Strong “bottom‐up” influences on small mammal populations: State‐space model analyses from long‐term studies

“Bottom‐up” influences, that is, masting, plus population density and climate, commonly influence woodland rodent demography. However, “top‐down” influences (predation) also intervene. Here, we assess the impacts of masting, climate, and density on rodent populations placed in the context of what is known about “top‐down” influences. To explain between‐year variations in bank vole Myodes glareolus and wood mouse Apodemus sylvaticus population demography, we applied a state‐space model to 33 years of catch‐mark‐release live‐trapping, winter temperature, and precise mast‐collection data. Experimental mast additions aided interpretation. Rodent numbers in European ash Fraxinus excelsior woodland were estimated (May/June, November/December). December–March mean minimum daily temperature represented winter severity. Total marked adult mice/voles (and juveniles in May/June) provided density indices validated against a model‐generated population estimate; this allowed estimation of the structure of a time‐series model and the demographic impacts of the climatic/biological variables. During two winters of insignificant fruit‐fall, 6.79 g/m² sterilized ash seed (as fruit) was distributed over an equivalent woodland similarly live‐trapped. September–March fruit‐fall strongly increased bank vole spring reproductive rate and winter and summer population growth rates; colder winters weakly reduced winter population growth. September–March fruit‐fall and warmer winters marginally increased wood mouse spring reproductive rate and September–December fruit‐fall weakly elevated summer population growth. Density dependence significantly reduced both species' population growth. Fruit‐fall impacts on demography still appeared after a year. Experimental ash fruit addition confirmed its positive influence on bank vole winter population growth with probable moderation by colder temperatures. The models show the strong impact of masting as a “bottom‐up” influence on rodent demography, emphasizing independent masting and weather influences; delayed effects of masting; and the importance of density dependence and its interaction with masting. We conclude that these rodents show strong “bottom‐up” and density‐dependent influences on demography moderated by winter temperature. “Top‐down” influences appear weak and need further investigation.     

“Enzyme Test Bench,” a high‐throughput enzyme characterization technique including the long‐term stability

A new high throughput technique for enzyme characterization with specific attention to the long term stability, called “Enzyme Test Bench,” is presented. The concept of the Enzyme Test Bench consists of short term enzyme tests in 96‐well microtiter plates under partly extreme conditions to predict the enzyme long term stability under moderate conditions. The technique is based on the mathematical modeling of temperature dependent enzyme activation and deactivation. Adapting the temperature profiles in sequential experiments by optimal non‐linear experimental design, the long term deactivation effects can be purposefully accelerated and detected within hours. During the experiment the enzyme activity is measured online to estimate the model parameters from the obtained data. Thus, the enzyme activity and long term stability can be calculated as a function of temperature. The engineered instrumentation provides for simultaneous automated assaying by fluorescent measurements, mixing and homogenous temperature control in the range of 10–85 ± 0.5°C. A universal fluorescent assay for online acquisition of ester hydrolysis reactions by pH‐shift is developed and established. The developed instrumentation and assay are applied to characterize two esterases. The results of the characterization, carried out in microtiter plates applying short term experiments of hours, are in good agreement with the results of long term experiments at different temperatures in 1 L stirred tank reactors of a week. Thus, the new technique allows for both: the enzyme screening with regard to the long term stability and the choice of the optimal process temperature regarding such process parameters as turn over number, space time yield or optimal process duration. The comparison of the temperature dependent behavior of both characterized enzymes clearly demonstrates that the frequently applied estimation of long term stability at moderate temperatures by simple activity measurements after exposing the enzymes to elevated temperatures may lead to suboptimal enzyme selection. Thus, temperature dependent enzyme characterization is essential in primary screening to predict its long term behavior. Biotechnol. Bioeng. 2009;103: 305–322. © 2008 Wiley Periodicals, Inc.     

“Capacity”, “best interests”, “will and preferences” and the UN Convention on the Rights of Persons with Disabilities

The United Nations (UN) Convention on the Rights of Persons with Disabilities (CRPD) is the most up‐to‐date international legal instrument concerning the rights of persons with disabilities. Such persons are taken to include those with serious mental disorders. According to an authoritative interpretation of a crucial Article (Article 12 ‐ Equal recognition before the law) by the UN CRPD Committee, involuntary detention and treatment of people with mental health disabilities are prohibited under the Convention. Both conventional mental health law and “capacity‐based” law are deemed to violate the Convention. However, some other UN bodies are not in full agreement (for example, the UN Human Rights Committee and the Subcommittee on Prevention of Torture and Other Cruel, Inhuman or Degrading Treatment or Punishment), while others are less explicitly absolutist (for example, the Human Rights Council). Furthermore, strong criticisms of the position of the CRPD Committee have been mounted from a number of academic quarters. These criticisms center on whether the role of a person's ability to make a decision can be ignored, no matter the circumstances. Much of the above debate turns on the concept of “legal capacity” and the now often‐repeated precept that one must always respect the “will and preferences” of the person with a disability. However, “will and preferences” remains undefined. In this paper, I offer an analysis of “will and preferences” that can clarify interventions that may be acceptable or non‐acceptable under the terms of the UN Convention.     

