Modelling the spatial and temporal dynamics of upland birds in Scotland

Population numbers change in space and time. The construction of models to investigate the spatial and temporal dynamics of populations may offer a means to identify the processes driving this change. In this thesis, we make use of models to examine the population ecology of three species of upland birds: red grouse, meadow pipit and capercaillie. Populations of red grouse in the British Isles exhibit cyclic fluctuations in abundance. Time series data from 287 grouse moors across the United Kingdom were analysed to investigate co-variation in these fluctuations. Results indicate high levels of synchrony between populations on neighbouring moors, with synchrony declining with increasing intermoor distance. At distances greater than 100km, populations exhibit only weak synchrony. Synchrony is shown to be a product of strong coupling events, which occur on average every one in six years. In the absence of such events, synchrony is shown to dissipate within three years. Further, we present evidence which suggests this coupling is driven (at least in part) by dispersal between populations. The density dependent structures are also found to be sufficiently homogeneous to allow correlations in climate to synchronise dynamics, but examination of three climate variables failed to detect a relationship. We also studied the population dynamics of meadow pipits in upland grassland ecosystems. Data, collected as part of an ongoing grazing field experiment, were analysed to construct a Bayesian model of population growth, and predict the effect of grazing intensity on meadow pipit populations. Results suggest grazing has a significant impact on population growth. Grazing may act to improve meadow pipit foraging efficiency and thus productivity. Finally, a spatially explicit population viability model was constructed to predict changes in the future abundance and distribution of capercaillie. Published estimates of key demographic variables were drawn from the literature to parameterise the model. The spatial structure of the population was inferred from spatial data, documenting the extent and configuration of remnant pine woodlands in Scotland. The model predicts a low probability of extinction for capercaillie in the future, and offers insights into key processes affecting the distribution and abundance of this species. The development of these models has advanced our understanding of the environmental processes driving changes in the spatial and temporal dynamics of these species. The results of these studies may be useful in anticipating the future consequences of various drivers of change on the ecology of upland species

Preferential invasion by Plasmodium merozoites and the self-regulation of parasite burden

The preferential invasion of particular red blood cell (RBC) age classes may offer a mechanism by which certain species of Plasmodia regulate their population growth. Asexual reproduction of the parasite within RBCs exponentially increases the number of circulating parasites; limiting this explosion in parasite density may be key to providing sufficient time for the parasite to reproduce, and for the host to develop a specific immune response. It is critical that the role of preferential invasion in infection is properly understood to model the within-host dynamics of different Plasmodia species. We develop a simulation model to show that limiting the range of RBC age classes available for invasion is a credible mechanism for restricting parasite density, one which is equally as important as the maximum parasite replication rate and the duration of the erythrocytic cycle. Different species of Plasmodia that regularly infect humans exhibit different preferences for RBC invasion, with all species except P. falciparum appearing to exhibit a combination of characteristics which are able to selfregulate parasite density

Preferential invasion of older RBCs and minimum RBC abundance under a 72 hour erythrocytic cycle duration.

<p>Minimum RBC abundance is mapped as a function of the maximum number of merozoites released per schizont, and the incrementally decreasing minimum age of susceptible RBCs.</p

Age class structure of host RBC population prior to infection.

<p>Age class structure of host RBC population prior to infection.</p

Assessing the significance of endemic disease in conservationkoalas, chlamydia, and koala retrovirus as a case study

It can be difficult to establish the conservation significance of endemic infectious diseasesthose that are well established in a populationin contrast with infectious diseases that are still invading. This difficulty can have important implications for designing policy to address species declines. The infectious diseases of koalas provide an ideal case study to examine issues involved in identifying the role of endemic disease in conservation biology. Koala populations are in decline, amidst claims for many years that infectious diseases, particularly those with chlamydial etiology, play a key role in this loss. However, weak associations between prevalence of infection, clinical signs of disease, and population decline mean that it remains unclear whether infectious disease is a primary driver of koala population decline. There are multiple causes of koala decline including drought, habitat destruction, and disease. Well-designed experiments, linked to appropriate models, are necessary to determine the true role of infectious disease in the current koala population declines and whether a focus on disease is likely to be a feasible, let alone the most cost-effective, means of preventing further declines

Preferential invasion of older RBCs and minimum RBC abundance in infected hosts.

