Multistate Occupancy Models Research Articles

Autonomous sound monitoring shows higher use of Amazon old growth than secondary forest by parrots

Forest regeneration may reduce the current loss of species due to tropical deforestation, but little is known about the extent and inter-specific variability of this effect. We compared the probability with which nine parrot species use old-growth and secondary forests in a ∼400km2 Amazonian landscape, while considering two types of habitat use: perching and flyover use. Perching use, when individuals stop at a sampling site, implies resting, foraging, or breeding activities; flyover merely implies that parrots fly through, above the canopy at a site. We established 155 sampling sites spanning old growth and approximately 30-year-old secondary forest, and sampled them repeatedly using autonomous audio recorders. Perching and flyover use were distinguished based on the temporal variation of intensity in parrot vocalization sonograms. We modeled our data with a set of species-specific, multi-state occupancy models that estimate the probability of each type of use for both habitats while accounting for imperfect species detection. Models were fit in a maximum likelihood framework and ranked according to the Akaike information criterion. All but one species fly over both habitats with the same probability, while seven out of nine show a higher probability of perching in old growth than in secondary forest. Interspecific variation in response to habitat change was not explained by variation in body mass or relative brain size. After three decades of forest regeneration in our study area, there are still measurable differences in habitat use, with a broad tendency for parrots to favor old growth over secondary forest.

Habitat use and population status of Yellow-billed and Pacific loons in western Alaska, USA

ABSTRACT Effective conservation of sympatric avian populations depends on unbiased estimates of population size, distribution, and habitat use. For populations of Yellow-billed Loons (Gavia adamsii) and Pacific Loons (G. pacifica) co-occurring in Arctic wetland communities in Alaska, USA, such data are limited and difficult to obtain, hindering population assessments and decision making. The Yellow-billed Loon is also under consideration for additional protections under the Endangered Species Act due to small global population size, specific habitat requirements, and low fecundity, further increasing the need for information at the landscape scale. To help evaluate the population status and habitat use of both species, we used repeated aerial surveys and a dynamic multistate occupancy modeling approach to jointly estimate 1) probability of lake use and 2) probability of use for nesting for Yellow-billed and Pacific loon populations at the landscape scale on the Seward Peninsula and Cape Krusenstern, Alask...

Community-managed forests and wildlife-friendly agriculture play a subsidiary but not substitutive role to protected areas for the endangered Asian elephant

Global conservation policy is increasingly debating the feasibility of reconciling wildlife conservation and human resource requirements in land uses outside protected areas (PAs). However, there are few quantitative assessments of whether or to what extent these ‘wildlife-friendly’ land uses fulfill a fundamental function of PAs—to separate biodiversity from anthropogenic threats. We distinguish the role of wildlife-friendly land uses as being (a) subsidiary, whereby they augment PAs with secondary habitat, or (b) substitutive, wherein they provide comparable habitat to PAs. We tested our hypotheses by investigating the influence of land use and human presence on space-use intensity of the endangered Asian elephant (Elephas maximus) in a fragmented landscape comprising PAs and wildlife-friendly land uses. We applied multistate occupancy models to spatial data on elephant occurrence to estimate and model the overall probability of elephants using a site, and the conditional probability of high-intensity use given that elephants use a site. The probability of elephants using a site regardless of intensity did not vary between PAs and wildlife-friendly land uses. However, high-intensity use declined with distance to PAs, and this effect was accentuated by an increase in village density. Therefore, while wildlife-friendly land uses did play a subsidiary conservation role, their potential to substitute for PAs was offset by a strong human presence. Our findings demonstrate the need to evaluate the role of wildlife-friendly land uses in landscape-scale conservation; for species that have conflicting resource requirements with people, PAs are likely to provide crucial refuge from growing anthropogenic threats.

Toxoplasma gondii exposure in arctic-nesting geese: A multi-state occupancy framework and comparison of serological assays.

