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242 results for “occupancy data”
Data from: Interspecific interactions among major carnivores in Panna Tiger Reserve: A multispecies occupancy approach
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Data and code for implementing time-to-detection occupancy model
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Data from: Occupancy winners in tropical protected forests: a pantropical analysis
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Data for: Considerations for fitting occupancy models to data from eBird and similar volunteer-collected data
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Data for: Occupancy–detection models with museum specimen data: Promise and pitfalls
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Data from: Improving inferences and predictions of species environmental responses with occupancy data
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Data from: Testing range-limit hypotheses using range-wide habitat suitability and occupancy for the scarlet monkeyflower (Erythranthe cardinalis)
Determining the causes of geographic range limits is a fundamental problem in ecology, evolution, and conservation biology. Range limits arise due to fitness and dispersal limitation, which yield contrasting predictions about habitat suitability and occupancy of suitable habitat across geographic ranges. If a range edge is limited primarily by fitness, occupancy of suitable habitat should be high, habitat suitability should decline towards the edge, and no suitable habitat should exist beyond it. In contrast, a range edge limited primarily by dispersal should have unoccupied but suitable habitat at and beyond the edge. We built ecological niche models relating occurrence records for the scarlet monkeyflower (Erythranthe cardinalis) to climatic variables, and applied these models to independent data from systematic, range-wide surveys of presence and absence to estimate the availability and occupancy of climatically suitable habitat. We found that fitness limitation predominated over dispersal limitation, but dispersal limitation also played a role at the poleward edge. These results are consistent with the hypothesis that dispersal limitation is more important along shallow environmental gradients and also suggest that synergy between dispersal and fitness limitation can contribute to colonization failure. The framework used here is validated by independent data and could be readily applied to inferring causes of range limits in many other species.
Data from: Validating dispersal distances inferred from autoregressive occupancy models with genetic parentage assignments
1.Dispersal distances are commonly inferred from occupancy data but have rarely been validated. Estimating dispersal from occupancy data is further complicated by imperfect detection and the presence of unsurveyed patches. 2.We compared dispersal distances inferred from seven years of occupancy data for 212 wetlands in a metapopulation of the secretive and threatened California black rail (Laterallus jamaicensis coturniculus) to distances between parent-offspring dyads identified with 16 microsatellites. 3.We used a novel autoregressive multi-season occupancy model that accounted for both unsurveyed patches and imperfect detection to quantify patch isolation using buffer radius (BRM) and incidence function (IFM) connectivity measures at 15 scales (1–10, 15, 20, 25, and 30 km). Connectivity measures were then fit as colonization covariates in occupancy models to estimate a model-averaged dispersal distance. 4.As predicted, colonization was more strongly related to connectivity at small spatial scales (< 10 km). AIC weights were greatest at 7 km for BRM and at 4 km for IFM. 5.Model-averaged dispersal distances (BRM = 7.46 km; IFM = 5.48 km) showed good agreement with the mean (± SE) dispersal distance from 23 parent-offspring dyads (5.58 ± 1.92 km), indicating reasonably accurate mean dispersal distances can be inferred from occupancy data when isolation strongly affects colonization.
Data from: Disentangling elevational richness: a multi-scale hierarchical Bayesian occupancy model of Colorado ant communities
Understanding the forces that shape the distribution of biodiversity across spatial scales is central in ecology and critical to effective conservation. To assess effects of possible richness drivers, we sampled ant communities on four elevational transects across two mountain ranges in Colorado, USA, with seven or eight sites on each transect and twenty repeatedly sampled pitfall trap pairs at each site each for a total of 90 days. With a multi-scale hierarchical Bayesian community occupancy model, we simultaneously evaluated the effects of temperature, productivity, area, habitat diversity, vegetation structure, and temperature variability on ant richness at two spatial scales, quantifying detection error and genus-level phylogenetic effects. We fit the model with data from one mountain range and tested predictive ability with data from the other mountain range. In total, we detected 105 ant species, and richness peaked at intermediate elevations on each transect. Species-specific thermal preferences drove richness at each elevation with marginal effects of site-scale productivity. Trap-scale richness was primarily influenced by elevation-scale variables along with a negative impact of canopy cover. Soil diversity had a marginal negative effect while daily temperature variation had a marginal positive effect. We detected no impact of area, land cover diversity, trap-scale productivity, or tree density. While phylogenetic relationships among genera had little influence, congeners tended to respond similarly. The hierarchical model, trained on data from the first mountain range, predicted the trends on the second mountain range better than multiple regression, reducing root mean squared error up to 65%. Compared to a more standard approach, this modeling framework better predicts patterns on a novel mountain range and provides a nuanced, detailed evaluation of ant communities at two spatial scales.
