Epidemiological models of rabies in domestic dogs: dynamics and control

Epidemiological models are frequently used to estimate basic parameters, evaluate alternative control strategies, and set levels for control measures such as vaccination, culling, or quarantine. However, inferences drawn from these models are sensitive to the assumptions upon which they are based. While many simple models provide qualitative insights into disease dynamics and control, they may not fully capture the mechanisms driving transmission dynamics and, therefore, may not be reasonable approximations of reality. This thesis examines how the predictions made by simple models are influenced by assumptions regarding the dispersion of the transition periods, alternative infection states, and transmission heterogeneity resulting from population structuring. More realistic models of rabies transmission dynamics among domestic dogs in Serengeti District (Tanzania) are developed and applied to the problem of assessing vaccination efficacy, and designing pulsed vaccination campaigns. Several themes emerge from the discussion of the models. First, the characteristics of outbreaks can be strongly influenced by the dispersion of the incubation and infectious period distributions, which has important implications for parameter estimation, such as the estimation of the basic reproductive number, R0. Similarly, alternative infection states, such as long incubation times, can substantially alter outbreak characteristics. Second, we find that simple SEIR models fail to accurately capture important aspects of rabies disease outbreaks among domestic dog populations in northern Tanzania, and therefore may be a poor basis for assigning control targets in this system. More complex models that included the role of human intervention in limiting outbreak severity, or that included population structure, were able to reproduce the observed outbreak size distribution. We argue that there is greater support for the structured population model, and discuss the implications of the three models on the evaluation of vaccination efficacy. Third, at a more regional scale, we build metapopulation models of rabies transmission among domestic dog sub-populations. We use a Bayesian framework to evaluate competing hypotheses about mechanisms driving transmission, and sources of reinfection external to the dog population. The distance between sub-populations, and the size of the sub-populations receiving and transmitting infection are identified as important components of transmission dynamics. We also find evidence for a relatively high rate of re-infection of these populations from neighbouring inhabited districts, or from other species distributed throughout the study area, rather than from adjacent wildlife protected areas. We use the highest ranked models to quantify the efficacy of vaccination campaigns that took place between 2002-2007. This work demonstrates how a coarse, proximate sentinel of rabies infection is useful for making inferences about spatial disease dynamics and the efficacy of control measures. Finally, we use these metapopulation models to evaluate alternative strategies of pulse vaccination in order to maximize the reduction in the occurrence of rabies. The strategies vary in both the way in which vaccine doses are allocated to sub-populations, and in the trade-off between the frequency and intensity of vaccination pulses. The most effective allocation strategy was based on a measure of the importance of sub-populations to disease dynamics, and it had 30-50% higher efficacy than the other strategies investigated. This work demonstrates the strong potential for the role of metapopulation models in optimizing disease control strategies

Fine-scale movement decisions of tropical forest birds in a fragmented landscape

The persistence of forest-dependent species in fragmented landscapes is fundamentally linked to the movement of individuals among subpopulations. The paths taken by dispersing individuals can be considered a series of steps built from individual route choices. Despite the importance of these fine-scale movement decisions, it has proved difficult to collect such data that reveal how forest birds move in novel landscapes. We collected unprecedented route information about the movement of translocated forest birds from two species in the highly fragmented tropical dry forest of Costa Rica. In this pasture-dominated landscape, forest remains in patches or riparian corridors, with lesser amounts of living fencerows and individual trees or "stepping stones." We used step selection functions to quantify how route choice was influenced by these habitat elements. We found that the amount of risk these birds were willing to take by crossing open habitat was context dependent. The forest-specialist Barred Antshrike (Thamnophilus doliatus) exhibited stronger selection for forested routes when moving in novel landscapes distant from its territory relative to locations closer to its territory. It also selected forested routes when its step originated in forest habitat. It preferred steps ending in stepping stones when the available routes had little forest cover, but avoided them when routes had greater forest cover. The forest-generalist Rufous-naped Wren (Campylorhynchus rufinucha) preferred steps that contained more pasture, but only when starting from non-forest habitats. Our results showed that forested corridors (i.e., riparian corridors) best facilitated the movement of a sensitive forest specialist through this fragmented landscape. They also suggested that stepping stones can be important in highly fragmented forests with little remaining forest cover. We expect that naturally dispersing birds and species with greater forest dependence would exhibit even stronger selection for forested routes than did the birds in our experiments

Group-size-mediated habitat selection and group fusion-fission dynamics of bison under predation risk

