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The Amazon rain forest is the most diverse ecosystem on Earth, harbouring more than ten thousand tree species. In this project, I used ecological and molecular information to explore how ecological factors and historical events have determined the species distributions and population genetic structure of tree species and the phylogenetic diversity of tree communities in the Amazon rain forest. Chapter 2 indicates that seasonally dry vegetation in northern South America represents a barrier to migration for Ficus insipida (Moraceae) and other wet-adapted Amazonian tree species as they have different plastid haplotypes restricted to Mesoamerica and Amazonia. Conversely, the ability of some pioneer species to survive seasonal drought may explain the weakly differentiated phylogeographic structure within these species, with some haplotypes occurring on both sides of this barrier. Chapter 3 explores whether patterns of population genetic structure in five widespread western Amazonian tree species are consistent with historical explanations. My results show that the genetic patterns among species are not entirely congruent suggesting that tropical rain forest species respond differently to long-term geological and climatic changes. Despite this, some tentative generalisations emerge, notably high genetic diversity and a strong geographic structure for plastid sequences suggesting long-term population stability across western Amazonia, and recent population expansions in the south-western Amazon. Chapter 4 uses 283 floristic inventories from the RAINFOR plot network to explore patterns of phylogenetic diversity across Amazonia. This study reveals that the species-rich communities of central Amazonia are dominated by phylogenetic close relatives compared to the equally species-rich communities of the north-west that tend to contain more distantly related species. Across Amazonia, an east-west gradient of the abundance of early divergent angiosperm clades was found, with the greatest percentage of tree species of Magnoliids and Monocots in the west. As these early diverging clades are also characteristic of pre-montane habitats, these results suggest that migration events from cooler environments at different geological times has played an important role in the assemblage of the most phylogenetically diverse communities in Amazonia. The findings from these three chapters corroborate the notion that both ecological factors and historical events have been important in determining species distributions and the phylogenetic diversity of tropical tree communities in Amazonia. Regional differences in genetic structure among populations, and phylogenetic diversity among communities, should both be taken into account in forest conservation planning and management.

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Common ancestry is a central tenet of evolutionary theory; phylogenies allow us to view this history, and more importantly, they provide a framework for generating and testing hypotheses of evolution. Hypotheses of macroevolution are centred on biodiversity: understanding and maintaining biodiversity is a key challenge of biology, whilst palaeobiology is mainly concerned with understanding the processes that generated this diversity. In recent years phylogenies have been employed to provide a timescale for evolution, and understand morphologicaJ evolution using Phylogenetic Comparative Methods (PCMs). However, whilst fossils were instrumental in initially integrating macroevolutionary thought into the modem evolutionary synthesis, the majority of PCMs have been applied to extant species only. Therefore, the main theme of this thesis is to incorporate fossils into analyses of major patterns in macroevolution, and simultaneously test the effectiveness of these method we use to do this. In Chapters One and Five, I study times of large macroevolutionary change - the origin of birds and the Permo- Triassic mass extinction - using phylogenies composed mainly of fossils. In Chapter Three, I investigate macroevolutionary patterns using extant taxa only, but incorporating modem PCMS. In Chapters Two and Four, I investigate the effects fossils and alternative methods can have on our understanding of modem macroevolutionary change. Overall, I show fossils are important in the understanding of past macroevolutionary change. The continued use of fossils in phylogenetics has great promise for our understanding species' diversification and trait evolution, but it is still possible to elucidate patterns from extant taxa. Throughout, I keep a firm focus on the appropriateness of methods, and consider best ways to integrate from the present day into deep time, and to combine modem genomic trees with sparse fossil data.

This thesis describes work that was undertaken to investigate the design of novel protocellular systems based on simple, positively charged polydiallyldimethylammonium chloride (PDDA)/adenosine triphosphate (ATP) or negatively charged PDDA/polyacrylic acid (PAA) coacervate phases. Coacervate phases were stabilised by encapsulation within a colloidosome formed from partially hydrophobised silica nanoparticles. The coacervate core colloidosomes were assembled via the formation of a Pickering emulsion, in which the coacervate bulk phase was suspended in a continuous phase of anhydrous dodecane. The colloidosomes were transferred out of the dodecane and into alternative solvents (acetone, ethanol and water) by cross-linking the colloidal particles with tetra methyl orthosilicate. The silica microstructures that were formed when the PDDA/PAA coacervate phase was used as the template had a homogeneous core, which was solidified throughout by the condensation of silica. Occasionally oil droplets were able to ingress into the coacervate phase, however they remained in close proximity to the coacervate/oil interface. Destabilisation of the Pickering emulsion interface was achieved by charge matching the positive PDDA/ATP coacervate phase with the negatively charged silica nanoparticles. This lead to significant ingress of oil droplets throughout the silica microstructures. The structures with complex interiors were characterised by a range of microscopy and X-ray tomographic techniques. Separately, photo active chloroplasts were extracted from Spinacia oleracea leaves into phosphate buffer, and then incorporated into coacervate microdroplets in aqueous suspensions. The activity of the chloroplasts within the coacervates was characterised by spectroscopic tracking of the reduction of the redox dye 2,6-dichorophenolindophenol from its blue form to its colourless form. A comparison of the stability and activity of the chloroplasts before and after sequestration into the coacervates was performed. Finally, artificial fossilisation experiments were attempted using a hydrothermal bomb or cold seal press on protocells formed from FMOC-tyrosine hydro gelled vesicles, yeast cells and the coacervate core microstructures. These systems were analysed by electron microscopy to check for evidence of the formation of microfossils.

