Showing papers by "James Cook University published in 2006"

Novel methods improve prediction of species' distributions from occurrence data

Abstract: Prediction of species' distributions is central to diverse applications in ecology, evolution and conservation science. There is increasing electronic access to vast sets of occurrence records in museums and herbaria, yet little effective guidance on how best to use this information in the context of numerous approaches for modelling distributions. To meet this need, we compared 16 modelling methods over 226 species from 6 regions of the world, creating the most comprehensive set of model comparisons to date. We used presence-only data to fit models, and independent presence-absence data to evaluate the predictions. Along with well-established modelling methods such as generalised additive models and GARP and BIOCLIM, we explored methods that either have been developed recently or have rarely been applied to modelling species' distributions. These include machine-learning methods and community models, both of which have features that may make them particularly well suited to noisy or sparse information, as is typical of species' occurrence data. Presence-only data were effective for modelling species' distributions for many species and regions. The novel methods consistently outperformed more established methods. The results of our analysis are promising for the use of data from museums and herbaria, especially as methods suited to the noise inherent in such data improve.

A Global Crisis for Seagrass Ecosystems

Abstract: Seagrasses, marine flowering plants, have a long evolutionary history but are now challenged with rapid environmental changes as a result of coastal human population pressures. Seagrasses provide key ecological services, including organic carbon production and export, nutrient cycling, sediment stabilization, enhanced biodiversity, and trophic transfers to adjacent habitats in tropical and temperate regions. They also serve as “coastal canaries,” global biological sentinels of increasing anthropogenic influences in coastal ecosystems, with large-scale losses reported worldwide. Multiple stressors, including sediment and nutrient runoff, physical disturbance, invasive species, disease, commercial fishing practices, aquaculture, overgrazing, algal blooms, and global warming, cause seagrass declines at scales of square meters to hundreds of square kilometers. Reported seagrass losses have led to increased awareness of the need for seagrass protection, monitoring, management, and restoration. However, seagrass science, which has rapidly grown, is disconnected from public awareness of seagrasses, which has lagged behind awareness of other coastal ecosystems. There is a critical need for a targeted global conservation effort that includes a reduction of watershed nutrient and sediment inputs to seagrass habitats and a targeted educational program informing regulators and the public of the value of seagrass meadows.

The Development of Constructivist Grounded Theory

Abstract: Constructivist grounded theory is a popular method for research studies primarily in the disciplines of psychology, education, and nursing. In this article, the authors aim to locate the roots of constructivist grounded theory and then trace its development. They examine key grounded theory texts to discern their ontological and epistemological orientation. They find Strauss and Corbin’s texts on grounded theory to possess a discernable thread of constructivism in their approach to inquiry. They also discuss Charmaz’s landmark work on constructivist grounded theory relative to her positioning of the researcher in relation to the participants, analysis of the data, and rendering of participants’ experiences into grounded theory. Grounded theory can be seen as a methodological spiral that begins with Glaser and Strauss’ original text and continues today. The variety of epistemological positions that grounded theorists adopt are located at various points on this spiral and are reflective of their underlying ontologies.

Governance and the Capacity to Manage Resilience in Regional Social-Ecological Systems

Abstract: The sustainability of regional development can be usefully explored through several different lenses. In situations in which uncertainties and change are key features of the ecological landscape and social organization, critical factors for sustainability are resilience, the capacity to cope and adapt, and the conservation of sources of innovation and renewal. However, interventions in social-ecological systems with the aim of altering resilience immediately confront issues of governance. Who decides what should be made resilient to what? For whom is resilience to be managed, and for what purpose? In this paper we draw on the insights from a diverse set of case studies from around the world in which members of the Resilience Alliance have observed or engaged with sustainability problems at regional scales. Our central question is: How do certain attributes of governance function in society to enhance the capacity to manage resilience? Three specific propositions were explored: (1) participation builds trust, and deliberation leads to the shared understanding needed to mobilize and self-organize; (2) polycentric and multilayered institutions improve the fit between knowledge, action, and social-ecological contexts in ways that allow societies to respond more adaptively at appropriate levels; and (3) accountable authorities that also pursue just distributions of benefits and involuntary risks enhance the adaptive capacity of vulnerable groups and society as a whole. Some support was found for parts of all three propositions. In exploring the sustainability of regional social-ecological systems, we are usually faced with a set of ecosystem goods and services that interact with a collection of users with different technologies, interests, and levels of power. In this situation in our roles as analysts, facilitators, change agents, or stakeholders, we not only need to ask: The resilience of what, to what? We must also ask: For whom?

