School of BioSciences - Research Publications

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    Two-step adaptive management for choosing between two management actions
    Moore, AL ; Walker, L ; Runge, MC ; McDonald-Maden, E ; McCarthy, MA (Ecological Society of America, 2017-06-01)
    Adaptive management is widely advocated to improve environmental management. Derivations of optimal strategies for adaptive management, however, tend to be case specific and time consuming. In contrast, managers might seek relatively simple guidance, such as insight into when a new potential management action should be considered, and how much effort should be expended on trialing such an action. We constructed a two‐time‐step scenario where a manager is choosing between two possible management actions. The manager has a total budget that can be split between a learning phase and an implementation phase. We use this scenario to investigate when and how much a manager should invest in learning about the management actions available. The optimal investment in learning can be understood intuitively by accounting for the expected value of sample information, the benefits that accrue during learning, the direct costs of learning, and the opportunity costs of learning. We find that the optimal proportion of the budget to spend on learning is characterized by several critical thresholds that mark a jump from spending a large proportion of the budget on learning to spending nothing. For example, as sampling variance increases, it is optimal to spend a larger proportion of the budget on learning, up to a point: if the sampling variance passes a critical threshold, it is no longer beneficial to invest in learning. Similar thresholds are observed as a function of the total budget and the difference in the expected performance of the two actions. We illustrate how this model can be applied using a case study of choosing between alternative rearing diets for hihi, an endangered New Zealand passerine. Although the model presented is a simplified scenario, we believe it is relevant to many management situations. Managers often have relatively short time horizons for management, and might be reluctant to consider further investment in learning and monitoring beyond collecting data from a single time period.
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    Disentangling the four demographic dimensions of species invasiveness
    Catford, JA ; Baumgartner, JB ; Vesk, PA ; White, M ; Buckley, YM ; McCarthy, MA ; Alpert, P (WILEY, 2016-11-01)
    A definitive list of invasive species traits remains elusive, perhaps due to inconsistent ways of identifying invasive species. Invasive species are typically identified using one or more of four demographic criteria (local abundance, geographic range, environmental range, spread rate), referred to here as the demographic dimensions of invasiveness. In 112 studies comparing invasive and nonâ invasive plant traits, all 15 combinations of the four demographic dimensions were used to identify invasive species; 22% of studies identified invasive species solely by high abundance, while 25% ignored abundance. We used demographic data of 340 alien herbs classified as invasive or nonâ invasive in Victoria, Australia, to test whether the demographic dimensions are independent and which dimensions influence invasive species listing in practice. Species' abundances, spread rates and range sizes were independent. Relative abundance best explained the invasiveness classification. However, invasive and nonâ invasive species each spanned the full range of each demographic dimension, indicating that no dimension clearly separates invasive from nonâ invasive species. Graminoids with longer minimum residence times were more frequently classified as invasive, as were forbs occurring near edges of native vegetation fragments. Synthesis. Conflating multiple forms of invasiveness, by not distinguishing invasive species that are identified using different demographic criteria, may obscure traits possessed by particular subsets of invasive species. Traits promoting high abundance likely differ from those enabling fast spread and broad ranges. Examining traits linked with the four demographic dimensions of invasiveness will highlight species at risk of becoming dominant, spreading quickly or occupying large ranges.
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    Improving the transparency of statistical reporting in Conservation Letters
    Fidler, F ; Fraser, H ; McCarthy, MA ; Game, ET (WILEY, 2018-03-01)
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    Plan S and publishing: reply to Lehtomaki et al. 2019
    McCarthy, MA ; Burgman, MA ; Wei, F ; Jarrad, FC ; Rondinini, C ; Murcia, C ; Marsh, HD ; Akcakaya, HR ; Esler, KJ ; Game, ET ; Schwartz, MW (WILEY, 2019-07-19)
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    Simultaneous-count models to estimate abundance from counts of unmarked individuals with imperfect detection
    Ryan, GE ; Nicholson, E ; Eames, JC ; Gray, TNE ; Loveridge, R ; Mahood, SP ; Sum, P ; McCarthy, MA (WILEY, 2019-06-01)
    We developed a method to estimate population abundance from simultaneous counts of unmarked individuals over multiple sites. We considered that at each sampling occasion, individuals in a population could be detected at 1 of the survey sites or remain undetected and used either multinomial or binomial simultaneous-count models to estimate abundance, the latter being equivalent to an N-mixture model with one site. We tested model performance with simulations over a range of detection probabilities, population sizes, growth rates, number of years, sampling occasions, and sites. We then applied our method to 3 critically endangered vulture species in Cambodia to demonstrate the real-world applicability of the model and to provide the first abundance estimates for these species in Cambodia. Our new approach works best when existing methods are expected to perform poorly (i.e., few sites and large variation in abundance among sites) and if individuals may move among sites between sampling occasions. The approach performed better when there were >8 sampling occasions and net probability of detection was high (>0.5). We believe our approach will be useful in particular for simultaneous surveys at aggregation sites, such as roosts. The method complements existing approaches for estimating abundance of unmarked individuals and is the first method designed specifically for simultaneous counts.
