The destruction of tropical forests is the most concerning current threat to biodiversity. Although protected areas have long been used as the primary tool for biodiversity conservation, there is an increasing need to find suitable conservation strategies for the growing area of human-modified land. This thesis addresses three themes that have been identified as the most pressing areas for research in human-modified landscapes: biodiversity conservation beyond protected areas, forest restoration, and the human–environment relationship. By studying the interactions between birds, plants, and people with isolated Ficus (Moraceae) trees in Assam, India, this thesis reports several important findings: 1) isolated Ficus trees are extraordinarily important to frugivorous bird communities that inhabit human-modified landscapes; 2) the frugivores visiting these isolated trees still sustained the majority of ecological function found in trees close to the forest edge; 3) isolated Ficus trees are also exceptionally important feeding sites for insectivorous birds in human-modified landscapes, compared to other trees; 4) Ficus trees are better restoration nuclei than other isolated trees; 5) although the sacred status of Ficus trees in Assam has a major influence on their abundance and distribution, faith-based values are insufficient in ensuring their conservation. In conclusion, this thesis finds that isolated Ficus trees are critically important micro-sites for conservation in human-modified landscapes, the loss of which may lead to avifaunal collapse and a reduction in restoration potential. However, by stressing their ecological and cultural properties, it may be possible to build a strong case for the conservation of isolated Ficus trees in Assam and elsewhere.

All wildlife populations harbour parasites. However, seabirds are likely to play a particularly important role in the maintenance and dispersal of infectious agents as a result of their colonial breeding habits. Seabird colonies are also known to be highly spatially structured, but little is known about the effects of this spatial structuring on seabird parasite dynamics. In this thesis, I use a tick-borne virus, Great Island virus (GIV), found in a large common guillemot (Uria aalge) colony bordering the North Sea as a model system to explore this relationship. I use a multidisciplinary approach, framed by a simple epidemiological model of the guillemot-tick-virus system. In Chapter 2, I describe a novel epidemiological model and parameterise it using the existing literature. The model suggests the importance of spatial structure within the guillemot colony, but also identifies a key missing parameter, the rate of virus transmission between pre-breeding and breeding areas. In Chapter 3, I go on to test the potential role of independent tick movement in driving transmission between these two areas, by quantifying the mobility of host-seeking seabird ticks, Ixodes uriae. I show the potential for ticks to walk ranges described anecdotally in the literature, in just a few minutes, but stress the importance of further experiments in the field. Chapter 4, I test the potential role of guillemot-mediated tick movement between pre-breeding and breeding areas. I show that pre-breeding guillemots spend a limited proportion of time ashore during daylight hours, which increases significantly as the season progresses and varies between individuals. A similar pattern is observed when considering how often they enter breeding areas when ashore; generally infrequently but varying spatiotemporally and between individuals. In Chapter 5, I apply finite mixture modelling techniques to improve existing estimates of age- and strain-specific GIV seroprevalence and force of infection in the guillemot colony. I also provide the first estimates of these parameters for eight strains, and highlight the importance of understanding strain-specific differences in GIV dynamics in future studies. Finally, I bring all four data chapters together in Chapter 6, by inputting my new parameter estimates (Chapters 3-5) into my existing model (Chapter 2). Taken together, my results suggest that GIV transmission within the guillemot colony may increase in the future as a result of declining breeding abundance and success, with more frequent or extreme disruption leading to a higher risk of infection within the colony. More generally, my results suggest that seabird colonies can be highly sensitive to changes in their spatial structure, and that endemic parasites have the potential to substantially impact, and hence to be an added threat to, their seabird hosts.

