DNA barcoding as a tool for coral reef conservation

DNA Barcoding (DBC) is a method for taxonomic identification of animals that is based entirely on the 5′ portion of the mitochondrial gene, cytochrome oxidase subunit I (COI-5). It can be especially useful for identification of larval forms or incomplete specimens lacking diagnostic morphological characters. DBC can also facilitate the discovery of species and in defining “molecular taxonomic units” in problematic groups. However, DBC is not a panacea for coral reef taxonomy. In two of the most ecologically important groups on coral reefs, the Anthozoa and Porifera, COI-5 sequences have diverged too little to be diagnostic for all species. Other problems for DBC include paraphyly in mitochondrial gene trees and lack of differentiation between hybrids and their maternal ancestors. DBC also depends on the availability of databases of COI-5 sequences, which are still in early stages of development. A global effort to barcode all fish species has demonstrated the importance of large-scale coordination and is yielding promising results. Whether or not COI-5 by itself is sufficient for species assignments has become a contentious question; it is generally advantageous to use sequences from multiple loci.     

Genetic monitoring as a promising tool for conservation and management

In response to ever-increasing anthropogenic changes to natural ecosystems, regional, national and international organizations have established guidelines for monitoring biological diversity. Most monitoring programs, however, do not take full advantage of the potential afforded by molecular genetic markers, which can provide information relevant to both ecological and evolutionary time frames, while costing less and being more sensitive and reliable than traditional monitoring approaches. As several molecular and computational approaches are relatively new, many technical and theoretical issues remain to be resolved. Here, we illustrate how DNA and population genetic data can provide valuable information, often unattainable via other approaches, for monitoring species of management, conservation and ecological interest.     

Mathematical modelling as a tool for management in eutrophication control of shallow lakes

The eutrophication model Delwaq-Bloom-Switch is developed to be a functional tool for water management. Therefore it includes nutrients, algal biomass and composition as well as water transparency. A module describing the interaction between water and bottom gives the model the flexibility to deal with measures, such as a decrease of the external phosphorus loading and flushing with water differing in composition from the lake water. This paper focuses on the functional aspects of the model, the results of an application on Lake Veluwe, The Netherlands, and the implications for water management.With one set of coefficients DBS reproduces the most important characteristics of Lake Veluwe for a period of two years before measures (reduction of the external loading and flushing during the winter months) and eight years after the measures. The phosphorus concentration decreased and became growth limiting for algae instead of nitrogen and light. Both in measurements and modelling results, the algal composition changed from blue-green algae dominance to green algae and diatom dominance. Lake Veluwe had a relatively short transient phase after reduction of external loading, because high nitrate concentrations in the flushing water inhibited a long period with high phosphorus releases from the bottom.Model calculations were carried out to investigate the effects of fish stock management and optimization of flushing. Both measures are promising.     

Ecohydrology as a new tool for sustainable management of estuaries and coastal waters

Throughout the world, estuaries and coastal waters have experienced degradation. Present proposed remedial measures based on engineering and technological fix are not likely to restore the ecological processes of a healthy, robust estuary and, as such, will not reinstate the full beneficial functions of the estuary ecosystem. The successful management of estuaries and coastal waters requires an ecohydrologybased, basin-wide approach. This necessitates changing present practices by official institutions based on municipalities or counties as an administrative unit, or the narrowly focused approaches of managers of specific activities (e.g., farming and fisheries, water resources, urban and economic developments, wetlands management and nature conservationists). Without this change in thinking and management concept, estuaries and coastal waters will continue to degrade, whatever integrated coastal management plans are implemented. To help in this process of change there is a need to (1) develop a profound understanding of the effects of biota and biotic processes on mediating estuary response to changing hydrology, sediment and nutrient flux and of the biota on hydrology at the river basin scale, and (2) to develop science-based remediation measures at the river basin scale, with elements of ecohydrology and phytotechnology at their core, to strengthen the ability of the biota to sustain and adapt to human-induced stresses.This revised version wa published online in March 2005 with corrections to the issue cover date.     