The zoonotic parasite, Toxoplasma gondii, has a worldwide distribution and a cosmopolitan suite of hosts. In arctic tundra regions, the definitive felid hosts are rare to absent and, while the complete transmission routes in such regions have yet to be fully elucidated, trophic and vertical routes are likely to be important. Wild birds are common intermediate hosts of T. gondii, and in the central Canadian arctic, geese are probable vectors of the parasite from temperate latitudes to the arctic regions. Our objective was to estimate seroprevalence of T. gondii in Ross's and Lesser Snow Geese from the Karrak Lake ecosystem in Nunavut, Canada. After harvesting geese by shotgun, we collected blood on filter paper strips and tested the eluate for T. gondii antibodies by indirect fluorescent antibody test (IFAT) and direct agglutination test (DAT). We estimated seroprevalence using a multi-state occupancy model, which reduced bias by accounting for imperfect detection, and compared these estimates to a naïve estimator. Ross's Geese had a 0.39 probability of seropositivity, while for Lesser Snow Geese the probability of positive for T. gondii antibodies was 0.36. IFAT had a higher antibody detection probability than DAT, but IFAT also had a higher probability of yielding ambiguous or unclassifiable results. The results of this study indicate that Ross's Geese and Lesser Snow Geese migrating to the Karrak Lake region of Nunavut are routinely exposed to T. gondii at some point in their lives and that they are likely intermediate hosts of the parasite. Also, we were able to enhance our estimation of T. gondii seroprevalence by using an occupancy approach that accounted for both false-negative and false-positive detections and by using multiple diagnostic tests in the absence of a gold standard serological assay for wild geese.

Spatial patterns of breeding success of grizzly bears derived from hierarchical multistate models.

Conservation programs often manage populations indirectly through the landscapes in which they live. Empirically, linking reproductive success with landscape structure and anthropogenic change is a first step in understanding and managing the spatial mechanisms that affect reproduction, but this link is not sufficiently informed by data. Hierarchical multistate occupancy models can forge these links by estimating spatial patterns of reproductive success across landscapes. To illustrate, we surveyed the occurrence of grizzly bears (Ursus arctos) in the Canadian Rocky Mountains Alberta, Canada. We deployed camera traps for 6 weeks at 54 surveys sites in different types of land cover. We used hierarchical multistate occupancy models to estimate probability of detection, grizzly bear occupancy, and probability of reproductive success at each site. Grizzly bear occupancy varied among cover types and was greater in herbaceous alpine ecotones than in low-elevation wetlands or mid-elevation conifer forests. The conditional probability of reproductive success given grizzly bear occupancy was 30% (SE = 0.14). Grizzly bears with cubs had a higher probability of detection than grizzly bears without cubs, but sites were correctly classified as being occupied by breeding females 49% of the time based on raw data and thus would have been underestimated by half. Repeated surveys and multistate modeling reduced the probability of misclassifying sites occupied by breeders as unoccupied to <2%. The probability of breeding grizzly bear occupancy varied across the landscape. Those patches with highest probabilities of breeding occupancy-herbaceous alpine ecotones-were small and highly dispersed and are projected to shrink as treelines advance due to climate warming. Understanding spatial correlates in breeding distribution is a key requirement for species conservation in the face of climate change and can help identify priorities for landscape management and protection.

Legacy effects of habitat degradation by Lesser Snow Geese on nesting Savannah Sparrows

Increased growth of the midcontinental population of Lesser Snow Geese (Chen caerulescens caerulescens) has led to overgrazing and habitat degradation at their Arctic and sub-Arctic breeding grounds. This habitat degradation has been shown to induce a trophic cascade that negatively affects plant, insect, and other avian species that share these habitats. In conjunction with a long-term study of the impacts of Lesser Snow Geese on habitat, we examined the dual influences of climate and long-term habitat change on the nesting occurrence of Savannah Sparrows near Churchill, Manitoba, Canada. Using multistate occupancy models, we found that variability in early-summer temperature and precipitation modulated year-to-year variability in nesting occurrence and detection probabilities. Extreme warm and wet conditions in early summer can benefit breeding Savannah Sparrows across the landscape. However, such events have not been prevalent enough to override the ~80% decline in Savannah Sparrow nesting occurrence over 36 yr. This dramatic decline can be attributed to the legacy of Lesser Snow Goose foraging, which has led to an 84% reduction in preferred shrub habitat for nesting Savannah Sparrows. Management actions targeted at reducing Lesser Snow Goose abundance and habitat restoration will be needed to allow sympatric Savannah Sparrows and functionally similar species to recover.

Metapopulation Dynamics of Species with Cryptic Life Stages

Quantifying metapopulation dynamics is a challenging task. Difficulties particularly arise in species that possess unobservable resistance forms that bias the estimation of colonization and persistence rates. Here, we develop a general multistate occupancy model that allows estimation of species persistence for both normal and resistant forms, even when the latter are not detectable. We apply this model to an 11-year data set on the tropical freshwater snail Drepanotrema depressissimum in a network of 229 ponds. These ponds frequently dry out, and the snails can persist by aestivating in the ground, where they are not detected. Our model adequately captures this feature because it infers a high persistence rate for the resistant form, while models ignoring aestivation tend to overestimate extinction and colonization. In addition, we find that, surprisingly, colonization and persistence are even higher in sites prone to desiccation and during years with low rainfall than in more humid sites and years, suggesting that D. depressissimum favors unstable sites where competitors are rare and where it can rely on aestivation to persist. Our model has the potential to provide valuable insights into the metapopulation dynamics of many species that otherwise could hardly be studied because of the existence of undetectable life forms.

