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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.

Population viability analyses are useful tools to predict abundance and extinction risk for imperiled species. In southeastern North America, the federally threatened gopher tortoise (Gopherus polyphemus) is a keystone species in the diverse and imperiled longleaf pine (Pinus palustris) ecosystem, and researchers have suggested that tortoise populations are declining and characterized by high extinction risk. We report results from a 30-year demographic study of gopher tortoises in southern Alabama (1991–2020), where 3 populations have been stable and 3 others have declined. To better understand the demographic vital rates associated with stable and declining tortoise populations, we used a multi-state hierarchical markrecapture model to estimate sex- and stage-specific patterns of demographic vital rates at each population. We then built a predictive population model to project population dynamics and evaluate extinction risk in a population viability context. Population structure did not change significantly in stable populations, but juveniles became less abundant in declining populations over 30 years. Apparent survival varied by age, sex, and site; adults had higher survival than juveniles, but female survival was substantially lower in declining populations than in stable ones. Using simulations, we predicted that stable populations with high female survival would persist over the next 100 years but sites with lower female survival would decline, become male-biased, and be at high risk of extirpation. Stable populations were most sensitive to changes in apparent survival of adult females. Because local populations varied greatly in vital rates, our analysis improves upon previous demographic models for northern populations of gopher tortoises by accounting for population-level variation in demographic patterns and, counter to previous model predictions, suggests that small tortoise populations can persist when habitat is managed effectively.

Novel infectious diseases, particularly those caused by fungal pathogens, pose considerable risks to global biodiversity. The amphibian chytrid fungus (Batrachochytrium dendrobatidis, Bd) has demonstrated the scale of the threat, having caused the greatest recorded loss of vertebrate biodiversity attributable to a pathogen. Despite catastrophic declines on several continents, many affected species have experienced population recoveries after epidemics. However, the potential ongoing threat of endemic Bd in these recovered or recovering populations is still poorly understood. We investigated the threat of endemic Bd to frog populations that recovered after initial precipitous declines, focusing on the endangered rainforest frog Mixophyes fleayi. We conducted extensive field surveys over 4 years at three independent sites in eastern Australia. First, we compared Bd infection prevalence and infection intensities within frog communities to reveal species‐specific infection patterns. Then, we analyzed mark‐recapture data of M. fleayi to estimate the impact of Bd infection intensity on apparent mortality rates and Bd infection dynamics. We found that M. fleayi had lower infection intensities than sympatric frogs across the three sites, and cleared infections at higher rates than they gained infections throughout the study period. By incorporating time‐varying individual infection intensities, we show that healthy M. fleayi populations persist despite increased apparent mortality associated with infrequent high Bd loads. Infection dynamics were influenced by environmental conditions, with Bd prevalence, infection intensity, and rates of gaining infection associated with lower temperatures and increased rainfall. However, mortality remained constant year‐round despite these fluctuations in Bd infections, suggesting major mortality events did not occur over the study period. Together, our results demonstrate that while Bd is still a potential threat to recovered populations of M. fleayi, high rates of clearing infections and generally low average infection loads likely minimize mortality caused by Bd. Our results are consistent with pathogen resistance contributing to the coexistence of M. fleayi with endemic Bd. We emphasize the importance of incorporating infection intensity into disease models rather than infection status alone. Similar population and infection dynamics likely exist within other recovered amphibian‐Bd systems around the globe, promising longer‐term persistence in the face of endemic chytridiomycosis.

