Dissertations / Theses on the topic 'Animal behaviour modelling'

This thesis considers mathematical models of the interaction between social and territorial behaviour in animals, mainly by probabilistic methods. Chapter 1 introduces the Resource Dispersion Hypothesis, which suggests that territorial behaviour plus dispersed food resources can explain the existence of social groups, and describes an existing model of the process, due to Carr and Macdonald. In Chapter 2 the model of Carr and Macdonald is analysed, and in Chapter 3 an improved model is suggested and its main properties derived, primarily using renewal theory. Chapters 4 and 5 consider various spatial models for territory formation, and the effect, of spatial factors on social behaviour, using analytic and simulation-based methods. Chapter 6 considers the evolution of social behaviour using both discrete-time deterministic models and branching processes to investigate the viability of different strategies of social behaviour in the presence of dispersed resources.

From the individual to species level, it is common for animals to have connections with one another. These connections can exist in a variety of forms; from the social relationships within an animal society, to hybridisation between species. The structure of these connections in animal systems can be depicted using networks, often revealing non-trivial structure which can be biologically informative. Understanding the factors which drive the structure of animal networks can help us understand the costs and benefits of forming and maintaining relationships. Multivariate modelling provides a means to evaluate the relative contributions of a set of explanatory factors to a response variable. However, conventional modelling approaches use statistical tests which are unsuitable for the dependencies inherent in network and relational data. A solution to this problem is to use specialised models developed in the social sciences, which have a long history in modelling human social networks. Taking predictive multivariate models from the social sciences and applying them to animal networks is attractive given that current analytical approaches are predominantly descriptive. However, these models were developed for human social networks, where participants can self-identify relationships. In contrast, relationships between animals have to be inferred through observations of associations or interactions, which can introduce sampling bias and uncertainty to the data. Without appropriate care, these issues could lead us to make incorrect or overconfident conclusions about our data. In this thesis, we use an established network model, the multiple regression quadratic assignment procedure (MRQAP), and propose approaches to facilitate the application of this model in animal network studies. Through demonstrating these approaches on three animal systems, we make new biological findings and highlight the importance of considering data-sampling issues when analysing networks. Additionally, our approaches have wider applications to animal network studies where relationships are inferred through observing dyadic interactions.

The emergence of collective patterns from repeated local interactions between individuals is a common feature to most living systems, spanning a variety of scales from cells to animals and humans. Subjects of this thesis are two aspects of emergent complexity in living systems: collective movement and transport network formation. For collective movement, this thesis studies the role of movement-mediated information transfer in fish decision-making. The second project on collective movement takes inspiration from granular media and soft mode analysis and develops a new approach to describe the emergence of collective phenomena from physical interactions in extremely dense crowds. As regards transport networks, this thesis proposes a model of network growth to extract simple, biologically plausible rules that reproduce topological properties of empirical ant trail networks.  In the second project on transport networks, this thesis starts from the simple rule of “connecting each new node to the closest one”, that describes ants building behavior, to study how balancing local building costs and global maintenance costs influences the growth and topological properties of transport networks. These projects are addressed through a modeling approach and with the aim of identifying minimal sets of basic mechanisms that are most likely responsible of large-scale complex patterns. Mathematical models are always based on empirical observations and are, when possible, compared to experimental data.

