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Reproductive patterns in the natural world are highly variable both between- and within-species. For example, mammalian females within a single population often vary substantially in their expenditure into offspring, both before and after birth. Understanding the causes of variation in reproductive behaviour remains a key aim within evolutionary ecology, due to its implications for understanding many aspects of biology, from population dynamics to life-history evolution. Nonetheless, little is known about how genetic differences between individuals and variation in individual space use influence investment into reproduction in the wild, particularly in terms of the parental care provided by females during lactation. In this thesis, I use the detailed phenotypic, relatedness, and census data available for the feral population of Soay sheep on the island of Hirta (St. Kilda, Scotland) to understand how differences between individuals driven by variation in genetics and access to resources influence a female's investment before and after birth. First, I present a field behavioural study to understand how a female's home range quality influenced maternal and lamb behaviour over the maternal care period. Despite previous work indicating that females with greater access to high quality vegetation had higher lifetime reproductive success, I found no evidence to suggest that home range quality influenced a mother's investment into care. Second, I used existing data to understand whether an individual's access to high quality vegetation influenced the costs incurred as a result of reproduction. Although I found evidence for significant survival costs, and identified reproductive costs for old animals in poor years, home range quality had no effect on the costs experienced by females. Nevertheless, I did find evidence that females with high quality home ranges were more likely to bear twins and this may explain the positive relationship between home range quality and lifetime reproductive success. Third, I explored methods for accounting for space sharing by related females within quantitative genetic analyses of three early-life (birth weight, birth date, and August weight) and two adult traits (jaw length and metacarpal length). This enabled me to understand the importance of spatial sources of phenotypic similarity in these traits, and to derive estimates of genetic variance components that were not biased by failing to incorporate the space sharing of related females. Females that used space more similarly tended to be more phenotypically similar and had lambs that had more similar trait values. However, contrary to my expectation accounting for home range overlap had little influence on heritability estimates. Finally, I used the models described above to select females that varied in their genetic merit for lamb growth. These females were then included in a second field study to understand whether genetically mediated differences in lamb growth were caused by variation in maternal care behaviours that were, to some degree, genetically determined. Females whose genetic merit was associated with faster lamb growth were less likely to reject sucking attempts and had lambs that spent more time resting, suggesting that maternal care in this population may have a genetic basis. I finish by discussing the implications of these results, drawing attention to limitations and areas worthy of future research.

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.