Passive recovery of small vertebrates following livestock removal in the Australian rangelands

In arid environments, grazing by exotic herbivores, including domestic livestock, can greatly influence native, small vertebrate assemblages. Whether the removal of livestock facilitates passive recovery of these assemblages depends on habitat condition and the species present. We explore changes in small mammal and reptile species richness, abundance, and composition in a degraded chenopod shrubland dominated by Acacia victoriae ssp. and open Acacia aneura (mulga) woodland destocked in 1976 and 1984, respectively. Data were obtained between 1997 and 2007, from two grazed and two ungrazed sites in each community. Species richness increased at a faster rate in ungrazed open A. aneura woodland, but did not differ significantly between ungrazed and grazed degraded chenopod shrubland. Subsequent analyses at a finer‐scale detected disparate responses in richness and abundance for microhabitat. At this scale, a greater number of species‐specific responses were also detected, including increased abundance of generalist species and decreased abundance of species requiring low cover. These results reiterate the potential for species‐specific responses to livestock that are more apparent in particular microhabitats. Furthermore, this investigation provides evidence for the gradual passive recovery of small mammal and reptile assemblages in both communities, which is facilitated by the removal of livestock in open A. aneura woodland in fair condition, but not degraded chenopod shrubland in poor condition.     

Major limitations to achieving “4 per 1000” increases in soil organic carbon stock in temperate regions: Evidence from long‐term experiments at Rothamsted Research,United Kingdom

We evaluated the “4 per 1000” initiative for increasing soil organic carbon (SOC) by analysing rates of SOC increase in treatments in 16 long‐term experiments in southeast United Kingdom. The initiative sets a goal for SOC stock to increase by 4‰ per year in the 0–40 cm soil depth, continued over 20 years. Our experiments, on three soil types, provided 114 treatment comparisons over 7–157 years. Treatments included organic additions (incorporated by inversion ploughing), N fertilizers, introducing pasture leys into continuous arable systems, and converting arable land to woodland. In 65% of cases, SOC increases occurred at >7‰ per year in the 0–23 cm depth, approximately equivalent to 4‰ per year in the 0–40 cm depth. In the two longest running experiments (>150 years), annual farmyard manure (FYM) applications at 35 t fresh material per hectare (equivalent to approx. 3.2 t organic C/ha/year) gave SOC increases of 18‰ and 43‰ per year in the 23 cm depth during the first 20 years. Increases exceeding 7‰ per year continued for 40–60 years. In other experiments, with FYM applied at lower rates or not every year, there were increases of 3‰–8‰ per year over several decades. Other treatments gave increases between zero and 19‰ per year over various periods. We conclude that there are severe limitations to achieving the “4 per 1000” goal in practical agriculture over large areas. The reasons include (1) farmers not having the necessary resources (e.g. insufficient manure); (2) some, though not all, practices favouring SOC already widely adopted; (3) practices uneconomic for farmers—potentially overcome by changes in regulations or subsidies; (4) practices undesirable for global food security. We suggest it is more realistic to promote practices for increasing SOC based on improving soil quality and functioning as small increases can have disproportionately large beneficial impacts, though not necessarily translating into increased crop yield.     

Invasive plants in Minnesota are “joining the locals”: A trait‐based analysis

Questions

Predicting which newly arrived species will establish and become invasive is a problem that has long vexed researchers. In a study of cold temperate oak forest stands, we examined two contrasting hypotheses regarding plant functional traits to explain the success of certain non‐native species. Under the “join the locals” hypothesis, successful invaders are expected to share traits with resident species because they employ successful growth strategies under light‐limited understorey conditions. Instead, under the “try harder” hypothesis, successful invaders are expected to have traits different from native species in order to take advantage of unused niche space.

Location

Minnesota, USA.

Methods

We examined these two theories using 109 native and 11 non‐native plants in 68 oak forest stands. We focused on traits related to plant establishment and growth, including specific leaf area (SLA), leaf carbon‐to‐nitrogen ratio (C:N), wood density, plant maximum height, mycorrhizal type, seed mass and growth form. We compared traits of native and non‐native species using ordinations in multidimensional trait space and compared community‐weighted mean (CWM) trait values across sites.

