Dynamic N-occupancy models: estimating demographic rates and local abundance from detection-nondetection data.

AimAdult survival is central to theories explaining latitudinal gradients in life history strategies. Life history theory predicts higher adult survival in tropical than north temperate regions given lower fecundity and parental effort. Early studies were consistent with this prediction, but standard‐effort netting studies in recent decades suggested that apparent survival rates in temperate and tropical regions strongly overlap. Such results do not fit with life history theory. Targeted marking and resighting of breeding adults yielded higher survival estimates in the tropics, but this approach is thought to overestimate survival because it does not sample social and age classes with lower survival. We compared the effect of field methods on tropical survival estimates and their relationships with life history traits.LocationSabah, Malaysian Borneo.Time period2008–2016.Major taxonPasseriformes.MethodsWe used standard‐effort netting and resighted individuals of all social and age classes of 18 tropical songbird species over 8 years. We compared apparent survival estimates between these two field methods with differing analytical approaches.ResultsEstimated detection and apparent survival probabilities from standard‐effort netting were similar to those from other tropical studies that used standard‐effort netting. Resighting data verified that a high proportion of individuals that were never recaptured in standard‐effort netting remained in the study area, and many were observed breeding. Across all analytical approaches, addition of resighting yielded substantially higher survival estimates than did standard‐effort netting alone. These apparent survival estimates were higher than for temperate zone species, consistent with latitudinal differences in life histories. Moreover, apparent survival estimates from addition of resighting, but not from standard‐effort netting alone, were correlated with parental effort as measured by egg temperature across species.Main conclusionsInclusion of resighting showed that standard‐effort netting alone can negatively bias apparent survival estimates and obscure life history relationships across latitudes and among tropical species.

[Extract] In our recent publication (Murray et al. 2009), we documented a marked disease-associated reduction in apparent survival of threatened frogs infected with pathogen Batrachochytrium dendrobatidis (Bd), despite a long period since its invasion. This result raises concern for hundreds of species of amphibians globally because it demonstrates that endemic chytridiomycosis can remain virulent for long periods, potentially placing ongoing pressure on amphibian populations that may elevate extinction risk. In response, Schmidt claims the apparent monthly survival estimates of Murray et al. are likely confounded with permanent emigration from study site… . If infected and uninfected frogs have different emigration probabilities, then one would obtain different apparent survival estimates from mark-recapture analysis for Bd-positive and Bd-negative frogs. Schmidt concludes, I believe that most of difference [in survival rate between infected and uninfected animals] is caused by permanent emigration from study site.

Estimates of species' vital rates and an understanding of the factors affecting those parameters over time and space can provide crucial information for management and conservation. We used mark–recapture, reproductive output, and territory occupancy data collected during 1985–2013 to evaluate population processes of Northern Spotted Owls (Strix occidentalis caurina) in 11 study areas in Washington, Oregon, and northern California, USA. We estimated apparent survival, fecundity, recruitment, rate of population change, and local extinction and colonization rates, and investigated relationships between these parameters and the amount of suitable habitat, local and regional variation in meteorological conditions, and competition with Barred Owls (Strix varia). Data were analyzed for each area separately and in a meta-analysis of all areas combined, following a strict protocol for data collection, preparation, and analysis. We used mixed effects linear models for analyses of fecundity, Cormack-Jolly-...

