Invader removal triggers competitive release in a threatened avian predator.

Changes in the distribution and abundance of invasive species can have far-reaching ecological consequences. Programs to control invaders are common but gauging the effectiveness of such programs using carefully controlled, large-scale field experiments is rare, especially at higher trophic levels. Experimental manipulations coupled with long-term demographic monitoring can reveal the mechanistic underpinnings of interspecific competition among apex predators and suggest mitigation options for invasive species. We used a large-scale before-after control-impact removal experiment to investigate the effects of an invasive competitor, the barred owl (Strix varia), on the population dynamics of an iconic old-forest native species, the northern spotted owl (Strix occidentalis caurina). Removal of barred owls had a strong, positive effect on survival of sympatric spotted owls and a weaker but positive effect on spotted owl dispersal and recruitment. After removals, the estimated mean annual rate of population change for spotted owls stabilized in areas with removals (0.2% decline per year), but continued to decline sharply in areas without removals (12.1% decline per year). The results demonstrated that the most substantial changes in population dynamics of northern spotted owls over the past two decades were associated with the invasion, population expansion, and subsequent removal of barred owls. Our study provides experimental evidence of the demographic consequences of competitive release, where a threatened avian predator was freed from restrictions imposed on its population dynamics with the removal of a competitively dominant invasive species.

Does coat colour influence survival? A test in a cyclic population of snowshoe hares.

Some mammal species inhabiting high-latitude biomes have evolved a seasonal moulting pattern that improves camouflage via white coats in winter and brown coats in summer. In many high-latitude and high-altitude areas, the duration and depth of snow cover has been substantially reduced in the last five decades. This reduction in depth and duration of snow cover may create a mismatch between coat colour and colour of the background environment, and potentially reduce the survival rate of species that depend on crypsis. We used long-term (1977-2020) field data and capture-mark-recapture models to test the hypothesis that whiteness of the coat influences winter apparent survival in a cyclic population of snowshoe hares (Lepus americanus) at Kluane, Yukon, Canada. Whiteness of the snowshoe hare coat in autumn declined during this study, and snowshoe hares with a greater proportion of whiteness in their coats in autumn survived better during winter. However, whiteness of the coat in spring did not affect subsequent summer survival. These results are consistent with the hypothesis that the timing of coat colour change in autumn can reduce overwinter survival. Because declines in cyclic snowshoe hare populations are strongly affected by low winter survival, the timing of coat colour change may adversely affect snowshoe hare population dynamics as climate change continues.

Range-wide sources of variation in reproductive rates of northern spotted owls.

We conducted a range-wide investigation of the dynamics of site-level reproductive rate of northern spotted owls using survey data from 11 study areas across the subspecies geographic range collected during 1993-2018. Our analytical approach accounted for imperfect detection of owl pairs and misclassification of successful reproduction (i.e., at least one young fledged) and contributed further insights into northern spotted owl population ecology and dynamics. Both nondetection and state misclassification were important, especially because factors affecting these sources of error also affected focal ecological parameters. Annual probabilities of site occupancy were greatest at sites with successful reproduction in the previous year and lowest for sites not occupied by a pair in the previous year. Site-specific occupancy transition probabilities declined over time and were negatively affected by barred owl presence. Overall, the site-specific probability of successful reproduction showed substantial year-to-year fluctuations and was similar for occupied sites that did or did not experience successful reproduction the previous year. Site-specific probabilities for successful reproduction were very small for sites that were unoccupied the previous year. Barred owl presence negatively affected the probability of successful reproduction by northern spotted owls in Washington and California, as predicted, but the effect in Oregon was mixed. The proportions of sites occupied by northern spotted owl pairs showed steep, near-monotonic declines over the study period, with all study areas showing the lowest observed levels of occupancy to date. If trends continue it is likely that northern spotted owls will become extirpated throughout large portions of their range in the coming decades.

What is the effect of poaching activity on wildlife species?

