Marine ecosystems provide essential goods and services to human populations, however anthropogenic offshore activities can adversely affect the functioning of ecosystems by reducing biodiversity. Temporal data on environmental fluctuations are required in order to implement effective ecosystem management. The health of marine ecosystems can be assessed using proximal measurements of biological data such as fishery catch statistics. However, these data are often patchily distributed and underreported. Seabirds have been shown to be useful indicators of the state of the marine environment. They are highly visible, charismatic species that are easy to count and observe in colonies and offshore foraging areas during the breeding season. In recent years the miniaturisation of electronic devices and the development of novel tracking methods have allowed a large variety of seabird species to be tracked to and from foraging areas and for environmental conditions in distant pelagic areas to be sampled. It has been suggested that seabird foraging and breeding behaviour provide more accurate measures of environmental change than demographic parameters such as adult mortality and productivity, as many species are able to buffer the effects of low food abundance during the breeding season by increasing foraging effort. In this thesis, demographic and behavioural data of several sympatrically breeding larid species were examined over extended temporal scales and the effectiveness of these data at indicating environmental change are assessed. Comparisons of annual fluctuations in demographic parameters were made among ecologically similar and dissimilar tern species breeding sympatrically at a North Sea colony. Species with similar foraging and breeding behaviour exhibited synchronous temporal population fluctuations, while dissimilar species showed no synchrony in population change. Similar and dissimilar species also showed differing responses to declines in predator abundance. To understand how seabird species with similar ecological requirements are able to coexist in the same area during the breeding season, foraging behaviour and reproductive parameters were examined among three morphologically similar terns (Sterna spp) breeding at the same colony. Species partitioned resources by both chick diet and foraging area and responded differently to increasing brood age. Sympatrically breeding Arctic (Sterna paradisaea) and Common Terns (S. hirundo) maintained comparable growth and survival rates of chicks, which suggests that species utilising different foraging strategies can be equally successful at raising chicks to fledging. However, Common Terns were found to exploit larger prey items with higher energetic contents than Arctic Terns, which may explain why this species was able to lay larger clutches and fledge more chicks. Temporal variation in foraging behaviour was examined further in Black-legged Kittiwakes (Rissa tridactyla) by comparing the foraging behaviour of individuals at the same colony during two stages of the breeding cycle (incubation and chick-rearing) and in two consecutive years (2011 and 2012). Diet, foraging areas and environmental variables associated with foraging were found to vary significantly throughout the breeding season and between years, with important consequences for marine conservation policy. Parental resource allocation in Kittiwake broods of two also varied throughout the chick development period as chick demand and environmental conditions surrounding the colony changed. This research illustrates how long-term seabird population and foraging behaviour data can be used to examine changes in the marine environment and to address ecological questions. Variation in chick demand, environmental conditions and species interactions can explain temporal changes in the foraging behaviour of sympatrically breeding species. These results also illustrate the value of considering seabird foraging behaviour when developing effectual offshore protected areas for marine predators.

This thesis tested hypotheses about the response of Baird’s tapir to rising anthropogenic pressure in Honduras. Baird’s tapir is the largest land mammal native to the Neotropics, and was previously abundant in all countries between Mexico and Ecuador. Patterns in Baird’s tapir occupancy in Honduras were modelled to test the effect of a range of environmental variables on the distribution and abundance of the species. Analyses of the genetic structure of Baird’s tapir in Honduras revealed very little genetic diversity at the mitochondrial genome. Only two haplotypes were identified from 69 samples successfully genotyped, representing a remarkably low level of diversity, which is likely to affect the viability of the species in the long-term. Occupancy and population estimates were generated for four protected areas, and for the remaining regions in Honduras where Baird’s tapir have been confirmed to remain. Occupancy was found to be associated with environmental variables relating to accessibility. Although the population estimates generated here exceed previous estimates, evidence of ongoing poaching and deforestation of tapir habitat suggests that Baird’s tapir populations in Honduras may not be viable outside of the protected areas of La Moskitia. Population Viability Analyses for the remaining areas of tapir occupancy in Honduras demonstrate the vulnerability of the species to habitat fragmentation and hunting pressure. Annual surveys in Cusuco National Park (PNC) from 2009 to 2012 investigated the conservation status of the species in this tapir stronghold over the duration of this PhD project. Patch occupancy analysis demonstrated that Baird’s tapir display a distribution bias in PNC associated with accessibility, and identified that Baird’s tapir are suffering a population decline that has the potential to cause the extirpation of the species from this Park within the next few years.

