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Sexually selected traits show large variation and rapid evolution across the aniaml kingdom. The genetic variation underlying sexually selected traits is often maintained despite apparent directional selection, with proposed explanations including sexually antagonistic selection or trade-offs with other life-history traits, such as survival. A key step in uncovering evolutionary drivers and constraints of these traits is to understand them at the genomci level. However, few empirical studies have attempted to investigate this aspect in the wild. Using long-term data from a population of red deer on the Isle of Rum, Scotland, this thesis both investigates the genomic basis of antler morphology, an important sexually selected trait, and genome-wide signals of sexually antagonistic selection through viability selection across the genome. Antlers are a form of sexual weaponry in male red deer and are assocaited with increased breeding success. I show that antler morphology is highly repeatable over an individual's lifetime, heritable and that almost all examined antler morphology traits are positively genetically correleated. The investigation of causative loci underlying antler morphology showed that it has a highly polygenic architecure, with some loci identified as having potential pleiotropic effects. The finding suggest that a large mutational target and genetic covariances among antler traits, in part maintained by pleiotropy, are lifely to contribute to the maintenance of genetic variation in antler morphology in this population. In species with two sexes, males and females largely share the same genome. However, due to differing biology and life histories, the sexes can have divergent itness optima for the same traits, thus resulting in sexually antagonistic selection, i.e., sexual conflict. Evidence for sex-specific transmission distortion was found in the deer, which pointed towards sexually divergent selection on parental gametes and prenatal viability. No genetic loci underlying differntial mortality between males and females at later life stages could be identified. Among the loci under sex-specific selection, several showed evidence of balancing selection could be linked to candidate genes. These results support onging sex-specific, but not sexually antagonistic. selection on parental haplotypes and offspring genotype during prenatal development, with potential trans-generational effects. These selection patterns likely contribute to the maintenance of genetic variance and thus eveolutionary potential in this population of red deer.

Parasites are a ubiquitous presence in nature that can profoundly impact the evolution and ecology of their hosts. Despite their longstanding interest for many branches of mammalian biology, there are relatively few large-scale longitudinal investigations of immunity and parasitism in large wild mammals. Furthermore, very few studies take full advantage of longitudinal studies’ ability to examine spatiotemporal variation, life history correlates, and fitness consequences of immunity and parasitism simultaneously. This thesis comprises the first parasitological and immunological investigation in the individually-monitored study population of red deer (Cervus elaphus) on the Isle of Rum in the Inner Hebrides, Scotland. Over the course of nine field seasons spanning 2016-2018, colleagues and I collected 2091 faecal samples from 447 identified individuals. I examined these faecal samples for eggs and larvae of gastrointestinal helminth parasites and protozoa. I particularly focussed on counts of three highly prevalent helminth taxa: strongyle nematodes, the common liver fluke Fasciola hepatica, and the tissue nematode Elaphostrongylus cervi. In addition, I adapted and employed a method of faecal antibody quantification originally developed for use in sheep. Samples were analysed for total immunoglobulin A (IgA) and anti- Teladorsagia circumcincta-specific IgA, giving measures of both general and specific immune allocation. I used these immune and parasite measures in several analyses, making use of the high-resolution life history, fitness, and behavioural data available for the Rum red deer population, focussing mainly on samples collected from adult females. The principal findings were: 1. The red deer were infected with multiple species of helminths and protozoa, present at high prevalence but relatively low intensity. These parasites showed seasonal patterns of infection with strong age and sex biases, all of which varied between parasite taxa. Generally, younger individuals had higher helminth intensities, and autumn and winter seasons featured the lowest parasite intensities. 2. Parasite counts were repeatable within individuals. However, repeatability varied according to the sampling timescale, with strongyle counts being more similar within sampling trips than between trips. This implied contrasting seasonal patterns in different individuals, so that sampling at different times of year would give different impressions of patterns of parasitism across the population. 3. Females that reproduced had lower antibody levels and higher parasite intensities in the following year. However, different components of reproduction had different costs for different immune and parasite measures: gestation was associated with lower total IgA levels, while only lactation resulted in increased parasite counts, implying an important role of exposure in mediating reproduction-parasitism tradeoffs in this system. 4. I investigated the impact of reproduction, immunity, and parasitism on fitness-related traits using path analysis. Parasite count in a given year was found to correlate negatively with reproduction the following year, indicating a possible cost of parasitism for multiple fitness-related traits, above and beyond that accounted for by current reproductive status itself. Increased anti-Teladorsagia circumcincta IgA was also found to be associated with increased probability of reproduction, beyond any association with strongyles themselves. 5. I quantified and controlled for spatial patterns of immunity and parasitism using Integrated Nested Laplace Approximation (INLA) models. These analyses revealed stark differences in the range and patterns of spatial heterogeneity for different immune and parasite measures. However, fixed effects remained largely unchanged by the incorporation of spatial effects, indicating that spatial variation was unlikely to be confounding my earlier findings. I discuss these findings and their implications for longitudinal studies of immunity and parasitism in wild animals and the further integration of spatiotemporal, life history, immune, and parasite data.

Demographic senescence is increasingly recognised as an important force shaping the dynamics of wild vertebrate populations. However, our understanding of the processes that underpin these declines in survival and fertility in old age remains limited. Evidence for age‐related changes in foraging behaviour and habitat use is emerging from wild vertebrate studies, but the extent to which these are driven by within‐individual changes, and the consequences for fitness, remain unclear. Using longitudinal census observations collected over four decades from two long‐term individual‐based studies of unmanaged ungulates, we demonstrate consistent within‐individual declines in home range area with age in adult females. In both systems, we found that within‐individual decreases in home range area were associated with increased risk of mortality the following year. Our results provide the first evidence from the wild that age‐related changes in space use are predictive of adult mortality.

Hunting is a common component in the management of ungulate species. Despite its widespread use, the influence of selective harvesting on phenotypic trait change is still ambiguous, and represents a critical gap in our understanding of the responses of wild populations under harvest. Using the long-term red deer (Cervus elaphus) dataset (1972–2012) from the Isle of Rum National Nature Reserve, Scotland, we assessed the relationship between antler length and key demographic processes (i.e., survival, recruitment, antler growth, parent-offspring trait correlation) for the male component of the population. We then constructed the first integral projection model for this species to examine the effects of simulated trophy hunting on 2 population-level parameters: the stable antler size distribution and the relative reproductive value of males. When male mortality rates due to hunting were