Ecological integrity assessment as a metric of biodiversity: are we measuring what we say we are?

As the recognition of the importance of biological diversity in biological conservation grows, an ongoing challenge is to develop metrics that can be used for effective conservation and management. The ecological integrity assessment has been proposed as such a metric. It is held by some to measure species composition, diversity, and habitat quality, as well as ecosystem structure, composition, and function. The methodology relies on proxy variables that include data on landscape characteristics such as patch size, abiotic factors such as hydrology, and some features of vegetation structure and composition. We suggest that the measure is flawed on four levels. First, its putative representation of general ecological form and function, and its lack of specific detail about how it actually represents those attributes, leaves the metric without the focus needed to be useful for measuring ecological features on the ground and testing associated hypotheses and predictions. Second, the proxy variables used to represent biological diversity, such as habitat (vegetation) metrics and vascular plant species diversity, are not empirically correlated with diversity of a range of taxa or of other components of the biota. Third, like other ecological indices that integrate many distinct features, the ecological integrity index is subject to the loss of information in its condensation of multi-dimensional variability into a one-dimensional index, and it may be subject to systematic bias from the conversion of raw data into categorical scores. Fourth, the sampling protocols are at risk of sampling bias, observer bias, and measurement error, any of which can confound the estimation of conservation value. In terms of biological diversity, the methodology produces an unreliable estimate of the number of vascular plant species and their relative percentages of occurrence, and an absence of any protocols for taxa other than plants. For these reasons we believe that ecological integrity assessment is currently of limited value as a measure of site-specific biological diversity and its change over time. A considerable amount of investigation is needed in order to have confidence in the results of an ecological integrity assessment, especially if it is to be used for regulatory purposes. We suggest further refinements and discuss alternative measures of biological diversity that provide reliable metrics for assessing change. A thoughtful choice among measures can help to identify the most appropriate assessment for conservation decisions.     

Is stress-induced analgesia a measure of stress severity?

When comparing magnitudes of "behavioural despair" (duration of immobility) and stress-induced analgesia in the tail suspension test and cold water swim test with SHR and NMRI male mice. The results might depend on saline injection prior the test and on the fact that exposure to cold water in swim test was sufficient to alter the response patterns. The findings show that the main parameters are closely related to each other. Stress-induced analgesia seems to be a measure of stress as the stress becomes stronger analgesia changes in linear dependence, whereas duration of immobility has an invert U-shaped function.     

When can a clonal organism escape senescence?

Abstract Some clonal organisms may live for thousands of years and show no signs of senescence, while others consistently die after finite life spans. Using two models, we examined how stage-specific life-history rates of a clone's modules determine whether a genetic individual escapes senescence by replacing old modules with new ones. When the rates of clonal or sexual reproduction and survival of individual modules decline with age, clones are more likely to experience senescence. In addition, the models predict that there is a greater tendency to find senescence in terms of a decline in the rate of sexual reproduction with clone age than in terms of an increase in the probability of clone mortality, unless rates of sexual reproduction increase dramatically with module stage. Using a matrix model modified to represent the clonal lifestyle, we show how a trade-off between sexual and clonal reproduction could result in selection for or against clonal senescence. We also show that, in contrast to unitary organisms, the strength of selection on life-history traits can increase with the age of a clone even in a growing population, countering the evolution of senescence.     

When can stress facilitate divergence by altering time to flowering?

Stressors and heterogeneity are ubiquitous features of natural environments, and theory suggests that when environmental qualities alter flowering schedules through phenotypic plasticity, assortative mating can result that promotes evolutionary divergence. Therefore, it is important to determine whether common ecological stressors induce similar changes in flowering time. We review previous studies to determine whether two important stressors, water restriction and herbivory, induce consistent flowering time responses among species; for example, how often do water restriction and herbivory both delay flowering? We focus on the direction of change in flowering time, which affects the potential for divergence in heterogeneous environments. We also tested whether these stressors influenced time to flowering and nonphenology traits using Mimulus guttatus. The literature review suggests that water restriction has variable effects on flowering time, whereas herbivory delays flowering with exceptional consistency. In the Mimulus experiment, low water and herbivory advanced and delayed flowering, respectively. Overall, our results temper theoretical predictions for evolutionary divergence due to habitat‐induced changes in flowering time; in particular, we discuss how accounting for variation in the direction of change in flowering time can either increase or decrease the potential for divergence. In addition, we caution against adaptive interpretations of stress‐induced phenology shifts.     

