Bayesian classification of catchments using spatial data: a first step to improved modelling of catchment effects on stream ecological condition

A major challenge facing freshwater ecologists and managers is the development of models that link stream ecological condition to catchment scale effects, such as land use. Previous attempts to make such models have followed two general approaches. The bottom-up approach employs mechanistic models, which can quickly become too complex to be useful. The top-down approach employs empirical models derived from large data sets, and has often suffered from large amounts of unexplained variation in stream condition.

We believe that the lack of success of both modelling approaches may be at least partly explained by scientists considering too wide a breadth of catchment type. Thus, we believe that by stratifying large sets of catchments into groups of similar types prior to modelling, both types of models may be improved. This paper describes preliminary work using a Bayesian classification software package, ‘Autoclass’ (Cheeseman and Stutz 1996) to create classes of catchments within the Murray Darling Basin based on physiographic data.

Autoclass uses a model-based classification method that employs finite mixture modelling and trades off model fit versus complexity, leading to a parsimonious solution. The software provides information on the posterior probability that the classification is ‘correct’ and also probabilities for alternative classifications. The importance of each attribute in defining the individual classes is calculated and presented, assisting description of the classes. Each case is ‘assigned’ to a class based on membership probability, but the probability of membership of other classes is also provided. This feature deals very well with cases that do not fit neatly into a larger class. Lastly, Autoclass requires the user to specify the measurement error of continuous variables.

Catchments were derived from the Australian digital elevation model. Physiographic data werederived from national spatial data sets. There was very little information on measurement errors for the spatial data, and so a conservative error of 5% of data range was adopted for all continuous attributes. The incorporation of uncertainty into spatial data sets remains a research challenge.

The results of the classification were very encouraging. The software found nine classes of catchments in the Murray Darling Basin. The classes grouped together geographically, and followed altitude and latitude gradients, despite the fact that these variables were not included in the classification. Descriptions of the classes reveal very different physiographic environments, ranging from dry and flat catchments (i.e. lowlands), through to wet and hilly catchments (i.e. mountainous areas). Rainfall and slope were two important discriminators between classes. These two attributes, in particular, will affect the ways in which the stream interacts with the catchment, and can thus be expected to modify the effects of land use change on ecological condition. Thus, realistic models of the effects of land use change on streams would differ between the different types of catchments, and sound management practices will differ.

A small number of catchments were assigned to their primary class with relatively low probability. These catchments lie on the boundaries of groups of catchments, with the second most likely class being an adjacent group. The locations of these ‘uncertain’ catchments show that the Bayesian classification dealt well with cases that do not fit neatly into larger classes.

Although the results are intuitive, we cannot yet assess whether the classifications described in this paper would assist the modelling of catchment scale effects on stream ecological condition. It is most likely that catchment classification and modelling will be an iterative process, where the needs of the model are used to guide classification, and the results of classifications used to suggest further refinements to models.

Sustainability and health : supporting global ecological integrity in public health

Radical changes in the biosphere and human interaction with the environment are increasingly impacting on the health of populations across the world. Diseases are crossing the species barrier, and spreading rapidly through globalized transport systems. From new patterns of cancer to the threat of global pandemics, it is imperative that public health practitioners acknowledge the interdependence between the sustainability of the environment and the sustainability of the human species.* Why are issues of global and local sustainability of increasing importance to the public's health?* Why do issues of sustainability require new practices within the professions of public health?* How can future and current public health practitioners develop those new practices?Drawing on scientific evidence of global and local environmental changes, Sustainability and Health offers a thorough background and practical solutions to the overlapping issues in environment and health. It examines potential and existing responses to global and local environment and health issues, involving individuals, community, industry and government. The authors introduce a range of emerging conceptual frameworks and theoretical perspectives, link IT and epidemiology and explain how scoping can link program design, delivery, data collection and evaluation in projects from their very beginning. Public health practitioners need to be able to manage health issues that cut across environmental, economic and social systems and to develop the capacity for leadership in facilitating change. Incorporating learning activities, readings, international case studies and an open learning approach, this is a valuable resource for students of public and environmental health, as well as medical, environmental and health science professionals.

