Solid surfaces that spend long periods of time in aquatic environments are susceptible to the accumulation of marine fouling organisms and this phenomenon is known as marine biofouling. This is a natural process which has significant impacts on marine industries. Research to develop new antifouling solutions focuses on the development of non-toxic solutions that can deter biofouling. A non-toxic antifouling approach that has gained interest in recent years is to modify the surface’s structure to disrupt organism settlement (Kirschner and Brennan 2012; Magin et al. 2010; Myan et al. 2013). Many studies determined that uniform arrays of single layered, micro-topographies are effective at deterring the initial settlement of fouling organisms. In contrast, most studies that tested uniform arrays of single layered, macro-topographies concluded that these topographies are not suitable for antifouling applications. Both single layered, micro-topographies and single layered, macro-topographies were determined to have limitations at mitigating biofouling. This resulted in the interest to develop hierarchical topographies. Hierarchical topographies are surfaces that consist of features that are varied in size and shape. It was suggested that the diverse nature of hierarchical topographies might be able to deter biofouling from a wider array of organisms. This research fabricated and tested a wide range of topographies (uniform, non-uniform, micro, macro, hierarchical, etc.) in a field study. A field study was preferred over lab experiments because results will reflect the antifouling efficacy of the surfaces in a marine environment. These results will indicate the topographies’ viability and future potential for industrial applications. Antifouling efficiency was evaluated by measuring fouling resistance (during the field test) and fouling removal (after the field test) of all topographies. Physical attributes (pattern geometry, pattern size, and surface roughness) of topographies were characterised with Scanning Electron Microscopy (SEM) and Laser Scanning Confocal Microscopy (LSCM). Statistical analysis was carried out to evaluate the significance of the topographies’ physical attributes on the antifouling efficiency of the topographies. The research hypotheses predicted that topography size, geometry and surface roughness will affect the topographies’ ability to resist biofouling. All patterned surfaces were predicted to have a higher resistance to biofouling in comparison to un-patterned control surfaces (i.e. smooth surfaces). The possibility that hierarchical topographies would have better fouling resistance properties than micro-topographies was considered as well. Hierarchical topographies and micro-topographies were also hypothesised to demonstrate better resistance to biofouling than macro-topographies. Topographies with straight ridges and hierarchical shapes were predicted to be more fouling resistant than sandpaper surfaces. Topographies with average roughness (RSa) that were less than 100µm were assumed to exhibit better antifouling efficacy in comparison to topographies with average roughness greater than 100µm. Results showed that pattern size and pattern geometry affects the antifouling efficiency of topographies. Unexpectedly, surface roughness did not show strong correlations with the fouling resistance of the topographies. With the exception of Sandpaper 50 and Sandpaper 1mm samples, all topographies were more fouling resistant than the control samples (i.e. smooth surfaces). Among the 16 topographies, sandpaper 1mm samples demonstrated the worst defence against biofouling. The mean total fouling coverage on these samples after 10 weeks of tests was 98.7%. Straight, single layer ridges demonstrated the best resistance to total fouling during the field test. Barnacle and polychaete settlement trends were affected by the size and geometry of single layer, single sized topographies. After 10 weeks, the mean total fouling coverage on these ridges was only 37.5%. The field test also showed that the topography with the best prolonged resistance to fouling was the 1mm straight ridges. The combination of structured surfaces and a low modulus material is likely to have contributed to the fouling removal properties of all topographies. Lastly, results from the field study also showed that hierarchical topographies do not necessarily have better antifouling properties than single layer, single sized topographies. The field study demonstrated that the physical attributes of topographies contributed to their antifouling efficiency. It has been suggested that the physical characteristics of topographies induces hydrodynamic variations that affects the surfaces’ antifouling properties. However, it is difficult to observe these changes in lab experiments or through field studies because these variations take place at a very small scale. Recent research has applied Computational Fluid Dynamics (CFD) to numerically simulate and analyse flow characteristics in the surrounding areas of antifouling topographies. As a continuation from the field study, the next study in this research applied CFD to analyse flow characteristics over several topographies that were tested in the field study. This was to determine if the settlement trends exhibited by organisms in the field study could have been affected by hydrodynamic variations that were induced by the presence of the topographies. The CFD analysis showed that rotational vortices formed between topography patterns. These vortices could have aided in the accumulation of biofouling material on all topographies during the field test. The analysis also showed that the topographies’ resistance to fouling could be attributed to high shear stress and strain rate zones at the peaks of the topographies. Comparisons between CFD and field test results indicate that higher stresses and strain rate zones around the topographies are likely to lead to a surface’s better resistance to marine biofouling. This is likely because high shear stress and strain rate zones could have disrupted organism motility and made the surface less conducive for settlement.