Results

We found few differences between trait spaces occupied by native and non‐native species. Non‐native species occupied smaller areas of trait space than natives, yet were within that of the native species, indicating similar growth strategies. We observed a higher proportion of non‐native species in sites with higher native woody species CWM SLA and lower CWM C:N. Higher woody CWM SLA was observed in sites with higher soil pH, while lower CWM C:N was found in sites with higher light levels.

Conclusions

Non‐native plants in this system have functional traits similar to natives and are therefore “joining the locals.” However, non‐native plants may possess traits toward the acquisitive end of the native plant trait range, as evidenced by higher non‐native plant abundance in high‐resource environments.

     

Accumulation of “Old Proteins” and the Critical Need for MS‐based Protein Turnover Measurements in Aging and Longevity

Aging and age‐related diseases are accompanied by proteome remodeling and progressive declines in cellular machinery required to maintain protein homeostasis (proteostasis), such as autophagy, ubiquitin‐mediated degradation, and protein synthesis. While many studies have focused on capturing changes in proteostasis, the identification of proteins that evade these cellular processes has recently emerged as an approach to studying the aging proteome. With advances in proteomic technology, it is possible to monitor protein half‐lives and protein turnover at the level of individual proteins in vivo. For large‐scale studies, these technologies typically include the use of stable isotope labeling coupled with MS and comprehensive assessment of protein turnover rates. Protein turnover studies have revealed groups of highly relevant long‐lived proteins (LLPs), such as the nuclear pore complexes, extracellular matrix proteins, and protein aggregates. Here, the role of LLPs during aging and age‐related diseases and the methods used to identify and quantify their changes are reviewed. The methods available to conduct studies of protein turnover, used in combination with traditional proteomic methods, will enable the field to perform studies in a systems biology context, as changes in proteostasis may not be revealed in studies that solely measure differential protein abundances.     

Boom‐bust dynamics in biological invasions: towards an improved application of the concept

Boom‐bust dynamics – the rise of a population to outbreak levels, followed by a dramatic decline – have been associated with biological invasions and offered as a reason not to manage troublesome invaders. However, boom‐bust dynamics rarely have been critically defined, analyzed, or interpreted. Here, we define boom‐bust dynamics and provide specific suggestions for improving the application of the boom‐bust concept. Boom‐bust dynamics can arise from many causes, some closely associated with invasions, but others occurring across a wide range of ecological settings, especially when environmental conditions are changing rapidly. As a result, it is difficult to infer cause or predict future trajectories merely by observing the dynamic. We use tests with simulated data to show that a common metric for detecting and describing boom‐bust dynamics, decline from an observed peak to a subsequent trough, tends to severely overestimate the frequency and severity of busts, and should be used cautiously if at all. We review and test other metrics that are better suited to describe boom‐bust dynamics. Understanding the frequency and importance of boom‐bust dynamics requires empirical studies of large, representative, long‐term data sets that use clear definitions of boom‐bust, appropriate analytical methods, and careful interpretations.     

Testing the limits of resistance: a 19‐year study of Mediterranean grassland response to grazing regimes

A synthesis of a long‐term (19 years) study assessing the effects of cattle grazing on the structure and composition of a Mediterranean grassland in north‐eastern Israel is presented, with new insights into the response of the vegetation to grazing management and rainfall. We hypothesized that the plant community studied would be resistant to high grazing intensities and rainfall variability considering the combined long history of land‐use and unpredictable climatic conditions where this community evolved. Treatments included manipulations of stocking densities (moderate, heavy, and very heavy) and of grazing regimes (continuous vs. seasonal), in a factorial design. The effect of interannual rainfall variation on the expression of grazing impacts on the plant community was minor. The main effects of grazing on relative cover of plant functional groups were related to early vs. late seasonal grazing. Species diversity and equitability were remarkably stable across all grazing treatments. A reduction in tall grass cover at higher stocking densities was correlated with increased cover of less palatable groups such as annual and perennial thistles, as well as shorter and prostrate groups such as short annual grasses. This long‐term study shows that interannual fluctuations in plant functional group composition could be partly accounted for by grazing pressure and timing, but not by the measured rainfall variables. Grazing affected the dominance of tall annual grasses. However, the persistence of tall grasses and more palatable species over time, despite large differences in grazing pressure and timing, supports the idea that Mediterranean grasslands are highly resistant to prolonged grazing. Indeed, even under the most extreme grazing conditions applied, there were no signs of deterioration or collapse of the ecosystem. This high resistance to grazing intensity and interannual fluctuation in climatic conditions should favor the persistence of the plant community under forecasted increasing unpredictability due to climate change.     