Ecological processes : a key element in strategies for nature conservation

A common approach to nature conservation is to identify and protect natural 'assets’ such as ecosystems and threatened species. While such actions are essential, protection of assets will not be effective unless the ecological processes that sustain them are maintained. Here, we consider the role of ecological processes and the complementary perspective for conservation arising from an emphasis on process. Many kinds of ecological processes sustain biodiversity: including climatic processes, primary productivity, hydrological processes, formation of biophysical habitats, interactions between species, movements of organisms and natural disturbance regimes. Anthropogenic threats to conservation exert their influence by modifying or disrupting these processes. Such threats extend across tenures, they frequently occur offsite, they commonly induce non-linear responses, changes may be irreversible and the full consequences may not be experienced for lengthy periods. While many managers acknowledge these considerations in principle, there is much scope for greater recognition of ecological processes in nature conservation and greater emphasis on long time-frames and large spatial scales in conservation planning. Practical measures that promote ecological processes include: monitoring to determine the trajectory and rate of processes; incorporating surrogates for processes in conservation and restoration projects; specific interventions to manipulate and restore processes; and planning for the ecological future before options are foreclosed. The long-term conservation of biodiversity and the wellbeing of human society depend upon both the protection of natural assets and maintaining the integrity of the ecological processes that sustain them.

A new approach to determining environmental flow requirements : sustaining the natural values of floodplains of the southern Murray-Darling Basin

Large overbank flood events play an important role in maintaining largescale ecological processes and connectivity along and across the floodplains and between the rivers and their floodplains in the southern Murray-Darling Basin. However, the regulation of rivers means that extensive overbank flooding can only occur in the rare circumstance of extreme flood events. Recent environmental water allocations have focussed on the largest floodplain blocks (‘icon’ sites) and a small set of specific values (e.g. colonial nesting waterbirds), as well as on trialling fine-scale manipulation of infrastructure (e.g. pumping) to water relatively small areas. There has been no comprehensive systematic assessment of the entire floodplain and its wider set of flood-dependent natural assets (such as ecosystems and species; herein referred to as ‘natural values’) to maximise the effectiveness of environmental water use and to catalogue values likely to be lost. This paper describes an assessment of some 220 000 ha found to support flood-dependent natural values in Victoria. We mapped the geographic distribution and estimated components of the flooding requirements (natural flooding frequency, and maximum period without flooding and minimum duration of each flooding event before significant deterioration) for each natural value. Using an example of one stretch of the River Murray, we show how the resultant spatial data can be used with floodplain inundation modelling to compare the outcomes of real or planned environmental watering events; potentially providing tools for management agencies to conserve a wider range of floodplain values than is currently the case. That is, water managers and the public can see what ecosystems and threatened species are intended to be maintained by environmental watering and what values are intended to be abandoned across the whole floodplain, rather than just seeing the small subset of values and ‘icon’ sites that are intended to be maintained. Examples are provided to illustrate how information about the location, water requirements and extent covered by potential floods for specific values can be used to build adaptive watering strategies for areas as large as the whole floodplain.

