Dilemmas in conservation for applied biologists

Prevention of the use of DDT has been made the target of a powerful propaganda drive in certain prosperous countries because, it is stated, DDT is a danger to man and harms wild life. On the other hand, DDT is by far the most economical, effective and safe insecticide for many uses, particularly for protecting men from certain insect-borne diseases and for enabling cotton to be grown in poor countries. Some risks can be reduced by eliminating those uses of DDT for which adequately safe, economical and effective substitutes exist, whether chemical or not; other risks can be reduced in other ways. The known risks to men are trivial, except when DDT concentrate is deliberately drunk, and the scare is made up of unknown risks -which could equally exist with any object or material, new or old. Risks to wild life have been greatly exaggerated and scares depending on falsehoods have become current. The postulated threat of progressive accumulation of DDT along a long food chain is not adequately supported by evidence, much of which has been misinterpreted. Thus the main dilemma is how to balance the great and undoubted benefits of DDT to millions of men, women and children against harm to wild life, sometimes genuine and remediable and sometimes dubious. People who campaign for banning have possibly failed to recognize this dilemma. On the other hand, they may have made a deliberate choice in favour of wild life. In that case, to be logical, they should also oppose all other means of preventing premature death of other people, which they might justify as a means of postponing over-population. The use or abuse of DDT is a minor component in the rise of the worl's population.     

Molecular marker-based pedigrees for animal conservation biologists

Pedigrees, depicting the genealogical relationships between individuals in a population, are of fundamental importance to several research areas including conservation biology. For example, they are useful for estimating inbreeding, heritability, selection, studying kin selection and for measuring gene flow between populations. Pedigrees constructed from direct observations of reproduction are usually unavailable for wild populations. Therefore, pedigrees for these populations are usually estimated using molecular marker data. Despite their obvious importance, and the fact that pedigrees are conceptually well understood, the methods, and limitations of marker-based pedigree inference are often less well understood. Here we introduce animal conservation biologists to molecular marker-based pedigrees. We briefly describe the history of pedigree inference research, before explaining the underlying theory and basic mechanics of pedigree construction using standard methods. We explain the assumptions and limitations that accompany many of these methods, before going on to explain methods that relax several of these assumptions. Finally, we look to future and discuss some recent exciting advances such as the use of single-nucleotide polymorphisms, inference of multigenerational pedigrees and incorporation of non-genetic data such as field observations into the calculations. We also provide some guidelines on efficient marker selection in order to maximize accuracy and power. Throughout we use examples from the field of animal conservation and refer readers to appropriate software where possible. It is our hope that this review will help animal conservation biologists to understand, choose, and use the methods and tools of this fast-moving field.     

Tackling the epigenome: challenges and opportunities for collaboration

What are the key considerations to take into account when large-scale epigenomics projects are being implemented?     

Factors influencing conservation attitudes of local people in Western Serengeti,Tanzania

Attitudinal studies are increasingly being adopted as tools for evaluating public understanding, acceptance and the impact of conservation interventions. The findings of these studies have been useful in guiding the policy interventions. Many factors affect conservation attitudes positively or negatively. The factors inspiring positive attitudes are likely to enhance the conservation objectives while those inducing negative attitudes may detrimentally undermine these objectives. The magnitude of the resultant effects of each particular factor is determined by the historical, political, ecological, socio-cultural and economic conditions and this may call for different management interventions. In this study we examined how conservation attitudes in western Serengeti are shaped by the following factors: level of conflicts with protected areas; wildlife imposed constraints (inadequate pasture, water, diseases, loss of livestock during migration, theft and depredation); participation in the community based project; and socio-demographic factors (age, education level, wealth, immigration, gender and household size). The results indicated that the level of conflicts, participation in the community based project, inadequate pasture, lack of water, diseases, wealth and education were important in shaping peoples’ attitudes. However, in a stepwise linear regression analysis, 59% of the variation in peoples’ attitudes was explained by three variables i.e., conflict level with protected areas, lack of water and participation in the community based project. In addition to these variables, level of education also contributed in explaining 51% of the variation in people’s attitude regarding the status of the game reserves. Five variables (lack of water, level of education, inadequate pasture, participation in the community based project and diseases) explained 12% of the variation in people’s attitude towards Serengeti National Park. The paper discusses the implications for conservation of these results and recommends some measures to realise effective conservation of wildlife resources.     

