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Restored wetlands, overgrown industrial sites, re-natured rivers, protected exclusion zones, abandoned farmland, and a host of new and returning animals including wolves, lynx, European elk, konik ponies and Highland cattle now feature in the rewilding landscape of the Oder Delta. Rewilding is a function of deliberate efforts by conservationists to facilitate natural processes, alongside myriad other social, economic, ecological and geomorphic factors. The relative insignificance of rewilding actions designing and managing nature in the Oder Delta prompts closer inspection of why rewilding happens here and what rewilding might entail more generally. Key drivers are identified through a critical biogeography of wildlife in the Oder Delta: How their distributions and movements are affected by a rich history; how individuals and species experience and shape rewilding futures; and how biopolitics governs animals' lives whilst occasionally offering them greater autonomy to rewild. An exploration of rewilding-positive forces is augmented by analysis of 'the business of rewilding'. Organisations operate in a competitive bioeconomy in which their aims and strategies must adapt to make rewilding pay and so the concepts of rewilding they proffer change. The Oder Delta offers an example of European rewilding in process where the effects of top-down nature conservation are largely absent on the ground and wildlife returns are somewhat serendipitous, challenging us to think beyond popular notions of rewilding as ecological restoration. On the other hand, rewilding cannot be explained away as nature 'filling the gaps'. Through developing a critical biogeography, distinct but interconnected political, ecological, social and economic processes emerge which begin to offer some explanations for why specific natures are appearing in specific places, in only some cases with associated conservation agendas.

Global change is putting unprecedented pressure on plants to adapt or migrate to avoid extinction. Studying the past responses of plants to environmental change can shed light on the potential evolutionary outcomes and sensitivity of species to future environmental change. These processes are especially relevant to highly diverse, evolutionarily rich, and ecologically vulnerable alpine ecosystems. My PhD aims to narrow the uncertainty about how plant lineages with a range of lowland and alpine species will be impacted by global change by studying the historical biogeography, trait and species diversification, and ecological strategies of alpine species in a phylogenetic framework. Chapter 1 reviews current knowledge about the relative roles of migration and adaptation in plant responses to climate change and how historical biogeographical and evolutionary modeling provide novel insights to these questions. Chapter 2 applies recent developments in sequencing methods to construct a new, near-complete phylogeny of a diverse species radiation, New Zealand Veronica, also addressing questions about how to resolve difficulties in reconstructing phylogenetic relationships in recent, rapid radiations such as Veronica. This group serves as an important case study for further evolutionary questions about the relationships between habitat, species diversity, and environmental change. Chapter 3 estimates the contributions of in situ cladogenesis (i.e., the formation of new species) and colonization from lowland habitat in generating mountain diversity in Veronica. Further, the chapter explores the importance of niche adaptation and divergence in contributing to cladogenesis, and presents a general, conceptual model to understand how mountain diversity accumulates. Chapter 4 compares the potential range and niche change required for plant species to respond to future climate change relative to the change undergone since the mid-Holocene. It also determines which niche traits can predict "winners" and "losers" under climate change. Chapter 5 discusses the main findings of the thesis and ends with proposed avenues for future research.

This dissertation statistically investigated putative biotic and abiotic drivers of ecological characteristics over the spatial scale of ocean basins and temporal scale of millennia to millions of years. For three fundamental hypotheses in evolutionary ecology, I compared patterns of natural experiments from the fossil record against expectations from theory. The first empirical study appraised the hypothesis that competition restricts geographic distributions at the species level, and thus taxa are more widespread when in the presence of fewer competitors, such as after mass extinction events. Contrary to the prediction of competitive exclusion, brachiopod and bivalve distributions were invariant to inferred biotic pressure, while habitat type and lineage age had detectable effects on range expansion or contraction on the scale of geologic stages across the Phanerozoic. The second study estimated the degree to which plankton modulate thermal preferences vs. migrate in response to glacial-interglacial climate fluctuations. Species conserved abiotic niches over the Middle-Late Pleistocene study interval, suggesting marine species will track preferred environments rather than adapt to Anthropogenic climate warming. The final study explored relative niche change within lineages vs. across an evolutionary tree of macroperforate planktonic foraminifera. The stark stasis observed within lineages could suggest niches evolve primarily during speciation, but any signal of such punctuated equilibrium was undetectable statistically with the small phylogenetic tree and large variance within and between species. Together, these results add perspective to longstanding debates about the scaling of population- to species-level ecology and micro- to macro-evolution.

