Objective Understanding the survival and movement of juvenile Gulf Sturgeon Acipenser desotoi is critical for improving recovery efforts under the U.S. Endangered Species Act. The river and estuary portions of the Choctawhatchee River watershed, a key part of the species' range, provide required habitat used by juvenile life stages. While the ecology and demographics of adult Gulf Sturgeon are well studied, similar information on juveniles remains limited.Methods We used acoustic telemetry data collected during 2020-2022 and applied multistate capture-recapture models to these data to estimate seasonal survival (Phi), transition probabilities between riverine and estuarine habitats (Psi), and detection probabilities (p) for juvenile Gulf Sturgeon. Tagged individuals (350-1,150 mm FL) were monitored using a fixed array of autonomous receivers within the Choctawhatchee River watershed, with emphasis on estuary and river habitats.Results The top-ranked statistical model indicated that survival varied by season and habitat type but was consistent across years and among our assumed age-classes based on length at capture. Transition probabilities revealed seasonal patterns, with movements from river to estuary peaking in winter (Psi = 0.41) and from estuary to river peaking in spring (Psi = 0.58). Detection probabilities also varied seasonally, reflecting differences in occupancy across habitats. These results suggest that Gulf Sturgeon >= 350 mm FL have surpassed an early life high-mortality phase characterized by Type III survivorship.Conclusions These findings improve our understanding of survival rates and seasonal habitat use in a critical life stage of Gulf Sturgeon. Transition probabilities can inform risk exposure timing to stressors such as dredging or infrastructure replacement. The consistency in juvenile survival across sizes suggests that the greatest recruitment compensatory potential is in size-classes <= 350 mm FL, which can inform ongoing monitoring and recovery planning for this threatened species. From 2020 to 2022, we used acoustic tags to track juvenile Gulf Sturgeon in the Choctawhatchee River and estuary system. Juveniles moved to the estuary in winter and to the river in spring. Survival was stable across years, similar among juvenile sturgeon of all sizes (350-1,150 mm fork length), and generally higher in the river.

Objective The expansion of nonnative Smallmouth Bass Micropterus dolomieu into the Grand Canyon ecosystem downstream of Glen Canyon Dam is widely seen as a potential threat to native fishes, particularly the Humpback Chub Gila cypha, which is listed as threatened under the Endangered Species Act. This concern stems from observations in the Green and upper Colorado rivers, where dam-modified habitats and reservoir introductions have allowed Smallmouth Bass to become established and impact native fish species. Our objective was to compare habitat conditions between a Smallmouth Bass population center in the Green River-where Humpback Chub are rare-and two major Humpback Chub population centers in the Colorado River in Grand Canyon, where Smallmouth Bass invasion is a conservation concern, to help assess invasion risk and inform management actions downstream of Glen Canyon Dam.Methods We developed a conceptual model of Smallmouth Bass recruitment potential emphasizing the roles of temperature, turbidity, and the timing of these conditions, based on literature for Smallmouth Bass and Largemouth Bass Micropterus nigricans. Using U.S. Geological Survey gauge station data, we summarized daily temperature and turbidity patterns near a known Smallmouth Bass population center in the middle Green River (near Jensen, Utah) and compared those with conditions in the Colorado River in Glen Canyon and Grand Canyon downstream from Glen Canyon Dam. We then used our conceptual model of Smallmouth Bass early life history, along with observed turbidity and temperature patterns, to explore how irregular recruitment could affect Smallmouth Bass population dynamics and individual growth potential using an age-structured population model and a bioenergetics model.Results Although warm reservoir releases due to low water storage in Lake Powell has made temperature regimes in Glen and Grand canyons more similar to those of the middle Green River, the Colorado River ecosystem in Grand Canyon has a very different turbidity regime from that of the middle Green River. The Colorado River in Grand Canyon becomes very turbid during late summer and fall, when tributaries experience flash floods during the North American monsoon season. These periods of high turbidity coincide with critical early life stages of Smallmouth Bass, likely limiting foraging efficiency, growth, and overwinter survival. Our population model indicates that rapidly growing and sustained Smallmouth Bass populations require successful recruitment at least once every 2 years, but empirical data suggest that these conditions occur only every 5-7 years in Grand Canyon. This would make long-term establishment of self-sustaining Smallmouth Bass populations in Grand Canyon unlikely or at least highly uncertain.Conclusions Despite the presence of nonnative predators, Humpback Chub populations in Grand Canyon have expanded during the past 10-15 years, very likely due to favorably warm river temperature. While Smallmouth Bass in Glen or Marble canyons (between Glen Canyon Dam and the Little Colorado River) may pose a downstream dispersal risk (and potentially a threat to Humpback Chub populations), high turbidity conditions downstream of the Little Colorado River reduce the likelihood of persistent local Smallmouth Bass recruitment. These results suggest that Smallmouth Bass invasion risk to Humpback Chub is not uniform across the Colorado River basin and should be evaluated in the context of the different site-specific water quality and flow regime conditions, other known risks to Humpback Chub, and Humpback Chub population size in different parts of the basin. Smallmouth Bass pose a potential but context-dependent threat to Humpback Chub in the Grand Canyon ecosystem. High turbidity in Grand Canyon downstream of the Little Colorado River may act as a natural barrier to sustained Smallmouth Bass recruitment, suggesting that risk assessments and management actions should be location-specific, include multiple abiotic and biotic factors, and be informed by long-term environmental conditions and time horizons.

