Mark-recapture Models Research Articles

Neckband loss and its effect on apparent survival estimates in Greylag Geese (Anser anser): variation with season, sex and age

Mark-recapture studies enable us to estimate population parameters such as survival, if marks do not impact survival and if marks are not lost. Mark loss can result from external wear and damage, but also behavioural factors may be important and could explain differences between seasons or sexes. We studied Greylag Geese (Anser anser) in eastern Netherlands, ringed with neckbands, leg bands and metal rings (912 geese), observed weekly during 1997–2019 (131,625 observations). Given the double marking and high annual resighting probabilities (neckbands: 0.974, leg rings: 0.639), we quantified neckband loss and the effect of neckbands on apparent survival, using multistate mark-recapture models. Annual neckband loss was 0.038, was higher in males (0.056) than females (0.021) and increased with years since marking, up to 0.098 for males more than 8 years after marking. Neckband loss tended to be higher during December–May than June–November, with most losses occurring in March–April. Both the higher loss in males and the peak in spring in both sexes could result from intraspecific fighting (pulling each other’s neck and neckband). Survival was underestimated in Cormack-Jolly-Seber models that did not account for neckband loss, by up to 0.096 for adult males 6–7 years after marking. Thus, ignoring neckband loss may give erroneous survival differences between sexes and seasons, and overestimate the effect of ageing on survival (i.e. senescence). We did not detect an effect of neckbands on mortality, but statistical power for this test was limited. Neckband loss, although lower nowadays than in studies of decades ago, still impacts survival estimates and should be considered in mark-recapture studies.

Are behaviour and stress-related phenotypes in urban birds adaptive?

Urbanisation is a world‐wide phenomenon converting natural habitats into new artificial ones. Environmental conditions associated with urbanisation represent great challenges for wildlife. Behaviour and stress tolerance are considered of major importance in the adaptation to novel urban habitats and numerous studies already reported behavioural and stress response phenotypes associated with urbanisation, often suggesting they represented adaptations, while rarely demonstrating it.The main goal of this study was to test the adaptive nature of urban shifts in behavioural and stress‐related traits, and by adaptive we mean phenotypic change favouring traits in the same direction as selection.Using 7 years of monitoring of urban and forest great tits, we first tested for differences in exploratory behaviour, aggressiveness and breath rate, between both habitats. Second, we performed habitat‐specific analyses of selection on the three former traits using (a) reproductive success and (b) survival estimated via capture–mark–recapture models, as fitness estimates, to determine whether shifts in these behavioural and stress‐related traits were aligned with patterns of ongoing selection.We found that urban birds displayed higher exploratory behaviour and aggressiveness, and higher breath rate, compared to forest birds. Selection analyses overall revealed that these shifts were not adaptive and could even be maladaptive. In particular, higher handling aggression and higher breath rate in urban birds was associated with lower fitness. Higher exploration scores were correlated with lower survival in both habitats, but higher reproductive success only in forest males. Overall, differences in patterns of selection between habitats were not consistent with the phenotypic divergence observed.Taken together, these results highlight that phenotypic shifts observed in cities do not necessarily result from new selection pressures and could be maladaptive. We hypothesise that divergences in behavioural traits for urban birds could result from the filtering of individuals settling in cities. We thus encourage urban evolutionary scientists to further explore the adaptive potential of behavioural traits measured in urban habitats (a) by replicating this type of study in multiple cities and species, (b) by implementing studies focusing on immigrant phenotypes and (c) by measuring selection at multiple life stages.

New abundance and survival estimates for the critically endangered Taiwanese white dolphin indicate no signs of recovery

