Dispersal is a fundamental process that shapes many aspects of population ecology and evolution. Dramatic local population declines brought about by anthropogenic-driven changes to ecological processes are unfortunately becoming ubiquitous and increasing the urgency to understand dispersal behaviour in many species. For species where direct methods of tracking movement and dispersal are unsuitable, other indirect methods need to be employed to understand and characterise these behaviours. The steep population decline, due to predation, at the largest EU population of Leach’s storm-petrels Oceanodroma leucorhoa (St Kilda, Scotland), and the potential part immigrant birds have in buffering this threat, highlighted the need to understand dispersal and connectivity of widely spaced colonies in this species. The implications for the persistence of local colonies and the wider population of Leach’s storm-petrels could then be assessed. A population genetic analysis of 9 colonies across the North Pacific and Atlantic distribution, using two DNA markers (mtDNA control region and microsatellites), revealed ocean basin differentiation (Global ST = 0.32 P <0.0001, Global FST = 0.04, P <0.0001) but also identified a migrant individual in the Pacific population (STRUCTURE migrant assignment). The Atlantic population was found to be genetically homogenous, with patterns of historical and contemporary gene flow, indicating that long-distance effective dispersal is prevalent in Leach’s storm-petrels within the ocean basin. Bayesian stable isotope analysis of carbon and nitrogen (13C & 15N) provides evidence for natal dispersal as an important dispersal mechanism, and reveals movement of immature birds between colonies during the breeding season as a likely mechanism to promote inter-colony exchange and gene flow. Stable isotope comparison also identified mixing on wintering grounds as another possible influence on dispersal. The potential for immigrant birds to offset the loss caused by predation at the St Kilda colony is supported by these studies, and will likely help the persistence of the colony in the short-term. However, future viability is debateable considering the evidence for both avian and mammalian predation. This research provides a better understanding of the extent and mechanism of dispersal in the Leach’s storm-petrel, which is important to predict the potential impact of environmental change and, where possible, implement effective population management for this species.

The major histocompatibility complex (MHC) is one of the most variable regions in the vertebrate genome. Many genes within the MHC play important roles in the development of an immune response, including the response to pathogens, by presenting pathogen fragments to T cells. Pathogen-mediated balancing selection is thought to be important in maintaining the high levels of allelic variation at these loci, though the precise mechanism remains unclear. The number of studies of MHC diversity in non-model organisms has increased dramatically in recent years as genotype data have become cheaper and easier to generate; however, key limitations in many such studies remain a lack of high quality MHC genotypes and associated phenotype data. Many studies focus on a single MHC locus, assuming that one locus will represent the full range of variation within each MHC haplotype. Alternatively, the products of different loci may co-amplify, preventing locus-specific genotypes and hence heterozygosity being accurately determined. Non-model systems are also often limited by small sample sizes and limited recording of associated host and pathogen measures, which, combined with high levels of allelic variation at MHC loci, can limit statistical power. Finally, few MHC studies control for the general effect of relatedness in explaining host traits before testing for MHC effects. With so many methodological impediments, it is challenging to identify robust associations between MHC variation and host phenotypes, such as parasite burden or fitness, and to draw conclusions about the mechanisms underpinning the maintenance of diversity at MHC loci. In this thesis, I address these problems by developing a SNP-based haplotyping system for a population of unmanaged Soay sheep (Ovis aries) on Hirta, St. Kilda, for which data is available on pedigree, phenotypic traits and fitness and its components over a 30- year study period. The ovine MHC consists of four classes of loci, within which loci are tightly clustered and show reduced recombination rates compared to the genome average. Although the mammalian MHC is usually highly variable, one would expect that the number of haplotypes within an MHC class in an island population of sheep with no immigration to be limited. The class IIa region of the ovine MHC includes the classical class II loci which are typically thought to be involved in the presentation of peptides derived from extracellular pathogens, including gastrointestinal helminths, in sheep and other mammals. In chapters 2 to 4, I describe the characterisation of class IIa haplotypic diversity in the Soay sheep using direct Sanger sequencing of PCR amplified fragments, which, in combination with cloning, revealed eight distinct haplotypes. With this knowledge of