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.

Exploring sensitivity of a multistate occupancy model to inform management decisions

1. Dynamic occupancy models are often used to investigate questions regarding the processes that influence patch occupancy and are prominent in the fields of population and community ecology and conservation biology. Recently, multistate occupancy models have been developed to investigate dynamic systems involving more than one occupied state, including reproductive states, relative abundance states and joint habitat-occupancy states. Here we investigate the sensitivities of the equilibrium-state distribution of multistate occupancy models to changes in transition rates. 2. We develop equilibrium occupancy expressions and their associated sensitivity metrics for dynamic multistate occupancy models. To illustrate our approach, we use two examples that represent common multistate occupancy systems. The first example involves a three-state dynamic model involving occupied states with and without successful reproduction (California spotted owl Strix occidentalis occidentalis), and the second involves a novel way of using a multistate occupancy approach to accommodate second-order Markov processes (wood frog Lithobates sylvatica breeding and metamorphosis). 3. In many ways, multistate sensitivity metrics behave in similar ways as standard occupancy sensitivities. When equilibrium occupancy rates are low, sensitivity to parameters related to colonisation is high, while sensitivity to persistence parameters is greater when equilibrium occupancy rates are high. Sensitivities can also provide guidance for managers when estimates of transition probabilities are not available. 4. Synthesis and applications. Multistate models provide practitioners a flexible framework to define multiple, distinct occupied states and the ability to choose which state, or combination of states, is most relevant to questions and decisions about their own systems. In addition to standard multistate occupancy models, we provide an example of how a second-order Markov process can be modified to fit a multistate framework. Assuming the system is near equilibrium, our sensitivity analyses illustrate how to investigate the sensitivity of the system-specific equilibrium state(s) to changes in transition rates. Because management will typically act on these transition rates, sensitivity analyses can provide valuable information about the potential influence of different actions and when it may be prudent to shift the focus of management among the various transition rates.

Investigating the population dynamics of California spotted owls without marked individuals

Understanding population dynamics is of great interest in many different contexts. Traditionally, population dynamics have often been considered in terms of individual-based demographic parameters (e.g., abundance, survival, and reproductive rates), estimation of which generally requires information from marked individuals. Alternatively, in some situations, it may be appropriate to consider population dynamics at a landscape level where the focus is shifted from numbers of individuals to the status of the population at places on the landscape. One consequence of doing so is that information from marked individuals is no longer required. Recently developed methods allow the estimation of landscape-level population vital rates in the realistic situation where the current status of the population might be misclassified via field methods (e.g., because of imperfect detection). Here, we consider the case of the California spotted owl (Strix occidentalis occidentalis) at the Eldorado study area in central Sierra Nevada, California, USA, where interest is in the occupancy rate of potential nesting territories, and in whether owls in an occupied territory successfully reproduced each year during 1997–2004. We analyzed the data using multistate occupancy models and found no evidence of annual variation in dynamic occupancy probabilities. There was strong evidence of annual variation in successful reproduction, with the pattern of variation being different depending on whether there was successful reproduction in the territory in the previous year. Of the three environmental variables considered, the Southern Oscillation Index appeared to be most important and explained some of the annual variation in reproduction probabilities.

Modeling species occurrence dynamics with multiple states and imperfect detection

Recent extensions of occupancy modeling have focused not only on the distribution of species over space, but also on additional state variables (e.g., reproducing or not, with or without disease organisms, relative abundance categories) that provide extra information about occupied sites. These biologist-driven extensions are characterized by ambiguity in both species presence and correct state classification, caused by imperfect detection. We first show the relationships between independently published approaches to the modeling of multistate occupancy. We then extend the pattern-based modeling to the case of sampling over multiple seasons or years in order to estimate state transition probabilities associated with system dynamics. The methodology and its potential for addressing relevant ecological questions are demonstrated using both maximum likelihood (occupancy and successful reproduction dynamics of California Spotted Owl) and Markov chain Monte Carlo estimation approaches (changes in relative abundance of green frogs in Maryland). Just as multistate capture-recapture modeling has revolutionized the study of individual marked animals, we believe that multistate occupancy modeling will dramatically increase our ability to address interesting questions about ecological processes underlying population-level dynamics.