The mammalian gut microbiota is an essential factor in intestinal function and thus overall health. In the post genomic era, culture independent studies into the gut microbiota, particularly that of humans have allowed great leaps forward in knowledge of a once cryptic ecosystem. Furthermore, recent advances in sequencing technologies have allowed acceleration and broadening of work in this research field. Despite this, the canine gut microbiome has remained relatively uncharacterised. This work investigates the faecal microbiota of a diverse multi-breed and multi-location group of 79 dogs, by amplifying and sequencing the 16S rDNA from these dogs using both Sanger sequencing of clone libraries and high throughput pyrosequencing. A robust census of the canine faecal microbiota was undertaken. The most abundant genera were the Bacteroides, Prevotella, Cetobacterium, Fusobacterium, Sutterella and Megamonas. A limited core microbiome was defined in 90% of the study population; this represented less than 0.5% of richness but more than 37.4% of abundance. Influences of host sex, diet and age were investigated but were found not significant. Some evidence was found for breed associated richness differences, most marked in Labrador retrievers and miniature Schnauzers. Furthermore, the microbiota of the Labradors appeared to cluster separately from the other breeds.

Tufted ducks were trained to dive to and from a respirometer box on a 1.7 m dive tank, so that measurements of respiratory gas exchange could be measured, along with time budget data. These data were combined with power cost estimates of diving to show that the optimal breathing model quantitatively predicted surface duration and the oxygen metabolised during foraging for the mean of all subject ducks but not for individual birds. Respirometry data also showed that both the oxygen and carbon dioxide stores were close to full adjustment after mean surface duration suggesting they have a similar influence on surface duration in tufted ducks, while pre-dive hyperventilation caused hypocapnia suggesting carbon dioxide is more often a limiting factor on dive duration. Oxygen uptake was not affected by hypercapnic exposure between dives and minimally affected by hypoxia, however dive time budgeting changed in both cases. This confirmed an influence of carbon dioxide on diving behaviour while estimates of respiratory exchange ratios above one during dives from hypoxia suggested the employment of anaerobic metabolic pathways in hypoxic conditions. Allometric studies investigating relationships between body mass and diving parameters across and within taxonomic groups of divers highlighted a number of limitations in our current knowledge of diving animals and also questioned some of the mass associated correlations that have been widely considered to exist across diving species.

Coronella austriaca is the United Kingdom’s rarest snake, being confined to the lowland heathlands of Dorset, Hampshire and Surrey. As a result, it remains the least understood; despite being listed as a key biodiversity action plan species. Substantial loss and fragmentation of its primary UK habitat - lowland heathland - has occurred in recent times, and yet research examining the population ecology and conservation genetics of this species remains limited. As a result, this PhD research was developed to fill this need. Based on three years of data collection, a combination of field studies, laboratory experiments, mathematical modelling and genetic analyses, were employed in an attempt to answer questions of relevance to the future conservation management of this species. Modelling smooth snake occupancy of remnant heathland patches using an information-theoretic approach showed patch size and the percentage of grassland in surrounding matrix habitats to be the primary determinants of smooth snake presence. Field-based studies based on 27 arrays of artificial refugia showed the size of trees and prey abundance to be important in determining mean smooth snake capture rates at occupied sites. Eight previously described microsatellite markers were used to complete the first assessments of the genetic population structure of C. austriaca at two spatial scales. Initial fine-scale analysis of structuring based on 11 sampling localities within a heathland/coniferous forest mosaic found significant population structuring as a result of isolation-by-distance effects, in addition to evidence of male-biased dispersal. At the wider scale, analysis of seven distinct populations across Dorset also found small but significant differences in genetic diversity. The observed patterns were not consistent with isolation-by-distance effects, nor was there any evidence of them being a result of habitat patch size or isolation. Phylogenetic analysis of the coarse-scale microsatellite data showed some evidence of population clustering based on their geographic locality in relation to the historical extent of Dorset’s heathland, suggesting they represent distinct management units. The reproductive ecology of C. austriaca was also examined using a combination of field data and microsatellite analysis. In contrast to continental populations, there was no relationship between female body size and litter size. However, there was a negative relationship between relative clutch mass and female body size, suggesting that there may be a trade-off between female survival and reproductive output. Microsatellite based genotyping of neonates from 16 litters born in the laboratory provides the first evidence of multiple paternity occurring in C. austriaca.

Nippostrongylus brasiliensis is a rodent intestinal nematode with an important pulmonary migrating stage. Previous studies have observed a lack of TNF-α production and minimal recruitment of neutrophils, which led us to the belief that anti-inflammatory mechanisms could be active in the lung stage. In this study, lipopolysaccharide (LPS) stimulated alveolar macrophages (NR8383) or rat lungs were used as in vitro or in vivo inflammation models respectively. Both live N.brasiliensis larvae and NES significantly reduced the production of LPS-induced pro-inflammatory mediators, TNF-α and NO, but not IL-1β, in NR8383 cells. The inhibition of TNF-α production was related to the heatlabile and trypsin-sensitive fraction of NES concentrate. 1-D protein gel of NES concentrate revealed that the molecular weights of proteins are between 6kDa and 100kDa. Glycoproteins were found abundant in NES concentrate. The inflammatory processes, including NF-κB translocation and TNF-α gene transcription were significantly inhibited by NES and/or NES concentrate. In vivo, we observed a significant reduction of neutrophil recruitment (≈ 40%) by NES on a background of LPS (100ng/ml) induced inflammation. This reduction was associated with the significant inhibition in gene transcriptions of proinflammatory mediators TNF-α, IL-1β, iNOS, ICAM-1 and MIP-2 in bronchoalveolar lavage (BAL) cells. The down-regulation of pro-inflammatory mediators and inflammatory processes observed in this study suggests that N.brasiliensis larvae and/or NES are capable of modifying the normally potent LPS inflammatory response, both in vitro and in vivo. This study and planned future studies could be fundamental in developing anti-inflammatory agents with immune-active molecules in N.brasiliensis-derived products.