Neural networks as a tool for control and management of a biological reactor for treating hydrogen sulphide

Based on an experimental database consisting of 194 daily cases, artificial neural networks were used to model the removal efficiency of a biofilter for treating hydrogen sulphide (H₂S). In this work, the removal efficiency of the reactor was considered as a function of the changes in the air flow and concentration of H₂S entering the biofilter. In order to obtain true representative values, the removal efficiencies (outputs) were measured 24 h after each input was changed. A MLP (multilayer perceptron 2-2-1) model with two input variables (unit flow and concentration of the contaminant fed into the biofilter) rendered good prediction values with a determination coefficient of 0.92 for the removal efficiency within the range studied. This means that the MLP model can explain 92% of the overall variability detected in the biofilter corresponding to a wide range of operating conditions.     

Behavior as a tool for welfare improvement and conservation management in the endangered lizard (Gallotia bravoana)

The study assessed the behavior of Gallotia bravoana (La Gomera, Canary Islands, one of the world's most threatened reptiles) to facilitate management decisions and improve welfare during initial stages of a species' recovery plan. The study analyzed—and remote-controlled video cameras filmed—the behavior of lizards housed in 3 outdoor enclosures, from May to September 2000. Daily activity showed a bimodal or unimodal pattern, all specimens basking more during June, with the largest male was the most active. Adults ate a higher percentage of vegetable items; subadults, a comparatively larger proportion of larvae and adult insects. The study analyzed individual compatibility; all interacted during 2 short periods. Aggression occurred mainly between males; because most directed high-intensity aggression toward a specific lizard, the study recommended isolating this lizard in a separate enclosure. The study recommended keeping 2 male-female pairs, who demonstrated social tolerance, as breeding pairs in separated terraria. Typical courtship behavior (head-bob sequences) occurred mainly during July, with highest frequency by the oldest male. Behavioral assessment provided data for improving the individuals' welfare in the enclosures and to select specific pairs for breeding.     

Niche-based modelling as a tool for predicting the risk of alien plant invasions at a global scale

Predicting the probability of successful establishment of plant species by matching climatic variables has considerable potential for incorporation in early warning systems for the management of biological invasions. We select South Africa as a model source area of invasions worldwide because it is an important exporter of plant species to other parts of the world because of the huge international demand for indigenous flora from this biodiversity hotspot. We first mapped the five ecoregions that occur both in South Africa and other parts of the world, but the very coarse definition of the ecoregions led to unreliable results in terms of predicting invasible areas. We then determined the bioclimatic features of South Africa's major terrestrial biomes and projected the potential distribution of analogous areas throughout the world. This approach is much more powerful, but depends strongly on how particular biomes are defined in donor countries. Finally, we developed bioclimatic niche models for 96 plant taxa (species and subspecies) endemic to South Africa and invasive elsewhere, and projected these globally after successfully evaluating model projections specifically for three well‐known invasive species (Carpobrotus edulis, Senecio glastifolius, Vellereophyton dealbatum) in different target areas. Cumulative probabilities of climatic suitability show that high‐risk regions are spatially limited globally but that these closely match hotspots of plant biodiversity. These probabilities are significantly correlated with the number of recorded invasive species from South Africa in natural areas, emphasizing the pivotal role of climate in defining invasion potential. Accounting for potential transfer vectors (trade and tourism) significantly adds to the explanatory power of climate suitability as an index of invasibility. The close match that we found between the climatic component of the ecological habitat suitability and the current pattern of occurrence of South Africa alien species in other parts of the world is encouraging. If species' distribution data in the donor country are available, climatic niche modelling offers a powerful tool for efficient and unbiased first‐step screening. Given that eradication of an established invasive species is extremely difficult and expensive, areas identified as potential new sites should be monitored and quarantine measures should be adopted.     