Emerging infectious disease and the loss of biodiversity in a Neotropical amphibian community

Abstract: Pathogens rarely cause extinctions of host species, and there are few examples of a pathogen changing species richness and diversity of an ecological community by causing local extinctions across a wide range of species. We report the link between the rapid appearance of a pathogenic chytrid fungus Batrachochytrium dendrobatidis in an amphibian community at El Cope, Panama, and subsequent mass mortality and loss of amphibian biodiversity across eight families of frogs and salamanders. We describe an outbreak of chytridiomycosis in Panama and argue that this infectious disease has played an important role in amphibian population declines. The high virulence and large number of potential hosts of this emerging infectious disease threaten global amphibian diversity.

Multiple disturbances and the global degradation of coral reefs: are reef fishes at risk or resilient?

Abstract: Increased frequency of disturbances and anthropogenic activities are predicted to have a devastating impact on coral reefs that will ultimately change the composition of reef associated fish communities. We reviewed and analysed studies that document the effects of disturbance-mediated coral loss on coral reef fishes. Meta-analysis of 17 independent studies revealed that 62% of fish species declined in abundance within 3 years of disturbances that resulted in >10% decline in coral cover. Abundances of species reliant on live coral for food and shelter consistently declined during this time frame, while abundance of some species that feed on invertebrates, algae and/or detritus increased. The response of species, particularly those expected to benefit from the immediate loss of coral, is, however, variable and is attributed to erratic replenishment of stocks, ecological versatility of species and sublethal responses, such as changes in growth, body condition and feeding rates. The diversity of fish communities was found to be negatively and linearly correlated to disturbance-mediated coral loss. Coral loss >20% typically resulted in a decline in species richness of fish communities, although diversity may initially increase following small declines in coral cover from high coverage. Disturbances that result in an immediate loss of habitat complexity (e.g. severe tropical storms), have a greater impact on fishes from all trophic levels, compared with disturbances that kill corals, but leave the reef framework intact (e.g. coral bleaching and outbreaks of Acanthaster planci). This is most evident among small bodied species and suggests the long-term consequences of coral loss through coral bleaching and crown-of-thorn starfish outbreaks may be much more substantial than the short-term effects currently documented.

Adopting a constructivist approach to grounded theory: implications for research design.

Abstract: Grounded theory is a popular research methodology that is evolving to account for a range of ontological and epistemological underpinnings. Constructivist grounded theory has its foundations in relativism and an appreciation of the multiple truths and realities of subjectivism. Undertaking a constructivist enquiry requires the adoption of a position of mutuality between researcher and participant in the research process, which necessitates a rethinking of the grounded theorist's traditional role of objective observer. Key issues for constructivist grounded theorists to consider in designing their research studies are discussed in relation to developing a partnership with participants that enables a mutual construction of meaning during interviews and a meaningful reconstruction of their stories into a grounded theory model.

Globalization, Roving Bandits, and Marine Resources

Abstract: Marine resource exploitation can deplete stocks faster than regulatory agencies can respond. Institutions with broad authority and a global perspective are needed to create a system with incentives for conservation.