Concern over unexplained population declines in the common toad (Bufo bufo) has led to it being recognised as a priority species for conservation research. The general consensus among herpetologists is that the most important cause of the declines seen as part of a global amphibian extinction crisis is habitat loss and degradation. The aim of thesis is to investigate the effect of habitat availability and quality on common toad populations in the United Kingdom, with a particular emphasis on the effect of land under agricultural use. I use occupancy modelling, resource selection function modelling and genetic techniques to determine the effects of both terrestrial and aquatic habitat on common toads. Based on my findings, I consider the impacts of habitat at local, landscape and national scales. My research revealed the importance of pond density and presence of woodland in increasing relative probability of toad occurrence in the terrestrial habitat (Chapters 2 and 3) and the importance of water quality, woodland coverage and available terrestrial habitat coverage in determining common toad presence in ponds. The isolating effect of urban areas is demonstrated in Chapter 4 where Isolation By Barriers (IBB) explains genetic distance between common toad breeding populations better than Isolation By Distance (IBD). In Chapter 5 I again use the resource selection function for terrestrial habitat use developed in Chapter 3, to investigate the importance of terrestrial habitat availability in determining pond use by common toads at a national scale. In my concluding chapter, I make recommendations for management and further research including consideration of potential interactions between the effect of habitat loss, fragmentation and degradation with other potential causes of common toad decline.

In this thesis I set out to further our understanding of two broad questions, 1) why it is that sexual selection favours the evolution of particular traits and 2) why do the patterns of sexual selection on such traits differ between groups and populations? Specifically, I focused on the role that variation in intrasexual competitive structure, the non-random distribution of socio-competitive environments across individuals, plays in shaping variation in the operation of sexual selection both within and across populations. I explore the roles of three main determinants of competitive structure, namely; population structure, polyandry and non-random variation in the distribution of the intensity of competition. To achieve this, I used a combination of empirical and theoretical tools, using the model system Red junglefowl, Gallus gallus. Throughout this thesis I both develop and employ network quantitative tools as a framework to describe variation in intrasexual competitive structure. Overall, this thesis demonstrates a complex relationship between competitive structure and the operation of sexual selection. This structure can modify the strength and direction of sexual selection operating on phenotypic traits, obscure the operation of selection at the population level and influence the relative roles of pre- and post-copulatory sexual selection. Furthermore, this thesis explores how differences in local ecology can shape competitive structure itself and in turn shape sexual selection. In doing so, this thesis sheds some light on the role that variation in competitive structure may play in shaping the operation of sexual selection both within and between populations and generating the great diversity in sexually-selected traits and behaviours between populations.

Brood parasitic birds lay eggs amongst the clutches of other species, which then assume all costs of parental care on their behalf. This thesis addresses several puzzles of avian brood parasitism, using field studies and theoretical modelling of the generalist parasite, the shiny cowbird (Molothrus bonariensis) and select hosts in Argentina. Key findings and conclusions were: • High parasitism intensity in a host population can result in a cost to hosts of removing parasite eggs from their clutches, and so help to maintain host’s acceptance of parasite eggs in evolutionary equilibrium. The cost is to host egg survival: hosts that remove parasite eggs from the clutch increase the risk that their eggs are destroyed by subsequent parasites that visit the nest. • The principal benefit of mobbing as a front-line defence of hosts may be to reduce egg loss due to parasite attack, rather than prevent parasitism itself. • Differences in the acoustic structure of begging calls between parasites and their host’s young can be to the parasite’s advantage. Parents provisioned unparasitized broods more during broadcast at the nest of shiny cowbird calls than calls of their own species’ chicks, in both a common host and a non-host. The long tremulous quality of a cowbird’s call functions analogously to a rapid call rate, thereby exploiting a common provisioning rule of avian parents. • A trade-off for maximum growth in parasite nestlings will variously favour or not favour the evolution of nestmate-killing behaviour, depending on a parasite’s abilities, relative to host young, to solicit and attain provisions from host parents. Generalist parasites can encounter both sides of the trade-off in different hosts. Meanwhile, indirect fitness costs are unlikely to constrain the evolution of nestmate-killing in shiny cowbirds, as they rarely, if ever, share the nest with siblings.