An accurate evaluation of total population density is required in many ecological and biological field. To protect crops from pest attacks, the population density of pests must be evaluated adequately. Accurate information obtained as a result of trapping in ecological monitoring is beneficial for decision-making purposes when implementing a control action. In pest monitoring, a classic technique of evaluating density based on a statistical method may result in poor accuracy. Accuracy can be optimised by applying alternative numerical integration methods to the problem. We explain how insufficient information regarding population density negatively affects the accuracy of estimation. Consequently, a coarse grid problem arises where the numerical integration methods are no longer valid. The evaluation of integration error is now a random variable and the probabilistic approach is used, due to the uncertainty in sampling data. In this thesis several population models have been considered to explain that the value of correlation coefficient on a coarse sampling grid is lost even if the true value is close to one. Phenomenon of ghost synchronization has been observed when the value of correlation coefficient on a coarse sampling grid is close to one but in reality the dynamics are not correlated.

The human polycore minisatellite probes 33.6 and 33.15 developed by Prof. Alec Jeffreys and colleagues have been shown to detect hypervariable minisatellites in many taxonomically dispersed species. The mRNA derivatives of these two probes, pSPT19.6 and pSPT18.15, have here been used to probe the genomes of four species currently maintained in captivity. The wild populations of these species, Rothschild's mynah, the Rodrigues fruit bat, the British Merlin and the New Zealand falcon, are threatened with extinction to varying degrees. By using the technique of DNA fingerprinting, it has been possible to assess the levels of minisatellite variation remaining in these stocks, to confirm or refute the parent/offspring allocations made within, and in the case of Rothschild's mynah, to demonstrate that at least two of the founders of the stock were closely related. In addition, it has been possible to show that there is a significant positive relationship between the similarity coefficient calculated between two adults and the inbreeding coefficient calculated for their offspring.

Within the UK, the continuing biodiversity crisis has led to a policy driven shift in the conservation sector; moving away from localized site scale conservation to a landscape-scale. This approach encourages fragmented habitat patches to be integrated into a much larger habitat network. Epiphytic lichens provide an ideal model system for studying the effectiveness of conservation initiatives within fragmented habitats, due to their metapopulation structures whereby individual trees within woodlands (and woodland stands within wooded landscapes), represent isolated habitat patches. Old-growth woodland in particular provides suitable habitat to a suite of lichens known as the Lobarion community, which are declining throughout Europe. Regeneration within these old growth areas, though essential for future habitat persistence, causes shading and ultimately leads to local extinctions of shade intolerant lichen epiphytes. A landscape scale conservation strategy that relies on habitat permeability to balance colonisation of post-regeneration woodland patches with extinctions in ageing woodland patches elsewhere in the landscape has been proposed as a management strategy to meet the needs of both lichen epiphytes and their woodland habitat. The unique conditions found in western Scotland, combining a relative abundance of high quality old growth habitat (in a European context) coupled with robust populations of some members of the Lobarion community, could provide an ideal opportunity to test such a management strategy. In this thesis, the plausibility of landscape-scale conservation as a management strategy for epiphytic lichens is explored, using a suite of nine target epiphytes of contrasting ecological traits set within Glen Creran, a temperate rainforest on the west coast of Scotland: 1. The habitat requirements of nine target epiphytes were identified and predictions of species distribution made over an entire glen using a species distribution modelling (SDM) approach. The SDM’s were found to apply more generally within the wider biogeographic area for five of the nine species, providing an evidence base for future conservation plans in Scotland’s rainforest zone. 2. A novel method to determine dispersal distance in lichen epiphytes was developed, combining a mechanized propagule trap with molecular techniques. This methodological advance allowed the first direct comparative study of lichen epiphytes in a natural context. 3. An agent based model was developed combining the results of 1. and 2. above to investigate the effect of habitat connectivity on colonisation in six contrasting lichen epiphytes, enabling inferences of species response to landscape-scale conservation scenarios within the study system to be made.

