scholarly journals Species occupancy estimation and imperfect detection: shall surveys continue after the first detection?

2017 ◽  
Vol 101 (4) ◽  
pp. 381-398 ◽  
Author(s):  
Gurutzeta Guillera-Arroita ◽  
José J. Lahoz-Monfort
Keyword(s):  
Imperfect Detection ◽  
Occupancy Estimation ◽  
Species Occupancy

Predicting fish species richness and habitat relationships using Bayesian hierarchical multispecies occupancy models

2020 ◽  
Vol 77 (3) ◽  
pp. 602-610
Author(s):  
Shannon White ◽  
Evan Faulk ◽  
Caleb Tzilkowski ◽  
Andrew Weber ◽  
Matthew Marshall ◽  
...  
Keyword(s):  
Species Richness ◽  
Fish Community ◽  
Fish Assemblages ◽  
Similar Species ◽  
Occupancy Models ◽  
Imperfect Detection ◽  
Modeling Framework ◽  
Bayesian Hierarchical ◽  
Recreation Area ◽  
Species Occupancy

Understanding how stream fishes respond to changes in habitat availability is complicated by low occurrence rates of many species, which in turn reduces the ability to quantify species–habitat relationships and account for imperfect detection in estimates of species richness. Multispecies occupancy models have been used sparingly in the analysis of fisheries data, but address the aforementioned deficiencies by allowing information to be shared among ecologically similar species, thereby enabling species–habitat relationships to be estimated for entire fish communities, including rare species. Here, we highlight the utility of hierarchical multispecies occupancy models for the analysis of fish community data and demonstrate the modeling framework on a stream fish community dataset collected in the Delaware Water Gap National Recreation Area, USA. In particular, we demonstrate the ability of the modeling framework to make inferences at the species-, guild-, and community-levels, thereby making it a powerful tool for understanding and predicting how environmental variables influence species occupancy probabilities and structure fish assemblages.

scholarly journals The costs of ignoring species detectability on functional diversity estimation

The Auk ◽  
2020 ◽  
Vol 137 (4) ◽  
Author(s):  
Facundo Xavier Palacio ◽  
René E Maragliano ◽  
Diego Montalti
Keyword(s):  
Functional Diversity ◽  
Functional Divergence ◽  
Habitat Type ◽  
Species Traits ◽  
Bird Communities ◽  
Imperfect Detection ◽  
East Central ◽  
Functional Types ◽  
Functional Richness ◽  
Species Occupancy

Abstract Functional diversity (FD) approaches have been increasingly used to understand ecosystem functioning in bird communities. These approaches typically rely on the assumption that species are perfectly detected in the field, despite the fact that imperfect detection represents a ubiquitous source of bias in biodiversity studies. This may be notably important in FD studies, because detection may depend on the functional traits used to compute FD metrics. However, little effort has been devoted to account for imperfect detection in FD studies, and therefore the degree to which species traits and detectability affects FD remains poorly understood. We predict that observed FD metrics may either underestimate or overestimate detection-corrected FD, because FD has multiple independent dimensions with different data properties. We assessed whether detection was related to bird traits (body mass, diet, and foraging stratum), accounting for habitat type, season, and phylogeny. We then used a multi-species occupancy model to obtain detection-corrected FD metrics (functional richness [FRic], functional evenness [FEve], and functional divergence [FDiv]), and compared observed and detection-corrected FD estimates in bird communities from east-central Argentina. Some functional types of birds (raptors and insectivores) were more easily overlooked, whereas others (seed and leaf eaters) were more easily detected. Some observed FD metrics underestimated detection-corrected FD (FRic and FDiv), whereas some others (FEve) overestimated detection-corrected FD. Both observed and detection-corrected FRic revealed differences between seasons, but not between habitat types. However, detection-corrected FEve and FDiv showed differences between seasons, contrary to observed estimates. Our results indicate that failure to account for unequal ease of detecting species can lead to erroneous estimates of FD because some functional types of birds are more easily overlooked. We outline some guidelines to help ornithologists identifying under which circumstances detection may be a concern and warn against the indiscriminate use of FD metrics without accounting for species detection.

