Behavioural ecology of the black-flanked rock-wallaby (Petrogale lateralis lateralis): Refuge importance in a variable environment

The black-flanked rock-wallaby (Petrogale lateralis lateralis) has suffered a significant decline in its distribution in Western Australia. This has been attributed to introduced predators (predominantly the red fox) and herbivores, fire, and habitat destruction due to clearing. Although since 2001 the Department of Environment and Conservation (DEC) had begun to reintroduce this species back into its former range, little was known of the behavioural ecology of this species. Fox control in the 1980s and 1990s resulted in population increases of rock-wallabies on several reserves in the central wheatbelt of WA. However, recently these populations have rapidly declined despite continuing fox control. All too often, management and conservation programs are based on little understanding on the natural history and ecology of animals, which can ultimately result in poor management. One of the major problems with our understanding of the ecology of P. l. lateralis was that there was little information on their behavioural, foraging and feeding patterns, and how these affect the population dynamics of the species. Although this species appears to be substrate bound, requiring complex rock structures that are believed to protect them from both predators and adverse climatic conditions, there was still little understanding of how these animals utilise this important resource, particularly in highly variable environments. There is a long-standing premise in behavioural ecology that highly variable environments can significantly affect the behaviour and demography of animal populations. Although this has been well documented in birds, and primates, behavioural elements are rarely incorporated into marsupial studies. For the success of any current and future reintroductions of rock- wallaby populations into new areas, we needed to understand the relationships between the landscape and climatic elements and the behavioural patterns and population dynamics of the species’. This study describes the behavioural ecology of the rock-wallaby subspecies P. l. lateralis in the central wheatbelt region of Western Australia. It focuses on environmental variables that have rarely been studied simultaneously, those of climate, fear of predation and conspecifics, and habitat structure. The Nangeen Hill Reserve population was chosen because it is one of seven small fragmented reserves, within a landscape, with strong seasonal climatic patterns. A methodological approach was developed that enabled identification of the key ecological determinants of the foraging and feeding behaviours of P. l. lateralis in this highly variable environment. The study included a comprehensive examination of all the behavioural characteristics and abilities of P. l. lateralis, compiling a detailed behavioural repertoire (ethogram), a first for this species, and included both nocturnal and diurnal observations. P. l. lateralis uses a complex arrangement of non-agonistic and agonistic behavioural acts that determines its social organisation, and indicates a linear dominance hierarchy. There is little vocal communication, and instead the rock-wallabies appear to rely on both ritualised behaviour acts and chemical cues to exchange information about the physiological or behavioural state of the individual, thus evolving very diverse and complex social behaviours. Nangeen Hill rock-wallabies occupy a permanent central rock refuge, with strong signs of site fidelity. Their foraging patterns reflect those of a central place forager, but distances travelled are restricted in open habitats, with stronger preferences for areas of rock structural complexity. Their foraging behaviour is not strictly nocturnal nor can it be considered crepuscular, exhibiting significantly different seasonal patterns. Time allocation for foraging is strongly affected by fear of predators and to a lesser extent conspecifics, and certain climatic conditions. Although rock-wallabies use multiple behavioural strategies to reduce predation risk, energy costs, and intraspecific agonistic interactions, they can only can survive in their present environment if they have access to complex rock refuge. This rock resource not only enables them to avoid extreme ambient temperatures, but also gives them protection against predators particularly when environmental conditions are unfavourable. In addition, their cave refuge also gives them protection from precipitation, reducing heat loss, and provides a safe environment for both rearing young and for courtship without the cost of predation. Rock refuge is the most important resource that defines this species and is central to all aspects of its life history. Although this reserve has been under a fox-baiting program since 1982, and subsequently resulted in a rock-wallaby population increase and habitat expansion, within the rocky outcrop (Kinnear et al., 1998), it was clear from my research that the ecological situation was more complex. There is a strong predation influence on the behaviour indicating that the population is now predominantly fear-driven. It is the fear of predators and dominant conspecifics that restricts both the foraging range and time spent feeding. This results in animals being tightly restricted to their rock refuge, resulting in overgrazing and habitat degradation. These concerns led me to believe that if the current situation was not alleviated, then a population crash was imminent.A population crash subsequently happened in 2010, and the cause of this decline is a result of a complex ecological relationship, that includes direct and indirect predatory effects, weed invasion, and drought. The results of this research and the subsequent recent population decline, show the importance of including behaviour into an ecological study to have a better understanding. It provides a better understanding of a species as well as providing important insights into its evolutionary past, and how this has shaped their social and demographic patterns. This research also demonstrates how the use of a permanent central rock refuge both contributes to the animal’s continued survival, and restricts its future distribution, particularly in ecologically altered landscapes. Although this study was not designed primarily to resolve conservation and management problems, its findings are already being used to design an active management plan for the central wheatbelt rock-wallaby populations. The complex relationships between how an animal obtains and uses its resources, the availability of different vegetation patches, and population demographics creates significant problems for the management of a species. This emphasises the need for future research on all animal groups, to understand the relationships between the habitat and landscape elements, and that of behaviour and population dynamics. Understanding how animals perceive their environment and how they adjust to its changes will be paramount for the future management and survival of many species

Invasion of a stream food web by a new top predator.