Planning for biodiversity conservation based on the knowledge of biologists

To conserve biodiversity, complementary approaches are necessary. Besides using museum data from sightings and specimens, the knowledge of experts can also be employed. Often such valuable information is lost on retirement or death. To investigate the value of this knowledge for nature conservation planning, we sent questionnaires to 124 professional conservationists in the province of KwaZulu-Natal, South Africa. Fifty-two replies illustrated that the historical context biases our concepts of nature and the conservation of biodiversity. Despite an awareness of all the spatial scales, complexities and dynamics of nature, there is still a strong focus on large-sized animals and visibly discrete ecosystems, such as wetlands. Nevertheless, the respondents illustrated that an awareness of infrequently-seen and less well known organisms is increasing. Harnessing this expert knowledge was valuable for conservation planning, but had the weakness that many taxa and localities were neglected. Similar problems arose with data from museum specimens. However, both these approaches were synergistic and highlighted the geographical areas that need far more exploration of their biodiversity. Such information gathering is an important ethical and practical exercise for conserving biodiversity.     

Tropical grassy biomes: linking ecology,human use and conservation

Tropical grassy biomes (TGBs) are changing rapidly the world over through a coalescence of high rates of land-use change, global change and altered disturbance regimes that maintain the ecosystem structure and function of these biomes. Our theme issue brings together the latest research examining the characterization, complex ecology, drivers of change, and human use and ecosystem services of TGBs. Recent advances in ecology and evolution have facilitated a new perspective on these biomes. However, there continues to be controversies over their classification and state dynamics that demonstrate critical data and knowledge gaps in our quantitative understanding of these geographically dispersed regions. We highlight an urgent need to improve ecological understanding in order to effectively predict the sensitivity and resilience of TGBs under future scenarios of global change. With human reliance on TGBs increasing and their propensity for change, ecological and evolutionary understanding of these biomes is central to the dual goals of sustaining their ecological integrity and the diverse services these landscapes provide to millions of people.This article is part of the themed issue ‘Tropical grassy biomes: linking ecology, human use and conservation’.     

生物多样性保护主流化的新机遇

<正>生物多样性是人类赖以生存和发展的物质基础。不断加剧的人类活动,致使生物多样性受到严重威胁,引起国际社会的广泛关注。生物多样性保护必须实现主流化,与社会经济可持续发展紧密结合,否则很难奏效。在全球尺度上,统领发展的最重要的理念即可持续发展(World Commission on Environment and Development,1987)。1992年联合国环境与发展大会通过了《21世纪议程》,被称为世界范围内可持续发展行动计划;2000年联合国世界首脑会议通过了     

Landscape scale conservation: resources, behaviour, the matrix and opportunities

Landscape scale conservation efforts are becoming more commonplace in conservation, with a move from single species to multi-species initiatives. These initiatives are reliant on modelling processes, largely underpinned by metapopulation models. We argue that generic models developed for individual species in particular landscapes over selected time periods may only be applicable to alternative landscapes and time periods in restricted circumstances. Variability in species responses to landscapes and environmental conditions is dependent on a range of species-specific intrinsic characteristics, dependent on their responses to resources, (including weather) and also individual states. We propose that the behavioural component of how species respond to resources needs to be taken into account in modelling species responses to landscape, and therefore how limited resources for conservation are deployed. Species behaviours are inherently complex. We argue that because of this complexity the conservation of the majority of species, especially of the least rare, may be best served if conservation effort is additionally focused on increasing landscape heterogeneity and disturbance. This may also facilitate persistence in the face of climate change. We suggest that heterogeneity should be promoted through agri-environment schemes.     

BioMEMS: forging new collaborations between biologists and engineers

This video describes the fabrication and use of a microfluidic device to culture central nervous system (CNS) neurons. This device is compatible with live-cell optical microscopy (DIC and phase contrast), as well as confocal and two photon microscopy approaches. This method uses precision-molded polymer parts to create miniature multi-compartment cell culture with fluidic isolation. The compartments are made of tiny channels with dimensions that are large enough to culture neurons in well-controlled fluidic microenvironments. Neurons can be cultured for 2-3 weeks within the device, after which they can be fixed and stained for immunocytochemistry. Axonal and somal compartments can be maintained fluidically isolated from each other by using a small hydrostatic pressure difference; this feature can be used to localize soluble insults to one compartment for up to 20 h after each medium change. Fluidic isolation enables collection of pure axonal fraction and biochemical analysis by PCR. The microfluidic device provides a highly adaptable platform for neuroscience research and may find applications in modeling CNS injury and neurodegeneration.     