As sessile organisms, plants had to develop various biochemical and physiological mechanisms to respond and adapt to abiotic stress conditions such as salt and drought and thus acquire stress tolerance. A particular interesting mechanism is the so called “priming effect”: an application of a mild short stress to plants at an early stage of development appears to enable them to cope better when stressed again at mature stage. However, the molecular effects of salt priming have not been systematically quantified and as a consequence the molecular basis of priming remains unknown. In this study an experimental procedure was established that allowed to test whether salt priming of young Arabidopsis thaliana plants had an effect on plants exposed to more severe salt stress at a later stage of development. To quantify how primed and non-primed plants responded to the second salt stress, global changes in their transcriptional expression profiles were monitored using Affymetrix GeneChip ATH1 microarray. Results showed that both primed and non-primed plants responded to the salt treatment modulating the same set of known stress responsive genes. However, primed plants differentially regulated a smaller set of genes. Furthermore, the vast majority of the stress responsive genes showed a weaker response in primed than in nonprimed plants. These results suggested that primed plants channelled the stress response using only selected genes. The next question addressed was how primed plants could “remember” the priming treatment after a period of extensive growth. Several studies had indicated that environmental stress induces changes in the chromatin structure thereby modifying the accessibility of the DNA for transcription factors and other regulatory proteins. This suggested a link between epigenetic modification and exposure of plants to stressful conditions, where the chromatin status might act as an epigenetic mark that could be maintained during plant growth and development. To investigate this hypothesis I carried out a comparative analysis of the epigenetic landscapes of primed and non-primed plants combining Chromatin Immuno-Precipitation with Illumina sequencing (ChIP-Seq). Genome-wide profiles of H3K4me2, H3K4me3, H3K9me2 and H3K27me3 were generated for roots and shoots of plants harvested immediately after the priming treatment. Roots of primed plants showed indeed numerous differences in their epigenetic profiles compared to non-primed roots, in particular at the level of H3K27me3. Therefore, I carried out an additional ChIP-Seq experiment before the application of the second stress to test if the priming induced changes in H3K27me3 were maintained over this period of extensive growth. Results showed that several epigenetic differences caused by priming were still maintained. Finally, to elucidate the relationship between epigenetic modifications and transcriptional responses the ChIP-Seq profiles were coupled with genome wide transcript profiles obtained by RNA-seq. Results shown that in the non-steady state there was no clear correlation between the differences detected at the transcriptional and at the epigenetic level. The results identified H3K27me3 as a potential mark for salt stress memory and they call for future studies extending both temporal and spatial resolution of epigenetic and transcriptional changes after salt priming.

