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Sea bass stocks in the UK are in decline as a result of increased fishing pressure and variable inter-annual recruitment. Recruitment variation is driven by survival in the early life stages; therefore, nursery habitats are thought to be able to stabilize recruitment through providing optimal growth conditions for juvenile fish. A thorough understanding of the factors that drive juvenile sea bass survival is needed, however, our understanding of what constitutes quality nursery habitat for juvenile sea bass is weak, with current knowledge based almost solely on saltmarshes. Juvenile sea bass were sampled using conventional seine and fyke nets across estuarine habitats, alongside dietary DNA metabarcoding to assess their distribution diet and condition, using measures of abundance, condition, stomach fullness, and diet. To determine whether the mechanism of larvae entering estuarine nurseries is an active or passive process the vertical distribution patterns of larval sea bass were compared across tidal cycles. Finally, over-winter survival was predicted based on energy budget modelling and temperature-dependent growth experiments, based on in-situ measurements of winter temperatures. Juvenile sea bass did not differentially select high tide habitats, but saltmarshes and sand provided increased foraging success. At low tide, however, sea bass were more abundant in complex habitat with lower foraging success. Diets mainly consisted of decapods and polychaete worms across habitats, but there was evidence of increased planktivory over mud. Larval sea bass did not show evidence of flood tide transport and likely rely on passive tidal forcing to migrate into estuaries, or they are trying to retain to deeper water. According to our models, winter thermal minima resulted in complete cohort loss in all scenarios on the East coast. The results of this study suggest that multiple habitats along the estuarine mosaic are important for juvenile sea bass at some point, and that a seascape approach to management is necessary, however, winter temperatures likely present a more extreme bottleneck to recruitment.

Deep-sea corals are under threat from anthropogenic factors such as destruction from bottom contact fishing gear, gas and oil exploration, deep-sea mining, pollution, and climate change. One unique coral, Acanella arbuscula (Isididae), is the only known species of branching coral that is found in large gardens stretching tens of kilometers where its shallow root-like hold fasts anchor it in soft sediment. They are incredibly fragile with fine branches only a few millimeters in diameter. These coral gardens provide habitat for commercially important fish species as well as several invertebrates that live obligately on A. arbuscula. Soft sediment coral gardens are heavily fished in the North Atlantic Ocean, and A. arbuscula are very commonly caught as by-catch. People working in the fisheries have reported gill nets on shore in Newfoundland, Canada containing upwards of one hundred dead Acanella colonies. Due to their importance to the deep-sea ecosystem, their unique nature, and the current threat to their survival, these octocorals are a sensible target for conservation. In order to conserve populations of deep-sea corals, it is imperative that researchers and stakeholders understand the connectivity of populations across the North Atlantic Ocean, because the recovery of areas decimated by bottom contact fishing gear will rely on larval recruitment from local populations. Recruited larvae are unlikely to survive if their source environment is largely different from where they settle, because corals are sensitive to changes in environmental conditions such as temperature, salinity, oxygenation, nutrient availability, and calcium carbonate concentration. Therefore, along with genetic connectivity, it is essential to understand the environmental seascape and what factors are contributing to local adaptation in populations. This research was carried out in three stages. First, the most beneficial methods of extracting DNA from deep-sea corals were investigated. Five different extraction methods were compared in the search for a method that produced high quality genomic DNA. The salting-out method and plant mini kit extractions were found to be the best methods for Acanella arbuscula. Second, Single Nucleotide polymorphisms (SNPs) generated from ultra-conserved elements (UCE) sequencing were used to investigate the connectivity of 362 colonies from 33 sites spanning depths of 60-2,300 m across nearly the entire geographical range of A. arbuscula from Greenland, Canada, Scotland, Ireland, and Spain. Four genetic clusters emerged, and trans-Atlantic connectivity of these octocorals was discovered with high levels of geneflow between Canadian samples and European samples at similar depths. A barrier to geneflow was discovered in the Eastern Atlantic where samples collected shallower than 1,200m showed almost no genetic connectivity to samples collected deeper than 1,200 m depth. Additionally, distinct genetic cluster formed exclusively for samples collected in the Bay of Biscay (Spain) around 860 m was identified. It is suspected that warm highly saline Mediterranean outflow water traveling northward creates a barrier to geneflow in this region. Finally, we used the SNPs generated from this study to investigate local adaptation to environmental factors across the 33 study sites in the North Atlantic. We compared 12 environmental variables such as seafloor temperature, oxygenation, nutrient availability, salinity, and pH across all of the sites with the genotypic diversity of the corals found at those sites for each UCE SNP marker. Twelve significant environment marker associations were found, and all of them were associated with seafloor temperature. Temperature on the seafloor appears to be the main driver of local adaptation in A. arbuscula. Using the associations between genotype and the environmental variables measured, it was possible to model the potential genotype for the entire study area and predict potential stepping-stones to connectivity. The combination of connectivity and migration data with local adaptation data was used to point out areas that are potentially vulnerable to climate change and destruction from direct anthropogenic threats. Some broad suggestions were made for potential MPA locations to help maintain populations in the North Atlantic such as Eastern Greenland, Southern Iceland, the Celtic Sea, and Cantabrian Sea.

Oviraptorosaurians were a group of theropod dinosaurs that reached high diversity in the Late Cretaceous (100.5-66 million years ago). Later diverging members evolved a distinctive cranium which was extensively pneumatised, short and tall, and ended in a robust, toothless beak. Their skull has been previously interpreted as adapted for a powerful bite as part of a herbivorous or omnivorous diet. This thesis focusses on testing whether these interpretations of oviraptorosaurian cranial function are accurate. Digital 3D models were created of four key oviraptorosaurian species - early diverging oviraptorosaurian Incisivosaurus gauthieri, and later diverging oviraptorid oviraptorosaurians Citipati osmolskae, Conchoraptor gracilis, and Khaan mckennai. Finite element analysis using scaled loads demonstrates oviraptorosaurian cranial shape was stronger (lower stresses) and more efficient (lower total strain energy) compared with other herbivorous theropod crania (Erlikosaurus and Ornithomimus) and performed similarly well or better compared with large carnivore Allosaurus. Digital volumetric reconstructions of jaw adductor musculature quantify elevated bite forces in oviraptorosaurians compared with other herbivorous theropods (349-499 N in Citipati down in order of cranial size to 53-83 N in Incisivosaurus). Maximum angles of oviraptorosaurian jaw gape were estimated as similar to but more limited than reported estimates for herbivorous theropod Erlikosaurus and greatly more limited than carnivorous theropods. When approaches were combined to model muscle driven biting, oviraptorosaurians display greater cranial stress than other theropods indicating that the increased relative force of their jaw adductor musculature outweighs the effect of a comparatively strengthened cranial morphology. Oviraptorid crania may function closer to structural safety limits while feeding due to the influence of other functional or developmental pressures acting on their cranial shape. Nevertheless, it appears Oviraptoridae were adapted for powerful bites as part of a predominately but not necessarily exclusively herbivorous diet, distinct from other herbivorous theropods, while cranial function varied among oviraptorids with different species favouring different positions of biting.

Anthropogenic activities are currently contributing to global wildlife populations declines in what some scientists have named the sixth mass extinction. Reptiles are not exempt from these declines, with species affected by the combined effects of habitat loss, climate change, over-exploitation, disease, and multiple other factors. In recent decades, emerging infectious diseases have become a more urgent concern on the conservation agenda, especially in those species or populations that are already threatened by human-mediated threats or changes. One example of these is ophidiomycosis, which was first detected in wild snake populations in Great Britain in 2016. The barred grass snake (Natrix helvetica) is a widespread species throughout Great Britain that has declined regionally in recent times. This thesis aims to answer: (1) What is the prevalence of skin lesions within the study population and its relationship to ophidiomycosis? (2) How do skin lesions caused by ophidiomycosis vary seasonally in barred grass snakes? (3) How do skin lesions affect the behaviour and survival of snakes? (4) What is the population size and annual survival and detectability of snakes within the population? A study site comprising an artificial wetland and associated habitats in eastern England measuring approximately 0.5 km2 in size, was monitored for N. helvetica through 264 surveys conducted by five surveyors from 2015 to 2021. A total of 1143 individual snakes were captured and identified by their ventral scale pattern, using Wild-ID. These data were then used to build a capture history to compare annual survival and detectability of snakes with and without skin lesions. Skin lesions were first identified in the population in 2016, which tested real-time PCR positive for Ophidiomyces ophidiicola DNA. Starting in 2019, targeted monitoring of skin lesions was undertaken to investigate their characteristics and aetiology, with snakes showing clinical signs being swabbed for later rtPCR analysis. Skin lesions were observed in 25.5% of individual snakes captured from 2019 to 2021 inclusive. The lesions occurred mainly on the ventral surface of snakes as discoloured areas of mild crusting on scales, or scale margin erosion. When present, a tailored severity classification system was used to score the severity of skin lesions. A total of 78.7% of the swabs taken from snakes with skin lesions, tested rtPCR positive for O. ophidiicola DNA. These results were reinforced through the use of histopathology of both tissue and slough samples, which supported use of skin lesions as a proxy for ophidiomycosis in later analyses. Skin lesions occurred more frequently in adults than sub-adults or neonates, and a higher occurrence of trauma was observed in snakes with skin lesions, indicating potential changes in behaviour leading to increased conflict with predators. Jolly-Seber models indicated a population size that fluctuated between 323-780 (SE: 66.15-179.67) snakes per year. Cormack-Jolly-Seber models showed that snakes with skin lesions had approximately half the apparent annual survival through time (φ = 0.224-0.225), than those snakes without skin lesions (φ = 0.531-0.639). Moreover, the detectability of snakes with skin lesions was also significantly higher (p = 0.693-0.721) than those without lesions (p = 0.08-0.163). Ophidiomycosis may therefore lead to changes in behaviour that could potentially expose snakes to higher predation pressure. Finally, the anti-predator behaviour of snakes was compared between snakes with and without skin lesions. Three anti-predator behaviours were observed, with musking being the most frequent, being recorded in over 75% of snakes upon initial capture. There were significant differences between the observed behaviour of snakes between both the capture and processing phases. The response of snakes to initial capture did not vary according to sex, size class, presence of skin lesions, or slough cycle. Snakes were less likely to feign death on subsequent captures than those encountered for the first time. Snakes with skin lesions also feigned death for a longer duration than those snakes without skin lesions. Changes in the behaviour of snakes affected by ophidiomycosis may lead to reduced survival rates, posing a threat to populations if recruitment is not high enough to compensate. The findings related to the prevalence of ophidiomycosis in N. helvetica could also have implications on survey design, such as employing a risk based surveillance strategy to improve the efficiency of ophidiomycosis detection.