What is antibiotic resistance and how can we measure it?

Antibiotic resistance is being found with increasing frequency in both pathogenic and commensal bacteria of humans and animals. Quantifying resistance within and between bacterial and host populations presents scientists with complex challenges in terms of laboratory methodologies and sampling design. Here, we discuss, from an epidemiological perspective, how antibiotic resistance can be defined and measured and the limitations of current approaches.     

Inferring landscape effects on dispersal from genetic distances: how far can we go?

Functional connectivity affects demography and gene dynamics in fragmented populations. Besides species-specific dispersal ability, the connectivity between local populations is affected by the landscape elements encountered during dispersal. Documenting these effects is thus a central issue for the conservation and management of fragmented populations. In this study, we compare the power and accuracy of three methods (partial correlations, regressions and Approximate Bayesian Computations) that use genetic distances to infer the effect of landscape upon dispersal. We use stochastic individual-based simulations of fragmented populations surrounded by landscape elements that differ in their permeability to dispersal. The power and accuracy of all three methods are good when there is a strong contrast between the permeability of different landscape elements. The power and accuracy can be further improved by restricting analyses to adjacent pairs of populations. Landscape elements that strongly impede dispersal are the easiest to identify. However, power and accuracy decrease drastically when landscape complexity increases and the contrast between the permeability of landscape elements decreases. We provide guidelines for future studies and underline the needs to evaluate or develop approaches that are more powerful.     

Neuronal jitter: can we measure the spike timing dispersion differently?

We propose a novel measure of statistical dispersion of a positive continuous random variable: the entropy-based dispersion (ED). We discuss the properties of ED and contrast them with the widely employed standard deviation (SD) measure. We show that the properties of SD and ED are different: while SD is a second moment characteristics measuring the dispersion relative to the mean value, ED measures an effective spread of the probability distribution and is more closely related to the notion of randomness of spiking activity. We apply both SD and ED to analyze the temporal precision of neuronal spiking activity of the perfect integrate-and-fire model, which is a plausible neural model under the assumption of high input synaptic activity. We show that SD and ED may give strikingly different results for some widely used models of presynaptic activity.     

When to rely on maternal effects and when on phenotypic plasticity?

Existing insight suggests that maternal effects have a substantial impact on evolution, yet these predictions assume that maternal effects themselves are evolutionarily constant. Hence, it is poorly understood how natural selection shapes maternal effects in different ecological circumstances. To overcome this, the current study derives an evolutionary model of maternal effects in a quantitative genetics context. In constant environments, we show that maternal effects evolve to slight negative values that result in a reduction of the phenotypic variance (canalization). By contrast, in populations experiencing abrupt change, maternal effects transiently evolve to positive values for many generations, facilitating the transmission of beneficial maternal phenotypes to offspring. In periodically fluctuating environments, maternal effects evolve according to the autocorrelation between maternal and offspring environments, favoring positive maternal effects when change is slow, and negative maternal effects when change is rapid. Generally, the strongest maternal effects occur for traits that experience very strong selection and for which plasticity is severely constrained. By contrast, for traits experiencing weak selection, phenotypic plasticity enhances the evolutionary scope of maternal effects, although maternal effects attain much smaller values throughout. As weak selection is common, finding substantial maternal influences on offspring phenotypes may be more challenging than anticipated.     

Abstraction from a sensori-motor perspective: can we get a quick hold on simple perception?