Tropical rainforests are the most diverse terrestrial biome, but their origins remain incompletely understood. Detailed analyses of the temporal and spatial context of the evolution of old and species-rich tropical rainforest lineages have potential to yield novel insights. However, only few such analyses are currently available. The palm subfamily Calamoideae is proposed here as an appropriate study system to address this knowledge gap. It has a rich fossil record, comprises 555 species, and has a pantropical distribution with the centre of diversity in the Asia-Pacific region. There is a general understanding of its taxonomy, phylogeny, and distribution, but species-level relationships, divergence times, and biogeographic history of the subfamily are known only in vague outlines. Here, three steps were undertaken to realise the full potential of the Calamoideae for providing new insights into the origins of tropical rainforests. First, targeted sequencing of 971 genes of 75 species was conducted, resulting in a robust phylogenomic framework of the Calamoideae. Second, sequencing was expanded to 653 calamoid specimens representing 502 species (90%) of the Calamoideae, resulting in 381 species (68%) in the final species-level phylogeny after data filtering. Divergence times were estimated based on four dating strategies, indicating an Early Cretaceous age of crown Calamoideae but an Oligocene and Miocene origin of most extant species. Finally, ancestral ranges and dispersal patterns were inferred for the Calamoideae in the Asia-Pacific region following the testing of 198 biogeographic models, showing that the subfamily reached its broad distribution during the Oligocene and Miocene convergence of Australia and Asia, and that migration pathways closely followed a stepping-stone model with dispersals out of the centre and into the periphery of the Asia-Pacific region. This work represents the largest densely sampled and dated molecular phylogeny of any major pantropical rainforest lineage to date and elucidates the biogeographic history of a characteristic component of the tropical rainforests in the Asia-Pacific region in unprecedented detail. It is hoped that it will serve as a detailed framework for future comparative analyses.

Accurately demarcating species distributions has long been at the core of ecology. Yet our understanding of the factors limiting species range limits is incomplete, especially for tropical species. Human-driven threats to the survival of many taxa are increasing, particularly habitat loss and climate change. Identifying distributional range limits of at-risk species can thus inform spatial conservation planning to mitigate these threats. The harpy eagle (Harpia harpyja) is a large raptor distributed across Neotropical lowland forests, from southern Mexico to northern Argentina, currently threatened by habitat loss and persecution. Coupled with climate change, harpy eagle distribution may contract or shift leading to uncertainty on its future conservation. Here, I use point process regression models and ordination to identify harpy eagle environmental range limits and recommend spatial conservation planning measures for the species. I propose a revised range size 11 % smaller and an Extent of Occurrence 26 % less than the current estimates. By including biotic interactions in model predictions, I show that prey resources are more important for limiting harpy eagle distribution than climatic conditions. When compared to crested eagle (Morphnus guianensis) distribution, the harpy eagle's primary competitor, both species shared identical habitat resource space, with only subtle differences in distribution. Range-wide habitat use indicated that harpy eagles prefer areas of 70-75 % evergreen forest cover, low elevation and high vegetation heterogeneity, but avoid cultivated land, mosaic forest and complex topography. The current Important Bird and Biodiversity Area (IBA) network covered 17 % of medium to high harpy eagle habitat exceeding the protected area target representation (10 %). Under a future high emissions climate change scenario, range size was predicted to decrease by 14.4 % by 2090, with the IBA network covering 14 % less of its current coverage. Despite its large range, the harpy eagle has specialized habitat requirements and would benefit from targeted conservation measures based on spatial models in order to maintain viable populations.