Cows in modern dairy systems are at risk of comprised health and welfare, and monitoring changes in behaviour can help identify early-warning signs. This thesis uses a local positioning system to detect changes in group-level behaviour. The proximity interaction network structure and consistency of a herd housed in a closed barn on a commercial farm in Essex is explored. Next, the network structure, alongside group-level space-use patterns, on the commercial farm in Essex are compared to those of a second dairy cow herd housed in an open barn (RVC Research farm). In the subsequent chapters, the relationship between barn temperature and bunching behaviour, a potentially maladaptive response to warmer than average temperatures, was investigated in both herds, through various bunching metrics: range size, inter-cow distance and nearest neighbour distance. The herd on the commercial farm in Essex was highly connected and temporally unstable, with inter-individual variation in interactions in the non-feeding zone, and social differentiation across functional zones. No social assortment by parity, days in milk or lameness state was detected. The herd on the RVC Research farm were less connected than the herd on the commercial farm in Essex. Inter-individual variation in proximity interactions was found in the feeding zoneof the RVC Research farm, alongside social differentiation across functional zones. Cows showed preferences for specific areas of the non-feeding zones, more so on the commercial farm in Essex than on the RVC Research farm. Cows increased their bunching behaviour ≥ 20°C in terms of all bunching metrics on the commercial farm in Essex. This pattern was observed for nearest neighbour distance on the RVC Research farm ≥ 15.91°C. This thesis demonstrates the use of precision livestock farming to monitor changes in group-level behaviour to improve the health and welfare of livestock.

The vast and dynamic swathes of pelagic ecosystems in the North-East Atlantic house multiple ecologically and economically important fish species. To ensure that humans do not over exploit these fish, and their habitats, multiple routine monitoring surveys take place. These surveys typically involve the use of hydroacoustic echosounders with trawling methods and collect information on the age, sex, size and weight of species that is used in dynamic models to predict changes in the mortality rate and stock size of cohorts of species. Although this method can be used to target pelagic fish, it has difficulty separating fish schools by species, typically requiring trawling validation methods to confirm the identity of the fish. However, trawling does not guarantee a representative catch of the fish schools which can skew the partitioning of hydroacoustic data, resulting in non-valid estimations of pelagic fish populations. Environmental DNA (eDNA) is a tool that has been utilised to detect pelagic fish species and is not impacted by the same bias as trawling. To investigate the use of eDNA to become a "net with no holes", validating fish schools detected by hydroacoustics, this thesis first aimed to refine the eDNA sampling strategy for marine pelagic fish. By collecting eDNA during routine pelagic hydroacoustic surveys this thesis first demonstrates that the sampling depth and hydrological conditions of the water do not significantly impact the number of pelagic fish species, communities, or the number of eDNA reads. Using these inferences on the eDNA sampling strategy for pelagic fish facilitated further investigations into the temporal utilisation of eDNA sampling for the highly migratory Atlantic bluefin tuna (ABT). Whereby surface water eDNA samples were collected from smaller, more cost effective, research vessels from summer to winter. I found that using this method ABT was detected across seasons while also revealing the presence of important potential prey species and marine predators providing useful information for future monitoring surveys. Additionally, the results of this thesis revealed significant correlations between the current trawl-validated and eDNA-validated hydroacoustics of pelagic fish. Fish species that were more abundant and widespread had stronger correlations, yet there were still large variances between species and sample years. Overall, this thesis demonstrates that eDNA can be used to verify the abundance of pelagic fish and suggests that the eDNA methods for validation are more appropriate for specific, high abundant, fish species where the DNA in the water column is more easily detected.

During embryonic development tissues are formed through a complex interplay of biochemical and physical signals. Along with morphogenic signals required for fate specification and patterning, cell and tissue mechanics are essential for shaping tissues. Generation of complex 3D tissues often requires simultaneous force-driven processes controlling cell and tissue rearrangements. Despite recent advances in the field, there is still much to be discovered about how distinct morphogenetic events in the embryo are linked and mechanically regulated during tissue formation. In this thesis I investigate how spatiotemporal coordination of local mechanical processes can help to regulate tissue morphogenesis by studying the formation of the early anterior neural plate (ANP) in the zebrafish embryo. We found that the ANP is dramatically reshaped during late gastrulation through large scale tissue flows generated by local internalisation events. We discovered that the neighbouring mesendoderm tissue is essential to initiate internalisation by causing mechanical instabilities in the ANP leading to local tissue buckling and inward folding. We propose that differential adhesive and migratory behaviour of the mesendoderm regulates ANP tissue morphogenesis. We further observed that continuous internalisation was critical to maintain proper tissue flows. Internalisation required E-Cadherin-mediated adhesion between mesendoderm and overlying neuroectoderm cells. Convergence extension movements were found to be dispensable for initiation of internalisation but required for ANP deep tissue extension and tissue shaping. We conclude that an interplay of extrinsic forces regulates ANP tissue morphogenesis. Theoretical modelling of tissue flows confirmed our experimental measurements and highlights that a spatiotemporal sequence of forces can in principle explain flow-driven reshaping of the ANP. Finally, we discovered an increase of cell extrusions that occur alongside these internalisation movements. Our observations provides new insights into mechanisms of early forebrain formation and adds to our understanding of how complex 3D tissues are shaped during embryonic development.

Sex determination is crucial for the maintenance and continuity of species. The specification of primordial germ cells and the development of a functional gonad are key steps, but the mechanisms are not fully understood in many organisms, including zebrafish. Germplasm is a component inherited by the primordial germ cells (PGCs) in zebrafish. Germplasm is localised to the Balbiani body, a conserved membrane-free structure found in all vertebrate oocytes, which gives rise to gametes. Germplasm components contribute to the oocyte polarity as well as the germ cell fate. However, to date, only a few mRNAs have been identified as germplasm components. Additionally, it is known the ovary must be actively maintained to keep the female fate, but little is known about how oocytes differentiate. I have identified a novel germplasm and oocyte component called zgc:163014. Here I show that transcripts of zgc:163014 are expressed exclusively maternally, localising to the Balbiani Body in early oocytes and to the vegetal pole in later oocytes. CRISPR/Cas genome editing was used to generate homozygous zgc:163014 mutant females and the mutants show that maternal zgc:163014 is required for oogenesis. Furthermore, maternal zgc:163014 mutant eggs display extra-numerary micropyles (-the opening through which sperm enters the egg during fertilisation-) such that zgc:163014 eggs appear punctured. Thus, I have named this novel gene pinchado (pin), which means punctured in Spanish. Pin protein is conserved across many teleost species and shows dynamic localisation in the centrosome, nuclei and cortex of cleavage-stage zebrafish embryos. pin RNA is bound by the conserved RNA-binding protein Ybx1, and Pin protein interacts with the Actin cytoskeleton through a beta-propeller domain. My work suggests that Pin plays a crucial role during oogenesis and germline development.

Heart development is a dynamic process that occurs rapidly in zebrafish embryos. Within 48 hpf heart looping is complete with the formation of two distinct chambers. During the next 5 days of development, endocardial cushions begin differentiating into mature heart valves that help to regulate the blood flow in zebrafish. Previous studies in mice and zebrafish have shown that pro-protein convertase FurinA has a role in cardiac morphogenesis. To date, the zebrafish genome has not been well annotated leaving sequences of many transcripts and their isoforms unknown. Here I describe a novel furina transcript X1, which interestingly has an unusually long 3'UTR sequence. The alternative 3'UTR furina isoform is expressed at embryonic stages prior to organ positioning. Computational analysis of the zebrafish transcriptome shows that a short sequence motif 'AGCAC' and a stem loop which we had previously studied in the 3'UTR of Nodal ligand sqt and inhibitors lefty1 and lefty2, is present in a variant 3'UTR transcript of furina. Reporter localization assays show that the furina 3'UTR element behaves similarly to the other 3'UTR motifs identified in the Nodal pathway. It also forms complexes in vivo with the RNA-binding protein and translational repressor, Ybx1. Analysis of the ybx1 mutant embryos revealed that they manifest leftright asymmetry and cardiac morphogenesis defects. I observed that the atrioventricular canal in these mutants is significantly larger than in the wild type controls. In a proportion of ybx1 mutant embryos, as a result of an enlargement of their atrioventricular canal, there is retrograde blood flow at the 5 dpf. In this work, I show an essential function for the 3'UTR element/Ybx1 regulon in translational repression of FurinA and reveal a new upstream regulatory mechanism that controls embryonic left-right asymmetry and heart development in zebrafish embryos.

Mastitis, the inflammation of the mammary gland, is the most prevalent disease among UK dairy cattle, imposing a significant burden on animal welfare, food security and antibiotic use. It is complex disease, with over 140 bacterial species being identified as etiological agents and general dysbiosis of the mammary gland bacterial community also being associated with mastitis incidence. A major driver of antibiotic use in dairy cows is in the administration of an intramammary infusion antibiotic and a teat sealant at drying off. This is to treat and prevent mastitis over the dry period and into early lactation when cows are particularly susceptible to mastitis. For responsible and justified use of antibiotics the effect of therapy on the mammary gland microbiota and udder health in sub-clinical mastitis cases need to be understood. In this study high-throughput sequencing techniques were used to analyse the bacterial community from 1231 milk samples collected from the udder quarters of 40 cows, in 2 independent farm studies, over 11 time points across the dry period into early lactation. Conclusions drawn from the first herd directed the specific selection of samples to analyse in the second herd, allowing the impact of antibiotic therapy on the milk microbiota to be more explicitly addressed. Data analysis and statistical modelling revealed that cows receiving antibiotic therapy had a similar outcome in the udder health and diversity metrics of the mammary gland microbiota in early lactation compared to those cows receiving just teatsealant therapy. A highly diverse composition and a dynamic nature of the milk microbiota was reported in both farms and treatment groups. Reporting that rapid changes to the bacterial community can occur within udder quarters, over subsequent time points, just 1 to 2 days apart. This study demonstrated the complexity and difficulty in describing a normal, stable microbiota in the mammary gland. It also suggests, in the context of these two farms, more evidence is required to show that omission of antibiotic therapy at drying off would be detrimental to healthy cows or cows with sub-clinical levels of mastitis.

Chondrichthyans, the cartilaginous fishes, are a highly successful clade of vertebrates that have occupied the aquatic realm for over 450 million years. Of these, the Palaeozoic represents a key time interval in terms of their origin and early diversification, yet much of their early macroevolutionary patterns remains unresolved because of the limitations of their fossil record. Their early fossil record is poor because their mostly cartilaginous skeletons are rarely well preserved and this, in turn, has restricted the data available for estimates of their evolutionary history. In this thesis, multiple statistical methods for quantifying the skeletal completeness and estimating diversity trends are combined to critically assess the quality of the Palaeozoic chondrichthyan fossil record. A novel metric is presented to quantify levels of soft tissue preservation next to skeletal completeness in the stem-chondrichthyan acanthodians which are known to preserve notoriously little skeletal features. The results identify a complex array of natural and human-driven biases that greatly influences our understanding of the Palaeozoic chondrichthyan fossil record. Variation in completeness impacts on the utility of characters for assessing phylogenetic relationships of the various chondrichthyan groups, specifically the stem-chondrichthyan lineages. An extensive assessment of early chondrichthyan diversity patterns give greater insight on their environmental and biological drivers but also highlight the impact sampling biases may have on them. Together, the quantified macroevolutionary patterns of completeness and diversity draw a more comprehensive picture of the evolutionary history and nature of the early chondrichthyan fossil record.