Poaching is a pervasive threat to wildlife, yet quantifying the direct effect of poaching on wildlife is rarely possible because both wildlife and threat data are infrequently collected concurrently. In this study, we used poaching data collected through the Management Information System (MIST) and wildlife camera trap data collected by the Tropical Ecology Assessment and Monitoring (TEAM) network from 2014 to 2017 in Volcanoes National Park, Rwanda. We implemented co-occurrence multi-season occupancy models that accounted for imperfect detection to investigate the effect of poaching on initial occupancy, colonization, and extinction of five mammal species. Specifically, we focused on two species of conservation concern (mountain gorilla [Gorilla beringei beringei] and golden monkey [Cercopithecus mitis kandti]), and three species targeted by poachers (black-fronted duiker [Cephalophus nigrifrons], bushbuck [Tragelaphus scriptus], and African buffalo [Syncerus caffer]). We found that the probability of local extinction was highest in sites with poaching activity for golden monkey and bushbuck. In addition, the probability of initial occupancy for golden monkey was highest in sites without poaching activity. We only found weak evidence of effects of poaching on parameters governing the occupancy dynamics of the other species. All species showed evidence of poaching presence affecting the probability of detection of the wildlife species. This is the first study to our knowledge to combine direct threat observations from ranger-based monitoring data with camera trap wildlife observations to quantify the effect of poaching on wildlife. Given the widespread collection of ranger-based monitoring and camera trap data, our approach is broadly applicable to numerous protected areas and has the potential to significantly improve conservation management. Specifically, the relationship between poaching activity and wildlife population dynamics can be combined with information on the relationship between ranger patrols and poaching activity to develop models useful for making wise decisions about ranger patrol deployment.

Estimating indices of range shifts in birds using dynamic models when detection is imperfect.

There is intense interest in basic and applied ecology about the effect of global change on current and future species distributions. Projections based on widely used static modeling methods implicitly assume that species are in equilibrium with the environment and that detection during surveys is perfect. We used multiseason correlated detection occupancy models, which avoid these assumptions, to relate climate data to distributional shifts of Louisiana Waterthrush in the North American Breeding Bird Survey (BBS) data. We summarized these shifts with indices of range size and position and compared them to the same indices obtained using more basic modeling approaches. Detection rates during point counts in BBS surveys were low, and models that ignored imperfect detection severely underestimated the proportion of area occupied and slightly overestimated mean latitude. Static models indicated Louisiana Waterthrush distribution was most closely associated with moderate temperatures, while dynamic occupancy models indicated that initial occupancy was associated with diurnal temperature ranges and colonization of sites was associated with moderate precipitation. Overall, the proportion of area occupied and mean latitude changed little during the 1997-2013 study period. Near-term forecasts of species distribution generated by dynamic models were more similar to subsequently observed distributions than forecasts from static models. Occupancy models incorporating a finite mixture model on detection - a new extension to correlated detection occupancy models - were better supported and may reduce bias associated with detection heterogeneity. We argue that replacing phenomenological static models with more mechanistic dynamic models can improve projections of future species distributions. In turn, better projections can improve biodiversity forecasts, management decisions, and understanding of global change biology.

Modeling spatiotemporal dynamics of outbreaking species: influence of environment and migration in a locust.

Many pest species exhibit huge fluctuations in population abundance. Understanding their large-scale and long-term dynamics is necessary to develop effective control and management strategies. Occupancy models represent a promising approach to unravel interactions between environmental factors and spatiotemporal dynamics of outbreaking populations. Here, we investigated population dynamics of the Australian plague locust, Chortoicetes terminifera, using density data collected between 1988 and 2010 by the Australian Plague Locust Commission over more than 3 million km2 in eastern Australia. We applied multistate and autologistic multi-season occupancy models to test competing hypotheses about environmental and demographic processes affecting the large-scale dynamics of the Australian plague locust. We found that rainfall and land cover predictors best explained the spatial variability in outbreak probability across eastern Australia. Outbreaks are more likely to occur in temperate than tropical regions, with a faster and more continuous response to rainfall in desert than in agricultural areas. Our results also support the hypothesis that migration tends to propagate outbreaks only locally (over distances lower than 400 km) rather than across climatic regions. Our study suggests that locust outbreak forecasting and management systems could be improved by implementing key environmental factors and migration in hierarchical spatial models. Finally, our modeling framework can be seen as a step towards bridging the gap between mechanistic and more phenomenological models in the spatial analysis of fluctuating populations.

The roles of competition and habitat in the dynamics of populations and species distributions.