Ecological correlates of the threat of extinction in neotropical bird species

Predicting the threat of extinction aids efficient distribution of conservation resources. This paper utilises a comparative macroecological approach to investigate the threat of extinction in Neotropical birds. Data on ecological variables for 1708 species are analysed using stepwise regression to produce minimum adequate models, first using raw species values and then using independent contrasts (to control for phylogenetic effects). The models differ, suggesting phylogeny has significant effects. The raw species analysis reveals that number of zoogeographical regions occupied, elevational range and utilisation of specialised microhabitats were negatively associated with threat, while minimum elevation and body mass were positively associated, whereas the independent contrasts analysis only identifies zoogeographical regions as important. Confining the analysis to the 582 species restricted to a single zoogeographical region reveals elevational range and number of habitats occupied to be negatively correlated with threat whether the analysis is based on the raw data or on independent contrasts. Analysis of four contrasting zoogeographical regions highlights regional variation in the models. In two Andean regions the threat of extinction declines as the elevation range across which the species occurs increases. In the presence of substantial human populations on high Andean plateaus, a species with a greater elevational range may be more likely to persist at some (relatively) unsettled altitudes. In Central South America, the strongest predictor of threat is minimum elevation of occurrence: species with a lower minimum are less threatened. The minimum elevation result suggests that lowland species experiencing an ecological limit to their minimum elevation (min. elevation >0 m) may be more at risk than those not experiencing such a limit (min. elevation = 0 m). Finally, in southern Amazonia, where there is little altitudinal variation, the only weak predictors of threat are body size, larger species being more threatened, and number of habitats, species occupying more habitats being less threatened. These contrasting results emphasise the importance of undertaking extinction risk analyses at an appropriate geographical scale. Since the models explained only a low percentage of total variance in the data, the effects of human-mediated habitat disturbance across a wide range of habitats may be important.

Predicting future ecological degradation based on modelled thresholds

Threshold models are becoming important in determining the ecological consequences of our actions within the environment and have a key role in setting bounds on targets used by natural resource managers. We have been using thresholds and related concepts adapted from the multiple stable-states literature to model ecosystem response in the Coorong, the estuary for Australia’s largest river. Our modelling approach is based upon developing a state-and-transition model, with the states defined by the biota and the transitions defined by a classification and regression tree (CART) analysis of the environmental data for the region. Here we explore the behaviour of thresholds within that model. Managers tend to plan for a set of often arbitrarily-derived thresholds in their natural resource management. We attempt to assess how the precision afforded by analyses such as CART translates into ecological outcomes, and explicitly trial several approaches to understanding thresholds and transitions in our model and how they might be relevant for management. We conclude that the most promising approach would be a mixture of further modelling (using past behaviour to predict future degradation) in conjunction with targeted experiments to confirm the results. Our case study of the Coorong is further developed, particularly for the modelling stages of the protocol, to provide recommendations to improve natural resource management strategies that are currently in use.

Does adding wood to agricultural streams enhance biodiversity? An experimental approach

Riparian clearing and the removal of wood from channels have affected many streams in agricultural landscapes. As a result, these streams often have depauperate in-stream wood loads, and therefore decreased habitat complexity and lower levels of in-stream biodiversity. The introduction of wood was investigated as a possible rehabilitation technique for agricultural streams. Wood was re-introduced to eight streams in two separate high-rainfall, intensively grazed regions of Victoria, Australia and the effect on aquatic macroinvertebrate communities was measured. The addition of wood increased overall family richness and the richness of most functional feeding groups occupying edge and benthic habitats within the stream. Wood addition led to less overlap between benthic and edge macroinvertebrate communities, suggesting increased habitat heterogeneity within the stream ecosystem. Of all sampled habitats, wood supported the greatest density of families and was colonised by all functional feeding groups. Wood habitats also had the highest overall richness and supported the most taxa that were sensitive to disturbance. These findings suggest that re-introducing wood to agricultural streams is an appropriate rehabilitation technique where those streams are affected by reduced habitat complexity. Additional work is needed to confirm these findings over larger spatial and temporal scales.

What are the policy priorities for sustaining ecological processes? A case study from Victoria, Australia

Developments in ecological theory indicate that ecological processes have major implications for sustaining biodiversity and the provision of ecosystem services. Consequently, conservation actions that focus solely on particular species, vegetation communities, habitats or sites ('assets') are unlikely to be effective over the long term unless the ecological processes that support them continue to function. Efforts to sustain biodiversity must embrace both 'assets' and 'process-oriented' approaches. Existing knowledge about ecological processes, incomplete though it is, has not been adequately considered in government decision making. It is, therefore, necessary to consider how to build consideration of ecological processes into legislative and institutional frameworks, policy and planning processes, and on-ground environmental management. Drawing on insights from interviews, a facilitated workshop, and a literature review, this paper identifies a suite of policy priorities and associated reforms which should assist in ensuring that ecological processes are given more attention in policy-making processes. It is concluded that a multi-pronged approach is required, because there are no 'silver bullets' for sustaining ecological processes.