Dinosaurs first appeared ~230 million years ago during the Late Triassic and dominated the global terrestrial ecosystems before the non-avian dinosaurs went extinct at the Cretaceous-Paleogene extinction. Given the broad geographical distribution and temporal range of non-avian dinosaurs, clarifying their feeding mechanisms and diets is essential for a fuller understanding of the macroevolution of non-avian dinosaurs, their trophic relationships with the contemporaneous organisms, as well as the global Mesozoic ecosystem. Oviraptorosauria is a clade of non-avian theropod dinosaurs that blossomed during the Late Cretaceous. Despite the long history of discovery, their diets remain controversial as the skeletons do not display obvious feeding adaptations. In this study, the mandibular anatomy and functional morphology of oviraptorosaurs are examined using approaches such as comparative anatomy, digital visualization and modelling, geometric morphometrics, and finite element analysis. It explores the feeding of oviraptorosaurs in the broad context of non-avian dinosaurs, compares the edentulous mandibles of phylogenetically distant vertebrates for dietary inference in oviraptorosaurs, identifies and describes an oviraptorid embryo exquisitely preserved inside an egg, and lastly estimates the bite forces of oviraptorids using musculature modelling. The results demonstrate that the feeding apparatus of oviraptorosaurs were functionally versatile, which facilitated niche-partitioning among contemporaneous oviraptorosaurs and other terrestrial vertebrates.

Four distinct cell-spanning waves of actin polymerisation and depolymerisation, as well as microtubule polymerisation and depolymerisation were found to occur during every cell cycle in zebrafish embryos during the cleavage stage, which corresponds to the 2-64 cell stage. Cell-spanning waves were imaged using fluorescent markers for actin and microtubules with a spinning disc microscope. A novel segmentation algorithm called 3-D ISO was developed for the purpose of segmenting the cell cortex and the cytoplasm from 3-D image stacks over time. Segmentation of the cell cortex and the cytoplasm enabled visualisation over each region, and quantitative analysis of the cell-spanning waves through the entire cell. Both actin and microtubule polymerisation waves were shown to initiate at the centrosomes upon entry into anaphase and expand outwards to the cell cortex. The polymerisation waves are characterised by redistribution of actin and microtubules markers from the cytoplasm to the cell cortex. Polymerisation waves for actin and microtubule were shown to be spatiotemporally correlated through the cytoplasm and cell cortex. Microtubule depolymerisation waves also initiate in the cytoplasm after anaphase and expand outwards to the cell cortex. They are not spatiotemporally correlated with actin depolymerisation waves through the cytoplasm but are correlated with them over the cell cortex. Thus, actin depolymerisation waves were shown to occur through the following cell cycle. The depolymerisation waves are characterised by redistribution of actin and microtubules markers from the cell cortex to the cytoplasm. Most importantly, the cytokinetic apparatus was shown to assemble in the wake of the polymerisation waves as they pass over the cell cortex. Cytokinesis is the final step in cell division during which a cell is separated into two daughter cells through ingression of a cytokinetic apparatus through the cell. Ingression of the cytokinetic apparatus was shown to occur as polymerisation and depolymerisation waves passed over the cell cortex, however, majority of ingression appeared to occur as the depolymerisation wave passed over the cell cortex.

The cabbage aphid, Brevicoryne brassicae L., is a Brassica specialist, and is among the most damaging pests of vegetable Brassica crops, causing significant yield losses due to direct feeding damage, virus transmission and crop contamination. It is normally managed using synthetic chemical pesticides. However, with emerging reports of insecticide-resistant B. brassicae clones and withdrawal of insecticides from the market because of environmental concerns, there is a need for alternative, sustainable approaches. In this project, a novel Integrated Pest Management (IPM) system was developed and evaluated, combining partially aphid resistant Brassica accessions with entomopathogenic fungi (EPF). In recent years it has been suggested that host plant resistance and biological controls such as EPF may interact favourably, resulting in greater than additive control. It was hypothesised that partial host plant resistance may extend the window of opportunity for successful EPF infection resulting in significantly higher levels of control. Through pre-selecting and screening a range of Brassica accessions, partially resistant accessions were identified which limited B. brassicae population development by approximately one third. Assessment of aphid life history traits showed that partial resistance significantly reduced the rate of juvenile aphid development, aphid weight and adult reproduction. Laboratory bioassays of 10 isolates of EPF showed that all were pathogenic to B. brassicae adults but were largely ineffective against nymphs with the exception of one isolate of Akanthomyces dipterigenus, which was highly virulent to nymphs. Experiments indicated that this may have resulted from faster germination and growth compared to other isolates. In experiments where B. brassicae were reared on partially resistant Brassica accessions and treated with the EPF A. dipterigenus or Beauveria bassiana, it was found that partial host plant resistance caused nymphs to become significantly more susceptible to infection by B. bassiana relative to nymph cohorts on more aphid-susceptible plants. Combining partial resistance with A. dipterigenus caused a significant increase in aphid population control as a result of a plant x EPF interaction. The results of this study demonstrate the potential of this combined IPM strategy, with the effects of partial resistance upon B. brassicae able to activate or improve EPF virulence to aphid nymphs, which appear to be the primary challenge for aphid control using EPF.

Greenhouse whitefly (Trialeurodes vaporariorum) are a major global pest, causing direct damage to >850 plant species and transmitting viral plant diseases. Management of T. vaporariorum is increasingly difficult because of widespread pesticide resistance. Many greenhouse growers rely on biological control agents to maintain T. vaporariorum. However, biological control agents are slow acting and variable in their efficacy, resulting in subsequent application of chemical insecticides when pest populations become unmanageable. There is an increasing drive to use integrated, multiple pest control strategies, limiting chemical application and increasing the use of sustainable alternatives. Entomopathogenic fungi (EPF) have the potential to be used as one of these alternative control methods, but EPF efficacy is highly variable between applications. Co-application of a chemical insecticide with an entomopathogenic fungus can result in improved pest control, assist resistance management, target multiple pest species and increase the range of environmental conditions over which control is effective. Combining chemical and biological pesticides has the potential to result in both positive and negative interactions, so it is important to understand how mixture components interact. Positive interactions result in synergism, whilst negative interactions cause antagonism and a reduction in pest control. In this thesis, EPF with potential to control T. vaporariorum were identified through a series of laboratory in vitro and in vivo tests. Co-application of a mixture of selected EPF and the chemical insecticide spiromesifen were evaluated in laboratory based bioassays. Using an ecotoxicological MixTox model, complex interactions between the EPF and insecticide were described; depending on the EPF and the concentrations applied, mixtures resulted in additivity, synergism or antagonism. The types of interactions were influenced by temperature and applications of a low concentration of spiromesifen with EPF resulted in additive mortality of T. vaporariorum in greenhouse trials. By understanding of the complex interactions between components of integrated pest management strategies, optimised approaches can be developed to control pests.

Infectious diseases are a major threat to the survival and fitness of all great ape species. Because of their close genetic relatedness, great apes share human susceptibility to a variety of viral, bacterial and parasitic infections. In the context of a growing human population and increasing habitat encroachment, pathogen transmission is of great concern for both humans and great apes. Therefore, monitoring great ape health status is key to understanding pathogen-host dynamics. Here, I studied two communities of habituated bonobos (Pan paniscus) at the LuiKotale field site in the Democratic Republic of the Congo (DRC) between December 2018 and July 2020. I first looked at health impairments and how they influence feeding behaviour and food choice in bonobos. I then investigated the consumption of Manniophyton fulvum leaves and stem bark by bonobos, and its association with parasite presence in faeces. Lastly, I measured individual urinary neopterin levels as a marker for the activation of cellular immunity, and studied how urinary neopterin varied with season, individual age, sex, reproductive status, and the presence of visual sickness symptoms. I found the presence of health impairments predicted neither a change in feeding behaviour nor an increased consumption of medicinal plant candidates. I hypothesized that bonobos used medicinal plant candidates as prophylaxis rather than cures. The consumption of M. fulvum leaves and stem bark was not associated with the presence of strongyle worms and cestode proglottids in faeces. My results suggest alternative triggers of the consumption of M. fulvum, including intestinal pain and discomfort. Finally, I found urinary neopterin levels increased with the presence of respiratory symptoms and fluctuated over a one-year period. I discussed the possible link to malaria and other infectious diseases in bonobo's neopterin variation. This study highlights the extent of medicinal plant use by bonobos at LuiKotale and sheds light on ecoimmunological aspects of the species. Further research is needed to understand the nature of diseases and infections carried by and affecting bonobos in order to better understand how individuals use medicinal plant candidates to maintain and restore health in the wild.

Halting the loss of biodiversity is one of our century's greatest challenges. In Southeast Asia, the biodiversity crisis is driven by unprecedented rates of forest clearance and degradation. Here, conservation efforts face the inherent complexity of trying to protect species in landscapes that also support human livelihoods. Most of our understanding of how bats are affected by land-use change in the tropics is limited to those species which can be monitored using live-trapping techniques. However, acoustic monitoring is an important survey method for monitoring the whole bat community in other regions of the world. In this thesis, advanced technological and statistical approaches are used to investigate how tropical bats respond to land-use change in Borneo. Specifically, the thesis explores the application of acoustic monitoring for bats in this region. In the first chapter, I outline how conservation zoning can be effective at protecting tropical bat diversity. To do so, I use a combination of live-trapping and acoustic monitoring to assess bat diversity and activity within The Crocker Range Biosphere Reserve compared to the surrounding agriculture. This includes demonstrating how acoustic data can be used to analyse differences in bat activity between habitats, even if it is not possible to classify calls to sonotype/species. Namely, this research highlights the importance of strict protective zones for conserving forest specialist species. Next, I refine the bat call classification process by using acoustic data manually classified sonotype/species to assess the value of conservation set-asides. These data were combined with forest structural metrics measured using airborne LiDAR to assess the effectiveness of riparian reserves (areas of native forest along waterways) for conserving bats in oil-palm landscapes. Using Bayesian occupancy modelling, I demonstrate how - unlike other components of tropical biodiversity - forest quality is more important than riparian reserve width for maintaining suitable habitat for bats. This provides important evidence for designing effective conservation policies for tropical mammals. The lack of reference call libraries and automated classification tools in Southeast Asia impedes ongoing acoustic monitoring for bats in this region. Acoustic monitoring generates large datasets - often approaching the scale of big data - which requires time and expertise to manually process. These costs limit the application of bioacoustics as a feasible method for monitoring bats in tropical regions, not least in Southeast Asia - thus, limiting our understanding of how bat communities persist in human-modified landscapes. Therefore, for the third data chapter, I focus on developing a semi-automated framework for classifying bat calls in Southeast Asia when reference libraries may be limited. As proof of concept, this viii framework is then used to develop a classifier for the bats of Borneo using reference calls for 52% of all 81 known echolocating species on the island. This classifier was developed using free software to ensure the same framework could be applied to other regions of Southeast Asia. Last, I apply the newly-developed classifier to examine patterns of bat activity in response to habitat disturbance at the Stability of Altered Forest Ecosystems Project in Sabah. The data used in this assessment represented a seven-fold increase in the number of recording hours compared to the combined effort of the previous studies. This acoustic dataset is combined with forest structural metrics measured using airborne LiDAR to assess responses across a gradient of habitat disturbance - comprising old-growth forest, logged forest, and monoculture tree plantations. In this chapter, I demonstrate how logged forests can provide important habitat for bats in human-modified landscapes, maintaining acoustic diversity and activity of many common species, particularly when compared to tree plantations. However, I also demonstrate how old-growth forest remains important for conserving forest specialist species. Collectively, in this thesis, I document how bats can benefit from conservation initiatives that protect landscape features within human-modified landscapes. Crucially however, I also demonstrate that as disturbance intensity increases, less resilient species are lost from humanmodified landscapes. Whilst I provide important empirical contributions for understanding bat responses to disturbance, there remain substantial questions about how best to conserve these species and promote sustainable land use. The pipeline and classifier provided in this thesis will help improve accessibility for future acoustic studies to address these questions in Borneo and other areas of Southeast Asia. Therefore, the findings and resources presented here are an important step towards evidence-based land management for conserving Southeast Asian bats in human-modified landscapes.