Les bancs de poissons sont des entités pouvant regrouper plusieurs milliers d'individus qui se déplacent de façon synchronisée, dans un environnement sujet à de multiples perturbations, qu'elles soient endogènes (e.g. le départ soudain d'un congénère) ou exogènes (e.g. l'attaque d'un prédateur). La coordination de ces bancs de poissons, décentralisée, n'est pas encore totalement comprise. Si les mécanismes sous-jacents aux interactions sociales proposés dans des travaux précédents reproduisent qualitativement les structures collectives observées dans la nature, la quantification de ces interactions et l'accord quantitatif entre ces mesures individuelles et les motifs collectifs sont encore rares dans les recherches récentes et forment l'objet principal de cette thèse. L'approche de ce travail repose sur une étroite combinaison entre les méthodes expérimentales et de modélisation dans l'objectif de découvrir les liens entre les comportements individuels et les structures observées à l'échelle collective. Nous avons caractérisé et quantifié les interactions et mécanismes à l'origine, d'abord, de la coordination des individus dans les bancs de poissons et, ensuite, de la propagation d'information, quand le groupe subit une perturbation endogène ou exogène. Ces travaux, tous réalisés en étudiant la même espèce de poisson d'eau douce, le nez-rouge (Hemigrammus rhodostomus), ont mobilisé une diversité de méthodes expérimentales, d'analyses statistique et de modélisation, à l'interface de l'éthologie, de la physique statistique et des sciences computationnelles
Fish schools are systems in which thousands of individuals can move in a synchronised manner in a changing environment, with endogenous perturbations (e.g. when a congener leaves the group) or exogenous (e.g. the attack of a predator). The coordination of fish schools, decentralised, is not completely understood yet. If the mechanisms underlying social interactions discussed in previous studies qualitatively match the social patterns observed in nature, the quantification of these interactions and the quantitative match between individual measurements and collective patterns are still sparse in recent works and are the main focus of this thesis. This work combines closely experimental and modelling methods in order to investigate the links between the individual behaviours and the patterns observed at the collective scale. We have characterised and quantified the interactions and mechanisms at the origin of, first, the coordination of individuals in fish schools and, second, the propagation of information, when the group is under endogenous or exogenous perturbations. This thesis focuses on one freshwater fish species, the rummy-nose tetra (Hemigrammus rhodostomus), and is the result of a diversity of experimental methods, statistical analyses and modelling, at the interface of ethology, statistical physics and computational sciences

The Allee effect corresponds to a positive relationship between population size and individual fitness. This positive relationship can cause thresholds, that is, critical population sizes below which the population becomes extinct. For species submitted to the Allee effect, the formation and cohesion of groups is therefore crucial to survival. Animals can achieve this collective behaviour through local interactions. Each individual interacts locally with conspecifics and, at the scale of the group, a unity of behaviour emerges: the animals move together, rest in the same place, or choose the same habitat patch to settle on.

We use a combination of mathematical modelling and experimental work to study certain mechanisms of collective behaviour. In particular we assess the extent to which different individual interactions can induce collective patterns and thereby influence the dynamics of dispersal and settlement of populations. First, we study the collective settlement induced by the arresting effect of a marker secreted by conspecifics. Then, two potential mechanisms for collective movement are examined: following the conspecifics and following a trail laid by conspecifics. Finally, we integrate explicit mechanisms of dispersal behaviour in a dynamic model involving a set of interconnected populations. This allows the study of the interplay between collective movements and Allee effects at the scale of the metapopulation.

Our work is inspired by the lifestyle of the two-spotted spider mite, Tetranychus urticae, a phytophagous pest of recognised agricultural importance. These subsocial mites live in aggregates on the leaf surface, protected by a collectively spun silk web. Experimental evidence suggests that its population dynamics are subject to the Allee effect. Moreover, these mites show a tendency to migrate collectively, which makes them an appropriate biological model.
Doctorat en Sciences
info:eu-repo/semantics/nonPublished

This thesis presents two studies where natural and sexual selection have interacted to evolve sexual behaviours. The thesis uses mathematical modelling to understand how these forces have caused each behaviour to evolve. This is useful because the results allow for reflection on the potential role of sexual selection in adaptation of these species to a changing environment. The first study is of early male arrival to spring breeding grounds in migratory avian species, this is termed protandry. The study explores the main hypotheses for avian protandry and then tests the susceptibility of each hypothesis to changing environment. The second study is of convenience polyandry in species where there is conflict over mating rate. Females have multiple strategies to avoid harassive males but strategies vary in cost and success rate; she must balance her strategy use to minimise her fitness depreciation. The study identifies the main factors that cause convenience polyandry to evolve and paves the way for future studies to investigate if sexual selection over resistance strategy provides these species a future advantage in adaptation to a changing environment.