Population genomics as a new tool for wildlife management

Admixture and introgression have varied effects on population viability and fitness. Admixture might be an important source of new alleles, particularly for small, geographically isolated populations. However, admixture might also cause outbreeding depression if populations are adapted to different ecological or climatic conditions. Because of the emerging use of translocation and admixture as a conservation and wildlife management strategy to reduce genetic load (termed genetic rescue), the possible effects of admixture have practical consequences ( Bouzat et al. 2009 ; Hedrick & Fredrickson 2010 ). Importantly, genetic load and local adaptation are properties of individual loci and epistatic interactions among loci rather than properties of genomes. Likewise, the outcome and consequences of genetic rescue depend on the fitness effects of individual introduced alleles. In this issue of Molecular Ecology, Miller et al. (2012) use model‐based, population genomic analyses to document locus‐specific effects of a recent genetic rescue in the bighorn sheep population within the National Bison Range wildlife refuge (NBR; Montana, USA). They find a subset of introduced alleles associated with increased fitness in NBR bighorn sheep, some of which experienced accelerated introgression following their introduction. These loci mark regions of the genome that could constitute the genetic basis of the successful NBR bighorn sheep genetic rescue. Although population genomic analyses are frequently used to study local adaptation and selection (e.g. Hohenlohe et al. 2010 ; Lawniczak et al. 2010 ), this study constitutes a novel application of this analytical framework for wildlife management. Moreover, the detailed demographic data available for the NBR bighorn sheep population provide a rare and powerful source of information and allow more robust population genomic inference than is often possible.     

Analysis of coastal lagoon metabolism as a basis for management

This work was carried out in a shallow eutrophic coastal lagoon (St. André lagoon, SW Portugal) which is artificially opened to the sea each year in early spring. Macrophytes, mainly Ruppia cirrhosa, are keystone species in this ecosystem covering up to 60% of its total area with peak biomasses over 500 g DW m^–2. The main objectives were to study ecosystem metabolism, to evaluate the metabolic contribution to the community of the macrophyte stands and their influence in the development of thermal stratification and bottom oxygen depletion.The work combined an experimental and a modelling methodology. The experimental approach included open water, mesocosm and microcosm seasonal experiments. During these experiments several physical, chemical and biological parameters were monitored in the lagoon and in plastic enclosures (mesocosms) for periods of 24 hours. The microcosm experiments followed the light-dark bottle technique. The simultaneous use of these different methodologies allowed the analysis of the contribution of the planktonic and benthic compartments to the ecosystem's oxygen budget.The modelling work was based on the mathematical simulation of heat and gas exchanges in a vertically resolved water column, under different macrophyte densities. Several simulations were carried out, in order to investigate the importance of the macrophytes in the development of water column stratification and anoxia.The simulation results suggest that macrophytes may greatly influence thermocline and oxycline development. This influence is proportional to their biomass and canopy height. It is suggested that controlled macrophyte biomass removal of up to 25% of available biomass in summer, may be useful in preventing bottom anoxia without compromising benthic net primary production.     

Mathematical modelling as a management tool for water quality control [2pt] of the tropical Beberibe estuary,NE Brazil

Sewage disposal in natural waters is a common problem in most countries. Large inputs of organic matter and nutrients from raw sewage to a weak hydrodynamic environment may lead to deterioration of the water quality. Widely available riverine and estuarine models such as QUAL-2E and MUDLARK can be used to adequately model these situations. Beberibe is a low hydrodynamic estuary that runs through a densely populated region in the Recife Metropolitan Area (RMA), Northeast Brazil, and receives untreated domestic sewage from aproximately 200000 inhabitants. The mouth of the estuary is shallow and tortuous, causing a large reduction in tidal propagation. The low river flow is strongly influenced by rain seasonality at the upstream boundary, with mean values varying from 4.9 m³ s^–1 in the wet winter to 1.4 m³ s^–1 during the dry summer. A major program to build sewage plants was planned to increase the water quality of the RMA rivers. This study focuses on water quality modelling of the Beberibe estuary basin, formed by the Beberibe River and two small tributaries. Numerical simulations of temperature, dissolved oxygen, biochemical oxygen demand, nitrate, ammonia, phosphate and faecal coliforms were carried out, targeting the expected population growth in the following 20 years. The QUAL-2E and the MUDLARK models were coupled at the tidal intrusion limit, with the estuarine sector modelled by the MUDLARK while QUAL-2E was used in the upper river. A longitudinal dispersion coefficient related to tidal excursion was introduced into the MUDLARK algorithm to better determine the tidal effect on the distribution of water quality variables. Both models were calibrated successfully and verified with a 4 year water quality data series from the Pernambuco State Environmental Agency (Companhia Pernambucana do Meio Ambiente – CPRH). Results showed that the river flow is a major factor controlling the water quality. Even the most efficient treatment applied was not able to bring water quality up to all desirable levels during dry summer months, mainly considering dissolved oxygen and biochemical oxygen demand. Results also confirm that the spring-neap cycle does not significantly affect water quality, probably due to the strong tidal attenuation at the estuary mouth.     

