Germination of seeds of desert annual plants is reduced where there are high densities of annual seedlings. This is interpreted as a response by seeds to avoid a severe biotic environment in which growth rate and fecundity are likely to be reduced by larger established competitors. This density-dependent germination response is due primarily to reduced germination of small-seeded annuals where densities of large-seeded annuals are high. Because of this germination response, and because of competition at the plant stage, large-seeded annuals could, in the absence of significant levels of predation by seed-eating rodents, dominate the annual plant community to a much greater extent than is commonly observed. By reducing densities of large-seeded annuals, rodents allow densities of small-seeded annuals to increase and thus exert a positive indirect effect on granivorous ants. Seed-eating rodents and a parasitic fungus both prey on Erodium cicutarium, a dominant annual plant. These two unrelated predators significantly influence each other's densities by their use of a common prey species. Dispersal of desert annual seeds that successfully germinate is apparently not as widespread as is suggested by observations that some desert annual seeds are redistributed throughout the year by wind and water. Removal of plants during seed set significantly reduced densities of seedlings on sample plots the next year.

The regulatory emigration hypothesis was tested experimentally using the crayfish Orconectes causeyi Jester. Varying amounts of food and shelter were provided to crayfish in tanks with escape routes. O. causeyi rapidly adjusted its numbers in harmony with available resources through density-dependent emigration. Shelter influenced the distribution and abundance of O. causeyi most. Response to food occurred but less and took longer than the response to shelter. The small amount of variance between numbers of crayfish that emigrated during both short-term and long-term replicate tests strongly supports the regulatory emigration hypothesis.

Land conversion is one of the greatest threats to terrestrial ecosystems around the world, and understanding its impacts on the biota is crutial for the management and conservation of species in and around human-modified landscapes, particularly in those where local declines can quickly translate into the extinction of endemic species or Evolutionary Significant Units.I investigated how habitat loss and fragmentation impacted dispersal and extinction risk in three small vertebrates (a phrynosomatid lizard Urosaurus nigricaudus, and two heteromyid rodents Chaetodipus arenarius and Dipodomys simulans), in a highly fragmented agricultural valley from the Sonoran Desert in the Baja California Peninsula, Mexico, where reptiles and rodents show high endemism and phylogenetic diversity. After reconstructing the history of habitat loss at the valley during the last 60 years, my approach involved the development and genotyping of 10 DNA microsatellite loci in 800 individuals from the three species that were sampled from continuous and fragmented habitat and analyzed using various population genetic methods.Although genetic diversity was not significantly affected by habitat loss and fragmentation, I observed an increase in genetic structure, relatedness, the spatial scale of individual movement and reversal of sex-biased dispersal in the three species, compared to continous habitat. I found evidence of a large and spatially localized extinction debt in the lizard, that showed individual dispersal restricted to<400 m in the fragmented habitat, while the two heteromyids seemed capable of dispersing over distances of few kilometers. Several observations supported a higher extinction risk in kangaroo rats compared to pocket mice. Continuous areas surrounding the fragmented landscape where identified as important sources of individuals to habitat fragments located nearby. Even the vegetation associated with a narrow wash across the fragmented landscape appeared to act as a corridor as high levels of dispersing individuals were inferred in the three species over a scale of several kilometers. This study provided an approach to evaluate the effects of distinct landscape features in preventing or allowing individual dispersal in multiple co-distributed species towards their conservation in human-modified landscapes.

African climate changed considerably throughout the Pleistocene (2.588 million (Ma) to 12 thousand years ago (ka)). The timing, rate, and magnitude of past climate change across the continent impacted the evolutionary and migratory history of many mammalian species, including hominins. Investigating paleoclimatic variability through time at local and regional scales allows for an assessment of the extent to which climate change affected hominin evolution in Africa. This dissertation presents three approaches for increasing the understanding of past climate change in Africa. One method is to critically synthesize the existing literature of African climate (n=85) and hominid demography (n=64) over a restricted time frame (150 ka to 30 ka) and specific spatial scale (regional). Results from this study are two-fold: 1) climate change in Africa during this period was variable by region, responding to different climate-forcing mechanisms, and 2) changes in population and climate were asynchronous and likely created alternating opportunities for migration into adjacent regions, including hominin migrations out of Africa (~140-80 ka). The second approach is to evaluate modern ecological relationships between species and their environment to better quantify interpretations of paleoecological records. A modern distribution study of 33 ostracode species from 104 sites in the southwest arm of Lake Malawi suggest that depth-dependent variables likely define species niches. Relationships between ostracodes, fish and the green algae Botryococcus, were used to inform the paleoecological interpretations in the third study of this dissertation. Additional results suggest that macrocharcoal is likely delivered to the lake basin via river rather than wind-borne methods. The third approach involves primary analysis of climatic indicators from the sedimentary record to chronicle paleoecological and paleoenvironmental change at the basin scale through time. Results from a 380.7 meter-long sediment core recovered from Lake Malawi indicate a change of state likely caused by local tectonism, which affected ostracode assemblages, but had little effect on lake level history through time. Furthermore, the local hydroclimate of Lake Malawi alternately covaried with global glacial/interglacial cycles and local insolation maxima over the past 1.25 Ma. The magnitude and frequency of hydroclimatic variability in the watershed will be further assessed in future research.