Objective We identified spatial and temporal variation in population trends for Gulf Sturgeon Acipenser desotoi (previously known as Acipenser oxyrinchus desotoi) across the species' range to inform recovery strategies. We also assessed whether adult survival or recruitment more strongly influences population change. Methods We analyzed adult Gulf Sturgeon capture-recapture data from 1990 to 2022 across seven Gulf of Mexico river systems. Using temporal symmetry models and fixed estimates of adult survival from a companion study, we estimated seniority probability (gamma(i + 1)), capture probability (p), recruitment (f), and population growth rate (lambda) for adult fish. Models were compared using Akaike information criterion adjusted for small sample sizes, and parameter estimates were derived at both river-specific and rangewide scales. Results Adult survival (phi) was the primary driver of lambda across the species' range, with gamma consistently >0.5 in most rivers and time periods. While rangewide lambda suggested stable or slightly increasing adult populations, river-level trends varied. Recent declines in lambda and f were observed in the Escambia, Apalachicola, and Suwannee rivers-systems affected by red tide, hurricanes, or oil exposure following the Deepwater Horizon spill. Capture probabilities remained low across rivers and time periods. Conclusions Long-term recovery of Gulf Sturgeon is likely more sensitive to adult survival than recruitment to the adult population. Population trajectories differ across rivers and may reflect both demographic changes and inconsistencies in monitoring. Restoring consistent, standardized adult monitoring in select rivers will improve the ability to detect meaningful trends and guide conservation efforts focused on minimizing adult mortality.