Using integrated state-of-environment reporting as a planning tool for resource management

The success of an ecosystems approach to river basin management depends greatly on the integration ofa wide range of information concerning the various components of the ecosystem, the formulation of realisticsolutions to complex problems, and finally, the support of all interested parties throughout the implementation phase:integrated State-of-Environment Reporting (SOER) can be an effective tool for meeting these challenges. Theecosystems approach is critical to the St. Lawrence Action Plan, a Canadian program which focuses on the protectionand conservation of the St. Lawrence River. The St. Lawrence Centre of Environment Canada not only acts asa catalyst in developing environmental partnerships among segments of the population, but synthesizes the resultsof these collective efforts. Its detailed evaluations on the state of the river environment perhaps best illustrate thenature of this task, because these reports must meet the particular environmental informational needs of many targetaudiences, which range from the general public to corporate decision-makers. SOER's practical nature facilitatesthe collection of data and the establishment of analysis targets and SOE indicators used in environmental monitoring.The integrated SOER framework developed at the St. Lawrence Centre represents a major challenge in the collection,integration, dissemination and use of environmental information. This framework is based in three majorobjectives: (1) information and education; (2) trend analysis and prediction; and (3) influence. Integrated SOER canbe a powerful tool: decision-makers will find it useful for designing action plans, while the general public can useit for assessing the state of the environment and the success of water management plans. Lastly, integrated SOERis also central to increasing public participation in the management of the environment, a factor essential to thesuccessful application of the ecosystems approach to water management.     

Application of LCA as a decision-making tool for waste management systems

Aim, Scope and Background  When materials are recycled they are made available for use for several future life cycles and can therefore replace virgin material more than just once. In order to analyse the optimal waste management system for a given material, the authors have analysed the material flows in a life cycle perspective. It is important to distinguish this approach for material flow analysis for a given material from life cycle analysis of products. A product life cycle analysis analyses the product system from cradle to grave, but uses some form of allocation in order to separate the life cycle of one product from another in cases where component materials are recycled. This paper does not address allocation of burdens between different product systems, but rather focuses on methodology for decision making for waste management systems where the optimal waste management system for a given material is analysed. The focus here is the flow of the given material from cradle (raw material extraction) to grave (the material, or its inherent energy, is no longer available for use). The limitation on the number of times materials can be recycled is set by either the recycling rate, or the technical properties of the recycled material. Main Features  This article describes a mathematical geometric progression approach that can be used to expand the system boundaries and allow for recycling a given number of times. Case studies for polyethylene and paperboard are used to illustrate the importance of including these aspects when part of the Goal and Scope for the LCA study is to identify which waste management treatment options are best for a given material. The results and discussion examine the different conclusions that can be reached about which waste management option is most environmentally beneficial when the higher burdens and benefits of recycling several times are taken into account. Results  In order to assess the complete picture of the burdens and benefits arising from recycling the system boundaries must be expanded to allow for recycling many times. A mathematical geometric progression approach manages to take into account the higher burdens and benefits arising from recycling several times. If one compares different waste management systems, e.g. energy recovery with recycling, without expanding the system to include the complete effects of material recycling one can reach a different conclusion about which waste management option is preferred. Conclusions  When the purpose of the study is to compare different waste management options, it is important that the system boundaries are expanded in order to include several recycling loops where this is a physical reality. The equations given in this article can be used to include these recycling loops. The error introduced by not expanding the system boundaries can be significant. This error can be large enough to change the conclusions of a comparative study, such that material recycling followed by incineration is a much better option than waste incineration directly. Recommendations and Outlook  When comparing waste management solutions, where material recycling is a feasible option, it is important to include the relevant number of recycling loops to ensure that the benefits of material recycling are not underestimated. The methodology presented in this article should be used in future comparative studies for strategic decision-making for waste management. The approach should not be used for LCAs for product systems without due care, as this could lead to double counting of the benefits of recycling (depending on the goal and scope of the analysis). For materials where the material cycle is more of a closed loop and one cannot truly say that recycled materials replace virgin materials, a more sophisticated approach will be required, taking into account the fact that recycled materials will only replace a certain proportion of virgin materials.     