Abstract Small populations of cetaceans with restricted ranges are particularly vulnerable to anthropogenic disturbances. The assessment of demographic parameters for these populations can provide meaningful insight into the ways in which they are being impacted by different threats. The Taiwanese white dolphin (TWD), Sousa chinensis taiwanensis, is a subspecies endemic to Taiwan and is classified as Critically Endangered. Multistate robust design mark–recapture models were fitted under a Bayesian framework to estimate demographic parameters and trends for the population from 2010 to 2018. Differences in these parameters by age category and the dolphins' use of their habitat were also explored. Abundance estimates varied from a maximum of 72 in 2010 (95% credible interval (CI) [65, 78]) to a minimum of 61 (95% CI [58, 64]) in 2017. In the oldest age category, abundance estimates varied from 10 (95% CI [10, 11]) in 2013 to 13 (95% CI [10, 13]) in 2016. Modelling showed that, over time, the abundance of dolphins in the oldest age group remained stable, while the remainder of the population, which includes reproductive individuals, experienced a steady decline. This decline is bound to affect the demographic recovery of TWD. Spatial heterogeneity indicated that some areas (i.e. with consistent high occurrences) likely represent important areas for biological functions of the TWD. This suggests that the recovery of the population may be enhanced with immediate and focused actions (such as the ban of gillnet fisheries) in these areas. However, with a small and declining population, reducing threats throughout their entire range is needed, including the new offshore windfarm development being constructed in and adjacent to the dolphin's range. Concerted actions to address known threats, continued monitoring of the population, and education of stakeholders are needed to prevent the extinction of the TWDs.

Physiological links with behavior and fitness: The acute adrenocortical response predicts trappability but not survival in male and female deermice

The “Cort-Fitness” hypothesis predicts a negative relationship between baseline glucocorticoids (GCs) and fitness, although evidence for this hypothesis remains mixed. Such ambiguity could partially exist because blood GCs, typically used in field studies, can fluctuate too rapidly to measure accurately, while the relationship between GCs and trappability is often neglected. Here, by addressing these factors, we examined relationships between GC measures and survival of North American deermice (Peromyscus maniculatus; hereafter deermice) as a model system. To do this, we used more stable GC measures, including the integrated measures of baseline and stress response fecal corticosterone metabolites (FCMs), and downstream measures of neutrophil/lymphocyte ratio (N/L ratio), and body condition score (BCS), to characterize their relationships with survival and trappability. Over two years, deermice were live-trapped monthly, evaluated for BCS, and sampled for feces and blood. Stress response FCMs were evaluated only at first capture. Mark-recapture models, with GC measures as predictors of either survival or trappability, were compared to identify top models. We found that stress response FCMs negatively predicted trappability, and weaker evidence that BCS positively predicted survival. Although the latter provides some support for the “Cort-Fitness” hypothesis, there was no support when using integrated measures. Instead, our findings suggest that deermice with a lower adrenocortical response (i.e. stress response FCMs) were more likely to be captured. Therefore, GC-trappability relationships must be investigated in field studies to avoid linking the wrong GC profile to fitness, and physiological measures other than blood GCs may be useful for detecting GC-fitness patterns.

Seasonal trends in adult apparent survival and reproductive trade-offs reveal potential constraints to earlier nesting in a migratory bird.

Birds aim to optimize resources for feeding young and self-maintenance by timing reproduction to coincide with peak food availability. When reproduction is mistimed, birds could incur costs that affect their survival. We studied whether nesting phenology correlated with the apparent survival of American kestrels (Falco sparverius) from two distinct populations and examined trends in clutch-initiation dates. We estimated apparent survival using multi-state mark-recapture models with nesting timing, nesting success, sex, age, and weather covariates. Nesting timing predicted the apparent survival of successful adults; however, the effect differed between populations. Early nesting kestrels had higher apparent survival than later nesters in the western population, where kestrels have a relatively long nesting season. At the eastern site, where kestrels have a relatively short nesting season, the pattern was reversed-later nesters had higher apparent survival than earlier nesters. Nesting timing did not affect the apparent survival of adults with failed nests suggesting that the energetic cost of producing fledglings contributed to the timing effect. Finally, clutch-initiation dates advanced in the western population and remained static in the eastern population. Given that both populations have seasonal declines in productivity, population-specific survival patterns provide insight into seasonal trade-offs. Specifically, nesting timing effects on survival paralleled productivity declines in the western population and inverse patterns of survival and reproduction in the eastern population suggest a condition-dependent trade-off. Concomitant seasonal declines in reproduction and survival may facilitate population-level responses to earlier springs, whereas seasonal trade-offs may constrain phenology shifts and increase vulnerability to mismatch.