Corneal avascularity is due to soluble VEGF receptor-1

Abstract: Corneal avascularity-the absence of blood vessels in the cornea-is required for optical clarity and optimal vision, and has led to the cornea being widely used for validating pro- and anti-angiogenic therapeutic strategies for many disorders. But the molecular underpinnings of the avascular phenotype have until now remained obscure and are all the more remarkable given the presence in the cornea of vascular endothelial growth factor (VEGF)-A, a potent stimulator of angiogenesis, and the proximity of the cornea to vascularized tissues. Here we show that the cornea expresses soluble VEGF receptor-1 (sVEGFR-1; also known as sflt-1) and that suppression of this endogenous VEGF-A trap by neutralizing antibodies, RNA interference or Cre-lox-mediated gene disruption abolishes corneal avascularity in mice. The spontaneously vascularized corneas of corn1 and Pax6+/- mice and Pax6+/- patients with aniridia are deficient in sflt-1, and recombinant sflt-1 administration restores corneal avascularity in corn1 and Pax6+/- mice. Manatees, the only known creatures uniformly to have vascularized corneas, do not express sflt-1, whereas the avascular corneas of dugongs, also members of the order Sirenia, elephants, the closest extant terrestrial phylogenetic relatives of manatees, and other marine mammals (dolphins and whales) contain sflt-1, indicating that it has a crucial, evolutionarily conserved role. The recognition that sflt-1 is essential for preserving the avascular ambit of the cornea can rationally guide its use as a platform for angiogenic modulators, supports its use in treating neovascular diseases, and might provide insight into the immunological privilege of the cornea.

Consumer–resource body-size relationships in natural food webs

Abstract: It has been suggested that differences in body size between consumer and resource species may have important implications for interaction strengths, population dynamics, and eventually food web structure, function, and evolution. Still, the general distribution of consumer-'resource body-size ratios in real ecosystems, and whether they vary systematically among habitats or broad taxonomic groups, is poorly understood. Using a unique global database on consumer and resource body sizes, we show that the mean body-size ratios of aquatic herbivorous and detritivorous consumers are several orders of magnitude larger than those of carnivorous predators. Carnivorous predator-prey body-size ratios vary across different habitats and predator and prey types (invertebrates, ectotherm, and endotherm vertebrates). Predator-prey body-size ratios are on average significantly higher (1) in freshwater habitats than in marine or terrestrial habitats, (2) for vertebrate than for invertebrate predators, and (3) for invertebrate than for ectotherm vertebrate prey. If recent studies that relate body-size ratios to interaction strengths are general, our results suggest that mean consumer-resource interaction strengths may vary systematically across different habitat categories and consumer types.

Abdominal aortic aneurysm : Pathogenesis and implications for management

Abstract: Abdominal aortic aneurysm (AAA) affects approximately 5% of elderly men and is responsible for a significant number of deaths in Western Countries. At present surgery by open or endovascular means is the only widely used therapy for this condition. In this review we examine the risk factors, serum, and genetic associations of AAA. Epidemiology studies suggest that smoking cessation and control of cholesterol and blood pressure should reduce the number of patients developing AAA. Natural history studies suggest that smoking cessation should reduce the rate of progression of AAA. Clear level 1 evidence for drug treatments of AAA are presently lacking; however, animal and human in vitro studies suggest that medication targeted at reducing inflammation and proteolysis are most likely to be beneficial, with limited data to support the use of statins, Angiotensin II inhibitors, and macrolides. Work has commenced in understanding which patients, identified by clinical, serum, and genotype, are more at risk of AAA progression and thus should be selected out for aggressive treatment. Well designed large multicenter randomized controlled trials are required to examine the medical treatment of AAA.

