Comparing estimates of population change from occupancy and mark–recapture models for a territorial species

Building engineers and managers often treat occupants as passive agents despite their important role in building energy performance. Meanwhile, neglecting occupants' preferences may lead to poor implementations of building controls. The overall goal of this research is to improve buildings' energy performance and occupants' satisfaction by considering occupant-building interactions. This research first assessed the impact of static and dynamic occupant modelling approaches in a simulation-based analysis using the existing occupant models. The results showed the discrepancies between these two approaches in predicting the energy performance. The analysis emphasized the importance of using dynamic modelling approach. Given that the existing occupant models are context-specific, the next steps of this research focused on conducting a monitoring campaign. Therefore, the various monitoring methods exist in the literature and the anecdotal evidence were critically reviewed. Among the methods, environmental conditions are more controllable as well as configuring building designs and control systems are more flexible with laboratories and virtual environments. However, researchers can achieve valuable information on the natural occupants' presence and behaviour by in-situ monitoring on a relatively large sample size at a lower cost in long-term studies. This research adopted the in-situ method in a case study.

Understanding how wide-ranging animals use landscapes in which human use is highly heterogeneous is important for determining patterns of human–wildlife conflict and designing mitigation strategies. Here, we show how biological sign surveys in forested components of a human-dominated landscape can be combined with human interviews in agricultural portions of a landscape to provide a full picture of seasonal use of different landscape components by wide-ranging animals and resulting human–wildlife conflict. We selected Asian elephants (Elephas maximus) in Nepal to illustrate this approach. Asian elephants are threatened throughout their geographic range, and there are large gaps in our understanding of their landscape-scale habitat use. We identified all potential elephant habitat in Nepal and divided the potential habitat into sampling units based on a 10 km by 10 km grid. Forested areas within grids were surveyed for signs of elephant use, and local villagers were interviewed regarding elephant use of agricultural areas and instances of conflict. Data were analyzed using single-season and multi-season (dynamic) occupancy models. A single-season occupancy model applied to data from 139 partially or wholly forested grid cells estimated that 0.57 of grid cells were used by elephants. Dynamic occupancy models fit to data from interviews across 158 grid cells estimated that monthly use of non-forested, human-dominated areas over the preceding year varied between 0.43 and 0.82 with a minimum in February and maximum in October. Seasonal patterns of crop raiding by elephants coincided with monthly elephant use of human-dominated areas, and serious instances of human–wildlife conflict were common. Efforts to mitigate human–elephant conflict in Nepal are likely to be most effective if they are concentrated during August through December when elephant use of human-dominated landscapes and human–elephant conflict are most common.

Strategic conservation efforts for cryptic species, especially bats, are hindered by limited understanding of distribution and population trends. Integrating long‐term encounter surveys with multi‐season occupancy models provides a solution whereby inferences about changing occupancy probabilities and latent changes in abundance can be supported. When harnessed to a Bayesian inferential paradigm, this modeling framework offers flexibility for conservation programs that need to update prior model‐based understanding about at‐risk species with new data. This scenario is exemplified by a bat monitoring program in the Pacific Northwestern United States in which results from 8 years of surveys from 2003 to 2010 require updating with new data from 2016 to 2018. The new data were collected after the arrival of bat white‐nose syndrome and expansion of wind power generation, stressors expected to cause population declines in at least two vulnerable species, little brown bat (Myotis lucifugus) and the hoary bat (Lasiurus cinereus). We used multi‐season occupancy models with empirically informed prior distributions drawn from previous occupancy results (2003–2010) to assess evidence of contemporary decline in these two species. Empirically informed priors provided the bridge across the two monitoring periods and increased precision of parameter posterior distributions, but did not alter inferences relative to use of vague priors. We found evidence of region‐wide summertime decline for the hoary bat (λ^ = 0.86 ± 0.10) since 2010, but no evidence of decline for the little brown bat (λ^ = 1.1 ± 0.10). White‐nose syndrome was documented in the region in 2016 and may not yet have caused regional impact to the little brown bat. However, our discovery of hoary bat decline is consistent with the hypothesis that the longer duration and greater geographic extent of the wind energy stressor (collision and barotrauma) have impacted the species. These hypotheses can be evaluated and updated over time within our framework of pre–post impact monitoring and modeling. Our approach provides the foundation for a strategic evidence‐based conservation system and contributes to a growing preponderance of evidence from multiple lines of inquiry that bat species are declining.