Objective Our objective was to quantify the relationship between oyster cultch mass (kg/m(3)) and density (oysters/m(2)) of live eastern oyster Crassostrea virginica on intertidal reefs in Suwannee Sound, Florida. We also evaluated the potential for a cultch-mass threshold below which recruitment declines (depensation) to inform oyster fishery management and restoration strategies.Methods During the winters of 2020-2022, we collected 185 standardized 0.025-m(3) grub-box samples of cultch from unrestored intertidal reefs in Suwannee Sound and conducted line-transect surveys to estimate live eastern oyster density. Cultch mass was converted to units of weight per area (kg/m(3)) for analysis. We modeled the relationship between cultch mass and live eastern oyster density using a Beverton-Holt recruitment framework coupled with two spat-settlement functions-one incorporating a minimum cultch threshold (Hmin) and one without. Models were fit in a Bayesian framework using Template Model Builder and No-U-Turn-Sampler, Markov chain-Monte Carlo sampling. We compared two biologically plausible parameter cases and evaluated model performance using Pareto-smoothed importance sampling leave-one-out cross validation.Results Live eastern oyster density increased in a saturating fashion with cultch mass. Models that included a minimum cultch threshold yielded median estimates of Hmin near 20 kg/m(3), with 86-88% of posterior samples exceeding 5 kg/m(3). However, the Pareto-smoothed importance sampling leave-one-out cross-validation model comparison did not favor threshold models over those without a threshold, and posterior distributions for Hmin were broad and included substantial probability density near zero. These findings suggest that recruitment limitation at low cultch mass is a plausible dynamic, but the exact location or existence of a cultch threshold remains uncertain.Conclusions Our findings highlight the potential for a cultch-mass threshold below which eastern oyster recruitment may be limited, consistent with ecological theory and field observations that larval settlement depends on suitable substrate. Although the precise value of this threshold remains uncertain, model results suggest that recruitment may decline when cultch mass falls below approximately 20 kg/m(3). We recommend that restoration and management efforts maintain cultch mass above a precautionary range of 5-20 kg/m(3) to reduce the risk of reef collapse and support recovery. Further research is needed to more precisely estimate system-specific thresholds and better understand how cultch mass interacts with other oyster reef characteristics. Our research in Suwannee Sound suggests that oyster populations may need a minimum of 5 to 20 kg of cultch per cubic meter of reef to support successful recruitment. While our models show a strong possibility that recruitment drops off below this level, the exact threshold is uncertain and may differ across locations. Because oyster larvae rely on suitable substrate (type and amount) to settle and grow, maintaining adequate cultch to support positive population growth should be a key focus for managing and restoring oyster reefs. More research is needed to refine these estimates and understand how cultch thresholds may vary across different reef systems.

Expansion of non-native brown trout ( Salmo trutta) in the Colorado River below Glen Canyon Dam motivated reevaluation of suppression strategies to minimize potential impacts to native fishes in the Grand Canyon, Arizona, USA. Brown trout are one of several non-native fish species of management concern in this river reach, and understanding their natal sources and movement patterns may assist managers in planning suppression strategies. We identified trace elements in brown trout otoliths, which, when coupled with location-specific water chemistry data, identified brown trout natal origins over 19 years. Strontium and manganese concentrations revealed distinct emigration patterns from natal tributary streams and the mainstem Colorado River over two periods. Adult brown trout collected from throughout our study area showed mixed tributary and mainstem natal origins, which persisted during suppression efforts in a known spawning tributary. Unexpectedly, we found evidence of brown trout reproduction in the Colorado River for at least a decade before documentation through field monitoring. Our findings may inform but complicate the development of management strategies for system-wide brown trout suppression.

Live oyster reefs are considered a critical recruitment habitat for estuarine faunal populations as localized in situ or mesocosm studies have demonstrated many faunal species prefer live oyster habitat. It has therefore been assumed that the loss of live oyster habitat would precipitate faunal population declines, but this has been largely untested at large (estuary) scales. Here, we assessed how estuary-wide faunal populations were affected by a 95% loss of live oyster habitat following the 2012 oyster collapse of Apalachicola Bay, FL, which previously supported one of the largest oyster fisheries in the United States. We standardized long-term fisheries-independent monitoring seine and trawl data to create relative indices of resident, associated, and transient faunal species' overall abundance and recruit abundance (restrictive to sizes between 15% and 35% of L-infinity). We expected that both relative abundance indices would decrease following the oyster collapse, particularly among species that reside on or recruit to oyster reefs. However, analyses via a series of one-sided Bayesian t tests did not indicate that faunal recruitment or overall abundance significantly declined in 2012 post-collapse. As the response of the faunal population could be lagged relative to the 2012 collapse, we also conducted change point analyses to search for lagged declines. Of the 24 relative abundance time series, only two had significant change points post-collapse, and only black sea bass overall relative abundance declined with an associated change point at the end of the time series. The surprising paucity of faunal decline following oyster loss may be due to the use of alternative habitat types, exceptionally lagged faunal responses, or, perhaps most compelling, a disconnect between preferred and required habitats. Our failure to detect faunal consequences following an oyster population collapse suggests that assumptions of habitat loss (or restoration) effects on estuarine fauna at ecosystem scales are not straightforward and the extrapolation of sub-estuary-scale studies may result in poor predictions of future outcomes.