All great ape species and subspecies are currently classified as endangered or critically endangered in the IUCN Red List, with wild populations declining at unprecedented rates. Among them, the bonobo (Pan paniscus) is perhaps the least known. With only 30% of its geographical range having been surveyed, the data needed for assessing its status and trend were lacking until 2016, preventing an update of its conservation status. Here, I investigated novel and traditional field methods for the assessment of bonobo populations, using data acquired in Salonga National Park (SNP), Democratic Republic of the Congo (DRC). First, I used 16,700 camera-trap videos to apply camera-trap distance sampling (CTDS), a recent method for estimating population density, to the bonobo and 13 other species. Second, I analysed 1,511 bonobo nests and 15 years of climatic data (2003-2018), to investigate factors involved in nest decay, evaluating the effects of inaccurate nest decay times on density estimates via traditional nest counts. Finally, I integrated datasets from 13 different surveys in SNP conducted over two time periods (2002-2008; 2012-2018) including detection/non-detection, count data and CTDS to estimate bonobo status and trend, using specifically calculated nest decay times. I showed that CTDS was an excellent method providing wildlife density and abundance, particularly important for threatened species, and highlighted issues in the application to different species, with reactivity to the cameras being the main source of bias for the bonobo. I found that decreasing precipitation triggered longer decay times of bonobo nests in SNP, with the number of storms being the main factor driving nest decay although a behavioural adaptation with bonobos strengthening nest structure in response to harsh precipitation. In addition, I showed that failure to account for nest-specific biotic and abiotic conditions, would lead to bonobo estimates biased up to 60%. Finally, I showed that an integrated analysis helped mitigating biases peculiar to specific survey methods, revealing an important, stable bonobo population in SNP. Here, a pristine habitat and the presence of rangers exerted a positive effect on bonobo abundance, as did ancestral taboos. The results of this thesis showed that new methodologies like CTDS, providing density estimates without the need of conversion factors, retain high potential for future population monitoring and conservation. Nevertheless, with necessary precautions such as application of time specific decay rates, implementation of traditional methods still provides accurate assessment of status and trend. The methods and recommendations described here are meant to serve as basis for a range-wide assessment, informing the new bonobo conservation strategy due in 2022.

Flight feathers are crucial for foraging, predator avoidance and large-scale movements in most avian populations. However, the structural integrity of these feathers can be compromised by growth defects, negatively impacting flight ability and survival. Poor feather condition is characterised by the presence of fault bars, which are weak areas displayed as translucent bands that appear through the width of the feather vane. Fault bars occur as a result of stressful or adverse environmental conditions during feather growth. The thesis investigated the macroscopic and microscopic characteristics of this growth defect in relation to current formation theories, assessed different feather quality measures and explored possible causes and consequences of fault bars. The study was carried out at RSPCA Stapeley Grange Wildlife Centre, which receive a large number of carrion crow Corvus corone admissions displaying poor feather condition each year. Firstly, the macroscopic and microscopic characteristics of fault bars were observed, reviewing existing fault bar formation theories and imagery with the use of advanced technology. Unique observational evidence was presented from this, identifying a 'squeezed' appearance to the barbules within fault bars, supporting the hypothesis of muscular constriction around the growing feather pin. Moreover, for the first time, images of fault bar occurrence within the growing feather pin were presented. Relationships between different measures of feather quality were then assessed, accounting for differences between feather type (primary, secondary and tail), in reference to the 'fault bar allocation' hypothesis (Jovani & Blas, 2004). In this, fault bars occur on feathers that are least important for flight, resulting in the majority of fault bars being located on the tail feathers, with the lowest numbers in the primary feathers. A variety of feather quality measures were assessed here, including the number of fault bars, average width of fault bars, feather iridescence and strength, in addition to the number of snapped and white feathers. A key finding in this study was the relationship between the average width of fault bars and average feather iridescence across all feather types. This information strengthens our knowledge of how dull feather portray honest communication signals of low fitness. Moreover, average feather strength was found to be an independent measure of quality, with generally no relationship found with other measures of quality. Average fault bar width measurements were used to investigate the causes of fault bar production in relation to chemical profile of feathers, parasite burden, sex and age (study aim 3). This made a valuable and novel discovery, identifying a possible link between calcium deficiency and fault bar occurrence. Calcium an essential element in skeletal mineralisation and eggshell formation. Therefore, the results of this study add to the knowledge of calcium and its role in fitness, expanding to feather quality. This study also found a potential trade-off between costly immune defences facilitated at the cost of feather quality, where low numbers of endoparasite species associated with wide fault bars in the wing feathers. Poor feather quality was not found to vary between sexes, as carrion crows are monomorphic and non-migratory. In regard to age differences, the tail feathers of younger individuals were found to have the widest fault bars. This supports many other studies in highlighting the vulnerability of juveniles during the feather growth period. Lastly, average feather strength measurements were used to investigate the consequences of poor feather quality in relation to the chemical profile of feathers, endoparasite burden, sex and age (study aim 4). A key finding here was that stress resistant bases were associated with a high proportion of chlorine in primary flight feathers. Links to parasite burden and sex were not identified; however, in line with the above findings, younger individuals were found to have low stress tolerance in the primary feathers compared to adults. Differences in feather strength in relation to fault bar occurrence was also reviewed. Contrary to predictions, no differences in strength were found between feather regions with fault bar occurrence and those with fault bar absence. Future research in this field could be extended to nestlings, an age group that was unfortunately excluded from this study due to the presentation of pin feathers. Moreover, research could also be broadened to additional species, as fault bars are found to impact a wide variety of passerine and non-passerine individuals. This may then open opportunities in understanding stressors faced by vulnerable species, aiding future conservation efforts.

Emerging viral zoonoses are a significant global health concern, brought into sharp focus in recent times by the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the subsequent global pandemic. Other emerging and re-emerging zoonotic viruses also continue to present significant threats to public health, including Crimean-Congo haemorrhagic fever virus (CCHFV), a tick-borne virus that can cause severe disease and high case fatality rates in people, but with a complex ecology that remains poorly understood in many areas of the world, particularly in Africa. Serological tools are vital for understanding emerging zoonotic viruses both at a population- and individual-level. Population-level surveillance of animal and human populations can shed light on patterns of viral circulation and aid in identification of risk factors associated with infection, while individual-level serological investigations help to characterise the immune response to infection, providing insights into the nature of protective immunity, possible vaccine targets and improving methods of disease detection. The initial focus of this thesis was the development of a diagnostic enzyme-linked immunosorbent assay (ELISA) for detection of CCHFV, and its subsequent use to explore the epidemiology of the virus in livestock and people in northern Tanzania. However, the start of the coronavirus disease 19 (COVID-19) pandemic part way through this research resulted in an additional set of research questions relating to SARS-CoV-2 diagnostic assay performance and epidemiology during the first wave of the pandemic in Glasgow, UK. This thesis therefore explores diagnostics assay development and epidemiology of CCHFV and SARS-CoV-2. Firstly, an indirect ELISA for detection of anti-CCHFV antibodies in livestock was developed and optimised. It showed good potential for use as an in-house assay for detection of CCHFV exposure in animals. Secondly, the performance of two indirect ELISA assays against the S1 subunit of the SARS-CoV-2 spike protein (S1) and the receptor binding domain (RBD) was investigated, establishing a cut-off value for interpretation of these assays, determining sensitivity and specificity, and exploring measures of assay precision. Both assays showed good ability to distinguish between positive or negative serum samples for anti-SARS-CoV-2 IgG antibodies. These ELISAs were then used to investigate levels of SARS-CoV-2 exposure in a patient population in Glasgow during the first wave of the COVID-19 pandemic, demonstrating that overall seroprevalence remained low throughout this period. Additionally, ELISA responses were compared against levels of neutralising antibodies (NAbs), measured using HIV(SARS-CoV-2) pseudotype virus neutralisation assays (PVNAs), demonstrating heterogeneity in IgG and NAb responses, and highlighting an association between disease severity and higher levels of IgG and neutralising antibodies. The epidemiology of CCHFV in northern Tanzania was explored through analysis of a large cross-sectional study of livestock and people in linked households, using a commercially produced species-independent ELISA. This study demonstrated for the first time that CCHFV is circulating in northern Tanzania. High levels of exposure were found in cattle (n = 1530/3098, 49.4%), goats (n = 823/2475, 33.3%), and sheep (n = 582/2124, 27.4%) across the region, and an overall seroprevalence of 15.1% (n = 53/351) was observed in people, despite an absence of confirmed clinical disease in the country (Temur et al., 2021). Substantial heterogeneities were observed in levels of exposure between study sites for both livestock and people, indicating that local context is important for determining exposure to CCHFV. However, patterns of village-level exposure varied between people and livestock, possibly suggesting different drivers of exposure. Risk factors associated with CCHFV seropositivity were also investigated in livestock, and demonstrated that increasing age, and extensive, pastoral agro-ecological settings were associated with higher levels of exposure. Additionally, a novel association was identified between pig keeping and higher exposure in cattle. The work presented in this thesis demonstrates the application of serological methods for investigation of two important emerging and re-emerging zoonotic viruses, SARS-CoV-2 and CCHFV. This research adds substantially to our knowledge of CCHFV epidemiology in northern Tanzania, demonstrating high levels of exposure to the virus in livestock populations and highlighting its potential as a public health concern in the country, while the work on SARS-CoV-2 provided important information on population-level immunity and the nature of the immune response during the early phases of the global pandemic.

With one million species at risk of extinction, there is an urgent need to regularly monitor threatened wildlife. In practice this is challenging, especially with wide-ranging, elusive and cryptic species or those that occur at low densities, such as chimpanzees (Pan troglodytes). Monitoring is needed to establish conservation actions, but also to assess population trends. For conservationists, key questions concern species distributions and densities. These data must be regularly updated, allowing conservation planners to effectively execute and assess conservation efforts. Conservationists benefit from methods that are time- and cost-efficient and simultaneously provide accurate and precise data. I evaluate passive acoustic monitoring (PAM) as a tool for detecting, localising, and estimating densities of chimpanzees. I compare with results from camera traps (CT), a more common method. I deployed two arrays of acoustic sensors in Issa Valley, Tanzania: one comprising twelve non-GPS-synchronised acoustic sensors across the whole study area for nine months to estimate chimpanzee presence/absence and density. I simultaneously deployed 53 CT for methodological comparison and used spatial capture-recapture (SCR) and distance sampling (DS) methods. Another acoustic array comprised four custom-built GPS synchronised acoustic sensors, deployed for a 3-month period around a single valley (~2km2), to localise chimpanzees. I found chimpanzee detectability varied over seasons. It is five times faster than an equivalent method using CT. Furthermore, I found that the estimated density of calling chimpanzees with acoustic SCR was lower than density derived from SCR with CT data, but within the 95% CI obtained with DS and CT data. Playback sounds were localisable with 27 ± 21.8m error and chimpanzee calls were localisable within 52m from the location of a researcher following the calling individuals. These results suggest PAM is a promising non-invasive method for chimpanzee monitoring. Despite the current challenges to automate data analysis, improvements of automatic call detection are promising. I anticipate that PAM will become more common in the conservationist's toolbox for loud calling terrestrial species monitoring such as chimpanzees, gibbons, orangutans, wolves or elephants.

