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

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.

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The peri-urban leopards of Kathmandu: assessing determinants of presence and predation on domestic animals

Oryx ◽

10.1017/s0030605320000423 ◽

2021 ◽

pp. 1-10

Author(s):

Ashish Bista ◽

Pranav Chanchani ◽

Naresh Subedi ◽

Siddhartha B. Bajracharya

Keyword(s):

Habitat Use ◽

Land Use Planning ◽

Urban Areas ◽

Domestic Animals ◽

Agricultural Landscapes ◽

Urban Landscapes ◽

Occupancy Models ◽

Rapid Response Teams ◽

Imperfect Detection ◽

Remnant Forest

Abstract The conservation of large carnivores in human-dominated landscapes needs to be reconciled with the safety of humans and domestic animals. This is especially true for the leopard Panthera pardus, which occurs extensively in agricultural landscapes and remnant forest tracts embedded within peri-urban areas such as Kathmandu district in Nepal. We carried out interviews in 321 households in this district to determine the extent of leopard habitat use and predation on domestic animals (dogs and goats) during October 2015–April 2016. We used multi-state occupancy models, and estimated probabilities of leopard habitat use (Ψ1) and predation on domestic animals (Ψ2) as a function of covariates, while accounting for imperfect detection. Our findings indicate that the rapidly urbanizing outskirts of Kathmandu city are used extensively by leopards. The estimated probability of fine-scale habitat use in 2 km2 sample units was 0.96 ± SE 0.05 and the probability of predation on domestic animals was 0.76 ± SE 0.15. Leopard attacks occurred in areas with high vegetation cover and abundant goats. Addressing the problem of leopard attacks on domestic animals will require developing a comprehensive mitigation plan that includes educational activities to raise awareness, measures to address grievances of affected local communities, interventions to prevent attacks on livestock, compensation programmes, and rapid response teams to ensure human and animal welfare in conflict-prone areas. Land-use planning in these peri-urban landscapes needs to facilitate the safe sharing of space between people and leopards.

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Using areas of known occupancy to identify sources of variation in detection probability of raptors: taking time lowers replication effort for surveys

Royal Society Open Science ◽

10.1098/rsos.160368 ◽

2016 ◽

Vol 3 (10) ◽

pp. 160368 ◽

Cited By ~ 4

Author(s):

Campbell Murn ◽

Graham J. Holloway

Keyword(s):

Detection Probability ◽

Spatial Scales ◽

Survey Methods ◽

A Priori ◽

Low Density ◽

Occupancy Models ◽

Imperfect Detection ◽

Factors Affecting ◽

Sources Of Variation ◽

Time Of Year

Species occurring at low density can be difficult to detect and if not properly accounted for, imperfect detection will lead to inaccurate estimates of occupancy. Understanding sources of variation in detection probability and how they can be managed is a key part of monitoring. We used sightings data of a low-density and elusive raptor (white-headed vulture Trigonoceps occipitalis ) in areas of known occupancy (breeding territories) in a likelihood-based modelling approach to calculate detection probability and the factors affecting it. Because occupancy was known a priori to be 100%, we fixed the model occupancy parameter to 1.0 and focused on identifying sources of variation in detection probability. Using detection histories from 359 territory visits, we assessed nine covariates in 29 candidate models. The model with the highest support indicated that observer speed during a survey, combined with temporal covariates such as time of year and length of time within a territory, had the highest influence on the detection probability. Averaged detection probability was 0.207 (s.e. 0.033) and based on this the mean number of visits required to determine within 95% confidence that white-headed vultures are absent from a breeding area is 13 (95% CI: 9–20). Topographical and habitat covariates contributed little to the best models and had little effect on detection probability. We highlight that low detection probabilities of some species means that emphasizing habitat covariates could lead to spurious results in occupancy models that do not also incorporate temporal components. While variation in detection probability is complex and influenced by effects at both temporal and spatial scales, temporal covariates can and should be controlled as part of robust survey methods. Our results emphasize the importance of accounting for detection probability in occupancy studies, particularly during presence/absence studies for species such as raptors that are widespread and occur at low densities.

