Capture–recapture models with heterogeneity to study survival senescence in the wild

Detecting senescence in wild populations and estimating its strength raise three challenges. First, in the presence of individual heterogeneity in survival probability, the proportion of high‐survival individuals increases with age. This increase can mask a senescence‐related decrease in survival probability when the probability is estimated at the population level. To accommodate individual heterogeneity we use a mixture model structure (discrete classes of individuals). Second, the study individuals can elude the observers in the field, and their detection rate can be heterogeneous. To account for detectability issues we use capture–mark–recapture (CMR) methodology, mixture models and data that provide information on individuals’ detectability. Last, emigration to non‐monitored sites can bias survival estimates, because it can occur at the end of the individuals’ histories and mimic earlier death. To model emigration we use Markovian transitions to and from an unobservable state. These different model structures are merged together using hidden Markov chain CMR models, or multievent models. Simulation studies illustrate that reliable evidence for survival senescence can be obtained using highly heterogeneous data from non site‐faithful individuals. We then design a tailored application for a dataset from a colony of black‐headed gull Chroicocephalus ridibundus. Survival probabilities do not appear individually variable, but evidence for survival senescence becomes significant only when accounting for other sources of heterogeneity. This result suggests that not accounting for heterogeneity leads to flawed inference and/or that emigration heterogeneity mimics survival heterogeneity and biases senescence estimates.     

Effect of haemosporidian infections on host survival and recapture rate in the blue tit

Parasites are ubiquitous in the wild and by imposing fitness costs on their hosts they constitute an important selection factor. One of the most common parasites of wild birds are Plasmodium and Haemoproteus, protozoans inhabiting the blood, which cause avian malaria and malaria‐like disease, respectively. Although they are expected to cause negative effects in infected individuals, in many cases studies in natural populations failed to detect such effect. Using data from seven breeding seasons (2008–2014), we applied a multistate capture–mark–recapture approach to study the effect of infection with malaria and malaria‐like parasites, individual age and sex on the probability of survival and recapture rate in a small passerine, the blue tit Cyanistes caeruleus, inhabiting the island of Gotland, Sweden. We found no effect of infection on survival prospects. However, the recapture rate of infected individuals was higher than that of uninfected ones. Thus, while our data do not support the presence of infection costs in terms of host survival, it suggests that parasites from the genera Plasmodium and Haemoproteus may affect some aspects of host behaviour, which translates into biased estimation of infection frequency at the population level.     

Estimability of migration survival rates from integrated breeding and winter capture–recapture data

Long‐distance migration is a common phenomenon across the animal kingdom but the scale of annual migratory movements has made it difficult for researchers to estimate survival rates during these periods of the annual cycle. Estimating migration survival is particularly challenging for small‐bodied species that cannot carry satellite tags, a group that includes the vast majority of migratory species. When capture–recapture data are available for linked breeding and non‐breeding populations, estimation of overall migration survival is possible but current methods do not allow separate estimation of spring and autumn survival rates. Recent development of a Bayesian integrated survival model has provided a method to separately estimate the latent spring and autumn survival rates using capture–recapture data, though the accuracy and precision of these estimates has not been formally tested. Here, I used simulated data to explore the estimability of migration survival rates using this model. Under a variety of biologically realistic scenarios, I demonstrate that spring and autumn migration survival can be estimated from the integrated survival model, though estimates are biased toward the overall migration survival probability. The direction and magnitude of this bias are influenced by the relative difference in spring and autumn survival rates as well as the degree of annual variation in these rates. The inclusion of covariates can improve the model's performance, especially when annual variation in migration survival rates is low. Migration survival rates can be estimated from relatively short time series (4–5 years), but bias and precision of estimates are improved when longer time series (10–12 years) are available. The ability to estimate seasonal survival rates of small, migratory organisms opens the door to advancing our understanding of the ecology and conservation of these species. Application of this method will enable researchers to better understand when mortality occurs across the annual cycle and how the migratory periods contribute to population dynamics. Integrating summer and winter capture data requires knowledge of the migratory connectivity of sampled populations and therefore efforts to simultaneously collect both survival and tracking data should be a high priority, especially for species of conservation concern.     