It is estimated that there are approximately 1030 ocean virioplankton (Suttle 2007; Parsons et al. 2012). A large component of the oceanic viriosphere are the cyanophages, viruses that specifically infect cyanobacteria. Recent advances in genomics has revealed such viruses encode a multitude of genes, often acquired horizontally, that act to redirect metabolism for their own gains (Mann et al. 2003; Lindell et al. 2004a; Millard et al. 2009; Sullivan et al. 2010; Hurwitz et al. 2013; Enav et al. 2014). These genes have been named auxiliary metabolic genes (AMGs). They include multiple subunits of complexes involved with photosynthetic electron transport (PET) and CO2 fixation (Mann et al. 2003; Lindell et al. 2004; Millard et al. 2009; Sullivan et al. 2010; Thompson et al. 2011; Puxty et al. submitted), leading to the hypothesis that cyanophages directly participate in photosynthesis to provide carbon and energy for their own replication. Cyanophages face a dynamically changing light environment during their rather lengthy infection cycles ~12hrs. Therefore, it was hypothesised that changes in light intensity may affect the physiology of phage infection in terms of photosynthesis, CO2 fixation and infection dynamics. During infection of the marine cyanobacterium Synechococcus sp. WH7803 with the well characterised cyanophage S-PM2 I show that decoupling of the photochemical and CO2 fixation reactions of photosynthesis occurs (Chapter 3), which presumably redirects metabolism towards energy generation and away from growth. Moreover, S-PM2 acts to modify the PET which results in improved functioning of PSII at HL. The result is that the lytic cycle is significantly shortened during infection of the Synechococcus host under HL compared with low light (LL) conditions. To understand whether this early lysis is a regulated process, whole transcriptome sequencing of S-PM2 was performed in HL and LL (Chapter 5). This revealed a general increase in expression of all genes in HL but only the cyanophage psbA gene was significantly up-regulated above this background. This AMG encodes a core complex of photosystem II (PSII) of the PET and therefore plays a vital role in supplying energy through photophosphorylation. It is concluded that light poses a metabolic constraint on cyanophage development that requires large amounts of energy for synthesis and assembly of the structural components of the virion. Cyanophages have therefore acquired and evolved coordinated expression of PSII genes to maintain this supply of energy. I further hypothesise that gene expression may pose a significant barrier in the acquisition of AMGs from their host due to incompatible gene regulation. To test this, the phage transcriptome was analysed (Chapter 4) to validate the model of temporal transcriptional regulation in cyanophage S-PM2 as previously proposed by comparison to enterobacteriophage T4. It is shown that the experimental data is largely congruent with the proposed model. This also revealed unpredicted characteristics of the transcriptome, including genome wide transcriptional read-through and antisense expression. It is suggested that this is facilitated by either inefficient transcriptional termination or pervasive transcription initiation and may be a biologically relevant process that allows for moderate expression of recently acquired genes. In addition, genome-wide antisense transcription may act to regulate the inventory or temporal expression of specific mRNAs in these regulatory limited phages. Attempts were therefore made to characterise a previously detected non-coding RNA (ncRNA) antisense to the light regulated S-PM2 psbA gene (Chapter 6). A model is proposed suggesting that the asRNA may act to tweak psbA expression under LL conditions to prevent accumulation of unnecessary PSII proteins. This mechanism has an interesting effect on the rate of splicing of a group I intron encoded by the psbA gene. This study provides an important leap forward in our understanding of the factors that regulate the infection dynamics and therefore ecology of cyanophages. In so doing it also reveals transcriptional constraints and adaptations that go some way to explaining the evolution of cyanophage genomes.

This thesis is divided into two main chapters. The first chapter relates to studies undertaken to gain insights into the mechanism of action on liver growth by the peroxisome proliferator (PP) ciprofibrate and the chemical cyproterone acetate (CPA) in rodents. Peroxisome proliferators are a class of chemicals that have diverse effects in rats and mice including increased DNA synthesis and peroxisome proliferation. Peroxisome proliferators include herbicides, plasticisers, hypolipidemic drugs and synthetic fatty acids. These chemicals act through ligand activation of nuclear membrane receptors termed ‘peroxisome-proliferator-activated receptors’ (PPARs), which ultimately activate nuclear transcription. PPs induce a cellular process in liver characterised by dramatic increases in the size and number of