A private management approach to coral reef conservation in Sabah,Malaysia

Many marine protected areas (MPAs), particularly in developing countries, have failed because of a lack of enforcement and monitoring due to limited public funds for conservation. Private investment and management in MPAs offers a potential solution, and has been applied with initial positive results at the Sugud Islands Marine Conservation Area (SIMCA) in Sabah, Malaysia. Conservation fees charged to visitors to Lankayan Island Dive Resort within the SIMCA have generated a sustainable source of financing to meet the majority of management costs for the conservation area, which is separately managed by a private organization called Reef Guardian. The availability of adequate funds has enabled Reef Guardian to invest in personnel training and surveillance technology to enforce the rules and regulations of the conservation area. In collaboration with government enforcement agencies, Reef Guardian has reduced threats such as illegal fishing and turtle egg poaching. As a result, there is a comparatively high abundance of commercially important fish, and turtle nestings at Lankayan Island have increased. Private management can be effective in conserving biodiversity in MPAs, and may well succeed regionally in suitable locations.

Recent changes in coral assemblages of a South African coral reef, with recommendations for long-term monitoring

Two-mile reef, Sodwana, South Africa is an unusual coral reef, being situated on a submerged fossilized sand dune and being very southerly (27°54). It is a popular Scuba diving venue receiving about 100000 dives year^–1. The line-intercept transect method, as recommended by the global coral reef monitoring network (GCRMN), was used to determine soft coral, hard coral and other benthos percentage cover. Physical coral damage, disease and bleaching were also recorded. Results were compared with those of B. Riegl (1993 – unpublished PhD thesis) 5 to 7 years earlier. The reef appears to be ecologically and highly dynamic. In the interim, there has been an increase in living benthos cover of 22.3% but also an increase in coral bleaching from 0% in 1993 to 1% in 1998. Physical damage, despite the large number of dives on the reef was minimal (1.52%), although it appears as if coral diseases may be increasing. The 20-m transects recommended by GCRMN are too long for this highly rugose reef with its distinct ridges and gullies. It is recommended that benthos cover, coral damage, bleaching and disease should be monitored annually using 40 5-m transects on the reef ridges and 40 5-m transects on the reef slopes.     

A simple model of growth form-dependent recovery from disease in coral reef sponges, and implications for monitoring

For clonal organisms that can suffer high levels of partial mortality and still recover, the conditions that influence infection and development of disease (e.g., abiotic stressors, population density) may be very different from the conditions that influence recovery. Recovery from infectious disease may increase if an individual can mount a defense before infection spreads throughout its body. If pathogens spread within an organism from an initial infection point, growth form—in conjunction with size—can influence the amount of time before all the tissue is diseased, and recovery precluded. A simple model of pathogen progression within individual sponges predicts that species with massive growth forms will be most susceptible to being overwhelmed by pathogen infection, and branching species will be most likely to recover. These predictions may help to explain the seemingly contradictory observations that branching species had the greatest prevalence of disease, and massive species the greatest rate of loss, in a monitored coral reef community. Disease may be observed disproportionately frequently in the organisms that are most likely to recover, resulting in underestimation, by standard monitoring procedures, of the effect of disease on losses from the community.     

BioPrEP – a regional, process-based approach for assessment of land with high conservation value for Bush Heritage Australia

Summary  A framework is presented for terrestrial conservation assessment that has been developed for Bush Heritage, an Australian non-profit organisation that manages land of outstanding conservation value through acquisition or working in partnership with other landowners. The framework is called Biodiversity Prediction using Ecological Processes and comprises seven conservation goals, with a set of candidate criteria and indicators for each goal. Particular emphasis is given to criteria that relate to habitat quality in addition to the more conventional focus on land quantity. The MCAS-S graphic user interface is used to help analyse the indicators and visualise the results in a transparent way that assists the decision-making process. The interface also allows indicators to be weighted differently, which among other things, allows analyses to reflect inter-regional differences in what represents high quality land. The framework was tested in a case study region (the Woodland region of south-eastern Australia), and the results reveal land that is potentially a priority for conservation investments. While the framework and case study results are indicative, and further analyses are required before they can be considered operational, the approach has potential application to other organisations in the private conservation sector.     

CLAP: A web-server for automatic classification of proteins with special reference to multi-domain proteins

Background

The function of a protein can be deciphered with higher accuracy from its structure than from its amino acid sequence. Due to the huge gap in the available protein sequence and structural space, tools that can generate functionally homogeneous clusters using only the sequence information, hold great importance. For this, traditional alignment-based tools work well in most cases and clustering is performed on the basis of sequence similarity. But, in the case of multi-domain proteins, the alignment quality might be poor due to varied lengths of the proteins, domain shuffling or circular permutations. Multi-domain proteins are ubiquitous in nature, hence alignment-free tools, which overcome the shortcomings of alignment-based protein comparison methods, are required. Further, existing tools classify proteins using only domain-level information and hence miss out on the information encoded in the tethered regions or accessory domains. Our method, on the other hand, takes into account the full-length sequence of a protein, consolidating the complete sequence information to understand a given protein better.

