Orangutans are the largest predominantly arboreal primate and consequently have a diverse repertoire of positional behaviour. Problems associated with travel on thin flexible supports worsen as body size increases; therefore locomotion should vary with body size. The aim of this thesis was to explore how orangutans solve problems related to life in wild and captive environments and how this changes with growth and development. A cross-sectional sample of wild orangutans (Pongo pygmaeus wurmbii) was studied at Tuanan Field Station in Central Borneo with subjects ranging from infant to adult. Results from wild orangutans showed that locomotion varied according to body size with larger orangutans using larger supports and gaining stability by bearing their weight in suspension. In contrast captivity promoted higher frequencies of terrestrial behaviours and these increased with age. Wild orangutans crossed large gaps in the canopy by oscillating compliant trunks. However I found that these skills are not fully mastered until 6 years old. Mothers were found to provide assistance during gap crossing according to the needs of their offspring. This thesis has shown that complex locomotor behaviour develops slowly during ontogeny and this may have implications for orangutan life history in different types of habitat.

Daphnia magna is gaining interest as a model for epigenetic research. It is easy to maintain under laboratory conditions and has low genetic diversity due to parthenogenetic reproduction. The D. magna genome is responsive to a wide range of stimuli and genomics resources are being developed for this species. Despite these great advantages, information regarding the epigenome of D. magna and its regulation is still lacking. Thus, the main aim of this work was to describe the methylome of D.magna and investigate its regulation and responsiveness to environmentally relevant exposure conditions. Despite the low levels of global DNA methylation, a defined profile could be identified. DNA methylation in D. magna is sporadic and mainly found at coding regions. These data suggest that D. magna encodes a complete set of genes for DNA methylation reactions. Evidence of direct effects on the DNA methylation profile were found in animals exposed to the DNA methylation inhibitor 5-azacytidine and these changes were persistent after the removal of the stressor. Acute and chronic exposures to environmentally relevant concentrations of stressors (arsenic and hypoxia) also induced changes in gene transcription levels and concentrations of onecarbon pathway metabolites. These findings indicate that the epigenome of D. magna is responsive to changes in the environment, supporting its use as an environmentally relevant model organism for epigenetics research. Furthermore, the maintenance of some of the epigenetic changes in the absence of the initial stressor supports the concept of ‘epigenetic memory’ and its potential use in chemical risk assessment.

Orangutans are the largest arboreal primate and have a diverse locomotor repertoire. The principal aim of this thesis was to explore the dynamic between morphology, behaviour and habitat to better understand the influences on orangutan locomotion. Positional behaviour data was collected at two peat-swamp forest sites: Sabangau, Central Kalimantan; and Suaq Balimbing, Aceh. We quantified forest structure and support availability in the dry-lowland forest of Ketambe, Aceh, in addition to the aforementioned peat-swamp forests and found that the three forests were structurally different. We used a remote measuring technique to compare limb morphology between species, and found they were similar suggesting selection for an optimal limb length. We found that habitat had a stronger influence on locomotion than either species or study site. Orangutans in different habitats had similar profiles of preferred supports, with the exception that the Sumatran species (Pongo abelii) had a preference for lianas. Orangutans in Sumatran peat-swamp forest used more compliant supports than recorded in dry-lowland forest. However, pronograde bridging was also used to negotiate the most flexible supports. This thesis has shown that habitat has a strong influence on orangutan locomotor behaviour, which is important since their habitat is becoming increasingly altered through human disturbance.

New Caledonian crows are amongst the most sophisticated tool-users in the animal kingdom. In this thesis I present my findings from various aspects of the crows’ behavioural ecology, morphology and cognition, contributing to our understanding of how this fascinating tool-use behaviour might have evolved. My studies in the field reveal new types of tool manufacture and foraging behaviour that help to build up a complete picture of the ecological importance of tool-use to wild crows. Additionally I demonstrate the subtlety and skill required to extract wood boring beetle larvae from their burrows, accounting for the slow development of tool-use proficiency in juvenile crows. Further work reveals how their unique visual field combines with a peculiarly straight bill to facilitate tool-use; perhaps the only evidence outside of the hominid hand for tool-use specific morphology. Recent studies suggest Corvus species are behaviourally and cognitively predisposed to become tool-users, however, through multiple lines of enquiry this thesis highlights the costs that New Caledonian crows bear in order to become successful tool-users. The unique ecological conditions in New Caledonia are likely to have made this costly form of foraging possible, helping to explain why tool-use is so rarely observed in other animals.