Persistent leatherback turtle migrations present opportunities for conservation

Effective transboundary conservation of highly migratory marine animals requires international management cooperation as well as clear scientific information about habitat use by these species. Populations of leatherback turtles (Dermochelys coriacea) in the eastern Pacific have declined by >90% during the past two decades, primarily due to unsustainable egg harvest and fisheries bycatch mortality. While research and conservation efforts on nesting beaches are ongoing, relatively little is known about this population of leatherbacks' oceanic habitat use and migration pathways. We present the largest multi-year (2004-2005, 2005-2006, and 2007) satellite tracking dataset (12,095 cumulative satellite tracking days) collected for leatherback turtles. Forty-six females were electronically tagged during three field seasons at Playa Grande, Costa Rica, the largest extant nesting colony in the eastern Pacific. After completing nesting, the turtles headed southward, traversing the dynamic equatorial currents with rapid, directed movements. In contrast to the highly varied dispersal patterns seen in many other sea turtle populations, leatherbacks from Playa Grande traveled within a persistent migration corridor from Costa Rica, past the equator, and into the South Pacific Gyre, a vast, low-energy, low-productivity region. We describe the predictable effects of ocean currents on a leatherback migration corridor and characterize long-distance movements by the turtles in the eastern South Pacific. These data from high seas habitats will also elucidate potential areas for mitigating fisheries bycatch interactions. These findings directly inform existing multinational conservation frameworks and provide immediate regions in the migration corridor where conservation can be implemented. We identify high seas locations for focusing future conservation efforts within the leatherback dispersal zone in the South Pacific Gyre.     

Writing and speaking: communication for biologists

A workshop for university biology teachers examined the teaching to undergraduates of writing and speaking. There was agreement that the communication of results and ideas was an integral part of scientific method. Proposals for the teaching of different aspects of communication during the undergraduate course are given and an Appendix lists some material which has been used with, and found suitable for biology students.     

Mahseer (Tor spp.) fishes of the world: status,challenges and opportunities for conservation

Reviews in Fish Biology and Fisheries - The mahseer fishes (Tor spp.) represent an iconic genus of large-bodied species of the Cyprinidae family. Across the 16 recognised species in the genus,...     

Perception of local people towards conservation of forest resources in Nanda Devi Biosphere Reserve,north-western Himalaya,India

This article examines the perception of the Bhotiya tribal community on the use and conservation of natural resources in Nanda Devi Biosphere Reserve (NDBR), north-western Himalaya in India with an objective of identifying the bottlenecks in the sustainable management of forest resources of NDBR through people’s participation. Despite, 85% of the respondents supporting the concept of conservation of forest resources, management decisions such as ban on mountaineering activities by creation of the Nanda Devi National Park (NDNP) in 1982 and NDBR in 1988, developed negative attitude among local people towards NDBR management, mainly because of restricted access to the forest resources for their livelihood. Promotion of some alternative income generating activities to reduce the dependence on natural resources was responded positively by the local people.     

GRIMD: distributed computing for chemists and biologists

Motivation: Biologists and chemists are facing problems of high computational complexity that require the use of several computers organized in clusters or in specialized grids. Examples of such problems can be found in molecular dynamics (MD), in silico screening, and genome analysis. Grid Computing and Cloud Computing are becoming prevalent mainly because of their competitive performance/cost ratio. Regrettably, the diffusion of Grid Computing is strongly limited because two main limitations: it is confined to scientists with strong Computer Science background and the analyses of the large amount of data produced can be cumbersome it. We have developed a package named GRIMD to provide an easy and flexible implementation of distributed computing for the Bioinformatics community. GRIMD is very easy to install and maintain, and it does not require any specific Computer Science skill. Moreover, permits preliminary analysis on the distributed machines to reduce the amount of data to transfer. GRIMD is very flexible because it shields the typical computational biologist from the need to write specific code for tasks such as molecular dynamics or docking calculations. Furthermore, it permits an efficient use of GPU cards whenever is possible. GRIMD calculations scale almost linearly and, therefore, permits to exploit efficiently each machine in the network. Here, we provide few examples of grid computing in computational biology (MD and docking) and bioinformatics (proteome analysis).

Availability

GRIMD is available for free for noncommercial research at www.yadamp.unisa.it/grimd

Supplementary information

www.yadamp.unisa.it/grimd/howto.aspx     

Gene network inference and visualization tools for biologists: application to new human transcriptome datasets

Gene regulatory networks inferred from RNA abundance data have generated significant interest, but despite this, gene network approaches are used infrequently and often require input from bioinformaticians. We have assembled a suite of tools for analysing regulatory networks, and we illustrate their use with microarray datasets generated in human endothelial cells. We infer a range of regulatory networks, and based on this analysis discuss the strengths and limitations of network inference from RNA abundance data. We welcome contact from researchers interested in using our inference and visualization tools to answer biological questions.