Precise spatial and temporal regulation of gene expression is critical for embryonic development. This is achieved in part via transcription factor binding to cis-regulatory modules (CRMs). However, in contrast to other germ layers, the gene regulatory network involved in endoderm formation is relatively understudied in vertebrates. In this study we use genomic approaches to study the chromatin landscape that governs endoderm specification and early endoderm organ formation in zebrafish embryos. Since the endoderm is a minor cell population, we employed two distinct methods to find to endoderm-specific CRMs: 1) to capture CRMs that regulate early endoderm-specific genes during early specification, we performed overexpression of the master regulator of endoderm formation, sox32, 2) to capture CRMs that function during early organogenesis, we have generated a three-colour transgenic line to specifically FACS isolate endoderm cells and study endoderm-specific CRMs at 28 hours post-fertilisation. Our results show that sox32 overexpression not only induces ectopic endoderm formation but also ectopic formation of progenitors of the zebrafish left/right organiser known as dorsal forerunner cells (DFCs), a phenomenon not previously discussed in literature. We also identified 16, 000 regions that exhibit enhanced accessibility by ATAC seq in embryos injected with sox32 mRNA compared to control and that a large number of these regions harboured motifs of transcription factors that play important roles during endoderm specification. Our findings also suggest that sorted GFP+ cells from the triple transgenic line comprise both endoderm and transdifferentiated Kupffer's vesicle cells, which are implicated in left/right asymmetry in zebrafish. We also show by ATAC-seq analysis that a large number of accessible regions are likely shared by GFP+ cells and cells that are devoid of fluorescence. Finally, we show that changes in the chromatin landscape correlate with changes in gene expression at both stages of endoderm development through comparison of data from ATAC-seq and RNA-seq, but also that the chromatin landscape changes between endoderm specification and early organogenesis. Our results provide inside into how the chromatin landscape changes in the endoderm during development and also reveals a number of potentially important CRMs that may help shed light into how endoderm is formed during embryogenesis.

Autophagy is an evolutionary conserved process of cellular self-degradation. It involves the lysosomal degradation of cellular materials, via an intermediate double membrane vesicle, where the degradation products can be reused by the cell. It is known that as well as bulk degradation autophagy can happen in a highly selective manner through receptors and adapters. One of the key players in this is the LC3 protein. This project investigates selective autophagy using Drosophila Melanogaster as a genetically modifiable organism. The Drosophila homologue of the mammalian LC3 proteins is ATG8a. ATG8a has a hydrophobic binding pocket (LDS) which binds autophagy substrates that contain a LC3 interacting region (LIR). Quantitative proteomics on Drosophila with a mutated LDS hydrophobic binding pocket was used to identify a panel of ATG8a interacting proteins. From this analysis, Drosophila GMAP (Golgi microtubule-associated protein) was discovered as a novel autophagy receptor. This study has shown that Drosophila GMAP has a role in golgiphagy, the selective degradation of the Golgi complex.

Understanding mosquito interaction with long-lasting insecticidal bednets is crucial in the development of more effective intervention methods to protect humans from malaria transmission. Accurate 3D time-series imaging of mosquito-bednet interaction has not previously been possible, but has the potential to offer full kinematic analysis of mosquito flight, accurately determine in situ insecticide dosages, and examine behaviours not yet welldocumented. The work presented in this thesis relates to utilising digital holography for the accurate 3D imaging of mosquito flight using a single-view recording setup. A scalable digital methodology for single object reconstruction and localisation is developed through simulations and physical validation, and a novel focus metric, based on the zero-crossing of the reconstructed complex wavefront, is introduced. This work examines the boundaries presented by a digital hologram recording setup, and utilises the lowest imaging resolution that still yields acceptable localisation errors. Real-world problems typical in mosquito imaging, such as multi-object close proximity and occlusions, and obscured-object localisation, are examined in detail. The methods provided to overcome these obstacles largely involve the development of novel post-process software solutions. Finally, a large field of view digital holographic experiment is developed and preliminary qualitative data of livemosquito reconstruction and localisation is presented. Further work involving techniques to improved the calibration of the large field of view system are suggested to improve the quantitative analysis of the data. The result of this study is a scalable digital holographic methodology to examine mosquito-bednet interaction in 3D at a level of accuracy previously only seen in 2D planar imaging of mosquitoes in a much smaller volume, as well as introducing novel post-processing techniques for accurate localisation.

The aim of this thesis is to investigate the cranial ecomorphology across Odontocetes clade by testing hypotheses of association between interspecific cranial morphological variation (mainly size and shape traits) and ecological adaptations. Very little previous research has focused on modularity in different species of toothed whales (Guidarelli et al, 2014; del Castillo et al., 2016; Churchill et al., 2019), and those that have, have tended to focus on common species such as Tursiops truncatus, Stenella coeruleoalba, and Delphinus delphis. Moreover, a comprehensive study of the cranial ecomorphology on the whole toothed whale clade is still lacking. The thesis is structured into four Chapters organised sequentially to cover the methodological approach (Chapter 2), the interspecific variation of odontocetes cranial morphology and its association with ecological adaptation (Chapter 3), the potential for cranial morphology to identify hybrids in two species of Monodontidae (Delphinapterus leucas and Monodon monoceros) in order to identify the potential of cranial morphology to identify hybrids and their evolutionary adaptation (Chapter 4), and finally the study of intraspecific skull variation in a stranded population of British false killer whale (Pseudorca crassidens, Chapter 5). Such a hierarchical taxonomic approach was designed specifically in order to provide a framework for interpreting skull size and shape variation in Odontocetes at all evolutionary scale from macro (=interspecific variation) to micro (one population). Ontogeny was not considered into this thesis because the aim of the proposed methodological framework is to identify its potential applicability to the study and interpretation of paleoecology from fossils, hence adult variation is more relevant due to clear change into feeding functions. Chapter 2 describes methods, statistical analyses, and protocol used to quantify cranial size and shape variation in three dimensions using three different digitising methods: Microscribe, Photogrammetry and Breuckmann laserscan. Also, this chapter supports Chapter 2 as sources/specimens from two different techniques and datasets used. In Chapter 3 I tested the hypothesis that ecological variables correlate with cranial shape and size of Odontocetes at macroevolutionary (= interspecifc) scales with the support of comparative methods. Similar analyses were presented in Churchill et al. (2018) and McCurry et al. (2017) although on a different selection of taxa and using different cranial 3D landmark configuration. Chapter 4, provides an analysis (by using GMM approach) of the genetically confirmed hybrid between Delphinapterus leucas and Monodon monoceros, was analysed by using GMM approach confirming the phenotypic dominance of one of his parental species. Sexual dimorphism in size, shape and integration of the skull was also examined within and between the two species. In Chapter 5, a stranded British population of Pseudorca crassidens was examined by comparing shape and size skull between sexes. A GMM approach was also used to study the morphological integration between crania and mandibles in separate sexes. Final remarks chapter summarizes all the previous findings and provides suggestions for future studies.

To survive and reproduce, primates must consume sufficient amounts of resource. Because they live in seasonal environments and mostly rely on vegetative foods, primates face temporal variations in food abundance and quality, and food shortages often have negative repercussions on their energy balance, fecundity, growth, and survival. To limit these impacts and maintain sufficient nutrient and energy intake during lean periods, primates exhibit a large range of adaptations including adjusting their diet, ranging behavior and/or group size. Chimpanzees (Pan troglodytes) are one of the most studied animals but despite nearly six decades of field research, gaps remain in our knowledge of the species, particularly when it comes to communities inhabiting savanna-woodlands, the ecological edge of the species range. Savanna-woodlands differ from forests in having substantially less rainfall, which is strongly seasonal, as well as lower plant density and diversity, all of which result in resource scarcity and important fluctuations in its availability. The selective pressures operating on chimpanzees in these landscapes are thus predicted to be different than those in forests, potentially eliciting adaptations distinct from adaptations to a forested habitat, especially during times of resource (both food and water) scarcity. However, to date, we have only limited behavioral data from habituated communities in savanna-woodlands, thus restricting our ability to explore these ideas. I investigated chimpanzee (P. t. schweinfurthii), diet, ranging and grouping patterns in the savanna-woodland environment of Issa valley, Tanzania, and particularly their correlations to seasonal fluctuations in resource availability. I also compared the diet, ranging and grouping patterns observed at Issa with those of other communities. I found that, when preferred foods were scarce, Issa chimpanzees consumed young leaves from tree species growing in the open woodland habitat. In contrast to previous reports from other chimpanzee communities, during periods of low food availability Issa chimpanzees significantly increased their daily path length. Water scarcity, however, did not influence their daily path length, and neither seasonal fluctuation in food nor water availability influenced habitat use. I found that party size at Issa was significantly influenced by seasonal variations in food but not water availability and was higher in open habitat, which is potentially characterized by a high predation risk. In general, Issa chimpanzees consumed less plant species than chimpanzees at more forested sites. Like elsewhere, they consumed mostly fruit, but other items such as leaves, flowers, and termites were also important in their annual diet probably because they provide essential proteins. Issa yearly home range was larger than most other communities for which data are available. Finally, compared to other communities, the Issa community was highly cohesive, possibly due to a combination of its small size and the potential threats (predators, neighboring communities) in their home range. By providing data from direct observations of a chimpanzee population living in an under‐studied biome, the present study brings new insights into chimpanzee behavioral responses to seasonal fluctuations in ressource availability, into the relationships between environment and behavior for this species, and into chimpanzee behavioral diversity in general. Furthermore, chimpanzee behavioral studies may be of great value to the paleoanthropological scientific community. The results of the current study could be useful to interpret archaeological records and infer extinct hominin behavior, as well as to highlight what adaptations may have set the principles for the differentiation between human and chimpanzee lineage.

