Potentials for monitoring gene level biodiversity: using Sweden as an example

Programs for monitoring biological diversity over time are needed to detect changes that can constitute threats to biological resources. The convention on biological diversity regards effective monitoring as necessary to halt the ongoing erosion of biological variation, and such programs at the ecosystem and species levels are enforced in several countries. However, at the level of genetic biodiversity, little has been accomplished, and monitoring programs need to be developed. We define “conservation genetic monitoring” to imply the systematic, temporal study of genetic variation within particular species/populations with the aim to detect changes that indicate compromise or loss of such diversity. We also (i) identify basic starting points for conservation genetic monitoring, (ii) review the availability of such information using Sweden as an example, (iii) suggest categories of species for pilot monitoring programs, and (iv) identify some scientific and logistic issues that need to be addressed in the context of conservation genetic monitoring. We suggest that such programs are particularly warranted for species subject to large scale enhancement and harvest—operations that are known to potentially alter the genetic composition and reduce the variability of populations.     

Inter-generational equity index for assessing environmental sustainability: An example on global warming

Inter-generational equity is essential for environmental sustainability. The current generation inherits an environment with a certain quality from the previous generation. The impact on the environment gradually exacerbates and accumulates over a period of time between two generations. However, currently there is no index available to assess inter-generational equity. Generally a typical environmental index is established to represent the environmental status in a specific year. This kind of index, although it presents the annual environmental variation, does not reflect the degree of change in environmental sustainability between two generations. Therefore, an inter-generational equity index (IGEI) and an endowment equation to examine the temporal trend of the changing environment are proposed for assessing inter-generational equity. To demonstrate the applicability of the endowment equation, an IGEI was established to assess the inter-generational equity of global warming. The global warming IGEI evaluates the status between two generations based on three sub-indexes; CO₂ emission, loss due to climate disasters, and the size of the existing forest area. The pressure–state–response (PSR) framework was adopted to explain the causal relationship between these three sub-indexes. According to the endowment rate determined by the proposed equation for each sub-index, the increase in CO₂ emission from 1980 to 2000 shows an obviously inequitable pattern between generations. Subsequently, the loss due to climate disasters between generations was also more serious. The size of the forest area, an important factor for reducing the impact of global warming, is unfortunately also decreasing significantly between generations. Using the endowment rate determined by the proposed endowment equation, the evaluation of the inter-generational equity is made possible and is demonstrated by the IGEI established for global warming.     

Measuring the sustainability of cities: An analysis of the use of local indicators

We analyze 17 studies of the use of urban sustainable development indicators (SDI) in developed western countries. The analysis reveals a lack of consensus not only on the conceptual framework and the approach favored, but also on the selection and optimal number of indicators. First, by performing different classifications and categorizations of SDI we identify problems inherent in territorial practices that use SDI. Second, we argue that the lack of consensus in several steps of the creation of SDI stems notably from the ambiguity in the definitions of sustainable development, objectives for the use of such indicators, the selection method and the accessibility of qualitative and quantitative data. Third, based on the reviewed studies, we propose a selection strategy for SDI through which we demonstrate the need to adopt a parsimonious list of SDI covering the sustainable development components and their constituent categories as broadly as possible while minimizing the number of indicators retained.     

Indicators of species richness at the local scale in an alpine region: a comparative approach between plant and invertebrate taxa

Studies investigating congruent variations in species richness patterns in alpine habitats are scarce. We investigated the potential of using the indicator taxa approach for species richness in alpine habitats of the Scandes (Norway). In four areas, we investigated seven functional and taxonomic terrestrial groups of organisms and evaluated their contribution to the species diversity. The function of each group as a surrogate for the overall species diversity or for the diversity of another taxon was analysed. Three groups of invertebrates (spiders without Lycosids, Lycosids only, and ground beetles), three groups of plants (shrubs, graminoids, and herbs), and lichens were used for a cross-taxon analysis of species diversity. Congruence in species richness was restricted to several significant results, with vascular plants and spiders (Araneae) being best suited as surrogate taxa in alpine habitats of the Scandes. In the cross-taxon analyses they showed strongest significant positive correlations, covering the total species richness of the alpine habitats best. Species counts in one group account for up to 70% of the variation in total species richness. We found only limited evidence for an ideal, efficient biodiversity indicator taxon that could be applied without restrictions at different alpine habitats in low and middle alpine areas. Thus, our results suggest that it is very important to use more than one taxon as indicator for species richness in terrestrial alpine habitats. This should facilitate future conservation planning in alpine areas.     