A simulation study of three methods for estimating selective values and survival rates from recapture data

The methods ofManly (1973),Manly (1975) andManly (1977) for estimating survival rates and relative survival rates from recapture data have been compared by computer simulation. In the simulations batches of two types of animal were “released” at one point in “time” and recapture samples were taken at “daily” intervals from then on. The various methods of estimation were then used to estimate, the daily survival rates of type 1 and type 2 animals, and also the survival rate of the type 2 animals relative to the type 1 animals. Simulation experiments were designed to examine (a) the bias in estimates, (b) the relative precision of different methods of estimation, (c) the validity of confidence intervals for true parameter values, and (d) the effect on estimates of the failure of certain assumptions.     

Observations of growth and postspawning survival of lumpfish Cyclopterus lumpus from mark‐recapture studies

Growth and postspawning survival of lumpfish Cyclopterus lumpus are described by mark‐recapture experiments using juveniles in offshore areas in the north‐east Atlantic Ocean and spawning adults in coastal Norway and Iceland. A female fish tagged as a juvenile and recaptured as an adult matured in a period of 18 months, providing the first observation on development in a wild C. lumpus. The von Bertalanffy growth function, fitted to data from recaptured fish, was used to estimate K and L_∞ and recaptured fish spawning after a year at liberty indicated a postspawning survival of c. 10% in Iceland.     

Movement patterns and study area boundaries: influences on survival estimation in capture–mark–recapture studies

The inability to account for the availability of individuals in the study area during capture–mark–recapture (CMR) studies and the resultant confounding of parameter estimates can make correct interpretation of CMR model parameter estimates difficult. Although important advances based on the Cormack–Jolly–Seber (CJS) model have resulted in estimators of true survival that work by unconfounding either death or recapture probability from availability for capture in the study area, these methods rely on the researcher's ability to select a method that is correctly matched to emigration patterns in the population. If incorrect assumptions regarding site fidelity (non‐movement) are made, it may be difficult or impossible as well as costly to change the study design once the incorrect assumption is discovered. Subtleties in characteristics of movement (e.g. life history‐dependent emigration, nomads vs territory holders) can lead to mixtures in the probability of being available for capture among members of the same population. The result of these mixtures may be only a partial unconfounding of emigration from other CMR model parameters. Biologically‐based differences in individual movement can combine with constraints on study design to further complicate the problem. Because of the intricacies of movement and its interaction with other parameters in CMR models, quantification of and solutions to these problems are needed. Based on our work with stream‐dwelling populations of Atlantic salmon Salmo salar, we used a simulation approach to evaluate existing CMR models under various mixtures of movement probabilities. The Barker joint data model provided unbiased estimates of true survival under all conditions tested. The CJS and robust design models provided similarly unbiased estimates of true survival but only when emigration information could be incorporated directly into individual encounter histories. For the robust design model, Markovian emigration (future availability for capture depends on an individual's current location) was a difficult emigration pattern to detect unless survival and especially recapture probability were high. Additionally, when local movement was high relative to study area boundaries and movement became more diffuse (e.g. a random walk), local movement and permanent emigration were difficult to distinguish and had consequences for correctly interpreting the survival parameter being estimated (apparent survival vs true survival).     

Combining capture–recapture data and known ages allows estimation of age‐dependent survival rates

In many animal populations, demographic parameters such as survival and recruitment vary markedly with age, as do parameters related to sampling, such as capture probability. Failing to account for such variation can result in biased estimates of population‐level rates. However, estimating age‐dependent survival rates can be challenging because ages of individuals are rarely known unless tagging is done at birth. For many species, it is possible to infer age based on size. In capture–recapture studies of such species, it is possible to use a growth model to infer the age at first capture of individuals. We show how to build estimates of age‐dependent survival into a capture–mark–recapture model based on data obtained in a capture–recapture study. We first show how estimates of age based on length increments closely match those based on definitive aging methods. In simulated analyses, we show that both individual ages and age‐dependent survival rates estimated from simulated data closely match true values. With our approach, we are able to estimate the age‐specific apparent survival rates of Murray and trout cod in the Murray River, Australia. Our model structure provides a flexible framework within which to investigate various aspects of how survival varies with age and will have extensions within a wide range of ecological studies of animals where age can be estimated based on size.     