Two main types of dissociation can be considered in order to articulate action and abstraction. Vision for action and vision for perception are often described as dissociated systems at both anatomical and functional levels. Within this framework, abstraction should be specific to perceptual representation, whereas the action system would simply analyse the objective metric of space. By contrast, one may focus on dissociations within the action system. In this case, one will accept that action may involve abstract representations, at least during movement preparation. But a specific visuomotor level of processing can be described that appears to comply with the spatial properties of the relationship between the actor and the environment. This system would be specialized for fast movement guidance towards pre-defined goals. Such an automatic piloting system would thus be free of abstraction.     

Linking oxidative and salinity stress tolerance in barley: can root antioxidant enzyme activity be used as a measure of stress tolerance?

Aims

A causal relationship between salinity and oxidative stress tolerance and a suitability of using root antioxidant activity as a biochemical marker for salinity tolerance in barley was investigated.

Methods

Net ion fluxes were measured from the mature zone of excised roots of two barley varieties contrasting in their salinity tolerance using non-invasive MIFE technique in response to acute and prolonged salinity treatment. These changes were correlated with activity of major antioxidant enzymes; ascorbate peroxidase, catalase, and superoxide dismutase.

Results

It was found that genotypic difference in salinity tolerance was largely independent of root integrity, and observed not only for short-term but also long-term NaCl exposures. Higher K⁺ retention ability (and, hence, salinity tolerance) positively correlated with oxidative stress tolerance. At the same time, antioxidant activities were constitutively higher in a sensitive but not tolerant variety, and no correlation was found between SOD activity and salinity tolerance index during large-scale screening.

Conclusion

Although salinity tolerance in barley correlates with its oxidative stress tolerance, higher antioxidant activity at one particular time does not correlate with salinity tolerance and, as such, cannot be used as a biochemical marker in barley screening programs.     

Does restoration work? It depends on how we measure success

The restoration of 4 partial stream barriers was evaluated in watersheds of Terra Nova National Park, Newfoundland, Canada from 2009 to 2011. Brook trout (n = 462) were tagged and tracked moving through our study sites using passive‐integrated transponder telemetry and the restoration actions were assessed using 3 different measures: passage success rates; the range of passable flows; and the availability of passable flows. We considered the observed results within a before‐after‐control‐impact (BACI) design that included reference reaches and pre‐restoration observations. The conclusions of BACI analyses were also contrasted with those that would have been obtained from commonly used before‐after (B‐A) or control‐impact (C‐I) study designs. While the restoration actions changed hydrological conditions in a way that should facilitate fish passage, our biological measures indicated that success was variable across culverts and within culverts depending on the measure evaluated. Furthermore, the natural temporal and spatial variability of fish movements often resulted in different conclusions between the more robust BACI design and the more commonly used B‐A and C‐I designs. Our results demonstrate that restoration of partial barriers may not always yield dramatic improvements. Furthermore, without suitable controls, the chances of drawing false conclusions regarding restorations in temporally and spatially dynamic systems are substantial.     

What do we measure by a luminol-dependent chemiluminescence of phagocytes?

The review presents a survey of published findings concerning the mechanism of luminol-dependent chemiluminescence in biological systems. The potential of various oxygen species (superoxide anion, hydrogen peroxide, hydroxyl radical) to react with luminol is discussed. The ability of commonly used enzymes (superoxide dismutase, catalase), inhibitors, and oxygen radical scavengers to discriminate between individual oxygen species is assessed together with the potential of a variety of substances encountered in biological systems to interfere in luminol-dependent chemiluminescence reactions. It is concluded that luminol-dependent chemiluminescence gives at present very little ability to discriminate between individual oxygen or radical species. Furthermore, luminol-dependent chemiluminescence used in biological systems is extremely prone to many interferences, which are very difficult to control.     

Antioxidants as therapies: can we improve on nature?