As Pacific salmon (Oncorhynchus spp.) decline across much of their range, it is imperative to further develop minimally invasive tools to quantify population abundance. One such advancement, trans‐generational genetic mark–recapture (tGMR), uses parentage analysis to estimate the size of wild populations. Our study examined the precision and accuracy of tGMR through a comparison to a traditional mark–recapture estimate for Chilkat River Chinook salmon (O. tshawytscha) in Southeast Alaska. We examined how adult sampling location and timing impact tGMR by comparing estimates derived using samples collected in the lower river mainstem to those using samples obtained in upriver spawning tributaries. Results indicated that tGMR estimates using a representative sample of mainstem adults were most concordant with, and 3% more precise than, the traditional mark–recapture estimate for this stock. Importantly, the timing and location of adult sampling were found to impact abundance estimates, depending on what proportion of the population dies or moves to unsampled areas between downriver and upriver sampling events. Additionally, we identified potential sources of bias in tGMR arising from violations of key assumptions using a novel individual‐based modeling framework, parameterized with empirical values from the Chilkat River. Simulations demonstrated that increased reproductive success and sampling selectivity of older, larger individuals, introduced negative bias into tGMR estimates. Our individual‐based model offers a customizable and accessible method to identify and quantify these biases in tGMR applications (https://github.com/swrosenbaum/tGMR_simulations). We underscore the critical role of system‐specific sampling design considerations in ensuring the precision and accuracy of tGMR projects. This study validates tGMR as a potentially useful tool for improved population enumeration in semelparous species.

Ecologists and conservation biologists increasingly rely on spatial capture–recapture (SCR) and movement modeling to study animal populations. Historically, SCR has focused on population-level processes (e.g., vital rates, abundance, density, and distribution), whereas animal movement modeling has focused on the behavior of individuals (e.g., activity budgets, resource selection, migration). Even though animal movement is clearly a driver of population-level patterns and dynamics, technical and conceptual developments to date have not forged a firm link between the two fields. Instead, movement modeling has typically focused on the individual level without providing a coherent scaling from individual- to population-level processes, whereas SCR has typically focused on the population level while greatly simplifying the movement processes that give rise to the observations underlying these models. In our view, the integration of SCR and animal movement modeling has tremendous potential for allowing ecologists to scale up from individuals to populations and advancing the types of inferences that can be made at the intersection of population, movement, and landscape ecology. Properly accounting for complex animal movement processes can also potentially reduce bias in estimators of population-level parameters, thereby improving inferences that are critical for species conservation and management. This introductory article to the Special Feature reviews recent advances in SCR and animal movement modeling, establishes a common notation, highlights potential advantages of linking individual-level (Lagrangian) movements to population-level (Eulerian) processes, and outlines a general conceptual framework for the integration of movement and SCR models. We then identify important avenues for future research, including key challenges and potential pitfalls in the developments and applications that lie ahead.

Mark-recapture (MR) methods are commonly used to study wildlife populations. Taking advantage of modern genetics one can generalize from \"recapture of self\" to \"recapture of closely-related kin\". Abundance and other demographic parameters of adults can then be estimated using, if necessary, only samples from dead animals (live-release is optional). This greatly widens the scope of MR, e.g. to commercial fisheries where large-scale tagging is impractical, and enhances the power of conventional MR studies where live release and tissue sampling is possible. We give explicit formulae for kinship (i.e., recapture) probabilities in general and specific cases. These yield a pseudo-likelihood based on pairwise comparisons of individuals in the samples. It is shown that the pseudo-likelihood approximates the full likelihood under sparse sampling of large populations. Experimental design is addressed via the principle of maximizing the Fisher information for parameters of interest. Finally, we discuss challenges related to kinship determination from genetic data, focusing on current limitations and future possibilities.

The rate of loss of tags used to mark individuals is an important consideration in wildlife research and monitoring. Passive integrated transponder (PIT) tags (or microchips) generally have high retention rates; however, tag loss rates for small mammals such as insectivorous bats are poorly understood. We double-marked a population of Gould's wattled bats (Chalinolobus gouldii) with forearm bands and PIT tags (with the injection site sealed with surgical adhesive) in January and February 2020 to determine rates of subsequent tag loss over the short- (1–2 months) and medium- (13–14 months) term. Loss of PIT tags occurred in 4 (2.7%) of 146 recaptured individuals, all within 2 months of microchipping. We also recorded 1 occurrence of band loss 11 months after banding. Our study supports assertions that PIT-tag retention rates in small mammals are high, and suggests that rates of tag loss in small bat species are low when surgical adhesive is applied. Quantifying the rate of tag loss enables this variable to be incorporated into mark-recapture models.

