Palearctic migrants, including barn swallows Hirundo rustica, responded to climate change in Europe from the mid to late 1900s with phenological changes, mostly showing earlier arrival and start of breeding. During this period, barn swallows in the Palearctic exhibited variable patterns of change in the timing of their arrival, breeding and departure from the breeding grounds. At the South African non-breeding grounds, the timing of migration shifted between the 1980s and 2000s, again with geographic variability. To explain these changes further, I examined geographic and temporal variability in the timing of flight feather ('primary') moult, and trends in body weight, in barn swallows ringed in South Africa between 1986 and 2012. Citizen science bird ringing, started in South Africa in 1948, generated all the data used in this project. All data were obtained from the South African Bird Ringing Unit (SAFRING).

Phylogenetic studies are providing powerful new insights into the evolution of complex traits. Metal hyperaccumulation is an unusual and complex physiological trait found in about 500 plant species and is associated with an exceptionally high degree of tolerance of metalliferous soils. Alyssum L. (Brassicaceae) is the largest known hyperaccumulator genus, comprising approximately 188 species distributed throughout the Mediterranean region and south-west Asia. Approximately one-quarter of these are largely restricted to areas of serpentine soils and have the ability to accumulate nickel to high concentrations in shoot tissue. This genus provides a good example in which to study the origins of a complex physiological trait, but its phylogeny is currently poorly understood. To produce a well-resolved phylogenetic tree to investigate the number and timing of origins of nickel hyperaccumulation within Alyssum, DNA sequences were generated for four chloroplast regions (matK, rps16–trnK, trnD–T and trnL–F) from 170 of 255 species in the tribe Alysseae. Additional sequencing was carried out for the chloroplast genes ndhF and rbcL and the nuclear gene PHYA. A Bayesian analysis employing a relaxed uncorrelated lognormal molecular clock and multiple fossil-age calibration points was carried out to reconstruct a time-calibrated phylogeny of this tribe using appropriate outgroups. Optimization of the nickel hyperaccumulation trait onto the resulting phylogenetic tree suggests that nickel hyperaccumulation arose twice in the Alysseae in the late Miocene/early Pliocene: 3.3–8.3 Mya in Alyssum and 6.3–8.8 Mya in Bornmuellera. The single origin in Alyssum is strongly associated with a significant acceleration in net species diversification rate, suggesting the ability to hyperaccumulate nickel could have provided a key evolutionary innovation facilitating rapid range expansion and subsequent species diversification. The scattered distribution of nickel hyperaccumulators across small island-like patches of serpentine soil suggests that allopatric speciation may have driven rapid diversification in this clade.

Photosynthesis is responsible for fixing approximately 111 – 117 Pg of CO₂ into organic carbon each year, of which about half is performed by algae in the oceans. Over geological timescales, photosynthesis by algae was instrumental in transforming Earth’s atmosphere. Despite the integral role algae play in the carbon cycle, the interaction and feedbacks between CO₂ fixation by algae and atmospheric CO₂ is poorly understood. This thesis expands upon our current knowledge by tracing the evolution of the key enzyme of photosynthesis, Rubisco, in algae through geological history. It was found that Rubisco underwent adaptation during distinct periods corresponding with falling atmospheric CO₂. The pattern of adaptation hints at physiological adaptation to varying concentrations of atmospheric CO2 and possibly indicates the emergence of carbon concentrating mechanisms (CCMs). This adaptation was probed further within the red and chromist algae, identifying key residues within the Rubisco protein sequence that may influence its kinetic properties. This research also provided new measurements of Rubisco CO2 affinity within the haptophyte algae. Finally, the importance of HCO₃- use by phytoplankton in the modern ocean was explored. HCO₃- utilisation was modelled through signals retained within stable carbon isotopes of organic matter estimate the response to anthropogenic increases of CO₂. The results indicate that phytoplankton utilise a large proportion HCO₃- which shows little sensitivity to anthropogenic increases of CO₂, even when model predictions are extended to 2100. This thesis demonstrates how algae can respond to CO₂ levels over geological and anthropogenic time scales.