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A sparse observation model to quantify species interactions in time and space

10.1101/815027 ◽

2019 ◽

Author(s):

Sadoune Ait Kaci Azzou ◽

Liam Singer ◽

Thierry Aebischer ◽

Madleina Caduff ◽

Beat Wolf ◽

...

Keyword(s):

Species Interactions ◽

Activity Patterns ◽

Niche Partitioning ◽

Camera Trap ◽

Camera Traps ◽

Observation Model ◽

Occupancy Models ◽

Time And Space ◽

Imperfect Detection ◽

Mobile Species

SummaryCamera traps and acoustic recording devices are essential tools to quantify the distribution, abundance and behavior of mobile species. Varying detection probabilities among device locations must be accounted for when analyzing such data, which is generally done using occupancy models. We introduce a Bayesian Time-dependent Observation Model for Camera Trap data (Tomcat), suited to estimate relative event densities in space and time. Tomcat allows to learn about the environmental requirements and daily activity patterns of species while accounting for imperfect detection. It further implements a sparse model that deals well will a large number of potentially highly correlated environmental variables. By integrating both spatial and temporal information, we extend the notation of overlap coefficient between species to time and space to study niche partitioning. We illustrate the power of Tomcat through an application to camera trap data of eight sympatrically occurring duiker Cephalophinae species in the savanna - rainforest ecotone in the Central African Republic and show that most species pairs show little overlap. Exceptions are those for which one species is very rare, likely as a result of direct competition.

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

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/cjfas-2019-0125 ◽

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.

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Application of Stochastic Patch Occupancy Models to Real Metapopulations

Ecology, Genetics and Evolution of Metapopulations ◽

10.1016/b978-012323448-3/50007-6 ◽

2004 ◽

pp. 105-132 ◽

Cited By ~ 29

Author(s):

Rampal S. Etienne ◽

Cajo J.F. ter Braak ◽

Claire C. Vos

Keyword(s):

Occupancy Models ◽

Patch Occupancy

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Patch-occupancy survey of elephant (Loxodonta africana) surrounding Livingstone, Zambia

Koedoe ◽

10.4102/koedoe.v59i1.1372 ◽

2017 ◽

Vol 59 (1) ◽

Author(s):

David A. Youldon ◽

Jackie Abell ◽

Joanne S. Briffitt ◽

Lackson Chama ◽

Michaela D. Channings ◽

...

Keyword(s):

Habitat Use ◽

National Park ◽

Species Abundance ◽

Patch Occupancy ◽

The North ◽

Core Habitat ◽

Abundance Estimates ◽

Ranging Behaviour ◽

Regular Sampling ◽

Human Wildlife Conflict

Wild elephants represent the biggest human–wildlife conflict issue in Livingstone, Zambia. However, little is known about their movements. This survey investigated elephants’ habitat use outside a core protected and fenced zone that forms part of Mosi-oa-Tunya National Park, Zambia. Using ‘patch-occupancy’ methodology, indications of elephant presence (feeding behaviour, dung and tracks) were surveyed. The survey aimed to assist proposed future monitoring exercises by defining the geographical extent that should be considered to improve accuracy in species abundance estimates. Results were supplemented using collected indications of elephant presence from prior monitoring exercises, and during this survey. Elephant presence was confirmed up to 8 km from the boundary of the protected core habitat, focussed in: (1) an unfenced zone of the national park, (2) along a road leading from the national park to the Dambwa Forest to the north and (3) along two rivers located to the west (Sinde River) and east (Maramba River) of the core area. Detection probability of elephant presence was high using these methods, and we recommend regular sampling to determine changes in habitat use by elephants, as humans continue to modify land-use patterns.Conservation implications: Identification of elephant ranging behaviour up to 8 km outside of the Mosi-oa-Tunya National Park in southern Zambia will assist in managing human– elephant conflict in the area, as well as in assessing this seasonal population’s abundance.