The mosquito Aedes polynesiensis, a member of the Aedes scutellaris complex, is the main vector in the South Pacific region of the Wuchereria bancrofti parasite, the causative agent of lymphatic filariasis (LF), and is also a major nuisance biter. Decades of Mass Drug treatment (MDA) have not been successful in elimination LF. Two non-vector species in the Ae. scutellaris complex were introgressed with Ae. polynesiensis to attempt to obtain lines that would produce cytoplasmic incompatibility (CI) with wild populations and/or LF-refractoriness. Despite selection of progeny from Brugia-challenged, non-infective females at each backcross, no refractory line was acquired. However, three lines from crosses between aposymbiotic Ae. polynesiensis and Ae. riversi displayed CI and male mating competiveness suitable for the purpose of population suppression using the incompatible insect technique (IIT). A population study was conducted of potential release sites and the evaluation of monitoring tools for Ae. polynesiensis on Moorea and Tetiaroa, French Polynesia. There was no evidence of active migration between selected islets on the atoll of Tetiaroa, suggesting it is a suitable site for field releases of CI males. The BioGents Sentinel trap was shown to be an efficient and convenient trap suitable for Ae. polynesiensis monitoring. The effects of temperature and larval density on life-table parameters relevant to IIT were examined, including: larval survivorship, developmental time to pupation, male to female ratio, male pupae yield, male size and adult male survival. These findings were used to design and conduct a 14-week field experiment testing CI male strain against an isolated population, using optimized rearing conditions. Approximately 8000 males were released weekly on motu Onetahi, Tetiaroa atoll. Significant sterility was induced by Wolbachia in the targeted female population, supporting the development and scale-up of this approach toward Ae. polynesiensis nuisance and LF transmission reduction.

Alterations of streams to facilitate highway construction and consumptive water use has become a fisheries management problem. To evaluate the effects of channeling concomitant to construction of Interstate 80 N. near Henefer, Utah, altered and unaltered sections of the Weber River were compared on the basis of fishes censused, population estimates and ordinations. Species compositions in particular areas were influenced by local rheologic conditions. Changes in species composition between samplings at a particular area were caused by fish movements. Data from altered sections, rehabilitated with deflectors and checkdams, were not noticeably different than data from unaltered areas. However, fish movements indicated an unstable environment throughout the study area. This shows that it may be possible to restore channeled streams to productive fisheries.

Our bodies contain a vast number and diversity of microbes. These microbes interact, and these interactions can define how microbes affect us. Microbial ecology and evolution, therefore, are important for both microbiology and human health. However, our understanding of microbial communities remains limited. There is a need for theory that dissects the complexity and identifies the key factors and processes affecting microbial groups. Here I develop realistic computer simulations and population models of microbial communities. My first project seeks to explain microbial communication (quorum sensing) and argues that quorum sensing is a way to infer when competing genotypes are no longer a threat. The second project proposes an evolutionary explanation for another major microbial trait: adhesion. I argue that adhesion is a weapon allowing cells to compete within microbial groups and push competitors out, particularly when growing on a host epithelium. The third project moves from microbes to the host and asks whether a host can control which microbes grow and persist inside it. I develop a model of the human gut epithelium and show that the gut architecture amplifies the ability of hosts to select helpful microbes over harmful ones using nutrient secretion. In addition to selecting particular microbial strains, a host will also benefit from stable symbiotic communities that behave in a predictable manner. But what determines whether host-associated communities are ecologically stable? My final project uses ecological network theory to show that ecological stability is likely to be a problem for gut communities that are diverse and contain species that cooperate with each other. However, I argue that the host should function as an ecosystem engineer that increases ecological stability by weakening the strong dependence of cooperating species upon one another. While host-associated communities are complex ecological systems, my thesis identifies key factors that affect their form and function.

