The use of fish in ecological assessments

Abstract Fish provide powerful tools for assessing aquatic environments. Three attributes are especially significant: the sensitivity of fish to most forms of human disturbance, their usefulness at all levels of biological organization and the favourable benefit-to-cost ratio offish assessment programmes. Fish can be used as indicators over wide temporal and spatial ranges. Because they cover all trophic levels of consumer ecology, fish can effectively integrate the whole range of ecological processes in waterways. Fish have been used in many different roles for assessing river health and monitoring responses to remedial management. Three of these applications appear to have particular value for management of Australian rivers: (i) automated systems monitoring fish ventilation can provide sensitive, broad-spectrum and continuous sensing of water quality to protect receiving waters or water-supply intakes; (ii) programmes collecting routine data on commercial or recreational fisheries can be designed and analysed so as to isolate confounding effects due to fishery-specific factors and, hence, used to detect and monitor environmental change on large scales; (iii) the Index of Biotic Integrity (IBI) can be modified to suit Australian conditions and fish communities to meet the important need for a predictive model of aquatic environmental quality. The IBI is a quantitative biological tool with a strong ecological foundation that integrates attributes from several levels of ecosystem organization. Examples of the use of IBI elsewhere suggest its robustness, flexibility and sensitivity can cope effectively with the low diversity of the Australian fish fauna and the dominance of ecological generalists. A provisional structure is suggested for a test of the IBI in four riverine regions of New South Wales.     

The role of experimental microcosms in ecological research

A number of recent and important developments in community ecology have been derived from experiments conducted in microcosms. Studies with microcosms have addressed a broad range of phenomena, including climate change, biodiversity, assembly rules, habitat restoration, trophic dynamics and mycorrhizal associations. The common factor linking these studies is that they manipulate an individual environmental axis and explore the role that axis plays in structuring communities. We discuss six recent studies to illustrate the use and design of microcosms for community ecology research.     

Herbivory simulations in ecological research

Because of the experimental advantages that they offer, mechanical simulations of grazing are more commonly used than true herbivory in ecological studies of the impact of herbivory on plants. However, few studies have explicitly compared plant responses to herbivory and to mechanical simulations. Most such comparisons report differences in plant responses to mechanical versus true herbivory, even though the amounts and types of tissue removed were similar. Moreover, studies that also attempted to mimic the timing of leaf damage report differences in plant responses to the different damage modes. Because a plant's response to herbivory is complex and is activated by more than merely the removal of tissue, exact mechanical simulations may prove difficult.     

The use of turbidimeters in suspended sediment research

Accurate characterisation of the trend in suspended sediment concentration in streams throughout runoff events requires a sampling interval much shorter than the one hour typically used. For logistical reasons this is not usually feasible, so continuously recording turbidimeters offer a potential alternative. The variety of correlations and relationships between sediment concentration and turbidity reported in the literature is not surprising in view of the many confounding effects present in natural stream systems. Data from five sites in a small forested catchment indicated variability in the turbidity-suspended sediment concentration relationship, but improvements were obtained by considering the effects of very fine sediment and background water colour. Throughout runoff events variations in sediment properties, organic acids concentration and turbulence can occur. It is concluded that a good linear relationship between turbidity and suspended sediment concentration should not necessarily be expected and any observed hysteresis could actually help explain erosion and transport processes. The detail and continuity of data generated by turbidimeters provides the opportunity for greater understanding of storm sediment dynamics, however, calibration requires careful consideration of site characteristics.     

生态土地分类研究进展

土地分类是土地评价,替代和管理的基础,对林业资源可持续利用具有重要的意义。生态土地分类是目前土地分类的主要方向和趋势。国际上早已开展此项研究。随着景观生态学和3S技术的发展,生态分类系统的研制已成为生态土地分类的重点。本文对生态土地分类的定义,特点,发展历史,生态分类系统理论,以及国际生态分类系统的发展趋势进行了系统的综述,并指出以资源（森林,土地,水域等）多目标管理为基础,定量与定性相结合的多因子多层次综合是未来生态土地研究发展的总趋势,有必要在我国大力开展相关研究。     

The use of ruminant models in biomedical perinatal research

Animal models are of critical importance in biomedical research. Although rodents and lagomorphs are the most commonly used species, larger species are required, especially when surgical approaches or new medical devices have to be evaluated. In particular, in the field of perinatal medicine, they are critical for the evaluation of new pharmacologic treatments and the development of new invasive procedures in fetuses. In some areas, such as developmental genetics, reproductive biotechnologies and metabolic programming, the contribution of ruminants is essential. The current report focuses on some of the most outstanding examples of great biomedical advances carried out with ruminant models in the field of perinatal research. Experiments recently carried in our research unit using ruminants are also briefly described.     

The use of transgenic systems in pharmaceutical research.