Signals of range expansions and contractions of vascular plants in the high Alps: observations (1994–2004) at the GLORIA* master site Schrankogel,Tyrol, Austria

High mountain ecosystems are defined by low temperatures and are therefore considered to react sensitively to climate warming. Responding to observed changes in plant species richness on high peaks of the European Alps, an extensive setup of 1 m × 1 m permanent plots was established at the alpine‐nival ecotone (between 2900 and 3450 m) on Mount Schrankogel, a GLORIA master site in the central Tyrolean Alps, Austria, in 1994. Recording was repeated in a representative selection of 362 quadrats in 2004. Ten years after the first recording, we observed an average change in vascular plant species richness from 11.4 to 12.7 species per plot, an increase of 11.8% (or of at least 10.6% at a 95% confidence level). The increase in species richness involved 23 species (about 43% of all taxa found at the ecotone), comprising both alpine and nival species and was pronouncedly higher in plots with subnival/nival vegetation than in plots with alpine grassland vegetation. Only three species showed a decrease in plot occupancy: one was an annual species, one was rare, and one a common nival plant that decreased in one part of the area but increased in the uppermost part. Species cover changed in relation to altitudinal preferences of species, showing significant declines of all subnival to nival plants, whereas alpine pioneer species increased in cover. Recent climate warming in the Alps, which has been twice as high as the global average, is considered to be the primary driver of the observed differential changes in species cover. Our results indicate an ongoing range contraction of subnival to nival species at their rear (i.e. lower) edge and a concurrent expansion of alpine pioneer species at their leading edge. Although this was expected from predictive distribution models and different temperature‐related habitat preferences of alpine and nival species, we provide first evidence on – most likely – warming‐induced species declines in the high European Alps. The projected acceleration of climate warming raises concerns that this phenomenon could become the major threat to biodiversity in high mountains.     

Long‐term farming systems and last crop sown shape the species and functional composition of the arable weed seed bank

Questions: The assembly of arable weed communities is the result of local filtering by agricultural management and crop competition. Therefore, soil seed banks can reflect the effects of long‐term cumulative field management and crop sequences on weed communities. Moreover, soil seed banks provide strong estimates of future weed problems but also of potential arable plant diversity and associated ecological functions. For this, we evaluated the effects of different long‐term farming systems under the same crop rotation sequence on the abundance, diversity and community assembly of weed seed bank, as well as on the functional diversity and composition. Location: DOK (biodynamic [D], bioorganic [O], conventional [K]) long‐term trial, Therwil, Switzerland. Methods: The effects of long‐term contrasted farming systems (i.e., biodynamic, organic, conventional, mineral and unfertilised systems) and last crop sown (i.e., wheat and maize) were evaluated on different indicators of species and functional diversity and composition of the weed soil seed bank. Results: The results showed significant influences of 40 years of contrasted farming systems on the diversity and composition of the seed bank, with higher diversities being found in unfertilised and organic farming systems, but also higher abundances than those found under conventional systems. Organic farming also allowed higher functional richness, dispersion and redundancy. Different farming systems triggered shifts in species and functional assemblies. Conclusions: The results highlight the importance of organic management for the maintenance of a diverse arable plant community and its functions. However, such results emphasise the need for appropriate yearly management to reduce the abundance of settled weediness and prevent affecting crop production. The farm management filtered community composition based on functional traits. Although the soil seed bank buffers the long‐term farming and crop sequence, the last crop sown and, thus, the yearly management were important determinants of seed bank composition.     

Managing for naturalness alone is not an effective way to preserve all the valuable natural features of the Białowieża Forest – a reply to Jaroszewicz et al.

Currently, Brzeziecki et al. 2016 (Journal of Vegetation Science 27: 460–467.) are using data from permanent study plots established in 1936 in Bia?owie?a National Park (NE Poland) to develop theoretical equilibrium tree size distributions and to then compare modelled and actual distributions with a view to assessing the population dynamics of the species involved. As part of their discussion, the authors address the question of possible consequences for the overall diversity of forest ecosystems under strict protection if long‐term trends relating to tree population densities and size structures are maintained. In the overall context of the above, the goal of the present paper is to respond to Jaroszewicz et al. (Journal of Vegetation Science 28: 218–222.) who suggest that the paper of Brzeziecki et al. (2016) is not representative for the whole Bia?owie?a National Park, and that – in this connection – strict protection should not be seen as a cause for concern. In this paper, we show that the data analysed by Brzeziecki et al. (2016) adequately characterize conditions in the wider Park. We also point out that the thorough scientific understanding of the long‐term dynamics of woodland communities under strict protection should indeed be taken into account as efforts are made to arrive at an effective conservation strategy capable of ensuring that the uniquely valuable features of the Bia?owie?a Forest are retained.