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    Open access and academic imperialism
    Burgman, M (WILEY, 2019-02-01)
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    The neglected tool in the Bayesian ecologist's shed: a case study testing informative priors' effect on model accuracy
    Morris, WK ; Vesk, PA ; McCarthy, MA ; Bunyavejchewin, S ; Baker, PJ (WILEY-BLACKWELL, 2015-01-01)
    Despite benefits for precision, ecologists rarely use informative priors. One reason that ecologists may prefer vague priors is the perception that informative priors reduce accuracy. To date, no ecological study has empirically evaluated data-derived informative priors' effects on precision and accuracy. To determine the impacts of priors, we evaluated mortality models for tree species using data from a forest dynamics plot in Thailand. Half the models used vague priors, and the remaining half had informative priors. We found precision was greater when using informative priors, but effects on accuracy were more variable. In some cases, prior information improved accuracy, while in others, it was reduced. On average, models with informative priors were no more or less accurate than models without. Our analyses provide a detailed case study on the simultaneous effect of prior information on precision and accuracy and demonstrate that when priors are specified appropriately, they lead to greater precision without systematically reducing model accuracy.
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    Scientific Foundations for an IUCN Red List of Ecosystems
    Keith, DA ; Rodriguez, JP ; Rodriguez-Clark, KM ; Nicholson, E ; Aapala, K ; Alonso, A ; Asmussen, M ; Bachman, S ; Basset, A ; Barrow, EG ; Benson, JS ; Bishop, MJ ; Bonifacio, R ; Brooks, TM ; Burgman, MA ; Comer, P ; Comin, FA ; Essl, F ; Faber-Langendoen, D ; Fairweather, PG ; Holdaway, RJ ; Jennings, M ; Kingsford, RT ; Lester, RE ; Mac Nally, R ; McCarthy, MA ; Moat, J ; Oliveira-Miranda, MA ; Pisanu, P ; Poulin, B ; Regan, TJ ; Riecken, U ; Spalding, MD ; Zambrano-Martinez, S ; Convertino, M (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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    Contending with uncertainty in conservation management decisions
    McCarthy, MA ; Ostfeld, RS ; Power, AG (BLACKWELL SCIENCE PUBL, 2014-01-01)
    Efficient conservation management is particularly important because current spending is estimated to be insufficient to conserve the world's biodiversity. However, efficient management is confounded by uncertainty that pervades conservation management decisions. Uncertainties exist in objectives, dynamics of systems, the set of management options available, the influence of these management options, and the constraints on these options. Probabilistic and nonprobabilistic quantitative methods can help contend with these uncertainties. The vast majority of these account for known epistemic uncertainties, with methods optimizing the expected performance or finding solutions that achieve minimum performance requirements. Ignorance and indeterminacy continue to confound environmental management problems. While quantitative methods to account for uncertainty must aid decisions if the underlying models are sufficient approximations of reality, whether such models are sufficiently accurate has not yet been examined.
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    Phylogenetic diversity meets conservation policy: small areas are key to preserving eucalypt lineages
    Pollock, LJ ; Rosauer, DF ; Thornhill, AH ; Kujala, H ; Crisp, MD ; Miller, JT ; McCarthy, MA (ROYAL SOC, 2015-02-19)
    Evolutionary and genetic knowledge is increasingly being valued in conservation theory, but is rarely considered in conservation planning and policy. Here, we integrate phylogenetic diversity (PD) with spatial reserve prioritization to evaluate how well the existing reserve system in Victoria, Australia captures the evolutionary lineages of eucalypts, which dominate forest canopies across the state. Forty-three per cent of remaining native woody vegetation in Victoria is located in protected areas (mostly national parks) representing 48% of the extant PD found in the state. A modest expansion in protected areas of 5% (less than 1% of the state area) would increase protected PD by 33% over current levels. In a recent policy change, portions of the national parks were opened for development. These tourism development zones hold over half the PD found in national parks with some species and clades falling entirely outside of protected zones within the national parks. This approach of using PD in spatial prioritization could be extended to any clade or area that has spatial and phylogenetic data. Our results demonstrate the relevance of PD to regional conservation policy by highlighting that small but strategically located areas disproportionally impact the preservation of evolutionary lineages.