Results

Our web-server, CLAP (Classification of Proteins), is one such alignment-free software for automatic classification of protein sequences. It utilizes a pattern-matching algorithm that assigns local matching scores (LMS) to residues that are a part of the matched patterns between two sequences being compared. CLAP works on full-length sequences and does not require prior domain definitions.Pilot studies undertaken previously on protein kinases and immunoglobulins have shown that CLAP yields clusters, which have high functional and domain architectural similarity. Moreover, parsing at a statistically determined cut-off resulted in clusters that corroborated with the sub-family level classification of that particular domain family.

Conclusions

CLAP is a useful protein-clustering tool, independent of domain assignment, domain order, sequence length and domain diversity. Our method can be used for any set of protein sequences, yielding functionally relevant clusters with high domain architectural homogeneity. The CLAP web server is freely available for academic use at http://nslab.mbu.iisc.ernet.in/clap/.     

Forty years of carabid beetle research in Europe - from taxonomy, biology, ecology and population studies to bioindication, habitat assessment and conservation

‘Carabidologists do it all’ (Niemelä 1996a) is a phrase with which most European carabidologists are familiar. Indeed, during the last half a century, professional and amateur entomologists have contributed enormously to our understanding of the basic biology of carabid beetles. The success of the field is in no small part due to regular European Carabidologists’ Meetings, which started in 1969 in Wijster, the Netherlands, with the 14th meeting again held in the Netherlands in 2009, celebrating the 40th anniversary of the first meeting and 50 years of long-term research in the Dwingelderveld. This paper offers a subjective summary of some of the major developments in carabidology since the 1960s. Taxonomy of the family Carabidae is now reasonably established, and the application of modern taxonomic tools has brought up several surprises like elsewhere in the animal kingdom. Progress has been made on the ultimate and proximate factors of seasonality and timing of reproduction, which only exceptionally show non-seasonality. Triggers can be linked to evolutionary events and plausibly explained by the “taxon cycle” theory. Fairly little is still known about certain feeding preferences, including granivory and ants, as well as unique life history strategies, such as ectoparasitism and predation on higher taxa. The study of carabids has been instrumental in developing metapopulation theory (even if it was termed differently). Dispersal is one of the areas intensively studied, and results show an intricate interaction between walking and flying as the major mechanisms. The ecological study of carabids is still hampered by some unresolved questions about sampling and data evaluation. It is recognised that knowledge is uneven, especially concerning larvae and species in tropical areas. By their abundance and wide distribution, carabid beetles can be useful in population studies, bioindication, conservation biology and landscape ecology. Indeed, 40 years of carabidological research have provided so much data and insights, that among insects - and arguably most other terrestrial organisms - carabid beetles are one of the most worthwhile model groups for biological studies.     

Ecology of the fruit spotting bug, Amblypelta lutescens lutescens Distant (Hemiptera: Coreidae) in cashew plantations, with particular reference to the potential for its biological control

Abstract  The fruit spotting bug, Amblypelta lutescens lutescens, is one of the principal insect pests of cashews in Australia. Its population dynamics were studied using field observations and long-term monitoring to find suitable management methods. Observations of bugs reared in netting bags showed a sequence of change in bug-damage symptoms after 12 h and up to 3 d. Field observations revealed that adults preferred to feed and rest on the shady side of the tree. The number of bugs observed accounted for only 17–35% of the total variability in the number of damaged shoots, suggesting that the number of flushing shoots (leaf, flower or young nuts) with fresh damage symptoms was a more reliable parameter for determining the presence and level of activity of bugs than was a direct estimate of the number of bugs. The green tree ant, Oecophylla smaragdina (F), was the most important factor regulating bug populations. When predation was excluded as a factor, the number of flushing shoots and maximum temperature accounted for 80% of the total variability in the bug damage. Green tree ants should be considered as an important biological control agent for fruit spotting bug, and monitoring should be commenced when cashew trees start to flush (using damaged shoots as indicator).     

A PCR system for detection of species and genotypes of the Echinococcus granulosus-complex, with reference to the epidemiological situation in eastern Africa

We describe the development of a specific and sensitive PCR/semi-nested PCR system for the rapid diagnosis of Echinococcus granulosus genotype G1, E. granulosus genotype G6/7, and Echinococcus ortleppi (G5). Diagnosis of G1 and the group G5/6/7 is performed by a simple PCR, while discrimination between E. ortleppi (G5) and G6/7 involves a subsequent semi-nested PCR step. The target sequence for amplification is part of the mitochondrial 12S rRNA gene. Specificity of the PCRs was 100% when evaluated with isolates of 16 species of cestodes, including Echinococcus multilocularis, Echinococcus equinus, E. ortleppi and three strains of E. granulosus (G1, G6 and G7). Sensitivity threshold was 0.25pg of DNA. This new approach was compared with published protocols of restriction fragment length polymorphism-PCR and sequencing of mitochondrial cytochrome c oxidase subunit 1 and NADH dehydrogenase 1 genes using Echinococcus isolates of human, sheep, goat, camel, cattle and pig origin from Kenya and Sudan. Additionally, two internal DNA probes were developed, one hybridising only with G1, the other with G5, G6 and G7 amplification products. Preliminary epidemiological results obtained with this PCR approach include the detection of a camel strain (G6) infection for the first time in a human patient from eastern Africa, and the first reports of E. ortleppi (G5) in livestock from Kenya and the Sudan.