Addressing aquaculture-fisheries interactions through the implementation of the ecosystem approach to aquaculture (EAA

This review addresses how the ecosystem approach to aquaculture (EAA) can optimize aquaculture-fisheries interactions considering different spatial scales from farm, aquaculture zone and watershed through to the global market. Aquaculture and fisheries are closely related subsectors with frequent interactions, largely due to the sharing of common ecosystems and natural resources. Interactions are also born from the flow of biomass from fisheries to aquaculture through fish-based feeds (e.g. fishmeal, fish oil and trashfish), through the collection of wild seed and brookstock, and genetic resources and biomass transfer from aquaculture to fisheries through culture-based fisheries (CBF) and escapees. Negative effects include modification of habitats affecting fisheries resources and activities (e.g. mangrove clearing for shrimp ponds, seabed disturbances through anchoring of aquaculture cages or pens, damage to seagrasses, alteration to reproductive habitats, biodiversity loss). Eutrophication of waterbodies due to excess nutrient release leading to anoxia and fish mortality can also impact negatively on biodiversity and wild fish stocks. Release of diseases and chemicals also imposes some threats on fisheries. Yet there could be beneficial impacts; for example, aquaculture is increasingly contributing to capture fisheries through CBF and could contribute to restore overfished stocks. Aquaculture can offer alternative livelihoods to fisherfolk, providing increased opportunity to them and also to their families, and especially to women. Aquaculture-increased production and marketing can also enhance and indirectly improve processing and market access to similar fishery products. The ecosystem approach to aquaculture (EAA) is a strategy for the management of the sector that emphasizes intersectoral complementarities by taking into account the interactions between all the activities within ecologically meaningful boundaries and acknowledging the multiple services provided by ecosystems. The main objective of this review is to understand the status of aquaculture-fisheries interactions associated with the biological, technological, social, economic, environmental, policy, legal and other aspects of aquaculture development and to analyze how these interactions are or could be addressed with an EAA. Therefore, the review involves aspects of scoping, identification of issues, prioritizing, devising management tools and plans for minimizing negative effects and optimizing positive ones within the context of social-ecological resilience, at different relevant geographical scales. Many of the management measures suggested in this review must involve not only EAA but also an ecosystem approach to fisheries (EAF), especially to deal with issues such as fishery of wild seed and the management of fisheries to produce fishmeal/oil for pelleted feeds or for direct feeding with wet fish. The implementation of EAA and EAF should help to overcome the sectoral and intergovernmental fragmentation of resource management efforts and assist in the development of institutional mechanisms and private-sector arrangements for effective coordination among various sectors active in ecosystems in which aquaculture and fisheries operate and between the various levels of government. Ecosystem-based management involves a transition from traditional sectoral planning and decision-making to the application of a more holistic approach to integrated natural resource management in an adaptive manner.

Overcoming data constraints to create meaningful ecological models

Many techniques used to model ecosystems cannot be meaningfully applied to large-scale ecological problems due to data constraints. Disparate collection methods, data types and incomplete data sets, or limited theoretical understanding mean that a wide range of modelling techniques used to model physical processes or for problems specific to species or populations cannot be used at an ecosystem scale. In developing an ecological response model for the Coorong, a South Australian hypersaline estuary, we combined several flexible modelling approaches in a statistical framework to develop an approach we call ‘ecosystem states’. This model uses simulated hydrodynamic conditions as input to predict one of a suite of states per space and time, allowing prediction of likely ecological conditions under a variety of scenarios. Each ecosystem state has defined sets of biota and physico-chemical parameters. The existing model is limited in that its predictions have yet to be tested and, as yet, no spatial or temporal connectivity has been incorporated into simulated time series of ecosystem states. This approach can be used in a wide range of ecosystems, where enough data are available to model ecosystem states. We are in the process of applying the technique to a nearby lake system. This has been more difficult than for the Coorong as there is little overlap in the spatial and temporal coverage of biological data sets for that region. The approach is robust to low-quality biological data and missing environmental data, so should suit situations where community or management monitoring programs have occurred through time.

