Estimating Site Occupancy, Colonization, and Local Extinction When a Species Is Detected Imperfectly

MacKenzie, Darryl I.; Nichols, James D.; Hines, James E.; Knutson, Melinda G.; Franklin, Alan B.

doi:10.1890/02-3090

Cited by 1,457 publications

(1,737 citation statements)

References 19 publications

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“…This model can then be compared with the standard occupancy model, which is identical in all respects except that the false positive is fixed to take the value 0 (see MacKenzie et al 2003;Royle and Kéry 2007). Under this model, the proportion of occupied sites p t fs can be calculated in the same way, but in the presence of potential random movements into and out of sites, is interpreted as proportional utilisation (the proportion of sites used by the species).…”

Section: State-space Occupancy Model Allowing For False Positivesmentioning

confidence: 99%

Accounting for false positive detection error induced by transient individuals

2013

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Context. In metapopulations, colonisation is the result of dispersal from neighbouring occupied patches, typically juveniles dispersing from natal to breeding sites. When occupancy dynamics are dispersal driven, occupancy should refer to the presence of established, breeding populations. The detection of transient individuals at sites that are, by definition, unoccupied (i.e. false positive detections), may result in misleading conclusions about metapopulation dynamics. Until recently, the issue of false positives has been considered negligible and current efforts to account for such error have been restricted to the context of species misidentification. However, the detection of transient individuals visiting multiple sites while dispersing is a distinct source of false positives that can bias estimates of occupancy because visited sites do not contribute to metapopulation dynamics in the same way as do sites occupied by established, reproducing populations. Although transient-induced false positive error presents a challenge to occupancy studies aiming to account for all sources of detection error and estimate occupancy without bias, accounting for it has received little attention.Aims. Using a novel application of an existing occupancy model, we sought to account for false positives that result from transient individuals being observed at truly unoccupied sites (i.e. where no establishment has occurred).Methods. We applied a Bayesian multi-season occupancy model correcting for false negative and false positive errors, to 3 years of detection or non-detection data from a metapopulation of water voles, Arvicola amphibious, in which both types of patch-state misclassification are suspected.Key results. We provide evidence that transient individuals can cause false positive detection errors. We then demonstrate the flexibility of the occupancy model to account for both false negative and false positive detection errors beyond the typical application to species misidentification. Accounting for both types of observation error reduces the bias in estimates of occupancy and avoids misleading conclusions about the status of (meta) populations by allowing for the distinction to be made between resident and transient occupancy.Conclusion. In many species, transience may result in patch-state misclassification which needs to be accounted for so as to draw correct inference about metapopulation status. Making the distinction between occupancy by established populations and visitation by transients will influence how we interpret patch occupancy dynamics, with important implications for the management of wildlife.Implications. The ability to estimate occupancy free of bias induced by false positive detections can help ensure that downward trends in occupancy are detected despite such declines being accompanied by increasing frequency of transients associated with, for example, reductions in mate availability or failure to establish. Our approach can be applied to any occupancy study in which false positive detecti...

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Section: State-space Occupancy Model Allowing For False Positivesmentioning

confidence: 99%

Accounting for false positive detection error induced by transient individuals

2013

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“…We utilized the robust design occupancy model framework (MacKenzie et al 2003) in Program MARK (White and Burnham 1999) to evaluate site occupancy and movement dynamics of odonates in response to landscape characteristics. Robust design occupancy models relax the assumption of single-season occupancy models that sites are closed to changes in occupancy state during the sampling interval, therefore allowing the evaluation of site occupancy dynamics over time by assuming that changes in occupancy state may occur during primary sampling periods but remain static during secondary sampling periods (MacKenzie et al 2002(MacKenzie et al , 2003.…”

Section: Occupancy Modelsmentioning

confidence: 99%

“…Robust design occupancy models relax the assumption of single-season occupancy models that sites are closed to changes in occupancy state during the sampling interval, therefore allowing the evaluation of site occupancy dynamics over time by assuming that changes in occupancy state may occur during primary sampling periods but remain static during secondary sampling periods (MacKenzie et al 2002(MacKenzie et al , 2003. In addition to site occupancy probability (ψ) and detection probability (p), robust-design occupancy models also estimate the probability of site colonization (γ) and the probability of site extinction (ε).…”