Those pharmaceutical companies whose goal is to generate novel innovative drugs are faced with the challenge that only a fraction of the compounds tested in clinical trials eventually become a registered drug. This problem of attrition is compounded by the fact that the clinical trial or development stage is by far the most costly phase of bringing a new drug to market, consuming around 80 per cent of the total spend. Transgenic technology represents an attractive approach to reducing the attrition rate of compounds entering clinical trials by increasing the quality of the target and compound combinations making the transition from discovery into development. Transgenic technology can impact at many points in the discovery process, including target identification and target validation, and provides models designed to alert researchers early to potential problems with drug metabolism and toxicity, as well as providing better models for human diseases. In target identification, transgenic animals harbouring large DNA fragments can be used to narrow down genetic regions. Genetic studies often result in the identification of large genomic regions and one way to decrease the region size is to do complementation studies in transgenic animals using, for example, inserts from bacterial artificial chromosome (BAC) clones. In target validation, transgenic animals can be used for in vivo validation of a specific target. Considerable efforts are being made to establish new, rapid and robust tools with general utility for in vivo validation, but, so far, only transgenic animals work reliably on a wide range of targets. Transgenic animals can also be used to generate better disease models. Predictive animal models to test new compounds and targets will significantly speed up the drug discovery process and, more importantly, increase the quality of the compounds taken further in the research and development process. Humanised transgenic animals harbouring the human target molecule can be used to understand the effect of a compound acting on the human target in vivo. Also, models mimicking human drug metabolism will provide a means of assessing the effect of human-specific metabolites and of understanding the pharmacokinetic properties of potential drugs. In toxicology studies, transgenic animals are providing more predictive models. A good example of this are those models routinely used to look for carcinogenicity associated with new compounds.     

The use of molecular data in mangrove plant research

The use of molecular data in plant studies has increased dramatically duringthe last decade. Recently, molecular techniques have been applied tomangrove plants to investigate population structure and phylogeneticrelationships. We briefly review research on mangrove plants based onprotein polymorphism and DNA data. Results of these molecular studieshave provided new insights into conservation issues, systematics,biogeography, and population biology of mangrove plants, in many casesrevealing unexpected and surprising patterns.     

The use of Caenorhabditis elegans in parasitic nematode research

There is increasing interest in the use of the free-living nematode Caenorhabditis elegans as a tool for parasitic nematode research and there are now a number of compelling examples of its successful application. C. elegans has the potential to become a standard tool for molecular helminthology researchers, just as yeast is routinely used by molecular biologists to study vertebrate biology. However, in order to exploit C. elegans in a meaningful manner, we need a detailed understanding of the extent to which different aspects of C. elegans biology have been conserved with particular groups of parasitic nematodes. This review first considers the current state of knowledge regarding the conservation of genome organisation across the nematode phylum and then discusses some recent evolutionary development studies in free-living nematodes. The aim is to provide some important concepts that are relevant to the extrapolation of information from C. elegans to parasitic nematodes and also to the interpretation of experiments that use C. elegans as a surrogate expression system. In general, examples have been specifically chosen because they highlight the importance of careful experimentation and interpretation of data. Consequently, the focus is on the differences that have been found between nematode species rather than the similarities. Finally, there is a detailed discussion of the current status of C. elegans as a heterologous expression system to study parasite gene function and regulation using successful examples from the literature.     

The next generation of microarray research: applications in evolutionary and ecological genomics

Microarray technology is one of the key developments in recent years that has propelled biological research into the post-genomic era. With the ability to assay thousands to millions of features at the same time, microarray technology has fundamentally changed how biological questions are addressed, from examining one or a few genes to a collection of genes or the whole genome. This technology has much to offer in the study of genome evolution. After a brief introduction on the technology itself, we then focus on the use of microarrays to examine genome dynamics, to uncover novel functional elements in genomes, to unravel the evolution of regulatory networks, to identify genes important for behavioral and phenotypic plasticity, and to determine microbial community diversity in environmental samples. Although there are still practical issues in using microarrays, they will be alleviated by rapid advances in array technology and analysis methods, the availability of many genome sequences of closely related species and flexibility in array design. It is anticipated that the application of microarray technology will continue to better our understanding of evolution and ecology through the examination of individuals, populations, closely related species or whole microbial communities.     

The evolutionary origins and ecological context of tool use in New Caledonian crows

New Caledonian (NC) crows Corvus moneduloides are the most prolific avian tool users. In the wild, they use at least three distinct tool types to extract invertebrate prey from deadwood and vegetation, with some of their tools requiring complex manufacture, modification and/or deployment. Experiments with captive-bred, hand-raised NC crows have demonstrated that the species has a strong genetic predisposition for basic tool use and manufacture, suggesting that this behaviour is an evolved adaptation. This view is supported by recent stable-isotope analyses of the diets of wild crows, which revealed that tool use provides access to highly profitable hidden prey, with preliminary data indicating that parents preferentially feed their offspring with tool-derived food. Building on this work, our review examines the possible evolutionary origins of these birds’ remarkable tool-use behaviour. Whilst robust comparative analyses are impossible, given the phylogenetic rarity of animal tool use, our examination of a wide range of circumstantial evidence enables a first attempt at reconstructing a plausible evolutionary scenario. We suggest that a common ancestor of NC crows, originating from a (probably) non-tool-using South-East Asian or Australasian crow population, colonised New Caledonia after its last emersion several million years ago. The presence of profitable but out-of-reach food, in combination with a lack of direct competition for these resources, resulted in a vacant woodpecker-like niche. Crows may have possessed certain behavioural and/or morphological features upon their arrival that predisposed them to express tool-use rather than specialised prey-excavation behaviour, although it is possible that woodpecker-like foraging preceded tool use. Low levels of predation risk may have further facilitated tool-use behaviour, by allowing greater expenditure of time and energy on object interaction and exploration, as well as the evolution of a ‘slow’ life-history, in which prolonged juvenile development enables acquisition of complex behaviours. Intriguingly, humans may well have influenced the evolution of at least some of the species’ tool-oriented behaviours, via their possible introduction of candlenut trees together with the beetle larvae that infest them. Research on NC crows’ tool-use behaviour in its full ecological context is still in its infancy, and we expect that, as more evidence accumulates, some of our assumptions and predictions will be proved wrong. However, it is clear from our analysis of existing work, and the development of some original ideas, that the unusual evolutionary trajectory of NC crows is probably the consequence of an intricate constellation of interplaying factors.