Genetic control strategies are a novel method for reducing populations of pest insects such as the yellow fever mosquito Aedes aegypti, a major vector of several important arboviral diseases. This thesis describes efforts to develop new tools to engineer the Ae. aegypti genome and to better understand existing tools, and furthermore to use these to engineer a gene drive system in Ae. aegypti. The piggyBac transposon was found to be extremely stable in the germline of Ae. aegypti, and transposons engineered into the germline could not be remobilized with either an endogenous or exogenous source of piggyBac transposase. Conversely, somatic remobilization of piggyBac transposons was found to be readily detectable in the presence of a source of active transposase, the first report of such remobilization in Ae. aegypti. Toward new tools for genome engineering, the site-specific integrase from the phage φC31 was successfully used to promote exchange between a transgene cassette inserted into the genome of Ae. aegypti and a cassette in a plasmid vector, in the first demonstration of recombinase mediated cassette exchange technology in a pest insect species. The integrases from phages φRV1 and Bxb1 were not found to be active in the germline of the mosquito. Finally, development of a gene drive system in Ae. aegypti using an RNAi-mediated killer-rescue mechanism was attempted. Tissue-specific expression of tTAV-regulated-toxic effectors genes, using the promoter regions of the blood meal induced genes Carboxypeptidase A-1, 30Kb and Vitellogenin A, was possible, but sex-specificity was not achieved. A blood meal inducible lethal phenotype was not possible using the chosen promoters, with expression of the effectors either leading to death in early development or to a sublethal phenotype. RNAi against tTAV fused to the Mnp fragment of the dengue virus’ genome was tissue specific, but was found to be highly effective in the fat body suggesting that the Vitellogenin A was the best candidate for the engineering of killer-rescue systems in the mosquito.

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.

Intraguild competition and predation have been recognised as important ecological factors influencing the population dynamics of carnivores. The effects of these interactions are often asymmetrical due to a size-related dominancy hierarchy. However, it has been suggested that competitively subordinate carnivores can minimise the costs of predation and competition through spatial and temporal avoidance. Here I investigate the ecological and behavioural mechanisms by which cheetahs (Acinonyx jubatus) coexist with competitively stronger lions (Panthera leo) and spotted hyaenas (Crocuta crocuta). Fieldwork was carried out in the Okavango Delta, northern Botswana, between October 2008 and August 2011. A total of 20 Global Positioning System (GPS) radio-collars were fitted on all known cheetahs (n=6), lion prides (n=5) and spotted hyaena clans (n=6) in the study area (approx. 3 000 km²). Pre-programmed radio-collars recorded locations and activity continuously for each individual and these data were complemented with direct behavioural observations. Cheetah data were analysed with respect to the temporal and spatial likelihood of encountering lions and spotted hyaenas. Results suggest that the response to the risks posed by other predators is species-specific, habitat-specific and dependent on the immediacy of the risk. Resource partitioning was not the main mechanism for coexistence as cheetahs overlapped extensively with lions and spotted hyaenas in time, space and habitat use. Instead, cheetahs adjusted their spatial distribution in response to immediate risks or adapted their habitat use depending on their vulnerability (e.g. behaviours such as feeding or with differing levels of moonlight at night). In general, cheetah temporal and spatial distribution is a hierarchal process, firstly driven by resource acquisition and thereafter fine-tuned by predator avoidance. In addition, habitat heterogeneity seemed to be key in facilitating coexistence. Understanding the behavioural mechanisms that interacting apex predators adopt to regulate these negative interactions could be crucial to carnivore conservation, especially as human-related habitat loss is forcing species into ever smaller areas.

In this thesis I apply new sequencing technologies and analytical methods derived from genomics and computer science to the neuroanatomy of gene expression. The first project explores characteristics of gene expression across adult neocortical layers in a representative mammal – the mouse. Amongst the thousands of genes and transcripts differentially expressed across layers, I found common functional characteristics of genes that define certain layers, candidate cases of isoform switching, and over a thousand apparent long intergenic non-coding RNA transcripts. The second project compares patterns of gene expression in the structurally diverged adult derivatives of the pallium in mice and chickens. Overall, gene expression levels were moderately correlated between the two species. While expression patterns of ‘marker’ genes were only poorly conserved in these regions, there nevertheless was significant conservation of cross-species marker genes for homologous structures, cell types and functionally analogous regions. Many aspects of these data from both projects can now be easily browsed and searched from custom-built web interfaces. In addition to generating unprecedented genome-wide resources for the neuroscience community to explore the functional and structural dimensions of gene expression amongst different pallial regions in mammals and birds, this work also provides new insights into the widespread evolutionary shuffling of adult marker gene expression.

