Studies of the evolution of the major histocompatibility complex (MHC) have been central to the understanding sexual selection and pathogen-mediated selection. The European badger Meles meles is well suited for exploring such questions because of its life history characteristics, reproductive biology and mating system. In this thesis, I examined both MHC class I and class II genes. Seven putatively functional sequences were found for class I genes and four for class II DRB genes. Evidence of past balancing selection of both genes was demonstrated by the d_Nd_S ratio, by positive selection at the antigen-binding site (ABS) and by trans-species polymorphism of alleles within other mustelids and carnivores. MHC class I genes also showed evidence of concerted evolution, but domains showed different evolutionary histories. MHC genes may influence microbiota and odour of an individual and influence mating preferences. I examined the bacterial community of the subcaudal gland secretion and demonstrated a high number of bacterial species (56 operational taxonomic units), which cubs exhibited a higher diversity than adults. The microbiota may lead to an individual-specific odour as a cue signaling the MHC genotype of potential mating partners. I report the first evidence for a MHC- based mating preference in carnivores. Female badgers showed a MHC-assortative mate choice towards breeding with males that had functionally similar MHC genes, for MHC class II DRB genes. This applied to neighbouring-group matings. I also found considerable annual fluctuation in the occurrence of MHC-based mate choice. Based on genome-wide background in the same mating randomizations I found no evidence of inbreeding, which indicated that MHC similarity was apparently the actual target of mate choice. In line with MHC-assortative mate choice, MHC heterozygosity had no influence on the co-infection status. Individual MHC alleles did, however, associate with resistance and susceptibility to specific pathogens, suggesting that MHC diversity may be driven and maintained by pathogen-mediated selection through rare-allele advantages and/or fluctuating selection. My study of genetic characteristics, mate choice and pathogen pressures in a wild population revealed past and contemporary evolutionary process of the MHC genes. This increases knowledge of how the MHC may affect mating behaviour and sexual selection, ultimately influencing population processes.

Termites are important ecosystem engineers in tropical and sub-tropical terrestrial regions where they influence ecosystem processes by altering the physical and chemical structure of the habitat. Termites affect nutrient availability by decomposition and comminution (shredding) of organic matter and act as agents of bioturbation as they re-work substrates during the construction of nests, tunnels and runways. At present we have a relatively good understanding of termite diversity patterns in the tropics through the extensive use of the standardised transect sampling protocol by Eggleton et al. (1995). These diversity data suggest that there is a functional difference in termite assemblage structure, and potentially in termite abundance and biomass, among comparable habitats across continents. However due to the lack of comparable abundance and biomass data from South America this has not previously been confirmed. In this thesis I, therefore, collected extensive data on termite taxonomic and functional assemblage structure in a South American site in Peru. The data were used to compare termite abundance and biomass from two comparable sites in Africa (Cameroon) and south east Asia (Malaysia) in order to gain better understanding of the role termites play in ecosystem processes. I found that there was an intercontinental difference in the abundance and biomass of termite feeding-groups mainly due to the dominance of soil-feeding termites in Cameroon and the absence of fungus-growing termites from Peru. The impact of certain lineages on the intercontinental differences suggests that the differences may be due to biogeographical evolution. Moreover, Eggleton et al. (1998) show that larger-bodied soil-feeding termites in Cameroon process more energy per unit area than predicted by their body size. Due to the need for an examination of the allometric relationships in termite assemblages outside Africa and the development of a more sophisticated feeding-group classification I explore the findings in Eggleton et al. (1998) further using population density - body mass relationships in three termite feeding-groups among the three continental sites in Cameroon, Peru and Malaysia. I found that large-bodied soil-feeding termites in Cameroon and large-bodied wood-feeding termites in Peru had higher population densities than expected by their body masses. As the population density - body mass relationship is inverse to that of the energy - body mass relationship the results suggest that the two feeding-groups also use more energy than expected by their body masses. Further, we have a relatively good understanding of the role termites play as ecosystem engineers e.g. in nutrient cycling and distribution, however, compared with our understanding of wood and litter decomposition in tropical forests quantitative data on the impact of termites in soil processes is poorly understood. In this thesis I conducted, to our knowledge, the first in situ soil macrofauna exclusion experiment using translocated soil in Peru to examine the impact of termites on soil C and N loss. I found that termites promote soil C and N loss which may be linked to the increase in microbial activity due to the passage of soil through the termite gut as well as the affect termites have on bioturbation and nutrient distribution. To conclude, in this thesis I present the first intercontinental comparison of abundance and biomass as well as the first in situ soil macrofauna exclusion experiment to date. The link between termite ecology, biogeography and evolution is discussed as well as the contribution of this thesis to the field of termite ecology.