Terrestrial gastropods are highly pestiferous and pose a significant global threat to sustainable agriculture, horticulture and floriculture. Current control methods rely on metaldehyde formulated bait pellets. However, metaldehyde can harm non target organisms and cause environmental pollution. Metaldehyde is also due to be banned for use in the UK by 2022. A viable alternative is the gastropod parasitic nematode Phasmarhabditis hermaphrodita, which has been formulated into a biological control agent (Nemaslug®) by BASF Agricultural Specialities. However, the same strain of P. hermaphrodita (DMG0001) has been produced in an artificial environment for over 25 years and research suggests this strain is losing beneficial traits (e.g. virulence and host finding) and failing to provide protection against slug damage. The primary aim of this thesis was to use a collection of wild isolated Phas marhabditis species (P. hermaphrodita, P. neopapillosa and P. californica) to investigate whether they are more virulent than the commercial strain of P. hermaphrodita (DMG0001) to the pestiferous slug Deroceras invadens and the snail Cornu aspersum in laboratory experiments. Host feeding inhibition, numbers of nematode dauers produced on gastropod cadavers and natural variation in chemotaxis behaviour were also investigated. Additionally, the impact of virulent strains on beneficial non- target organisms and the mechanism of host behavioural manipulation were explored. Multiple wild strains were found to perform better than the commercial strain in regards to virulence, feeding inhibition, proliferation on cadavers and locating host cues. This research has demonstrated that other members of the Phasmarhabditis genus can be utilised as safe and effective biological control agents. This thesis presents which Phasmarhabditis species show the most potential for pathogenic ability and host seeking.

The study of Neanderthal behaviour and ecology has been shaped by the overarching question of Neanderthal cognitive modernity. The debates concerning Neanderthal cultural complexity and subsistence strategies cross paths in the study of birds. Recent research has shed light on the contribution of bird remains as a proxy in interpretations of Middle Palaeolithic diet and behaviour. Additionally, birds function as excellent indicators of past climate and environmental conditions because some species have highly restricted niche requirements. This thesis contributes new information to our understanding of Neanderthal behaviour and ecology across their geographical and temporal range by employing ecological and taphonomic methods to bird remains recovered from five Neanderthal sites: Gorham's Cave and Devil's Tower Rockshelter in Gibraltar, Cova Negra, Spain, Scladina Cave, Belgium, and Tabun Cave, Israel. Intra- and inter-site analyses establish that Neanderthals exploited gamebirds and wetland species for subsistence purposes in all five locations. Ecological results indicate that the Neanderthal bioclimatic and habitat niche did not vary by geographic position. Within their niche, Neanderthals efficiently exploited birds as a regular addition to their diet, focussing their efforts on specific taxa. This conflicts with earlier research, which proposed that Neanderthals were incapable of conceptualising the complex strategies necessary for hunting birds and small, fast game.

Attention bias (AB) describes a tendency to differentially allocate attention towards one of two or more emotional stimuli. In humans these biases reliably map onto physiological and self-reported measures of affect. AB tasks have been shown to detect shifts in emotional state and have been proposed as a novel method of animal welfare assessment. This PhD aimed to determine which factors might influence AB in rhesus macaques (Macaca mulatta) through triangulation of these cognitive data with behavioural observations, physiological measures (salivary cortisol) and key genetic polymorphisms related to oxytocin, serotonin, dopamine, and cortisol. Key factors of interest were condition (baseline and post-stressor) sex, age, and time of day. AB trials were conducted with 61 (45 female, 16 male) adult rhesus macaques (Macaca mulatta) using an automated computer operated apparatus with threat-neutral conspecific face stimuli presented on screens. Duration of looking at these stimuli was recorded. Two looking time measures were used throughout the thesis: duration looking at the threat face stimulus (THR), total duration looking at the threat and neutral face stimuli (TL). AB trials were conducted before and after the macaques' annual veterinary health check, which is thought to be acutely stressful. A total of 640 AB trials were conducted. The main findings were the relationship between AB measures and the interaction between condition and sex. Female macaques became less attentive to social information from baseline to post-stressor, while male macaques became more attentive. Further, an association between AB measures and time of day was revealed. This thesis demonstrated that the inclusion of pedigree (relatedness) data is vital when conducting genetic analysis to avoid type I errors. Without pedigree data, six genotypes had a significant association with the AB measures; however, with pedigree data only one statistically significant association was found. The cognitive, behavioural, and physiological results suggested that the veterinary health check may be too mild a stressor for use in future AB studies. The use of a more stressful event or procedure may be more informative while the AB measure is studied and developed. This project has shown AB to be a promising tool for welfare assessment, highlights some important influencing variables and should act as a guide for further research.

This thesis examines the potential for the inheritance of environmental information in the highly social teleost fish, Danio rerio. I performed a series of studies over four data chapters that examined the effects of varying levels of environmental enrichment (EE) across three generations. I aimed to examine the effects of EE on physiology, brain function and behaviour. To do this, I utilized a combination of video tracking in a novel open tank group shoaling test, larvae movement trials, high resolution imaging of morphology, and adult whole brain gene expression analysis. Taken together, these studies indicate that variation in levels of enrichment is associated with changes in complex behaviours and morphologies, which can be inherited through the paternal germline. The analysis of larvae movement and shape performed here shows that changes in locomotor activity may be established in early development, as subtle changes in developmental timing are found. The results here also show that changes in locomotor activity are stably inherited between generations, whereas changes in social traits are not. Although there were changes in social behaviours within generations, there were no inherited effects of on shoal cohesion. I targeted the expression of two nonapeptides known to be involved in the regulation of social behaviour in fish species, arginine vasotocin (AVT) and isotocin (IT) and found that changes to social traits in the first generation appear to be associated with changes in whole-brain AVT expression. The disparity in the heritability of these two behavioural realms found here is particularly interesting and provides the potential for further investigation.

Seasonal reproduction is a strategy conserved across nature. The duration of light (photoperiod) regulates the reproductive molecular control within the Hypothalamic-Pituitary-Gonadal Axis of seasonal species, and supplementary cues fine-tune the exact timing of breeding. In recent years, epigenetic mechanisms have been shown to be involved in an array of circannual rhythms, including reproduction. The aim of this thesis was to explore the molecular reproductive neuroendocrine processes that underlie the onset of reproduction in two summer-breeding animal models, the Japanese quail (Coturnix japonica) and the Siberian hamster (Phodopus sungorus). In birds, light penetrates the skull and is detected by deep-brain photoreceptors (DBPs) within the hypothalamus, stimulating the photoperiodic reproductive response. However, the identity of these DBPs is unclear to this day. In the present thesis, the expression of two photoreceptors, Vertebrate-Ancient Opsin (VA Opsin) and Neuropsin (OPN5), was repressed through adeno-associated viral injection, and the breeding response was monitored in control and treated birds maintained under short-days (SD), or long-days (LD) for 2, 7 or 28 days. The data revealed that both opsins may be involved in seasonal reproduction in the Japanese quail, and that OPN5's role includes modulating gonadal sensitivity to gonadotropins during breeding. It was also found that hypothalamic OPN5, GNRH and DNAmethyltransferase (Dnmt) expression increases at embryonic day 14 in this species. In addition, higher global methylation levels were found in the pituitary gland of adult LD quail, compared to SD. In the Siberian hamster, two studies were conducted to investigate the effect of triiodothyronine (T3) on the photoperiod-dependent regulation of reproductive physiology and hypothalamic DNA methyltransferase enzyme expression in both males and females. Two weeks of daily T3 injections induced gonadal growth in SD males, but not in females. Female SD hamsters, but not males, were found to express lower levels of de novo Dnmts compared to LD individuals. However, exogenous T3 did not affect hypothalamic Dnmt expression in neither males or females. The data indicated sex differences in the gonadal response to T3, as well as in the regulation of hypothalamic DNA methyltransferase expression. It is likely that female Siberian hamsters require additional cues to initiate reproductive processes. The studies presented allowed for an exploration of reproductive mechanisms in both an avian and a mammalian model, including the role of epigenetic processes in seasonal breeding. Future studies are required to elucidate the precise mechanisms of DBPs, as well as identify downstream targets of maintenance and de novo Dnmts.

Heteropody is the phenomenon in which the manus and pes of quadrupedal animals differ substantially in size and shape. The term is most often used in reference to the extreme foot size differences present in fossils and trackways of some non-avian dinosaurs, particularly sauropods. Previous studies have asserted the possibility that extreme heteropody developed in these animals as a mechanism to equalise underfoot pressure, compensating for unusually anterior/posterior centre of mass positions. This thesis sets out to test this hypothesis by answering the following questions: 1. Can skeletal surface area predict soft tissue foot surface area? 2. Is antero-posterior centre of mass position correlated with heteropody in extant taxa? 3. Do underfoot forces and pressures in extant taxa indicate the presence of a pressure equalisation mechanism? 4. Is there evidence in the fossil record for a link between centre of mass and extreme heteropody in dinosaurs? These questions were answered using the corresponding methods: 1. Using CT scans of the feet of extant animals and a custom Matlab script to derive underfoot surface area for skeletal and soft tissue and if they correlate. 2. Using digitized skeletons and convex hulls of quadrupedal extant animals to gather centre of mass and heteropody data for a range of extant animals, and seeing how they correspond with CoM positions. 3. Combining new pressure mat recordings with recordings in the literature for quadrupedal animals and seeing how they correspond with CoM positions. 4. Gathering heteropody data from sauropodomorph fossil trackways and some quadrupedal dinosaur body fossils, and testing how they correspond with previously established CoM position estimates. From these lines of enquiry, no link between CoM position and heteropody was definitively established. Results for live animal studies showed more signal for a correlation than in skeleton-only studies, and dinosaur trackway analysis showed potential for a link in sauropodomorphs, but neither of these studies provided enough evidence to establish a correlation between CoM and heteropody in tetrapods. This thesis does not support the hypothesis that heteropody is used as a pressure equalisation mechanism in tetrapods, especially as a universal rule. This thesis also found that soft tissue underfoot surface area is highly predictable from skeletal underfoot surface area. In addition, it found that underfoot surface area based on soft tissue is larger in forefeet compared to hindfeet that would be expected from skeletal surface area alone.