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Migration patterns and seasonal forest use by birds in the Brazilian Pantanal

Bird Conservation International ◽

10.1017/s0959270916000290 ◽

2017 ◽

Vol 27 (3) ◽

pp. 371-387 ◽

Cited By ~ 7

Author(s):

JOÃO BATISTA DE PINHO ◽

MÔNICA ARAGONA ◽

KARLO YOSHIHIRO PIOTO HAKAMADA ◽

MIGUEL ÂNGELO MARINI

Keyword(s):

Habitat Use ◽

Bird Species ◽

Occupancy Models ◽

Neotropical Forests ◽

Migration Patterns ◽

Point Counts ◽

Run Off ◽

Forest Use ◽

Migratory Patterns ◽

Landscape Units

SummaryThe use of forest habitats and migratory patterns are still unclear for tropical birds. Some are described herein for the Pantanal wetlands of Brazil. Thus, our aim was to describe different patterns of forest habitat use by birds and classify the birds’ migration patterns for the northern Pantanal region, Brazil. From September 1999 to December 2003, we sampled four forest types, during which we collected standardised data with mist-net captures and point counts, with additional ad lib. observations. We recorded 214 bird species: 113 (52.8%) were total habitat generalists; 41 (19.2%) were forest generalists; 19 (8.9%) were flooded habitat specialists; and 28 (13.1%) were not classified due to the low number of records; three other categories of habitat use divide the remaining 6% of records. About half of the species showed some migratory behaviour, these were classified by us according to the season they spent in the area: 121 species (56.5%) as residents, 28 (13.1%) as run-off and dry migrants, 11 (5.1%) as run-off (winter) migrants, eight (3.7%) as dry (breeding) migrants, eight (3.7%) as dry and flooding (summer) migrants, eight (3.7%) as flooding migrants, three (1.4%) as flooding and run-off migrants, and 27 (12.6%) as uncommon. We constructed community occupancy models with six of the eight patterns of migration described; flooding migrants and run-off migrants were not modelled since the few species recorded also had very few detections. As expected, the model confirmed that species from all six tested migration patterns arrive and depart from the Pantanal across the seasons. Contrary to most Neotropical forests, there was a high percentage (43.5%) of non-resident species. The results show the need of investing heavily in preserving different landscape units within the Pantanal, but also in the surrounding Cerrado region, in order to conserve resident and short distance intra-tropical migrants.

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Determining carnivore habitat use in a rubber/forest landscape in Brazil using multispecies occupancy models

PLoS ONE ◽

10.1371/journal.pone.0195311 ◽

2018 ◽

Vol 13 (4) ◽

pp. e0195311 ◽

Cited By ~ 4

Author(s):

Andrea Dechner ◽

Kevin M. Flesher ◽

Catherine Lindell ◽

Téo Vega de Oliveira ◽

Brian A. Maurer

Keyword(s):

Habitat Use ◽

Forest Landscape ◽

Occupancy Models

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Habitat Occupancy by Spruce Grouse (Canachites canadensis) in the south of its range, Québec, Canada

Canadian Journal of Zoology ◽

10.1139/cjz-2021-0115 ◽

2021 ◽

Author(s):

Clara Casabona i Amat ◽

Pierre Blanchette ◽

André Desrochers

Keyword(s):

Bird Species ◽

Probability Of Detection ◽

Coniferous Forests ◽

Range Limit ◽

Isolated Populations ◽

Imperfect Detection ◽

Occupancy Modelling ◽

Habitat Occupancy ◽

Management Measures ◽

Temperate Deciduous Forests

Studying habitat occupancy at the margins of species’ distributions can be helpful in clarifying species’ requirements and planning management measures. Spruce grouse (Canachites canadensis Linnaeus, 1758), a bird species associated with northern short-needle coniferous forests in North America, has its southeastern range limit where coniferous forests are mixed with temperate deciduous forests and agricultural lands. Some isolated populations are found in these habitats. Using a single-season occupancy modelling approach, we investigated habitat use by spruce grouse, accounting for imperfect detection, in the lowlands of the St. Lawrence River in southern Québec, Canada. We conducted call-response spruce over three years at 279 sites (59 sites in 2007, 100 sites in 2008 and 120 sites in 2009). At the site level, the probability of occupancy was 21% (IC: 10.7% - 37.9%) and probability of detection was 54% (IC: 34.7% - 73.0%). Based on the covariates in the models, occurrence increased with higher cover of coniferous trees and low deciduous shrubs, and decreased with higher cover of deciduous trees. Finally, detection probability was highest at the beginning of the survey (50% in late April) and was influenced by year.

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