Biophysical models have become the 'go-to' tool for predicting the dispersive trajectories of planktic marine organisms, and are used to design Marine Protected Areas (MPAs), identify pathways of invasion, and understand metapopulation dynamics and biogeography. Yet, despite this relatively long history of development, continued technological advancement and increased usage, models continue to often fail to predict patterns in nature. As biophysical models are able to accurately predict the dispersal of abiotic particles, it is argued that it is how we incorporate larval behaviour (sensu vertical swimming) in models that may be decoupling predictions of dispersal and species distribution patterns. Yet, despite the recognised importance of vertical distribution/position to dispersal by advection, especially in smaller organisms, there is currently no general consensus of how, what, and when behaviours can and should be included in models, perhaps because the drivers of larval behaviour are inherently complex and as yet, not fully understood (Chapter 1). The typical approach is to parameterise behaviours as 'rules' based on laboratory observed responses to cues, but it this approach appropriate given the complexity of larval decision-making in the presence of multiple cues in nature in comparison to single cue responses in controlled environments? In Chapter 2 I explored the movements larvae must undertake to achieve the vertical distribution patterns observed in nature. Results suggest that behaviours are not consistent with those described under the Tidal Vertical Migration (TVM) hypothesis, instead, showing a need for swimming speed and direction to vary over the tidal cycle -- with upward swimming needing to be 2.5x faster than downwards swimming and a change in direction from upwards to downwards needing to occur around the midpoint of the flood tide - and low model compatibility during the ebb tide. Next, I looked to identify the environmental drivers of larval vertical distribution during the ebb tide, where the model compatibility of Chapter 2 was low. Explored external drivers (density, salinity, temperature, turbulence) explained very little of the vertical distribution patterns of the larvae, however, results suggest differential usage of environmental cues based on ontogenetic stage, and vertical distribution patterns observed differed from previous observations of a similar species at a different location. Finally, I presented a framework for assessing how behavioural parameterisation can influence dispersal trajectories in marine systems (Chapter 4), comparing a novel approach of reverse engineering larval swimming from in-situ observations (Chapter 2: REVM behaviours) against simulations adopting passive dispersal, and particles attributed a tidal vertical migration (TVM) signature. Results highlight how the implementation of behaviour within biophysical models can lead to fundamentally different dispersal outcomes, and specifically, that the inclusion of vertical migration behaviour is a mechanism that significantly reduces dispersal distances, but depending on the approach to implementation can lead to fundamental differences in dispersal direction. This thesis makes significant steps towards improving the parameterisation of behaviour within dispersal models by considering larval movement as a manifestation of behaviour influenced by the larva's in-situ environment. The methodologies and analytical techniques designed and applied within the data chapters can be applied to any species with a planktonic dispersal phase in any location, and provide an important step towards improving the biological 'realism' of behavioural parameterisation in dispersal models in the absence of an understanding of the complex drivers of active larval movement.

Antarctica has long been isolated from its nearest landmasses and has been at least partially glaciated for the past ~35 million years. This long-term isolation combined with the fragmentation of habitats creates a unique environment for the examination of biogeographic patterns. Previously it was believed that the repeated full glaciation of Antarctica wiped out the pre-existing terrestrial fauna and flora and that the continent was, therefore, subsequently re-colonised after periods of glacial retreat, such as from the particularly extensive Last Glacial Maximum. However, recent molecular studies of a variety of taxonomic groups have shown that much of the current terrestrial life found on the continent is generally ancient and must have survived these glaciation events. The main body of Antarctica (East or continental Antarctica) and West Antarctica and the Antarctic Peninsula show differing geological histories and distinct biogeographic patterns in a variety of invertebrates including mites, springtails and nematodes, indicating distinct evolutionary histories. However, despite tardigrades being the most common and widespread invertebrate within Antarctica there has been limited study of their Antarctic biogeography. This thesis set out to investigate the evolutionary and biogeographic patterns of two eutardigrade species (Acutuncus antarcticus and Mesobiotus furciger). At the initiation of this study, A. antarcticus was believed to be a pan-Antarctic species, with a Gondwanan distribution, and M. furciger a globally common taxon and a Southern hemisphere species with a widespread Antarctic distribution. Individuals were sampled that originated from multiple locations across Antarctica. These individuals were then used to document a range of morphometric characters and underwent molecular extraction targeting the three gene regions of 18S, 28S and COX1. Further sequence data were added from GenBank. Phylogenetic analyses using both Maximum Likelihood and Bayesian methods showed that both species are likely to be species groups, with highly distinct lineages in the maritime and continental Antarctic regions. The levels of divergence detected strongly support cryptic speciation. This conclusion was further supported by morphological analyses, which identified significant differences between material sampled from each of these regions. Ancestral state and molecular clock analyses showed that both of these species groups had ancient Antarctic origins, requiring long-term regional survival within Antarctica, consistent with patterns identified in other invertebrate taxa. Morphological comparisons between individuals within single genetic clades obtained from different habitats also identified significant differences, supporting phenotypic plasticity in response to environmental conditions. This finding, not noted previously in tardigrades, has important taxonomic implications, as species identification relying on morphological characters alone may now result in miss-identification.