Data from: Distinguishing distribution dynamics from temporary emigration using dynamic occupancy models
1. Dynamic occupancy models are popular for estimating dynamic distribution rates (colonization and extinction) from repeated presence/absence surveys of unmarked animals. This approach assumes closure among repeated samples within primary periods, allowing estimation of dynamic rates between these periods. However, the impact of temporary emigration (reversible changes in sampling availability) on dynamic rate estimates, has not been tested. 2. Using simulated data, we investigated the degree to which temporary emigration could mislead researchers interested in quantifying dynamics. We then compared results from three avian point count datasets to evaluate the likelihood that temporary emigration confounds estimates of dynamics for 19 species under a popular sampling protocol. 3. Simulated experiments indicated that when secondary periods were open to temporary emigration, presence of dynamics was correctly identified ≥ 95.1% of the time, and dynamic rate estimates were accurate. However, dynamic rate estimates were biased when secondary periods were closed to temporary emigration. In empirical datasets, dynamic occupancy models had greater support than closed models for all species when secondary sampling periods occurred in immediate succession (i.e., 3 samples within 10 minutes); however, our results suggest that this is because these estimates were heavily influenced by temporary emigration. When counts within a primary period were separated by 24-48 hours, we found evidence of dynamics for less than half of these species. We recommend an alternative sampling approach that allows accurate estimation of dynamic rates when temporary emigration is of no interest, and introduce a novel model for estimating both processes simultaneously in rare cases where they are both of biological interest. 4. Concern for violating the occupancy modeling closure assumption has led to widespread recommendations that samples within primary periods be conducted extremely close in time. However, this may not be the best approach when interest is in quantifying dynamic rates. While dynamic occupancy models provide estimates of 'colonization' and 'extinction,' these values do not inherently represent dynamics unless temporary emigration has been explicitly modeled, or accounted for with sampling design. Naiveté to this fact can result in incorrect conclusions about biological processes.
Data from: Ultra-fine scale spatially-integrated mapping of habitat and occupancy using structure-from-motion
Organisms respond to and often simultaneously modify their environment. While these interactions are apparent at the landscape extent, the driving mechanisms often occur at very fine spatial scales. Structure-from-Motion (SfM), a computer vision technique, allows the simultaneous mapping of organisms and fine scale habitat, and will greatly improve our understanding of habitat suitability, ecophysiology, and the bi-directional relationship between geomorphology and habitat use. SfM can be used to create high-resolution (centimeter-scale) three-dimensional (3D) habitat models at low cost. These models can capture the abiotic conditions formed by terrain and simultaneously record the position of individual organisms within that terrain. While coloniality is common in seabird species, we have a poor understanding of the extent to which dense breeding aggregations are driven by fine-scale active aggregation or limited suitable habitat. We demonstrate the use of SfM for fine-scale habitat suitability by reconstructing the locations of nests in a gentoo penguin colony and fitting models that explicitly account for conspecific attraction. The resulting digital elevation models (DEMs) are used as covariates in an inhomogeneous hybrid point process model. We find that gentoo penguin nest site selection is a function of the topography of the landscape, but that nests are far more aggregated than would be expected based on terrain alone, suggesting a strong role of behavioral aggregation in driving coloniality in this species. This integrated mapping of organisms and fine scale habitat will greatly improve our understanding of fine-scale habitat suitability, ecophysiology, and the complex bi-directional relationship between geomorphology and habitat use.
