ABSTRACTBiology is considered the most visual of the sciences. Historically it has relied on the skill set of observation, experimentation, and (less acknowledged) drawing. Many scientists, who have contributed to the foundations of biology and medicine, were also artists (Smith 2009). The drawing methods employed by these pioneers of biology have been overlooked in history and rarely considered a methodology for research or educational practices related to complex biological topics like evolutionary processes. According to botanist and artist Agnes Arbor, “There is a close association between fingers and brain, that the handing over either the technical or the interpretive side of research to another worker cannot but mean a serious loss of integration” (Arbor 1954). The integrated drawing-experimental methods of the past combined the observational naturalist’s skill set with the experimental biologist skill set. As a result, the drawing methods themselves became a complex conceptualization of living systems and illuminated them. Today, biology disciplines are converging on a consensus that living systems are multi-dimensional, networked, dynamic, interdependent, and evolutionary complex webs. Understanding a complex moving web of life for students may require. It may benefit from a non-linear, creative approach for a continued perception of biological phenomena, as it did in the past. Benefits from this historical method may also emerge in the education of future life scientists and physicians. It has been verified that even simple drawing is an activity that increases observational skills, focus, and divergent thinking (Kozbelt 2010). Technology has sped up the discovery process and increased the data output. However, it has had a side-effect of marginalizing those deliberate, mindful, and methodical biology skills, such as observation and drawing from Nature. Alongside the growing technology is a resurgence and a strong need for complementary measured, meditative arts and drawing practice. With this realization, the paradigm of STEAM (science, technology, engineering, art, and math) has become colloquially popular. However, despite the use of “art” in science education and even the presence of artists in laboratories, the historical drawing biology approach has not been revisited, developed further, explored, or practiced in any rigorous way. This is a significant oversight in biological science education, considering that scientists of the past made huge leaps in their iii discoveries using simple technologies and drawing. This genuine unification of biology and drawing is generally not a domain that professional or academic artists or educators can easily address. It requires a deep understanding and intimate relationship with Nature and biological systems. As an authentic merger, it is content-heavy and skill-dependent. Developing a drawing-based model for biology is essential and, perhaps, best undertaken by biology sectors. My interest in this dissertation has been the synthesis that occurs within the learner or researcher of this amalgamated domain. It has not been developed or taught as a model of scientific inquiry today and does not exist in the science or biology curriculum. Yet, it is the core of the visual arts and visual STEAM-based experiences, which assert that they employ the visual arts to enhance biology education. To reveal the potential of the drawing discovery process, I have examined the multidimensional history of drawing for biology and visualizing biological mechanisms. Also, I have developed artistic-narrative methods, retaining the essence of the past and applicable in modern biology courses of today. These efforts address the deficit of a foundational visual skill set, which is the focus of this work. / Biology

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.

Japan is one of the world’s 34 biodiversity hotspots, according to Conservation International (CI). The methods used by various organisations to define priorities differ, however, and all have weaknesses when trying to identify hotspots at finer resolutions. The goal of this thesis is to investigate how biodiversity hotspots in Japan could be revealed and mapped in order to encapsulate conservation elements of biodiversity in practical ways and at various scales. Bioquality is a term that emphasises the concentration within a community of elements of biodiversity with high conservation value. It evaluates the global rarity and taxonomic distinctiveness of plant species or infra-specific taxa using four Star categories. At a plant community level, the Genetic Heat Index (GHI), which is a standardised global range size rarity score, is calculated using weighted Star statuses of species in the community. Bioquality hotspots are assessed here for the first time for the flora and vegetation in Japan – and for temperate Asia – by categorising the Japanese flora into Stars and by applying GHI to survey data and literature-based sources. Keys to Stars are developed for the Japanese flora, with adjustments for variability in species geographic range size information and for taxonomic relatedness. A Flora of Japan (FOJ) database was compiled as a BRAHMS database, containing 8,262 accepted names (30,656 taxon names in total, including synonyms) in 258 families – the first full database of Japanese vascular plants. A total of 7,145 taxa are assigned Stars; from the rarest to the widespread class, there are 884 Black, 756 Gold, 833 Blue, and 4,672 Green Star taxa, confirming that Japan as a whole contains a high proportion of globally rare taxa (23% taxa in Black or Gold). A protocol for calibrating the weight of Stars based on species geographic range is developed based on fine-resolution distribution maps within Japan and coarse–resolution Taxonomic Database Working Group (TDWG) code information. The protocol optimises calculation for temperate regions. The first ever bioquality hotspot maps of Japan are produced using two independent data sources on species distribution at national level: 1) 50 botanical prefectures using 4,830 species from the FOJ database; 2) 1,418 Horikawa ‘geoquadrats’ (0.1° latitude by 0.15° longitude grid) maps covering 829 species. The Ryukyu Islands and Ogasawara Islands are identified as bioquality hotspots, and high mountain ranges in mainland Japan are predicted to contain areas potentially high in GHI; the spatial patterns of GHI are generally concordant between maps of different resolutions. These findings highlight that bioquality assessment can be applied meaningfully at various spatial resolutions. Using field sampling data and existing literature, three study sites are further investigated on a local level: 1) the satochi-satoyama landscape, the current national priority area for biodiversity conservation; 2) various vegetation types of Okinawa-jima Island, the Ryukyu Islands; and 3) the Utaki sacred groves within the predicted hotspot of the Ryukyu Islands. The Ryukyu Islands are confirmed to contain bioquality hotspots within many individual sites, while there was generally low GHI across the satochi-satoyama landscape. The field study outcomes, together with a gap analysis of the existing coverage of protected areas, highlight three important points that are directly relevant to national biodiversity conservation planning: 1) the Ryukyu Islands urgently need newly designated protected areas; 2) the satochi-satoyama landscape conservation should redirect its focus on cultural benefits to the public; 3) the existing protected areas, particularly on mountain areas, need re-evaluation in terms of upgrading their status in light of the bioquality assessment.