My thesis explores how the information content of fossil Glires (rodents + rabbits) effects phylogenetic reconstruction and the implications for downstream analysis and interpretation. The first two chapters take a detailed look at the phylogenetic signal contained within fossil Glires, while the third and fourth chapters put interpretation of fossils into practice through analyses of phylogeny, biogeographic history, anatomy and geometric morphometrics. In the final chapter, I discuss the importance of my biogeographic, anatomical and phylogenetic results within the context of Glires evolution. I also recommend the inclusion of fossil data in total-evidence approaches where possible and give suggestions for future work.

The aim of this study was to develop survey methodologies to examine marine invertebrate communities inhabiting the shallow benthic and intertidal regions of the Falkland Islands, of which little was previously known of their diversity and distribution. A better understanding of the factors influencing shallow benthic community structure has been presented. From surveys of a Macrocystis kelp forest, spatial scales (depth) were found to influence benthic invertebrate communities more than temporal scales (season). Hermit crab Pagurus comptus and Spirorbid annelids were found to be drivers of the community variation. By combining DNA barcoding techniques with occurrence data from open access databases, the Falkland Islands exhibited the greatest taxonomic distinctness of algae in the southern South Atlantic, which can be attributed to time of deglaciation at the end of the Last Glacial Maximum. The first Southern hemisphere distribution of Pylaiella washingtoniensis was recorded. The first description of zonation of the intertidal zone has been reported, an examination across spatial scales determined that the north-west of the Islands displayed the greatest diversity. Exposure was found to be a more influential factor in structuring communities than steepness. The first temporal littoral surveys were employed at a sub-Antarctic site in the east and cold-temperate site in the west of the Falklands to examine seasonal variation of benthic communities. Diversity was found to be greatest in Austral autumn and summer in the east and west, respectively. This work has addressed key gaps in the ecology of shallow marine communities of the Falkland Islands, contributing knowledge of biogeographical patterns of the wider region of southern South America.

Understanding better the impact of climate and changing environmental conditions on species and ecosystems has become one of the pressing research priorities. In addition, a need for more realistic field-based climate change experiments and focus on community and ecosystem functioning has grown in the last decade. The main aim of this PhD work was to study the effect of mainly temperature variation on species and ecosystems, by studying small-scale aspect (slope orientation) on both intertidal gullies and hedgerows/road verges in SW England. Such paralleled studies between terrestrial and marine ecosystem are sparse. I especially investigated (1) abiotic variations, (2) species distribution and richness, (3) species physiology (osmotic regulation) and phenology (gonad development), (4) leaf-litter decomposition as a key ecological process, and (5) comparison of conspecific species with different biogeographic origins, all between north- and south-facing aspects in both ecosystems. In both the intertidal and terrestrial ecosystems, south-facing slopes were much warmer (annual mean) and experienced more hot extreme events (more intense and frequent) than the opposite north-facing slopes; which corrobotate some future predictions by the IPCC. In addition, south-facing terrestrial slopes were significantly drier than the north-facing ones. Abundance and richness was greater on cooler north- than south-facing aspect on the rocky shore at all studied levels of organisation. Osmotic regulation did not seem to explain distributional change between two closely related limpet species, suggesting that other ecosphysiological or behavioural thermoregulation are factors involved. There was no variation with aspect in soil mesofauna, little variation in decomposition process, while greater differences were detected in terrestrial plants at most levels of organisation, except at the community level. This work showed that intertidal gullies and road verges are good systems to study the impact of temperature variations on ecosystem patterns and processes, and that aspect seem to buffer temperature extremes, offering refugia for cold-adapted and moist-tolerant species on the cooler and moister habitats (e.g. north-facing aspect). Aspect influenced species distribution at different levels (community, taxonomic, functional, species, and biogeographic origins), and differences between north- and south-facing aspects were more marked, however, on the intertidal than on land. In the future, slope aspect could be at interest for the conservation and management sector as a way to locally buffer global warming.