Despite the importance of tropical birds in the development of life history theory, we lack information about demographic rates and drivers of population dynamics for most species. We used a 7-year (2007–2013) capture-mark-recapture dataset from an exceptionally wet premontane forest at mid-elevation in Costa Rica to estimate apparent survival for seven species of tropical passerines. For four of these species, we provide the first published demographic parameters. Recapture probabilities ranged from 0.21 to 0.53, and annual estimates of apparent survival varied from 0.23 to 1.00. We also assessed the consequences of inter-annual variation in rainfall on demographic rates. Our results are consistent with inter-annual rainfall increasing estimates of apparent survival for two species and decreasing estimates for three species. For the three species where we could compare our estimates of apparent survival to estimates from drier regions, our estimates were not consistently higher or lower than those published previously. The temporal and spatial variability in demographic rates we document within and among species highlights the difficulties of generalizing life history characteristics across broad biogeographic gradients. Most importantly, this work emphasizes the context-specific role of precipitation in shaping tropical avian demographic rates and underscores the need for mechanistic studies of environmental drivers of tropical life histories. Factores que afectan la supervivencia aparente de aves tropicales en un bosque húmedo premontano A pesar de la importancia de las aves tropicales en el desarrollo de teorías de historia de vida, aún no entendemos bien los patrones o factores causales en la dinámica de poblaciones para la mayoría de las especies tropicales. Usamos datos de una comunidad de aves paseriformes del sotobosque, marcando y recapturando individuos por siete años (2007–2013) en un bosque premontano altamente pluvial en Costa Rica con el fin de estimar las tasas de supervivencia aparente. Pudimos modelar la supervivencia aparente para siete especies, proporcionando los primeros parámetros demográficos publicados para cuatro de ellas. Las probabilidades de recaptura varían entre 0.21 y 0.53 mientras que las tasas de supervivencia aparente varían entre 0.23 y 1.00. También, evaluamos la relación entre precipitación y tasas demográficas. Se relacionó con la variación interanual en la supervivencia aparente en modelos competitivos de cuatro especies, pero el efecto de la precipitación varió, siendo positivo en dos especies y negativo en tres especies. Más aun, nuestras estimaciones de supervivencia aparente fueron a la misma vez mayores y mucho más bajas que otras estimaciones de poblaciones que experimentan regímenes de precipitación diferentes. La variabilidad en las tasas demográficas entre especies y poblaciones que encontramos demuestra la dificultad de generalizar a través de gradientes biogeográficos. Aún más importante, este trabajo destaca, en un contexto específico, el papel de la precipitación en los cambios de las tasas demográficas en aves tropicales, y destaca la necesidad de conducir estudios mecánicos de los factores ambientales que impulsan las historias naturales en el trópico. Table S1. Cormack-Jolly-Seber model selection results for seven Neotropical bird species in Costa Rica. Fig. S1. Variation in sampling effort across years measured in number of hours a 12-m mist-net was open during the sampling event. Fig. S2. Variation in precipitation measured in millimeters during the biological year preceding sampling event (e.g., March 2007–February 2008). Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

The Strait of Gibraltar is an important habitat for cetaceans due to its high marine productivity. However, it is also the second most navigated channel in the world, subjecting cetaceans to a high level of vessel traffic, including an established whale‐watching fleet. Both maritime traffic and whale‐watching activities have been shown to impact the behaviour of cetaceans, but little is known about their impact on the demography and dynamics of cetacean populations. The aim of this study was to evaluate the impacts of both ferry traffic and whale‐watching vessels on the apparent survival probability of a bottlenose dolphin (Tursiops truncatus) population that occurs in the Strait. A Bayesian hierarchical mark–recapture modelling approach was applied to 8 years of photo‐identification data (2002–2009). Apparent annual survival probability was negatively correlated with ferry traffic, which explained >70% of temporal variation in survival, in contrast to whale‐watching, the effect of which was almost negligible. Despite these results, other natural and human‐related factors are likely to drive apparent survival in the study area. Abundance increased between 2002 and 2005, and then decreased between 2006 and 2009, while local per‐capita recruitment decreased from 2004 until the end of the study period. These shifts correlated temporally with the construction of a large harbour on the Moroccan coast, which increased maritime traffic significantly, including a 40% increase in ferry traffic that regularly transited the Strait. These results highlight the need to better understand the impact of maritime traffic on the demography of the dolphin population in the Strait, in order to implement evidence‐based conservation regulations in a region of high cetacean occurrence.

ABSTRACTKnowledge of survival rates of Neotropical landbirds remains limited, with estimates of apparent survival available from relatively few sites and species. We used capture–mark–recapture models to estimate apparent survival of 31 species from eastern Ecuador based on data collected from 2001 to 2006. Models assuming constant survival had highest support for 27 species; models incorporating effects of transients were highest for four. Average apparent survival across 30 species of passerines was 0.58 (± 0.02 SE); apparent survival was lower during the first interval after initial capture (φ1: mean = 0.49 ± 0.03) than during subsequent intervals (φ2: mean = 0.60 ± 0.02). Apparent survival was similar among three families represented by at least four species (Thamnophilidae: 0.57 ± 0.03,N= 10; Furnariidae: 0.59 ± 0.03,N= 5; Pipridae: 0.56 ± 0.02,N= 4). There was no indication that species that occur in flocks had higher survival than nonflocking species (obligate flock members: 0.57 ± 0.03,N= 10; facultative flock members: 0.56 ± 0.04,N= 5; nonflocking: 0.59 ± 0.03,N= 15). Comparisons of published estimates of apparent survival of tropical species demonstrated substantial differences among species and, in some cases, within species across different sites in the Neotropics. Our results support previous studies that concluded that early estimates of high (> 85%) survival in tropical birds may not be representative of all tropical species. Future studies should focus on understanding factors (e.g., life‐history traits) that promote differences in survival among species within tropical forests.