State–space models (SSMs) are an important modeling framework for analyzing ecological time series. These hierarchical models are commonly used to model population dynamics, animal movement, and capture–recapture data, and are now increasingly being used to model other ecological processes. SSMs are popular because they are flexible and they model the natural variation in ecological processes separately from observation error. Their flexibility allows ecologists to model continuous, count, binary, and categorical data with linear or nonlinear processes that evolve in discrete or continuous time. Modeling the two sources of stochasticity separately allows researchers to differentiate between biological variation and imprecision in the sampling methodology, and generally provides better estimates of the ecological quantities of interest than if only one source of stochasticity is directly modeled. Since the introduction of SSMs, a broad range of fitting procedures have been proposed. However, the variety and complexity of these procedures can limit the ability of ecologists to formulate and fit their own SSMs. We provide the knowledge for ecologists to create SSMs that are robust to common, and often hidden, estimation problems, and the model selection and validation tools that can help them assess how well their models fit their data. We present a review of SSMs that will provide a strong foundation to ecologists interested in learning about SSMs, introduce new tools to veteran SSM users, and highlight promising research directions for statisticians interested in ecological applications. The review is accompanied by an in-depth tutorial that demonstrates how SSMs can be fitted and validated in R. Together, the review and tutorial present an introduction to SSMs that will help ecologists to formulate, fit, and validate their models.

Marine protected areas (MPAs) are increasingly implemented as tools to conserve and manage fisheries and target species. Because there are opportunity costs to conservation, there is a need for science-based assessment of MPAs. Here, we present one of the northernmost documentations of MPA effects to date, demonstrated by a replicated before–after control-impact (BACI) approach. In 2006, MPAs were implemented along the Norwegian Skagerrak coast offering complete protection to shellfish and partial protection to fish. By 2010, European lobster (Homarus gammarus) catch-per-unit-effort (CPUE) had increased by 245 per cent in MPAs, whereas CPUE in control areas had increased by 87 per cent. Mean size of lobsters increased by 13 per cent in MPAs, whereas increase in control areas was negligible. Furthermore, MPA-responses and population development in control areas varied significantly among regions. This illustrates the importance of a replicated BACI design for reaching robust conclusions and management decisions. Partial protection of Atlantic cod (Gadus morhua) was followed by an increase in population density and body size compared with control areas. By 2010, MPA cod were on average 5 cm longer than in any of the control areas. MPAs can be useful management tools in rebuilding and conserving portions of depleted lobster populations in northern temperate waters, and even for a mobile temperate fish species such as the Atlantic cod.

Long-term datasets are required to understand the response of long-lived organisms (e.g., gopher tortoises [Gopherus polyphemus]) to management actions, such as prescribed burns. Our objective was to estimate the effects of prescribed burning on gopher tortoise population dynamics over decadal time frames at Fort Stewart Army Reserve, southeastern Georgia, USA. We captured and marked adult tortoises from 1994–2020. In addition, since the early 1990s, managers at Fort Stewart collected spatial records of prescribed burns; thus, we could compare demography of the population to prescribed burning. We used a Bayesian hierarchical model (open population Jolly-Seber model) to estimate population parameters (emigration and survival, immigration and recruitment, and adult abundance) and their relationships with years since burn. We observed opposing responses to years since burn at 2 sites: abundance and the probability of staying (survival plus not emigrating) increased within 1 site when it had been more recently burned (F zones), but abundance and probability of staying in a second site increased when it had been longer since the site was burned (E zones). Some of these effects were weak but indicative of different responses to burning between the sites. Although the sites experienced similar burning regimes, they differed substantially in other habitat features: the F zones had almost twice the tree cover and lower soil sand composition, indicating that tortoise population responses to burning depend on habitat context. We inferred that the primary mechanism for demographic responses to years since burn was likely emigrating adults, which indicates the need for more detailed movement data. Our results demonstrate that gopher tortoise population responses to prescribed burning are complex, context dependent, and primarily influenced by tortoise movements. Therefore, prescribed burn plans may best accommodate spatially dynamic tortoise populations when they create spatial heterogeneity in burn ages within the range of typical tortoise movements.