In the Americas, arbovirus transmission is concentrated within urban settings in tropical zones, where high human population densities and environmental conditions enhance the survival and reproduction of Aedes aegypti. Since its re-emergence in South America in the 70's, dengue virus has been expanding and increasing in urban settings where it is now endemic. Additionally, the recent arrival of new arboviruses into the region, such as chikungunya (2013) and Zika virus (2015), have triggered major epidemics leading significant public health and economic impacts. These pathogens are linked in sharing a common mosquito vector in Ae. aegypti. Given the absence of effective licenced vaccines, vector control is thus the primary strategy for reducing the transmission of all of these pathogens. Effective vector control and public health preparedness require detailed understanding of vector ecology and human exposure risk within foci of transmission. Both vector populations and viral dynamics are highly dependent on environmental conditions, but the nature of environmental impacts likely depends on local ecological context. Ecuador bears an important burden of arboviral transmission in South America. Most transmission is concentrated in coastal cities where dengue is endemic and rising, and major outbreaks of chikungunya and Zika have recently occurred. However, there has been limited investigation of vector ecology in these rapidly expanding urban settings, and its association with seasonal patterns of arboviral transmission. To address this gap, this study aimed to assess the environmental drivers of Ae. aegypti ecology, infection rates and arboviral transmission within two major urban hotspots in Coastal Ecuador. This was accomplished through a series of field studies of vector ecology, laboratory analyses of arboviruses, and modelling investigations designed to identify environmental determinants of human exposure and infection incidence. The first chapter reviews what is known about the most important Aedes-borne viruses and their vectors in South America, with particular focus on Ecuador, vector control, and the global and regional disease burden. The second chapter presents results from a field study carried out in a urban neighbourhood of Quinindé, Ecuador, that evaluated a novel trapping method, the Mosquito Electrocuting Trap (MET), for direct estimation of human exposure to Ae. aegypti bites. The third chapter describes results of a 6-month field study aimed to characterize the environmental determinants of Ae. aegypti abundance and distribution, behaviour and arboviral infection rates within two cantons in Coastal Ecuador at the tail end of the 2016-17 Zika outbreak. The fourth chapter presents an analysis of seasonal and annual variation in dengue, chikungunya and Zika virus within these 2 cantons, and associations with climatic and entomological variables. The fifth chapter discusses the key results of each of the chapters and the implications of the findings towards an effective vector control in Ecuador and beyond the country. It was found that the MET was effective for measuring Ae. aegypti host-seeking behaviour, and generated representative estimates of their biting rate and activity time relative to the standard BG-sentinel trap (BGS). Analysis of Ae. aegypti ecology indicated that its abundance varied significantly between cantons, neighbourhoods within cantons associated with urbanization gradient, temporal timing of collection and past rainfall. Additionally, there was significant variation in Ae. aegypti resting behaviour (resting in or outside houses) between cantons. This demonstrates the existence of heterogeneity in Ae. aegypti population dynamics and behaviour between and within the study sites, which highlights the importance of localized surveillance to guide vector control. Likewise, arboviral incidence of dengue and chikungunya (as reported to the health system) also differed between the two study sites, being dengue 1.5 and chikungunya 2.5 times higher in Portoviejo than in Quinindé during the peaking week. The seasonal pattern of disease incidence varied among the three arboviruses, with a difference of 5 weeks between each of their peak of incidence. Intra-annual incidence was also found to be linked with climatic and entomological variables, with dengue and chikungunya incidence being positively associated with temperature and rainfall, while Zika incidence negatively associated with such climatic variables. Outdoor Aedes collections with Prokopack aspirators and BGS were positively related to dengue incidence, while indoor Prokopack aspirations were negatively associated with this variable. The interannual incidence of dengue differed between years analysed (2013-2018) with 2015 being the year with highest dengue incidence. Such findings highlight the importance of conducting focalized epidemiological surveillance on each site, but also differentiating between arboviruses, rather than assuming they all will follow dengue trends. Findings from this work have provided new entomological and epidemiological information to the study sites and despite the short period of study, fine spatial scale heterogeneity was detected in arbovirus transmission dynamics.

Groups of animals often compete over resources, such as territory, food, or mates, which are critical for survival. Successful groups tend to be those in which individuals cooperate effectively, and thus intergroup competition is thought to exert a selective pressure favouring the evolution of behavioural traits that promote intragroup affiliation. However, no cohesive pattern has emerged to describe the effect of intergroup conflict (IGC) on intragroup social behaviour. Furthermore, because most studies focus on intragroup behaviour during or immediately after conflict, we know relatively little about how groups perceive and respond to the risk of encountering rivals. Here, I investigate the function of intragroup behaviour in response to the threat and occurrence of IGC in three wild crested macaque (Macaca nigra) social groups. I use relative risk maps based on the timing and locations of intergroup encounters (IGEs) in conjunction with behavioural observations to test predictions that changes in intragroup behaviour function to increase social cohesion. Group spread, behavioural synchrony, and pre- and post-encounter focal observation data indicate that crested macaques remember the frequency, location, and outcome of previous IGEs: Also, that individuals in dominant and subordinate groups may perceive encounters differently. However, I found no evidence that intragroup behaviour functions to promote cohesion. Rather, my results indicate that both pre- and post-conflict behaviour functions primarily to minimise individual costs and reduce physiological anxiety. Rather than collective action being impeded by the lack of cohesion-enhancing behaviours, I suggest that this population may not need them in the context of IGC. These findings raise the possibility that (a) when food resources are abundant and mating access is easily monopolised, not all groups that engage in IGC have something worth fighting for, and (b) that we need to find ways of incorporating this into future models of intergroup hostility.

This study explores the fourth genre, creative nonfiction, as the means to retell the stories of lived experiences. The aim of the study was to gather stories of ordinary people working to conserve orang-utans in Sarawak through in-depth interviews based on narrative inquiry principles, and then to re-tell the stories by crafting a creative nonfiction artefact composed of different subgenres such as Shorts, Portraits, Literary Journalism, hybrid nonfiction pieces and stories partially or wholly told in the participants' own voices in a subgenre that the narrative inquirer-writer identified and named the Crafted Interview. Nineteen individuals were identified and interviewed, using semi-structured interview questions that allowed for digressions, follow-up questions and gentle probing with empathy and understanding by the researcher. Not just a detached observer, the researcher was a participant involved in orang-utan conversation, with a background in journalism and conservation, close to the research participants and their work. She became the interviewer as research instrument and a collaborator in the interviews, gathering stories - the lived experiences of participants through in-depth interviews. The product of the study, the creative nonfiction artefact, tells stories in various nonfiction subgenres spanning fifty years of orang-utan conservation in Sarawak. Through this montage of stories, the narrative inquirer-writer re-tells the storied lives of men and women who have worked in orang-utan conservation in different capacities. These were "ordinary" people, not privileged Western primatologists, but the individuals on the ground, doing their daily work as forest guards and keepers, wildlife biologists and researchers, eco-tour operator and fundraiser for wildlife rehabilitation each contributing to the long-term survival of the iconic primate in its wild habitats or to the orphaned orang-utans that had been confiscated from poachers or illegal exotic pet owners. These stories reflect not just work to save the endangered species, but also the larger issue of species extinction. It is acknowledged that though important, this study has focused only on a small population of orang-utans found in Sarawak; there are other populations in Borneo and Sumatra threatened by human avarice and ignorance. The human species' lack of humanity is evident in the lives of the orphaned orang-utans and the semi-wild animals that cling to a tenuous life in a tiny patch of forest in the middle of human settlements. This leads us to the final level of meaning and understanding; that the human species may be forcing itself into extinction. We exist in a large ecosystem; our fate inextricably linked to that of our cousin, the red ape. While it teeters on the brink of extinction, we realise that we could soon follow suit. Despite the naysayers who believe that reading as a pleasurable pastime will soon disappear, the future of the creative nonfiction seems promising; it will thrive in both traditional and new forms as writers and readers alike continue to "hunger for the real." The future of the orang-utan is not so clear-cut. What is evident is that species conservation is a real need around the world. More creative projects beckon, appealing to us to research and write imaginatively, telling true stories, to support other endangered species and to share the stories of men and women toiling to save them on this uneven battlefield. This is a baton we can and should take up; the spark has been lit and this is a flame that needs to keep burning.

Asian elephants (Elephas maximus) are among the last remaining megaherbivores in the Sundaic rainforests. In this thesis, I aimed to improve our understanding of the ecological roles of rainforest-dwelling Asian elephants through their herbivory and seed dispersal behaviours. A comprehensive review in Chapter One revealed that there have been few investigations of their interactions with the community and the habitats they live in. In Chapter Two, I advanced our understanding of Asian elephants in modifying the rainforest structure by quantifying their diet selection and herbivory impacts. The principal foods of Asian elephants in rainforests were palms (39% of total trunkfuls consumed) and trees (30%). They preferred monocots, particularly palms (preference ratio=4.6; below 1=avoidance) that are not abundant in the forest, and most monocots sustained high damage due to elephant foraging (above 40% in foraged patches). Their feeding behaviour was associated with a reduced palm density in the Royal Belum rainforest where elephants roam, as compared to a forest lacking elephants in Krau Wildlife Reserve. Although large tree saplings (around 21 cm diameter) were vulnerable to elephant damage, they had high recovery rates, and elephant herbivory is likely not the sole factor causing lower tree sapling density in Belum. Asian elephants are important seed dispersers. In Chapter Three, I recorded rare interactions of Asian elephants and a large-fruited rainforest tree, Irvingia malayana (Irvingiaceae) through the use of camera-traps. The removal rate of fruits by elephants was low, yet seed dispersal by elephants allowed Irvingia malayana seeds to escape from high levels of seed predation by wild boars. In Chapter Four, using network analysis, I identify Asian elephants as dominant functional generalists promoting seed dispersal diversity within the community. This is the first highly diverse seed dispersal network in the Sundaic region, built using an inter-disciplinary approach, which combines ethnobotany knowledge, feeding signs on fruits, camera-trapping, and published literature. Elephants had high species strength and were important to both the dispersal of plants central to the network and the dispersal of large-fruited species. Along with other important seed dispersers such as gibbons (the most efficient seed dispersers), binturong, civets, and the Malayan sun bear, they promoted network nestedness and functional redundancy. Simulation of defaunation of important, highly-connected seed dispersers caused adverse co-extinctions of seed dispersal interactions. Urgent protection of important and vulnerable rainforest species is needed in the Sundaic region. This thesis confirms the importance of Asian elephants as selective feeders for palms and tree saplings. It describes their interactions with tropical Sundaic fruits and confirms Asian elephants as functionally dominant seed dispersers within the seed dispersal community.

While coral reefs worldwide are threatened by unprecedented environmental change, some reef-building corals can already be found living under extreme conditions within marginal habitats. Learning how corals can survive high temperature fluctuations and multiple other stressors experienced in mangroves, relative to typical reefs, is a key step in understanding the adaptive capacity of reef-building corals to future environmental change. The role of the coral host, symbiotic algae, and diverse microbiota, and how these components of the holobiont interact to define the adaptive capacity of reef-building corals requires further exploration. In this thesis, the thermal tolerance limits of conspecific corals from a mangrove versus a reef habitat were tested in a 20-day heat-ramping experiment. Heating corals beyond their regional thermal maxima caused severe decreases in productivity, irrespective of which habitat the coral came from, but corals from the mangrove habitat suffered less thermally induced bleaching. Amplicon sequencing coral holobionts from reef and mangrove habitats in Indonesia and the Seychelles revealed significant habitat-dependent differences in coral microbiome compositions. A potentially novel coral-bacteria symbiosis between a mangrove-dwelling merulinid coral and an unclassified spirochaete, which accounted for 47% of the coral’s bacterial community, was also uncovered, though its role in the holobiont remains unknown. Reciprocal translocations of corals between reef and mangrove habitats resulted in rapid reorganisation of coral-associated bacterial communities. Within four days of translocation, coral-associated bacterial communities had changed. Corals demonstrated local adaptation and exhibited increased survivability when back-transplanted in their native habitat than when cross-transplanted to a new habitat. Experimental manipulation of the coral microbiome by antibiotic treatment demonstrated its sensitivity to disturbance, with rapid shifts in bacterial abundance, diversity, and composition taking place within 36 hours. These findings demonstrate the conservation value of mangrove coral habitats and highlight the rapid habitat-dependent flexibility of the coral microbiome.

