Yung En Chee

Transparency in ecology and evolution: Real problems, real solutions

To make progress scientists need to know what other researchers have found and how they found it. However, transparency is often insufficient across much of ecology and evolution. Researchers often fail to report results and methods in detail sufficient to permit interpretation and meta-analysis, and many results go entirely unreported. Further, these unreported results are often a biased subset. Thus the conclusions we can draw from the published literature are themselves often biased and sometimes might be entirely incorrect. Fortunately there is a movement across empirical disciplines, and now within ecology and evolution, to shape editorial policies to better promote transparency. This can be done by either requiring more disclosure by scientists or by developing incentives to encourage disclosure.

Spatial data for modelling and management of freshwater ecosystems

Fluvial habitats are inherently variable. They are shaped by flow magnitude, frequency, timing and duration, by the effects of upstream and downstream features along flow paths and by bioclimatic processes and human activities in upstream contributing catchments. Managing freshwater ecosystems requires tools and data that effectively account for these multi-scale processes. We tackle these challenges in this analysis of the distribution of 17 native and alien fish species in south-eastern Australia. A fine-scale, stream-link-based GIS database comprising an extensive set of ecologically meaningful attributes at multiple scales was developed to characterise the multidimensional environmental space of freshwater biota. This article describes the methods and data required to construct such a database. Boosted regression tree models were employed to analyse relationships between species and 20 candidate environmental predictors. For some species, competitors/predators were also included as predictors. Models were evaluated from several viewpoints: the ecological plausibility and intuition arising from them, their ability to predict to river links within the training area and for 11 species for which data were sufficient, their ability to predict to an adjacent but geographically distinct region. Despite modest environmental contrasts in the study area, these data and species distribution models (SDMs) produced predictions with useful predictive ability and discriminatory power. Critically, predictors of distribution identified as important for the various species modelled were ecologically interpretable. Several – but not all – of the models tested for transferability also predicted distributions reasonably well in the adjacent region. The GIS stream database and SDMs have immediate applications, but also provide a valuable foundation for developing more sophisticated tools for management and conservation in Australian freshwater environments.

Modelling spatial and temporal changes with GIS and Spatial and Dynamic Bayesian Networks

State-and-transition models (STMs) have been successfully combined with Dynamic Bayesian Networks (DBNs) to model temporal changes in managed ecosystems. Such models are useful for exploring when and how to intervene to achieve the desired management outcomes. However, knowing where to intervene is often equally critical. We describe an approach to extend state-and-transition dynamic Bayesian networks (ST-DBNs) - incorporating spatial context via GIS data and explicitly modelling spatial processes using spatial Bayesian networks (SBNs). Our approach uses object-oriented (OO) concepts and exploits the fact that ecological systems are hierarchically structured. This allows key phenomena and ecological processes to be represented by hierarchies of components that include similar, repetitive structures. We demonstrate the generality and power of our approach using two models - one developed for adaptive management of eucalypt woodland restoration in south-eastern Australia, and another developed to manage the encroachment of invasive willows into marsh ecosystems in east-central Florida. We extend Dynamic Bayesian Network technology to model spatial processes.A novel application of object-oriented concepts helps handle BN modelling complexity.We demonstrate proof-of-concept with two environmental management case studies.We include model templates and algorithms for spatio-temporal scenario simulations.

Metaresearch for evaluating reproducibility in ecology and evolution

Abstract Recent replication projects in other disciplines have uncovered disturbingly low levels of reproducibility, suggesting that those research literatures may contain unverifiable claims. The conditions contributing to irreproducibility in other disciplines are also present in ecology. These include a large discrepancy between the proportion of “positive” or “significant” results and the average statistical power of empirical research, incomplete reporting of sampling stopping rules and results, journal policies that discourage replication studies, and a prevailing publish‐or‐perish research culture that encourages questionable research practices. We argue that these conditions constitute sufficient reason to systematically evaluate the reproducibility of the evidence base in ecology and evolution. In some cases, the direct replication of ecological research is difficult because of strong temporal and spatial dependencies, so here, we propose metaresearch projects that will provide proxy measures of reproducibility.

