Sequence Conservation in the Prediction of Catalytic Sites

Predicting catalytic sites of a given enzyme is an important open problem of Bioinformatics. Recently, many machine learning-based methods have been developed which have the advantage that they can account for many sequential or structural features. We found that although many kinds of features are incorporated, protein sequence conservation is the main part of information they used and should play an important role in the future. So we tested several conservation features in their ability to predict catalytic sites by using the Support Vector Machine classifier. Our results suggest that position specific scoring matrix performs better than other features and incorporating conservation information of sequentially adjacent sites is more effective than that of structurally adjacent ones. Moreover, although conservation information is effective in predicting catalytic sites, it is a difficult problem to optimize the combination of conservation features and other ones.     

Strategic Grassland Bird Conservation throughout the Annual Cycle: Linking Policy Alternatives,Landowner Decisions,and Biological Population Outcomes

Grassland bird habitat has declined substantially in the United States. Remaining grasslands are increasingly fragmented, mostly privately owned, and vary greatly in terms of habitat quality and protection status. A coordinated strategic response for grassland bird conservation is difficult, largely due to the scope and complexity of the problem, further compounded by biological, sociological, and economic uncertainties. We describe the results from a collaborative Structured Decision Making (SDM) workshop focused on linking social and economic drivers of landscape change to grassland bird population outcomes. We identified and evaluated alternative strategies for grassland bird conservation using a series of rapid prototype models. We modeled change in grassland and agriculture cover in hypothetical landscapes resulting from different landowner decisions in response to alternative socio-economic conservation policy decisions. Resulting changes in land cover at all three stages of the annual cycle (breeding, wintering, and migration) were used to estimate changes in grassland bird populations. Our results suggest that successful grassland bird conservation may depend upon linkages with ecosystem services on working agricultural lands and grassland-based marketing campaigns to engage the public. With further development, spatial models that link landowner decisions with biological outcomes can be essential tools for making conservation policy decisions. A coordinated non-traditional partnership will likely be necessary to clearly understand and systematically respond to the many conservation challenges facing grassland birds.     

Plant reintroductions: the need for a global database

Plant reintroductions include labor-intensive, costly, and time-consuming work and often cannot guarantee a successful outcome. In order to maximize the chances of success, it is therefore of utmost importance to appropriately select target species, release site, cultivation and reintroduction methodology, and management technique of the out-planting site. Case studies, best practice and experiences of plant reintroductions are however not sufficiently disseminated to the plant conservation community, most often remaining in unpublished internal reports to which access is difficult. We suggest that this is a major problem for conservationists and it requires the establishment of a framework for rapid and effective broadcasting of information on plant reintroduction programs. We propose a set of variables for a centralized web-based interface which could provide the necessary information in a standardized and accessible form.     

SmeltCam: Underwater Video Codend for Trawled Nets with an Application to the Distribution of the Imperiled Delta Smelt

Studying rare and sensitive species is a challenge in conservation biology. The problem is exemplified by the case of the imperiled delta smelt Hypomesus transpacificus, a small delicate fish species endemic to the San Francisco Estuary, California. Persistent record-low levels of abundance and relatively high sensitivity to handling stress pose considerable challenges to studying delta smelt in the wild. To attempt to overcome these and other challenges we have developed the SmeltCam, an underwater video camera codend for trawled nets. The SmeltCam functions as an open-ended codend that automatically collects information on the number and species of fishes that pass freely through a trawled net without handling. We applied the SmeltCam to study the fine-scale distribution of juvenile delta smelt in the water column in the upper San Francisco Estuary. We learned that during flood tides delta smelt were relatively abundant throughout the water column and that during ebb tides delta smelt were significantly less abundant and occurred only in the lower half and sides of the water column. The results suggest that delta smelt manipulate their position in the water column to facilitate retention in favorable habitats. With the application of the SmeltCam we increased the survival of individual delta smelt by 72% compared to using a traditional codend, where all of the fish would have likely died due to handling stress. The SmeltCam improves upon similar previously developed silhouette photography or video recording devices and demonstrates how new technology can be developed to address important questions in conservation biology as well as lessen the negative effects associated with traditional sampling methods on imperiled species.     