Tanzania’s Ruaha landscape is an international priority area for large carnivore conservation, harbouring roughly 10% of the world’s lions, and important populations of leopards and spotted hyaenas. However, these large carnivore populations are threatened by intense retaliatory killing due to human-carnivore conflict on village land around Ruaha National Park (RNP), mostly as a result of livestock predation by lions, leopards and spotted hyaenas. Moreover, a current lack of ecological data on the distribution of these carnivores hinders the development of effective strategies for conservation and targeted conflict mitigation in this landscape. This study aimed to identify the most significant ecogeographical variables (EGVs) influencing the distribution of lions, leopards and spotted hyaenas across the Ruaha landscape, and to map areas of conservation importance for these species. In addition, the study assessed the influence of EGVs on livestock predation risk by these carnivores in the village land around RNP, and generated a predictive map of predation risk. The relative importance of livestock husbandry practices and EGVs in terms of influencing predation risk within enclosures was also investigated. Proximity to rivers was the most important variable influencing the distribution of large carnivores in Ruaha, and contributed to predation risk of grazing livestock. The traditional livestock husbandry adopted in bomas appeared insufficient to alleviate the inherent risk of predation by large carnivores. The study produced the first detailed maps of lion, leopard and spotted hyaena distribution in the critically important Ruaha landscape, and identified likely livestock depredation hotspots. These results will target conflict mitigation approaches around Ruaha, by identifying particularly high-risk areas for livestock enclosures and grazing stock. Improving husbandry in these areas could help reduce livestock depredation and retaliatory carnivore killing, therefore reducing one of the most significant conservation threats in this critically important landscape.

Peregrines Falco peregrinus and Gyrfalcons F. rusticolus were studied in Low and High Arctic Greenland, comparing populations within and between areas. Analyses of weather data from northwest Greenland (1979–2005) revealed a general warming trend, resulting in a lengthened breeding window for many bird species. Both falcon species depend on cliffs for nesting, and take a similar range of bird species as prey. However, Gyrfalcons lay six weeks earlier than Peregrines in Kangerlussuaq and one month earlier than Peregrines in Thule, and occupy more sheltered nest-sites. Being larger than Peregrines, Gyrfalcons also take some larger prey species. In addition, both species move to lower latitudes for the winter, but while most Gyrfalcons migrate relatively short distances, Peregrines are complete long-distance migrants to Central and South America. One Peregrine, satellite-tracked from its breeding site at 76.5° N, travelled ~12,500 km and >100° in latitude, one of the longest migrations ever documented for a raptor. Around Thule in northwest Greenland (at 76.5° N), scientists had historically documented no breeding Peregrines, but six occupied sites were discovered during this study, comprising what is probably the most northern nesting population in the world. Over the same period, breeding Gyrfalcons have apparently disappeared from southern Greenland, and may have declined in central-west Greenland (67° N). The ultimate cause of this retraction may be climate warming, but the proximate cause is probably competition from an increasing Peregrine population. Gyrfalcons tagged with satellite-received transmitters showed characteristics associated with both obligate and facultative migration. Their winter ranges varied greatly in size, with the largest, ~172,000 km2, being the biggest ever documented for a raptor. Many individuals made long movements within a winter, and some spent up to a month at sea. They may have rested on ice and fed upon seabirds. Carbon dating of stratified faecal accumulation from Gyrfalcon nests in central-west and northwest Greenland showed use of sites for up to ~2,500 and ~650 years, respectively. The age of nest sites correlated significantly with the current distance to the Greenland Ice Sheet, and probably reflects colonization patterns following glacial retreat. In central-west Greenland the ratio of Peregrine to Gyrfalcon pairs changed from 1:1 in the early 1970s to nearly 14:1 in 2005. Over this period, competition for nest sites and prey is likely to have intensified. The crucial prey for Gyrfalcons when they start nesting in early spring are resident ptarmigan, whose numbers are probably depleted by Peregrines during the months they are present. If recent trends in climate change continue, Peregrines may continue to increase in Greenland, and spread north into areas previously occupied only by Gyrfalcons. At the same time, Gyrfalcons may retreat north from many currently-occupied areas.