Few studies of tropical fish communities compare fish distributions across the full range of near-shore tropical marine habitats. As a result, our understanding of tropical marine fish communities is often biased towards habitats preferred by researchers. The distribution and habitat preferences of all 136 fish species occurring at 106 stations in three bays off Tortola in the British Virgin Islands were assessed. At a species level, habitat type was often the key factor influencing fish distribution. Of the 44 species occurring at more than 10 stations, 3 were sand specialists, 5 were strongly associated with mangroves, 7 were dependent on seagrass and algal beds and 14 were found only on the forereef. Eleven species were widely distributed both on the forereef and in bays, and 9 of them showed clear evidence of ontogenetic partitioning. The juveniles all preferred bay habitat types and moved onto the forereef as they approached sexual maturity. At a community level, five distinct fish assemblages were found. The assemblage types were classified according to their distribution: 1) forereef, 2) reef flat, 3) non-mangrove associated seagrass, 4) mangrove associated seagrass and 5) eutrophic areas. Forereef stations were the most species-rich with 24 species per station while eutrophic stations had the most depauperate communities with only 4 species per station. Variation in fish species richness at each station was largely explained by a simple habitat complexity index. It accounted for 70% of the variation in fish species richness and 21% of the variation in fish abundance. Rugosity and variety of growth forms were the most important predictors of species richness, but the height of the habitat architecture was the most useful predictor of fish abundance. Artificial reefs were constructed to test the effects of each habitat complexity variable experimentally. Increasing rugosity, variety of growth forms and percentage hard substrate increased the observed number of species but increasing the variety of hole-sizes, and height had no effect. The only complexity variable that had a significant effect on fish abundance was percentage hard substrate. In addition to the static substrate structure, long-spined sea urchins Diadema antillarum affected fish distribution because small fish shelter from predators in their spines. The urchins increase species richness and abundance in low complexity seagrass beds, but on artificial reefs, where shelter was not a limiting factor, the effect was less pronounced. Organic pollution is another factor that negatively affects the fish community by reducing fish species richness and abundance. Poor water quality often alters the natural habitat, confounding observations, but fish species richness was reduced in polluted areas even when artificial reefs were used as habitat controls. The applications of these findings to the management and conservation of fish in the British Virgin Islands are discussed.

Dendritic cells (DC) play a key role in immunity and represent a great target for modulation, because of their ability to prime T cells and direct their polarisation into effector subsets. Ticks release immunomodulatory compounds in their saliva, possibly in order to evade host immune responses during feeding. We have recently reported that Rhipicephalus appendiculatus ticks produce ‘Japanin’, a secretory lipocalin that arrests differentiation of monocytes into DC and reprogrammes maturation of DC in response to various stimuli towards a tolerogenic phenotype . Japanin was cloned and recombinantly expressed in a baculovirus system for subsequent immunological and biochemical analysis. This study was set out to further investigate the immunomodulatory activity of Japanin as well as the underlying mechanism of action. We have discovered that Japanin prevents DC-mediated proliferation and polarisation of allogeneic T cells. Experiments with labelled Japanin have demonstrated that it binds predominantly to ex vivo generated human monocyte-derived DC (moDC) and to a reduced degree to monocyte and DC populations in peripheral blood, yet to no other blood leucocytes. We have identified CD206, also known as the mannose receptor, as a Japanin-binding receptor on moDC. This identification has been achieved by crosslinking and subsequent pull-down of Japanin-receptor complexes from moDC. Affinity studies with recombinant CD206 constructs have confirmed the binding to Japanin. Moreover, the binding has been verified by specific siRNA knock-down of CD206 in moDC, which resulted in significantly decreased binding of Japanin. Unexpectedly, CD206 has appeared to be dispensable for at least most of the DC-modulatory activity of Japanin. Therefore, attempts were made to determine other factors in the mode of action of Japanin, through which we have found that IL-10 is not essentially involved. Further results have suggested that the activity of Japanin demands cell contact. Collectively, we have come to the conclusion that the mechanism of action of Japanin might require internalisation by DC, potentially enabling modulation of intracellular pathways involved in the regulation of DC maturation.

