Susan J. Nichols

Analyzing cause and effect in environmental assessments: using weighted evidence from the literature

Abstract.  Sound decision making in environmental research and management requires an understanding of causal relationships between stressors and ecological responses. However, demonstrating cause–effect relationships in natural systems is challenging because of difficulties with natural variability, performing experiments, lack of replication, and the presence of confounding influences. Thus, even the best-designed study may not establish causality. We describe a method that uses evidence available in the extensive published ecological literature to assess support for cause–effect hypotheses in environmental investigations. Our method, called Eco Evidence, is a form of causal criteria analysis—a technique developed by epidemiologists in the 1960s—who faced similar difficulties in attributing causation. The Eco Evidence method is an 8-step process in which the user conducts a systematic review of the evidence for one or more cause–effect hypotheses to assess the level of support for an overall question. In contrast to causal criteria analyses in epidemiology, users of Eco Evidence use a subset of criteria most relevant to environmental investigations and weight each piece of evidence according to its study design. Stronger studies contribute more to the assessment of causality, but weaker evidence is not discarded. This feature is important because environmental evidence is often scarce. The outputs of the analysis are a guide to the strength of evidence for or against the cause–effect hypotheses. They strengthen confidence in the conclusions drawn from that evidence, but cannot ever prove causality. They also indicate situations where knowledge gaps signify insufficient evidence to reach a conclusion. The method is supported by the freely available Eco Evidence software package, which produces a standard report, maximizing the transparency and repeatability of any assessment. Environmental science has lagged behind other disciplines in systematic assessment of evidence to improve research and management. Using the Eco Evidence method, environmental scientists can better use the extensive published literature to guide evidence-based decisions and undertake transparent assessments of ecological cause and effect.

The influence of extreme climatic events and human disturbance on macroinvertebrate community patterns of a Mediterranean stream over 15 y

Abstract We analyzed long-term changes in macroinvertebrate communities in a Mediterranean temporary stream in southern Portugal over 15 y (1993–2008) at 10 locations with 3 degrees of physicochemical disturbance (reference, high disturbance, and mild disturbance). We related year-to-year variation of macroinvertebrate communities to long-term (59 y) information on precipitation and temperature. Our goals were to: 1) determine the stability of macroinvertebrate communities in the stream, 2) establish the influence of physicochemical disturbance on community stability, 3) assess the influence of climate change on the macroinvertebrate communities, and 4) assess the interactive effects of climate change and disturbance level on macroinvertebrate communities. Community structure varied naturally from year to year, but changes in taxon richness and evenness were much stronger and more unpredictable in disturbed than in other sites. In the long term, the more diverse (reference) and the poorest (disturbed) communities were stable, whereas communities affected by mild disturbance slowly decreased in taxon richness (slope  =  −0.07, r2  =  0.38). This decrease could be a response to the continuous stress or to climate change. The multivariate patterns over time of invertebrate communities at mildly disturbed sites were the only patterns significantly correlated with climatic patterns. In the past 59 y in this Mediterranean area (southeastern Europe), winter temperature has increased 1°C and precipitation has decreased 1.5 mm/d. Marked changes in community composition (70–80% Bray–Curtis dissimilarity) occurred only in years of extremely low precipitation or temperature. In years of climatic extremes and at chemically disturbed sites, Orthocladiinae and Simuliidae became dominant. In this stream, a shift in community equity occurs before species elimination. This shift might be useful as an early warning for biodiversity loss because of disturbance or climate change. We recommend continued sampling of reference sites for monitoring purposes so that effects of climate change can be established and so that contemporary human disturbance can be assessed relative to an adjusted reference condition.

Big data opportunities and challenges for assessing multiple stressors across scales in aquatic ecosystems

Aquatic ecosystems are under threat from multiple stressors, which vary in distribution and intensity across temporal and spatial scales. Monitoring and assessment of these ecosystems have historically focussed on collection of physical and chemical information and increasingly include associated observations on biological condition. However, ecosystem assessment is often lacking because the scale and quality of biological observations frequently fail to match those available from physical and chemical measurements. The advent of high-performance computing, coupled with new earth observation platforms, has accelerated the adoption of molecular and remote sensing tools in ecosystem assessment. To assess how emerging science and tools can be applied to study multiple stressors on a large (ecosystem) scale and to facilitate greater integration of approaches among different scientific disciplines, a workshop was held on 10–12 September 2014 at the Sydney Institute of Marine Sciences, Australia. Here we introduce a conceptual framework for assessing multiple stressors across ecosystems using emerging sources of big data and critique a range of available big-data types that could support models for multiple stressors. We define big data as any set or series of data, which is either so large or complex, it becomes difficult to analyse using traditional data analysis methods.