Population viability analysis (PVA) is a central tool for conservation decision-making. To ensure the reliability of PVA projections, it is important to identify factors that can introduce biases. This study addresses two general but overlooked related issues in PVAs that can significantly affect the reliability of their projections. First, we examined the effects of using apparent versus true survival estimates on PVA outcomes. Second, we incorporated emigration and immigration into the models to assess their influence on the accuracy of projections based on each type of survival estimate. To evaluate these concerns, we implemented PVAs structured by age, sex, and breeding status using as a study system a threatened raptor population (Bonelli's eagle, Aquila fasciata) from which apparent and true survival were available (2008–2020). The performances of PVA projections based on each survival type and dispersal process were assessed by evaluating their fit to census data. Our findings revealed that using apparent survival underestimated census data, while true survival showed a considerably better fit. However, models including dispersal processes showed that each survival type may only deliver precise projections at very specific levels of emigration and immigration. Given the potentially large differences found when using true and apparent survival, we suggest that the relevance of this issue should be elevated to that of other widely reported PVA limitations. Recently developed, accessible analytical methods may permit an easier estimation of true survival and dispersal processes. Otherwise, calibrating projections against observed data may be fundamental to test the adequacy of survival estimates.

Population parameter estimates from mark–recapture studies are dependent on individuals retaining marks or tags. Therefore, tag retention estimates are needed for different tag types and anatomical tagging locations. Few studies have empirically quantified the bias from tag retention on fish population parameters that are derived from mark–recapture studies. We examined differences in retention between T-bar anchor tags and PIT tags as well as among four anatomical locations for PIT tags in Brown Trout Salmo trutta in a tailwater fishery in Arkansas, USA. We also estimated the relative bias of tag type and PIT tag location on apparent survival estimates from Cormack–Jolly–Seber models. Tag retention for the anchor tags was 15.1% lower than that for the PIT tags after 1 year and 46.1% lower after 4 years. Greater PIT tag retention resulted in less biased estimates of apparent survival for PIT tags (average −7.1%) than for anchor tags (average −37.8%). However, PIT tags that were placed in different anatomical locations had varying retention rates, so the degree of relative bias that was associated with their apparent survival estimates also varied. Inserting the PIT tags in the cheek or dorsal musculature provided the greatest retention for Brown Trout and may provide the least biased apparent survival estimates from future mark–recapture studies.

It is well known that, due to that inherent differences in their underlying causal mechanisms, different types of crime will have variable impacts on different groups of people. Furthermore, the locations of vulnerable groups of people are highly temporally dynamic. Hence an accurate estimate of the true population at risk in a given place and time is vital for reliable crime rate calculation and hotspot generation. However, the choice of denominator is fraught with difficulty because data describing popular movements, rather than simply residential location, are limited. This research will make use of new ‘crowd-sourced’ data in an attempt to create more accurate estimates of the population at risk for mobile crimes such as street robbery. Importantly, these data are both spatially and temporally referenced and can therefore be used to estimate crime rate significance in both space and time. Spatio-temporal cluster hunting techniques will be used to identify crime hotspots that are significant given the size of the ambient population in the area at the time.

In some animal populations, immigrants have lower survival than philopatric individuals. Costs of dispersal or low phenotypic quality of dispersers may explain the pattern. However, apparent adult survival estimates, which describe real survival combined with site fidelity cannot be separated from permanent emigration. Thus, heterogeneity in breeding dispersal propensities of immigrants and philopatrics can bias fitness correlates of dispersal. Differences in breeding dispersal propensities may be caused by different strategies in response to environmental cues inducing dispersal, such as reproductive success. In such cases, the reported differences between immigrants and philopatric individuals may not reflect true variation in survival.We studied whether dispersal status specific apparent adult survival is associated with reproductive success in a Temminck's stint Calidris temminckii population. We analysed two long term capture–recapture datasets characterised by low and high nest predation levels. Philopatric individuals had higher apparent adult survival than immigrants in both datasets and the difference was highlighted during the high nest predation period. By contrasting return rates between successful and unsuccessful breeders as a proxy for dispersal, we found that unsuccessful immigrants breeding for the first time dispersed more likely than successful immigrants, but such a pattern was not found among philopatric individuals. Our results support the hypothesis that immigrant and philopatric individuals have different breeding dispersal strategies following reproductive failure and that their apparent adult survival differences are at least partly explained by different breeding dispersal propensities. Our results also suggest that the recent decline of the study population reflects a multiple response to increased nest predation through decreased local recruitment and increased emigration.