Ecological determinism in Australia : tracing the legacy of McHarg downunder and its key precedents

Ecological planning, as advocated by Ian McHarg, filtered extensively through North America following the publication of Design with Nature (1965). The integrated design and planning approach was also advanced by numerous graduates of McHarg's studios at the University of Pennsylvania where this approach was extensively trialled and proven. While a clear synthesis and theoretical framework was articulated and reinforced through a plethora of projects, monographs, and articles, the majority of these perspectives were North American, lacked clarity about the translation of the approach into legal strategic and statutory planning instruments, nor shed light upon what transpired in Australia. This paper reviews the development of the Conservation Plan created for the southern Mornington peninsula in Victoria, Australia, as well as its intent, structure and internal workings as a successful model of ecological statutory planning, in the context of the wider WPRPA activities that draws directly from the McHarg theory. Known as the Conservation Plan for the southern Mornington Peninsula in Victoria, a revolutionary planning structure devised in the early 1970s by several Australian proponents. The Conservation Plan continues in operation today curating a high scenic valued landscape protecting it from intrusion from the growing metropolitan city of Melbourne thus fulfilling its objectives of landscape quality conservation whilst still permitting sympathetic building and land use growth. Contextually, the Conservation Plan appears to be only statutory equivalent translation of the approach internationally other than the Pinelands Commission planning processes in New Jersey.

Does urbanization have the potential to create an ecological trap for powerful owls (Ninox strenua)?

Landscape transformation associated with urbanization is one of the most damaging and pervasive impacts humans have on natural ecosystems. The response of species to increasing urbanization has become a major focus of research globally. Powerful owls ( Ninox strenua) are a top-order predator the have been shown to reside in urban environments, but increasing urbanization has also been demonstrated to significantly reduce available habitat. In this paper we use species distribution models established for key food and nesting resources of powerful owls across an urban-forest gradient to constrain habitat predictions from a previously developed powerful owl species distribution model. This multi-criteria decision analysis (MCDA) approach allowed us to investigate the impacts of urbanization on potential powerful owl habitat when challenged with food and nesting requirements. As powerful owls only use tree cavities for nesting we propose that the cue for settlement in an area is associated with the presence of habitat and food and as such breeding requirements may be disconnected from settlement requirements.Our results demonstrate that incorporation of a general prey resource (at least one group of arboreal marsupials) as a cue for settlement does not reduce the amount of available habitat for powerful owls substantially. Further constraining the model with a tree cavity resource, however, leads to a substantial reduction in powerful owl habitat in the urban and urban fringe environments. If a diverse prey resource (two or more groups of arboreal marsupials) is used as the cue for settlement, this sees a substantial reduction in available habitat in urban environments. Incorporation of tree cavities into this model does not reduce the available habitat for powerful owls substantially.We propose that powerful owls do not need a diverse prey base for survival, and that breeding resources are unlikely to be a cue for settlement. As such, we argue in this paper that increasing urbanization has the potential to create an ecological trap for powerful owls as there is a significant difference between habitat capable of supporting powerful owls, and habitat in which owls can breed.Management of powerful owls in urban environments will be difficult, but this research highlights the potential for the use of nest boxes to enhance the breeding activities in increasingly urbanized environments. Replacement of this critical resource may be able to reverse any potential ecological trap that is occurring. © 2014 Elsevier Ltd.