In the first half of the nineteenth century, the Himalaya were finally being recognised as the highest mountains on the globe. Simultaneously, they were becoming the insecure northern frontier of the East India Company's burgeoning Indian empire. This thesis examines the scientific, political and imaginative understandings of the Himalaya that emerged from this context. It traces two overlapping sets of arguments through the mountains. Firstly, it examines the laboriousness of scientific practice in the high spaces of the Himalaya, and the inherent dependency of European surveyors and naturalists on pre-existing networks of labour and expertise. Secondly, it details the role of global comparison in the rise of verticality as a framework for understanding both human and nonhuman worlds. The thesis consists of five thematic chapters, each of which deals with a different type of science: measurement, physiology, geology, botany, and biogeography. By addressing a range of interrelated sciences rather than focusing on only one, it becomes possible to explain how the mountains became both spaces and subjects of scientific practice. Methodologically, the five chapters do so by examining the practical aspects of doing science in remote and often topographically challenging locations. They concentrate especially on the moments that instruments, bodies and practices broke down, which are revealing of the social relationships that underpinned the knowledge they produced. A close focus is also maintained on everyday interactions between travellers and their guides (especially Bhotiya, Tartar, and Lepcha), which often highlight the limits of imperial mastery. Tracing the reconfiguration of these networks and practices ultimately reveals the many ways that the mountains were rendered as marginal spaces in this period in relation to lowland norms. More broadly, this thesis demonstrates the value of using geographical features as sites and scales for histories that transcend traditional national and area studies framings. By placing mountains at the centre of the analysis, it shows that travellers in the Himalaya were constantly measuring their experiences against expectations arising from the Alps and the Andes. It thus offers a methodology for examining the formation of what were inherently both sciences of the globe and global sciences in practice. At the same time, it shows that these global comparisons could be contradictory, often only adding to scientific and imperial uncertainties. Ultimately, this thesis thus argues that we need to pay attention to disconnection as much as connection in the making of supposedly global categories in the nineteenth century.

This thesis investigates the long term biogeographic factors which may have contributed towards subspecific variation within modern populations of the lion (Panthera leo) and tiger (Panthera tigris). Present day morphological variation in both species is examined in light of this biogeographical modelling, existing genetic research, and further analysis of the effects of phenotypic plasticity. This research provides a spatially explicit view of the recent evolutionary history of the lion and tiger, and examines their morphology using an unprecedentedly large sample of specimens, from both captive and wild populations, and with known geographic origins. These strands of investigation are important, as it can corroborate, or challenge existing phylogenetic and morphological studies, thereby lending support to or challenging the validity of subpecific taxonomy, management units and clines. This thesis is organised around two main research themes: 1) Biogeographical range shifts in the tiger and lion: Species distribution modelling techniques, incorporating palaeoclimatic models form the basis of understanding the changing ranges of the lion and tiger through glacial/interglacial and pluvial/interpluvial cycles of the Late Pleistocene and Holocene. Models are augmented with palaeoenvironmental evidence including fossil records, rock art and historical records and evidence of large scale stochastic events. Standard species distribution models are built upon by creating Global Environmental Zones and Strata, which aids in their descriptive power. 2) Phenotypic variation within modern populations: Morphology is examined using an unprecedentedly large sample of linear craniometric measurements of lion and tiger specimens. The effect of phenotypic plasticity is examined by comparing the vastly different environmental conditions found between captive and wild lion and tigers. This preliminary analysis supports the interpretation of wild variation by separating the influences of life history, from evolutionary history. Geo-referenced specimens of wild lions and tigers are used to examine geographical patterns and potential environmental influences on modern day variation, in light of the biogeographical modelling and phenotypic analysis. Core Findings: Whilst interglacial conditions have largely benefitted the population extent of the tiger, allowing northward and westward dispersal, the opposite is true in the lion where combined interglacial and interpluvial conditions have decreased their potential range. The biogeographical modelling broadly supports contiguous potential populations of both species through changing climatic cycles, except where sea level change has isolated the Sunda populations of the tiger. Such broad scale analysis may not fully account for narrow, yet enduring barriers and conduits to dispersal such as rivers. Significant phenotypic plasticity is found within lion and tiger skull morphology, which is likely related to differences in the mechanical properties of diet. Morphological variation between wild populations is largely determined by clinal size differences in the tiger, although the similarly sized Amur and Indian populations are separable on multiple skull parameters which likely relate to phenotypic plasticity. Clinal size variation occurs less strongly in the lion with no step change in size or shape between the northern and southern subspecies. The Asian lion population shows shape differences from populations in Africa, likely due to a combination of environmental effects on skull plasticity, and the recent population bottleneck of the Asian population.