Using multistate occupancy estimation to model habitat use in difficult-to-sample watersheds: bridle shiner in a low-gradient swampy stream

2013 ◽  
Vol 70 (10) ◽  
pp. 1429-1437 ◽  
Author(s):  
Timothy Jensen ◽  
Jason C. Vokoun
Keyword(s):  
Habitat Use ◽  
Aquatic Organisms ◽  
Probability Of Detection ◽  
High Abundance ◽  
Occupancy Models ◽  
Imperfect Detection ◽  
Patch Occupancy ◽  
Rare Minnow ◽  
Occupancy Estimation ◽  
Bridle Shiner

We used multiseason, multistate patch occupancy models to investigate habitat use of a regionally rare minnow (bridle shiner, Notropis bifrenatus) within a difficult-to-sample, swampy stream system by defining occupancy states as coarse abundance categories (i.e., none, some, many). Habitat patches were repeatedly subsampled during three sampling periods spanning June to August 2011 using a nonstandard purse-and-lift method with a seine net, as poorly defined shorelines, unconsolidated substrate, and emergent vegetation limited beaching and restricted possible sampling locations. Detection probabilities increased from June to August, likely due to increasing catch per effort as age 0 became vulnerable to the gear, supported by the probability of detection being greater when the species was at high abundance, given occupancy. The probability of a habitat patch being occupied increased with the percent of macrophyte cover and decreased with increasing distance from another occupied patch. Decreasing mean depth showed a weak relationship to high abundance, given a patch was occupied. In summary, the multistate occupancy analytical approach was highly informative for developing quantitative habitat relationships and was seen as an effective framework for evaluating habitat use of aquatic organisms that inhabit environments inherently difficult to sample for which imperfect detection and sampling efficiency are of concern.

scholarly journals Improving species occupancy estimation when sampling violates the closure assumption

Ecography ◽  
2013 ◽  
Vol 36 (12) ◽  
pp. 1299-1309 ◽  
Author(s):  
Clint R. V. Otto ◽  
Larissa L. Bailey ◽  
Gary J. Roloff
Keyword(s):  
Occupancy Estimation ◽  
Species Occupancy ◽  
Closure Assumption

scholarly journals Validating metabarcoding-based biodiversity assessments with multi-species occupancy models: a case study using coastal marine eDNA

2019 ◽  
Author(s):  
Beverly McClenaghan ◽  
Zacchaeus G. Compson ◽  
Mehrdad Hajibabaei
Keyword(s):  
Model Comparison ◽  
Environmental Dna ◽  
Model Assessment ◽  
Occupancy Models ◽  
Ecological Inference ◽  
Biodiversity Data ◽  
Imperfect Detection ◽  
Coastal Marine ◽  
Species Occupancy

AbstractEnvironmental DNA (eDNA) metabarcoding is an increasingly popular method for rapid biodiversity assessment. As with any ecological survey, false negatives can arise during sampling and, if unaccounted for, lead to biased results and potentially misdiagnosed environmental assessments. We developed a multi-scale, multi-species occupancy model for the analysis of community biodiversity data resulting from eDNA metabarcoding; this model accounts for imperfect detection and additional sources of environmental and experimental variation. We present methods for model assessment and model comparison and demonstrate how these tools improve the inferential power of eDNA metabarcoding data using a case study in a coastal, marine environment. Using occupancy models to account for factors often overlooked in the analysis of eDNA metabarcoding data will dramatically improve ecological inference, sampling design, and methodologies, empowering practitioners with an approach to wield the high-resolution biodiversity data of next-generation sequencing platforms.

A field ecologist's guide to environmental DNA sampling in freshwater environments

2020 ◽  
Vol 40 (4) ◽  
pp. 641-651
Author(s):  
Emily F. McColl-Gausden ◽  
Andrew R. Weeks ◽  
Reid Tingley
Keyword(s):  
Environmental Samples ◽  
Environmental Dna ◽  
Single Species ◽  
Freshwater Ecosystems ◽  
False Positives ◽  
Imperfect Detection ◽  
Occupancy Detection ◽  
Multiple Species ◽  
Methodological Considerations ◽  
Species Occupancy

Environmental DNA, or eDNA—DNA shed from organisms and extracted from environmental samples—is an emerging survey technique that has the potential to transform biodiversity monitoring in freshwater ecosystems. We provide a brief overview of the primary methodological aspects of eDNA sampling that ecologists should consider before taking environmental samples in the field. We outline five key methodological considerations: (i) targeting single species vs multiple species; (ii) where and when to sample; (iii) how much water to collect; (iv) how many samples to take; and (v) recognising potential sources of false positives. The need to account for false negatives and false positives in eDNA surveys, and the power of species occupancy detection models in accounting for imperfect detection, is also discussed.