Odonata (Insecta) as a tool for the biomonitoring of environmental quality

Despite the fundamental dependence of human populations on water resources, a range of anthropogenic impacts, in particular the removal of riparian vegetation, threaten freshwater environments. One of the most effective means of evaluating the effects of anthropogenic disturbance in aquatic ecosystems is the use of bioindicators, and the insects of the order Odonata are among the most efficient indicators, due to their enormous sensitivity to environmental changes. In this context, the present study aimed to verify which parameters of the odonate community (species richness, abundance/biomass, composition, taxonomic diversity and taxonomic/phylogenetic distinctness) are most effective for the evaluation of the loss of environmental integrity. The study focused on 50 streams in the northeast of the Brazilian state of Pará. The streams were sampled during the dry season, between June and August 2011. The physical characteristics of each stream were evaluated using a Habitat Integrity Index (HII). The species composition provided the best parameter for the evaluation of ecological integrity, providing a relatively accurate assessment at a lower mean research cost than other parameters. Taxonomic diversity and distinctness also provided relatively reliable results, contributed additional information on the evolutionary relationships among the odonate taxa, and also provided a low-cost approach. Deconstructing communities is necessary to detect impacts, considering the considerable variation in the environmental requirements of the different species. Overall, the parameter that best responded to gradients of disturbance was species composition, followed by diversity and taxonomic distinctness. Given these findings, odonate-based biomonitoring should focus on these parameters to guarantee the optimal detection and evaluation of habitat alterations.     

Multiplex PCR panel of microsatellite markers for the tambaqui, Colossoma macropomum, developed as a tool for use in conservation and broodstock management

The tambaqui, Colossoma macropomum, native to Brazil, is widely used in aquaculture systems. We developed a multiplex PCR panel for this species, comprising 12 microsatellite loci. This panel was used to genotype 73 specimens collected from Juruti, a city in the Brazilian Amazon. The mean number of alleles per locus was 8.8, the mean observed heterozygosity was 0.76, and the combined power of discrimination and the combined power of exclusion were 0.99999999999999993 and 0.999991762, respectively. We observed no significant deviation from Hardy-Weinberg equilibrium in this population. All amplified alleles were clearly typed, and easily interpretable results were obtained. This method will be useful for paternity analysis, population genetics and conservation studies, as well as for selective breeding programs for C. macropomum.     

Linear patterns of Alzheimer's disease mutations along alpha-helices of presenilins as a tool for PS-1 model construction

We performed an analysis of mutation patterns in all 10 hydrophobic regions (HRs) of presenilin-1 (PS-1) and PS-2 using a recent database of Alzheimer's disease (AD) mutations. The linear patterns were confirmed and extended to areas spanning as many as three faces of a given HR. The complementary areas of residues free of AD mutations were identified based on the location of non-pathogenic polymorphisms and PS-1 versus PS-2 amino acid discordances. Taking into account the location of areas of AD mutations and mutation-free areas/regions, we proposed a preliminary model of PS-1 structure using a general stick-out-mutation rule. To build a molecular structure of PS-1 and preserve features of the preliminary model, we used bacteriorhodopsin template in homology/comparative modelling. Two molecular models were built differing in the location of C-terminal fragment helices. The models properly distinguish residues belonging to AD-affected sites and non-pathogenic areas, and may be used for classification purposes. They also comply with experimental results, such as differences in accessibility of the catalytic residues in uncleaved PS-1, and binding of PEN-2 by the PS-1 NF motif.     