Automated detection of blue whale D-calls using deep learning with a double-observer performance assessment

An automated algorithm for passive acoustic detection of blue whale D-calls is developed based on established deep learning methods for image recognition via the DenseNet architecture. Koogu—an open-source Python package—was used for developing the detector. The detector was trained on annotated acoustic recordings from the Antarctic, and the performance of the detector was assessed by calculating precision and recall using a separate independent dataset also from the Antarctic. Detections from both the human analyst and automated detector were then inspected by a more experienced analyst to identify any calls missed by either approach and to adjudicate whether the apparent false-positive detections from the automated approach were actually true-positives. Lastly, an additional performance assessment was conducted using double-platform methods (via a closed-population Huggins mark recapture model) to assess the probability of detection of both the human analyst and automated detector, based on the assumption of false-positive-free and reconciled detections. According to our double-platform analysis, the automated detector performed very well with higher recall and fewer false-positives that the original human analyst.

Abundance and effect of health status on apparent survival of Guiana dolphins, Sotalia guianensis, in an open embayment in north‐eastern Brazil

Abstract Guiana dolphins (Sotalia guianensis) inhabit shallow waters of the tropical western Atlantic, an area that is now mostly occupied by cities and harbours. Demographic studies have been concentrated in sheltered areas of south/south‐eastern Brazil. This study investigated site fidelity and estimated population abundance and apparent survival of Guiana dolphins in Mucuripe Embayment (ME), on the north‐eastern Brazilian coast, through photo‐identification surveys and closed and open population mark–recapture models, from October 2009 to September 2011. Forty‐six Guiana dolphin groups were recorded (in groups of between one and eight dolphins, with a mean ± SD of 3.49 ± 2.33) in 27 out of 40 surveys. Twenty‐five animals were photo‐identified, with eight considered to have a ‘poor health’ status. The standardized site fidelity index (SSFI) was low (0.25). Using the program capture, the time and heterogeneity model (Mth) resulted in a total abundance estimate of 39, with a Coefficient of Variation (CV) of 21% (95% CI 35–80%). In program mark, model averaging resulted in a total abundance estimate of 33 (CV 32%, 95% CI 30–100%). Using a CV of 21%, the power to detect a decline of 50% during the study period was 0.44 and the power to detect a decline of 5% a year was 0.11. To detect these declines with a 0.90 power, 12 years of monitoring would be necessary. The annual adult apparent survival rate was low (0.71; CV 19%; 95% CI 0.40–0.90), and differed for dolphins in ‘good’ (0.64; CV 28%, 95% CI 0.27–0.89) and ‘poor’ (0.85; CV 22%; 95% CI: 0.23–0.99) health. The low abundance of Guiana dolphins in ME indicates that conservation actions should start immediately, such as creating a marine protected area, continuing awareness campaigns, using by‐catch reduction technologies, developing new regulations, and promoting law enforcement. Monitoring studies must continue with increased effort to reduce uncertainty in estimates and to improve the power to detect trends of decline.

Mark–Recapture Models Accurately Predict Growth Trajectories of Known‐Age Muskellunge in Green Bay, Lake Michigan

AbstractLength‐at‐age data are commonly used to describe growth of fish, and obtaining these data typically involves estimating ages from calcified structures (e.g., fin spines or rays, otoliths, or cleithra). Verifying the accuracy of age and growth estimates for long‐lived fish is often difficult because known‐age fish are not available for all ages in a population. Mark–recapture methods offer nonlethal alternatives for estimating growth of fish that do not require age data. However, few studies have compared growth trajectories estimated from mark–recapture data with trajectories estimated using the standard von Bertalanffy growth function (VBGF) incorporating length‐at‐age data from known‐age fish. We used a robust data set of Muskellunge Esox masquinongy sampled from Green Bay, Lake Michigan, during 1990–2018 to compare growth trajectories estimated from three mark–recapture models and a VBGF fitted to length‐at‐age data from known‐age individuals. Growth trajectories estimated with mark–recapture models were similar to trajectories estimated with a VBGF using known‐age fish. Our results suggest that using recapture of tagged fish provides a viable alternative for describing Muskellunge growth trajectories compared with using ages estimated from calcified structures, where incorrect age estimates represent an additional source of error.

Increasing numbers of killer whale individuals use fisheries as feeding opportunities within subantarctic populations.