Two-Stage Bayesian Study Design for Species Occupancy Estimation

2014 ◽  
Vol 19 (2) ◽  
pp. 278-291 ◽  
Author(s):  
Gurutzeta Guillera-Arroita ◽  
Martin S. Ridout ◽  
Byron J. T. Morgan
Keyword(s):  
Study Design ◽  
Two Stage ◽  
Occupancy Estimation ◽  
Species Occupancy

An Investigation of Crowd Speech for Room Occupancy Estimation

2017 ◽  
Author(s):  
Siyuan Chen ◽  
Julien Epps ◽  
Eliathamby Ambikairajah ◽  
Phu Ngoc Le
Keyword(s):  
Occupancy Estimation

scholarly journals Population estimates of Antillean manatees in Puerto Rico: an analytical framework for aerial surveys using multi-pass removal sampling

2019 ◽  
Vol 100 (4) ◽  
pp. 1340-1349
Author(s):  
Jaime A Collazo ◽  
Matthew J Krachey ◽  
Kenneth H Pollock ◽  
Francisco J Pérez-Aguilo ◽  
Jan P Zegarra ◽  
...  
Keyword(s):  
Puerto Rico ◽  
Detection Probability ◽  
Analytical Framework ◽  
Population Estimates ◽  
High Concentration ◽  
Imperfect Detection ◽  
Factors Affecting ◽  
Management Actions ◽  
Aerial Surveys ◽  
Population Size Estimates

AbstractEffective management of the threatened Antillean manatee (Trichechus manatus manatus) in Puerto Rico requires reliable estimates of population size. Estimates are needed to assess population responses to management actions, and whether recovery objectives have been met. Aerial surveys have been conducted since 1976, but none adjusted for imperfect detection. We summarize surveys since 1976, report on current distribution, and provide population estimates after accounting for apparent detection probability for surveys between June 2010 and March 2014. Estimates in areas of high concentration (hotspots) averaged 317 ± 101, three times higher than unadjusted counts (104 ± 0.56). Adjusted estimates in three areas outside hotspots also differed markedly from counts (75 ± 9.89 versus 19.5 ± 3.5). Average minimum island-wide estimate was 386 ± 89, similar to the maximum estimate of 360 suggested in 2005, but fewer than the 700 recently suggested by the Puerto Rico Manatee Conservation Center. Manatees were more widespread than previously understood. Improving estimates, locally or island-wide, will require stratifying the island differently and greater knowledge about factors affecting detection probability. Sharing our protocol with partners in nearby islands (e.g., Cuba, Jamaica, Hispaniola), whose populations share genetic make-up, would contribute to enhanced regional conservation through better population estimates and tracking range expansion.El manejo efectivo del manatí antillano amenazado en Puerto Rico requiere estimados de tamaños de poblaciónes confiables. Dichas estimaciones poblacionales son necesarias para evaluar las respuestas a las acciones de manejo, y para determinar si los objetivos de recuperación han sido alcanzados. Se han realizado censos aéreos desde 1976, pero ninguno de ellos han sido ajustados para detecciones imperfectas. Aquí resumimos los censos desde 1976, actualizamos la distribución, y reportamos los primeros estimados poblacionales ajustados para la probabilidad de detección aparente en los censos de Junio 2010 a Marzo 2014. Las estimaciones poblacionales en áreas de mayor concentración del manatí promedió 317 ± 103, tres veces más abundante que los conteos sin ajuste (104 ± 0.56). Las estimaciones poblacionales en tres áreas fuera de las áreas de mayor concentración del manatí también fueron marcadamente diferentes (75 ± 9.89 vs 19.5 ± 3.5). El estimado mínimo poblacional en la isla entera fue de 386 ± 89, similar al estimado máximo de 360 sugerido en el año 2005, pero menor a los 700 sugeridos recientemente por el Centro de Conservación de Manatíes de Puerto Rico. Documentamos que el manatí tiene una distribución más amplia de lo que se sabía con anterioridad. El mejoramiento de los estimados poblacionales locales o a nivel de isla requerirá que se estratifique a la isla en forma diferente y que se investiguen los factores que influencian a la probabilidad de detección. Compartir protocolos como este con colaboradores de islas vecinas (por. ej., Cuba, Jamaica, Española), cuyas poblaciones de manatíes comparten material genético, contribuiría a la conservación regional mediante mejores estimaciones poblacionales y monitoreo de la expansión de su ámbito doméstico.

Sign in / Sign up

Export Citation Format

Share Document