Seabird breeding success and population size on many oceanic islands have declined in recent years as a result of predation by non-native mammals. On Ascension Island, South Atlantic the sooty tern Onychoprion fuscatus breeding population declined precipitously in size in the 1970s. Despite cat eradication in 2003 and a cull of predatory mynas, the tern population between 1990 and 2012 consistently contained 350,000 birds. Shortages of small fish within foraging range of Ascension driven to the sea surface by once more prevalent tuna rather than cat predation probably caused the 1970s decline. Abundance and size of rats increased in response to cat eradication with the impact of rats on the size of the seabird population similar to the combined impact of both cats and rats. Ascension sooty terns have adopted a life-history strategy of sub-annual breeding as a viable alternative to seasonal breeding. The population consistently bred every 289 days, as did most individual birds. Despite an increase in lifetime reproductive rate resulting from sub-annual breeding, I predict a slow but sure decline in the population size unless rats are controlled. Studies of sooty tern migratory ecology are required and the species’ current IUCN Red List category should be reviewed.

Shallow water tropical and temperate marine habitats are changing dramatically in response to many stressor-driven effects. The change in turn threatens the associated fish communities relying on their maintenance for habitat provision. At present, a much better understanding of the interaction between changing habitats and the associated fish is necessary. To address the lack of understanding of the habitat – fish association, mechanisms which underpin the habitat driven responses of reef fish were examined, from entire communities down to species level, across tropical and temperate ecosystems. Using a highly biodiverse ecosystem as the model system, effects of changing habitat on the associated fish community were observed, consequently demonstrating how important, in terms of shelter and food resources, the overall habitat is in structuring the fish community. Furthermore, patterns of habitat use of certain fish species within and across tropical and temperate ecosystems were examined. Variation in the size of the habitat used and its overlap between species within systems, and uniform patterns in habitat use and comparable fish habitat size and overlap across systems, were discovered. By looking at fish habitat use within systems, invaluable knowledge was gained on ecological interactions between habitat and fish on a small scale. At the same time, detection of similar mechanisms of fish habitat use across ecosystems indicates to possible uniform response of fish communities to habitat change at a large-scale. Finally, by looking at fish habitat selection using olfaction, in a temperate model system, a range of subtle behavioural responses displayed during habitat selection were detected. These results highlighted the extent of complexity of the mechanisms used in fish habitat selection and the ubiquitous importance of the habitat and its properties for the associated fish. In addition to, and based on the ecological significance of the findings, a number of potential management and conservational applications of the research were given within the thesis.

CO2 storage in the oceans is strongly affected by biological processes. Production of organic matter through phytoplankton photosynthesis drives CO2 sequestration, which feeds back to atmospheric CO2 and global climate. The ongoing increase in atmospheric CO2 and temperature is strongly associated with changes in ocean chemistry and increasing seawater temperatures. To investigate these impacts on coastal phytoplankton under conditions predicted for the year 2100 (pCO2 elevated to 800 μatm and +4 °C temperature), three factorial experiments were conducted with natural communities sampled from the western English Channel (WEC). Elevated pCO2 increased phytoplankton biomass by up to 20-fold while elevated temperature resulted in an increase of up to 14-fold. Light-saturated photosynthetic carbon fixation rates increased > 6-fold under elevated pCO2 while an increase of up to 3-fold resulted from elevated temperature. The combined effects of elevated pCO2 and temperature reduced biomass in late summer and had no effects on biomass in the autumn with no significant effects on photosynthetic carbon fixation rates in either season. Individual treatments of elevated pCO2 and temperature resulted in near mono-specific communities: diatoms in late summer and nanophytoplankton in autumn. Combined effects of both factors resulted in the most diverse phytoplankton communities and promoted increased dinoflagellate and Synechococcus biomass at the expense of diatoms and nanophytoplankton. Elevated pCO2 alone promoted dominance of the harmful algal bloom (HAB) species, Phaeocystis in spring and autumn, while the combination of elevated pCO2 and temperature promoted biomass of the HAB species, Prorocentrum minimum in autumn. The results indicate that experimental simulations of year 2100 pCO2 and temperature may significantly modify phytoplankton community structure with a positive feedback on atmospheric CO2 in late summer and no change on feedback in autumn. In either scenario, no increase in phytoplankton productivity during a period of changes in bulk carbonate chemistry resulting from ongoing anthropogenic carbon uptake, may be expected to negatively influence carbon biogeochemistry in the WEC.