Is wildlife research useful for wildlife conservation in the tropics? A review for Borneo with global implications

The urgency of the tropical biodiversity crisis continues to be a major justification for wildlife research and its funding. To examine the benefits of this research for on-the-ground conservation, we focused on Borneo, where conservation has a long history and we have direct experience. We compiled, categorized and evaluated 284 publications from a broad variety of sources, 153 from peer-reviewed journals. We found that few studies address threats to species and fewer still provide input for or guidance to effective management. We consider various reasons for these shortcomings. Research is seldom judged on its relevance to pragmatic problem solving. Furthermore, many research programs lack the necessary long-term vision and organizational structure for useful applied research. We consulted conservation leaders about our conclusions and all responses suggest that our concerns are not unique to Borneo but reflect wider problems. We conclude that conservation research across most of the tropics is failing to address conservation needs. We make a number of recommendations based on our findings. Conservation biologists should place a higher priority on addressing practical conservation needs and goals.     

Advances in linking wintering migrant birds to their breeding-ground origins using combined analyses of genetic and stable isotope markers

An enduring problem in avian ecology and conservation is linking breeding and wintering grounds of migratory species. As migratory species and populations vary in the degree to which individuals from distinct breeding locales mix on stop-over sites and wintering grounds, establishing migratory connectivity informs our understanding of population demography and species management. We present a new Bayesian approach for inferring breeding grounds of wintering birds of unknown origins in North America. We incorporate prior information from analysis of genetic markers into geographic origin assignment based upon stable-hydrogen isotope analysis of feathers (δ(2)H(f)), using the Loggerhead Shrike (Lanius ludovicianus). Likely geographic origins derived from analyses of DNA microsatellites were used as priors for Bayesian analyses in which birds were assigned to a breeding-ground origin using their δ(2)H(f) values. As with most applications of Bayesian methods, our approach greatly improved the results (i.e. decreased the size of the potential area of origin). Area of origin decreased by 3 to 5-fold on average, but ranged up to a 10-fold improvement. We recommend this approach in future studies of migratory connectivity and suggest that our methodology could be applied more broadly to the study of dispersal, sources of productivity of migratory populations, and a range of evolutionary phenomena.     

Bayesian adaptive survey protocols for resource management

Transparency in resource management decisions requires a proper accounting of uncertainty at multiple stages of the decision-making process. As information becomes available, periodic review and updating of resource management protocols reduces uncertainty and improves management decisions. One of the most basic steps to mitigating anthropogenic effects on populations is determining if a population of a species occurs in an area that will be affected by human activity. Species are rarely detected with certainty, however, and falsely declaring a species absent can cause improper conservation decisions or even extirpation of populations. We propose a method to design survey protocols for imperfectly detected species that accounts for multiple sources of uncertainty in the detection process, is capable of quantitatively incorporating expert opinion into the decision-making process, allows periodic updates to the protocol, and permits resource managers to weigh the severity of consequences if the species is falsely declared absent. We developed our method using the giant gartersnake (Thamnophis gigas), a threatened species precinctive to the Central Valley of California, as a case study. Survey date was negatively related to the probability of detecting the giant gartersnake, and water temperature was positively related to the probability of detecting the giant gartersnake at a sampled location. Reporting sampling effort, timing and duration of surveys, and water temperatures would allow resource managers to evaluate the probability that the giant gartersnake occurs at sampled sites where it is not detected. This information would also allow periodic updates and quantitative evaluation of changes to the giant gartersnake survey protocol. Because it naturally allows multiple sources of information and is predicated upon the idea of updating information, Bayesian analysis is well-suited to solving the problem of developing efficient sampling protocols for species of conservation concern. © 2011 The Wildlife Society.     

Protected area networks and savannah bird biodiversity in the face of climate change and land degradation

The extent to which climate change might diminish the efficacy of protected areas is one of the most pressing conservation questions. Many projections suggest that climate‐driven species distribution shifts will leave protected areas impoverished and species inadequately protected while other evidence suggests that intact ecosystems within protected areas will be resilient to change. Here, we tackle this problem empirically. We show how recent changes in distribution of 139 Tanzanian savannah bird species are linked to climate change, protected area status and land degradation. We provide the first evidence of climate‐driven range shifts for an African bird community. Our results suggest that the continued maintenance of existing protected areas is an appropriate conservation response to the challenge of climate and environmental change.     