Although oxidative damage contributes to many pathologies the use of naturally occurring, small-molecule antioxidants as therapies for these disorders has not been successful. Here I discuss some of the reasons this may be so. Paramount among these are the difficulties in delivering enough of the antioxidant to the intracellular location required to decrease pathological oxidative damage and the challenge of assessing whether the intervention has actually decreased oxidative damage in the patient to a therapeutically useful extent. To develop effective antioxidant therapies the best strategy may be to create new chemical entities designed to detoxify a defined reactive oxygen species-dependent process that underlies a particular pathology, in the same way a conventional drug is designed to modulate a biochemical process, rather than applying antioxidants in an unfocused manner. In developing new antioxidants it will be useful to utilize endogenous processes to activate and recycle the molecules in parallel with the targeting of compounds to cells and organelles in ways that are not limited by the constraints that impair the distribution of endogenous antioxidants. In short, I suggest that the future development of antioxidant therapies should be viewed as an arm of drug development, utilizing focused approaches similar to those of medicinal chemistry and pharmacology, rather than as a branch of nutrition.     

The number domain- can we count on parietal cortex?

Does the primate brain contain a dedicated and localized neural circuitry for processing generic numerical information? The human parietal cortex, particularly the intraparietal sulcus (IPS), has long been implicated in processing symbolic (verbal) number information. If the IPS is indeed the site of generic numerical processing, however, its neurons should also encode nonsymbolic numerosity information. Two recent studies by Shuman and Kanwisher and by Piazza et al. published in this issue of Neuron tested this assumption...with quite different results.     

When does stress end? Evidence of a prolonged stress reaction in shiftworking truck drivers

This study aimed to analyze individual cortisol levels in relation to work conditions, sleep, and health parameters among truck drivers working day shifts (n = 21) compared to those working irregular shifts (n = 21). A total of 42 male truck drivers (39.8 (+/-) 6.2 yrs) completed questionnaires about sociodemographics, job content, work environment, health, and lifestyle. Rest-activity profiles were measured using actigraphy, and cardiovascular blood parameters were collected. Salivary cortisol samples were obtained: (i) at waking time, (ii) 30?min after waking, and (iii) at bedtime, during both one workday and one day off from work. Irregular-shift workers, compared to day-shift workers, showed significantly higher waist-hip ratio, very-low-density lipoprotein (VLDL) cholesterol, tiredness after work, years working as a driver, truck vibration, and less job demand (p < .05). High cortisol levels in irregular-shift workers were correlated with certain stressors, such as short sleep duration and low job satisfaction, and to metabolic parameters, such as total cholesterol, high-density lipoprotein (HDL), low-density lipoprotein (LDL), VLDL, and triglycerides. Day-shift workers had higher cortisol levels collected 30?min after waking (p = .03) and a higher cortisol awakening response (CAR; p = .02) during workdays compared to off days. Irregular-shift workers had higher cortisol levels on their off days compared to day-shift workers (p = .03). In conclusion, for the day-shift workers, a higher cortisol response was observed on workdays compared to off days. Although no direct comparisons could be made between groups for work days, on off days the irregular-shift workers had higher cortisol levels compared to day-shift workers, suggesting a prolonged stress response in the irregular-shift group. In addition, cortisol levels were correlated with stressors and metabolic parameters. Future studies are warranted to investigate further stress responses in the context of irregular work hours.     

When can the cause of a population decline be determined?

Inferring the factors responsible for declines in abundance is a prerequisite to preventing the extinction of wild populations. Many of the policies and programmes intended to prevent extinctions operate on the assumption that the factors driving the decline of a population can be determined. Exogenous factors that cause declines in abundance can be statistically confounded with endogenous factors such as density dependence. To demonstrate the potential for confounding, we used an experiment where replicated populations were driven to extinction by gradually manipulating habitat quality. In many of the replicated populations, habitat quality and density dependence were confounded, which obscured causal inference. Our results show that confounding is likely to occur when the exogenous factors that are driving the decline change gradually over time. Our study has direct implications for wild populations, because many factors that could drive a population to extinction change gradually through time.