Electronic Thesis and Dissertation Repository

Thesis Format

Integrated Article


Doctor of Philosophy


Statistics and Actuarial Sciences

Collaborative Specialization

Scientific Computing


Bonner, Simon J.


Mark-recapture (MR) models typically assume that individuals under study have independent survival and recapture outcomes. One such model of interest is known as the Cormack-Jolly-Seber (CJS) model. In this dissertation, we conduct three major research projects focused on studying the impact of violating the independence assumption in MR models along with presenting extensions which relax the independence assumption. In the first project, we conduct a simulation study to address the impact of failing to account for pair-bonded animals having correlated recapture and survival fates on the CJS model. We examined the impact of correlation on the likelihood ratio test (LRT), the 𝑐 Μ‚ correction, and the achieved coverage of 95% confidence intervals around the recapture and survival probabilities estimated from the CJS model. We find that correlated fates between mated animals may result in underestimated standard errors for parsimonious models, deflated LRT statistics, and underestimated values of 𝑐 Μ‚ for models taking sex-specific effects into account. In the second project, we present a novel conditional data approach to estimating recapture and survival correlations between mates. We provide a simulation study which demonstrates that for sufficiently large sample sizes the estimators of recapture and survival correlations between mated pairs are unbiased and achieve at least nominal coverage for 95% confidence intervals. The study shows that the variance correction using an alternative 𝑐 Μ‚ estimator addresses the issue of undercoverage and demonstrate the application of my model extension to a mark-recapture dataset of Harlequin ducks (Histrionicus histrionicus), a large monogamous waterfowl species. The final project in this work is focused on presenting extensions to both the CJS and Jolly-Seber (JS) model which allow mortality of members within a group to influence the future survival outcomes of remaining members with Bayesian methods. We conduct a simulation study which demonstrated that the models produce unbiased estimates and credible intervals which achieve nominal coverage. Finally, we apply the CJS model extension to a dataset of Wild Turkeys (Meleagris gallopavo silvestris) and find that there is evidence to suggest that mortality results in reduced survival rates for remaining group members.

Summary for Lay Audience

In the field of statistical ecology, mark-recapture studies are a standard method of estimating the survival outcomes and size of wildlife populations. These studies involve sending researchers to the home range of some species of interest, capturing a subset of the population, placing a non-invasive marking on them, and releasing them back into the wild. The process is repeated over several occasions with researchers making note of which animals they have previously marked, and which marks are new. Once the data has been gathered, demographic parameters are estimated with an ecological model. Two such models are the Cormack-Jolly-Seber and the Jolly-Seber models. These are considered to be standard reliable approaches to estimating survival rates over a period of time. These models have been adapted to account for several different species-specific traits and environmental stressors that may impact survival rates and population sizes such as age, harsh climate, and potential human interference. One long-standing assumption of these modelling techniques is that animals are assumed to have independent fates. Namely, if an animal is killed or leaves their home, this event will not impact the chance of the same thing happening to other members of the population. In many cases, the assumption of independence is likely violated by the complex behaviour of the animal population under study. In this dissertation, we conducted three major research projects to address situations in which the independence assumptions are violated. In the first project, we study the impact that unmodelled correlation between mated pairs, animals that form long-term partnerships with the intention of reproduction, can have on estimates of survival and recapture outcomes in the CJS model. In the second, we follow up on the first study by providing an extension to the CJS model that allows for estimation of recapture and survival correlations between mated pairs. Finally, in the last project, we present extensions to both the JS and CJS models for group-living species, animals which travel in flocks or packs, that allows for within group mortality to impact the survival outcomes of surviving members in future occasions.

Creative Commons License

Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.