Cadaver decomposition in terrestrial ecosystems

Abstract: A dead mammal (i.e. cadaver) is a high quality resource (narrow carbon:nitrogen ratio, high water content) that releases an intense, localised pulse of carbon and nutrients into the soil upon decomposition. Despite the fact that as much as 5,000 kg of cadaver can be introduced to a square kilometre of terrestrial ecosystem each year, cadaver decomposition remains a neglected microsere. Here we review the processes associated with the introduction of cadaver-derived carbon and nutrients into soil from forensic and ecological settings to show that cadaver decomposition can have a greater, albeit localised, effect on belowground ecology than plant and faecal resources. Cadaveric materials are rapidly introduced to belowground floral and faunal communities, which results in the formation of a highly concentrated island of fertility, or cadaver decomposition island (CDI). CDIs are associated with increased soil microbial biomass, microbial activity (C mineralisation) and nematode abundance. Each CDI is an ephemeral natural disturbance that, in addition to releasing energy and nutrients to the wider ecosystem, acts as a hub by receiving these materials in the form of dead insects, exuvia and puparia, faecal matter (from scavengers, grazers and predators) and feathers (from avian scavengers and predators). As such, CDIs contribute to landscape heterogeneity. Furthermore, CDIs are a specialised habitat for a number of flies, beetles and pioneer vegetation, which enhances biodiversity in terrestrial ecosystems.

Evolution of the continental crust

Abstract: The continental crust covers nearly a third of the Earth's surface. It is buoyant—being less dense than the crust under the surrounding oceans—and is compositionally evolved, dominating the Earth's budget for those elements that preferentially partition into silicate liquid during mantle melting. Models for the differentiation of the continental crust can provide insights into how and when it was formed, and can be used to show that the composition of the basaltic protolith to the continental crust is similar to that of the average lower crust. From the late Archaean to late Proterozoic eras (some 3–1 billion years ago), much of the continental crust appears to have been generated in pulses of relatively rapid growth. Reconciling the sedimentary and igneous records for crustal evolution indicates that it may take up to one billion years for new crust to dominate the sedimentary record. Combining models for the differentiation of the crust and the residence time of elements in the upper crust indicates that the average rate of crust formation is some 2–3 times higher than most previous estimates.

Nano-Emulsion Production by Sonication and Microfluidization—A Comparison

Abstract: The efficiency of sonication and microfluidization to produce nano-emulsions were evaluated in this study. The purpose was to produce an oil-in-water nano-emulsion of d-limonene to apply it in the next step for nano-particle encapsulation. In the entrapment and retention of volatiles or for the microencapsulation efficiency, emulsion size is one of the critical factors. In this study, a bench-top sonicator and an air-driven microfluidizer were used to prepare the emulsions. Results show that, while both methods were capable of producing nano-emulsions of the size range of 150-700 nm, the microfluidizer produced emulsions with narrower size distributions and sonication was more convenient in terms of operation and cleaning. In general, the size of the emulsions decreased with increasing sonication time, or the microfluidization pressure and duration. However, for both sonication and microfluidization, optimal conditions were necessary for emulsification beyond which the emulsion sizes would either increase or have little change with further processing.

How can experience in clinical and community settings contribute to early medical education? A BEME systematic review.

Abstract: Review date: Review period January 1992–December 2001. Final analysis July 2004–January 2005.Background and review context: There has been no rigorous systematic review of the outcomes of early exp...

Will human-induced changes in seawater chemistry alter the distribution of deep-sea scleractinian corals?

Abstract: The answer to the title question is uncertain, as very few manipulative experiments have been conducted to test how deep-sea scleractinians (stony corals) react to changes in seawater chemistry. Ocean pH and calciumcarbonate saturation are decreasing due to an influx of anthropogenic CO2 to the atmosphere. Experimental evidence has shown that declining carbonate saturation inhibits the ability of marine organisms to build calcium carbonate skeletons, shells, and tests. Here we put forward a hypothesis suggesting that the global distribution of deep-sea scleractinian corals could be limited in part by the depth of the aragonite saturation horizon (ASH) in the world's oceans. Aragonite is the metastable form of calcium carbonate used by scleractinian corals to build their skeletons and the ASH is the limit between saturated and undersaturated water. The hypothesis is tested by reviewing the distribution of deep-sea, bioherm-forming scleractinian corals with respect to the depth of the ASH. Results indicate that > 95% of 410 coral locations occurred in saturated waters during pre-industrial times. Projections indicate that about 70% of these locations will be in undersaturated waters by 2099. Lab experimentation, in situ experimentation, and monitoring efforts are needed to quantify the effects of changing seawater chemistry on deep-sea coral ecosystems.