Mark–recapture statistics have rarely been applied to plants, yet they can be useful for estimating plant demographic traits where individuals may be missed or unobservable. We applied mark–recapture statistics based on an information theory approach to estimate annual probabilities of dormancy in a five-year study of a threatened, perennial plant, the small yellow lady's slipper orchid (Cypripedium calceolus ssp. parviflorum (Salisb.) Fernald). The aboveground states of 548 genets in eight patches were monitored over five years. Apparent survival probabilities (φ), corrected for dormancy, were calculated. The best-fit model suggested that apparent survival was constant throughout the study for all patches, while dormancy varied additively with time among patches. The mean probability of dormancy was 0.320 ± 0.024, with a mean maximum overestimation of 0.067 as calculated using an estimate of the probability of detection. Dormancy typically lasted for no longer than two consecutive years, although dormancy as long as four years was observed. Dormancy displayed a strong covariate relationship with spring frost days, although effects of precipitation and mean spring temperature were almost equally strong. Mean apparent survival probabilities were high in each patch (φ = 0.878), but dormancy probabilities varied considerably among patches (d = 0.188–0.672). Conventional resprouting probabilities underestimated apparent survival by a mean difference of 0.288 (range: 0.150–0.589). This novel application of mark–recapture statistics to plant demography allowed robust survival estimates that accounted for uncertainty due to an unobservable, dormant life stage.

This is the second in a series of periodic monitoring reports on northern spotted owl (Strix occidentalis caurina) population and habitat trends on federally administered lands since implementation of the Northwest Forest Plan in 1994. Here we summarize results from a population analysis that included data from longterm demographic studies during 1985–2008. This data was analyzed separately by study area, and also in a meta-analysis across all study areas to assess temporal and spatial patterns in fecundity, apparent survival, recruitment, and annual rates of population change. Estimated rates of annual population decline ranged from 0.4 to 7.1 percent across federal study areas (weighted average of 2.8 percent). Covariates for barred owls (Strix varia), weather, climate, habitat, and reproductive success were analyzed and had varying degrees of association with owl demographic parameters. We now have more evidence that increasing numbers of barred owls and loss of nesting/roosting habitat contributed to demographic declines in some study areas. We also summarize results from a habitat analysis that used the above data in conjunction with remotely sensed data from 1994 to 2007 to develop “habitat suitability” models and habitat maps. These maps were used to quantify the amount and distribution of owl habitats. We also report on causes of habitat change during this period. On federal lands, nesting/roosting habitat declined by 3.4 percent rangewide, with some physiographic provinces experiencing losses of 10 percent. Dispersal habitat increased by 5.2 percent, but dispersal-capable landscapes declined by 1 percent. Wildfire remains the leading cause of habitat loss. We developed a rangewide “wildfire suitability” model and map to illuminate the portions of the owl’s range where suitable nesting/roosting habitat overlaps with landscapes suitable for the occurrence of large wildfires. Barred owls and management of owl habitat in fire-prone areas continue to be topics for future monitoring, research, and management consideration.

This paper will critically assess the utility of conventional and novel data sources for building fine-scale spatio-temporal estimates of the ambient population. It begins with a review of data sources employed in existing studies of the ambient population, followed by preliminary analysis to further explore the utility of each dataset. The identification and critiquing of data sources which may be useful for building estimates of the ambient population are novel contributions to the literature. This paper will provide a framework of reference for researchers within urban analytics and other areas where an accurate measurement of the ambient population is required. This work has implications for national and international applications where accurate small area estimates of the ambient population are crucial in the planning and management of urban areas, the development of realistic models and informing policy. This research highlights workday population estimates, in conjunction with footfall camera and Wi-Fi sensors data as potentially valuable for building estimates of the ambient population.

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.

Occupancy information can help us to achieve high energy-efficient buildings. Previous works mainly focus on predicting the presence and absence of occupants in homes or single person offices. We attempt to predict regular occupancy level in a commercial building deployment scenario. The occupancy prediction models can be divided into two categories of occupancy models and data mining approaches. For the occupancy models, we shall investigate the efficiencies of two widely used multi-occupant models, that is, inhomogeneous Markov chain and multivariate Gaussian. For the data mining approaches, we propose the application of autoregressive integrated moving average, artificial neural network and support vector regression. Experiments have been conducted using actual occupancy data under four different prediction horizons, that is, 15 min, 30 min, 1 and 2 h. The results demonstrated a guideline in how to choose a proper method for the prediction of occupancy in commercial buildings under different prediction horizons.