Biodiversity and monitoring of colorless filamentous bacteria in sulfide aquatic systems of North Caucasus region

Bacterial mats in sulfide aquatic systems of North Caucasus are basically composed by the species of genera Thiothrix and Sphaerotilus. Additionally, several non-filamentous sulfur-oxidizing bacteria were isolated from the mats and several minor 16S rRNA phylotypes were found in clone libraries from these mats. The minor components were affiliated with Proteobacteria, Chlorobia, Cyanobacteria and Firmicutes. Even in an individual mat population heterogeneity of Thiothrix spp. was revealed by analysis of 16S rRNA gene and RAPD-PCR. Five Thiothrix isolates were described as new species Thiothrix caldifontis sp. nov. and Thiothrix lacustris sp. nov. In the Thiothrix-Sphaerotilus type of bacterial mat the proportion of dominant organisms might be influenced by sulfide concentration in the spring water. The higher sulfide concentration (more than 10 mg/l) in the spring water is more favorable for the development of bacterial mats with dominant Thiothrix organisms than for Thiothrix-Sphaerotilus type of sulfur mat.     

Dynamic sustainability assessment of countries at the macro level: A principal component analysis

Monitoring progress toward sustainable development requires the identification of operational indicators that provide manageable units of information on institutional, environmental, economic and social dimensions. This paper is an attempt to develop macro sustainability indicators of selected countries in order to track sustainability in a dynamic manner. Therefore, as a first step, sustainability pillar variables for 131 countries were defined and derived for the period 2000–2007. Three different methods, i.e., standardization, min–max and cyclical techniques, were used to normalize data and finally a principal component analysis (PCA) was applied for weighting selected variables. In the last step, countries were ranked based on their principal components (PCs) and spatially aggregated sustainability was tracked in four dimensions. The paper finds that while progress was observed for the institutional, economic and social dimensions, the environmental conditions deteriorated successively over the studied period. It is concluded that when institutional, environmental and economic pillars are strongly correlated, economic development cannot solely explain environmental deterioration.     

Assessing facilitative responses to a nurse shrub at the community level: the example of Potentilla fruticosa in a sub‐alpine grassland of northwest China

Biotic interaction studies have revealed a large discrepancy among experiments in target responses to the effects of neighbours, which may in part be due to both high species‐specificity of plant responses and low number of target species used in experiments. Our aim was to assess facilitative responses at the community level and the role of both functional groups and ecological attributes of target species. In a sub‐alpine grassland on the eastern Tibet plateau, we assessed growth responses of all species in the community to removal of a dominant shrub. We also measured changes in the main environmental variables. Species responses were analysed by functional group and in relation to their mean regional altitudinal distribution. All significant interactions were positive and affected one‐third of the total species richness of the community. All functional groups were facilitated but forbs were less strongly facilitated than in the two other groups. High‐alpine species were less strongly facilitated than low‐sub‐alpine species, but the strength of this relationship was weaker than that reported in previous work. There was evidence of a decrease in extreme temperatures below the canopy of the shrub but no variations in soil moisture. We conclude that the highly stressful conditions induced by the dry continental climate of the eastern Tibet plateau are a main driver of the exclusive dominance of positive interactions. Assessing interactive responses at the community level is likely to provide a useful tool to better understand the role of biotic interactions in community responses to environmental changes.     

Improving benchmarking by using an explicit framework for the development of composite indicators: an example using pediatric quality of care

Background

The measurement of healthcare provider performance is becoming more widespread. Physicians have been guarded about performance measurement, in part because the methodology for comparative measurement of care quality is underdeveloped. Comprehensive quality improvement will require comprehensive measurement, implying the aggregation of multiple quality metrics into composite indicators.

Objective

To present a conceptual framework to develop comprehensive, robust, and transparent composite indicators of pediatric care quality, and to highlight aspects specific to quality measurement in children.

Methods

We reviewed the scientific literature on composite indicator development, health systems, and quality measurement in the pediatric healthcare setting. Frameworks were selected for explicitness and applicability to a hospital-based measurement system.

Results

We synthesized various frameworks into a comprehensive model for the development of composite indicators of quality of care. Among its key premises, the model proposes identifying structural, process, and outcome metrics for each of the Institute of Medicine's six domains of quality (safety, effectiveness, efficiency, patient-centeredness, timeliness, and equity) and presents a step-by-step framework for embedding the quality of care measurement model into composite indicator development.

Conclusions

The framework presented offers researchers an explicit path to composite indicator development. Without a scientifically robust and comprehensive approach to measurement of the quality of healthcare, performance measurement will ultimately fail to achieve its quality improvement goals.