<p>Minimum RBC abundance is mapped as a function of the maximum number of merozoites released per schizont, and the incrementally decreasing minimum age of susceptible RBCs (simulated with an erythrocytic cycle duration of 48 hours).</p

Current trends and future directions in koala chlamydial disease research

Infectious diseases can be key threatening processes for biodiversity conservation. However, establishing the relative importance of disease (among other threatening processes) as a driver of species declines can be challenging. Bias in the directions that a research field may take as it develops due to factors such as conservation policy, funding, public perception, and available expertise and technology may exacerbate this difficulty. Chlarhydiosis (infection with bacteria in Family Chlamydiaceae) is an example of an infectious disease with a poorly understood role in koala (Phascolarctos cinereus) population dynamics. The arboreal folivorous koala is an internationally recognized iconic species of high conservation, sociocultural and economic value. To date, no studies have quantitatively examined the breadth and scope of research related to koala chlamydiosis, nor systematically identified the current research gaps. We systematically and quantitatively reviewed a comprehensive database of literature related to koala chlamydiosis, classified and examined the main foci of the research, and evaluated research gaps with the goal of assisting policy planning for funding further koala chlamydiosis research. We examined published literature with regard to journal category, authorship, funding, spatiotemporal scope, study foci and type, chlamydial species examined, methodological design and overall findings. Among the 117 peer-reviewed papers published between 1970 and 2016 that fit our criteria, the most striking finding was the relative lack of population-level disease studies within the last two decades to examine mechanisms of chlamydial infection dynamics. This research gap is of particular concern given the potential role of Chlamydia in koala population declines, and the recent dramatic changes in our understanding of pathogen phylogeny and improved diagnostic approaches. Our results demonstrate a pressing need for future in situ comprehensive longitudinal population-level studies from diverse geographic regions. These studies must utilize up-to-date diagnostic methods capable of distinguishing chlamydial species and strains to elucidate the role of chlamydial infection in koala population declines and the underlying mechanisms involved. They should also employ rigorous epidemiological methodologies and evaluate co-infection, habitat, climatic and demographic data. Our findings suggest some key research gaps concerning koala chlamydiosis, and are hence important for guiding future research into koala chlamydiosis and conservation

Data from: Infection of the fittest: devil facial tumour disease has greatest effect on individuals with highest reproductive output

Emerging infectious diseases rarely affect all members of a population equally and determining how individuals’ susceptibility to infection is related to other components of their fitness is critical to understanding disease impacts at a population level and for predicting evolutionary trajectories. We introduce a novel state-space model framework to investigate survival and fecundity of Tasmanian devils (Sarcophilus harrisii) affected by a transmissible cancer, devil facial tumour disease. We show that those devils that become host to tumours have otherwise greater fitness, with higher survival and fecundity rates prior to disease-induced death than non-host individuals that do not become infected, although high tumour loads lead to high mortality. Our finding that individuals with the greatest reproductive value are those most affected by the cancer demonstrates the need to quantify both survival and fecundity in context of disease progression for understanding the impact of disease on wildlife populations

Infection of the fittest: devil facial tumour disease has greatest effect on individuals with highest reproductive output

Emerging infectious diseases rarely affect all members of a population equally and determining how individuals’ susceptibility to infection is related to other components of their fitness is critical to understanding disease impacts at a population level and for predicting evolutionary trajectories. We introduce a novel state‐space model framework to investigate survival and fecundity of Tasmanian devils (Sarcophilus harrisii) affected by a transmissible cancer, devil facial tumour disease. We show that those devils that become host to tumours have otherwise greater fitness, with higher survival and fecundity rates prior to disease‐induced death than non‐host individuals that do not become infected, although high tumour loads lead to high mortality. Our finding that individuals with the greatest reproductive value are those most affected by the cancer demonstrates the need to quantify both survival and fecundity in context of disease progression for understanding the impact of disease on wildlife populations