Source-sink dynamics refer to systems with some units as sources of juveniles, and others as sinks. The same pattern can theoretically occur at a small spatial scale, within single populations. Under these circumstances, varying quality of breeding habitats/territories determines different levels of survival and/or reproduction, which in turn result in varying contributions of territories to the population dynamics. Territory occupancy has been proposed as an indirect measure of habitat quality. Here, we used territory occupancy and productivity from a long-termmonitoring of an Eagle Owl Bubo bubo population in NW Italy to (i) show how different contributions to population dynamicsmay characterize territories over limited geographical scale in a strongly territorial species, and (ii) investigate the potential use of territory occupancy as a proxy for habitat quality in this species. Three out of 10 territories appeared to producemost fledglings (potential sources), whereas the others were characterized by extremely low productivity (possible sinks). The overall productivity is likely to nearly balancemortality, but the general equilibriummasks complex variation in the contributions of territories to the population dynamic. Territory occupancywas affected by average productivity, and thus long-term occupancy could be used as a proxy for habitat quality. In long-lived and scarce territorial species, such as the Eagle Owl, preservation of suitable conditions at key territories can be crucial for the population survival.

Occupancy‐based monitoring has become an important tool in wildlife conservation and management. Nonetheless, meeting occupancy modeling assumptions and providing biologically accurate information are difficult tasks over long time periods, large areas, or when monitoring multiple species. In occupancy modeling frameworks, derived grids are commonly used to divide landscapes into discrete units. Grid sizes that match the home range size of the species of interest are considered optimal, but this practice is complicated as home range size may vary by sex, habitat quality, or among species. Additionally, studies often assume their survey methods sample an entire grid cell when the actual effective sampling area may be much smaller. The effect of reduced effective sampling area on occupancy estimation has received little attention to date, despite being flagged as a critical issue. In this study, we assessed (1) how the relationship between effective area, home range size, and grid size affects power to detect trends in occupancy; (2) how varying the sampling design factors of effective area, duration, detection probability, and resurvey interval influence monitoring efficiency; and (3) determine whether a single sampling design can simultaneously detect declines in two species with different home range sizes. We used a spatially explicit simulation framework to create biologically realistic declining populations over 10 yr and assessed statistical power to detect known declines using occupancy modeling. We found that effective area and detection probability had the greatest influence on statistical power. We could not reliably detect declines when detection probability was low or when effective sampling area was <1/4 cell. We conclude that failing to account for effective area less than the cell size will result in overestimation of statistical power. Our simulations suggest occupancy models can detect declines for two species with different home range sizes using the same grid cell size under certain conditions, for instance, surveying >25% of the landscape, ≥25% effective area, and fixed sampling locations. Further, increasing resampling interval greatly increased monitoring efficiency. Our results show monitoring planning requires explicit consideration of effective sampling area and methods with sufficient detectability to detect population declines.

The ability to monitor changes in biodiversity is fundamental to demonstrating sustainable management practices of natural resources. Disturbance studies generally focus on responses at the plot scale, whereas landscape-scale responses are directly relevant to the development of sustainable forest management. Modeling changes in occupancy is one way to monitor landscape-scale responses. We used understory vegetation data collected over 16 years from a long-term study site in southeastern Australia. The site was subject to timber harvesting and frequent prescribed burning. We used occupancy models to examine the impacts of these disturbances on the distribution of 50 species of plants during the study. Timber harvesting influenced the distribution of 9 species, but these effects of harvesting were generally lost within 14 years. Repeated prescribed fire affected 22 species, but the heterogeneity of the burns reduced the predicted negative effects. Twenty-two species decreased over time independent of treatment, and only 5 species increased over time. These changes probably represent a natural response to a wildfire that occurred in 1973, 13 years before the study began. Occupancy modeling is a useful and flexible technique for analyzing monitoring data and it may also be suitable for inclusion within an adaptive-management framework for forest management.