peroxisomes, correlated with both hepatocyte hypertrophy (i.e. an increase in the size of liver cells) and hyperplasia (i.e. an increase in the number of liver cells during replicative DNA synthesis and cell division). However, the mechanism of action of increased hepatocyte growth is not currently understood. Understanding the mechanism by which increased liver growth is induced by PPs in rodents will hopefully provide insights into how natural liver growth occurs and might have medical benefits for human health if the mechanism of PP toxicity can be overcome. Knowledge gained from the mechanism of PP activation might also then be applied to other chemical carcinogens. Therefore, firstly the mode of action of the peroxisome proliferator ciprofibrate was investigated. Previous work had indicated that two successive doses of ciprofibrate treatment separated by 24hr led to two rounds of liver cell replication, but it was not clear whether the same or different hepatocytes were involved in this growth response. To study this phenomenon, histochemical experimental work was undertaken to assess whether the same or different hepatocyte cells were stained during the two rounds of cell division following ciprofibrate treatment. The two histochemical stains used were EdU and BrdU, which are both base-pair analogues that stain nuclei undergoing DNA replication. It was hypothesized that if EdU was used to stain cells at 24 hr and then BrdU at 48 hr, that if the same cells were responding to ciprofibrate treatment then cells would be co-stained by both dyes, whereas if different cells were responding then there would be little or no double staining of hepatocyte cells. It was found that different cells were stained by the two dyes, indicating that ciprofibrate treatment was targeting different cells. Secondly, the mode of action of the carcinogen cyproterone acetate (CPA) on hepatocyte growth was investigated. Previous work had investigated the effects of CPA on hepatocyte growth in male and female rats and had suggested differences in response between the sexes. In the present study female rats were treated with CPA, to assess whether differences in labelling indices were present compared to previous male results. Female F-344/NHsd rats, aged 14-15 weeks, were treated with CPA and then injected with BrdU at 22 hr, and rats were killed 2 hr later. Results confirmed that the female rats had a considerably higher labelling index (50%) compared to male rats (6%). This suggested that upregulation of gene expression in female rats was much higher, which might provide an exciting opportunity to identify sets of genes involved in carcinogenic responses. To investigate whether there was any overlap between genes induced by ciprofibrate and CPA treatment a preliminary study was designed where female rats were gavaged with CPA and then killed 3 hr later. Real-time PCR analysis of a small number of target genes showed no consistent changes in expression between the present CPA and previous ciprofibrate treatment results, suggesting largely different modes of action of these chemicals. The second chapter of this thesis relates to studies undertaken to gain insights into neurodegenerative disorders. Neurodegeneration is a gradual loss of structure or function of neurons, which may lead to neuronal death. Neurodegenerative diseases including Parkinson’s, Alzheimer’s, and Huntington’s occur as a result of neurodegenerative changes. Several studies have suggested that PPARs have critical roles in reducing the brain inflammation which in turn might have a significant effect on reducing the fundamental processes involved. Work was performed using a mouse model of dementia with lewy body disease (Psmc1fl/fl; CaMKIIα-Cre) to represent neurodegenerative disorder, and involved parallel, in vivo and in vitro investigations to determine whether the development of neurodegenerative diseases occurs at the same rate in vitro and in vivo i.e. a comparison of rapidity of pathogenicity progression was made. Astrocytes were used to track the development of disease, given that these play a key role in neurological disorders, using an immunohistochemistry approach. A PPAR-γ analogue was used to investigate the role of PPARs in reducing astrocytes proliferation. To optimise the validity of the results, four controls were used including an antagonist T0070907 which abolished the effect of rosiglitazone treatment alone. The results on the effect of PPAR-γ agonist and rosiglitazone, after a week of treatment, showed that the PPAR-γ agonist inhibited astrocytes activation in both the cortex and hippocampus of the mutant mice organotypic slice culture. The number of GFAP +ve astrocytes was significantly decreased in mutant mice with 100 µM rosiglitazone in both areas, whereas 50 µM rosiglitazone showed a decrease in the number of astrocytes in the cortex, but the effect was less in the region of the hippocampus. This finding suggests that PPs such as rosiglitazone may have potential uses as therapeutic drugs to inhibit neurodegeneration.