Across many taxa, there is wide intra- and interspecific variation in metabolic rate and in the microbial community composition within the gut. In separate studies, both the metabolic rate and the gut microbiota of an organism have been shown to be related to diet, environment and ontogeny or life history, all of which can have repercussions on survival. Nonetheless, few studies have examined a host’s gut microbiota and metabolic rate concurrently. The experiments within this thesis explore whether a relationship exists between the gut microbiota and metabolic rate in juvenile Atlantic salmon. In addition, this thesis examines whether the genetic origin of the fish can account for any variation in the gut microbial community composition, host physiology, or in host behaviour. To the author's knowledge, these experiments are the first to demonstrate a link between the metabolic rate and the gut microbiota in Atlantic salmon. importantly, the use of common garden experiments uncovered that the genetic background of the fish had an impact on both fish physiology and the gut microbiota. Additionally, rearing environment was shown to impact fish behaviour, which could have consequences for fish physiology, metabolic rate and their gut microbiota. These findings not only highlight the need to consider the gut microbiota when studying host physiology, but also has implications for aquaculture, particularly within the context of fish farm escapees.

Understanding why populations change in size and distribution can help us assess a species' vulnerability to future environmental change (e.g. climate warming) and their conservation status. This thesis focuses on a population of sooty terns, a small seabird, that breed in huge numbers on Ascension Island in the South Atlantic. By combining long-term data on population size and breeding movements with genetic relatedness and chick survival, we explore the effects of environmental and social processes that may underlie population trends. We found evidence for a shift in population size between two breeding sites on the island. Despite high population genetic diversity and low levels of relatedness we found fine-scale genetic structure between neighbours. There was evidence that birds breeding earlier were genetically different to those breeding over one month later. Chick sociality was a key factor influencing daily survival together with the use of habitat cover, both of which are likely responses to predation risk. The shift in population size between breeding sites suggests instability in habitat quality, with potential declines in breeding success driving breeder movements. Overall our findings suggest differences in animal behaviour can have significant effects on population ecology, genetic structure, breeding timing and breeding outcomes.

Environmental enrichment (EE) has a variety of positive cognitive effects and the mitogen- and stress-activated protein kinase 1 (MSK1) is in an optimal location for orchestrating translational changes in response to altered neuronal activity. It has been seen that the kinase function of MSK1 is necessary for regulating basal synaptic transmission strength, increasing mEPSCs amplitude after EE and for allowing cognitive flexibility. Changes in AMPA receptor (AMPAR) expression, particularly at the cell surface, is one possible explanation for MSK1- and EE- dependent effects on synaptic transmission. In this thesis, I have compared wild-type mice and mice containing an inactive form of MSK1 (MSK1 KD), raised under either standard or EE conditions. After 3 months of EE, significant interactions between housing and genotype were identified in the AMPAR subunit GluA2, alongside two plasticity-related immediate early genes (IEGs), Arc and EGR1. This homeostatic regulation of IEG transcription corroborated what has previously been identified at the RNA level and these changes may reflect the alterations seen previously at the electrophysiological level. Using electron microscopy, I discovered that under basal conditions, the PSD length is shorter in MSK1 KD animals, suggestive of reduced protein accumulation at the post-synaptic membrane. I also performed behavioural studies and identified MSK1 KD animals to have significantly reduced exploratory behaviour and improved spatial working memory, which may reflect the underlying behavioural trait for the impairment in cognitive flexibility. These studies provide new insights into the role that MSK1 plays in regulating key-plasticity related proteins and ultrastructural alterations and provides further clarity of the molecular pathways linking the long-lasting enrichmentinduced alterations underpinning cognitive and behavioural adaptations. Greater understanding of this pathway could provide new therapeutic avenues for patients with cognitive impairments.

From the strange pieces of material covering our feet to the shape of the hair on our head, culture pervades every aspect of the modern human condition. Our culture has changed more in the brief time in which our species, as we recognise it today, has existed than perhaps any of the flora or fauna that co-inhabit this planet of ours. However, the cultures of non-human animals (hereafter: animals) are, arguably, mostly stationary, the mechanisms underlying them and influencing the expression of them are highly debated in the comparative psychology, anthropology, biology and cultural evolutionary literature. This thesis sits at the intersection of these literatures and asks and attempts to answer some questions about the cultures of our closest extant relatives, the non-human great apes (henceforth: apes). For example, can ape cultures emerge without the inclusion of special variants of social learning? What are the social learning capacities of apes (do apes "ape")? Overall, what are the factors influencing ape cultures, and how do these compare to what we know of our own culture. In this thesis, I will build on already existing methodologies, e.g., the Latent Solutions methodology (Tennie & Hedwig, 2009), and apply them in novel ways. In doing so I will target some of the more controversial issues in the aforementioned fields and attempt, using controlled and consistent testing procedures, to add new understanding of culture and social learning in apes to the literature surrounding it.

For most brain regions the only realistic approach to theory is a top down, systems view because the evidence is too sparse to 'join the dots'. For a number of reasons the cerebellum is probably the best-suited large brain structure to take a different, evidence-based approach. That is the approach here, combining evidence of anatomy, electrophysiology, molecular biology and behavioural conditioning studies with mathematical and computational modelling, to build a model of the way the cerebellum derives output from input. Modelling is used to test predictions and to generate hypothetical data not available with current experimental techniques, which feed back into the model. This allows modelled behaviour of different parts of the circuit to be tested against evidence of other parts. The focus is on circuits involved in control of axial and limb movements, although parts of an explanation are likely to be portable to other circuits (because cerebellar circuit wiring is modular). An important part of the proposals is that the functions of pattern recognition and output coding are separate. It is a function of recoding in the granular layer to turn input variables into independent (and fewer) internal variables. Independence means they can be used in different functions without mutual interference of the execution of those functions with each other. Pattern recognition determines which circuits have output and when, but does not code output. Instead, the response to a known pattern following training is permissive, creating a time window in which output cells are controlled ad hoc by internally generated information about movement. Recoding in the granular layer, as well as having a long-suspected role in pattern detection, also has a role in control of output rates, by turning (what is from a cerebellar view) an arbitrary range and frequency distribution of input rates into a narrow range of granule cell rates with a fixed bandwidth and a frequency distribution with a fixed shape, so that the only functional variable of internal signals traffic at the scale of input to a Purkinje cell is the adjustable range.

Autophagy is a fundamental and evolutionarily conserved process, in which cytoplasmic material is degraded through the lysosomal pathway. Nutrient deprivation is one of the main stresses known to induce autophagy and is tightly regulated by autophagic machinery. However, many of these mechanisms of regulation remain to be elucidated. One of the most well studied autophagy-related proteins is Atg8a (Drosophila homolog to mammalian LC3), which participates in autophagosome formation and autophagy cargo selection in the cytoplasm. Despite growing evidence that LC3/Atg8a is also enriched in the nucleus, mechanisms by which it is targeted to this compartment, and the nuclear components with which it interacts with remain poorly understood. Atg8-family interacting proteins have been shown to harbour a LC3-interacting region (LIR), which is highly conserved in Eukaryotes. Bioinformatical screening for this region has provided a gateway for the identification of Atg8a-interacting proteins. Here, a novel LIR containing nuclear protein, named Sequoia, is characterised. Following the discovery of a LIR-dependent interaction between Atg8a and Sequoia, results presented here show that sequoia-depletion induces autophagy in nutrient-rich conditions through the enhanced expression of autophagy genes. Harbouring a zinc-finger binding domain, Sequoia is also found to bind to promoter regions of a wide set of autophagy genes, thereby repressing their transcriptional expression. Consistent with reports that indicate that the acetylation status of Atg8-family proteins is fundamental in their ability to interact with nuclear components, we piece together a mechanism of autophagic control within the nucleus by uncovering the roles of YL-1, a member of a component of a nuclear acetyltransferase complex, and deacetylase Sir2 (mammalian homolog SIRT1). Taken together, results here suggest a mechanism for the regulatory control of autophagy genes by transcription factor Sequoia and Atg8a, highlighting the importance of acetylation events in the induction of autophagy under starvation condition. Furthermore, we also uncover a potential role of dDOR (mammalian homolog DOR/ TP53INP2) and its ubiquitin-interacting motif in the cellular redistribution of Atg8a.

Insects and their fragments are often recovered from crime scenes and archaeological deposits as essential evidence in support of forensic and environmental archaeological investigations. Insects colonise the most diverse natural and anthropic environments, however different taxa show different ecological preferences and their development and phenology are species-specific and temperature dependent. Therefore, species identification is of primary importance to make any interpretation of the case. Today, insects identification can be achieved using two different approaches: 1) the morphological analysis of diagnostic features is currently well-established, irreplaceable and traditionally widely used method; 2) on the other hand, the DNA-based identification method has been integrated more recently (second half of 1980s) as a consequence of the rapid advance of molecular biology techniques. The main objective of this thesis is to provide an accurate framework of how to proceed to analyse entomological remains collected from contexts where conservation status is not optimal. A strong focus is directed on Diptera, using both approaches and providing a pragmatic and critic workflow of analysis for reliable interpretative purposes. In particular, the lack of descriptions of immature stages of poorly studied species is considered and investigated. To achieve this, three macro-projects concerning either archaeoentomological or forensic entomological investigations are presented through the analysis of two case-studies, respectively. The outcomes of the whole research include: i) an original contribution to molecular archaeology research, through the ex novo design of a DNA-based workflow applied to Diptera puparia; ii) an innovative contribution to the environmental archaeology research belonging to the Italian heritage, through the analysis of mineralised findings recovered from a Sardinian medieval urban well, and found in association to human remains within a Roman grave; iii) an essential contribution to forensic entomology, through the generation of new morphological data of immature stages of Physiphora alceae (Diptera: Ulidiidae) and through the comparative descriptions of puparia of ten species of Piophilidae, along with the design of a dichotomy key. Although the results are overall promising, further research is needed within molecular archaeology field applied on Diptera puparia. An improved workflow which meets all the essential authenticity criteria will be a great achievement and will provide an extra tool of analysis for archaeological records. The great potential of the archaeoentomological investigations in deriving interpretations of the human past and practices has been demonstrated not only through the identification of taxa but also through the analysis of taphonomic processes involved in their preservation. Finally, an integrated taxonomy-DNA based approach is beneficial, whether applicable, to strengthen the accuracy of the identifications; however, a continuous research is necessary to generate new data especially of unexplored and poorly studied taxa of forensic interest.

Ancestral reconstruction can be understood as an interpolation between measured characteristics of existing populations to those of their common ancestors. Doing so provides an insight into the characteristics of organisms that lived millions of years ago. Such reconstructions are inherently uncertain, making this an ideal application area for Bayesian statistics. As such, Gaussian processes serve as a basis for many probabilistic models for trait evolution, which assume that measured characteristics, or some transformation of those characteristics, are jointly Gaussian distributed. While these models do provide a theoretical basis for uncertainty quantification in ancestral reconstruction, practical approaches to their implementation have proven challenging. In this thesis, novel Bayesian methods for ancestral reconstruction are developed and applied to bat echolocation calls. This work proposes the first fully Bayesian approach to inference within the Phylogenetic Gaussian Process Regression framework for Function-Valued Traits, producing an ancestral reconstruction for which any uncertainty in this model may be quantified. The framework is then generalised to collections of discrete and continuous traits, and an efficient approximate Bayesian inference scheme proposed, representing the first application of Variational inference techniques to the problem of ancestral reconstruction. This efficient approach is then applied to the reconstruction of bat echolocation calls, providing new insights into the developmental pathways of this remarkable characteristic. It is the complexity of bat echolocation that motivates the proposed approach to evolutionary inference, however, the resulting statistical methods are broadly applicable within the field of Evolutionary Biology.