Dioxins are extremely widespread, toxic and persistent pollutants, as well as a major concern for human health. The Aryl hydrocarbon receptor (Ahr) is the key component in the metabolic response to dioxins. Ahr is a cytoplasmic bHLH-PAS transcription factor that, upon binding with dioxin, translocates to the nucleus. There it forms a complex with the Ah receptor nuclear transloator (Arnt), another bHLH-PAS protein, and binds to the eight-nucleotide XRE motif to control gene expression. Previous work with Ahr knock-out mice revealed the existence of dioxin-independent activity for Ahr in development, but the relationship between the two activities of Ahr remains unclear. Our work uses Drosophila to clarify this question, which is central for therapies seeking inactivation of Ahr. The Drosophila Ahr homologue, spineless(ss), does not bind dioxins, however, it physically interacts with Tango (Tgo), Arnt's fly homologue, and controls gene expression through the XRE motif during development. Here I show that, in the absence of dioxin, Ahr can still bind Tango and Arnt and rescues ss- phenotypes, indicating equivalent dioxin-independent activities. I next demonstrate that exposure to dioxin produces an in vivo hyperactivation of Ahr, which can also be achieved by increasing the dosage of either Tango or Arnt. Thus Ahr shows different levels of activity, from basal to toxic, depending on the presence of specific ligands and cofactors, and the toxic effects of dioxins represent an excess of the Ahr developmental function. I have also carried out a genetic screen in the search of genes that interact with ss. From this screen I have found that the genes that code for the Krüppel-type zinc-finger proteins Squeeze (Sqz) and Rotund (Rn) interact functionally with ss. I demonstrate that Rn and Ss interact physically in vivo. Ahr is also able to interact functionally with rn and sqz indicating that the interaction with zinc-finger proteins might be an ancestral feature of the dioxin receptor.

Alcohol intake causes gene expression changes resulting in cellular and molecular adaptations that could be associated with a predisposition to alcohol dependence. Expression profiling using high-throughput microarrays has recently been used to identify changes in gene expression that may be associated with alcohol dependence. To clarify the mechanisms and biology underlying alcohol dependence, bioinformatics, behavioural and genetics methodologies were employed to analyse obtained raw microarray data set that was previously generated from Drosophila exposed to an acute dose of ethanol. Classical linear statistical modeling coupled with clustering and functional enrichment analyses were implemented to evaluate whole-head time series microarray data from ethanol-treated and control samples, and implicated many genes or pathways affected by acute ethanol treatment in Drosophila head including those involved in stress signaling, inter and intra cellular signaling, ubiquitinmediated signaling, metabolic switches, and possible transcriptional regulatory components. Further analysis identified interaction networks and patterns of transcriptional regulation within the set of identified genes. Seven of these genes, ana, Axin, hiw, hop, hsp26, hsp83, and mbf1, were verified and linked with novel roles in ethanol behavioural responses using functional tests. Additional work on two of these genes namely, hiw and hsp26 also revealed a role for glia, mushroom bodies and ellipsoid body neurons as important regulators of acute ethanol response in Drosophila. Finally, these studies have demonstrated that microarray analysis is an efficient method for identifying candidate genes and pathways that may be fundamental to human alcohol dependence or abuse.

Johnston, who discovered the mosquito auditory organ at the base of the antennae 150 years ago, speculated that audition was involved in mating behaviour. Indeed, the Johnston's organ (JO) is now known to detect the whine of flying mosquitoes. Analysis of sound recordings of flight tones from tethered, flying, mosquitoes revealed that opposite-sex pairs, when within their acoustic near-fields, attempt to frequency-match the harmonic components of their flighttones. Same-sex pairs actively avoid frequency-matching. Mosquitoes of the species Toxorhynchites brevipalpis, where the flight-tone frequencies of males and females are similar, attempt to match the fundamental frequency of their flight-tones. Haemophilic, vector-carrying mosquitoes Culex quinquefasciatus and Anopheles gambiae ss, where the fundamental frequency of the male flight tone is about 1.5 times that of the female, frequency-match harmonic components of their flight tones. Usually the male's 1st harmonic with the 2nd harmonic of the female flight-tone. In Burkina Faso, where two morphologically similar molecular forms aggregate in the same swarms but rarely hybridise, frequency-matching of flight-tones may perform a pre-mating barrier and a form of subspecies recognition. We discovered that frequency-matching occurred significantly more frequently between same-form male-female pairs of flying, tethered mosquitoes, than when each member of the pair was of a different molecular form. The bandwidth and tuning of sound-evoked flagellum vibrations and the JO's electrical responses to this mechanical input were measured using laser interferometry and extracellular electrodes, respectively. For the first time we showed that distortion products, recorded from the flagellum and JO, could provide the neural basis for frequency-matching at frequencies beyond the range of the JO's electrical responses. We also discovered that spontaneous oscillations of the antennae are produced by physiologically-sensitive mosquitoes. Through temperature-control and injection of pharmacological agents into the JO, evidence is presented advocating dynein as the molecular motor responsible for powering these oscillations.