The bioaccumulation of persistent organic pollutants (POPs) is of particular environmental concern in top predators, which accumulate high concentrations of POPs that can cause adverse effects. Previous small scale studies found high concentrations of POPs in adult great skuas, Stercorarius skua, a top predator in the marine environment. This thesis investigates the factors affecting concentrations and patterns of POPs (contribution of individual POPs to the ΣPOPs) in the great skua across its breeding range in the north-east Atlantic. Clear differences between colonies in both concentration and pattern of POPs in adult plasma were not indicative of being caused by long range transport of POPs in the atmosphere. Variation in diet between colonies is the mostly likely explanation for these colony differences, with great skuas from some colonies having a greater proportion of fish in their diet whilst others eat more seabird prey. Although seabirds are often used in studies of POPs in the environment, the effect of migratory behaviour has not previously been studied in detail. By using a combination of global location sensor (GLS) loggers and feather stable isotopes from winter grown feathers, the wintering areas of individuals from three breeding populations of great skuas were identified. Great skuas spend the winter in three distinct areas across the North Atlantic, with birds from the same breeding colonies wintering in different areas. In two of the three breeding populations, wintering area explained a significant proportion of variation in organochlorines (OCs) concentrations and pattern. However in the colony with the highest concentrations of OCs, no effect of wintering area was found, possibly as a result of these great skuas feeding at a higher trophic level during the breeding season than other populations. Temporally, concentrations of OCs were higher in 1980 than 2008 in eggs, whilst newer contaminants polybrominated diphenyl ethers (PBDEs) and perfluorinated chemicals (PFASs) show the opposite trend. In conclusion, concentrations of POPs in the great skua were influenced primarily by breeding season diet with wintering area and sex also having small but significant effects on POPs. Wintering area explained the most variation in the pattern of POPs in great skuas. The POP concentrations found in this study exceeded those which have been found to cause adverse effects on the immune system and reproduction in other species of seabird.

This thesis examines how extrinsic and intrinsic factors affect dispersal, foraging, aggression and energy reserves in a winter population of a small, migratory flocking bird, the Snow Bunting Plectrophenax nivalis. Previous observations of this species, and consideration of its northern ground-feeding open country niche, suggested that Snow Buntings were less likely to show as strong a degree of site fidelity as many other winter-studied species. This may therefore have led to opportunities for the Snow Bunting's winter behavioural ecology to diverge from that of more sedentary species. The distribution of age and sex categories of wintering Snow Buntings was examined at eleven sites in North-East Scotland which varied markedly in altitude (and consequently habitat and climate). The proportions of adult males and adult females trapped at these sites increased with altitude, whilst the proportion of juvenile females decreased. Because males are the larger sex, and adult birds have the advantage of previous experience, the distribution of age and sex categories suggested that the more elevated sites were of higher quality. Consequently, I suggest several environmental factors (reduced competition, fewer predators, and similarity to breeding conditions) which may be responsible for altitudinal segregation and argue that these may also help explain intraspecific latitudinal segregation patterns in this and other species. More detailed observations of Snow Bunting numbers and behaviour were made at one high altitude site, Cairn Gorm during 1987/88 to 1992/93. There was evidence that, even within this site, birds selected higher altitude feeding areas when possible. However, snowfalls caused some birds, particularly young or naive individuals or females, to leave the site, although population composition recovered during subsequent thaws.