<p>This dissertation is an investigation of the systematics, phylogeography, and ecology of a globally distributed fungal family, the Elaphomycetaceae. In Chapter 1, we assess the literature on fungal phylogeography, reviewing large-scale phylogenetics studies and performing a meta-data analysis of fungal population genetics. In particular, we examined the possible effects of asexuality, trophic niche, dispersal method, and ocean barriers on population structure. In Chapter 2, we examine the systematics and phylogeography of the Elaphomycetaceae, a family consisting of the truffle genus Elaphomyces and the stalked genus Pseudotulostoma, hypothesizing that the mammal-dispersed truffle would show evidence of dispersal limitation. Using DNA sequence data, we determined that Pseudotulostoma is derived from a lineage of Elaphomyces, indicating that Elaphomyces as currently defined is paraphyletic. The distribution of each subgenus of Elaphomyces is nearly global; representative species have been found on every continent save Africa and Antarctica. This biogeographic pattern does not follow the pattern expected by a scenario of continental vicariance. Dating analysis in BEAST confirmed that broadly distributed clades are, in most cases, too young for this pattern to be explained by continental vicariance, indicating that occasional long-distance dispersal has been a significant component in the biogeographic history of the Elaphomycetaceae. This finding contradicts our initial hypothesis that the mammal-dispersed truffles would be dispersal- limited. In Chapter 3, we investigate the role of Elaphomyces as a host for the fungal parasite Elaphocordyceps, a parasite derived from insect pathogens that attacks both insect larvae and Elaphomyces, its only fungal host. We examined the biogeography of Elaphocordyceps isolated from Elaphomyces specimens in order to test whether it, like its host, showed recent connections between the Southern and Northern Hemispheres. We also evaluated the pathogenicity of infection as determined by a visual rubric for the truffle gleba, the phylogenetic distribution of Elaphocordyceps species on its host, testing for seasonal, climate, and host-parasite effects. In Chapter 4, based on the phylogeographic pattern seen in Elaphomyces that resembles that of some air-dispersed fungi, we used theoretical and experimental methods to test whether Elaphomyces could be dispersed by air. We tested the capacity for air dispersal with an experimental test of passive air dispersal on the powdery spores of Elaphomyces morettii and found that these large spores could disperse over a short distance (10 m) in comparable numbers with the spores of the giant puffball Calvatia cyathiformis, which is known to be air-dispersed. The major findings of this thesis are that 1) fungi in general show high dispersal ability, but that trophic niche and dispersal mode may affect population structure, 2) that Pseudotulostoma, a stalked genus, is derived from the truffle Elaphomyces, 3) that the Elaphomycetaceae have experienced frequent long-distance dispersal despite 4) that the fitness of Elaphomyces as indicated by glebal development varies with host-parasite interactions based on species identity, but not with climate or season, and that 5) Elaphomyces spores, should they be released into the air, can remain in the air long enough to be dispersed long distances by the wind. The overall conclusion of this thesis is that, while Elaphomyces is clearly reliant on animal vectors for excavation and dispersal, its past history of long-distance dispersal and current spore trajectories indicate it can be passively air-dispersed as well.</p> / Dissertation