This study explores the principles of echolocation in bats which can be potentially adopted for bio-inspired sonar systems. Using a biological signal processing technique which was developed based on bat’s hearing system, the effect of auditory processing on the object discrimination is investigated for both CF (constant frequency) and FM (frequency modulated) signals respectively. These signals are considered as two representative types of echolocating calls. This study has simulated returning echoes from target discs using different types of calls by applying measured impulse responses of the objects. The simulated echoes were then processed through auditory models. The results have shown that the auditory processing contributes not only to increase the gain but also to enhance the ability to discriminate the sizes of discs. The peak and notch characteristics appearing in the auditory spectrum also confirms the flexibility of designing auditory models to manipulate spectral and temporal characteristics of the echo signals. Secondly, the effect of the bat’s head on the received signals at the two ears for varying distances was investigated by measuring the head-related transfer function (HRTF) of a bat-head cast. It has been reported that a bat changes bandwidth and duration of its echolocating call as it approaches a target. Adaptive change in the echolocating calls has been well explained in previous studies in terms of characteristics of signal structure. However, the range-dependent adaptive change in emitted signals also implies that the reflected signals reaching the two ears (i.e. binaural hearing) change in gain and frequency as the distance between the bat and the target varies. The result of measured HRTF has provided insights to range-dependent binaural information regarding the adaptive change of the echolocating calls. The results of measured data show that relatively higher gain at low frequencies (below 10 kHz1) is observed than that at high frequencies (above 10 kHz) as the bat-head cast approaches the sound source. It is also noted that interaural level differences (ILDs) at a fixed distance have less sensitive changes at low frequencies than at high frequencies as the angle of the source direction changes in the frontal axis. However, the sensitivity of the ILDs at low frequencies increase more than at high frequencies as the range reduces. It is concluded that the low frequency implies a more significant role during the target approaching stage in echolocation including distance perception. Also, the systematic change in sensitivity of the ILDs in various ranges suggests that the bat might be able to calibrate the angular resolution by broadening the bandwidth at low frequencies. Furthermore, the HRTF results calculated from a computational sphere model confirms the potential function of low frequency to calibrate the ILDs sensitivity for varying distances. Overall, this study has shown that customised auditory processing of the echolocating signal improves the quality of sonar representation and the results of investigations using the HRTFs of the bat-head cast guide the future design of effective adaptive signals based on the range-dependent HRTFs, to potentially enhance the performance of sonar systems. 1This study has defined the range of the low and the high frequencies based on the acoustical diffraction and reflection of the sound around the bat-head. The diffraction effect appeared to be prominent below 10 kHz.

The mind of the chimpanzee poses something of a paradox. In captivity, chimpanzees show cognitive abilities which seem only rarely used in the wild. The contention of this thesis is that the added complexity which a fission-fusion social system imposes on a Machiavellian primate requires complex decision-making, and that it is in making these decisions that wild chimpanzees use their cognitive abilities. The extent of social complexity in the relationships between male chimpanzees was investigated in an unprovisioned community in the Budongo Forest, Uganda. Statistical modelling and the construction of mutually exclusive hypotheses were used to determine the extent of tactical behaviour and decision-making in the social lives of these animals. Male chimpanzees were found to live in a highly dynamic social milieu, showing complex patterns of associations which appeared to be tactical. Chimpanzee males changed their associates frequently every day, and it is argued that each change represents a decision. In pursuit of association strategies, each decision is tactical, and requires cognitive representations of strategic goals and the relationships between individuals. Individual males appeared to deliberately select their association partners. Over time, the tendency a dyad had to associate changed, as individuals sought to alter their relationships, in pursuit of association, and broader social, strategies. Two such association strategies were distinguished; one in which individuals maintained an even level of association with other males, another where males concentrated on associating with only a few others. Individuals switched from one strategy to another as their social status changed, although both strategies could lead to increased status. A preference for higher status males as nearest neighbours lead to competition for proximity partners, and individuals, particularly the middle to high status males, appeared to use proximity tactically. In choosing between grooming partners, male chimpanzees appeared to to select the individual with whom they had the stronger association relationship. This implied a cognitive comparison of the value of each relationship. Male ranging patterns were examined, and the majority of time was spent within small core areas which were both partially overlapping and distinct. Each male?s core area had a similar habitat composition, and overlap between core areas was positively related to dyadic association tendencies. It is hypothesised that these core areas function to enable the location of individuals to be predicted by other members of the community. The cognitive demands of decision-making by wild chimpanzees is discussed in relation to the demonstrated abilities of captive individuals, as are the implications for an understanding of the evolution of the chimpanzee mind.