An Application of Qualitative Risk Assessment in Park Management

The identification and prioritisation of natural values and the potential threats to them is an essential part of the management of parks and reserves by Parks Victoria, which regularly explores alternative ways to undertake and improve the efficiency of this process. Here we describe an application of ecological risk assessment techniques for identifying and analysing risks to natural values in the mallee national parks of north-western Victoria. Utilizing a workshop setting and multiple assessors, hazards were identified with the aid of a hazard matrix. A modification of the risk analysis protocol from the Australian Standard for Risk Management, AS/NZS 4360, was used to facilitate assessment by multiple participants and to capture the full range of their judgements so as to best characterise threats to natural values. An iterative process provided opportunity to resolve uncertainty due to linguistic ambiguity and vagueness, and genuine differences of opinion that remained were explicitly represented in the final ranking of the hazards. A fault tree was then used to explore the ecological complexities behind one particular issue of concern in the mallee parks.

Alternatives to biodiversity offsets for mitigating the effects of urbanization on stream ecosystems: Alternatives to Biodiversity Offsets

Globally, offset schemes have emerged in many statutory frameworks relating to development activities, with the aim of balancing biodiversity conservation and development. Although the theory and use of biodiversity offsets in terrestrial environments is broadly documented, little attention has been paid to offsets in stream ecosystems. Here we examine the application of offset schemes to stream ecosystems and explore whether they suffer similar shortcomings to those of offset schemes focused on terrestrial biodiversity. To challenge the applicability of offsets further, we discuss typical trajectories of urban expansion and their cascading physical, chemical and biological impacts on stream ecosystems. We argue that the highly connected nature of stream ecosystems and urban drainage networks can transfer impacts of urbanization across wide areas, complicating the notion of like-for-like exchange and the prospect of effectively mitigating biodiversity loss. Instead, we identify in-catchment options for stormwater control, which can avoid or minimize the impacts of development on downstream ecosystems, while presenting additional public and private benefits. We describe the underlying principles of these alternatives, some of the challenges associated with their uptake, and policy initiatives being trialed to facilitate adoption. In conclusion, we argue that stronger policies to avoid and minimize the impacts of urbanization provide better prospects for protecting downstream ecosystems, and can additionally, stimulate economic opportunities and improve urban liveability.

Fraud Not a Primary Cause of Irreproducible Results: A Reply to Clark et al.

We welcome the comment from Clark et al. [1xSee all References][1] and are gratified that they found value in our article. In response, we would like to state that our paper was devoted to exploring relatively well-developed empirical evidence of insufficient transparency in ecology and evolution. We did not review fraud because there is an absence of empirical evidence indicating that fraud is a major problem in ecology and evolution. However, as Clark et al. also note, despite possible growth in fraud in other disciplines over recent decades, it still accounts for only a very small proportion of irreproducible results in those fields [2xMisconduct accounts for the majority of retracted scientific publications. Fang, F.C. et al. Proc. Natl Acad. Sci. U.S.A. 2012; 109: 17028–17033Crossref | PubMed | Scopus (215)See all References][2]. This would be true even if only 1% of fraud is detected. Thus, the available evidence suggests that fraud is not a primary hindrance to scientific progress. We agree with Clark et al. that increased transparency might help limit fraud and we look forward to continued discussion of various ways to promote transparency.

Correcting common misconceptions to inspire conservation action in urban environments: Urban Conservation

Abstract Despite repeated calls to action, proposals for urban conservation are often met with surprise or scepticism. There remains a pervasive narrative in policy, practice, and the public psyche that urban environments, although useful for engaging people with nature or providing ecosystem services, are of little conservation value. We argue that the tendency to overlook the conservation value of urban environments stems from misconceptions about the ability of native species to persist within cities and towns and that this, in turn, hinders effective conservation action. However, recent scientific evidence shows that these assumptions do not always hold. Although it is generally true that increasing the size, quality, and connectivity of habitat patches will improve the probability that a species can persist, the inverse is not that small, degraded, or fragmented habitats found in urban environments are worthless. In light of these findings we propose updated messages that guide and inspire researchers, practitioners, and decision makers to undertake conservation action in urban environments: consider small spaces, recognize unconventional habitats, test creative solutions, and use science to minimize the impacts of future urban development.