Fisheries can generate feeding opportunities for large marine predators in the form of discards or accessible catch. How the use of this anthropogenic food may spread as a new behaviour, across individuals within populations over time, is poorly understood. This study used a 16-year (2003-2018) monitoring of two killer whale Orcinus orca subantarctic populations (regular and Type-D at Crozet), and Bayesian multistate capture-mark-recapture models, to assess temporal changes in the number of individuals feeding on fish caught on hooks ('depredation' behaviour) of a fishery started in 1996. For both populations, the number of depredating individuals increased during the study period (34 to 94 for regular; 17 to 43 for Type-D). Increasing abundance is unlikely to account for this and, rather, the results suggest depredation was acquired by increasing numbers of existing individuals. For regular killer whales, a plateau reached from 2014 suggests that it took 18 years for the behaviour to spread across the whole population. A more recent plateau was apparent for Type-Ds but additional years are needed to confirm this. These findings show how changes in prey availability caused by human activities lead to rapid, yet progressive, innovations in killer whales, likely altering the ecological role of this top-predator.

Applying Multistate Mark-Recapture Models with State Uncertainty to Estimate Survival and Reproduction of Quail

Obtaining unbiased estimates of vital rates and understanding how vital rates change in response to environmental stimuli are a continual pursuit of ecologists. Multistate mark-recapture (MSMR) models provide a flexible framework for evaluating dependent vital rates in a comprehensive analysis. For example, a bird must remain alive during breeding season to initiate a nest (i.e., transition from a nonbreeding to a breeding state); thus, the probability that a bird initiates a nest is dependent on the probability that it is still alive. Traditional MSMR models allow only for the estimation of survival, detection, and state transition parameters and depend on the assumption that observers can correctly classify the true state of the animal without error. If the potential for state misclassification exists, incorporating parameters to estimate state uncertainty will reduce biases in the biological parameters of interest. I applied an MSMR model with state uncertainty (MSMR-SU) to estimate short-term survival, dispersal, and reproduction in translocated scaled quail (Callipepla squamata) reintroduced to a large landscape in West Texas, USA. I tested for the effects of release treatment, source population, age, release location, and year on demographic parameters (e.g., survival, dispersal, nest initiation, renesting rate, and nest success). I demonstrated a novel method of estimating nest initiation and renesting rate for avian species using a MSMR-SU model. MSMR-SU models provide a flexible and rigorous approach for evaluating effects of variables on demographic parameters for quail and other species.

Estimating Pacific walrus abundance and survival with multievent mark-recapture models

Arctic marine ecosystems are undergoing rapid physical and biological change associated with climate warming and loss of sea ice. Sea ice loss will impact many species through altered spatial and temporal availability of resources. In the Bering and Chukchi Seas, the Pacific walrus Odobenus rosmarus divergens is one species that could be impacted by rapid environmental change, and thus, population assessments are needed to monitor changes in the status of this ecologically and culturally important marine mammal. We conducted a 5 yr genetic mark-recapture study to estimate demographic parameters for the Pacific walrus. We developed a Bayesian multievent mark-recapture model to estimate walrus survival and abundance while accounting for age misclassification. We estimated the probability of juvenile annual survival as 0.63 (95% credible interval [CrI]: 0.39-0.87) and adult female annual survival as 0.90 (95% CrI: 0.74-1.00). We estimated total abundance as 256434 (95% CrI: 171047-364659). We provide the first estimate of total Pacific walrus abundance since an aerial survey in 2006, which generated a substantially less precise total population size estimate (129000; 95% CI: 55000-507000). The emerging ecosystem state in the northern Bering and Chukchi Seas will likely result in a decline in Pacific walrus abundance, but there is substantial uncertainty regarding the magnitude of the anticipated decline. Our demographic estimates provide critical information to evaluate future population trends of this subsistence resource vital to communities that border the Bering and Chukchi Seas in the USA and Russia.