This thesis proposes a collection of analytical and computational methods for inferring an underlying social structure of a given population, observed only via timestamped occurrences of its members across a range of locations. It shows that such data streams have a modular and temporally-focused structure, neither fully ordered nor completely random, with individuals appearing in "gathering events". By exploiting such structure, the thesis proposes an appropriate mapping of those spatio-temporal data streams to a social network, based on the co-occurrences of agents across gathering events, while capturing the uncertainty over social ties via the use of probability distributions. Given the extracted graphs mentioned above, an approach is proposed for studying their community organisation. The method considers communities as explanatory variables for the observed interactions, producing overlapping partitions and node membership scores to groups. The aforementioned models are motivated by a large ongoing experiment at Wytham woods, Oxford, where a population of Parus major wild birds is tagged with RFID devices and a grid of feeding locations generates thousands of spatio-temporal records each year. The methods proposed are applied on such data set to demonstrate how they can be used to explore wild bird sociality, reveal its internal organisation across a variety of different scales and provide insights into important biological processes relating to mating pair formation.

The drivers of fidelity and divorce of pair-bonded individuals, along with their fitness consequences, are of great interest as they influence mating systems, population structure and productivity, and gene flow. Socially monogamous birds offer an ideal opportunity to study divorce since they show great variability in the extent to which pair bonds are maintained. However, there has been little consensus as to whether divorce is a behavioural adaptation to improve a mating situation, or a consequence of other processes. Moreover, the biological and ecological correlates of fidelity are difficult to address because previous work has been based on indirect and potentially biased methods. Finally, in terms of process, the link between the process of mate choice and subsequent mating decisions has been largely inaccessible to study. My doctoral thesis addressed these significant gaps in our understanding of cause, process and consequence in the formation and dissolution of pair bonds in socially monogamous birds. I accomplished this in three principal ways. First, I conducted a robust phylogenetic meta-analysis on 84 studies across 64 species to assess the existing empirical evidence that divorce in socially monogamous birds is adaptive (in terms of breeding success). This analysis revealed that divorce is, in general, adaptive as it is both triggered by relatively low breeding success and leads to improvement in success. Next, I developed a novel probabilistic multievent capture–mark–recapture framework that provides joint estimates of survival and fidelity while explicitly accounting for imperfect detection, capture heterogeneity, and uncertainty in pair status. By applying this model to breeding data on a wild great tit population I showed that birds that remain faithful to their partner exhibit higher survival rates and are more likely to remain faithful in the next breeding season than do birds that change partners. Subsequently, I confirmed the generality of a survival benefit by applying the model to breeding data on other tit populations. Then, by applying the model to data from a population of mute swans, I showed that fidelity decreases the likelihood of skipping breeding and mortality in this long-lived species, and that these effects depended on age, individual quality, and immigration status. Finally, I investigated how the timing of pair formation influences breeding success and divorce probability using five years of data on the over-winter social behaviour of great tits. I showed that early pair formation had a positive effect on fitness components, influencing the likelihood of divorce only indirectly, through breeding success. Further, my work revealed that males, but not females, with higher numbers of the female associates in winter, and males whose future breeding partners were ranked low amongst these, divorced more often. My research makes a significant contribution to our understanding of divorce and fidelity, and generates a number of important implications for future studies. First, my work establishes that divorce is adaptive for breeding success. Second, my results highlight that survival is an important (and likely, widespread) fitness consequence of pairing decisions. Third, I provide a novel statistically rigorous modelling framework for estimating fidelity-rates and testing hypothesis about fidelity that overcomes many of the inherent biases in traditional estimates. Fourth, it provides the first evidence for a selective advantage of early pair formation in wild, thus highlighting that there are benefits to pair familiarity that manifest via social associations of individuals prior to breeding. Finally, my work reveals the selective pressures operating via the social environment can ultimately influence the mating strategies individuals adopt.