haplotypic diversity, and genotypes for a sample of Soay sheep typed on the Ovine Infinium HD chip (approximately 600K SNPs), I developed a panel of 13 SNPs which could be used to impute the class IIa haplotypes. This panel was genotyped by KASP (Kompetitive Allele Specific PCR) in 6034 samples and used to impute the class IIa haplotypes. After quality control measures, class IIa haplotypes were successfully imputed for 5349 individuals. Evidence of balancing selection was identified using the Ewens-Watterson test at different life history stages and within the standing population each year between 1985 and 2012, showing that allele frequencies were more even than would be expected under neutrality. However, there was no evidence of deviation from Hardy-Weinberg equilibrium identified at different life stages or in the standing population in any year. In chapter 5, I investigate associations between the MHC class IIa haplotypes and individual-level data on host phenotypes - body weight, plasma immunoglobulin levels (measured as anti-Teladorsagia circumcincta third larval stage IgA, IgE and IgG) and strongyle faecal egg counts (FEC). Associations were tested within mixed effects models which were used to account for repeated measures and control for fixed effects known to affect the response variables, as well as within an animal model framework to account for relatedness between individuals. Haplotype heterozygosity was unrelated to any of the traits investigated, suggesting a general heterozygote advantage is unlikely to be operating within the Soay sheep. Six of the eight class IIa haplotypes were associated with multiple traits in different age-sex classes, although many of these associations were removed after inclusion within animal models. The evidence of balancing selection and associations between class IIa haplotypes and phenotypes related to health offers a promising glimpse into the evolutionary mechanisms which may be operating to maintain diversity within this region.

An island subspecies endemic to the remote St Kilda archipelago, Apodemus sylvaticus hirtensis is considered of national importance but has been little studied, despite its inclusion in the criteria for the islands’ designation as a World Heritage Site. This study expands our knowledge of the core ecology of the mice; distribution, morphology, age structure, breeding phenology, population density, range size, survival and fecundity are all described and quantified using data collected from 4462 captures of 787 individuals between 2009-2012 on three sites (Carn Mor, Glen Bay & Village Bay), 1-2km apart on the main island of Hirta. Morphological analysis confirmed the reputed gigantism the mice, with maximum body weights of 60g for males and 50.5g for a non-gravid female both being approximately double that of a mainland specimen (the heaviest gravid female caught weighed 56g). Sexual dimorphism was evident, with males >1 year old being 8.7% heavier than females on average. Significant geographical variation in size was also found; mice on the seabird breeding colony of Carn Mor were heavier, longer and in better condition than mice elsewhere. Mice were observed to have a well-defined breeding season between April and September, shorter than on the mainland, with most individuals not breeding until their second year and very few surviving two winters. No geographical differences were found in the proportion of adult mice more than a year old that were in breeding condition at any given time, although there were significant geographical differences in the proportion of individuals in breeding condition for ‘young adult’ mice entering their first spring and sub adult mice in the autumn of the year in which they were. Spatially explicit capture-recapture (SECR) methods were used to quantify population densities free from ad hoc methods of trapping area estimation. Temporal variation in population size typical of temperate small mammals was found, with densities as low as 2 mice/ha in spring, increasing through summer and autumn with juvenile recruitment until reaching a peak at the beginning of winter of up to 50 mice/ha. Geographical variation was again observed, with frequent significant differences between trapping sites and an overall trend of highest population densities on the seabird breeding site. Mean individual range sizes varied between 0.3-3.0ha and were largest in Village Bay and in males in breeding condition. Pradel robust design recruitment models were used to quantify monthly survival (0.67-1.00) and fecundity (0.03- 0.41) and overall rate of population change (0.81-1.52) between sessions. Survival varied little between grids outside of the breeding season, but tended to be greater in Carn Mor than Village Bay during the summer. Fecundity rates varied little between years and grids, with one exception where increased summer fecundity followed a severe winter decline on Carn Mor. The possible role of differences in the quality of the food supply (in particular the seabird breeding colony and spatial variation in sheep grazing pressure) on creating geographical variation in body size, condition, breeding phenology, density and population dynamics are discussed in detail, as is the overall pattern of insular traits found in the mice.