The larvae (wireworms) of some click beetle genera inhabit the soil in agricultural land and are crop pests. In the UK, a pest complex of Agriotes species, A. obscurus, A. sputator and A. lineatus, has been identified as the cause of the majority of damage. However, studies on their ecology are lacking, despite knowledge of this being important for the development of sustainable risk assessment and pest management strategies, in part due to the morphologically cryptic nature of wireworms. The ecology of economically important click beetle species was investigated, focusing on UK Agriotes species. The relationship between sex pheromone trapped male Agriotes adults and wireworms, identified using a molecular tool (T‐RFLP), was influenced by sampling method, and some environmental variables significantly correlated with species distributions. Scale of sampling influenced the observed distribution of wireworms and other soil insect larvae. Other wireworm species were trapped together with Agriotes species, but mitochondrial 16S rRNA sequences could not be matched to those of other UK species. Sequences from Canadian wireworm samples revealed possible cryptic species. Differences in adult movement rates were found in laboratory tests (A. lineatus > A. obscurus > A. sputator). Molecular markers (AFLPs) were developed to assess dispersal in adult male Agriotes but further protocol optimisation is required. The results show the importance of identifying wireworms to species for assessing adult and wireworm distributions, since the Agriotes pest complex may not be present or as 3 widespread as previously assumed. Sex pheromone trapping of adults may not be appropriate for risk assessment as the relationship between aboveground adult and belowground wireworm species distribution is not straightforward. The differences observed in Agriotes species’ ecology have implications for the implementation of pest management strategies. The techniques used here can be applied in future studies to provide information on other economically important click beetle species worldwide.

This thesis is an analysis of the integration of dispersed asylum seekers in Glasgow. It is a qualitative case study that uses data from participant observation with community groups, interviews with asylum seekers and those involved in service provision and policy, and documentary analysis. It examines the impact of policy within a local context, and the difficulties of defining and promoting integration for asylum seekers. The research makes both an empirical and theoretical contribution, building on the knowledge of the impact of dispersal and asylum policy, with a Scottish perspective analysing the issues when implementing reserved asylum policy within a devolved context. The research contributes to debates on integration with an analysis of the conceptual and practical difficulties of promoting integration for asylum seekers. The research findings are structured around three key analytic themes, the impact of policy on asylum seekers and other stakeholders, defining and promoting integration, and challenges. The research indicates tensions between devolved and reserved responsibilities in relation to asylum. The different approaches to integration create difficulties for those working within devolved services, but implementing a reserved policy. Promoting integration for asylum seekers is seen as beneficial for both asylum seekers and host communities in Scotland, but there are both conceptual and practical challenges. There are difficulties of how far and in what ways temporary integration can be measured, which are analysed in relation to existing frameworks for integration. Practice related debates have formed the basis of a shift to a more strategic platform for integration work. Contexts and procedures continue to change, however, bringing fresh challenges. The concept of social capital has been influential in the structures that have been set up to facilitate the processes of integration and dispersal within Glasgow. Yet there are difficulties with the usage of a social capital based framework. Whilst social capital is a useful concept, there is a risk that its usage may mask issues of inequality and exclusion, and the fundamental difficulties of the asylum process remain.

The past two decades have witnessed an unprecedented decline in Lepidopteran species, with more than a third of the UK’s butterflies now either considered threatened, or already lost from the country. The vulnerable marsh fritillary, Euphydryas aurinia, after a long term loss in the UK of 73% in abundance, has become an almost iconic species as the target of many well-funded conservation projects across the UK. Despite extensive ecological studies, populations of E. aurinia are shown in Chapter 2 to still be declining in south-west UK even after recommended management strategies have been implemented. This necessitates the need for prompt research beyond that of management requirements and butterfly habitat preferences. In Chapter 3, microsatellite markers (EST-SSRs) were developed for E. aurinia and using these markers in Chapter 4, it is shown that E. aurinia populations in southern UK and Catalonia, Spain, are severely genetically differentiated at all geographical scales, and genetically depauperate, causing huge concerns for the conservation of this enigmatic and ecologically important species. Dispersal is fundamental to metapopulation existence and survival. Phosphoglucose isomerase (PGI – an enzyme in the glycolysis pathway) is a well-endorsed candidate gene for dispersal, extensively studied in the Glanville fritillary (Melitaea cinxia) and Orange Sulphur (Colias eurytheme). In Chapter 5, an analysis across 27 sites in the UK discovered six non-synonymous SNPs (single nucleotide polymorphisms) within PGI. A single charge-changing SNP of interest showed no evidence of balancing selection, contrary to findings in M. cinxia, instead appearing to be neutral when analysed alongside microsatellite markers developed in Chapter 3. No link was found between genotype and flight, morphology or population trend. These findings challenge the emerging perspective that PGI could be used as an adaptive molecular marker for arthropods. Wolbachia are endosymbiotic bacteria capable of dramatically altering the reproductive system of their host. In Chapter 6, a PCR-based diagnostic in conjunction with MLST (multi-locus sequence typing) identified 100% prevalence of a single strain of Wolbachia across all sampled E. aurinia populations in the UK. Total prevalence suggests that Wolbachia probably has little phenotypic impact on its host, but the potential impacts of this endosymbiont on uninfected populations should be considered during any management plans for the conservation of E. aurinia. Current management plans will need to incorporate all areas of research, from basic ecological requirements to molecular adaptation and unseen manipulators of host biology, to be able to fully and effectively conserve declining fragmented species.

