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      Assessing the utility of statistical adjustments for imperfect detection in tropical conservation science

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          Abstract

          1. In recent years, there has been a fast development of models that adjust for imperfect detection. These models have revolutionized the analysis of field data, and their use has repeatedly demonstrated the importance of sampling design and data quality. There are, however, several practical limitations associated with the use of detectability models which restrict their relevance to tropical conservation science.

          2. We outline the main advantages of detectability models, before examining their limitations associated with their applicability to the analysis of tropical communities, rare species and large-scale data sets. Finally, we discuss whether detection probability needs to be controlled before and/or after data collection.

          3. Models that adjust for imperfect detection allow ecologists to assess data quality by estimating uncertainty and to obtain adjusted ecological estimates of populations and communities. Importantly, these models have allowed informed decisions to be made about the conservation and management of target species.

          4. Data requirements for obtaining unadjusted estimates are substantially lower than for detectability-adjusted estimates, which require relatively high detection/recapture probabilities and a number of repeated surveys at each location. These requirements can be difficult to meet in large-scale environmental studies where high levels of spatial replication are needed, or in the tropics where communities are composed of many naturally rare species. However, while imperfect detection can only be adjusted statistically, covariates of detection probability can also be controlled through study design. Using three study cases where we controlled for covariates of detection probability through sampling design, we show that the variation in unadjusted ecological estimates from nearly 100 species was qualitatively the same as that obtained from adjusted estimates. Finally, we discuss that the decision as to whether one should control for covariates of detection probability through study design or statistical analyses should be dependent on study objectives.

          5. Synthesis and applications. Models that adjust for imperfect detection are an important part of an ecologist's toolkit, but they should not be uniformly adopted in all studies. Ecologists should never let the constraints of models dictate which questions should be pursued or how the data should be analysed, and detectability models are no exception. We argue for pluralism in scientific methods, particularly where cost-effective applied ecological science is needed to inform conservation policy at a range of different scales and in many different systems.

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          Most cited references69

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          Beyond the Fragmentation Threshold Hypothesis: Regime Shifts in Biodiversity Across Fragmented Landscapes

          Ecological systems are vulnerable to irreversible change when key system properties are pushed over thresholds, resulting in the loss of resilience and the precipitation of a regime shift. Perhaps the most important of such properties in human-modified landscapes is the total amount of remnant native vegetation. In a seminal study Andrén proposed the existence of a fragmentation threshold in the total amount of remnant vegetation, below which landscape-scale connectivity is eroded and local species richness and abundance become dependent on patch size. Despite the fact that species patch-area effects have been a mainstay of conservation science there has yet to be a robust empirical evaluation of this hypothesis. Here we present and test a new conceptual model describing the mechanisms and consequences of biodiversity change in fragmented landscapes, identifying the fragmentation threshold as a first step in a positive feedback mechanism that has the capacity to impair ecological resilience, and drive a regime shift in biodiversity. The model considers that local extinction risk is defined by patch size, and immigration rates by landscape vegetation cover, and that the recovery from local species losses depends upon the landscape species pool. Using a unique dataset on the distribution of non-volant small mammals across replicate landscapes in the Atlantic forest of Brazil, we found strong evidence for our model predictions - that patch-area effects are evident only at intermediate levels of total forest cover, where landscape diversity is still high and opportunities for enhancing biodiversity through local management are greatest. Furthermore, high levels of forest loss can push native biota through an extinction filter, and result in the abrupt, landscape-wide loss of forest-specialist taxa, ecological resilience and management effectiveness. The proposed model links hitherto distinct theoretical approaches within a single framework, providing a powerful tool for analysing the potential effectiveness of management interventions.
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            Some Practical Aspects of a Conditional Likelihood Approach to Capture Experiments

            R Huggins (1991)
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              In Defense of Indices: The Case of Bird Surveys

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                Author and article information

                Contributors
                Role: Handling Editor
                Journal
                J Appl Ecol
                J Appl Ecol
                jpe
                The Journal of Applied Ecology
                Blackwell Publishing Ltd (Oxford, UK )
                0021-8901
                1365-2664
                August 2014
                02 June 2014
                : 51
                : 4
                : 849-859
                Affiliations
                [1 ]Grand Challenges in Ecosystems and the Environment, Department of Life Sciences, Imperial College London Silwood Park Campus, Ascot, SL5 7PY, UK
                [2 ]Departmento de Ecologia, Instituto de Biociências, Universidade de São Paulo Rua do Matão, 101, trav. 14, São Paulo, SP, 05508-090, Brazil
                [3 ]Departmento de Zoologia, Instituto de Biociências, Universidade de São Paulo Rua do Matão, 101, trav. 14, São Paulo, SP, 05508-090, Brazil
                [4 ]Departamento de Biologia, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo - USP Av. Bandeirantes 3900, Ribeirão Preto, 14040-901, Brazil
                [5 ]Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz Campus Prof. Soane Nazaré de Andrade, Km 16 - Rodovia Jorge Amado, Ilhéus, BA, 45662-900, Brazil
                [6 ]Lancaster Environment Centre, Lancaster University Lancaster, LA1 4YQ, UK
                [7 ]Museu Paraense Emílio Goeldi Av. Magalhães Barata 376, Belém, Pará, CEP 66040-170, Brazil
                Author notes
                *Correspondence author. E-mail: c.banks@ 123456imperial.ac.uk
                Article
                10.1111/1365-2664.12272
                4144333
                25177046
                9585524b-bdf2-4a84-b12f-7af92e519b56
                © 2014 The Authors. Journal of Applied Ecology © 2014 British Ecological Society

                This is an open access article under the terms of the Creative Commons Attribution 4.0 License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 22 October 2013
                : 14 April 2014
                Categories
                Improving Methodological Approaches
                Review

                Ecology
                biodiversity conservation,capture–recapture models,detectability,detection probability,imperfect detection,monitoring,occupancy models,species richness

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