Documenting Biogeographical Patterns of African Timber Species Using Herbarium Records: A Conservation Perspective Based on Native Trees from Angola

In many tropical regions the development of informed conservation strategies is hindered by a dearth of biodiversity information. Biological collections can help to overcome this problem, by providing baseline information to guide research and conservation efforts. This study focuses on the timber trees of Angola, combining herbarium (2670 records) and bibliographic data to identify the main timber species, document biogeographic patterns and identify conservation priorities. The study recognized 18 key species, most of which are threatened or near-threatened globally, or lack formal conservation assessments. Biogeographical analysis reveals three groups of species associated with the enclave of Cabinda and northwest Angola, which occur primarily in Guineo-Congolian rainforests, and evergreen forests and woodlands. The fourth group is widespread across the country, and is mostly associated with dry forests. There is little correspondence between the spatial pattern of species groups and the ecoregions adopted by WWF, suggesting that these may not provide an adequate basis for conservation planning for Angolan timber trees. Eight of the species evaluated should be given high conservation priority since they are of global conservation concern, they have very restricted distributions in Angola, their historical collection localities are largely outside protected areas and they may be under increasing logging pressure. High conservation priority was also attributed to another three species that have a large proportion of their global range concentrated in Angola and that occur in dry forests where deforestation rates are high. Our results suggest that timber tree species in Angola may be under increasing risk, thus calling for efforts to promote their conservation and sustainable exploitation. The study also highlights the importance of studying historic herbarium collections in poorly explored regions of the tropics, though new field surveys remain a priority to update historical information.     

Adult tiger spiketail (<Emphasis Type="Italic">Cordulegaster erronea</Emphasis> Hagen) habitat use and home range observed via radio-telemetry with conservation recommendations

The Tiger Spiketail dragonfly (Cordulegaster erronea Hagen) is geographically restricted to the eastern half of North America, patchily distributed within the range and a habitat specialist of small spring and seepage fed headwater streams running through mature forest. These habitats are highly sensitive to disturbance and the Tiger Spiketail is of conservation concern throughout most of its range. Yet little is known about the habitat use of either sex away from the breeding stream hampering conservation strategies. In this study we use miniaturized radio transmitters to investigate the habitat use and home range of individual males and a female Tiger Spiketail in New Jersey. This is the first and only radio-telemetry for this species. We also provide recommendations for habitat protection and conservation. Our studies demonstrate that this species is critically dependent upon mature forest and the high quality, perennial headwater streams that run through them. These habitats are particularly sensitive to disturbance. Except when patrolling and ovipositing, both sexes are in the canopy above the breeding stream and in the adjacent mature forest, indicating the inseparable linkage between the aquatic and forested terrestrial habitat for this species. Our observations also suggest that C. erronea occurs in a metapopulation of nearby streams in our study area. Conservation of this species may therefore require forest protection far beyond the breeding stream. In New Jersey, and in other places throughout the range, there are many potential pressures on these habitats and current regulatory protections are not likely suitable. These same habitats may also be important for other Odonate species of conservation concern suggesting that protection of C. erronea may benefit a suite of species. We hope the information obtained from this study can assist resource managers in developing conservation and habitat protection measures.     

Applied conservation services of the evolutionary theory

Having quantitative data to use in a reliable model in conservation can be extremely limiting because of the usual scarcity of such information. The body of theory accumulated so far in evolutionary ecology, and particularly in the evolution of life-history traits, can also come in the aid of conservation practitioners and provide them with some help in the absence of quantitative data. Although some attempts have been made already to bridge the gap between evolution and applied conservation, this interface remains to be properly delineated. Here we present a diverse number of examples of the applicability of evolutionary knowledge to the effective solution of diverse applied conservation problems. We first deal with the opposed strategies of animal and plant species inhabiting survival versus reproduction habitats, and the most adequate management approaches in both cases, with special emphasis in assessing the risks of supplementing food and nest boxes for conservation purposes. Secondly, we deal with invasion biology and suggest that a better understanding of the problem of biological invasions, and a better management of it, is gained if the focus is moved from invasive species characteristics to the properties of the invaded community from an evolutionary perspective. Finally, we show how the management of complex predator–prey interactions can benefit from the application of knowledge on life-history evolution and discuss the particularities of culling programs applied either to short-lived or long-lived species in order to be effective.     

How ethnobotany can aid biodiversity conservation: reflections on investigations in the semi-arid region of NE Brazil

Ethnobotany is a relatively new discipline but its social and scientific roles are becoming more consistently defined and its importance as a tool for complimenting management and conservation strategies at local and regional levels is now well recognized by the scientific community throughout the world. In the present work we have collected information from four years of ethnobotanical study in an area of caatinga vegetation in the semi-arid region of northeastern Brazil with the goal of defining a model for conservation and management actions in the region. Drawing on ethnobotanical and ecological information obtained through traditional techniques of ethnobotanical and vegetation surveys, we discuss the uses of 166 native and exotic plant species and suggest specific actions and specific groups of species for conservation and sustainable use programs. We also discuss the limitations of our approach and indicate what information must still be collected in order to construct robust and workable plans of action.     

Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data.

Mounting evidence shows that many protein complexes are conserved in evolution. Here we use conservation to find complexes that are common to the yeast S. cerevisiae and the bacteria H. pylori. Our analysis combines protein interaction data that are available for each of the two species and orthology information based on protein sequence comparison. We develop a detailed probabilistic model for protein complexes in a single species and a model for the conservation of complexes between two species. Using these models, one can recast the question of finding conserved complexes as a problem of searching for heavy subgraphs in an edge- and node-weighted graph, whose nodes are orthologous protein pairs. We tested this approach on the data currently available for yeast and bacteria and detected 11 significantly conserved complexes. Several of these complexes match very well with prior experimental knowledge on complexes in yeast only and serve for validation of our methodology. The complexes suggest new functions for a variety of uncharacterized proteins. By identifying a conserved complex whose yeast proteins function predominantly in the nuclear pore complex, we propose that the corresponding bacterial proteins function as a coherent cellular membrane transport system. We also compare our results to two alternative methods for detecting complexes and demonstrate that our methodology obtains a much higher specificity.     

The comparative method in conservation biology

The phylogenetic comparative approach is a statistical method for analyzing correlations between traits across species. Whilst it has revolutionized evolutionary biology, can it work for conservation biology? Although it is correlative, advocates of the comparative method hope that it will reveal general mechanisms in conservation, provide shortcuts for prioritizing conservation research, and enable us to predict which species will experience (or create) problems in the future. Here, we ask whether these stated management goals are being achieved. We conclude that comparative methods are stimulating research into the ecological mechanisms underlying conservation, and are providing information for preemptive screening of problem species. But comparative analyses of extinction risk to date have tended to be too broad in scope to provide shortcuts to conserving particular endangered species. Correlates of vulnerability to conservation problems are often taxon, region and threat specific, so models must be narrowly focused to be of maximum practical use.     

Avoiding costly conservation mistakes: the importance of defining actions and costs in spatial priority setting

Background

The typical mandate in conservation planning is to identify areas that represent biodiversity targets within the smallest possible area of land or sea, despite the fact that area may be a poor surrogate for the cost of many conservation actions. It is also common for priorities for conservation investment to be identified without regard to the particular conservation action that will be implemented. This demonstrates inadequate problem specification and may lead to inefficiency: the cost of alternative conservation actions can differ throughout a landscape, and may result in dissimilar conservation priorities.

Methodology/Principal Findings

We investigate the importance of formulating conservation planning problems with objectives and cost data that relate to specific conservation actions. We identify priority areas in Australia for two alternative conservation actions: land acquisition and stewardship. Our analyses show that using the cost surrogate that most closely reflects the planned conservation action can cut the cost of achieving our biodiversity goals by half. We highlight spatial differences in relative priorities for land acquisition and stewardship in Australia, and provide a simple approach for determining which action should be undertaken where.

Conclusions/Significance

Our study shows that a poorly posed conservation problem that fails to pre-specify the planned conservation action and incorporate cost a priori can lead to expensive mistakes. We can be more efficient in achieving conservation goals by clearly specifying our conservation objective and parameterising the problem with economic data that reflects this objective.     

Improving biodiversity monitoring

Effective biodiversity monitoring is critical to evaluate, learn from, and ultimately improve conservation practice. Well conceived, designed and implemented monitoring of biodiversity should: (i) deliver information on trends in key aspects of biodiversity (e.g. population changes); (ii) provide early warning of problems that might otherwise be difficult or expensive to reverse; (iii) generate quantifiable evidence of conservation successes (e.g. species recovery following management) and conservation failures; (iv) highlight ways to make management more effective; and (v) provide information on return on conservation investment. The importance of effective biodiversity monitoring is widely recognized (e.g. Australian Biodiversity Strategy). Yet, while everyone thinks biodiversity monitoring is a good idea, this has not translated into a culture of sound biodiversity monitoring, or widespread use of monitoring data. We identify four barriers to more effective biodiversity monitoring in Australia. These are: (i) many conservation programmes have poorly articulated or vague objectives against which it is difficult to measure progress contributing to design and implementation problems; (ii) the case for long‐term and sustained biodiversity monitoring is often poorly developed and/or articulated; (iii) there is often a lack of appropriate institutional support, co‐ordination, and targeted funding for biodiversity monitoring; and (iv) there is often a lack of appropriate standards to guide monitoring activities and make data available from these programmes. To deal with these issues, we suggest that policy makers, resource managers and scientists better and more explicitly articulate the objectives of biodiversity monitoring and better demonstrate the case for greater investments in biodiversitymonitoring. There is an urgent need for improved institutional support for biodiversity monitoring in Australia, for improved monitoring standards, and for improved archiving of, and access to, monitoring data. We suggest that more strategic financial, institutional and intellectual investments in monitoring will lead to more efficient use of the resources available for biodiversity conservation and ultimately better conservation outcomes.     