Current trends and future challenges in the experimental, theoretical and computational analysis of intervalence charge transfer (IVCT) transitions

Abstract: Mixed-valence chemistry has a long and rich history which is characterised by a strong interplay of experimental, theoretical and computational studies. The intervalence charge transfer (IVCT) transitions generated in dinuclear mixed-valence species (particularly of ruthenium and osmium) have received considerable attention in this context, as they provide a powerful and sensitive probe of the factors which govern electronic delocalisation and the activation barrier to intramolecular electron transfer. This tutorial review discusses classical, semi-classical and quantum mechanical theoretical treatments which have been developed over the past 35 years for the analysis of IVCT absorption bands. Particular attention is drawn to the applicability of these models for the analysis of mixed-valence complexes which lie between the fully localised (Class II) and delocalised (Class III) limits in the “localised-to-delocalised” (Class II–III) regime. A clear understanding of the complex interplay of inter- and intramolecular factors which influence the IVCT process is crucial for the design of experimental studies to probe the localised-to-delocalised regime and in guidance of the development of appropriate theoretical models.

The predation gauntlet: early post-settlement mortality in reef fishes

Abstract: Most marine fishes have pelagic larvae that settle to benthic juvenile/adult habitats. Ecologists have argued that mortality rates are particularly high during the settlement transition, but relevant data have been sparse. Recently, researchers have used several novel techniques to estimate the magnitude of predation mortality during the settlement transition. We used meta-analysis to determine that for 24 taxonomically diverse species in geographically widespread locations, an estimated 55.7% (CI: 43.0–65.5%) of juveniles were consumed within 1–2 days of settlement. Such high mortality highlights this brief period as a key phase in the life history of fishes and supports the view that these communities are strongly influenced by predation. Additionally, we argue that because predators have such strong effects on juvenile survival, the population and community dynamics of reef fishes may be linked to human exploitation of reef predators.

Case study: a bridge across the paradigms.

Abstract: Case study as a teaching and research tool has an extensive history in health and social sciences. Despite its suitability for many of the research questions that face nurses, nurses have not fully embraced case study as a comprehensive approach for research. The vagaries of the real-life clinical setting can confound methodologically purist researchers. Case study provides a milieu in which nurse researchers can respond to these vagaries and move towards a paradigmatic openness. In this paper, we argue that case study offers, as yet, under-explored and under-utilised potential as a bridge across the traditional research paradigms. We argue that case study has broad research application and epistemological, ontological and methodological flexibility. When used as a research approach, case study is both the process and end product of research. It provides a delineated boundary for inquiry, and a structural process within which any methods appropriate to investigating a research area can be applied.

Diversity and flexibility of sex-change strategies in animals.

Abstract: Here, we review recent empirical advances that have improved our understanding of why and when sex change occurs. We show that sex-changing animals use a greater diversity of strategies to increase their reproductive success than was previously recognized: some individuals change sex early, others change sex late, some individuals change sex more than once, and others do not change sex at all. These different strategies can be unified by the principle that individuals change sex when it increases their reproductive value. The breeding tactics (male, female or non-breeder) adopted by individuals often appear to be adaptive responses to their own social–ecological context and variation in these conditions results in significant differences in the timing of sex change within and between species.

Ecological consequences of major hydrodynamic disturbances on coral reefs

Abstract: A recent tsunami and an apparent increase in the frequency of severe tropical storms underscore the need to understand and predict the ecological consequences of major hydrodynamic disturbances. Reef corals provide the habitat structure that sustains the high biodiversity of tropical reefs, and thus provide the foundation for the ecosystem goods and services that are critical to many tropical societies. Here we integrate predictions from oceanographic models with engineering theory, to predict the dislodgement of benthic reef corals during hydrodynamic disturbances. This generalizes earlier work, by incorporating colonies of any shape and by explicitly examining the effects of hydrodynamic gradients on coral assemblage structure. A field test shows that this model accurately predicts changes in the mechanical vulnerability of coral colonies, and thus their size and shape, with distance from the reef crest. This work provides a general framework for understanding and predicting the effects of hydrodynamic disturbances on coral reef communities; such disturbances have a major role in determining species zonation and coexistence on coral reefs, and are critical determinants of how coral assemblages will respond to changes in the frequency and intensity of tropical storms associated with a changing climate.