Structural habitats support high biodiversity by providing refuge, forage resources, and recruitment habitat that upwardly influence the broader faunal community structure. However, there are few system-wide studies that empirically measure communities before and after major shifts in habitat structure or availability, limiting our ability to predict the consequences of changes in structural habitat above local scales. We used the collapse of the Apalachicola Bay, Florida oyster population as a natural experiment to assess the impacts of estuary-wide structural habitat loss on the nekton community through long-term faunal monitoring data. Habitat losses of this magnitude are expected to decrease diversity and alter composition, so we expected to observe these changes in Apalachicola Bay after the oyster population collapse. We assessed changes in Gini-Simpson diversity and composition over a 21-year period encompassing the 2012 oyster collapse using generalized linear mixed models to account for confounding drivers. We surprisingly found no evidence that Gini-Simpson diversity or composition differed immediately before or following the collapse, which may be explained if estuarine fauna were able to effectively use other habitats. This suggests that proportional changes in diversity or composition from loss or gain of structural habitats cannot be assumed at the system-wide scale.

The collapse of oyster populations and the fisheries they support has been a worldwide phenomenon, but studies of oyster demography in situ prior to and after the collapse have been rare. We used time series of stage-based counts of eastern oysters Crassostrea virginica in Apalachicola Bay, Florida, to help understand how abundance and demographic rates may have changed in the decade after the 2012 collapse relative to the period before the collapse. We relied on a Bayesian hierarchical model in which the latent stage structure of the oyster population (i.e., densities of spat, sublegal oysters, and legal oysters) was governed by a system process and where the count data represented summaries of that latent structure. Count data were sufficient to conduct this on two large oyster bars that had some of the highest precollapse oyster densities. We also examined nine other bars with less data for any temporal trends in postcollapse abundance that might be associated with recent restoration efforts. Among the 11 bars examined, oyster densities were often increasing prior to the collapse and were very low, without detectable trends, afterward. Based on our demographic analyses, mortality rates of Apalachicola Bay oysters in the decade after the collapse generally exceeded (often greatly so) those during the precollapse period for all oyster stages. On the other hand, spat settlement rates apparently were increasing prior to the collapse and remained high during the postcollapse period. Simulations of postcollapse demography suggest that without improved survival rates, further declines of the oyster population can be expected. We discuss these findings in light of ongoing restoration and management efforts and suggest ways in which rapid transitions to undesirable socio-ecological regimes might be avoided in the future.

Objective: Depressed eastern oyster Crassostrea virginica populations in the northern Gulf of Mexico have been the target of numerous post-Deepwater Horizon restoration projects. These projects primarily have focused on replacing oyster cultch (substrate) to promote spat settlement, increase recruitment, and bolster adult oyster populations. This study assessed the outcomes of six such efforts, which used different cultch types and densities between 2015 and 2022 in three estuaries on the Florida panhandle (Pensacola, St. Andrew, and Apalachicola bays). Total restoration costs for these projects were more than US$14 million.Methods: Using generalized linear models, we analyzed oyster count data collected from diver surveys in three size-classes (spat, seed, and adult). We tested whether oyster population responses in the six restoration efforts varied over time, location, or study design.Result: Oyster counts did not persistently increase after restoration, regardless of cultch type or density. Positive responses to restoration efforts were irregular and short-lived and seemed only to occur for spat-size oysters immediately after restoration. None of the restoration efforts significantly improved the abundance of oysters of any size-class in any of the study estuaries. Factors contributing to these results likely include design and implementation elements, such as the materials used and the height of the restored reefs. However, monitoring programs have not been able to deliver a clear picture of what is hindering restoration success.Conclusion: For oyster restoration efforts to succeed, changes are needed-both in their implementation and in the way they are monitored-in order to promote continuous learning and improvement in restoration outcomes.