For gregarious animals the cost-benefit trade-offs that drive habitat selection may vary dynamically with group size, which plays an important role in foraging and predator avoidance strategies. We examined how habitat selection by bison (Bison bison) varied as a function of group size and interpreted these patterns by testing whether habitat selection was more strongly driven by the competing demands of forage intake vs. predator avoidance behavior. We developed an analytical framework that integrated group size into resource selection functions (RSFs). These group-size-dependent RSFs were based on a matched casecontrol design and were estimated using conditional logistic regression (mixed and populationaveraged models). Fitting RSF models to bison revealed that bison groups responded to multiple aspects of landscape heterogeneity and that selection varied seasonally and as a function of group size. For example, roads were selected in summer, but not in winter. Bison groups avoided areas of high snow water equivalent in winter. They selected areas composed of a large proportion of meadow area within a 700-m radius, and within those areas, bison selected meadows. Importantly, the strength of selection for meadows varied as a function of group size, with stronger selection being observed in larger groups. Hence the bison-habitat relationship depended in part on the dynamics of group formation and division. Group formation was most likely in meadows. In contrast, risk of group fission increased when bison moved into the forest and was higher during the time of day when movements are generally longer and more variable among individuals. We also found that stronger selection for meadows by large rather than small bison groups was caused by longer residence time in individual meadows by larger groups and that departure from meadows appears unlikely to result from a depression in food intake rate. These group-size-dependent patterns were consistent with the hypothesis that avoidance of predation risk is the strongest driver of habitat selection

Establishing the link between habitat selection and animal population dynamics

Although classical ecological theory (e.g., on ideal free consumers) recognizes the potential effect of population density on the spatial distribution of animals, empirical species distribution models assume that species–habitat relationships remain unchanged across a range of population sizes. Conversely, even though ecological models and experiments have demonstrated the importance of spatial heterogeneity for the rate of population change, we still have no practical method for making the connection between the makeup of real environments, the expected distribution and fitness of their occupants, and the long-term implications of fitness for population growth. Here, we synthesize several conceptual advances into a mathematical framework using a measure of fitness to link habitat availability/selection to (density-dependent) population growth in mobile animal species. A key feature of this approach is that it distinguishes between apparent habitat suitability and the true, underlying contribution of a habitat to fitness, allowing the statistical coefficients of both to be estimated from multiple observation instances of the species in different environments and stages of numerical growth. Hence, it leverages data from both historical population time series and snapshots of species distribution to predict population performance under environmental change. We propose this framework as a foundation for building more realistic connections between a population's use of space and its subsequent dynamics (and hence a contribution to the ongoing efforts to estimate a species' critical habitat and fundamental niche). We therefore detail its associated definitions and simplifying assumptions, because they point to the framework's future extensions. We show how the model can be fit to data on species distributions and population dynamics, using standard statistical methods, and we illustrate its application with an individual-based simulation. When contrasted with nonspatial population models, our approach is better at fitting and predicting population growth rates and carrying capacities. Our approach can be generalized to include a diverse range of biological considerations. We discuss these possible extensions and applications to real data

Leopards provide public health benefits in Mumbai, India

Populations of large carnivores are often suppressed in human-dominated landscapes because they can kill or injure people and domestic animals. However, carnivores can also provide beneficial services to human societies, even in urban environments. We examined the services provided by leopards (Panthera pardus) to the residents of Mumbai, India, one of the world's largest cities. We suggest that by preying on stray dogs, leopards reduce the number of people bitten by dogs, the risk of rabies transmission, and the costs associated with dog sterilization and management. Under one set of assumptions, the presence of leopards in this highly urbanized area could save up to 90 human lives per year. A further indirect benefit of leopard presence may be an increase in local abundance of other wildlife species that would otherwise be predated by dogs. The effective conservation of carnivores in human-dominated landscapes involves difficult trade-offs between human safety and conservation concerns. Quantitative assessments of how large carnivores negatively and positively affect urban ecosystems are critical, along with improved education of local communities about large carnivores and their impacts

‘You shall not pass!’: quantifying barrier permeability and proximity avoidance by animals