Ecological Responses to Flow Alteration: Assessing Causal Relationships with Eco Evidence

The environment is being increasingly recognized as a legitimate user of water. However, tension between environmental and consumptive uses remains and environmental water allocations may be subject to legal challenge. Current predictions of ecological response to altered flow regimes are not sufficiently transparent or robust to withstand such challenges. We review the use of causal criteria analysis to systematically review ecological responses to changes in flow regimes. Causal criteria analysis provides a method to assess the evidence for and against cause-effect hypotheses. Relationships supported by sufficient evidence can inform transparent and robust environmental flow recommendations. The use of causal criteria analysis in environmental science has been facilitated by the development of the Eco Evidence method and software—a standardized approach for synthesizing evidence from the scientific literature. Eco Evidence has thus far been used to assess the evidence concerning responses of vegetation, fish, macroinvertebrates, and floodplain geomorphology to changes in flow regime, and provides a robust and transparent assessment of this evidence. There is a growing movement internationally to shift from experience-based to evidence-based methods in environmental science and management. The research presented here is at the leading edge of a fundamental change in the way environmental scientists use evidence.

River condition assessment may depend on the sub-sampling method: field live-sort versus laboratory sub-sampling of invertebrates for bioassessment

Aquatic macroinvertebrates are commonly used biological indicators for assessing the health of freshwater ecosystems. However, counting all the invertebrates in the large samples that are usually collected for rapid site assessment is time-consuming and costly. Therefore, sub-sampling is often done with fixed time or fixed count live-sorting in the field or with preserved material using sample splitters in the laboratory. We investigate the differences between site assessments provided when the two sub-sampling approaches (Live-sort and Lab-sort) were used in conjunction with predictive bioassessment models. The samples showed a method bias. The Live-sort sub-samples tended to have more large, conspicuous invertebrates and often fewer small and, or cryptic animals that were more likely to be found in Lab-sort samples where a microscope was used. The Live-sort method recovered 4–6 more taxa than Lab-sorting in spring, but not in autumn. The magnitude of the significant differences between Live-sort and Lab-sort predictive model outputs, observed to expected (O/E) taxa scores, for the same sites ranged from 0.12 to 0.53. These differences in the methods resulted in different assessments of some sites only and the number of sites that were assessed differently depended on the season, with spring samples showing most disparity. The samples may differ most in spring because many of the invertebrates are larger at that time (and thus are more conspicuous targets for live-sorters). The Live-sort data cannot be run through a predictive model created from Lab-sort data (and vice versa) because of the taxonomic differences in sub-sample composition and the sub-sampling methods must be standardized within and among studies if biological assessment is to provide valid comparisons of site condition. Assessments that rely on the Live-sorting method may indicate that sites are ‘less impaired’ in spring compared to autumn because more taxa are retrieved in spring when they are larger and more visible. Laboratory sub-sampling may return fewer taxa in spring, which may affect assessments relying on taxonomic richness.

Using the reference condition maintains the integrity of a bioassessment program in a changing climate.

Abstract Climate change is gradual and long-term, consistently collected data are required to detect resulting biological responses and to separate such responses from local effects of human activities that monitoring programs usually are designed to assess. The reference-condition approach is commonly used in freshwater assessments that use predictive modeling, but a consistent reference condition is required to maintain the relevance and integrity of results over the long term. We investigated whether external influences, such as climate change, inhibited clear interpretation of bioassessment results in a study design using reference vs test sites. Macroinvertebrates were collected from 16 sites (11 sites affected by ski resorts and 5 reference sites) on 5 streams in 4 seasons each year from 1994 to 2008 within Kosciuszko National Park, Australia. We analyzed trends over 15 y to address questions regarding climate-change and macroinvertebrate bioindicators of stream condition (observed/expected [O/E] taxa; Stream Invertebrate Grade Number Average Level [SIGNAL] 2 scores; Simpsons Diversity; Ephemeroptera, Plecoptera, Trichoptera [EPT] richness ratio; and Oligochaeta abundance). Climate became slightly warmer and less humid (p < 0.0001), but no significant relationships between climate variables and bioindicators were evident. All bioindicators consistently distinguished between test and reference sites in all seasons. All bioindicators except for O/E taxa scores differed among streams (regardless of site type). O/E taxa are inherently adjusted for specific stream characteristics, and, thus, were robust to differences in stream type while remaining sensitive to reference and test site variation. Generally, reference and test sites did not respond differently to any gradual climate changes. Furthermore, the reference sites sampled through time remained in a condition equivalent to the previously defined reference condition and provided a valid comparison for current test sites of unknown condition. The bioindicators used here were insensitive to the small but significant changes in climate detected over the 15-y study. However, extreme climate-related events (such as severe drought and extensive bushfire) were detected by the chosen bioindicators at both reference and test sites. Ecological outcomes of climate change can be accounted for only by an appropriate study design that includes standardized sampling of fixed sites (both test and reference) over long periods.