A range-wide collection of Juglans regia seeds was undertaken in autumn 1997 from 12 countries, including 25 provenances and 375 half-sib progenies. 2200 seedlings were produced using innovative nursery techniques. The seedlings were planted in three provenance trials in southern England in 1999, the largest of which acted as a combined provenance/progeny trial. After one growing season, survival was 98.9 %, mean height growth 35 cm, and mean stem diameter increment 5 mm. Provenance differences for both height and stem diameter increment were highly significant (p<0.001). There were no significant genotype × environment interactions. Flushing assessments revealed few significant differences between provenances and flushing was complete by early April. Family heritability for tree height was 0.19 at one site and, with combined selection, genetic gain was estimated at 8 %. The effects of three types of treeshelter and a stumping treatment on walnut establishment were tested over three growing seasons. Treeshelters were found beneficial to height increment. However, 120 cm tall shelters promoted early flushing, and consequent risk of increased frost damage, and caused more stem die-back than 75 cm shelters. Stumping promoted rapid early height increment but gave no longer-term benefit. The crown (cd) and stem (dbh) diameter at breast height relationship of open growing trees in Britain was assessed and was highly significant (r2 = 0.96, p<0.001). The regression equation (cd = 2.71 + 17.6dbh) permitted the estimation of suitable planting densities for the provenance trials and the calculation of a thinning regime. Isozyme analysis of the 375 genotypes identified 20 loci in 15 enzyme systems with seed embryo extracts. Using young leaf extracts, the polymorphic locus Pgm-1 indicated low expected heterozygosity of 0.06 both within populations and at the species level. FST and GST estimates, both 0.05, indicated high uniformity among populations. Genetic distance estimates did not identify significant clustering consistent with geographic origin.

Little is known about the composition of tropical epiphytic communities and the influence of environmental variables on community composition. In this thesis I quantify the diversity and biomass of bromeliads, and other vascular epiphytes along an altitudinal transect on the eastern slope of the southeast Peruvian Andes and then look for species’ adaptations related to patterns of diversity and biomass. I compare patterns with those of woody species. Bromeliad species, like tree species, were found to form ecological zones related to climate. The lowest altitude ecological zone (below 1250 m) is the lowland rainforest (LRF), which has the warmest climate and highest evapotranspiration. In LRF vascular epiphytes are less prominent than other ecological zones, with the lowest bromeliad species richness and lowest vascular epiphyte biomass. However, low water-availability gives rise to most variable shoot morphology of bromeliads. The tropical montane forest (TMF), between 1250 m and 2250 m, is intermediate in climate between the LRF and the tropical montane cloud forest (TCF). The TMF has the highest α-diversity, but species richness is lower than the TCF. The shoot morphology of bromeliads is intermediate between TCF and LRF. The highest altitude ecological zone with forest is the TCF (above 2250 m). The TCF has the highest bromeliad species richness, and lowest diversity of shoot forms. The low diversity of shoot forms represents the need for a large phytotelm (water-impounding shoot) to intercept and store precipitation. The TCF has the highest vascular epiphyte biomass, although the biomass is variable as a consequence of the natural disturbance caused by landslides. Along the transect bromeliad species with CAM photosynthesis are only present in the LRF. Terrestrial bromeliad distribution records covering the Neotropics show CAM photosynthesis is more prevalent in drier environments showing that CAM photosynthesis is primarily an adaptation to drought. Epiphytic bromeliads, pre-adapted to a water-stressed environment show no differences in presence along rainfall gradients, but species with CAM photosynthesis occupy warmer environments.