The latent dsDNA viruses of the genus Phaeovirus (family Phycodnaviridae, clade Nucleo-cytoplasmic Large DNA Viruses; NCLDVs) employ genome integration in their brown algae hosts (class Phaeophyceae). The only phaeoviruses described in detail infected the order Ectocarpales, though Phaeovirus major capsid protein (MCP) occurs in 4 kelp (order Laminariales) species. Phaeoviruses are a major knowledge gap because brown algae are ecologically and economically important and have independently evolved complex multicellularity. This study aimed to investigate kelp Phaeovirus morphology, evolution, host range, distribution, host impacts, and genomics. Microscopy of Laminaria digitata gametophytes revealed particles and cell morphology typical of Phaeovirus infections. This putative Laminaria digitata virus 1 (LdV-1) infection, unlike the Ectocarpales phaeoviruses, often occurred in vegetative cells. L. digitata Phaeovirus symptoms were ~3 times more common in 18 versus 15 oC culture, but overall were uncommon and highly variable. No impact on gametophyte reproduction was observed. Broad-scale MCP PCRs and subsequent phylogeny identified 4 novel kelp phaeoviruses, placing the phaeoviruses of Ecklonia maxima, Ecklonia radiata, and Undaria pinnatifida in subgroup A, a Macrocystis pyrifera Phaeovirus in subgroup C, and a Saccharina japonica Phaeovirus in the novel subgroup D. Kelp phaeoviruses may follow the Ectocarpales Phaeovirus evolutionary trend of genome reduction (in subgroups B, C, and D versus A). Combined with all available data, 26 % of kelp were Phaeovirus MCP-positive. Genomic data from LdV-1 and 3 available kelp genomes contained Phaeovirus orthologs from the following putative, integrated phaeoviruses: LdV-1, Ecklonia radicosa virus (ErcV), Saccharina japonica virus (SjV), and Undaria pinnatifida virus (UpV). Subsequent phylogeny of 9 Phaeovirus core genes showed similar subgroups as before and non-core orthologs had implications for Phaeovirus evolution. For kelp phaeoviruses, this study has revealed a partial infection cycle, preliminary observations of viral symptoms, a broader distribution and host range, and evolutionary insights for both viruses and hosts.

The insular Caribbean is a prefect arena for the study of evolution and biogeography. One exceptional feature of the Caribbean islands is the colonisation of this archipelago by terrestrial mammal fauna. Historic changes in climate, colonisation of new species and the arrival of humans has greatly affected the endemic fauna of the Caribbean. Due to the extinction of much of the Late Quaternary Caribbean mammal fauna during the Holocene, many aspects of taxonomy in this group remains unresolved, preventing a complete study of evolutionary questions surrounding speciation, colonisation and extinction and critically, hindering the conservation of endangered species. This study has incorporated three groups of endemic Caribbean mammals: eulipotyphlan insectivores, rodents and primates, in order to investigate patterns in colonisation and evolutionary histories. Advanced techniques in extraction and sequencing of degraded or ancient DNA were utilised as part of this study in order to successfully able to extract and sequence DNA from museum and zooarchaeological specimens, despite the high degradation indicative of DNA from tropical regions. This study has found that whilst the Caribbean is home to ancient relic species, the islands are also hotspots for the generation of new species, as shown by the recent intra-island speciation of Hispaniolan Nesophontes species. This study has also been able to demonstrate patterns of insular evolution including accelerated evolution and the generation of unusual morphology, both exhibited by the Jamaican primate Xenothrix and extinct caviomorph rodents. Colonisation histories differ between groups, but both rodent and primate taxa looked at as part of this study colonised the Caribbean via over water dispersal during the mid-late Miocene, a period of low global sea level, when a riverine connection may have facilitated faunal movement between the Caribbean and South America. Previous taxonomy in many of the species looked as part of this study were based on morphology and needs to be re-assessed in light of the results of this molecular analysis. This is particularly important for the living Cuban hutia in the genera Capromys and Mesocapromys where the conservation of declining populations is vital for the continued survival of these unqiue taxa.