An online database and desktop assessment software to simplify systematic reviews in environmental science

We describe software to facilitate systematic reviews in environmental science. Eco Evidence allows reviewers to draw strong conclusions from a collection of individually-weak studies. It consists of two components. An online database stores and shares the atomized findings of previously-published research. A desktop analysis tool synthesizes this evidence to test cause-effect hypotheses. The software produces a standardized report, maximizing transparency and repeatability. We illustrate evidence extraction and synthesis. Environmental research is hampered by the complexity of natural environments, and difficulty with performing experiments in such systems. Under these constraints, systematic syntheses of the rapidly-expanding literature can advance ecological understanding, inform environmental management, and identify knowledge gaps and priorities for future research. Eco Evidence, and in particular its online re-usable bank of evidence, reduces the workload involved in systematic reviews. This is the first systematic review software for environmental science, and opens the way for increased uptake of this powerful approach. Systematic review is a powerful, but underused, technique in environmental science.We developed software and a database designed to simplify such reviews.The online database stores and shares evidence, reducing the workload for users.The analysis software guides users through a previously-published review method.The software produces a standard report to maximize transparency and repeatability.

Contribution of national bioassessment approaches for assessing ecological water security: an AUSRIVAS case study

River managers in Australia are managing in the face of extremes to provide security of water supply for people, production and the environment. Balancing the water requirements of people, environments and economies requires that water security is viewed holistically, not just in terms of the water available for human consumption. Common definitions of water security focus on the needs of both humans and ecosystems for purposes such as drinking, agriculture and industrial use, and to maintain ecological values. Information about achieving water security for the environment or ecological purposes can be a challenge to interpret because the watering requirements of key ecological processes or assets are not well understood, and the links between ecological and human values are often not obvious to water users. Yet the concepts surrounding river health are inherently linked to holistic concepts of water security. The measurement of aquatic biota provides a valuable tool for managers to understand progress toward achieving ecological water security objectives. This paper provides a comprehensive review of the reference condition approach to river health assessment, using the development of the Australian River Assessment System (AUSRIVAS) as a case study. We make the link between the biological assessment of river health and assessment of ecological water security, and suggest that such an approach provides a way of reporting that is relevant to the contribution made by ecosystems to water security. The reference condition approach, which is the condition representative of minimally disturbed sites organized by selected physical, chemical, and biological characteristics, is most important for assessing ecological water security objectives.

Challenges for evidence-based environmental management: what is acceptable and sufficient evidence of causation?*

Investigators attempting to demonstrate causal relationships in environmental systems face challenges associated with natural variability, multiple stressors, the difficulty of performing rigorous experiments, and the time and money required to undertake such studies. Rapid, transparent, and logical methods are needed to synthesize and evaluate evidence from multiple existing scientific research studies. Eco Evidence was developed for this purpose. It provides a synthesis method, online database, and analysis software for use in environmental causal assessments. Eco Evidence provides a definition of ‘acceptable’ and ‘sufficient evidence’ to establish causation. To illustrate its capabilities, we provide an example in which Eco Evidence informed a review of groundwater abstraction limits for environmental flow guidelines in the Australian Capital Territory. The synthesis of available evidence from peer-reviewed and unpublished sources was deemed sufficient and acceptable to inform a decision to keep groundwater abstraction limits <10% of long-term recharge. However, the definitions of acceptable and sufficient evidence might differ based upon the reasons for conducting an environmental causal assessment and on the perceived risk and consequences of making particular decisions.

A DNA barcode database of Australia’s freshwater macroinvertebrate fauna

Macroinvertebrates are widely used for monitoring freshwater ecosystems. In most monitoring programs, identifications take substantial time and expense. Methods that improve the speed, accuracy and cost-effectiveness of macroinvertebrate identification would benefit such programs. Increasingly, DNA barcodes are being used to provide accurate species-level identifications and have the potential to change how macroinvertebrates are routinely identified. Herein we discuss the need for DNA barcodes of freshwater macroinvertebrates with particular reference to Australia. We examine the use of DNA barcodes for species identification and compare DNA barcoding efforts of macroinvertebrates from Australia with those globally. We consider the role of high-throughput sequencing of DNA barcodes in freshwater bioassessment and its potential use in biosurveillance. Finally, we outline a strategy for developing a comprehensive national DNA barcode database for Australian freshwater macroinvertebrates and present the initial efforts in creating this database.