Doctor of Philosophy in Interdisciplinary Studies (PhD)
Bridging Indigenous Knowledge and western science to better understand animal behaviour and habitat use
Fun amongst the Gentoo colony with @AugerMethe. Much learned, hilarious field moments had, and all the penguins tagged! Cheers to a #GreatSupervisor at #UBC @UBCoceans
Dissertations completed in 2010 or later are listed below. Please note that there is a 6-12 month delay to add the latest dissertations.
Animal behaviour may represent an early response to variation in habitat suitability. Identifying factors that promote behaviours may be particularly important in areas undergoing environmental change. Recent advances in remote tracking, satellite imagery, and associated methodologies have enabled behavioural research in animals occupying remote environments where direct observation is impractical. Moving habitats (e.g., drifting sea ice) elicit complex behaviours, affect the apparent movement of animals, and are associated with high observation error. In this thesis, I investigated the foraging ecology of polar bears (Ursus maritimus) during the winter. First, I investigated the accuracy of a commonly used model for sea ice motion using dropped GPS collars. I showed that these satellite-based models underestimate the drift speed and have large errors estimating its direction at low speeds. Second, I developed models for remote-tracking data to study behaviours with orientation bias (e.g., relative to wind). Using a popular class of statistical models, hidden Markov models, I developed movement models that allow for error-prone environmental data. I showed that my method effectively recovered behaviour and outperformed other methods when faced with coarse environmental data. Last, I developed a model to correct for sea ice drift and investigated the effect of diurnal, seasonal, and environmental covariates on polar bear behaviour. I identified a peak in diurnal activity later in the day compared to other populations, as well as an increase in activity as the season progressed, which may be indicative of an increase in active foraging. I also identified spatial patterns of distribution with respect to season, ice concentration, and bear age that may reflect high habitat quality in western Hudson Bay and the potential presence of competitive exclusion. My thesis provides a novel assessment of the error present in remotely-sensed sea ice drift models and data that can be used to improve them in the future. In addition, my thesis presents models that can be applied to investigate important, and previously difficult to model, behaviours with orientation bias across taxa. Finally, my thesis expands on our understanding of polar bear foraging ecology with novel insights on its association with the environment.
Spatio-temporal statistical methods are widely used to model natural phenomena across both space and time. Example phenomena include the concentrations of airborne pollutants and the distributions of endangered species. A spatio-temporal process is said to have been preferentially sampled when the locations and/or times chosen to observe it depend stochastically on the values of the process at the chosen locations and/or times. When standard statistical methodologies are used, predictions of a preferentially sampled spatio-temporal process into unsampled regions and times may be severely biased. Preferential sampling within spatio-temporal data may be the rule rather than the exception in practice. The work demonstrated in this dissertation addresses the issue of preferential sampling. We develop the first general framework for modelling preferential sampling in spatio-temporal data and apply it to historical UK black smoke measurements. We demonstrate that existing estimates of population-level black smoke exposures may be highly inaccurate due to preferential sampling. By leveraging the information contained in the chosen sampling locations, we can adjust estimates of black smoke exposure to the presence of preferential sampling. Next, we develop a fast, intuitive, powerful, and general test for preferential sampling. A user-friendly R-package we wrote performs the test. We demonstrate its utility in both a thorough simulation study and by successfully replicating previously-published results on preferential sampling. Finally, we adapt our ideas on preferential sampling to the setting of spatio-temporal point patterns. By considering the observed point pattern as a spatio-temporal thinned, marked log-Gaussian Cox process, we show that preferential sampling can be directly accounted for within the model. Under certain assumptions, the true distribution of locations can then be attained. Using these ideas, we develop a framework for combining multiple data sources to estimate the spatio-temporal distribution of an animal. We then apply our framework to estimate effort-corrected space-use of an endangered ecotype of killer whales. Ultimately, we hope that investigations into preferential sampling will become an essential component within spatio-temporal analyses, akin to model diagnostics. The methods developed in this dissertation are widely applicable, allowing researchers to routinely perform such investigations.
Theses completed in 2010 or later are listed below. Please note that there is a 6-12 month delay to add the latest theses.