Information characterising site fidelity and abundance for common bottlenose dolphins (Tursiops truncatus) along the southwest coast of Florida is important for defining stock structure for management purposes. Long-term site fidelity and ranging patterns of bottlenose dolphins in Charlotte Harbor and Pine Island Sound, Florida were investigated using photo-ID data collected during 566 boat-based surveys from 1982 through 2007. Seasonal abundance estimates were generated from seven multi-week field seasons during 2001 through 2006, before and after a major hurricane and red tide event occurred in the area. In total, 1,154 distinctive dolphins were identified up to 34 times each with 84% of individuals resighted on more than one day. Multiple year residency rates were high with 81% of dolphins sighted in at least two years and 30% over ten or more years. Seventy-six percent of individuals with sightings on two or more days were observed in both summer and winter. Of 249 dolphins sighted on ten or more days in the study area, 83% were never observed outside the study area, indicating strong site-fidelity. Two years after a devastating Category 4 hurricane in 2004 and following two years of Karenia brevis harmful algal blooms, 94% of dolphins were observed in the same region within the study area and abundance estimates remained stable. Documenting range and site fidelity patterns of individuals over long periods of time is helpful for characterizing population structure and for examining changes attributable to environmental factors and perturbations such as hurricanes, harmful algal blooms and climate change.

Understanding fish population status and trends are fundamental to effective research and management. Challenges in understanding population status include recognizing and accounting for sources of variation in capture probability (p<^>) that can obscure patterns in count data and bias inferences about the population. In systems where management actions such as invasive species removals are implemented based on population triggers, errors in abundance estimation can propagate to missed management opportunities simply due to variation in p<^>, rather than actual population status. We assessed the relative importance of individual heterogeneity (species and fish size), environmental (stream discharge, temperature) and spatial variation, and interspecific interactions (density) on electrofishing p<^> for native (Speckled Dace Rhinichthys osculus, Bluehead Sucker Catostomus discobolus, Flannelmouth Sucker Catostomus latipinnis) and invasive (Brown Trout Salmo trutta, Rainbow Trout Oncorhynchus mykiss) fishes. We fit closed-population depletion models with combinations of covariates using 6 years of data collected during invasive salmonid suppression efforts. We found that the relative importance of spatially and temporally varying environmental influences on p<^> differed between native and introduced species. Temperature was important for explaining variability in p<^> for two of three native species, and discharge had a significant influence on p<^> for both Brown Trout and Rainbow Trout. We also found that p<^> declined with increasing Brown Trout density, which would limit precision and potentially bias abundance, for two of the three native species. These results illustrate the potential importance of interspecific interactions in influencing p<^> and understanding implications of management actions, such as invasive species suppression. Our results demonstrate the need for cautious interpretation of uncalibrated catch-per-unit-effort data for abundance-triggered management actions, including those designed to promote conservation of endangered or economically valuable species.

A multitude of different statistical models are commonly used to monitor trends in wildlife populations. Most are used to estimate abundance or survival (or both), and these estimates are then examined over time to infer trends in a population. The choice of which model to use is influenced by the key research question of interest and the types of data available. The accuracy and precision of any estimate from a population model are determined by whether the data meet the model assumptions. We assessed the performance of both closed and open capture–recapture models for determining trends in abundance and survival of River Cooters, Pseudemys concinna, in the Santa Fe River, Florida from 2009–2019. We fit three closed models to estimate abundance, one open model to estimate survival, and two robust design models to estimate both abundance and survival. We then used simulation to generate three datasets that represented different sampling designs, including one that mimics our field data, to assess model performance and compare tradeoffs in sampling design. We recommend using the robust design framework when possible as this design and model estimation returned accurate and precise estimates of abundance and survival. This model estimated survival ranging from 0.69–0.95 and capture probability from 0.21–0.25. This design requires consistent sampling of at least three events per year during a closed period, repeated over at least five years, to estimate survival between years. In situations where samples could not be repeated across years, closed population models are likely the most reliable framework in terms of model precision and accuracy. Overall, sampling designs that allow for repeated sampling and align the biology of the study species and the assumptions of the statistical model are likely the most informative approaches for sampling River Cooters and similar species.