Animal personality is found in a wide range of taxa, yet our knowledge of what maintains consistent among-individual variation in behaviour is still incomplete. Many personality traits are associated with fitness, leading to the expectation that, under selection, genetic (and among-individual) variation will be eroded over time. Several adaptive models have been developed in order to explain this maintenance of variation. These include state-dependence, state-behaviour feedback loops, life-history and behavioural coadaptation and the Pace of Life syndrome. These models represent good starting points for thinking about what drives and maintains among-individual variation in behaviour, and while empirical support for these models is mixed, one thing they do have in common is the assumption of a significant genetic basis underpinning personality traits. Significant heritability is required for an evolutionary response to selection and for among-individual variation to be adaptive. The univariate estimates of heritability for personality traits that are growing in the literature, while useful, are likely insufficient to predict how personality traits will respond to selection. This thesis uses the Trinidadian guppy, Poecilia reticulata, and other species to explore patterns of among-individual and genetic variation in personality traits, advocating the benefits of using multivariate perspectives throughout. Firstly, the among-individual covariance structure between measures of boldness, growth and metabolic rate are estimated in a test of the Pace of Life syndrome. Secondly, an appraisal of the relative strength of maternal and genetic effects on offspring personality and how it changes over ontogeny. Next, a comprehensive treatment of sexual dimorphism in behaviour and size followed by analysis of genotype-by-sex interactions using both univariate and multivariate methods. Finally, a comparative analysis of personality in 7 species of small fish, identifying the main axis of among-individual variation from a single assay in each and quantifying the phylogenetic signal.

Using trap data the Hawdon, Poulter and South Branch valleys, a spatial distribution model was created for Stoats (Mustela erminea), Ship Rats (Rattus rattus) and Weasels (Mustela nivalis) in the North Branch of the Hurunui River. Ten spatial attributes were analysed in this thesis as potential spatial predictors of Stoats, Ship rats or Weasels; four of which were distance related measurements (distance from ecotonal edge, distance from river, distance from river tributary and distance from trapping edge); three were climate based variables (mean maximum temperature, mean minimum temperature and mean precipitation) and three were topographical based variables (elevation, aspect and slope). Relationships that existed between each spatial attribute and the number of Stoats, Ship Rats and Weasels caught were quantified by comparing the significance of the mean trapping rate with each spatial attribute and expressed spatially as maps in a Geographical Information System (GIS). Results from this thesis found elevation, aspect and distance from ecotonal edge as potential spatial predictors of Stoat populations. Elevation and aspect were found to be potential predictors of Ship rat and Weasel populations. GIS is able to predict the spatial distribution of pest species to a similar (or better) level compared to more formal associative models. The potential of GIS is however, restrained by the same limitations associated with these models. By using a larger trapping data set and identifying a number of social interactions between Stoats, Ship Rats and Weasels, one can improve the accuracy of spatially modelling each species within a Beech forest environment. Therefore, improve our understanding how landscapes influence the distribution of each pest species.