PhDA large predator, the nymph of the dragonfly Cordulegaster boltonii (Anisoptera) (Donovan), has recently invaded Broadstone Stream, an acid headwater in southern England. Because of its large size, the invader established itself as a new top predator. The Broadstone Stream food web is exceptionally detailed and the community has been studied since the early 1970s. The invasion of C boltonii, therefore, provided a rare opportunity to investigate the effects of a potentially strong perturbation upon a well-described system. At the peak of the invasion C boltonii density exceeded seventy nymphs per square metre, comparable to the abundance of the previous top predators. The invasion appeared to part of a long-term trend, within an otherwise persistent community, towards a fauna less tolerant of profound acidity. Mobile, epibenthic prey were particularly vulnerable to C boltonii, due to high encounter rate. In field experiments,t he invader depressedth e abundanceo f two such species, a previous top predator and a detritivorous stonefly, whereas many other taxa were largely unaffected. Predator impact was strongest during peak prey abundance in the summer and autumn, and weakest in the spring when prey were scarce. The diets of the resident predators and C boltonii overlapped extensively when prey were seasonally abundant, but resource-partitioning increased as prey abundance declined. The recent decline in the abundance of P. conspersa, which had the most similar diet to C boltonfl, may be due to competitive and predatory interactions with the larger predator. Cordulegaster boltonii preyed upon virtually every animal taxon within the food web. Consequently, the complexity of the web (e. g. linkage density, omnivory and chain length) increased following the invasion. However, most taxa were rare and most feeding links were weak when the web was quantified.Natural Environment Research Counci

Dynamics of marine zooplankton : social behavior ecological interactions, and physically-induced variability

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2008Marine ecosystems reflect the physical structure of their environment and the biological processes they carry out. This leads to spatial heterogeneity and temporal variability, some of which is imposed externally and some of which emerges from the ecological mechanisms themselves. The main focus of this thesis is on the formation of spatial patterns in the distribution of zooplankton arising from social interactions between individuals. In the Southern Ocean, krill often assemble in swarms and schools, the dynamics of which have important ecological consequences. Mathematical and numerical models are employed to study the interplay of biological and physical processes that contribute to the observed patchiness. The evolution of social behavior is simulated in a theoretical framework that includes zooplankton population dynamics, swimming behavior, and some aspects of the variability inherent to fluid environments. First, I formulate a model of resource utilization by a stage-structured predator population with density-dependent reproduction. Second, I incorporate the predator-prey dynamics into a spatially-explicit model, in which aggregations develop spontaneously as a result of linear instability of the uniform distribution. In this idealized ecosystem, benefits related to the local abundance of mates are offset by the cost of having to share resources with other group members. Third, I derive a weakly nonlinear approximation for the steady-state distributions of predator and prey biomass that captures the spatial patterns driven by social tendencies. Fourth, I simulate the schooling behavior of zooplankton in a variable environment; when turbulent flows generate patchiness in the resource field, schools can forage more efficiently than individuals. Taken together, these chapters demonstrate that aggregation/ schooling can indeed be the favored behavior when (i) reproduction (or other survival measures) increases with density in part of the range and (ii) mixing of prey into patches is rapid enough to offset the depletion. In the final two chapters, I consider sources of temporal variability in marine ecosystems. External perturbations amplified by nonlinear ecological interactions induce transient excursions away from equilibrium; in predator-prey dynamics the amplitude and duration of these transients are controlled by biological processes such as growth and mortality. In the Southern Ocean, large-scale winds associated with ENSO and the Southern Annular Mode cause convective mixing, which in turn drives air-sea fluxes of carbon dioxide and oxygen. Whether driven by stochastic fluctuations or by climatic phenomena, variability of the biogeochemical/physical environment has implications for ecosystem dynamics.Funding was provided by the Academic Programs Office of the MIT-WHOI Joint Program, an Ocean Ventures Fund Award, an Anonymous Ys Endowed Science Fellowship, and by NSF grants OCE-0221369 and OCE-336839