Ecological responses to a changing climate have been well documented in a broad range of species, predominantly in terms of range movements and phenological changes. When faced with a changing environment, species survival will depend on the ability to: 1) evade changes in climate, via dispersal; 2) evolve, via natural selection; and/or 3) plastically change their phenotype, without underlying genetic changes. The potential for an organism to evade, evolve or plastically respond to a changing environment can be predicted by inferring relationships with current climatic conditions. Altitudinal gradients have been proposed as being particularly suitable for environmental change studies due to the rapid variation in climate even over short geographical distances. Species that inhabit altitudinal gradients experience a range of climatic conditions across their range and are thus subject to varying selection pressures. Changes in temperature are predicted to particularly influence ectotherms due to the direct effect on physiological processes. The common frog (Rana temporaria) occurs from zero to over a thousand metres along altitudinal gradients in Scotland, offering the opportunity to assess the influence of temperature on organism responses. The overall aim of this thesis was to assess population-level relationships with climate, in order to make predictions regarding susceptibility to a changing climate, focussing on R. temporaria in Scotland. In Chapter 2, I inferred colonisation patterns within Europe following the last glacial maximum by combining new and previously compiled mitochondrial cytochrome b DNA sequences. I found that the mitochondrial DNA sequences from my Scottish samples were identical to, or clustered with, the common haplotype previously identified from Western Europe. This clade showed very low mitochondrial genetic variation, consistent with a leptokurtic model of range expansion, where low numbers of long-distance dispersers cause multiple founder events. Second, I assessed fine-scale genetic variation in relation to current temperature gradients using microsatellites. No population structure was found within or between altitudinal gradients at any scale (3-50km; average FST= 0.02), despite a mean annual temperature difference of 4.5°C between low- and high-altitude sites. Levels of genetic diversity and heterozygosity were considerable but did not vary by site, altitude or temperature. In Chapter 3, common temperature treatments were used to assess phenotypic differentiation and phenotypic plasticity variation in relation to altitude in terms of larval fitness traits. Local adaptation to altitude was assessed using QST-FST analyses and adaptive phenotypic divergence was then related to environmental parameters using Mantel tests, to look for drivers of selection. I found that R. temporaria showed evidence of local adaptation in all larval fitness traits measured. However, only variation in larval period and growth rate was consistent with adaptation to altitude. Moreover, this was only evident in the three mountains with the highest high-altitude sites (at least 900m). Adaptive divergence in traits that were locally adapted to altitude was correlated with spring temperature, suggesting that temperature acts as a strong environmental selection pressure influencing local adaptation even in the face of high gene flow. In Chapter 4, the physiological and behavioural responses that facilitate survival in high-altitude environments were evaluated, in terms of routine metabolic rate and freeze tolerance in tadpoles, and breeding temperature in adults. I found that routine metabolic rate was lower for individuals sampled from high- than low-altitude sites but only from the three mountains with the highest high-altitude sites (at least 900m). Glucose accumulation during freezing was not significantly different based on altitude. However, individuals from low-altitude survived freezing significantly better than those from high-altitude, across all mountains. Breeding did not occur below 5˚C at any site and there was no significant difference in breeding temperature between high- and low-altitude sites, leading to high-altitude individuals spawning 30 days later than those at low-altitude. My results suggest that tadpoles are adapted physiologically to surviving at high-altitude via reduced routine metabolic rate, but only at the highest breeding sites. Finally, in Chapter 5, I assessed the spatial variation in species presence and composition of parasitic water moulds in the genus Saprolegnia found on R. temporaria eggs. Thirteen samples isolated from four sites were identified as members of the Saprolegniaceae. Four putative species of Saprolegnia were isolated overall, multiple Saprolegnia water moulds were isolated from within sites, and species composition varied between sites. Acidity was significantly lower at sites where 4 Saprolegniaceae were present, but genetic distance between samples was not correlated with environmental or geographic distance. These findings question the previous focus on S. ferax as the primary agent of Saprolegnia infection in amphibians and suggest that future studies of virulence need to consider the synergistic effect of multiple Saprolegnia species. In conclusion, R. temporaria show the potential for evasion, evolution and plastic responses to a changing climate and my results suggest that the outlook is positive for survival of the common frog in Scotland.