1. Impediments to animal movement are ubiquitous and vary widely in both scale and permeability. It is essential to understand how impediments alter ecological dynamics via their influence on animal behavioural strategies governing space use and, for anthropogenic features such as roads and fences, how to mitigate these effects to effectively manage species and landscapes.2. Here, we focused primarily on barriers to movement, which we define as features that cannot be circumnavigated but may be crossed. Responses to barriers will be influenced by the movement capabilities of the animal, its proximity to the barriers, and habitat preference. We developed a mechanistic modelling framework for simultaneously quantifying the permeability and proximity effects of barriers on habitat preference and movement.3. We used simulations based on our model to demonstrate how parameters on movement, habitat preference and barrier permeability can be estimated statistically. We then applied the model to a case study of road effects on wild mountain reindeer summer movements.4. This framework provided unbiased and precise parameter estimates across a range of strengths of preferences and barrier permeabilities. The quality of permeability estimates, however, was correlated with the number of times the barrier is crossed and the number of locations in proximity to barriers. In the case study we found that reindeer avoided areas near roads and that roads are semi-permeable barriers to movement. There was strong avoidance of roads extending up to c. 1 km for four of five animals, and having to cross roads reduced the probability of movement by 68·6% (range 3·5–99·5%).5. Human infrastructure has embedded within it the idea of networks: nodes connected by linear features such as roads, rail tracks, pipelines, fences and cables, many of which divide the landscape and limit animal movement. The unintended but potentially profound consequences of infrastructure on animals remain poorly understood. The rigorous framework for simultaneously quantifying movement, habitat preference and barrier permeability developed here begins to address this knowledge gap

Incorporating habitat availability into systematic planning for restoration: A species-specific approach for Atlantic Forest mammals

AimSpecies persistence often depends not only on habitat protection, but also on habitat restoration. The effectiveness of species conservation through habitat restoration can be enhanced by explicitly considering habitat availability', the combined effects of the total amount of habitat and its spatial configuration. We develop an approach for prioritizing land for restoration in a complex biome, considering habitat availability, land acquisition cost and biogeographical representation

Biodiversity impacts of bioenergy production: microalgae vs. first generation biofuels

Energy and fuel demands, which are currently met primarily using fossil fuels, are expected to increase substantially in the coming decades. Burning fossil fuels results in the increase of net atmospheric CO2 and climate change, hence there is widespread interest in identifying sustainable alternative fuel sources. Biofuels are one such alternative involving the production of biodiesel and bioethanol from plants. However, the environmental impacts of biofuels are not well understood. First generation biofuels (i.e. those derived from edible biomass including crops such as maize and sugarcane) require extensive agricultural areas to produce sufficient quantities to replace fossil fuels, resulting in competition with food production, increased land clearing and pollution associated with agricultural production and harvesting. Microalgal production systems are a promising alternative that suffer from fewer environmental impacts. Here, we evaluate the potential impacts of microalgal production systems on biodiversity compared to first generation biofuels, through a review of studies and a comparison of environmental pressures that directly or indirectly impact biodiversity. We also compare the cultivation area required to meet gasoline and distillate fuel oil demands globally, accounting for spatial variation in productivity and energy consumption. We conclude that microalgal systems exert fewer pressures on biodiversity per unit of fuel generated compared to first generation biofuels, mainly because of reductions in direct and indirect land-use change, water consumption if water is recycled, and no application of pesticides. Further improvements of technologies and production methods, including optimization of productivities per unit area, colocation with wastewater systems and industrial CO2 sources, nutrient and water recycling and use of coproducts for internal energy generation, would further increase CO2 savings. Overall pollution reductions can be achieved through increased energy efficiencies, along with nutrient and water recycling. Microalgal systems provide strong potential for helping in meeting global energy demands sustainably

The threats endangering Australia's at-risk fauna

Reducing the rate of species extinctions is one of the great challenges of our time. Understanding patterns in the distribution and frequency of both threatened species and the threatening processes affecting them improves our ability to mitigate threats and prioritize management actions. In this quantitative synthesis of processes threatening Australian at-risk fauna, we find that species are impacted by a median of six threats (range 1–19), though there is considerable variation in numbers of threats among major taxonomic groups. Invasive species, habitat loss, biological resource use, natural systems modification and climate change are the processes most commonly affecting Australian threatened species. We identified an uneven distribution of research knowledge among species, with half of the total number of species-specific peer-reviewed scientific publications associated with only 11 threatened species (2.7%). Furthermore, the number of threats associated with each species was correlated with the research effort for that species, and research effort was correlated with body mass. Hence, there appears to be a research bias towards larger-bodied species, and certain charismatic species, that could result in inferences biased towards these favored species. However, after accounting for these effects we found that for birds, amphibians, reptiles and marine mammals body mass is positively correlated with the number of threats associated with each species. Many threats also co-occur, indicating that threat syndromes may be common