A key process in evolution is the adaptation of a species to a new environment that can be achieved by the gain of an advantageous novel function. The importance of gene duplication in generating functional innovation is currently being revealed. In order to determine whether gene duplication plays a role in environmental adaptation it is necessary to show that duplicate retention is dictated by the environment. Furthermore, investigating the genetic mechanisms of duplicate divergence will further our understanding of how these genes develop new functions and contribute to adaptation. In this thesis I examine the extent of gene duplication in yeast and investigates the mechanisms by which these duplicates diverge. Identifying gene duplicates in multiple yeast strains reveals that there are large differences in duplicate gene content between the strains. Interestingly, the retention of genes in duplicate is not random and correlates with a strain's natural environment. Next, parsimony and maximum likelihood methods are developed for determining the duplication and loss events in the evolution of {\it Drosophila} gene families. The performance of these methods is tested and their strengths and weaknesses are characterised. Duplicate divergence is also considered. Firstly, by examining transcription factor binding sites that may indicate divergence of expression between duplicates. Here, there is evidence of high rates of change in binding sites, which is consistent with positive selection and may indicate functional innovation. Interestingly, it is possible to find large differences in binding site gain and loss between the strains that can be rationalised by analysing their natural environments, suggesting a role for duplicate divergence in environmental adaptation. Secondly, duplicate divergence through changes in specificity of physical interactions is considered. Here, I show that as duplicates age they share fewer interactions. I develop a method to predict whether changes in interface regions will alter specificity and show that changes in specificity are best explained by examining functional atom contacts between residues. The investigations of duplicate divergence highlight the genetic mechanisms that lead to changes in expression and interactions through subfunctionalisation or neofunctionalisation, that could potentially lead to functional innovation. The correlation of duplicate retention with natural environment indicates that selection is shaping genome content. I argue that this has important implications for environmental adaptation and speciation.

The Negativicutes are a class of bacteria within the predominantly Grampositive phylum Firmicutes that possess a diderm Gram-negative cell envelope along with lipopolysaccharides. Remarkably, some members of this class of Gram-negative bacteria can form endospores. The evolutionary origins of this enigmatic class were investigated through bioinformatics analyses, which defined and characterised their Gram-negative and Gram-positive toolkits, while analyses of Gram-negative signature proteins provided insights into the origins of the Gram-negative toolkit. The genome of Sporomusa sphaeroides, a sporulating species from the Negativicutes, was sequenced and annotated for the first time. In addition, the transcriptional landscapes of Veillonella parvula and Sporomusa sphaeroides during logarithmic and stationary phase growth were investigated using RNA-Seq, expanding the repertoire of known genome features, including non-coding RNAs within these species.

This thesis analyses the process of construction of linguistic meaning from a diachronic perspective. The analysis is based on the theories of intertextuality and social construction and applies a corpus analysis of collocations and paraphrases of key notions discussed in Darwin’s correspondence. In particular, the focus of the analysis is on the terms \(species\) and \(varieties\) with the aim to observe how the meanings of these terms are formed in a process of social negotiation. The thesis analyses the difference in the meanings of these terms, but also focuses on the diachronic dimension of their use in the correspondence, which allows for the observation of how different interpretations of meanings emerge in discourse. Thus far, diachronic studies in the field of corpus linguistics focused on comparing different historical corpora rather than observing the diachronic change of the immediate contextual environment of particular terms. The results presented in this thesis show that the meanings of terms are not only formed of different interpretations in discourse, but that these interpretations can be specific to particular temporal spans in discourse.

This thesis examines the nature of biological species, and argues that species are real. The thesis starts with a descriptive account of species drawn from biology. This includes taxonomic views, theories of speciation and theories in ecology. In this chapter a particular definition of species, 'the biospecies', is reached. The thesis continues in Chapter Two with a philosophical account of species, which aims at reaching an understanding of the kind of entities species are. The chapter concludes that species are natural kinds, but not as traditionally construed. Chapter Three looks closely at the use biologists make of species terms, and argues that biological theories are committed to such terms. That species terms cannot be dispensed with in biological statements indicates that species are real. If species are real, they are entities for which questions of identity make sense. Chapter Four reviews different criteria for the individuation and identity of species. All the criteria are found to suffer from problems of vagueness. In view of the difficulty of providing criteria for species identity, the thesis turns in the fifth chapter to two biological views---numerical taxonomy and neo-Darwinism---which claim that biological theories can dispense with species terms. But a look at these reductive theories shows that one loses a certain measure of explanation if species are dispensed with. In the light of the failure of the reductive theories, a fresh attempt is made in Chapter Six at giving a criterion for species sameness. This last chapter also serves as a general conclusion to the thesis.