Global environmental change fundamentally affects plants and their interactions with other species, and this has profound impacts on communities and ultimately ecosystems. In order to understand the mechanisms involved, we need to elaborate on the combined effects of different global change drivers on multiple levels of plant organization, including the biochemical level (production of defence compounds), the whole organism, the population, and the plant-herbivore interaction level. This thesis investigates (1) the combined effects of factors related to climate change and habitat fragmentation on Brassica nigra and (2) the effects of Zn soil pollution on the heavy metal hyperaccumulator Noccaea caerulescens at these different levels. Common garden and greenhouse experiments with B. nigra applied drought stress and elevated CO₂ to examine climate change impacts, while crossing treatments (inbreeding and between-population outbreeding) were used to investigate habitat fragmentation effects. Heterosis was lost under drought stress, and there were several interactive effects of the experimental treatments that varied within and among populations. In a greenhouse experiment with N. caerulescens, plants were grown on soil with different amounts of zinc. Plants had greater herbivore resistance when grown on Zn-amended soil, and invested more in herbivore tolerance when grown on soil without added Zn. In general, the results indicate that factors related to global environmental change have complex and interactive effects on different levels of plant organization. The findings are discussed in terms of their implications for ecology, evolution and conservation.

The relative contributions of biome history and geological setting to historical assembly of species richness in biodiversity hotspots remain poorly understood. The tropical Andes is one of the world’s top biodiversity hotspots, and with its diverse biomes and the relatively recent but dramatic uplift, the Andes provides an ideal study system to address these questions. To gain insights into the historical species assembly of the tropical Andes, this study focuses on investigating patterns of plant species diversification in the Andean seasonally dry tropical forest (SDTF) biome. Three plant genera are used as study groups: Amicia (Leguminosae, Papilionoideae), Tecoma (Bignoniaceae), and Mimosa (Leguminosae, Mimosoideae). Species limits are re-evaluated to enable dense sampling of species and intraspecific diversity for phylogeny reconstruction for each group. Time-calibrated phylogenies for Amicia and Mimosa are presented and used to determine patterns of species diversification in time and space. For Tecoma, incongruence between nuclear and chloroplast gene trees precludes straightforward estimation of a species tree and this incongruence is attributed to possible reticulation caused by hybridization. Divergence time estimates and patterns of diversification for Amicia and Mimosa are compared with other Andean SDTF groups (Cyathostegia, Coursetia, Poissonia; Leguminosae) using isolation by distance and phylogenetic geographic structure analyses. Consistently deep divergences between sister species and high geographic structure across all five groups suggest that Andean SDTF lineages have persisted over the past 10 million years (My) with high endemism driven by dispersal limitation, caused by geographic isolation, following the most recent episode of rapid mountain uplift 5-10 My ago. This prolonged stasis of the Andean SDTF biome is in line with Miocene fossil and paleoclimate evidence. Finally, wider analyses of the contrasting evolutionary timescales of older SDTF and more recent high-altitude grassland diversity suggest that the exceptional plant species diversity in the Andes is the outcome of highly heterogeneous evolutionary histories reflecting the physiographical heterogeneity of the Andean biodiversity hotspot.