1. Ecologists have long been interested in the processes that determine patterns of species occurrence and co-occurrence. Potential short-comings of many existing empirical approaches that address these questions include a reliance on patterns of occurrence at a single time point, failure to account properly for imperfect detection and treating the environment as a static variable. 2. We fit detection and non-detection data collected from repeat visits using a dynamic site occupancy model that simultaneously accounts for the temporal dynamics of a focal prey species, its predators and its habitat. Our objective was to determine how disturbance and species interactions affect the co-occurrence probabilities of an endangered toad and recently introduced non-native predators in stream breeding habitats. For this, we determined statistical support for alternative processes that could affect co-occurrence frequency in the system. 3. We collected occurrence data at stream segments in two watersheds where streams were largely ephemeral and one watershed dominated by perennial streams. Co-occurrence probabilities of toads with non-native predators were related to disturbance frequency, with low co-occurrence in the ephemeral watershed and high co-occurrence in the perennial watershed. This occurred because once predators were established at a site, they were rarely lost from the site except in cases when the site dried out. Once dry sites became suitable again, toads colonized them much more rapidly than predators, creating a period of predator-free space. 4. We attribute the dynamics to a storage effect, where toads persisting outside the stream environment during periods of drought rapidly colonized sites when they become suitable again. Our results support that even in highly connected stream networks, temporal disturbance can structure frequencies with which breeding amphibians encounter non-native predators. 5. Dynamic multi-state occupancy models are a powerful tool for rigorously examining hypotheses about inter-species and species-habitat interactions. In contrast to previous methods that infer dynamic processes based on static patterns in occupancy, the approach we took allows the dynamic processes that determine species-species and species-habitat interactions to be directly estimated.

ABSTRACTMany territorial species use vocalizations as a primary form of territory defense, and the areas actively defended do not necessarily correspond with an individual's home range. As passive acoustic monitoring becomes a primary population assessment method for soniferous species, often in combination with occupancy modeling, effective conservation will require more detailed information on species‐specific space use to refine interpretation. Northern spotted owls (Strix occidentalis caurina) actively vocalize during the breeding season, but interpreting acoustic data is complicated by variable detectability—particularly for females—and interference from competitive barred owls (Strix varia). Using a dense network of autonomous recording units deployed 0–3 km from known northern spotted owl activity centers, we quantified vocal activity by sex, reproductive status, landscape features, and intensity of barred owl vocalizations. Additionally, we compared detections from overlapping regional monitoring sites to refine our understanding of detectability. Male territorial calls were detected more frequently and consistently than female territorial calls. Female calls were infrequent and restricted to the activity center and immediately adjacent areas, especially when nesting. Vocal space use areas were similar in size but smaller than published home ranges, reinforcing that territorial calls represent high‐use areas, not full spatial use. We propose a detection‐based spectrum of weeks with detection for inferring occupancy that accounts for calling rate, caller sex, and project objectives. Stricter thresholds can minimize false positives in population assessments, while inclusive thresholds reduce false negatives when used to determine habitat protection. Our results support nuanced, objective‐based thresholds for interpreting northern spotted owl detections from passive acoustic monitoring. This approach balances accuracy with conservation risk tolerance, elucidating that acoustically inferred territory does not reflect total landscape used. By clarifying vocal behavior, this study advances the application of passive acoustic monitoring for habitat management and occupancy estimation amid intense interspecies pressures and ongoing landscape change.

Unintended effects of recreational activities in protected areas are of growing concern. We used an adaptive-management framework to develop guidelines for optimally managing hiking activities to maintain desired levels of territory occupancy and reproductive success of Golden Eagles (Aquila chrysaetos) in Denali National Park (Alaska, U.S.A.). The management decision was to restrict human access (hikers) to particular nesting territories to reduce disturbance. The management objective was to minimize restrictions on hikers while maintaining reproductive performance of eagles above some specified level. We based our decision analysis on predictive models of site occupancy of eagles developed using a combination of expert opinion and data collected from 93 eagle territories over 20 years. The best predictive model showed that restricting human access to eagle territories had little effect on occupancy dynamics. However, when considering important sources of uncertainty in the models, including environmental stochasticity, imperfect detection of hares on which eagles prey, and model uncertainty, restricting access of territories to hikers improved eagle reproduction substantially. An adaptive management framework such as ours may help reduce uncertainty of the effects of hiking activities on Golden Eagles.