New Caledonian crows (NC crows; Corvus moneduloides) are the most prolific avian tool-users and crafters, using up to three unique tool types derived from numerous plant materials. Since the discovery that wild populations of NC crows use and manufacture different tools in different locations with no measured environmental correlates to these distributions, the process by which NC crows acquire their tool-oriented behavior has been investigated. Two major findings were discovered in 2005: NC crows have a genetic predisposition to manipulate stick like objects, and they increase their rate of manipulation when exposed to social influences. Since then, much of the research into the sociality of wild NC crows has focused on direct social influences, especially the parent-juvenile relationship, yet no social network of wild NC crows has been described. In my thesis, I characterized a new proximity-logging device, Encounternet, and outline a four-step plan to assess error in animal borne devices; uncovered drivers, such as relatedness, space-use, and environmental factors, of wild NC crow sociality, and experimentally manipulated the social network, revealing immediate changes to the number of day-time and roosting partners, the breakdown of first-order relatedness driving sociality, and an increase in the amount of time NC crows associate; and revealed an indirect pathway via tools left behind by conspecifics allowing for the transmission of tool-properties between unrelated NC crows. Altogether, I furthered our understanding of wild NC crow sociality through the use of an animal-borne device, experimental manipulation in the wild measuring the response of the NC crow social network, and demonstrated the utility of animal-borne devices in mapping the network of a population of wild birds.

Inbreeding occurs when relatives mate and have offspring. Inbreeding depression is hypothesized to have influenced the evolution of mating systems and behavioural mechanisms of inbreeding avoidance in the animal kingdom. Inbreeding in the wild is difficult to measure, as in order to build a pedigree allowing us to identify matings between relatives, the identity of as many as possible members of a population needs to be known. For a long time, the main source of knowledge about inbreeding depression was based on laboratory and agricultural studies, which did not reflect the array of environmental pressures wild populations have to cope with. In consequence, the deleterious consequences of inbreeding have often been underestimated. This is problematic because accurate estimates of the effect size of inbreeding depression are needed to study the strength of selection on inbreeding avoidance mechanisms, and are also of importance to conservation genetics. The aim of this thesis was to use pedigree data to infer the occurrence and effects of inbreeding using over forty years of breeding events of the great tit Parus major from Wytham Woods, Oxfordshire. The effects of inbreeding on fitness were investigated across a life-history continuum, and across environments. I found that close inbreeding (f=0.25) resulted in pronounced inbreeding depression, which acted independently on hatching success, fledging success, and recruitment success, and reduced the number of fledged grand-offspring by 55%. My results therefore suggest that estimates of fitness costs of inbreeding must focus on the entire life cycle. I also show that the variation in the strength of inbreeding depression varies across environments, particularly so the more the environmental variable considered is linked to fitness. These results emphasise the need of using relevant environmental contrasts when investigating inbreeding by environment interactions. I further asked whether individuals involved in matings with relatives differed relative to individuals mating with unrelated partners. I did not find any evidence for clear predictors of inbreeding, and I show that inbreeding depression in our population is entirely independent of any tendency for low quality parental genotypes, or phenotypes, to inbreed. Neither did I find any evidence for active inbreeding avoidance: great tits did not mate less often with kin than expected based on several scenarios of random mating, nor did I find increased rates of extra-pair paternity among birds breeding with relatives. In fact, I observed quite the contrary, as birds mating with kin exhibited a higher than average rate of close inbreeding relative to all scenarios of random mating investigated, showed lower rates of extra-pair paternity and divorce than birds mated to unrelated partners. I hypothesise that cases of occasional inbreeding in this population may result from mis-imprinting or a related process whereby some birds develop particularly strong bonds that are at odds with all predictions of avoiding inbreeding. Finally, I asked to what extent natal dispersal, a behaviour that is often hypothesized to play an important role in avoiding inbreeding, indeed reduces the likelihood of inbreeding. I found that male and female individuals breeding with a relative dispersed over several-fold shorter distances than those outbreeding. This led to a 3.4 fold increase (2.3-5, 95% CI) in the likelihood of close inbreeding relative to the population average when individuals dispersed less than 200m. This thesis demonstrates that inbreeding has deleterious effects on a wild population of birds, occurring throughout an individual’s life, and is of varying strength across environments. My findings strongly support the theory that natal dispersal should be considered as a mechanism of prime importance for inbreeding avoidance.