In North America, the grizzly bear (Ursus arcos) is one of many species increasingly threatened by the consequences of human-wildlife conflict, with human-bear encounters on the rise due to increased human activity near or in bear habitat. As a result, a growing number of bears are subjected to management measures such as translocations in which animals are moved to areas with lower risk of human conflict, although these measures are not always successful. Previous research has attempted to understand factors associated with translocation success, but new methods are needed to address the continuous and complex nature of issues related to how animals move and learn about their surroundings as well as how they adapt to novel environments. The objective of my MSc thesis is to develop and employ a novel agent-based computer simulation model to analyze how grizzly bears learn and respond following a translocation event. This modelling effort attempts to capture how bears make decisions based on multiple factors, and represent how grizzly bears interact with their environment and make movement decisions based on learned behaviours. First, an agent-based movement model was developed for female grizzly bears using GPS-location data for bears within a region in west-central Alberta, Canada. The model, which incorporates multi-scale decision-making and machine learning, generated movement patterns similar to those observed in radio-collared females in the study area. Home range sizes and movement metrics produced by the model were consistent with those observed in female grizzly bears in the area. The model was then used to simulate translocation events in which bears with varying “exploration” propensities were translocated to habitats with familiar or novel landscape characteristics. In general, bears translocated to habitats with similar landscape features to their original habitat were more likely to use high-quality habitat than bears moved to areas with very different landscape features. However, while increased exploration led to greater use of high-quality habitat in the long run, exploratory behaviour was found to be mostly detrimental during the first years following a translocation, the period considered critical for translocation success. Model results were found to be scale-dependent with results varying both in time and space, highlighting the need for a multi-scale approach to animal movement studies. The findings presented here also emphasize the need to account for behavioural traits of wildlife and habitat characteristics of the capture and release sites when selecting suitable translocation locations. This work highlights the potential for agent-based modelling as a tool to study animal movement as a continuous and complex process and evaluate conservation policies.
Graduate
2021-08-24

Seabird species are increasingly threatened around the world due to a range of anthropogenic impacts affecting at-sea and breeding habitat. One such species is the Ancient Murrelet, an Alcid species nesting on the Pacific Coast of Canada. Ancient Murrelets are an important species in Canadian waters as approximately 50 % of the world’s breeding population nest in a small region of the British Columbia coast. Ancient Murrelets are listed as a species of Special Concern, due to threats in their breeding colonies; threats to their at-sea habitat, such as disturbance from shipping traffic, oil pollution, and fisheries bycatch, are currently poorly- documented due to the challenges associated with studying seabirds in their offshore environments. Conservation efforts to protect this species require information on movements and habitat use at sea. Therefore, there exists a critical need for research that provides new knowledge on where murrelets are travelling and the habitats in which they are foraging. The objective of this thesis research is to investigate movement behaviour and at-sea habitat of Ancient Murrelets during breeding season foraging trips. Movement modelling using hidden Markov models differentiated the tracks into behaviour states, and identified foraging locations at sea. Foraging locations were used in regression modelling to investigate the degree to which variability in Ancient Murrelet foraging locations could be explained by seafloor depth, slope and tidal current, and spatial measures such as distance from the breeding colony. From characteristics of movement paths, hidden Markov models identified three movement behaviour states, which were interpreted as transit, resting, and foraging behaviours. Logistic regression models suggested that depth, seafloor slope, tidal speed, and distance from the colony exhibited a negative influence on locations where birds chose to forage. Nevertheless, of the locations where foraging took place, foraging intensity was found to be higher in deeper areas suggesting Ancient Murrelets may be focusing efforts in areas of higher prey abundance. The combination of individual movement analysis and habitat analysis provides an important first step in gaining a greater understanding of Ancient Murrelet behaviour and foraging habitat at sea. These findings can inform marine management planning in this region and conservation of this vulnerable species.
Graduate
2021-04-17

Pathogens and parasites are increasingly recognized as important components within host populations, communities, and ecosystems. Parasite contributions to ecosystem function most likely manifest as density-mediated impacts of parasites on their hosts, the direct contributions of parasite biomass to a system, and via parasite-induced changes in host behavior and physiology (trait-mediated impacts). Here, a framework was constructed that can be used to conceptualize parasite contributions to ecosystem function (Chapter 1). Then the influence of parasite attack on host movement was explored to further evince the mechanistic underpinnings of trait-mediated parasite impacts (Chapter 2). Additionally, mesocosms were created across a gradient of parasitism to examine how these mechanisms are likely to unfold at larger biological scales (Chapter 3). Lastly, a series of differential equations was created to model host-parasite-ecosystem interactions and generate theoretical predictions about how and when parasites are likely to influence ecosystem processes (Chapter 4). Parasites have many characteristics of ecosystem engineers, but their role has historically been ignored. These studies begin to explore the role that parasitism may have as one of the drivers of ecosystem processes.