Studying the spermatogenesis of horse is beneficial for the horse industry by identifying the causes of chromosomal abnormalities, which cause embryonic loss, congenital abnormalities and infertility. Little is known about the spermatogenesis in horse. This is the first report that investigates the horse spermatogenesis in detail, particularly metaphase I (MI) and prophase I (PI) stages of the first meiotic division. Meiotic recombination is considered to be the major outcome of meiosis. It is essential for proper chromosome segregation and formation of normal haploid gametes. Analysis of recombination frequency and distribution are crucial for genomic and association studies. Any alteration of the recombination frequency and positioning can cause non-disjunction and generation of aneuploidy. The frequency and distribution of chiasmata were estimated at MI chromosomes from fourteen fertile stallions. The average frequency of autosomal chiasmata was 49.45 ± 2.07, corresponding to a genetic length of 2,472.5 cM. All autosomal bivalents had at least one chiasma. The majority of chromosomes have one or two chiasmata, which are mostly distally localized. The frequency and the distribution as well as the genetic length of chiasmata were also estimated for the first time in eight different individual autosomes. Immunofluorescent localization was used to characterize the early stages of the first meiotic division as well as to examine the frequency and the distribution of DNA mismatch repair protein MutL Homologous Protein 1 (MLH1) foci on synaptonemal complexes (SCs) from sex fertile stallions. The mean frequency of autosomal recombination foci was 50.11±2.35. All autosomal bivalents had at least one recombination focus. In general, foci were located near the distal ends with some foci interstitially distributed. The distribution of MLH1 foci indicated positive interference; however, foci were very close to one another in rare instances. The average SCs relative length was highly correlated with the average number of MLH1 foci. MLH1 have been proposed to mark crossover sites at PI since the frequency and distribuation of MLH1 foci closely correspond to the frequency and distribution of chiasmata on MI chromosomes. iii | P a g e Spermatozoa viability, which include spermatozoa head and tail membrane integrity, acrosomal integrity and mitochondrial function assessment are the main sperm analysis parameters considered in this thesis to evaluate the stallion fertility using epididymal collected semen samples. The mean percentage of spermatozoa with viable heads and tails, using Chicago sky blue stain, was 81.26 ± 5.06. FITC-Pisum sativum agglutinin (FITC-PSA) and MitoTracer green were used successfully to assess the spermatozoal acrosomal status as well as the mitochondrial function, respectively. The mean percentage of spermatozoa with integrated acrosome was 93.85 ± 1.9, while for functional mitochondria was 95.63 ± 1.63. In conclusion, this finding is the cornerstone to understanding the genetic basis of normal horse spermatogenesis. Simultaneous assessment of different functional sperm parameters as well as investigating the synapsis and recombination frequency and distribution, at PI or MI, would assist with predictions of stallion fertility prior to breeding. In addition, this study will enable investigators to use linkage analysis in identifying and localising different genetic loci associated with specific traits.

Amphibian metamorphosis is a post-embryonic process that systematically transforms different tissues in a tadpole. This transformation requires extensive remodelling of almost every tissue in the animal. Thyroid hormone plays a causative role in this complex process by inducing a cascade of gene regulation. One of the more dramatic effects of thyroid hormone (triiodothyronine T 3) is to induce a complete regression of tadpole tail in culture in a simple chemically defined medium. The technique of differential display proposed by Liang and Pardee in 1992, has been applied in an attempt to isolate and then characterise responsive genes induced by thyroid hormone triiodothyronine (T3). Library screens using the PCR fragment xL52 as a probe allowed the isolation of -2.5kb clone termed xth-2. Sequence analysis and database searches at the amino acid level revealed that this clone (xth-2) showed approximately 91% identity to some of the members of a recently discovered family of tissue-specific transmembrane proteins called Hem proteins. Temporal expression of xth-2 using RT-PCR technique revealed that this gene is developmentally regulated. Whole mount in situ hybridisation used for detecting the location of this mRNA in Xenopus laevis embryos at different developmental stages indicated that xth-2 protein was highly expressed in the brain and the pattern of expression has been extended along the central nervous system (CNS) and the caudal region (tail bud). Expression of xth-2 protein in Xenopus embryos, did not show any significant effect on the phenotypic features of the embryos examined. The Nap1 protein, a member of Hem family proteins has recently been found to associate with the SH3 domain of Nck protein, and is thought to play an important role in signalling transduction. We could therefore, speculate that protein xth-2 will have the same function as does the Nap1 on the basis of their sequence similarity, tissue distribution and also the expression pattern.

