Explaining the birds and the bees: deriving habitat restoration targets from multi‐species occupancy models

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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Model selection and assessment for multi-species occupancy models

Ecology ◽

10.1890/15-1471.1 ◽

2016 ◽

Vol 97 (7) ◽

pp. 1759-1770 ◽

Cited By ~ 54

Author(s):

Kristin M. Broms ◽

Mevin B. Hooten ◽

Ryan M. Fitzpatrick

Keyword(s):

Model Selection ◽

Occupancy Models ◽

Species Occupancy ◽

Selection And Assessment

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Designing an occupancy framework to monitor an endemic rainforest duck: Methodological and modelling considerations

10.1101/2020.02.03.931543 ◽

2020 ◽

Author(s):

Shah Nawaz Jelil ◽

Murchana Parasar ◽

Laura Cancino ◽

Kimberly Cook

Keyword(s):

Detection Probability ◽

Site Occupancy ◽

Optimal Number ◽

Occupancy Models ◽

Occupancy Detection ◽

Habitat Factors ◽

Long Term Ecological Research ◽

Species Occupancy ◽

Future Population

AbstractUnderstanding species trend, decline or growth, is vital to further conservation efforts. Species-habitat relationship studies are equally important for conservation as it helps in understanding the habitat a particular species depends upon, i.e. habitat conservation. However, rare and endemic species are inherently difficult to study and occupancy models are especially useful in such cases. We conducted the first detection, non-detection survey for the white winged duck in Dehing Patkai Wildlife Sanctuary, India to assess site occupancy and test habitat factors that explain its occupancy. We found that white winged duck occupancy was low (0.27 ± 0.21 SE) and detection probability was 0.44 ± 0.30 SE. We found that increasing tree richness and decreasing elevation increased species occupancy. Detection probability was influenced by our effort in that detection increased with increasing number of survey hours. Using two standard approaches, we estimated the optimal number of sites and replicate surveys for future occupancy studies. We further present considerations for future surveys. Considering the sporadic and fragmented information available, we recommend long-term ecological research to better understand the present and future population trends of the species.

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Dynamic multi-species occupancy models of birds of high-altitude grasslands in eastern South Africa

10.7287/peerj.preprints.26932 ◽

2018 ◽

Author(s):

David H Maphisa ◽

Hanneline Smit_Robinson ◽

Res Altwegg

Keyword(s):

High Altitude ◽

Habitat Preferences ◽

Bird Species ◽

Bird Diversity ◽

Grass Cover ◽

Occupancy Models ◽

Occupancy Dynamics ◽

Pumped Storage ◽

Species Occupancy ◽

High Altitude Grasslands

Moist, high-altitude grasslands of eastern South African harbour rich avian diversity and endemism. This area is also threatened by increasingly intensive agriculture and land conversion for energy production. This conflict is particularly evident at Ingula, an Important Bird and Biodiversity Area located within the least conserved high-altitude grasslands and which is also the site of a new Pumped Storage Scheme. The new management seeks to maximise biodiversity through manipulation of the key habitat variables: grass height and grass cover through burning and grazing to make habitat suitable for birds. However, different species have individual habitat preferences, which further vary through the season. We used a dynamic multi-species occupancy model to examine the seasonal occupancy dynamics of 12 common grassland bird species and their habitat preferences. We estimated monthly occupancy, colonisation and persistence in relation to grass height and grass cover throughout the summer breeding season of 2011/12. For majority of these species, at the beginning of the season occupancy increased with increasing grass height and decreased with increasing grass cover. Persistence and colonisation decreased with increasing grass height and cover. However, the 12 species varied considerably in their responses to grass height and cover. Our results suggest that management should aim to provide plots which vary in grass height and cover to maximise bird diversity. We also conclude that the decreasing occupancy with increasing grass cover and low colonisation with increasing grass height and cover is a results of little grazing on our study site. We further conclude some of the 12 selected species are good indicators of habitat suitability more generally because they represent a range of habitat needs and are relatively easy to monitor.

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A Network Extension of Species Occupancy Models in a Patchy Environment Applied to the Yosemite Toad (Anaxyrus canorus)

PLoS ONE ◽

10.1371/journal.pone.0072200 ◽

2013 ◽

Vol 8 (8) ◽

pp. e72200 ◽

Cited By ~ 10

Author(s):

Eric L. Berlow ◽

Roland A. Knapp ◽

Steven M. Ostoja ◽

Richard J. Williams ◽

Heather McKenny ◽

...