Movile Cave is an isolated cave ecosystem that receives no input of photosynthetically fixed carbon. Instead, carbon is primarily fixed through light- independent bacterial processes such as chemolithoautotrophy and methanotrophy. Distinctive microbial floating mats appear at the surface of groundwater flooding the cave, at the redox interface between the oxygenated air above (7-10%) and the anaerobic water below. Methane, of geological origin, bubbles up into the cave and is present in the cave atmosphere (0.5-1%). The in situ methanotroph community of Movile Cave microbial floating mat was determined by examination of metagenomic sequencing and pmoA gene microarray data sets. The metagenonomic sequencing approach indicated a Methylococcus capsulatus -like organism to be the most abundant methanotroph in Movile Cave. pmoA microarray analysis indicated a high abundance of Methylocystis pmoA gene sequences with Methylococcus capsulatus-like pmoA gene sequences being relatively abundant. The methane oxidising bacterium Methylomonas strain LWB was isolated from a sample of lake water from Movile Cave. Phylogenetic analysis of the genes encoding 16S rRNA and the soluble and particulate methane monooxygenase functional gene markers pmoA and mmoX, respectively, confirmed that strain LWB belongs to the genus Methylomonas. Methylomonas LWB has a second putative copy of the particulate methane monooxygenase pXM which displays an unusual gene orientation. The Methylomonas LWB genome contains all genes encoding the typical Type I methanotroph ribulose monophosphate pathway for formaldehyde assimilation and all genes required for a complete TCA cycle. Active methane oxidisers in Movile Cave were identified by DNA Stable-isotope probing. Organisms belonging to the genera Methylomonas, Methylocystis, Methylococcus and Methylobacter- were identified from 13C-enriched DNA. Cross-feeding of the 13C label into non-methanotrophic organisms identified from the 13C-enriched DNA indicated that methanotrophs provide a carbon source for other microorganisms in Movile Cave.

Upland headwater streams are important sources of freshwater in mountainous temperate to sub-arctic latitude European countries like Scotland. Yet much less is known about the ecology of small, characteristically oligotrophic, mountain streams supporting periphyton and aquatic bryophyte dominated vegetation, and their potential bioindicator capacity of environmental water quality, than lowland rivers impacted by anthropogenic disturbance, in this context. This scarcity of knowledge has significant implications for the success of the recently implemented Water Framework Directive (WFD: 2000/60/EC). The WFD is a major piece of environmental legislation for water policy and sustainable water management in Europe. New contributions are fundamental to environment agencies, such as the Scottish Environment Protection Agency (SEPA), tasked with the responsibility of enforcing WFD statutory requirements and developing effective biomonitoring tools for assessing water quality status in Scotland. A major aim of the WFD is to achieve at least ‘good’ ecological status of inland waterbodies by 2015. Further, in doing so, to ascertain ecological benchmark communities of near-pristine (or minimally-impacted) reference conditions as indicators of high water quality status. The objective is to improve understanding of the environmental processes driving the production and diversity of freshwater plant species-assemblages in upland streams. Such information can be used for assessing perturbations threatening the ecological integrity of rivers impacted by anthropogenic disturbances (human pressure). This enables environment agencies such as SEPA, to respond appropriately by implementing corrective measures and sustainable management strategies. This project monitored a range of near-pristine headwater streams of contrasting underlying geology in the Scottish Highlands. The approach adopted was compatible with current WFD river characterisation and biomonitoring strategies. These were used to investigate the structural and functional response of freshwater plant communities (chiefly diatoms and other algal groups; aquatic bryophyte and vascular submerged macrophyte vegetation) to environmental drivers (e.g. flow, substrate morphology, nutrient inputs, water chemistry, underwater light availability). The work was carried out with the aim of contributing to future development of baseline monitoring tools for assessing upland stream habitat quality in Scotland.