<b>Cardamine hirsuta</b> L. is an emerging model system in developmental genetics, where natural genetic variation within <b>C. hirsuta</b> provides the means to investigate the genetic basis of morphological traits. This thesis investigates the geographical structure and genealogical history of genetic variation within <b>C. hirsuta</b> and identifies its closest relatives. This will enable the accurate selection of species for comparison with <b>C. hirsuta</b> when making interpretations of evolutionary processes, and provide a better understanding of morphological character evolution in <b>C. hirsuta</b>. The phylogeographic history of <b>C. hirsuta</b> was reconstructed using multiple chloroplast and nuclear markers and widespread accession sampling from across its native range. A distinct group was identified within <b>C. hirsuta</b>, restricted to the high mountains of East Africa. Climate suitability modelling showed that Pleistocene glacial dynamics have had a strong effect on the distribution of genetic variation within <b>C. hirsuta</b>. The phylogeographical data generated here was used to investigate the origin of <b>C. hirsuta</b> in the Azores, an oceanic archipelago. The Azores are dominated by an endemic chloroplast haplotype which is associated with an endemic phenotype. Thus, <b>C. hirsuta</b> appears to have diversified <b>in situ</b> in the Azores. Phylogenetic analyses of Cardamine, restricted to diploid species to remove the confounding effects of polyploids, found that <b>C. hirsuta</b> is most closely related to <b>C. oligosperma</b>, a western North American species. Multiple loci and extensive intraspecific sampling were brought to bear to demonstrate that <b>C. hirsuta</b> and <b>C. oligosperma</b> are reciprocally monophyletic. <b>Cardamine pattersonii</b>, a restricted endemic from north-west Oregon is likely to be an allopolyploid, with <b>C. oligosperma</b> as the maternal parent and possibly <b>C. nuttallii</b> as the paternal parent.

Neopterygian fishes represent over half of vertebrate richness in the Recent and display staggering phenotypic variety, yet little is known about the first 150 million years of their evolution. Furthermore, neopterygian richness and disparity is highly unevenly partitioned between teleost fishes, with ~29,000 species expressing a plethora of phenotypes, and holostean fishes, with 8 species and just two morphological styles. Fossil phenotypes have the unique ability to illuminate the assembly of neopterygian disparity, and can reveal the pattern by which the uneven partitioning of disparity arose. Morphology and function were quantified with landmarks and six functional traits, respectively, for 356 neopterygian species known globally throughout the first 150 million years of their history. The main axes of morphological and functional variation were derived and used to examine a series of evolutionary questions. Pertinently, they revealed how disparity was accumulated for 60% of the neopterygian radiation; morphological disparity increased through time, whereas functional disparity remained stable. The morphological dataset was expanded to include shape data for 398 species and size data for 471 species. Time scaled supertrees containing 671 mostly Mesozoic, but also living neopterygian species, were created. Together, the trees and traits were used to quantify evolutionary rates and innovation and test the predictions of genome duplication enhanced morphological diversification in teleosts, and the presence of 'living fossil' characteristics in holosteans. The analyses revealed higher rates and greater innovation in teleosts guaranteed to possess duplicated genomes, consistent with the predictions of genome duplication enhanced diversification. The only 'living fossil' characteristic of holosteans is their poor capacity for size innovation, yet they possess relatively high rates of shape evolution. However, estimates of rates and innovation are heavily influenced by timescale choice, emphasising the need for workers to perform their analyses on a variety of plausible timescales to determine the limits of their conclusions.

Neisseria meningitidis is the bacterium responsible for meningococcal meningitis and septicaemia in humans. Meningococcal disease is primarily a disease of young children, characterized by rapid deterioration from first symptoms to death, with an 11% fatality rate and a global distribution. Patterns of genetic diversity in meningococcal populations provide an account of their evolutionary history and structure, which can be inferred by population genetics modelling. Understanding these phenomena can inform control and prevention strategies, and provides interesting case studies in evolution. The aim of this thesis is to develop population genetics techniques for inferring the evolutionary history of meningococci. I begin by reviewing the field, and justifying the use of coalescent methods in modelling microparasite populations. Inference on carriage populations of meningococci under the standard neutral model and the neutral microepidemic model is performed using a modification to approximate Bayesian computation. AMOVA and Mantel tests are used to quantify the differentiation between carriage and disease populations, and the extent to which geography and host age structure carriage populations. The results are used to propose revised coalescent models for meningococcal evolution. The role of natural selection in shaping meningococcal diversity is investigated using a novel method that utilises an approximation to the coalescent and reversible-jump Markov chain Monte Carlo to detect sites under selection in the presence of recombination. Having performed a simulation study to assess the statistical properties of the method, I apply it to the porB antigen locus and seven housekeeping loci in N. meningitidis. There is strong evidence for selection imposed by the host immune system in the antigen locus, but not the housekeeping loci which are functionally constrained. Finally I discuss the future direction of population genetic approaches to understanding infectious disease.