Intervalence charge transfer (IVCT) in trinuclear and tetranuclear complexes of iron, ruthenium, and osmium.

Abstract: Electron and energy transfer are ubiquitous in biological, chemical, and physical processes, which has led to extensive multidisciplinary research efforts to elucidate the factors influencing mechanistic pathways. Of considerable importance in these studies have been investigations of intramolecular electron and energy transfer within polymetallic assemblies as a result of the diversity (coordination number, ligand environment, stereochemistry, and redox characteristics) provided by the metal centers in such structures. Because of their multicomponent nature, these structures have considerable design potential to exploit the cooperation between the metals and/or other redox-active centers. Novel photochemical molecular devices (PMDs) may be constructed which are capable of performing useful light- and redox-induced functionsincluding artificial photosynthesis and photoinduced energy- and electron-transfer processes in light-harvesting “antenna” systems. Metallosupramolecular assemblies have also been designed to mimic the photoinduced charge separation function in photosynthetic organisms, in an attempt to elucidate the complex electron- and energy-transfer mechanisms which occur in natural systems. The possibility of multiple electron transferby absorption of several photons by linked chromophores, or the design of systems which generate more than one electron upon absorption of one photonhas significant implications in catalytic schemes, as well as understanding long-range electron transfer in biological systems, and the conductivity of “molecular wires”. In molecules involving delocalized unpaired electrons, polarizability may be present so that the species exhibit interesting nonlinear optical or magnetic properties. Polypyridyl complexes of the d^6 metals Fe^II, Ru^II, and OsII have attracted particular attention as the basis of these assemblies due to a combination of favorable photophysical and redox characteristics, the longevity of their excited states, and their chemical inertness in a variety of oxidation states. An important feature of these complexes is the capability of systematic variation of the ground- and excited-state properties by the judicious choice of the coordinating ligands.

Coral bleaching, reef fish community phase shifts and the resilience of coral reefs

Abstract: The 1998 global coral bleaching event was the largest recorded historical disturbance of coral reefs and resulted in extensive habitat loss. Annual censuses of reef fish community structure over a 12-year period spanning the bleaching event revealed a marked phase shift from a prebleach to postbleach assemblage. Surprisingly, we found that the bleaching event had no detectable effect on the abundance, diversity or species richness of a local cryptobenthic reef fish community. Furthermore, there is no evidence of regeneration even after 5–35 generations of these short-lived species. These results have significant implications for our understanding of the response of coral reef ecosystems to global warming and highlight the importance of selecting appropriate criteria for evaluating reef resilience.

Introduced Macroalgae – a Growing Concern

Abstract: Introductions of non-indigenous species to new ecosystems are one of the major threats to biodiversity, ecosystem functions and services. Globally, species introductions may lead to biotic homogenisation, in synergy with other anthropogenic disturbances such as climate change and coastal pollution. Successful marine introductions depend on (1) presence of a transport vector, uptake of propagules and journey survival of the species; (2) suitable environmental conditions in the receiving habitat; and (3) biological traits of the invader to facilitate establishment. Knowledge has improved of the distribution, biology and ecology of high profile seaweed invaders, e.g. Caulerpa taxifolia, Codium fragile ssp. tomentosoides, Sargassum muticum, and Undaria pinnatifida. Limited, regional information is available for less conspicuous species. The mechanisms of seaweed introductions are little understood as research on introduced seaweeds has been mostly reactive, following discoveries of introductions. Sources of introductions mostly cannot be determined with certainty apart from those directly associated with aquaculture activities and few studies have addressed the sometimes serious ecological and economic impacts of seaweed introductions. Future research needs to elucidate the invasion process, interactions between invaders, and impacts of introductions to support prevention and management of seaweed introductions.