Bird ringing is a key ecological research technique that involves the capture and handling of birds. It is used extensively to obtain information on population dynamics of wild birds, and many aspects of avian behavior, physiology and life-history, which would otherwise be unfeasible to obtain. Despite millions of birds ringed every year, little is known about the short- or long-term impacts on birds, and whether there are negative welfare, conservation and scientific consequences, which can ultimately bias the interpretation of data from wild bird studies. In this thesis I study the type of intrusion that capture and handling causes to the bird, by analyzing their interlinked physiological and behavioral responses to capture stress, including hormonal and immunological responses, energy regulation decisions (feeding behavior and thermal regulation) and breeding effort. I further study the immediate effects that capture and handling has on birds through analyzing types of injuries and the rates at which injuries and mortality occur. I have focused mainly on mist-netting, which is the most widely used capture technique, and captures of passerine birds, which is the most frequently sampled taxon. However, I also demonstrate how the impacts of capture and handling can be studied in marine birds and applied to other capture methods. These studies reveal the range of short-term impacts that capture and handling may have on wild birds, and highlight aspects of methodology that have a strong effect on these impacts. The longer term consequences for lifetime fitness and demographic change require further study. This thesis demonstrated the importance for researchers to be aware of the potential effects of their activities on their study subjects, particularly for susceptible species and situations, and to continuously reasses their methods for effective improvement. I propose several guidelines, which aim to promote the birds’ welfare in regards to data collection.

A basic aim of evolutionary biology is to explain the enormous diversity among animal and plant species. But also within species there is often large genetic and phenotypic variation, and such variation is necessary for evolution to create new reproductively isolated species. The present thesis is directed to explain differentiation within populations highlighting and discussing the significance of phenotypic plasticity as an evolutionary process that leads to the expression of alternative phenotypes within a species. Such phenotypic expressions are particularly interesting, because the process by which new species are formed typically involves a temporary stage within the splitting species, that is, different heritable and distinct types that coexist within the same population. Such phenotypes may be raw material for full species formation, and the study of alternative-phenotype species should therefore be particularly worthwhile in speciation research. When alternative phenotypes are not entirely genetic they may arise as a result of developmental plasticity, when organisms develop in accordance with local abiotic and biotic conditions. Subject to developmental plasticity, alternative phenotypes, take different developmental routes depending on the local selection pressures, or depending on the environmental conditions experienced during development. Here, laboratory experiments showed that three-spined sticklebacks exhibit alternative phenotypes as a plastic response to physical environment and diet, demonstrating and supporting the idea that environmental inputs modulate the expression of traits through phenotypic plasticity during ontogeny. When, morphological differences arise, discrete morphological characteristics are originated and may be reinforced by the continuous presence of same environmental conditions. Here is demonstrated that these discrete morphological characteristics lead the individuals to specialise on specific prey or habitat types. Moreover, it is showed that plasticity may also play a role in the final stages of species formation, when reproductive isolation completes the speciation process. It is shown that diet-induced morphology has an important influence in mate preferences representing a strong potential to generate reproductive isolation via assortative mating, and this mate preferences may be highly efficient to maintaining isolation, thus the hypothesis of ecological speciation is supported. Finally, in this study, two alternative-phenotype lakes are described. It is suggested that the origin of the segregated alternative phenotypes in both lakes is a consequence of ecological traits divergences; however in one of the lakes the alternative phenotypes arose from a founder population, meanwhile in the second lake the alternative phenotypes may arose by the ecological adaptation of the forms in allopatry.

Natural selection should favour individuals who are able to adjust their life history strategy and resource allocation in response to changing environmental and social conditions. I examined the flexibility of reproductive resource allocation by female mice in response to manipulation of their nutritional, immunological and social environment. I considered the consequences of their investment decisions for the next generation. In five separate experiments I found that: 1. Food restricted females skewed their offspring sex ratio in favour of sons. 2. Ambient disease cues caused females to produce more resistant and less aggressive sons. 3. Direct parasitic infection prior to pregnancy caused females to produce more resistant sons with an altered hormonal response to socialisation. 4. Dominant females were less likely to become pregnant, suckled litters less post-partum, and produced more aggressive offspring. 5. Despite a mate-choice preference for subordinates, females which were mated with dominant males had bigger litters. These responses by females to variation in their local environment are likely to have fitness consequences for their offspring, and as such would be acted upon by selection. Further work should seek to gain insight into the mechanisms underlying these responses, and determine the adaptive or non-adaptive nature of the flexibility observed.