Data from: Nine-banded Armadillo (Dasypus novemcinctus) occupancy and density across an urban to rural gradient
<p>The nine-banded Armadillo (<em>Dasypus novemcinctus</em>) is the only species of Armadillo in the United States and alters ecosystems by excavating extensive burrows used by many other wildlife species. Relatively little is known about its habitat use or population densities, particularly in developed areas, which may be key to facilitating its range expansion. We evaluated Armadillo occupancy and density in relation to anthropogenic and landcover variables in the Ozark Mountains of Arkansas along an urban to rural gradient. Armadillo detection probability was best predicted by temperature (positively) and precipitation (negatively). Contrary to expectations, occupancy probability of Armadillos was best predicted by slope (negatively) and elevation (positively) rather than any landcover or anthropogenic variables. Armadillo density varied considerably between sites (ranging from a mean of 4.88 – 46.20 Armadillos per km<sup>2</sup>) but was not associated with any environmental or anthropogenic variables.</p>
Data from: Kirtland's warbler occupancy and plantation density
<p>Early studies into the habitat preferences of the Kirtland's warbler (KW; <em>Setophaga kirtlandii</em>) suggested that these birds exhibited a preference for areas with high jack pine stem densities; therefore, jack pine plantations established as part of the KW recovery and conservation programs have been planted using a 1.5 x 1.8 m spacing (3,588 trees ha<sup>-1</sup>). In contrast, traditional pine plantations in the Lake States established for roundwood production are typically planted on a 2.1 x 2.4 m spacing that equates to 1,922 trees ha<sup>-1</sup>. Over more than 40 years, tree spacing in KW habitat plantations has gone largely unchanged, and until very recently there has never been an attempt to verify that these tighter spacings actually provide better KW habitat than would a traditional forestry spacing. We used a retrospective approach to assess the impacts of tree density on KW occupancy and observed an unexpected negative relationship between realized plantation density and maximum occupancy by KW singing males. This finding should be interpreted with caution due to the limited nature of this study; however, a lack of a positive relationship is entirely plausible given the narrow range of densities encountered in plantations, as well as the fact that uniform spacing of plantations should allow for the achievement of optimal jack pine cover at lower densities than would be required in a natural-origin stand.</p>
Data from: Camera traps reveal seasonal variation in activity and occupancy of the Alpine mountain hare (Lepus timidus varronis)
<p>Mountain hare is a cold-adapted species threatened by climate change, but despite its emblematic nature, our understanding of the causes of population decline remains limited. Camera traps are increasingly used in ecology as a tool for monitoring animal populations at large spatial and temporal scales. In mountain environments where field work is constrained by difficult access and harsh conditions, camera traps constitute a promising tool for surveying rare and elusive species such as the mountain hare. Our study explored the use of camera traps as a tool for studying seasonal habitat occupancy and daily activity patterns of the mountain hare, in order to carry out long-term monitoring of populations. We installed 46 camera traps along elevation gradients in the Mont-Blanc massif (France) from January 2018 to June 2022. We measured habitat variables at each camera trap site in order to define vegetation composition and habitat structure. We performed multi-season and single-season occupancy models to respectively describe habitat occupancy of the mountain hare throughout the year and identify the environmental variables influencing mountain hare presence during the breeding season. Mountain hares occupy coniferous forest in winter, and then switch to mixed areas of shrubland and grassland above treeline in spring and the beginning of summer. In spring, occupancy probability of the mountain hare increases with relative cover of mixed low shrub and herbaceous layer (i.e. the 10-40 cm vegetation layer), suggesting a link to food resources and protection from predation. Our results also confirm the nocturnal and crepuscular activity of the mountain hare during the breeding season, and strictly nocturnal activity in winter. Our results demonstrate the efficiency of camera traps as tools for monitoring mountain hare habitat occupancy in mountain environments and underline the importance of diverse habitat mosaics for the preservation of the species.</p>
Data from: Northern pikas experience reduced occupancy due to surrounding human land use despite the occurrence of suitable microclimates