Ordovician samples have been collected from various places from within three separate terranes in Scotland; the Highland Border Complex, the Southern Uplands and the Midland Valley. The samples have been palynologically processed and their assemblages studied with the aim of understanding some of the palaeoecological, biostratigraphical and thermal relationships of the three areas.Seventy one samples have been processed from nine localities of the Highland Border Complex and these have yielded fifteen species of chitinozoans in four genera, as well as indeterminate species of those genera. There are also five species of acritarchs in four genera as well as other microfossils. Black shales from the Complex yield the most diverse palynomorph assemblages, and were probably deposited from Arenig through to Caradoc although not necessarily at the same time in different parts of the basin. The preservation of palynomorphs appears to be better in the west of Scotland than in the east.From the Southern Uplands samples have been processed from Coldingham Bay and proved barren, from Barrhill the assemblages are poor, but from the Ordovician-Silurian bondary beds (C. peltifer to P. acuminatus Zones) at Dob's Linn they are quite diverse although abundance is very low, with forty three samples yielding thirty three species of acritarchs in eighteen genera, thirty one species of chitinozoans in thirteen genera and various other microfossils. The boundary cannot be delineated using the palynological assemblages, and although Tylotopalla sp. A and Ancyrochitina ancyrea Eisenack 1931 are common in most of the samples from the boundary the palynomorphs do not appear to mirror the changes that occur in the graptolite assemblages.From the Midland Valley samples have been processed from eight miscellaneous localities in the region of Girvan, giving very little biostratigraphical data, although one sample from Doularg Hill is dated as upper Arenig to lower Llanvirn. A section of twelve samples processed from the Mill and Shalloch Formations (D. complanatus and D. anceps Zones) at Woodland Point, Girvan, has yielded thirty five species of chitinozoans in twelve genera including a new species Angochitina woodlandensis and five new combinations; Belonechitina comma (Eisenack 1959), Belonechitina hirsuta (Laufeld 1967). Belonechitina micracantha (Eisenack 1931), Belonechitina schopfi subsp. americana (Taugourdeau 1965), and Belonechitina seriespinosa (Jenkins 1969). There are also forty seven species of acritarchs in twentyone genera, including two new species; Actinotodissus woodlandense, and Goniosphaeridium girvanense, and many scolecodonts. Spores are common and three species are recognised at Woodland Point. The samples are dated as Upper Ordovician and Calpichitina lenticularis (Bouche 1965) and Acanthochitina barbata appear to be important Upper Ordovician indicators, possibly being near-shore species as they are not found in rocks of the same age at Dob's Linn. Calpichitina lenticularis is very important in one sample and less so in all the others and it is suggested that it may be reworked. The palaeoecological picture at Woodland point shows an offshore situation in the Mill Formation, becoming more near-shore at the base of the Shalloch Formation and then more off-shore again.The palaeoecology of both Dob's Linn and Woodland Point are discussed and chitinozoans found to be more common in black shales than grey mudstones, although the acritarchs do not appear to be preferentially found in grey mudstones or black shales. Netromorph acritarchs are less common at Dob's Linn than was expected, but are very common at Woodland Point which may suggest that the sediments at Woodland Point were deposited more offshore than those at Dob's Linn but were more greatly influenced by turbiditic material. Sphaeromorph acritarchs at Woodland Point are very common and due to the variable thickness of the walls it is suggested that there is a mixing of near-shore and off-shore species, possibly by the turbiditic action mentioned above. Belonechitina is markedlymore important at Woodland Point than at Dob's Linn the reverse of which is true with Cyathochitina . The suggested reason for this is that Belonechitina is a near-shore species whilst Cyathochitina is an off-shore species. Veryhachium appears to become more important towards the end of the Ordovician, as a sample each from Woodland Point and Dob's Linn contain three species of this relatively rare genus, although the significance of this is not yet known.The sample from Dob's Linn and Woodland Point are compared with published works using the jacquard Coefficient and the results presented. The samples at Dob's Linn are compared with the Ordovician-Silurian boundary sediments elsewhere, and although different species are present at Dob's Linn and on Anticosti Island, and the abundance and diversity is lower at Dob's Linn, the boundary in Scotland has a much better palynomorph assemblage than was expected. The boundary assemblage presented here is quite similar to the one in Skane, Sweden.Finally the thermal history of the samples is discussed, and a general trend appears, with the samples from Girvan being the least altered, those from the Southern Uplands being moderately altered and finally the Highland Border Complex samples which have been subjected to temperatures probably between 200 and 300oC, and thus strongly altered.