The role of competition in structuring biotic communities at fine spatial scales is well known from detailed process-based studies. Our understanding of competition's importance at broader scales is less resolved and mainly based on static species distribution maps. Here, we bridge this gap by examining the joint occupancy dynamics of an invading species (Barred Owl, Strix varia) and a resident species (Northern Spotted Owl, Strix occidentalis caurina) in a 1000-km study area over a 22-year period. Past studies of these competitors have focused on the dynamics of one species at a time, hindering efforts to parse out the roles of habitat and competition and to forecast the future of the resident species. In addition, while these studies accounted for the imperfect detection of the focal species, no multi-season analysis of these species has accounted for the imperfect detection of the secondary species, potentially biasing inference. We analyzed survey data using models that combine the general multistate-multi-season occupancy modeling framework with autologistic modeling, allowing us to account for important aspects of our study system. We found that local extinction probability increases for each species when the other is present; however, the effect of the invader on the resident is greater. Although the species prefer different habitats, these habitats are highly correlated at the patch scale, and the impacts of invader on the resident are greatest in patches that would otherwise be optimal. As a consequence, competition leads to a weaker relationship between habitat and Northern Spotted Owl occupancy. Colonization and extinction rates of the invader are closely related to neighborhood occupancy, and over the first half of the study the availability of colonists limited the rate of population growth. Competition is likely to exclude the resident species, both through its immediate effects on local extinction and by indirectly lowering colonization rates as Northern Spotted Owl occupancy declines. Our analysis suggests that dispersal limitation affects both the invasion dynamics and the scale at which the effects of competition are observed. We also provide predictions regarding the potential costs and benefits of managing Barred Owl populations at different target levels.

Determinants of extinction-colonization dynamics in Mediterranean butterflies: the role of landscape, climate and local habitat features.

Many species are found today in the form of fragmented populations occupying patches of remnant habitat in human-altered landscapes. The persistence of these population networks requires a balance between extinction and colonization events assumed to be primarily related to patch area and isolation, but the contribution of factors such as the characteristics of patch and matrix habitats, the species' traits (habitat specialization and dispersal capabilities) and variation in climatic conditions have seldom been evaluated simultaneously. The identification of environmental variables associated with patch occupancy and turnover may be especially useful to enhance the persistence of multiple species under current global change. However, for robust inference on occupancy and related parameters, we must account for detection errors, a commonly overlooked problem that leads to biased estimates and misleading conclusions about population dynamics. Here, we provide direct empirical evidence of the effects of different environmental variables on the extinction and colonization rates of a rich butterfly community in the western Mediterranean. The analysis was based on a 17-year data set containing detection/nondetection data on 73 butterfly species for 26 sites in north-eastern Spain. Using multiseason occupancy models, which take into account species' detectability, we were able to obtain robust estimates of local extinction and colonization probabilities for each species and test the potential effects of site covariates such as the area of suitable habitat, topographic variability, landscape permeability around the site and climatic variability in aridity conditions. Results revealed a general pattern across species with local habitat composition and landscape features as stronger predictors of occupancy dynamics compared with topography and local aridity. Increasing area of suitable habitat in a site strongly decreased local extinction risks and, for a number of species, both higher amounts of suitable habitat and more permeable landscapes increased colonization rates. Nevertheless, increased topographic variability decreased the extinction risk of bad dispersers, a group of species with significantly lower colonization rates. Our models predicted higher sensitivity of the butterfly assemblages to deterministic changes in habitat features rather than to stochastic weather patterns, with some relationships being clearly dependent on the species' traits.

Relaxing the closure assumption in occupancy models: staggered arrival and departure times.

Occupancy statistical models that account for imperfect detection have proved very useful in several areas of ecology, including species distribution and spatial dynamics, disease ecology, and ecological responses to climate change. These models are based on the collection of multiple samples at each of a number of sites within a given season, during which it is assumed the species is either absent or present and available for detection while each sample is taken. However, for some species, individuals are only present or available for detection seasonally. We present a statistical model that relaxes the closure assumption within a season by permitting staggered entry and exit times for the species of interest at each site. Based on simulation, our open model eliminates bias in occupancy estimators and in some cases increases precision. The power to detect the violation of closure is high if detection probability is reasonably high. In addition to providing more robust estimation of occupancy, this model permits comparison of phenology across sites, species, or years, by modeling variation in arrival or departure probabilities. In a comparison of four species of amphibians in Maryland we found that two toad species arrived at breeding sites later in the season than a salamander and frog species, and departed from sites earlier.

Decline in small mammal species richness in coastal-central California, 1997-2013.