High-resolution bio-logging tools were used to examine the fine-scale foraging behaviors of humpback whales (Megaptera novaeangliae) in the coastal waters of the Western Antarctic Peninsula during the austral autumn of 2009 and 2010. Discrete feeding events (i.e., lunges) were inferred from the biologging records of thirteen whales, including a mother and her calf. In general, humpback whales exhibited efficient foraging behaviors that allowed them to maximize energetic gains and minimize energetic costs as predicted by optimal foraging theory. They fed at a continuous and high rate in the upper portion of the water column (< 100 m) from approximately dusk to dawn when their prey (Antarctic krill, Euphausia superba) were most vulnerable and less costly to acquire (i.e., near the surface). When forced to dive to greater depths, they adjusted their behaviors (e.g., descent and ascent rates) so that they could maximize their foraging durations and increase their lunging rates. In addition, humpbacks appeared to accept short term (i.e., dive by dive) costs associated with depleted oxygen stores in favor of maximizing long term (i.e., daily) energetic gains. Such efficient behaviors are particularly beneficial for mother-calf pairs who have additional energetic costs associated with foraging, such as lactation (mother), growth (calf), and maintaining proximity. In addition, because the physiology of humpback whales is poorly understood yet critically important for predicting their behaviors in response to fluctuations in their environmental conditions, foraging behaviors inferred from the bio-logging records were used to estimate their metabolic rates, oxygen storage capacities, and oxygen replenishment rates under the framework of optimal foraging theory. This research suggests that the current techniques used to estimate humpback whale oxygen stores is appropriate but that the estimation of metabolic rates of humpbacks while foraging and while traveling need to be addressed further. This work aims to increase the current understanding of humpback whale foraging behaviors along the Western Antarctic Peninsula so that appropriate measures can be taken to aid in their recovery and in the sustainability of the Antarctic marine ecosystem.