Fecundity and density dependence can be estimated from mark–recapture data for making population projections

Abstract Forecasting changes in size and distributions of populations is an essential component of conservation assessments. Such forecasts are only useful for species conservation and management when they are based on robust estimators of fecundity, survival, and density dependence. While apparent survival estimation is the main focus of mark–recapture modeling, fecundity and density dependence are rarely the subject of these models. Here, we present a Bayesian hierarchical framework that can estimate fecundity and density dependence along with age-based survival using only robust-design capture–recapture data. We refer to this framework as RD-pop. We used simulated capture histories to demonstrate that RD-pop can estimate vital rates and their density dependence with little bias. We applied RD-pop to capture history data from Brown Creeper (Certhia americana) and showed that estimates of fecundity are consistent with the breeding biology of this species. Finally, we illustrate that density dependence, even when estimated with uncertainty in the RD-pop framework, regularizes population dynamics and reduces the frequent population extinctions and explosions observed under density-independent models. RD-pop is a useful addition to the current mark–recapture modeling toolbox especially when the goal is to build population models that can make medium- and long-term projections. It can be applied to any population for which long-term robust-design mark–recapture data are available, and with slight modifications (incorporation of weather and climate effects on vital rates) has the potential to facilitate demographic projections under climate change.

The impacts of marking on bats: mark-recapture models for assessing injury rates and tag loss

AbstractThe individual identification of animals is essential for long-term population ecology studies. Injuries and tag loss can negatively impact animal welfare and parameter estimates. We used time-to-failure curves and multistate mark-recapture models to estimate injury rates, body condition decline, tag loss and survival probabilities associated with two tags commonly used in bats: metallic arm bands and steel ball chain collars. We monitored two colonies of Carollia perspicillata at União Biological Reserve, southeastern Brazil, from 2013 to 2019. Every other month, we marked individuals with arm bands, collars or both. Collars did not cause noticeable injuries, but were lost at a higher rate than arm bands (1.5–2.5 times). The arm band-related injury probability between captures was ~ 0.2, and after 17 months half the marked animals developed injuries. Animals marked as juveniles were less likely to get injured than adults. Injuries were associated with a lower body condition in females. Body condition was positively associated with apparent survival; however, a direct effect of arm band injuries on survival estimates was not observed. The tag loss rates caused a negative bias in survival estimates. Mark-recapture studies should evaluate the efficacy of the marking technique, accounting for potential animal injury, tag loss, and bias in parameter estimation. Marking individuals should be limited to studies that monitor species with high recapture probability, using the least harmful tags possible, and balancing the burden to the animals with the potential to generate knowledge.

Population structure, residency, and abundance of whale sharks in the coastal waters off Nosy Be, north‐western Madagascar

Abstract Between September and December, whale sharks (Rhincodon typus) aggregate in the coastal waters off Nosy Be, an island in north‐western Madagascar. Swimming with these sharks has become an important tourism activity, but no formal protection is in place in Madagascar to protect this endangered species from the potential negative effects of tourism or other human impacts. Boat‐based surveys (n = 405) were conducted from tourism vessels from September to December, 2015–2019. For most sightings (98%), whale sharks were sighted while foraging for bait fish at the surface, in association with mackerel tuna (Euthynnus affinis) and seabirds (Sternidae). A total of 408 individual whale sharks were individually photo‐identified over this period. All individuals were immature, and 82% of sexed sharks were male. Sharks ranged from 3.0 to 8.0 m in total length (TL), with a mean TL of 5.65 ± 0.94 m (n = 66) for females and 5.46 ± 1.09 m for males (n = 295). Most sharks (72% of the identified individuals) were only identified once within the study period. Movement modelling showed an open population with a short mean residence time of 7.2 days. Resightings were recorded from up to 12 years apart (2007–2019). Ten sharks were seen in all five seasons during 2015–2019. A basic POPAN mark–recapture model estimated a total population size of 681 (608–763) sharks over the 2015–2019 period. Nosy Be waters are an important foraging ground for juvenile whale sharks. Sighting data demonstrate that a high proportion of the sharks’ preferred habitat lies outside existing protected areas, but within an identified Key Biodiversity Area. National species‐level protection and increased spatial management is warranted to secure the continued presence of whale sharks in this region.