Intensive resource extraction activity in the oil sands of Canada alters the quantity, structure and distribution of native ecosystems, which in turn creates substantive challenges for conservation, land management and habitat reclamation. Progressive reclamation occurs on active mine sites in the Athabasca oil sands region (AOSR) of Canada, along with concurrent assessments of reclamation effectiveness. Yet, little is known about the ability of reclaimed habitats to mitigate for the short‐ and long‐term impacts associated with open‐pit mines and provide functional habitat for wildlife. We used a robust quasi‐experiment that combined camera trap data from an observational study with an innovative occupancy model to assess the effectiveness of upland reclamation to provide habitat for wildlife in the AOSR. The dynamic occupancy models were applied to 15 years of camera trap data to assess wildlife usage patterns of nine species of wildlife over seven types of habitats. The habitats sampled ranged from mining‐disturbed habitats reclaimed to upland forest ecosites common in the region, habitats disturbed by natural (fire) and human disturbances (clear‐cut logging), with comparisons to mostly intact mature forests. Our results indicate that the nine species of wildlife assessed used habitats in a manner consistent with expectations: some preferred disturbance‐dominated habitats while others used mature forest to a higher degree. We demonstrate that the application of dynamic occupancy models to camera trap data reliably discerned these trends, providing the means to predict wildlife usage patterns in an ever‐changing landscape, including one containing bitumen extraction as a contributor to landscape‐level modifications. Practical implication : Our work illustrates how continued monitoring of wildlife using camera traps contributes to assessments of reclamation effectiveness with respect to wildlife occurrence, distribution and usage patterns in anthropogenically and naturally disturbed landscapes. Evaluating the effectiveness of reclamation is especially important given the expected increase in habitat reclamation on active oil sands mines over the next several decades, coupled with the need to ensure that disturbed habitats regain ecological function able to sustain wildlife in the future.

Nonsystematically collected, a.k.a. opportunistic, species observations are accumulating at a high rate in biodiversity databases. Occupancy models have arisen as the main tool to reduce effects of limited knowledge about effort in analyses of opportunistic data. These models are generally using long closure periods (e.g., breeding season) for the estimation of probability of detection and occurrence. Here, we use the fact that multiple opportunistic observations in biodiversity databases may be available even within days (e.g., at popular birding localities) to reduce the closure period to 1 day in order to estimate daily occupancies within the breeding season. We use a hierarchical dynamic occupancy model for daily visits to analyze opportunistic observations of 71 species from nine wetlands during 10 years. Our model derives measures of seasonal site use within seasons from estimates of daily occupancy. Comparing results from our “seasonal site use model” to results from a traditional annual occupancy model (using a closure criterion of 2 months or more) showed that our model provides more detailed biologically relevant information. For example, when the aim is to analyze occurrences of breeding species, an annual occupancy model will over‐estimate site use of species with temporary occurrences (e.g., migrants passing by, single itinerary prospecting individuals) as even a single observation during the closure period will be viewed as an occupancy. Alternatively, our model produces estimates of the extent to which sites are actually used. Model validation based on simulated data confirmed that our model is robust to changes and variability in sampling effort and species detectability. We conclude that more information can be gained from opportunistic data with multiple replicates (e.g., several reports per day almost every day) by reducing the time window of the closure criterion to acquire estimates of occupancies within seasons.