Sensitivity analysis of Repast computational ecology models with R/Repast

Computational ecology is an emerging interdisciplinary discipline founded mainly on modeling and simulation methods for studying ecological systems. Among the existing modeling formalisms, the individual-based modeling is particularly well suited for capturing the complex temporal and spatial dynamics as well as the nonlinearities arising in ecosystems, communities, or populations due to individual variability. In addition, being a bottom-up approach, it is useful for providing new insights on the local mechanisms which are generating some observed global dynamics. Of course, no conclusions about model results could be taken seriously if they are based on a single model execution and they are not analyzed carefully. Therefore, a sound methodology should always be used for underpinning the interpretation of model results. The sensitivity analysis is a methodology for quantitatively assessing the effect of input uncertainty in the simulation output which should be incorporated compulsorily to every work based on in-silico experimental setup. In this article, we present R/Repast a GNU R package for running and analyzing Repast Simphony models accompanied by two worked examples on how to perform global sensitivity analysis and how to interpret the results

Sensitivity analysis of Repast computational ecology models with R/Repast

Computational ecology is an emerging interdisciplinary discipline founded mainly on modeling and simulation methods for studying ecological systems. Among the existing modeling formalisms, the individual-based modeling is particularly well suited for capturing the complex temporal and spatial dynamics as well as the nonlinearities arising in ecosystems, communities or populations due to individual variability. In addition, being a bottom up approach, it is useful for providing new insights on the local mechanisms which are generating some observed global dynamics. Of course no conclusions about model results could be taken seriously if they are based on a single model execution and they are not analyzed carefully. Therefore, a sound methodology should always be used for underpinning the interpretation of model results. The sensitivity analysis is a methodology for quantitatively assessing the effect of input uncertainty in the simulation output which should be incorporated compulsorily to every work based on in silico experimental setup. In this paper we present R/Repast a GNU R package for running and analyzing Repast Simphony models accompanied by two worked examples on how to perform global sensitivity analysis and how to interpret the results

Context Dependency of Community Dynamics: Predator-Prey Interactions Under Ecological Disturbances

Numerous studies have focused on the drivers of diversity and stability of communities, especially under global change. However, multi-dimensionality of ecosystems due to biotic components (e.g predation, competition and adaptive dynamics) and abiotic factors (e.g. disturbances, resource dynamics and their distinct attributes) cause context-dependent outcomes and challenge the predictions. There are still controversies around complex community dynamics under varying regimes, however, finding mechanistical explanations will illuminate the fate of multispecies assemblages. Using model microbial communities, consisting of bacterial prey and protist predator, combined with simulation modelling and advanced statistics, this thesis investigated the impact of imposed disturbances (i.e. increased dilution rates that simulate density-independent mortality as press or pulse disturbances) (i) on transient recovery dynamics of a simple microbial food web, and (ii) on bacterial abundance, diversity and community structure in the absence or presence of a protist predator. In addition, this thesis questioned the impacts of species interactions and rapid trait shifts, as a response to predation and competition, on the community dynamics and stability. Our results revealed that the predator suffered more from disturbances over longer time periods. Reduced predation pressure caused a transient phase of prey release during and even after disturbances. Recovery time depended on the strength and duration of disturbances, however, coupling to an alternative resource increased the chance of fast recovery and stabilized the communities. In multi-species prey communities, bacterial abundance, diversity, and community composition were more affected by predation than by the disturbances and resource dynamics. Predator abundance, on the other hand, was strongly affected by the type of disturbance imposed. Importantly, community attributes had differential sensitivities, as reflected by their different response and recovery dynamics. Prey community dynamics varied more temporally andwere less stable under predation stress, while prey diversity increased significantly. Predation rapidly induced anti-predation traits, which altered population dynamics of both prey and predator. More importantly, predator and the resistant prey, in turn, elevated the number of direct cause-effect relationships between the community members. Our findings are not limited to the studied system and can be used to understand the dynamic response and recovery potential of many natural predator-prey or host-pathogen systems. They can be used as a base for future studies to illuminate the debates on the future communities.:Summary Zusammenfassung 1 Scope and Outline 2 General Introduction 2.1 Context dependency of community dynamics 2.2 Ecological disturbances 2.2.1 Transient dynamics and stability 2.2.2 Catastrophic shifts 2.3 Species interactions and evolutionary dynamics under environmental change 2.3.1 Species interactions and coexistence 2.4 Eco-evolutionary dynamics 2.5 Community assembly mechanisms 2.6 Dealing with complexities 2.6.1 Microbial model systems as a tool in ecology 2.6.2 Correlation, causation and the future of predictions 2.7 Aims of this study 3 Community Dynamics under Disturbances 3.1 Transient recovery dynamics of a predator-prey system 4 Interactions of Community Drivers 4.1 Interactions between predation and disturbances shape prey communities 5 Species Interactions and Evolutionary Dynamics Shaping Communities 5.1 Summary 5.2 Introduction 5.2.1 Predator-Prey Dynamics and Community Stability 5.2.2 Causal inferences 5.3 Aim of the study 5.4 Methods 5.4.1 Organisms 5.4.2 Microcosm experiments and estimation of species abundances 5.4.3 Statistical analysis 5.5 Results 5.5.1 Community dynamics 5.5.2 Dynamics of prey diversity and community stability 5.5.3 Causal links between the species dynamics 5.6 Discussion 5.7 Synopsis 6 General Discussion 6.1 Communities under disturbances: Predator{ prey dynamics 6.2 Temporal species dynamics and community assembly Synthesis and Outlook 7.1 Increasing complexity of species interactions 7.2 Going further from causal links 7.3 Metacommunities References 8 Appendix 8.1 Declaration of the authorship 8.2 Author contributions of published articles 8.3 List of publications and conference contributions 8.4 Acknowledgments 8.5 Supplementary material for Chapter 3 8.6 Supplementary material for Chapter 4 8.7 Supplementary material for Chapter