Cord-forming fungi (CFF) are an assemblage of saprotrophic fungi which can use complex foraging organs of longitudinally arranged hyphae to join up disparate substrates in a patchy resource environment. Their importance to woodlands lies, mainly, in their ability to modify nutrient cycling and soil structure. Therefore, in order to enable woodlands to continue to thrive in terms of their health and ecosystem function, it is necessary to understand the factors contributing to the establishment, success and diversity of this group. Whilst work to date on CFF has focussed on their physiology and interactions in laboratory conditions, little work has been carried out on their taxonomy and establishment/presence in the field. The work in this thesis begins to address these crucial unanswered questions in CFF ecology. By carrying out investigations at a range of scales, from phylogenetic analysis to UK wide Species Distribution Modelling, this thesis reaches a number of surprising results with potentially important implications for woodland management. This is most evident in Chapter 3 where our hypothesis that fungal communities develop over time in plantations of different woodland ages was disproved, illustrating that even 13 years after planting, fungal communities in plantations on ex-agricultural land had not begun to reach those in established ASNW. These unexpected results continue into Chapter 4, where the thesis demonstrates that dominant canopy species has a greater impact on community composition than any other woodland factor. Chapter 5 continues this theme, by showing that removal of invasive species is not always beneficial for the cord-forming fungal communities, especially if it involves removing the woody substrate. The work described, detailed and analysed in this thesis has initiated further investigations, proposed changes to woodland management practices and laid the foundations for future work relating to CFF and their role and function in British woodlands.

The Mercurialis annua L. (Euphorbiaceae) species complex comprises a group of closely related lineages that present a wide range of sexual-systems, making it a valuable model for the study of plant sexual-system evolution. Within this polyploid complex, diploid populations are dioecious, and polyploid populations either monoecious or androdioecious (males coexist with functional hermaphrodites). The primary aim of this thesis was to use patterns of genetic diversity to elucidate the evolutionary origin and maintenance of the sexual-system diversity in M. annua. The phylogeny of the M. annua complex was reconstructed using chloroplast and ITS DNA sequence. This, in conjunction with morphometric analysis, showed that both hexaploid M. annua, and a novel species from the Canary Islands (newly described here as Mercurialis canariensis), were allopolyploid in origin. Such an origin for hexaploid M. annua suggests that androdioecy may have been able to arise in this group as a consequence of hybridisation between a monoecious lineage, tetraploid M. annua, and a dioecious lineage, M. huetii. Artificial crosses were used to show that hexaploid M. annua has disomic marker inheritance, and a statistical approach was developed to quantify genetic diversity and differentiation in polyploids with disomic inheritance. Strong gradients in genetic (allozyme) diversity at a pan-European scale were used to infer the existence of separate glacial refugia for dioecious and monoecious races of M. annua, at the eastern and western ends of the Mediterranean basin, respectively. A metapopulation model had previously been proposed to explain the ecological maintenance of androdioecy in M. annua. Here, population-level patterns of genetic diversity were used as an indirect test of this model. The discovery of lower within-population diversity, and of greater genetic differentiation between populations, for monoecious populations than for androdioecious populations was consistent with the metapopulation model, and suggests that androdioecy is maintained by the occurrence of regular local extinction.