Consistency and use of information about threats in the participatory process for identification of priority conservation areas in the Brazilian Amazon

Despite the increasing number of scientific papers on the subject, conservation planning has failed to actively prioritise the creation of new protected areas. Strategies proposed to increase the creation of new protected areas based on conservation plans include broad stakeholder participation in decision-making processes in order to include their concerns and facilitate social acceptance of proposed actions. However, there are controversial views about the effectiveness of stakeholder participation. The quality of the decision depends both on the information used by stakeholders and on how it is used, so it is necessary to evaluate both these aspects of a decision-making process. Threats are intrinsically related to conservation decisions because they are more easily understood by people than biodiversity values, and they can affect both decisions and outcomes of conservation actions. This article analyses how information about threats was used in the decision-making process conducted by the Brazilian Government in 2006 to indicate priority areas for the conservation of the Amazon biome. We first verified the consistency of the information on threats attributed by stakeholders to these new priority areas, and then assessed whether the existence, levels and types of threats influenced the choice of areas for conservation. The results showed that there were some successes in recognising threats, but also many inconsistencies, especially in assigning levels of intensity for some types of threats such as fishing. The decision-making process also did not fully use available information to indicate areas for conservation. The lack of understanding on the motivation behind these inconsistencies could suggest the presence of political opportunism. A more quantitative approach to assigning priorities is needed: one that is less dependent on the individual input of stakeholders and more accurately reflects the actual emergency status of proposed areas. This indicates that greater effort should be allocated to combining a participatory approach with a robust decision support system.     

No Reef Is an Island: Integrating Coral Reef Connectivity Data into the Design of Regional-Scale Marine Protected Area Networks

We integrated coral reef connectivity data for the Caribbean and Gulf of Mexico into a conservation decision-making framework for designing a regional scale marine protected area (MPA) network that provides insight into ecological and political contexts. We used an ocean circulation model and regional coral reef data to simulate eight spawning events from 2008–2011, applying a maximum 30-day pelagic larval duration and 20% mortality rate. Coral larval dispersal patterns were analyzed between coral reefs across jurisdictional marine zones to identify spatial relationships between larval sources and destinations within countries and territories across the region. We applied our results in Marxan, a conservation planning software tool, to identify a regional coral reef MPA network design that meets conservation goals, minimizes underlying threats, and maintains coral reef connectivity. Our results suggest that approximately 77% of coral reefs identified as having a high regional connectivity value are not included in the existing MPA network. This research is unique because we quantify and report coral larval connectivity data by marine ecoregions and Exclusive Economic Zones (EZZ) and use this information to identify gaps in the current Caribbean-wide MPA network by integrating asymmetric connectivity information in Marxan to design a regional MPA network that includes important reef network connections. The identification of important reef connectivity metrics guides the selection of priority conservation areas and supports resilience at the whole system level into the future.     

Could taxonomic misnaming threaten the ex situ conservation and the usage of plant genetic resources?

Ex situ conservation of plant germplasm, especially seed banking, is a favourable and widely used method for the conservation of plant genetic resources (PGR). The long-term conservation of these resources is fundamental for food security and plant breeding in order to stem the losses in agrobiodiversity and to meet the global challenges that agriculture is facing. The conservation and accessibility of PGR relies on their correct taxonomic labelling and on the building of a searchable database that links ex situ collections together. In the current study, we analysed the impact of taxonomic misnaming in the two major PGR databases (Genesys PGR, EURISCO), listing accessions conserved worldwide. The aim was to understand if taxonomic misnaming issues prevent PGR conservation. We chose as a case-study seed collections of accessions of the genus Citrullus (watermelon genepool), the taxonomy and nomenclature of which have been largely revised in recent times. We observed that taxonomic misnaming greatly limits PGR conservation with only 3% of the accessions listed in the databases correctly named; moreover, 28% were affected by taxonomic errors that prevent the establishment of the accessions’ taxonomic identity, with consequences on their conservation and exploitation. The existence of the problem was also confirmed by the experimental propagation of three misnamed accessions. We suggest herein a series of actions that, put in place, could solve the extant misnaming issues in the databases and prevent their reoccurrence, allowing the correct conservation and the usability by the stakeholders of all the accessions.