvious that a lot of work is needed to fully understand the conditions and individual situations under which ROS are beneficial or detrimental.     

Genetic Allee effects on performance, plasticity and developmental stability in a clonal plant

Negative effects of small population size on fitness, so-called Allee effects, may threaten population persistence even in intact habitat remnants. We studied genotypes of 14 isolated populations of the clonal plant Ranunculus reptans, for which molecular genetic (RAPD-) variability is higher for large than for small populations. In a competition-free greenhouse environment vegetative offspring of genotypes from large populations produced more rosettes and flowers, indicating higher fitness. Within-genotype coefficients of variation in performance traits, indicating developmental instability, were lower for genotypes from populations with higher RAPD-variability. In competition with a taller grass, we found relative reduction in leaf length less pronounced for plants from large populations, suggesting higher adaptive plasticity. Our experimental study of a plant with predominantly vegetative reproduction suggests, that negative genetic effects of recent habitat fragmentation, which so far rather were expected in plants with frequent sexual reproduction, are more severe and more common than previously acknowledged.     

Blinded and unblinded internal pilot study designs for clinical trials with count data

Internal pilot studies are a popular design feature to address uncertainties in the sample size calculations caused by vague information on nuisance parameters. Despite their popularity, only very recently blinded sample size reestimation procedures for trials with count data were proposed and their properties systematically investigated. Although blinded procedures are favored by regulatory authorities, practical application is somewhat limited by fears that blinded procedures are prone to bias if the treatment effect was misspecified in the planning. Here, we compare unblinded and blinded procedures with respect to bias, error rates, and sample size distribution. We find that both procedures maintain the desired power and that the unblinded procedure is slightly liberal whereas the actual significance level of the blinded procedure is close to the nominal level. Furthermore, we show that in situations where uncertainty about the assumed treatment effect exists, the blinded estimator of the control event rate is biased in contrast to the unblinded estimator, which results in differences in mean sample sizes in favor of the unblinded procedure. However, these differences are rather small compared to the deviations of the mean sample sizes from the sample size required to detect the true, but unknown effect. We demonstrate that the variation of the sample size resulting from the blinded procedure is in many practically relevant situations considerably smaller than the one of the unblinded procedures. The methods are extended to overdispersed counts using a quasi‐likelihood approach and are illustrated by trials in relapsing multiple sclerosis.     

A validation framework to assess performance of commercial deformable image registration in lung radiotherapy

IntroductionDeformable image registration (DIR) can play an important role in the context of adaptive radiotherapy. The AAPM Task Group 132 (TG-132) has described several quantitative measures for DIR error assessment but they can only be accurately defined when there is a ground-truth present in high-contrast regions. This work aims to set out a framework to obtain optimal results for CT-CT lung DIR in clinical setting for a commercially available system by quantifying the DIR performance in both low- and high-contrast regions.MethodsFive publicly available thorax datasets were used to assess the DIR quality. A “Ghost fiducial” method was implemented by windowing the contrast in a new feature provided by Varian Velocity v4.1. Target registration error (TRE) of the landmarks and Dice-similarity coefficient of the tumour were calculated at three different contrast settings to assess the algorithm in high- and low-contrast scenarios.ResultsFor the original unedited dataset, higher resolution DIR methods showed best performance acceptable within the recommended limit according to TG-132, when actual displacements were less than 10 mm. The relation of the actual displacement of the landmarks and TRE shows the limited capacity of the algorithm to deal with movements larger than 10 mm.ConclusionThis work found the performance of DIR methods and settings available in Varian Velocity v4.1 to be a function of contrast level as well as extent of motion. This highlights the need for multiple metrics to assess different aspects of DIR performance for various applications related to low-contrast and/or high-contrast regions.     

Ways of Learning: Observational Studies Versus Experiments

Abstract Manipulative experimentation that features random assignment of treatments, replication, and controls is an effective way to determine causal relationships. Wildlife ecologists, however, often must take a more passive approach to investigating causality. Their observational studies lack one or more of the 3 cornerstones of experimentation: controls, randomization, and replication. Although an observational study can be analyzed similarly to an experiment, one is less certain that the presumed treatment actually caused the observed response. Because the investigator does not actively manipulate the system, the chance that something other than the treatment caused the observed results is increased. We reviewed observational studies and contrasted them with experiments and, to a lesser extent, sample surveys. We identified features that distinguish each method of learning and illustrate or discuss some complications that may arise when analyzing results of observational studies. Findings from observational studies are prone to bias. Investigators can reduce the chance of reaching erroneous conclusions by formulating a priori hypotheses that can be pursued multiple ways and by evaluating the sensitivity of study conclusions to biases of various magnitudes. In the end, however, professional judgment that considers all available evidence is necessary to render a decision regarding causality based on observational studies. (JOURNAL OF WILDLIFE MANAGEMENT 72(1):4–13; 2008)