The richness and composition of a small mammal community inhabiting semiarid California oak woodland may be changing in response to climate change, but we know little about the causes or consequence of these changes. We applied a capture-mark-recapture model to 17 years (1997-2013) of live trapping data to estimate species-specific abundances. The big-eared woodrat was the most frequently captured species in the area, contributing 58% of total captures. All small mammal populations exhibited seasonal fluctuations, whereas those of the California mouse, brush mouse, and pinyon mouse declined during the study period. We also applied a multispecies dynamic occupancy model to our small mammal detection history data to estimate species richness, occupancy (ψ), detection (p), local extinction (ϵ), and colonization (γ) probabilities, and to discern factors affecting these parameters. We found that ψ decreased from 0.369 ± 0.088 in 1997 to 0.248 ± 0.054 in 2013; γ was lower during the dry season (May-September) than the wet season (October-April) and was positively influenced by total seasonal rainfall (slope parameter, ß = 0.859 ± 0.371; 95% CI = 0.132-1.587). Mean mammalian species richness decreased from 11.943 ± 0.461 in 1997 to 7.185 ± 0.425 in 2013. With highly variable climatic patterns expected in the future, especially increased frequency and intensity of droughts, it is important to monitor small mammal communities inhabiting threatened California oak woodlands.

On valuing patches: estimating contributions to metapopulation growth with reverse-time capture-recapture modelling.

Metapopulation ecology has historically been rich in theory, yet analytical approaches for inferring demographic relationships among local populations have been few. We show how reverse-time multi-state capture-recapture models can be used to estimate the importance of local recruitment and interpopulation dispersal to metapopulation growth. We use 'contribution metrics' to infer demographic connectedness among eight local populations of banner-tailed kangaroo rats, to assess their demographic closure, and to investigate sources of variation in these contributions. Using a 7 year dataset, we show that: (i) local populations are relatively independent demographically, and contributions to local population growth via dispersal within the system decline with distance; (ii) growth contributions via local survival and recruitment are greater for adults than juveniles, while contributions involving dispersal are greater for juveniles; (iii) central populations rely more on local recruitment and survival than peripheral populations; (iv) contributions involving dispersal are not clearly related to overall metapopulation density; and (v) estimated contributions from outside the system are unexpectedly large. Our analytical framework can classify metapopulations on a continuum between demographic independence and panmixia, detect hidden population growth contributions, and make inference about other population linkage forms, including rescue effects and source-sink structures. Finally, we discuss differences between demographic and genetic population linkage patterns for our system.

Neighborhood and habitat effects on vital rates: expansion of the Barred Owl in the Oregon coast ranges.

In this paper, we modify dynamic occupancy models developed for detection-nondetection data to allow for the dependence of local vital rates on neighborhood occupancy, where neighborhood is defined very flexibly. Such dependence of occupancy dynamics on the status of a relevant neighborhood is pervasive, yet frequently ignored. Our framework permits joint inference about the importance of neighborhood effects and habitat covariates in determining colonization and extinction rates. Our specific motivation is the recent expansion of the Barred Owl (Strix varia) in western Oregon, USA, over the period 1990-2010. Because the focal period was one of dramatic range expansion and local population increase, the use of models that incorporate regional occupancy (sources of colonists) as determinants of dynamic rate parameters is especially appropriate. We began our analysis of 21 years of Barred Owl presence/nondetection data in the Tyee Density Study Area (TDSA) by testing a suite of six models that varied only in the covariates included in the modeling of detection probability. We then tested whether models that used regional occupancy as a covariate for colonization and extinction outperformed models with constant or year-specific colonization or extinction rates. Finally we tested whether habitat covariates improved the AIC of our models, focusing on which habitat covariates performed best, and whether the signs of habitat effects are consistent with a priori hypotheses. We conclude that all covariates used to model detection probability lead to improved AIC, that regional occupancy influences colonization and extinction rates, and that habitat plays an important role in determining extinction and colonization rates. As occupancy increases from low levels toward equilibrium, colonization increases and extinction decreases, presumably because there are more and more dispersing juveniles. While both rates are affected, colonization increases more than extinction decreases. Colonization is higher and extinction is lower in survey polygons with more riparian forest. The effects of riparian forest on extinction rates are greater than on colonization rates. Model results have implications for management of the invading Barred Owl, both through habitat alteration and removal.

Estimating parameters of hidden Markov models based on marked individuals: use of robust design data.