<p>Aim: Despite warming temperatures, some species are found persisting at the trailing edge of their distribution. Microclimates provided by complex topography are considered a key factor in these cases of range stationarity, buffering stress from exposure to warming and enabling persistence. However, for species with trailing-edges located in human-modified landscapes, refugial conditions provided by microclimates could be disrupted by human activities. Here, we aimed to understand the determinants of trailing-edge occupancy for a small lagomorph found in rocky patches harboring cool microclimates.</p> <p>Location: Hokkaido Island, Japan</p> <p>Taxon: Northern pika (<em>Ochotona hyperborea</em>)</p> <p>Methods: We surveyed the occupancy of northern pikas across a wide elevational gradient (350–2200 m) for two consecutive summers. Ambient air and microhabitat (i.e., rock interstices) thermal conditions were measured to assess their relationship. We then analyzed their effects on occupancy at two nested spatial scales: (1) whole-distribution, and (2) at identified trailing-edge sites where we explored the effects of microclimates and surrounding human activities (i,e., distance to nearest road and area of human land use such as plantation forests or agricultural fields).</p> <p>Results: Overall, rock interstices exhibited cooler conditions than ambient air with temperature differences of 1–2 ºC. The overall distribution of northern pikas was affected by both mean ambient temperature and microhabitat availability, with warmer (lower elevation) sites with less microhabitats corresponding to the trailing edge of its distribution. Interestingly, trailing edge occupancy patterns were best explained by the negative effect of surrounding human land despite the existence of suitable microclimates in the rocky patches.</p> <p>Main conclusions: Our findings suggest that the local refugial conditions supported by cool microclimates are likely to be disrupted by the effects of human land at the larger landscape scale. This result highlights the importance of considering the effects of human activities and landscape alteration for effective microrefugia conservation. --</p>
Processed data for the analysis of human mobility changes from COVID-19 lockdown on bird occupancy in North Carolina, USA
<p>The COVID-19 pandemic lockdown worldwide provided a unique research opportunity for ecologists to investigate the human-wildlife relationship under abrupt changes in human mobility, also known as Anthropause. Here we chose 15 common non-migratory bird species with different levels of synanthrope and we aimed to compare how human mobility changes could influence the occupancy of fully synanthropic species such as House Sparrow (<em>Passer domesticus</em>) versus casual to tangential synanthropic species such as White-breasted Nuthatch (<em>Sitta carolinensis</em>). We extracted data from the eBird citizen science project during three study periods in the spring and summer of 2020 when human mobility changed unevenly across different counties in North Carolina. We used the COVID-19 Community Mobility reports from Google to examine how community mobility changes towards workplaces, an indicator of overall human movements at the county level, could influence bird occupancy.</p>
Dynamics of tree-cavity occupancy: Data and code
<h3>Supplementary data and code to the paper entitled “Resource suitability drives low use of avian-excavated tree cavities: a multi-state occupancy dynamics approach”</h3> <p> </p> <p>The following list indicates the names of files included as supplementary data and code, as well as a brief description of their content. File names are given by headings in italic, followed by content description.</p> <p> </p> <p><em>CavNestMisiones.rds</em> </p> <p>Contains the data used to fit the model in file <em>MSODynModel.R</em>. It includes the following objects:</p> <p> <strong>y</strong> An array with dimensions 452x20x16 showing the observed cavity states for each of 452 cavities, a maximum of 20 visits per cavity per year, and 16 years. This array contains NAs prior to the first year of cavity registration, after cavity loss, and in any year*visit combination for which there was no data for the corresponding cavity.</p> <p><strong>origen </strong>A vector with length 452 with ‘1’ for excavated and ‘2’ for non-excavated cavities.</p> <p> </p> <p><em>MSODynModel.R</em></p> <p>Model code including preliminary data processing, JAGS code for the dynamic multi-state occupancy model, and call to JAGS to fit the model. Model code includes posterior predictive checking for goodness-of-fit.</p> <p> </p> <p><em>MSMO60k.Rdata</em></p> <p>JAGs output with MCMC samples from the posterior probability distribution of model parameters.</p> <p> </p> <p><em>SimCavs.R</em></p> <p>Code for simulating cavity use.</p> <p> </p> <p><em>SimCavsFunctions.R</em></p> <p>Functions used in <em>SimCavs.R.</em></p>
Data from: Long-term trends in the occupancy of ants revealed through use of multi-sourced datasets