This thesis tests models on the dispersal of hominin populations in the Upper Pleistocene, specifically in relation to the Arabian Peninsula. It does so by conducting a quantified comparison of lithic assemblages from northeast Africa and southwest Asia. Lithic data from new excavations at the Jubbah Palaeolake in northern Saudi Arabia is compared to assemblages from Ethiopia, Sudan, Egypt, Jordan, Iran, Oman and other localities in Saudi Arabia. This is the first detailed inter-regional study of this area for Marine Isotope Stages 5 to 3, a critical spatial and temporal context in debates on both early modern human and Neanderthal demography and dispersal. The spatial and temporal character of the rich Arabian archaeological record correlate with emerging evidence for environmental change in Arabia; in particular the repeated dating of archaeological contexts to periods of climatic amelioration suggests that demographic growth was associated with periods of increased precipitation. The various factors influencing lithic variability and the methodologies by which they can be elucidated are reviewed. In particular this highlights the need for quantified and comparative analyses. A variety of analytical approaches are applied in this thesis, including the use of Correspondence and Principal Components Analyses to develop a nuanced view of lithic variability. Variability in cores is shown to largely reflect the related factors of size and reduction intensity. With analyses of debitage and retouched lithics a broadly similar picture emerges: assemblages which are heavily reduced have small cores and blanks and higher levels of retouch, and elements of shape variation also change in relation to reduction intensity. Elements of residual variability may reflect cultural differences. While it is felt that the evidence presented broadly orientates the Upper Pleistocene Middle Palaeolithic of Arabia to dispersals from Africa, this suggestion is subsumed with a problematization of using lithic evidence to understand dispersals. Aside from the need for further dated archaeological material from Arabia and surrounding countries, lithic analyses need to more thoroughly consider factors such as reduction intensity if we are to make robust inferences on population dispersals.

Biofilms are communities of microorganisms associated with surfaces encased in a protective extracellular matrix. These communities often pose clinical and industrial challenges due to their ability to tolerate biocidal treatments and removal strategies. Understanding the ecological interactions that take place during biofilm establishment is a key element for designing future treatment strategies. In this work, I utilized unique methods for studying factors contributing to cooperative antibiotic detoxification in a polymicrobial biofilm model. Subsequently, I tested a novel compound mixture that exhibited promising antibiofilm properties. Escapin is an L-amino acid oxidase that acts on lysine to produce hydrogen peroxide (H2O2), ammonia, and equilibrium mixtures of several organic acids collectively called Escapin intermediate products (EIP). Previous work showed that the combination of synthetic EIP and H2O2 functions synergistically as an antimicrobial toward diverse planktonic bacteria. To test the combination of EIP and H2O2 on bacterial biofilms, Pseudomonas aeruginosa was selected as a model, due to its role as an important opportunistic pathogen. Specifically, I examined concentrations of EIP and H2O2 that inhibited biofilm formation or fostered disruption of established biofilms. High-throughput assays of biofilm formation using microtiter plates and crystal violet staining showed a significant effect from pairing EIP and H2O2, resulting in inhibition of biofilm formation relative to untreated controls or to EIP or H2O2 alone. Similarly, flow cell analysis and confocal laser scanning microscopy revealed that the EIP and H2O2 combination reduced the biomass of established biofilms relative to controls. Area layer analysis of biofilms post-treatment indicated that disruption of biomass occurs down to the substratum. Only nanomolar to micromolar concentrations of EIP and H2O2 were required to impact biofilm formation or disruption, which are significantly lower concentrations than those causing bactericidal effects on planktonic bacteria. Micromolar concentrations of EIP and H2O2 combined enhanced P. aeruginosa swimming motility compared to either EIP or H2O2 alone. Collectively, these results suggest that the combination of EIP and H2O2 may affect biofilms by interfering with bacterial attachment and destabilizing the biofilm matrix.