Given the global collapse of most oyster fisheries, we explored the conditions under which the interaction of oysters and fishers can lead to multiple system equilibria, and how those conditions might affect management strategies and recovery efforts. Using simple, but plausible, models of oyster fisheries, we identified tipping points, multiple equilibria, and hysteresis under a wide range of realistic model parameterizations. In collapsed systems with hysteresis, recovery of the system will require far less harvest than that which precipitated the collapse, and recovery times can be on decadal scales. We also derived optimal, non-equilibrium, state-dependent fishing policies and found that these policies can perform well, but are accompanied by high variation in the allowable harvest. Critically, these optimal policies also require constant monitoring of system state and frequent control of fishing effort. Finally, we examined habitat-enhancement scenarios that mimic proposed and ongoing restoration programs. We found that these efforts can increase the number of fishers the system can support and reduce otherwise long recovery times in collapsed systems.

The Gulf Sturgeon Acipenser oxyrinchus desotoi is an anadromous species that inhabits Gulf of Mexico coastal waters from Louisiana to Florida and is listed as threatened under the U.S. Endangered Species Act. Seasonal cues (e.g., freshwater discharge) determine the timing of spawning and migration and may influence the availability of critical habitat during winter months in six estuaries. Large information gaps, especially related to critical estuarine habitat for juveniles, hinder recovery efforts to protect these habitats and assess risks from emerging threats. Using Apalachicola Bay, Florida, as a model system, we developed and analyzed a preliminary Bayesian network model so that we could identify knowledge gaps (i.e., where expert knowledge was lacking) and data gaps (i.e., where data were unavailable) that limit the ability to assess the quantity of critical estuarine habitat for juvenile Gulf Sturgeon. The model hypothesized habitat availability per winter month in estuarine habitat under alternative scenarios of river discharge and length of the winter foraging season. A search for geospatial data sets revealed that the largest gap involved salinity, temperature, and oxygen (i.e., water condition) monitoring data, with data available only for Apalachicola Bay. For the Apalachicola Bay model, data gaps prevented the development of 53% of water condition geospatial data sets and a sensitivity analysis showed that water condition data most limited the ability to predict habitat availability. Expert knowledge was low, and conditional certainty scores showed that the relationships with the lowest certainty were abiotic suitability and habitat availability. Reducing information gaps could aid the development of a model that is appropriate for informing management. Future efforts could prioritize the expansion of water monitoring within critical habitat estuaries and predicting abiotic suitability and habitat availability. Bayesian network models can easily incorporate prior and new information for complex systems. Thus, our model could be updated as future research and monitoring efforts close these information gaps.

These data represent counts of live and dead oysters from line-transect surveys used to evaluate status and trends in intertidal Eastern Oyster (“oyster”) reefs in the Suwannee Sound region of the northeastern Gulf of Mexico. For details on methods and example application see Moore et al. 2020.

The objective of many fish and wildlife restoration programs is to utilize management actions to change the state of a system. Because restoration programs are often expensive, iteratively assessing whether the restoration is having the desired outcome is a critical aspect of learning how to inform ongoing and sampling designs to evaluate proposed restoration programs. We provide an example of how we are using data resampling as part of an adaptive restoration process to test the effectiveness of a restoration action and associated monitoring program to restore the degraded Lone Cabbage oyster reef in Suwannee Sound, Florida in the northeast Gulf of Mexico. We use a resampling framework through simulations to inform the progress of the restoration efforts by examining the direction and magnitude of the differences in live oyster counts between restored and unrestored (wild) reefs over time. In addition, we evaluated the effort (number of sites sampled) needed to determine the effect of restoration to understand how many surveys should be conducted in subsequent sampling seasons. These efforts allow us to provide timely insight into the effectiveness of both our monitoring efforts and restoration strategy which is of critical importance not only to the restoration of Lone Cabbage Reef but to larger restoration efforts within the Gulf of Mexico as part of the consolidated Deepwater Horizon settlements and funded restoration efforts.

