School of BioSciences - Research Publications
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ItemPlan S and publishing: reply to Lehtomaki et al. 2019(WILEY, 2019-10)
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ItemOpen access and academic imperialism(WILEY, 2019-02)
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ItemNo Preview AvailableScientific Foundations for an IUCN Red List of Ecosystems(PUBLIC LIBRARY SCIENCE, 2013-05-08)An understanding of risks to biodiversity is needed for planning action to slow current rates of decline and secure ecosystem services for future human use. Although the IUCN Red List criteria provide an effective assessment protocol for species, a standard global assessment of risks to higher levels of biodiversity is currently limited. In 2008, IUCN initiated development of risk assessment criteria to support a global Red List of ecosystems. We present a new conceptual model for ecosystem risk assessment founded on a synthesis of relevant ecological theories. To support the model, we review key elements of ecosystem definition and introduce the concept of ecosystem collapse, an analogue of species extinction. The model identifies four distributional and functional symptoms of ecosystem risk as a basis for assessment criteria: A) rates of decline in ecosystem distribution; B) restricted distributions with continuing declines or threats; C) rates of environmental (abiotic) degradation; and D) rates of disruption to biotic processes. A fifth criterion, E) quantitative estimates of the risk of ecosystem collapse, enables integrated assessment of multiple processes and provides a conceptual anchor for the other criteria. We present the theoretical rationale for the construction and interpretation of each criterion. The assessment protocol and threat categories mirror those of the IUCN Red List of species. A trial of the protocol on terrestrial, subterranean, freshwater and marine ecosystems from around the world shows that its concepts are workable and its outcomes are robust, that required data are available, and that results are consistent with assessments carried out by local experts and authorities. The new protocol provides a consistent, practical and theoretically grounded framework for establishing a systematic Red List of the world's ecosystems. This will complement the Red List of species and strengthen global capacity to report on and monitor the status of biodiversity.
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ItemMetaresearch for Evaluating Reproducibility in Ecology and Evolution(OXFORD UNIV PRESS, 2017-03)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.
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ItemPrioritizing plant eradication targets by re-framing the project prioritization protocol (PPP) for use in biosecurity applications(Springer, 2017-03-01)The eradication of newly detected alien plant species is often prescribed, but rarely successful. Eradication programs fail for many reasons, however, for eradication to remain a cost-efficient management option it is clear that good decisions must be made at the outset. Here we re-frame the project prioritization protocol (PPP), a tool widely used in conservation biology, for use with the metrics typically used by a biosecurity agency. We then use existing methods to estimate the cost-efficiency of eradicating 50 hypothetical species incursions and compare the reduction in weed risk achieved by allocating resources using the PPP framework with the allocation based on risk ranking. By allocating resources to plant eradication programs using the PPP our analysis indicated that it is possible to improve the return on public expenditure by 25% compared to investing based solely on weed risk assessment scores. We also demonstrate how the cost-efficiency of the overall portfolio is influenced by the choice of planning horizon; including the decline in overall portfolio performance that arises when attempting to eradicate individual species too quickly. Finally, we discuss the logistical benefits to a management agency that arise from the use of a generic overarching framework such as the PPP. We believe that the PPP has considerable potential for use in biosecurity and can help focus attention on those species where management can make the biggest difference.
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ItemIdentifying hotspots of alien plant naturalisation in Australia: approaches and predictions(SpringerLink, 2016)Her Majesty the Queen in Right of Australia as represented by: Sally Salmon The early detection of newly naturalised alien species is vital to ensuring the greatest chance of their successful eradication. Understanding where species naturalise most frequently is the first stage in allocating surveillance effort. Using Australia’s Virtual Herbarium, we compiled the collection records for all plant species in Australia. We controlled for potential spatial biases in collection effort to identify areas that have an elevated rate of first records of alien species’ occurrence in Australia. Collection effort was highly variable across Australia, but the most intense collection effort occurred either close to herbaria (located in cities) or in remote natural environments. Significant clusters of first records of occurrence were identified around each state’s capital city, coinciding with higher collection effort. Using Poisson point process modelling, we were able to determine the relative influence of environmental and anthropogenic factors on the spatial variation in the risk of species naturalisation. Effort-corrected naturalisation risk appeared to be strongly related to land use, road and human population densities, as well as environmental factors such as average temperature and rainfall. Our paper illustrates how the risk of naturalisation at a location can be estimated quantitatively. Improved understanding of factors that contribute to naturalisation risk enhances allocation of surveillance effort, thereby detecting novel species sooner, and increasing the likelihood of their eventual eradication.