Arctic terns are iconic seabirds, famous for annual migrations between the Arctic and Antarctic. Recent assessment suggests they are one of the most vulnerable seabirds to climate change. Its wide geographical range hinders the detection of hazards faced by the species during its annual bi-hemispheric movements. Although Arctic terns breed in the Pacific, Atlantic and Arctic coasts of North America, few tracking studies have been conducted on North American Arctic terns, and none in Canada, which represents a significant proportion of their circumpolar breeding range. Using light-level geolocators, I tracked 53 Arctic terns from 5 breeding colonies across a wide latitudinal and longitudinal range within North America. In Chapter 2, I compared the routes taken by terns in our study to those previously tracked from Greenland, The Netherlands, Sweden, Norway, Maine (USA), and Alaska (USA). Most Arctic terns tracked globally used one of three southbound migration routes: 1) Atlantic West Africa; 2) Atlantic Brazil; 3) Pacific coastal, and one of two northbound migration routes: 1) Mid-ocean Atlantic; 2) Mid-ocean Pacific. These migration corridors were also used by many other trans-equatorial seabirds, suggesting that Arctic tern routes are important for multiple seabird species. However, my results show little overlap between these routes and internationally-recognized Waterbird Flyways. This research suggests that Arctic tern migration habitat, where they spend 4-6 months per year, is currently mostly unprotected and that identification of seabird-specific flyways would benefit seabird conservation. These novel findings could inform international discussions for the protection of primary migratory corridors of vulnerable seabirds. In Chapter 3, I analyzed the factors that explained individual migratory variation among Arctic terns by using wet-activity data simultaneously recorded by the geolocators. Southbound migration was longer in duration than northbound, and colony latitude best explained this seasonal difference and total duration of each migration. Daily individual variation was also greater during the northbound migration, suggesting breeding terns potentially travel faster than non-breeding terns. Two individuals exhibited previously-unknown migration strategies of staying on-land or resting mid-flight. While migration routes are shared, migration duration is variable across colonies and individuals, suggesting that timing should be considered in flyways conservation.
In contrast with the endangered southern resident killer whales (SRKWs), the northern resident killer whales (NRKWs) have been thriving in their habitats. The main hypotheses proposed to explain the differences in survival of these population are associated with differential reproductive output, body compositions, and feeding rates. Testing some of these hypotheses requires researchers to identify prey captures for these animals. As these events are difficult to directly observe through field operations, researchers equip whales with suction-cup attached biologgers and use kinematic variables during the bottom phase of a dive to predict prey captures. However, universal definitions of the bottom phase have not been established and often appear arbitrarily chosen, leading to potentially over or underestimating foraging events. Using the diving and kinematic data collected from three NRKWs, I show that modifying the bottom phase greatly impacts existing methods used to predict prey capture events. To investigate bottom phase definition variability, I then asked several whale researchers to identify the bottom phase of various dives via an interactive study. Linear mixed-effects model analyses showed that there exists substantial variation in bottom phase definitions across different researchers and across different dive types. I compared several statistical models of the start and end of the bottom phase of a dive, including modifications to existing methods, linear regression models, and functional linear regression models. Compared to the currently used bottom phase definitions, using the model based definitions resulted in significant improvements when predicting prey capture dives. Furthermore, these proposed models offer substantial increases in prediction accuracy of the bottom phase of a dive when comparing these model predictions and the currently used methods to the user-provided bottom phases. Finally, I formulated two methods to determine an adequate sample size for fitting these statistical models. The results of both methods show that an adequate sample size of approximately 50-100 dives can be used to obtain satisfactory model predictions for this data. This work shows that dive phase definitions may impact the results of many existing studies and should be emphasized as an important part of analyzing diving data.
Within any population, certain individuals outperform other members of their species. However, the precise basis for their advantage largely remains a mystery in ecology. In the last decade, research on the variability in foraging behaviour and diet between individuals has become a focus for ecologists as a potential mechanism for individual advantage. The numbers of breeding pairs of gentoo penguins in the Falkland Islands fluctuate annually, and while the precise cause of deferred breeding is unknown, carryover effects from the previous winter period are likely an important factor. Blood oxygen-carrying capacity and body mass are proposed to be critical carryover effects from winter influencing the reproductive trade-off of participating in breeding in the following spring, given their proposed influence on the diving ability and hence foraging capacity of penguins. In this thesis, I investigate (1) if interindividual variation in diving efficiency is associated with the condition of oxygen stores through i) blood oxygen-carrying capacity, using blood hemoglobin (Hb) and hematocrit (Hct) as indicators, and ii) body mass, and (2) if pre-breeding foraging effort differs between individuals based on their condition of oxygen stores and breeding status. Through monitoring penguins with time-depth recorders, I explored how Hb, Hct, and body mass influenced a penguin’s ability to dive efficiently (maximize bottom time) over their natural range of foraging depths. Subsequently, I monitored breeding participation and egg lay date to assess the reproductive status of individuals. Reduced blood oxygen-carrying capacity was found to negatively impact dive efficiency, and the effect was most influential during deeper dives. Penguins with higher Hb and an apparent optimum Hct of 52 % performed best. Pre-breeding foraging effort was predictive of reproductive status, as early laying penguins exhibited lower foraging effort and spent less time at sea than non-breeding penguins. How diving behaviour corresponds to breeding participation is essential to understand the effects ecosystem changes have on populations, and knowledge gained here could have broad implications for the conservation of this genus and many diving species.