Gastrointestinal ischemia monitoring through impedance spectroscopy as a tool for the management of the critically ill

Impedance spectroscopy (IS) has been proposed as a tool for monitoring mucosal tissue ischemia and damage in the gut of critically ill patients resulting from shock and hypoperfusion. A specific device and system have been developed and tested for this specific application over the past 12 years by our research group. This paper reviews previously published studies as well as unpublished experimental results, and puts the whole in context and perspective to help understand this technology. Results presented include summaries of gastric reactance measurement understanding, in vivo measurements in animal models, clinical significance of the measurement, and future perspectives of clinical use of this technology. All of the experimental work done to date has been designed to determine the evolving device prototypes’ performance and limitations from an instrumentation point of view. Although there are still questions to be answered with regard to the IS measurement, we conclude that we have reached enough confidence in the measurement and the device’s performance and safety to begin clinically oriented research to learn how this technology may be useful in the diagnosis and management of different populations of the critically ill.     

A methodology for screening haemolymph of intertidal mussels, Mytilus edulis, using FT-IR spectroscopy as a tool for environmental assesment

Developing effective, rapid and inexpensive methods for monitoring and conserving aquatic resources is an important issue for environmental managers. This study focuses on Mytilus edulis, a keystone species of many coastal marine communities, which is frequently used as a biomonitor for a range of pollutants. Recent advances in post-genomic technologies have provided new methods of biochemical screening, and Fourier transform-infrared spectroscopy (FT-IR) is one such method that could enable bioindicator species to be used for environmental assessment. This paper develops a methodology to apply the FT-IR approach to marine intertidal M. edulis and addresses three methodological issues: First, the optimum physical location for biofluid sampling is examined (i.e. laboratory versus field). Secondly, the effects of transportation of frozen biofluid sampling from either the field-site or laboratory to the analytical facility are considered. Finally, the effect of repeated FT-IR measurements on collected M. edulis haemolymph samples is examined. From these results we suggest sampling haemolymph from M. edulis at the top of the shore prior to immediate snap-freezing in liquid nitrogen. Sample transportation can occur on ice for up to eight hours before storage at −80 °C. FT-IR measurements should occur within three months of collection and samples should not be used or thawed more than twice. We show how this method can be used to differentiate successfully between four different estuarine environments. Ultimately, through addressing these methodological questions, we provide a protocol to allow efficient sampling and FT-IR measurement of M. edulis as collected from the intertidal areas of rocky and muddy shores. We conclude that due to current monitoring needs presented by the European Water Framework Directive such an approach could prove to be an invaluable future tool for assessing coastal water quality.     

An axis for risk management in classificatory sys-tems as a contribution to efficient clinical practice

Comprehensive clinical assessment and patient management plans have been enhanced by the development of multiaxial classificatory systems. Assessment of risk is an essential clinical task for which the conclusions are not currently reflected in the multiaxial diagnostic schemata. Developments in the understanding of risk and its management make possible consideration of its place in multiaxial systems. The structure and principles of a potentially workable axis, summarizing current knowledge of risk in the domains of suicide, self-neglect and violence to others, are described. Clinicians are more likely to use this axis than the multiple, emerging, risk assessment guidelines. Incorporating risk management would be a practical addition to presently available axes and be very widely clinically applicable.     

Modelling past and present geographical distribution of the marine gastropod Patella rustica as a tool for exploring responses to environmental change

A climate envelope approach was used to model the distributions of the intertidal gastropod Patella rustica , to test the robustness of forecast responses to climate change. The model incorporated variables that were likely to determine the abundance and the northern range limit of this species in the NE Atlantic. The model was built using classification and regression tree analysis (CART) trained with historical distribution data from the mid 1950s and a set of corresponding climatic and oceanographic variables. Results indicated air and sea temperature, in particular during the reproductive and settlement periods, as the main determinants of the Atlantic distribution of P. rustica . The model was subsequently fed with contemporary climatic data and its output was compared with the current distribution and abundance of P. rustica , assessed during a 2002–2003 survey. The model correctly hindcasted the recent collapse of a distributional gap in northern Portugal, as well as an increase in abundance at locations within its range. The predicted northward expansion of the northern range limit did not occur because the absence of the species was confirmed in a survey encompassing the whole Atlantic French coast up to Brest. Stretches of unsuitable habitat too long to be overcome by dispersal are the likely mechanism controlling the northern limit of the distribution of this intertidal species.