Testing the focal species approach to making conservation decisions for species persistence

Aim: Most risk assessments and decisions in conservation are based on surrogate approaches, where a group of species or environmental indicators are selected as proxies for other aspects of biodiversity. In the focal species approach, a suite of species is selected based on life history characteristics, such as dispersal limitation and area requirements. Testing the validity of the focal species concept has proved difficult, due to a lack of theory justifying the underlying framework, explicit objectives and measures of success. We sought to understand the conditions under which the focal species concept has merit for conservation decisions. Location: Our model system comprised 10 vertebrate species in 39 patches of native forest embedded in pine plantation in New South Wales, Australia. Methods: We selected three focal species based on ecological traits. We used a multiple-species reserve selection method that minimizes the expected loss of species, by estimating the risk of extinction with a metapopulation model. We found optimal reserve solutions for multiple species, including all 10 species, the three focal species, for all possible combinations of three species, and for each species individually. Results: Our case study suggests that the focal species approach can work: the reserve system that minimized the expected loss of the focal species also minimized the expected species loss in the larger set of 10 species. How well the solution would perform for other species and given landscape dynamics remains unknown. Main conclusions: The focal species approach may have merit as a conservation short cut if placed within a quantitative decision-making framework, where the aspects of biodiversity for which the focal species act as proxies are explicitly defined, and success is determined by whether the use of the proxy results in the same decision. Our methods provide a framework for testing other surrogate approaches used in conservation decision-making and risk assessment. © 2013 John Wiley & Sons Ltd.

Modelling the benefits of habitat restoration in socio-ecological systems

Decisions affecting the management of natural resources in agricultural landscapes are influenced by both social and ecological factors. Models that integrate these factors are likely to better predict the outcomes of natural resource management decisions compared to those that do not take these factors into account. We demonstrate how Bayesian Networks can be used to integrate ecological and social data and expert opinion to model the cost-effectiveness of revegetation activities for restoring biodiversity in agricultural landscapes. We demonstrate our approach with a case-study in grassy woodlands of south-eastern Australia. In our case-study, cost-effectiveness is defined as the improvement in native reptile and beetle species richness achieved per dollar spent on a restoration action. Socio-ecological models predict that weed control, the planting of trees and shrubs, the addition of litter and timber, and the addition of rocks are likely to be the most cost-effective actions for improving reptile and beetle species richness. The cost-effectiveness of restoration actions is lower in remnant and revegetated areas than in cleared areas because of the higher marginal benefits arising from acting in degraded habitats. This result is contingent on having favourable landowner attitudes. Under the best-case landowner demographic scenarios the greatest biodiversity benefits are seen when cleared areas are restored. We find that current restoration investment practices may not be increasing faunal species richness in agricultural landscapes in the most cost-effective way, and that new restoration actions may be necessary. Integrated socio-ecological models support transparent and cost-effective conservation investment decisions. Application of these models highlights the importance of collecting both social and ecological data when attempting to understand and manage socio-ecological systems.

Evolutionary history of a secondary terrestrial Australian diving beetle (Coleoptera, Dytiscidae) reveals a lineage of high morphological and ecological plasticity

The evolution of a secondary terrestrial lifestyle in diving beetles (Coleoptera: Dytiscidae) has never been analysed in a phylogenetic framework before. Here we study Terradessus caecus Watts, a terrestrial species of the subfamily Hydroporinae endemic to Australia. We infer its phylogenetic placement using Bayesian inference and maximum-likelihood methods based on a multilocus molecular dataset. We also investigate the divergence time estimates of this lineage using a Bayesian relaxed clock approach. Finally, we infer ancestral ecological preferences using a likelihood approach. We recover T. caecus nested in the genus Paroster Sharp with strong support. Therefore, we establish a synonymy for both species of Terradessus with Paroster: Paroster caecus (Watts) n.comb. and Paroster anophthalmus (Brancucci & Monteith) n.comb. Paroster is an endemic Australian genus that has a remarkable number of subterranean species in underground aquifers with highly derived morphologies. Our results highlight one of the most remarkable radiations of aquatic beetles with independent ecological pathways likely linked to palaeoclimatic disruptions in the Neogene. Paroster caecus (Watts) n.comb. originated from a mid-Miocene split following the onset of an aridification episode that has been ongoing to the present day. The deep changes in ecological communities in association with the drying-out of palaeodrainage systems might have pushed this lineage to colonize a new niche in terrestrial habitats.