Dissertation

Le caribou forestier est une espèce menacée au Canada, la principale hypothèse au déclin des populations étant l’intensification de la prédation provoquée par les perturbations anthropiques du paysage. Afin de faire face à cette situation, il est nécessaire d’étudier et comprendre l’impact de l’environnement sur les interactions prédateur-proies entre le caribou et le loup, ainsi qu’avec l’orignal, qui est sa principale proie alternative. Pour cela, cette thèse présente la conception d’un modèle centré sur l’individu des déplacements de ces trois espèces en fonction de leur environnement, dont résulteront les interactions prédateur-proies. Afin de permettre l’application de ce modèle sur de longues périodes, et donc pour un environnement changeant, une méthodologie a été développée, qui s’articule atour de deux aspects principaux. Tout d’abord, la notion de niveaux d’émergence est introduite, permettant d’ordonner les comportements observables du système selon leurs interdépendances, afin de choisir comme trait du modèle un com- portement correspondant au domaine d’applicabilité visé. Ordonner les comportements selon leurs niveaux d’émergence permet également d’identifier la redondance entre les patrons, qui peut être à l’origine d’un phénomène de sur-apprentissage lorsqu’ils sont utilisés lors de la calibration. Dans un second temps, un nouveau protocole pour la calibration et la validation du ou des traits choisis à l’aide des niveaux d’émergence, nommé réplication de système basé sur l’individu (Individual Based System Replication - IBSRtion) est également présenté. Ce protocole met l’emphase sur la modélisation directe, contrairement au principal protocole existant, la modélisation orientée patrons (Pattern Oriented Modelling - POM), et permet une approche empirique en générant artificiellement des données non disponibles ou ne pouvant être récoltées par des études de terrains. IBSRtion a également l’avantage de pouvoir être intégrée dans POM, afin de contribuer à la création d’une méthodologie universelle pour la conception de modèles centrés sur l’individu. Le processus de conception de ce modèle aura entre autre permis de faire une synthèse des connaissances et d’identifier certaines lacunes. Une étude visant à palier le manque de connaissances satisfaisantes sur les réponses comportementales à court-terme des proies face au risque de prédation a notamment permis d’observer que celles-ci sont une combinaison de comportements chroniques et éphémères, et que les mécanismes qui en sont à l’origine sont complexes et non-linéaires. Le résultat de ce travail est un modèle complexe utilisant de nombreux sous-modèles, et calibré de façon empirique, applicable à une grande variété d’environnements. Ce modèle a permis de tester l’impact de l’enfeuillement sur les relations prédateur-proies. Des simulations ont été effectuées pour différentes quantités d’enfeuillement, suivant deux configurations spatiales différentes. Les résultats de simulation suggèrent que des plans d’aménagement considérant également l’habitat de l’orignal pourraient être bénéfiques pour le caribou forestier, car ils permettraient d’améliorer la ségrégation spatiale entre les deux espèces, et donc entre le caribou et le loup. En le couplant avec un module de naissances et de morts naturelles ainsi qu’un modèle d’évolution du paysage, ce modèle permettra par la suite d’évaluer l’impact de plans d’aménagement forestier sur la viabilité des populations de caribou forestier.
Forest-dwelling woodland caribou are considered threatened in Canada. The main hypothesis to the decrease of populations is the intensification of predation provoked by anthropogenic perturbations in the landscape. To deal with this situation, it is necessary to study and to understand the impact of the environment on the predator-prey interactions between the caribou and the wolf, and with the moose, its main alternative prey. In this perspective, this thesis presents the design of an individual-based model of displacements of these three species with respect to their environment, from which the predator-prey interactions will result. To allow for the application of this model for long periods of time, i.e. for changing environments, a methodology has been developed, which is based on two key points. First, the notion of levels of emergence is introduced, allowing to order the different observable comportments of the system according to their inter-dependencies, to help with choosing a trait of the model corresponding to the intended domain of applicability. Ordering the comportments according to their levels of emergence also permits to identify redundancy between patterns, which can lead to over-fitting when they are used for calibration. Second, a new methodology for calibration and validation of the trait(s) chosen by means of the levels of emergence framework is also presented, named Individual Based System Replication (IBSRtion). This protocol emphasizes forward modelling, contrary to the main existing methodology, Pattern Oriented Modelling (POM), and allows to use an empirical approach by artificially generating data that are unavailable or that cannot be obtained by means of field studies. IBSRtion can also be integrated into POM, to contribute to the establish- ment of a universal methodology for the design of individual based models. The design process of this model allowed for a synthesis of existing knowledge and to point out some gaps. More specifically, a study conducted to deal with the lack of sufficient information on the short-term response of prey to predation risk allowed to observe that their behavioural responses to prior presence of predators are a combination of chronic and ephemeral behaviours, and that the mechanisms that produce them are complex and non-linear. The outcome of this work is a complex model, using many sub-models, and calibrated in an empirical fashion, that can be applied to a wide variety of environments. This model allowed to test the impact of the encroachment of deciduous trees on predator-prey relations. Simulations have been run for different quantities of encroachment, according to two different spatial configurations. Simulation results suggest that management plans taking into account the moose’s habitat might benefit woodland caribou, because they could increase spatial segregation between the two species, and thus between caribou and wolf. Coupling this model with a module of birth and natural death, along with a model of landscape transformation, would allow the assessment of the impact of different forest management plans on the viability of woodland caribou populations.