One step forward: contrasting the effects of Toe clipping and PIT tagging on frog survival and recapture probability

Amphibians have been declining worldwide and the comprehension of the threats that they face could be improved by using mark–recapture models to estimate vital rates of natural populations. Recently, the consequences of marking amphibians have been under discussion and the effects of toe clipping on survival are debatable, although it is still the most common technique for individually identifying amphibians. The passive integrated transponder (PIT tag) is an alternative technique, but comparisons among marking techniques in free‐ranging populations are still lacking. We compared these two marking techniques using mark–recapture models to estimate apparent survival and recapture probability of a neotropical population of the blacksmith tree frog, Hypsiboas faber. We tested the effects of marking technique and number of toe pads removed while controlling for sex. Survival was similar among groups, although slightly decreased from individuals with one toe pad removed, to individuals with two and three toe pads removed, and finally to PIT‐tagged individuals. No sex differences were detected. Recapture probability slightly increased with the number of toe pads removed and was the lowest for PIT‐tagged individuals. Sex was an important predictor for recapture probability, with males being nearly five times more likely to be recaptured. Potential negative effects of both techniques may include reduced locomotion and high stress levels. We recommend the use of covariates in models to better understand the effects of marking techniques on frogs. Accounting for the effect of the technique on the results should be considered, because most techniques may reduce survival. Based on our results, but also on logistical and cost issues associated with PIT tagging, we suggest the use of toe clipping with anurans like the blacksmith tree frog.     

On the design of closed recapture experiments

We propose a method to plan the number of occasions of recapture experiments for population size estimation. We do so by fixing the smallest number of capture occasions so that the expected length of the profile confidence interval is less than or equal to a fixed threshold. In some cases, we solve the optimization problem in closed form. For more complex models we use numerical optimization. We detail models assuming homogeneous, time‐varying, subject‐specific capture probabilities, behavioral response to capture, and combining behavioral response with subject‐specific effects. The principle we propose can be extended to plan any other model specification. We formally show the validity of the approach by proving distributional convergence. We illustrate with simulations and challenging examples in epidemiology and ecology. We report that in many cases adding as few as two sampling occasions may substantially reduce the length of confidence intervals.     

Resident and transient dynamics, site fidelity and survival in wintering Blackcaps Sylvia atricapilla: evidence from capture–recapture analyses

In their winter quarters, migrant birds may either remain within a small area (resident strategy) or move frequently over a large area looking for locally abundant food (transient strategy). It has been suggested that both strategies could simultaneously occur in the same population. We used time-since-marking capture–recapture models to infer the coexistence of these two behavioural strategies (transient and resident) among wintering Blackcaps Sylvia atricapilla using weekly recapture data over a 7-year period. A related question is whether Blackcaps, if surviving to the next winter, always return to the same wintering area, so we also used this approach to analyse winter site fidelity and to estimate annual survival probabilities. Model selection supported the existence of heterogeneity in survival estimates for both the within-season and the interannual survival probabilities, i.e. there was evidence for the existence of transients. It was estimated that 26% of the Blackcaps were resident during the winter. Mean apparent annual survival probability was 0.46 (se = ±0.11). However, there was some evidence suggesting that not all individuals showed winter site fidelity. The estimated proportion of individuals that, if alive, returned to the wintering area was 28%. This is the first study to show the existence of these two behavioural strategies (residence and transience) among wintering Blackcaps, and the first confirming this pattern using capture–recapture models. These models considering transient and resident dynamics may become an important tool with which to analyse wintering strategies.     

Mark‐recapture modeling accounting for state uncertainty provides concurrent estimates of survival and fecundity in a protected harbor seal population

Harbor seal breeding behavior and habitats constrain opportunities for individual‐based studies, and no current estimates of both survival and fecundity exist for any of the populations studied worldwide. As a result, the drivers underlying the variable trends in abundance exhibited by harbor seal populations around the world remain uncertain. We developed an individual‐based study of harbor seals in northeast Scotland, whereby data were collected during daily photo‐identification surveys throughout the pupping seasons between 2006 and 2011. However, a consequence of observing seals remotely meant that information on sex, maturity‐stage, or breeding status was not always available. To provide unbiased estimates of survival rates we conditioned initial release of individuals on the first time sex was known to estimate sex‐specific survival rates, while a robust design multistate model accounting for uncertainty in breeding status was used to estimate reproductive rate of multiparous and ≥3‐yr‐old females. Survival rates were estimated at 0.95 (95% CI = 0.91–0.97) for females and 0.92 (0.83–0.96) for males, while reproductive rate was estimated at 0.89 (0.75–0.95) for multiparous and 0.69 (0.64–0.74) for ≥3‐yr‐old females. Stage‐based population modeling indicated that this population should be recovering, even under the current shooting quotas implemented by the recent management plan.