Foraging strategies of two sympatric lagomorphs: Implications of habitat fragmentation

I studied the effects of variation in food patch quality and predation risk on the foraging patterns and measures of foraging behavior of New England (S. transitionalis) and eastern (S. floridanus) cottontails, and their survivorship and weight change during these experiments. I then superimposed the results of these experiments onto real habitat patches to determine the amount of habitat each species could occupy and maintain similar survivorship. Finally, I measured an adaptation (eye size), and predator detection of both species in an effort to explain the difference in survival between S. floridanus and S. transitionalis. In outdoor enclosures (5.7 x 45.7-m) I manipulated food quality and predation risk among four food patches. I measured the give-up-density (GUD) of food at each feeder daily, and weighed animals on a weekly basis. I also developed a break-beam sensor device to measure the time cottontails spent foraging at feeders that in predation risk. Neither species varied their behaviors with predation risk, though S. transitionalis spent marginally more total time at risk. During this experiment when no food was available in cover, S. transitionalis had lower survival than S. floridanus. However, when food was available in cover, the survivorship curves of the two species did not differ. When food quality and predation risk varied among food patches, S. floridanus avoided the poorer quality patches and foraged at higher quality patches with greater predation risk, whereas S. transitionalis avoided only the poorest quality food patches. When I applied these foraging patterns onto real habitat patches I found that S. floridanus could occupy 99% of a habitat patch whereas S. transitionalis could only occupy 32% of a patch. As snow accumulated in winter, S. transitionalis lost a significant amount of suitable habitat whereas, S. floridanus did not. One mechanism that may explain the paradox in the survivorship and habitat use of the two species is the bulginess of their eyes and the distance that they can detect an approaching predator. S. floridanus has larger eyes, and can detect an approaching predator at a greater distance than S. transitionalis

Emergent Behaviour in Game AI: A Genetic Programming and CNN-based Approach to Intelligent Agent Design

Emergent behaviour is behaviour that arises from the interactions between the individual components of a system, rather than being explicitly programmed or designed. In this work, genetic programming is used to evolve an adaptive game AI, also known as an intelligent agent, whose job is to capture up to twenty-five prey agents in a simulated pursuit environment. For a pursuit game, the fitness score tallies each prey the predator captured during a run. The fitness is then used to evaluate each agent and choose who moves forward in the evolutionary process. A problem with only choosing the best performing agents is that genetic diversity becomes lost along the way, which can result in monotonous behaviour. Diverse behaviour helps agents perform under situations of uncertainty and creates more interesting computer opponents in video games, as it encourages the agent to explore different possibilities and adapt to changing circumstances. Inspired by the works of Cowan and Pozzuoli in diversifying agent behaviour, and Chen’s work in L-system tree evaluation, a convolutional neural network is introduced to automatically model the behaviour of each agent, something previously done manually. This involves training the convolutional neural network on a large data set of behaviours exhibited by the agents, which take the form of image-based traces. The resulting model is then used to detect interesting emergent behaviour. In the first set of experiments, the convolutional neural network is trained and tested on several sets of traces, then the performance of each run is analyzed. Results show that the convolutional neural network is capable of identifying 6 emergent behaviours with 98% accuracy. The second set of experiments combine genetic programming and the convolutional neural network in order to produce unique and interesting intelligent agents, as well as target specific behaviours. Results show that the system is able to evolve more innovative and effective agents that can operate in complex environments and could be extended to perform a wide range of tasks