     

Elephant calling patterns as indicators of group size and composition: the basis for an acoustic monitoring system

The paper gives evidence that the vocal activity of elephants varies with group size, composition and reproductive status, and that elephants' calling patterns could therefore provide the basis for a remote monitoring system. We examined a 3‐week set of array‐based audio recordings of savanna elephants (Loxodonta africana), searching for diagnostic acoustic parameters. An acoustic array made it possible to locate recorded sounds and attribute the calls to particular elephants or elephant groups. Simultaneous video recordings made it possible to document visible behaviour and roughly correlate it with vocalizations. We compared several measures of call density in elephant groups containing up to 59 individuals, and found that rates of calling increased with increasing numbers of elephants. We divided all call events into three structural types (single‐voice low‐frequency calls, multiple‐voice clustered low‐frequency calls, and single‐voice high frequency calls), and found that the incidence of these varies predictably with group composition. These results suggest the value of a network of listening systems in remote areas for the collection of information on elephant abundance and population structure.     

Biodiversity indicators in European ground waters: towards a predictive model of stygobiotic species richness

1. Estimates of species richness obtained from exhaustive field inventories over large spatial scales are expensive and time-consuming. For this reason, efficiency demands the use of indicators as 'surrogates' of species richness. Biodiversity indicators are defined herein as a limited suite of taxonomic groups the species richness of which is correlated with the species richness of all other taxonomic groups present in the survey area.
2. Species richness in ground water was assessed at different spatial scales using data collected from six regions in Europe. In total, 375 stygobiotic species were recorded across 1157 sites and 96 aquifers. The taxonomic groups collected from more than one site and with more than two species (Oligochaeta, Gastropoda, Cyclopoida, Harpacticoida, Ostracoda, Isopoda, Amphipoda, Bathynellacea and Acari) were used to develop nonparametric models to predict stygobiotic biodiversity at the aquifer scale.
3. Pair-wise correlations between taxonomic groups were low, i.e. variation in species richness of a single taxonomic group did not usually reflect variation of the other groups. In contrast, multiple regressions calculated between species richness of any combination of taxa and extra-group species richness along the six regions resulted in a number of significant relationships.
4. These results suggest that some taxonomic groups (mainly Copepoda and Amphipoda and, to a lesser extent, Oligochaeta and Gastropoda) combined in different ways across the regions, were good biodiversity indicators in European groundwater ecosystems. However, the uneven distribution of taxonomic groups prevented selection of a common set of indicators for all six regions. Faunal differences among regions are presumably related to both historical and ecological factors, including palaeogeography, palaeoecology, geology, aquifer fragmentation and isolation, and, less clearly, anthropogenic disturbance.     

A directional strategy for monitoring Cre-mediated recombination at the cellular level in the mouse

Functional redundancies, compensatory mechanisms, and lethal phenotypes often prevent the full analysis of gene functions through generation of germline null mutations in the mouse. The use of site-specific recombinases, such as Cre, which catalyzes recombination between loxP sites, has allowed the engineering of mice harboring targeted somatic mutations, which are both temporally controlled and cell-type restricted. Many Cre-expressing mouse lines exist, but only a few transgenic lines are available that harbor a reporter gene whose expression is dependent on a Cre-mediated event. Moreover, their use to monitor gene ablation at the level of individual cells is often limited, as in some tissues the reporter gene may be silenced, be affected by position-effect variegation, or reside in a chromatin configuration inaccessible for recombination. Thus, one cannot validly extrapolate from the expression of a reporter transgene to an identical ablation pattern for the conditional allele of a given gene. By combining the ability of Cre recombinase to invert or excise a DNA fragment, depending on the orientation of the flanking loxP sites, and the availability of both wild-type (WT) and mutant loxP sites, we designed a Cre-dependent genetic switch (FLEx switch) through which the expression of a given gene is turned off, while the expression of another one is concomitantly turned on. We demonstrate the efficiency and reliability of this switch to readily detect, in the mouse, at the single cell level, Cre-mediated gene ablation. We discuss how this strategy can be used to generate genetic modifications in a conditional manner.     