Harmonia axyridis is a ladybird native to Asia, but introduced widely as a biocontrol agent. It is invasive and detrimental to native species in North America, which meant its arrival in Britain was met with concern. Establishment was seen as an opportunity to track the spread of an invasive alien species (IAS) whilst also monitoring impacts on native species. The aims of this thesis were to examine the responses of native British ladybirds to the arrival of H. axyridis, to establish the effect of the IAS on native ladybirds when compared to other drivers, and to investigate the possible facilitation of the H. axyridis invasion by natural enemy release. Modelling ladybird distributions with life-history and resource-use traits found that species predatory on a wide range of prey families had larger range sizes than those which ate fewer prey types. This suggests that the wide diet breadth of the IAS is likely to have played a critical role in the species’ rapid spread. Dietary niche overlap between H. axyridis and native ladybirds showed positive correlation with declines of native ladybirds. This indicates that the IAS is playing an important role, but the significance of urbanisation suggests habitat destruction is also significant. Abundance of H. axyridis was influenced by habitat type and aphid abundance, but not by the native ladybird community, suggesting the spread of the IAS will not be slowed by biotic resistance. Harmonia axyridis is attacked by native parasitoids, but at a much lower rate than is the native Coccinella septempunctata, in line with natural-enemy release theory. There was no evidence of attack rate increasing with time since arrival in an area. Overall, H. axyridis is an extremely successful IAS, with detrimental effects on native ladybirds which are likely to continue.

Studies of mating systems and social organisation have been central to understanding of the evolution of social behaviour. The European badger Meles meles is a good species in which to study these processes, as its complex social system provides an opportunity to investigate how both natural and kin selection shape the evolution of mating systems and social structure. In this thesis, I use behavioural and genetic data to describe the mating system and social organisation of a high-density badger population and examine the occurrence of cooperative breeding. I genotyped 915 (85%) badgers trapped in Wytham Woods (1987–2005), 630 of which were cubs, and assigned both parents to 331 cubs with 95% confidence. This revealed a polygynandrous mating system, with up to five mothers and five fathers per social group. Mounting behaviour was also polygynandrous and I show the strongest evidence to date for multiple-paternity litters. I demonstrate, for the first time, that groups consisted of close and distant kin: approximately one third of group members were first-order kin, and overall group members had slightly lower relatedness levels than half-siblings. Within groups, adult and yearling females had higher pairwise relatedness than males, and neighbouring groups contained relatives. These findings result from the high level (42%) of extra-group paternities, 86% of which were assigned to neighbouring males. For the first time I show that females avoided inbreeding by mating with extra-group males; however, incestuous matings did occur. Promiscuous and repeated mountings were observed, which may reduce male–male aggression and infanticide, but may also promote sperm competition, genetic diversity, and / or genetic compatibility. Just under a third of adult males and females were assigned parentage each year and I quantify, for the first time, reproductive skew within badger groups. Correlations between relatedness, group productivity, and reproductive skew were not consistent with the predictions of incomplete-control models; rather, resource availability may play a role. Older and younger badgers displayed reduced annual breeding success, with male success increasing initially with experience. The Restraint, Constraint, and Selection Hypotheses did not explain the age-related breeding pattern in females. Variance in lifetime breeding success (LBS) was greater for males. Males that only bred within or only outside of their groups had half the LBS of males that did both. Females that were assigned maternity probably bred cooperatively and allonursed non-offspring, which has not been demonstrated previously. No benefit was established, however, in terms of litter size, probability of offspring breeding, or offspring lifetime breeding success, with more mothers in a group. In conclusion, badger social groups are fostered through kinship ties. Polygynandry and repeated mounting may have evolved originally to reduce male–male aggression and infanticide by males, through paternity masking. Although plural breeding occurs, group living appears to be costly. Motivation to disperse may be reduced through high-levels of extra-group paternities, which may also reduce inbreeding. Cooperative breeding among mothers may represent a low-cost behaviour with indirect benefits due to high levels of relatedness between female group-members. Badger sociality therefore represents an early stage in the evolution of social behaviour.