Keyword(s):

Patchy Environment ◽

Occupancy Models ◽

Yosemite Toad ◽

Species Occupancy ◽

Anaxyrus Canorus ◽

Network Extension

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Spatial Gaussian processes improve multi‐species occupancy models when range boundaries are uncertain and nonoverlapping

Ecology and Evolution ◽

10.1002/ece3.7629 ◽

2021 ◽

Author(s):

Wilson J. Wright ◽

Kathryn M. Irvine ◽

Thomas J. Rodhouse ◽

Andrea R. Litt

Keyword(s):

Gaussian Processes ◽

Occupancy Models ◽

Species Occupancy

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Peer Review #2 of "Dynamic multi-species occupancy models reveal individualistic habitat preferences in a high-altitude grassland bird community (v0.1)"

10.7287/peerj.6276v0.1/reviews/2 ◽

2019 ◽

Keyword(s):

High Altitude ◽

Peer Review ◽

Habitat Preferences ◽

Bird Community ◽

Occupancy Models ◽

Grassland Bird ◽

High Altitude Grassland ◽

Species Occupancy

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Living in the concrete jungle: carnivore spatial ecology in urban parks

10.1101/2020.06.09.142935 ◽

2020 ◽

Author(s):

Siria Gámez ◽

Nyeema C. Harris

Keyword(s):

Spatial Ecology ◽

Interspecific Interactions ◽

Spatial Association ◽

Occupancy Models ◽

Urocyon Cinereoargenteus ◽

Anthropogenic Pressures ◽

Red Foxes ◽

Striped Skunk ◽

Species Occupancy ◽

Human Shield

ABSTRACTPeople and wildlife are living in an increasingly urban world, replete with unprecedented human densities, sprawling built environments, and altered landscapes. Such anthropogenic pressures can affect multiple processes within an ecological community, from spatial patterns to interspecific interactions. We tested two competing hypotheses, human shields versus human competitors, to characterize how humans affect the carnivore community using multi-species occupancy models. From 2017-2020, we conducted the first camera survey of city parks in Detroit, Michigan, and collected spatial occurrence data of the local native carnivore community. Our 12,106-trap night survey captured detected data for coyotes (Canis latrans), red foxes (Vulpes vulpes), gray foxes (Urocyon cinereoargenteus), raccoons (Procyon lotor), and striped skunks (Mephitis mephitis). Overall occupancy varied across species (Ψcoyote=0.40, Ψ raccoon=0.54, Ψred fox =0.19, Ψstriped skunk =0.09). Contrary to expectations, humans did not significantly affect individual occupancy for these urban carnivores. However, co-occurrence between coyote and skunk only increased with human activity. The observed positive spatial association between an apex and subordinate pair supports the human shield hypothesis. Our findings demonstrate how urban carnivores can exploit spatial refugia and coexist with humans in the cityscape.

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Relative species abundance and population densities of the past; developing multi-species occupancy models for fossil data

10.22541/au.163254515.50135373/v1 ◽

2021 ◽

Author(s):

Trond Reitan ◽

Torbjørn Ergon ◽

Lee Hsiang Liow

Keyword(s):

Species Abundance ◽

Biased Sampling ◽

Occupancy Models ◽

Geological Time ◽

Population Densities ◽

Time Intervals ◽

Relative Population ◽

Modelling Framework ◽

Wide Range ◽

Species Occupancy

The number of individuals of species within communities varies, but estimating abundance, given incomplete and biased sampling, is challenging. Here, we describe a new occupancy model in a hierarchical Bayesian framework with random effects, where multi-species occupancy and detection are modeled as a means to estimate relative species abundance and relative population densities. The modelling framework is suited for occupancy data for temporal samples of fossil communities with repeated sampling including multiple species with similar preservation potential. We demonstrate our modelling framework using a fossil community of benthic organisms to estimate changing relative species abundance dynamics and relative population densities of focal species in 9 (geological) time-intervals over 2.3 million years. We also explored potential explanatory factors (paleoenvironmental proxies) and temporal autocorrelation that could provide extra information on unsampled time-intervals. The modelling framework is applicable across a wide range of questions on species-level dynamics in (palaeo)ecological community settings.

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