The population of beluga whales in Cook Inlet, Alaska, USA, declined by nearly half in the mid-1990s, primarily from an unsustainable harvest, and was listed as endangered in 2008. In 2014, abundance was ~340 whales, and the population trend during 1999-2014 was -1.3% yr -1 . Cook Inlet beluga whales are particularly vulnerable to anthropogenic impacts, and noise that has the potential to reduce communication and echolocation range considerably has been documented in critical habitat; thus, noise was ranked as a high potential threat in the Cook Inlet beluga Recovery Plan. The current recovery strategy includes research on effects of threats potentially limiting recovery, and thus we examined the potential impact of anthropogenic noise in critical habitat, specifically, spatial displacement. Using a subset of data on anthropogenic noise and beluga detections from a 5 yr acoustic study, we evaluated the influence of noise events on beluga occupancy probability. We used occupancy models, which account for factors that affect detection probability when estimating occupancy, the first application of these models to examine the potential impacts of anthropogenic noise on marine mammal behavior. Results were inconclusive, primarily because beluga detections were relatively infrequent. Even though noise metrics (sound pressure level and noise duration) appeared in high-ranking models as covariates for occupancy probability, the data were insufficient to indicate better predictive ability beyond those models that only included environmental covariates. Future studies that implement protocols designed specifically for beluga occupancy will be most effective for accurately estimating the effect of noise on beluga displacement.

SummaryBiodiversity monitoring is crucial for effective conservation efforts. Effective monitoring allows managers to determine the status and trends of biodiversity, as well as the success of conservation actions. The population of the Broad‐toothed Rats (Mastacomys fuscus) in the Barrington Tops National Park New South Wales, Australia has been monitored since 1999 via scat and live‐trapping surveys. We reviewed the methods used and analysed the data produced with the aim of describing patterns of population change over time using a range of outcome variables and identifying different climate correlates. A secondary aim was to explore the use of population statistics that account for imperfect detection by comparing naïve occupancy, with an index of relative abundance based on trap effort, the latency to find scats during scat surveys and an occupancy model based on trapping surveys. Neither of these three methods accounts for detectability variation. Naïve occupancy decreased slightly over time, while the relative abundance based on trap effort revealed no evidence of change. Additionally, naïve occupancy decreased with increasing temperature while temperature had no clear impact on relative abundance. Finally, precipitation had no impact on either naïve occupancy or relative abundance. We found no evidence of a relationship between the latency to find scats and the index of relative abundance, suggesting that one or neither is related to actual abundance. Finally, a multi‐season occupancy model found occupancy probability to be 0.78 ± 0.23 (standard error); detection probability as 0.51 ± 0.06; seasonal colonisation rate as 0.36 ± 0.13 and seasonal extinction rate at 0.44 ± 0.13. We conclude that despite significant investment in monitoring, this historical data set does not allow managers to ascertain whether population change has occurred and to identify potential drivers of change. Careful consideration of future methods, in particular, whether there is imperfect detection in scat surveys, will help to inform future monitoring.

Old growth forests are declining globally, threatening dependent wildlife. Many arboreal old‐growth obligates, such as the threatened red tree vole, are difficult to monitor for changes in habitat occupancy, and abundance. Yet, conservation planning relies on this information to prevent population declines. We integrated a range of species, habitat, and landscape change information to develop a dynamic habitat‐population model. The spatial individual‐based model simulated dynamic patterns of occupancy that responded to annual habitat maps, describing 36 years of observed change. We simulated population dynamics and local movement to characterize changes in occupancy and abundance, and the capacity of remaining habitat to support red tree voles. Red tree vole redistribution patterns strongly corresponded to wildfire footprints and timber extraction locations. Population strongholds are likely to exist in clumped pockets of old‐growth forest that were unaffected by wildfire and in protected old forest reserves. However, the exact number and locations of local clusters remain uncertain. Simulated population losses occurred at different paces in different places, underscoring the need for recurring evaluation of population changes with field occupancy surveys and modeled evaluations that can anticipate potential connectivity and extirpation thresholds. This modeling approach was effective at leveraging existing information for a data‐light species to assess how historical changes to the quantity, quality, and configuration of habitat likely influenced the potential landscape capacity, species abundance, and distribution. Dynamic individual‐based modeling can benefit conservation planning for red tree vole and other reclusive forest species by providing biologically nuanced assessments of abundance and distribution. Such models can also project the long‐term benefits and impacts of spatially explicit land management plans.

Post-hurricane recovery and long-term viability of the Alabama beach mouse