Biodiversity in the Gulf of Guinea: an overview

Patterns of species-richness and endemism in the Gulf of Guinea reflect the region's biogeographic history. Bioko is a continental-shelf island that was recently connected to the African mainland, whereas Príncipe, São Tomé and Annobón are truly oceanic and have never been connected with each other or with the mainland. As a result, Bioko supports a much more diverse flora and fauna but with relatively low levels of endemism at the species level, whereas the oceanic islands are relatively depauperate because of their isolation but rich in endemic taxa. Species endemism is 0–3% on Bioko for angiosperms, bats, birds, reptiles and amphibians, compared with much higher values on Principe for these same taxa of 8% (plants) to 100% (amphibians), on São Tomé between 14% (plants) and 100% (amphibians), and on Annobón 0% (bats) to 71% (reptiles). On a global scale, for their size both Príncipe and São Tomé support unusually high numbers of single-island endemic species of birds, reptiles and amphibia. For its tiny size, Annobón is also notable for its endemic birds and reptiles. Among terrestrial molluscs the rates of endemism are in general higher than for plants and vertebrates, from ca 50% on Bioko to ca 80% on the oceanic islands. In contrast and as might be expected, only Bioko supports a rich freshwater fish fauna and it contains many endemic taxa, whereas the oceanic islands support only a few salt-tolerant species. The Gulf of Guinea islands are also important for their marine organisms, amongst which coral reef fish and marginellid molluscs show high levels of endemism, though they are not especially species-rich. The Gulf of Guinea islands are of great interest to conservationists and evolutionary biologists. Each island, of greatly differing size and degree of isolation, has acquired its unique sub-set of plants and animals separately from the neighbouring mainland, followed by adaptive radiations in situ. For this reason the conservation value of the archipelago as a whole is greater than the sum of the biodiversity contained in its individual islands. Conservation initiatives in the Gulf of Guinea should therefore ensure that representative terrestrial, freshwater and marine habitats and groups of organisms are targeted in a co-ordinated manner among the islands.     

Airborne fungi as indicators of ecosystem disturbance: an example from selected Tatra Mountains caves (Poland)

We report on the determination of the spore concentration and the species composition of the airborne fungi in selected caves of the Tatra Mountains, Poland. The following caves were surveyed: Mylna, Ob?azkowa, Mro?na, Zimna and Naciekowa. The sampling was carried out in July 2015 and in January 2016. The aeromycological analyses were performed with the impact method, using the Air Ideal 3P apparatus and potato dextrose agar (PDA, Biocorp) culture medium. In the course of the July 2015 analysis, 17 species of fungi were isolated and 11 species were isolated in January 2016. In Mylna and Naciekowa caves, the dominant species were Cladosporium cladosporioides and Stachybotrys cylindrospora. In Ob?azkowa cave, Rhizoctonia predominated and in Zimna cave—the colonies of the yeast-like fungi, along with S. cylindrospora. In Mro?na cave, Penicillium notatum was the most abundant taxon. In the winter time, in the majority of the caves Penicillium spp. predominated, with the exception of Mro?na and Naciekowa caves where Aspergillus niger was dominant. We propose that aeromycological monitoring be performed regularly in the following caves: Mro?na, Naciekowa and Zimna.     

Emergy-based indicators of regional environmental sustainability: A case study in Shanwei,Guangdong, China

Understanding which factors mainly affect the environmental sustainability of a Region is a very crucial concern for many Chinese planners and policy-makers. In this study, the emergy accounting method is applied to the production and consumption activities of the city of Shanwei, a seaside urban area in Guangdong region, China. The emergy method provides a comprehensive assessment of a system, by generating a consistent set of indicators capable to capture the dynamics of the system as a whole and its efficiency in converting resources into an economic product and welfare. At the same time, the approach is capable to provide details about a system's performance over time, its use of renewable versus nonrenewables sources, local versus imported, concentrated versus dispersed and finally labor intensive versus fuel intensive processes. The main local renewable and nonrenewable emergy flows supporting the investigated area were included in the accounting, together with the flows of imported energy, goods, machinery, labor and services. Coal plays a crucial role for electricity generation, industrial uses, but also gasoline and diesel for transport affect the overall sustainability to a non-negligible extent. An Emergy Sustainability Indicator (ESI) of the local economic and social system is calculated and compared with the average value of the Chinese economy, based on the assumption that a process or system is unsustainable if it contributes to lower the overall sustainability of the region or country. This is quantified by the requirement that always must be ESI_local ≧ ESI_country. Results confirm that the most crucial factor for this region sustainability is the use of coal as a non-renewable and imported energy source. The calculated emergy indicators translate into a set-aside buffer land demand capable to mitigate, dilute, and uptake the environmental impact of human-dominated activities. Unfortunately, such buffer land demand is much higher than the land actually available. As a result, both the ESI-based sustainability equation as well as the lack of support land make the city's production and consumption patterns unsustainable and call for different lifestyles and environmental policies.