Development and use of multistate mark-recapture models, which provide estimates of parameters of Markov processes in the face of imperfect detection, have become common over the last 20 years. Recently, estimating parameters of hidden Markov models, where the state of an individual can be uncertain even when it is detected, has received attention. Previous work has shown that ignoring state uncertainty biases estimates of survival and state transition probabilities, thereby reducing the power to detect effects. Efforts to adjust for state uncertainty have included special cases and a general framework for a single sample per period of interest. We provide a flexible framework for adjusting for state uncertainty in multistate models, while utilizing multiple sampling occasions per period of interest to increase precision and remove parameter redundancy. These models also produce direct estimates of state structure for each primary period, even for the case where there is just one sampling occasion. We apply our model to expected-value data, and to data from a study of Florida manatees, to provide examples of the improvement in precision due to secondary capture occasions. We have also implemented these models in program MARK. This general framework could also be used by practitioners to consider constrained models of particular interest, or to model the relationship between within-primary-period parameters (e.g., state structure) and between-primary-period parameters (e.g., state transition probabilities).

Joint estimation of habitat dynamics and species interactions: disturbance reduces co-occurrence of non-native predators with an endangered toad.

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.

Multiple coping strategies maintain stability of a small mammal population in a resource-restricted environment.

In semi-arid environments, aperiodic rainfall pulses determine plant production and resource availability for higher trophic levels, creating strong bottom-up regulation. The influence of climatic factors on population vital rates often shapes the dynamics of small mammal populations in such resource-restricted environments. Using a 21-year biannual capture-recapture dataset (1993 to 2014), we examined the impacts of climatic factors on the population dynamics of the brush mouse (Peromyscus boylii) in semi-arid oak woodland of coastal-central California. We applied Pradel's temporal symmetry model to estimate capture probability (p), apparent survival (φ), recruitment (f), and realized population growth rate (λ) of the brush mouse and examined the effects of temperature, rainfall, and El Niño on these demographic parameters. The population was stable during the study period with a monthly realized population growth rate of 0.993 ± SE 0.032, but growth varied over time from 0.680 ± 0.054 to 1.450 ± 0.083. Monthly survival estimates averaged 0.789 ± 0.005 and monthly recruitment estimates averaged 0.175 ± 0.038. Survival probability and realized population growth rate were positively correlated with rainfall and negatively correlated with temperature. In contrast, recruitment was negatively correlated with rainfall and positively correlated with temperature. Brush mice maintained their population through multiple coping strategies, with high recruitment during warmer and drier periods and higher survival during cooler and wetter conditions. Although climatic change in coastal-central California will likely favor recruitment over survival, varying strategies may serve as a mechanism by which brush mice maintain resilience in the face of climate change. Our results indicate that rainfall and temperature are both important drivers of brush mouse population dynamics and will play a significant role in predicting the future viability of brush mice under a changing climate.

The shrinking ark: patterns of large mammal extinctions in India.

Mammal extinctions are widespread globally, with South Asian species being most threatened. We examine local extinctions of 25 mammals in India. We use historical records to obtain a set of locations at which each species was known to have been present at some time in the last 200 years. We then use occupancy estimation models to draw inferences about current presence at these same locations based on field observations of local experts. We examine predictions about the influence of key factors such as protected areas, forest cover, elevation, human population density and cultural tolerance on species extinction. For all 25 species, estimated local extinction probabilities (referenced to a 100 year time frame) range between 0.14 and 0.96. Time elapsed since the historical occurrence record was an important determinant of extinction probability for 14 species. Protected areas are positively associated with lower extinction of 18 species, although many species occur outside them. We find evidence that higher proportion of forest cover is associated with lower extinction probabilities for seven species. However, for species that prefer open habitats (which have experienced intensive land-use change), forest cover alone appears insufficient to ensure persistence (the complement of extinction). We find that higher altitude is positively associated with lower extinction for eight species. Human population density is positively associated with extinction of 13 species. We find that 'culturally tolerated' species do exhibit higher persistence. Overall, large-bodied, rare and habitat specialist mammals tend to have higher extinction probabilities.

Two-species occupancy models: a new parameterization applied to co-occurrence of secretive rails.

Two-species occupancy models that account for false absences provide a robust method for testing for evidence of competitive exclusion, but previous model parameterizations were inadequate for incorporating covariates. We present a new parameterization that is stable when covariates are included: the conditional two-species occupancy model, which can be used to examine alternative hypotheses for species' distribution patterns. This new model estimates the probability of occupancy for a subordinate species conditional upon the presence of a dominant species. It can also be used to test if the detection of either species differs when one or both species are present, and if detection of the subordinate species depends on the detection of the dominant species when both are present. We apply the model to test if the presence of the larger Virginia Rail (Rallus limicola) affects probabilities of detection or occupancy of the smaller California Black Rail (Laterallus jamaicensis coturniculus) in small freshwater marshes that range in size from 0.013 to 13.99 ha. We hypothesized that Black Rail occupancy should be lower in small marshes when Virginia Rails are present than when they are absent, because resources are presumably more limited and interference competition should increase. We found that Black Rail detection probability was unaffected by the detection of Virginia Rails, while, surprisingly, Black and Virginia Rail occupancy were positively associated even in small marshes. The average probability of Black Rail occupancy was higher when Virginia Rails were present (0.74 +/- 0.053, mean +/- SE) than when they were absent (0.36 +/- 0.069), and for both species occupancy increased with marsh size. Our results contrast with recent findings from patchy forest systems, where small birds were presumed to be excluded from small habitat patches by larger competitors.