Recent Invaders in Small Mediterranean Islands: Wild Boars Impact Snakes in Port-Cros National Park

Mediterranean islands host unique ecosystems that are particularly vulnerable to invasive species. However, knowledge regarding the precise impact of invasive species on local biodiversity remains limited for many of these systems. Here we report on the negative impacts of invasive wild boars (Sus scrofa) on native snakes on islands in the Mediterranean basin. Capture-mark-recapture was initiated in 2012 on two snake species (Montpellier snake, Malpolon monspessulanus and Ladder snake, Zamenis scalaris) across two islands of Port-Cros National Park. Several wild boars, an invasive species, reached the islands in 2007. They remained confined to small areas of the islands for several years. In Port-Cros, the numbers of wild boars suddenly increased in 2015, and rapidly colonized the whole island damaging vast land surfaces. In Porquerolles, wild boars did not proliferate. This offered an opportunity to examine the impact of wild boar outbreak with a Before-After Control-Impact design (BACI). Snake counts and mark-recapture modeling showed that demographic traits were stable before 2016 for both snake species on both islands. As well as abundance, recruitment, and population growth rate of Montpellier snakes significantly declined where wild boars proliferated but remained constant on the island where they did not. Wild boars probably impacted snake numbers through habitat destruction and direct killing. The rapid decline of snakes (apex predators) and intensive uprooting that strongly damage ground dwelling species (plants, animals) suggest that wild boars represent a serious threat to island biodiversity. As elsewhere around the world, these invasive ungulates proliferate in the Mediterranean basin, they are proficient swimmers and exhibit a remarkably high invasive potential. We recommend vigilance and fast eradication to prevent population outburst; even a few a localized non-proliferating individuals contain the latent potential for devastating outbreaks.

A novel approach to estimate postrelease survival for estuarine fishes

Effective adaptive management of aquaculture-based fisheries enhancement programs requires iterative feedback on the impact of stocking activities. For estuarine finfishes, postrelease survival is particularly challenging to assess where recapture rates are low or difficult to obtain. We describe a novel approach to assess short-term apparent survival of hatchery-reared fish stocked into open estuarine systems and address postrelease behavioral states to quantify weekly survival of common snook (Centropomus undecimalis) after one year of monitoring. Following a weekly spatial and temporal replicate-release design for two experimental releases, 1922 juvenile snook (133–281 mm fork length) were marked with passive integrated transponder (PIT) tags and released among two regions of Phillippi Creek, Florida. Marine-adapted PIT tag antenna arrays detected 79% of released individuals and provided daily resighting histories for analysis with multistate mark-recapture models. Resighting histories were best explained by short-term differences in apparent survival among the first few weeks, and long-term patterns in detectability driven by residency behaviors. Weekly apparent survival rates increased from between 0.25 and 0.52 after the first week to >0.9 after week five. Fork length positively influenced survival for both releases and water height positively influenced detectability for the fall release. The highest survival was observed for individuals released in lower Phillippi Creek in the spring, suggesting lower reaches of tidal creek systems provide ideal release locations for juvenile snook. Further application of this approach will help refine optimal release locations, times, and procedures, promote adaptive management of enhancement programs, and maximize the benefits of strategic, science-based stocking on receiving populations.

Survival and abundance of polar bears in Alaska's Beaufort Sea, 2001-2016.

The Arctic Ocean is undergoing rapid transformation toward a seasonally ice‐free ecosystem. As ice‐adapted apex predators, polar bears (Ursus maritimus) are challenged to cope with ongoing habitat degradation and changes in their prey base driven by food‐web response to climate warming. Knowledge of polar bear response to environmental change is necessary to understand ecosystem dynamics and inform conservation decisions. In the southern Beaufort Sea (SBS) of Alaska and western Canada, sea ice extent has declined since satellite observations began in 1979 and available evidence suggests that the carrying capacity of the SBS for polar bears has trended lower for nearly two decades. In this study, we investigated the population dynamics of polar bears in Alaska's SBS from 2001 to 2016 using a multistate Cormack–Jolly–Seber mark–recapture model. States were defined as geographic regions, and we used location data from mark–recapture observations and satellite‐telemetered bears to model transitions between states and thereby explain heterogeneity in recapture probabilities. Our results corroborate prior findings that the SBS subpopulation experienced low survival from 2003 to 2006. Survival improved modestly from 2006 to 2008 and afterward rebounded to comparatively high levels for the remainder of the study, except in 2012. Abundance moved in concert with survival throughout the study period, declining substantially from 2003 and 2006 and afterward fluctuating with lower variation around an average of 565 bears (95% Bayesian credible interval [340, 920]) through 2015. Even though abundance was comparatively stable and without sustained trend from 2006 to 2015, polar bears in the Alaska SBS were less abundant over that period than at any time since passage of the U.S. Marine Mammal Protection Act. The potential for recovery is likely limited by the degree of habitat degradation the subpopulation has experienced, and future reductions in carrying capacity are expected given current projections for continued climate warming.