The evolution of extra-group paternity (EGP) is a contentious issue in evolutionary biology. This thesis examines the factors and adaptive benefits driving EGP in a high-density, group-living population of European badgers (Meles meles). To improve power to assign parentage, I isolated and characterised 21 new polymorphic microsatellite markers. I genotyped 83% of 1410 badger trapped 1987‒2010 using 35 autosomal microsatellite markers. Maternity and paternity were assigned at 80% confidence ca. 82% of individuals. 48% of paternities were extra-group, where 85% were attributable to neighbouring-group males and EGP was detected in 47% of litters; thus badger social group do not correspond with a breeding unit. I tested whether indirect genetic benefits explain these high EGP rates. (1) ‘Good-gene-as-heterozygosity Hypothesis’: Paternal heterozygosity, but not maternal or an individual’s own heterozygosity, associated positively with first-year survival probability. Under benign environmental conditions, cubs fathered by more heterozygous males had a higher first year survival probability. Despite this correlation, the EGP rate per litter correlated with neither average nor maximum within-group heterozygosity of candidate fathers. (2) Fitness benefit Hypothesis: Extra-group offspring (EGO) had lower first-year survival probability and lived 1.3 years less than within-group offspring (WGO). Female WGO produced more litters and offspring over their lifetime than female EGO, whereas male EGO produced more offspring than male WGO. (3) Inbreeding avoidance hypothesis: The EGP rate within a litter increased with greater average pair-wise relatedness between mothers and within-group candidate fathers. No inbreeding depression on first-year survival probability was detected, but small sample sizes limited statistical power. Socio-ecologically, at the litter level, EGP correlated negatively with the number of within-group candidate fathers, and positively with neighbouring-group candidate fathers. In conclusion, EGP in badgers may reduce inbreeding and be maintained in the population through a sex-specific antagonistic selection and indirect genetic benefits may occur when the total fitness benefits of producing extra-group sons outweigh the costs of producing extra-group daughters. These indirect genetic benefits only partially explain the evolution of promiscuity in European badgers, highlighting that evolutionary factors underlying promiscuity remain unclear.

Single-species research dominates the field of ecology; however there is a growing appreciation of the importance of a multi-species approach to holistic conservation. Carnivores exert a top-down control on other species, and are vital components of stable ecosystem functioning. Physiologically adapted for predation upon other animals, competition between carnivores can be particularly aggressive; frequently resulting in mortality, and even population suppression. Big cat research has historically focused on those species that are most easily observable; in particular the lion Panthera leo. The majority of the Felidae however are secretive and elusive, and receive relatively little scientific attention. In particular, there are few data available that measure the effect of direct intraguild interactions between carnivores. Using leopards Panthera pardus as a model species, this research aimed to investigate the impact of lions on the behavioural ecology of a socially subordinate carnivore. Leopards are the most abundant large carnivore in Africa, and have the largest global range of all felids; their ecological niche overlapping with that of both lions and tigers. The knowledge gained from examining their competitive interactions is therefore widely relevant, and may be applicable to other subordinate carnivore species that remain unstudied. Biotelemetry and camera-trap data were modelled using novel algorithms to show that lions impact on leopard population density, demographics and spatial ecology. Faecal analyses suggest that dietary niche segregation may facilitate sympatry. These results indicate the level of impact that large carnivores can exert over smaller species, and the potential for a focus on single-species conservation to undermine holistic conservation. The manifestation of intraguild competition has a significant influence on an animal’s ecology; leopards are generalist species that cope with persecution by adapting their behaviour and niche. Ecological specialists may not fare as well under competitive pressure, and proactive conservation initiatives may be required for endangered species.