<p><span>We combined participatory science data and museum records to understand long-term changes in occupancy for 29 ant species in Denmark over 119 years. Bayesian occupancy modelling indicated change in occupancy for 15 species: five increased, four declined and six showed fluctuating trends. We consider how trends may have been influenced by life-history and habitat changes. Our results build on an emerging picture that biodiversity change in insects is more complex than implied by the simple insect decline narrative.</span></p>
Data from: Sequential use of niche and occupancy models identifies conservation and research priority areas for two data-poor endemic birds from the Colombian Andes
<p>The lack of high-quality information on data-poor species can hinder efforts to inform conservation actions via spatial distribution modeling. This is particularly true for tropical birds of conservation concern, for which ecological studies and assessments of their conservation status have received limited funding. Here we use a cost- and time-efficient protocol for assessing the distribution of range-restricted taxa and to identify priority areas for their conservation based on a sequential application of Environmental Niche Models (ENMs) and Occupancy-Detection Models. This approach first uses available geographical information and niche-theory to prioritize potential study sites, which can later be surveyed to obtain high-quality presence-absence data to accurately model distributional ranges with limited resources. We apply this protocol to identify priority areas for two Neotropical birds of conservation concern endemic to the Colombian Andes: Yellow-headed Brush-finch (<i>Atlapetes flaviceps</i>) and Tolima Dove (<i>Leptotila conoveri</i>). We first fitted ENMs using spatially-filtered datasets containing all available records up to 2018. We then conducted field surveys across climatically suitable areas identified for both species, carrying out a total of 1750 counts to generate input data for the occupancy models. Overall, our results suggested more extended and more continuous distribution ranges for both species than previously reported, but also identified population strongholds that are not currently represented within the national protected areas system. Both species occupied a narrow elevational belt (~1300–2600) of the Central Andes of Colombia primarily on the slopes of the Magdalena River valley, with isolated populations in the Western and Eastern Andes; these areas have undergone some of the most marked landscape transformations in Colombia. This straightforward protocol maximizes available information and minimizes costs, while allowing for estimation of occurrence probabilities for range-restricted, data-poor taxa.</p>
Data from: Sharing detection heterogeneity information among species in community models of occupancy and abundance can strengthen inference
<p>1. The estimation of abundance and distribution and factors governing patterns in these parameters is central to the field of ecology. The continued development of hierarchical models that best utilize available information to inform these processes is a key goal of quantitative ecologists. However, much remains to be learned about simultaneously modeling true abundance, presence, and trajectories of ecological communities.</p> <p>2. Simultaneous modeling of the population dynamics of multiple species provides an interesting mechanism to examine patterns in community processes and, as we emphasize herein, to improve species-specific estimates by leveraging detection information among species. Here we demonstrate a simple but effective approach to share information about observation parameters among species in hierarchical community abundance and occupancy models, where we use shared random effects among species to account for spatiotemporal heterogeneity in detection probability.</p> <p>3. We demonstrate the efficacy of our modeling approach using simulated abundance data, where we recover well our simulated parameters using N-mixture models. Our approach substantially increases precision in estimates of abundance compared to models that do not share detection information among species. We then expand this model, and apply it to repeated detection/non-detection data collected on six species of tits (Paridae) breeding at 119 1 km<sup>2</sup> sampling sites across a <em>P. montanus</em> hybrid zone in northern Switzerland (2004-2020). We find strong impacts of forest cover and elevation on population persistence and colonisation in all species. We also demonstrate evidence for interspecific competition on population persistence and colonization probabilities, where the presence of marsh tits reduces population persistence and colonisation probability of sympatric willow tits, potentially decreasing gene flow among willow tit subspecies.</p> <p>4. While conceptually simple, our results have important implications for the future modeling of population abundance, colonization, persistence, and trajectories in community frameworks. We suggest potential extensions of our modeling in this paper, and discuss how leveraging data from multiple species can improve model performance and sharpen ecological inference.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.