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ItemThe changing patterns of plant naturalization in Australia(WILEY, 2015-09)Abstract Aim To identify the temporal patterns of plant naturalization in Australia, particularly the interaction between taxonomy, geographic origin and economic use. Location Australia. Methods From Australia's Virtual Herbarium, we compiled a database of information for the entire naturalized flora of Australia. We then examined the database in discrete time intervals to determine the changes in patterns of naturalized species taxonomy, geographic origin and economic use over time. Results Contrary to prevailing hypotheses, we found no evidence to indicate that the rate of alien flora naturalization is increasing in Australia. The number of naturalized species has grown linearly during the period 1880–2000, with the underlying rate of new species detected per thousand specimens declining over the same time period. Despite this, the diversity of both species taxonomy and geographic origin has increased over the last 120 years, leading to increased rates of growth in the total phylogenetic diversity of the Australian flora. Main Conclusions By classifying species according to their likely origin and economic use, we are able to infer the circumstances driving the patterns of naturalization. In particular, we identify how the contribution of individual pathways has changed since European settlement corresponding with the socio‐economic development of the continent. Our study illustrates how the changing nature of ‘high‐risk’ pathways is relevant to directing interventions such as biosecurity regulation.
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ItemPlant extirpation at the site scale: implications for eradication programmes(WILEY, 2015-02)Abstract Aim To identify the relative importance of commonly available site and species factors on the probability of extirpating a plant species at the site scale. Location Australia. Methods We reviewed the plant eradication literature and listed the factors commonly cited as influencing eradication success. We then analysed a database of 408 site‐scale extirpation attempts, across 17 species eradication programmes, by modelling the time until extirpation to determine the relative influence of these factors on the probability of extirpation, given time. Results The most commonly cited factors influencing eradication success can be classified into two groups as follows: those related to the ‘organisation’, being typically binary variables and amenable to management; and those related to the ‘site/species’, which typically were continuous values and usually beyond the control of the management agency. Detectability period, search distance, monitoring rate, infestation size, propagule longevity, time to reproductive maturity and previous eradication success all influenced the extirpation rate. Conversely, climate suitability, land use and general accessibility (distance to nearest manager) were relatively unimportant. By relating the influential site/species factors to a time‐dependent model, managers and policymakers can explicitly estimate the probability of successful extirpation at a site, given a particular time horizon. These estimates can then be aggregated up to the species scale to allow managers to set realistic goals regarding eradication time frames and resource requirements. Main conclusions Our paper illustrates how the probability of extirpation at the site scale can be quantitatively estimated and how these estimates can be used to inform decisions regarding broader species‐scale eradication programmes. We expect that the use of such quantitative approaches to select better eradication targets will improve eradication success rates over time.
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ItemTraits influence detection of exotic plant species in tropical forests(PUBLIC LIBRARY SCIENCE, 2018-08-22)Detecting exotic plant species is essential for invasive species management. By accounting for factors likely to affect species' detection rates (e.g. survey conditions, observer experience), detectability models can help choose search methods and allocate search effort. Integrating information on species' traits can refine detectability models, and might be particularly valuable if these traits can help improve estimates of detectability where data on particular species are rare. Analysing data collected during line transect distance sampling surveys in Indonesia, we used a multi-species hierarchical distance sampling model to evaluate how plant height, leaf size, leaf shape, and survey location influenced plant species detectability in secondary tropical rainforests. Detectability of the exotic plant species increased with plant height and leaf size. Detectability varied among the different survey locations. We failed to detect a clear effect of leaf shape on detectability. This study indicates that information on traits might improve predictions about exotic species detection, which can then be used to optimise the allocation of search effort for efficient species management. The innovation of the study lies in the multi-species distance sampling model, where the distance-detection function depends on leaf traits and height. The method can be applied elsewhere, including for different traits that may be relevant in other contexts. Trait-based multispecies distance sampling can be a practical approach for sampling exotic shrubs, herbs, or grasses species in the understorey of tropical forests.