Simultaneous modeling of habitat suitability, occupancy, and relative abundance: African elephants in Zimbabwe.

The recent development of statistical models such as dynamic site occupancy models provides the opportunity to address fairly complex management and conservation problems with relatively simple models. However, surprisingly few empirical studies have simultaneously modeled habitat suitability and occupancy status of organisms over large landscapes for management purposes. Joint modeling of these components is particularly important in the context of management of wild populations, as it provides a more coherent framework to investigate the population dynamics of organisms in space and time for the application of management decision tools. We applied such an approach to the study of water hole use by African elephants in Hwange National Park, Zimbabwe. Here we show how such methodology may be implemented and derive estimates of annual transition probabilities among three dry-season states for water holes: (1) unsuitable state (dry water holes with no elephants); (2) suitable state (water hole with water) with low abundance of elephants; and (3) suitable state with high abundance of elephants. We found that annual rainfall and the number of neighboring water holes influenced the transition probabilities among these three states. Because of an increase in elephant densities in the park during the study period, we also found that transition probabilities from low abundance to high abundance states increased over time. The application of the joint habitat-occupancy models provides a coherent framework to examine how habitat suitability and factors that affect habitat suitability influence the distribution and abundance of organisms. We discuss how these simple models can further be used to apply structured decision-making tools in order to derive decisions that are optimal relative to specified management objectives. The modeling framework presented in this paper should be applicable to a wide range of existing data sets and should help to address important ecological, conservation, and management problems that deal with occupancy, relative abundance, and habitat suitability.

Demography of snowshoe hare population cycles.

Cyclic fluctuations in abundance exhibited by some mammalian populations in northern habitats ("population cycles") are key processes in the functioning of many boreal and tundra ecosystems. Understanding population cycles, essentially demographic processes, necessitates discerning the demographic mechanisms that underlie numerical changes. Using mark-recapture data spanning five population cycles (1977-2017), we examined demographic mechanisms underlying the 9-10-yr cycles exhibited by snowshoe hares (Lepus americanus Erxleben) in southwestern Yukon, Canada. Snowshoe hare populations always decreased during winter and increased during summer; the balance between winter declines and summer increases characterized the four, multiyear cyclic phases: increase, peak, decline, and low. Little or no recruitment occurred during winter, but summer recruitment varied markedly across the four phases with the highest and lowest recruitment observed during the increase and decline phase, respectively. Population crashes during the decline were triggered by a substantial decline in winter survival and by a lack of subsequent summer recruitment. In contrast, initiation of the increase phase was triggered by a twofold increase in summer recruitment abetted secondarily by improvements in subsequent winter survival. We show that differences in peak density across cycles are explained by differences in overall population growth rate, amount of time available for population growth to occur, and starting population density. Demographic mechanisms underlying snowshoe hare population cycles were consistent across cycles in our study site but we do not yet know if similar demographic processes underlie population cycles in other northern snowshoe hare populations.

Perturbation analysis for patch occupancy dynamics.

Perturbation analysis is a powerful tool to study population and community dynamics. This article describes expressions for sensitivity metrics reflecting changes in equilibrium occupancy resulting from small changes in the vital rates of patch occupancy dynamics (i.e., probabilities of local patch colonization and extinction). We illustrate our approach with a case study of occupancy dynamics of Golden Eagle (Aquila chrysaetos) nesting territories. Examination of the hypothesis of system equilibrium suggests that the system satisfies equilibrium conditions. Estimates of vital rates obtained using patch occupancy models are used to estimate equilibrium patch occupancy of eagles. We then compute estimates of sensitivity metrics and discuss their implications for eagle population ecology and management. Finally, we discuss the intuition underlying our sensitivity metrics and then provide examples of ecological questions that can be addressed using perturbation analyses. For instance, the sensitivity metrics lead to predictions about the relative importance of local colonization and local extinction probabilities in influencing equilibrium occupancy for rare and common species.