Section: Occupancy Modelsmentioning

confidence: 99%

“…In addition to site occupancy probability (ψ) and detection probability (p), robust-design occupancy models also estimate the probability of site colonization (γ) and the probability of site extinction (ε). Site colonization probability is defined as the probability a site becomes occupied at time t + 1 given it is not occupied at time t (MacKenzie et al 2003).…”

Section: Occupancy Modelsmentioning

confidence: 99%

“…Conversely, site extinction probability is the probability a site becomes unoccupied at time t + 1 given it is occupied at time t (MacKenzie et al 2003).…”

Section: Occupancy Modelsmentioning

confidence: 99%

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Evaluating the effects of landscape configuration on site occupancy and movement dynamics of odonates in Iowa

2014

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Odonates contribute highly to global biodiversity and are considered good indicators of environmental quality, but they are under-studied and quantitative information on their habitat associations is lacking. Our objective was to examine the effects of landscape configuration on site occupancy and movement dynamics of four odonate species in Iowa: Tramea onusta, Epitheca princeps, Pantala flavescens, and Calopteryx maculata. We conducted standardized visual encounter surveys for odonates at 233 public properties in Iowa from 2007 to 2011 and computed landscape variables within a 200, 600 m, and 1 km radius of each surveyed site. Using a robust design occupancy model in Program MARK, we estimated detection probability and site occupancy, site extinction, and site colonization probabilities for each species. We found few significant effects of landscape variables on site occupancy, extinction, or colonization, although landscape variables at 600 m were included in the best model for all species. Detection probability (SE) ranged from 0.30 (0.04) for Pantala flavescens to 0.49 (0.04) for Calopteryx maculata. Our study provides information to aid habitat restoration and management efforts on sites having suitable characteristics in the surrounding landscape and ultimately help conserve odonates. 2 AbstractOdonates contribute highly to global biodiversity and are considered good indicators of environmental quality, but they are under-studied and quantitative information on their habitat associations is lacking. Our objective was to examine the effects of landscape configuration on site occupancy and movement dynamics of four odonate species

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Demographic and spatial responses of resident bird populations to the arrival of migratory birds within an urban environment

et al. 2019

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Long-distance migration allows many bird species to overcome the severe climatic changes that occur in seasonal environments. Migration is highly demanding, and given its cyclical nature, we currently know that it has substantial effects on the population parameters of migratory birds during both breeding and wintering seasons. However, the potential effects of the presence of migratory birds in their wintering grounds on populations of resident birds have remain largely unexplored. Here, we propose the hypothesis that migratory birds negatively affect the habitat occupancy and population abundance of resident birds because of the arrival of numerous individuals during the most limiting months of the year. Here, we studied different species of migratory and resident birds that coexist during winter in an urban ecological reserve located within Mexico City. We used single-species multiseason occupancy models, two-species occupancy models, and distance sampling techniques to evaluate changes in occupancy and population density of resident bird species during three consecutive winters. We found an aggregation pattern between two resident species (Psaltriparus minimus and Thryomanes bewickii) with three migratory warblers (Cardellina pusilla, Setophaga coronata and Setophaga townsendi). Thus, our results provide evidence of the formation of mixed-species flocks in our study area. We also conclude that resident birds experience different demographic and behavioral processes during winter that not necessarily result from interspecific interactions with migratory birds. K E Y W O R D Sdistance sampling, long-distance migration, occupancy models, population density, resident birds

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Estimating Site Occupancy, Colonization, and Local Extinction When a Species Is Detected Imperfectly

Cited by 1,457 publications

References 19 publications

Accounting for false positive detection error induced by transient individuals

Accounting for false positive detection error induced by transient individuals

Evaluating the effects of landscape configuration on site occupancy and movement dynamics of odonates in Iowa

Demographic and spatial responses of resident bird populations to the arrival of migratory birds within an urban environment

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