Within‐year and among‐year variation in impacts of targeted conservation management on juvenile survival in a threatened population

Abstract Overall impacts of targeted conservation interventions on population growth rate (λ) will depend on within‐year and among‐year variation in exposure of target individuals to interventions, and in intervention efficacy in increasing vital rates of exposed individuals. Juvenile survival is one key vital rate that commonly varies substantially within and among years, and consequently drives variation in λ. However, within‐year, among‐year and overall impacts of targeted interventions on population‐wide survival probabilities of potentially mobile juveniles are rarely quantified, precluding full evaluation and evidence‐based refinement of interventions. We applied multi‐state mark–recapture models to 8 years of ring–resighting data from a threatened red‐billed chough Pyrrhocorax pyrrhocorax population to quantify within‐year and among‐year variation in juvenile exposure to a targeted intervention of supplementary feeding and parasite treatment, and to estimate efficacy in increasing juvenile survival probability. We then combined and up‐scaled these estimated effects to evaluate the impact of the 8‐year intervention on overall population‐wide survival probability and resulting population size. High proportions of surviving juveniles (>70%) were exposed to the intervention across the annual biological cycle in all years. Exposure was associated with higher short‐term survival probabilities through the full annual cycle. Consequently, management increased estimated population‐wide annual juvenile survival by approximately 0.14. However, such effects were only evident in cohorts with low overall annual survival. Population models projected that these impacts on annual juvenile survival substantially reduced population decline, such that population size at the end of the 8‐year intervention was approximately double that without management. Synthesis and applications. Our results show how complex patterns of within‐year and among‐year variation in exposure and efficacy of targeted conservation interventions can arise and scale up to affect population‐level outcomes. We demonstrate overall positive effects of a joint supplementary feeding and parasite treatment intervention on the focal chough population, but also highlight potential routes to improve efficacy, for example, through more precise targeting of interventions and agricultural management actions in the context of among‐year variation in environmental conditions.

Incorporating antenna detections into abundance estimates of fish

Autonomous passive integrated transponder (PIT) tag antennas are commonly used to detect fish marked with PIT tags but cannot detect unmarked fish, creating challenges for abundance estimation. Here we describe an approach to estimate abundance from paired physical capture and antenna detection data in closed and open mark–recapture models. Additionally, for open models, we develop an approach that incorporates uncertainty in fish size, because fish size changes through time (as fish grow bigger) but is unknown if fish are not physically captured (e.g., only detected on antennas). Incorporation of size uncertainty allows for estimation of size-specific abundances and demonstrates a generally useful method for obtaining state-specific abundances estimates under state uncertainty. Simulation studies comparing models with and without antenna detections illustrate that the benefit of our approach increases as a larger proportion of the population is marked. When applied to two field data sets, our approach to incorporating antenna detections reduced uncertainty in abundance substantially. We conclude that PIT antennas hold great potential for improving abundance estimation, despite the challenges they present.

From drought to deluge: spatiotemporal variation in migration routing, survival, travel time and floodplain use of an endangered migratory fish

We developed a novel statistical model to relate the daily survival and migration dynamics of an endangered anadromous fish to river flow and water temperature during both extreme drought and severe flooding in an intensively managed river system. Our Bayesian temporally stratified multistate mark–recapture model integrates over unobserved travel times and route transitions to efficiently estimate covariate relationships and includes an adjustment for telemetry tag battery failure. We applied the model to acoustic-tagged juvenile Sacramento River winter-run Chinook salmon (Oncorhynchus tshawytscha) and found that survival decreased with decreasing river flows and increased water temperatures. We found that fish were likely to enter a large floodplain during flood conditions and that survival in the floodplain was comparable to the mainstem Sacramento River. Our study demonstrates the response of an endangered anadromous fish population to extreme spatial and temporal variability in habitat accessibility and quality. The general model framework we introduce here can be applied to telemetry of migratory fish through systems with multiple routes to efficiently estimate spatiotemporal variation in survival, travel time, and routing.