Introduction: In 2011, authorities of Quito, the capital city of Ecuador, approved an ordinance to promote public health and animal welfare through responsible pet ownership promotion. The population of dogs was not known, and the relationships between dog abundance, socioeconomic factors, prevalence of zoonotic gastrointestinal parasites, and pet ownership responsibility had not been investigated. The objectives of this study were (1) to estimate the human:dog (HD) ratio, (2) to examine the relationship between household factors and responsible pet ownership, and (3) to estimate the prevalence of households with one or more dogs infected with intestinal parasites in Quito, Ecuador. Methods: Space-based random sampling procedures were used for estimation of HD ratios in free-roaming dogs and confined owned dogs. The relationship between household factors and a Responsible Pet Ownership Index was examined using logistic regression. Dog fecal samples were tested for intestinal parasites. Results: Among stray dogs, the observed HD ratio was 58:1. Among dogs kept indoors, the observed HD ratio was 3.5:1. A positive interaction effect between number of dogs in study households and household living conditions (a proxy for household wealth) on responsible pet ownership was observed, which we discuss in this report. Prevalence of households with dogs infected with intestinal parasites was 28% (95% confidence interval [CI] = 21–37). Ancylostoma spp. was the most frequent intestinal parasite in study dogs kept indoors. Conclusion: This study provides new information that can be used by policy makers to formulate, implement, and evaluate public policies and education programs aimed at enhancing animal welfare and health in Ecuador.

Self-organization is a process of establishing and reinforcing local structures through feedbacks between internal population dynamics and external factors. In reef-building systems, substrate is collectively engineered by individuals that also occupy it and compete for space. Reefs are constrained spatially by the physical environment, and by mortality, which reduces production but exposes substrate for recruits. Reef self-organization therefore depends on efficient balancing of production and occupancy of substrate. To examine this, we develop a three-dimensional individual-based model (IBM) of oyster reef mechanics. Shell substrate is grown by individuals as valves, accumulates at the reef level, and degrades following mortality. Single restoration events and subsequent dynamics are simulated for a case study in South Carolina (USA). Variability in model processes is included on recruitment, spatial environmental constraints, and predation, over multiple independent runs and five predator community scenarios. The main goal for this study is to summarize trends in dynamics that are robust across this uncertainty, and from these generate new hypotheses and predictions for future studies. Simulation results demonstrate three phases following restoration: initial transient dynamics with considerable shell loss, followed by growth and saturation of the live population, and then saturation of settlement habitat several years later. Over half of simulations recoup initial shell losses as populations grow, while others continue in decline. The balance between population density, substrate supporting the reef, and exposed surfaces for settlement is mediated by overall population size and size structure, presence of predators, and relative amounts of live individuals and intact dead shells. The efficiency of settlement substrate production improves through time as population size structure becomes more complex, and the population of dead valves accumulates.

Estimates of animal abundance are widely used to support conservation and resource management. For populations in open systems, abundance estimates from tagging data can be highly uncertain or biased. Here, we develop a novel approach to estimate abundance of an open population by pairing two models, each utilizing distinct tagging data. Using data from telemetry tags, we infer movement rates to and from the study site with a Markovian model allowing for an environmental effect. Then, using data from conventional passive tags, we apply a Lincoln–Petersen abundance estimator modified to account for mortality and movement. After developing the model within a Bayesian framework, we demonstrate its application to data on gray triggerfish (Balistes capriscus) tagged in the Atlantic Ocean off North Carolina, USA. For this open population, we estimate site abundance to be ∼1000 fish (∼2000 fish·km–2) and additionally find evidence for an effect of hurricanes on movement. The general approach may be useful for fisheries, wildlife, and other ecological studies utilizing multiple tag types, particularly for estimating abundance of an open population.