There is ample evidence that climate change is impacting on phenology and it has been suggested that this may generate trophic mismatches. A key system for investigating phenology and trophic mismatch occurs in spring in temperate deciduous woodlands, where folivorous caterpillars and their predators, insectivorous passerines, are reliant upon ephemeral resources for reproductive success and survival. However, studies are primarily conducted within single-site, oak- (Quercus sp) dominated woodland and focus on a single caterpillar species, winter moth (Operophtera brumata), despite these passerines being habitat generalists with large geographic ranges. It remains to be seen whether insights gained from these studies can be generalised on the landscape scale across different habitats. In this thesis, I explore the extent to which geographic and habitat variation operates in this system and attempt to expand the system beyond a linear single-species food chain into a more biologically realistic multi-species food web. I also identify the most important environmental factors predicting the phenology of the passerines to allow better predictions of how their phenology could alter under future climate change scenarios. To address these questions, I established a novel 220km transect of Scotland incorporating 40 field sites that vary in elevation and the type of deciduous woodland habitat, monitoring six blue tit (Cyanistes caeruleus) nestboxes, tree and invertebrate phenology and abundance, at each site throughout the springs of 2014-16. Firstly, I assess how blue tit occupancy and productivity are affected by the variation in fine-scale woodland habitat, latitude, elevation and prey availability that exists along the transect (Chapter 2). I find that habitat variables strongly affect fledging success but not occupancy or clutch size, whilst occupancy exhibits biogeographic trends, revealing that the relationship between breeding decisions and outcomes differs among habitats and implies that it may be difficult to generalise results from one habitat to others. Next, I aim to identify the environmental aspects which play a role in regulating blue tit reproductive phenology by examining the ability of temperature, tree phenology, invertebrate prey abundance and photoperiod to predict nest initiation and laying dates (Chapter 3). I find that night-time temperature in early spring is the most important predictor of both nest initiation and lay date (slopes ~ -3days/°C) and I suggest that this supports the hypothesis that temperature acts as a constraint on timing rather than a cue. Invertebrate abundance is also a positive correlate of lay date, possibly allowing fine-tuning of timing. This knowledge provides clearer foundations from which to predict future phenological change and possible trophic mismatch in this system. There is the potential that the apparent effect of temperature on blue tit reproductive phenology is indirect and mediated by diet, which is largely undescribed in the period prior to breeding. Therefore, in Chapter 4 I examine how blue tit diet varies across habitat, geography and time, and whether there is a dietary cue utilised to initiate breeding phenology, using data from metabarcoding faeces collected from nestbox-roosting adults in early spring. Geographic variation in diet is substantial, with high site-to-site dietary turnover (β-diversity), as well as high turnover along the elevational and latitudinal gradients studied. Dietary α-diversity (richness) is unaffected by geographical variables, but increases over time, with significant pre-breeding dietary increases in Lepidoptera and Hemiptera signifying a possible cue. In addition, these data provide the most comprehensive next-generation insights into the diet of a wild bird to date and identify 432 prey taxa. Finally, I analyse how biogeographic and habitat variables affect the phenology, abundance and diversity of caterpillars (Chapter 5). Host tree species’ varied significantly in their likelihood of hosting a caterpillar, with oak and willow (Salix sp.) the most likely. Biogeography had less effect on the likelihood of caterpillar occurrence, but elevation delayed peak date by 3.7 days/100m increase. There was also support for the spring caterpillar peak being dominated by a few key species, with over half of all caterpillars identified being of just three of the 62 total species, including winter moth. These findings contribute to understanding how the temporal distribution of caterpillars varies across habitats on the landscape scale. Taken together, the findings of this thesis reveal considerable geographic and habitat variation throughout this system, in both the composition of the food web and the impacts on blue tit productivity, demonstrating why caution must be exercised when extrapolating findings from one location or habitat to others.

The geographical distributions of many species are changing in response to rapid environmental change, and lags between the emergence and colonisation of new habitat areas are common. Given many species distributions are not at equilibrium with the environment, a greater understanding of the processes that underpin range expansion is required to predict where lags might emerge. Here I explore how population processes lead to emergent patterns of occupancy from the core to the edge of the species range. Working with water voles (Arvicola amphibius) in the UK, I carry out large scale surveys of a recovering metapopulation to explore the contribution of environment and the colonisation process in limiting range extent. I then use experimental translocations of water voles to quantify drivers of colonisation and local persistence, and the spatial scale over which these processes operate. I also explore the role of sociality and conspecific attraction in driving the formation of local populations at low landscape densities, and investigate the potential for between-individual variation in a behavioural trait to influence the formation of these spatial structures. Onward expansion was limited by the spatial scale of the colonisation process, and abrupt declines in occupancy at the range edge suggest that immigration increased the chance of local persistence. Social attraction led to build up of local populations, while more distant, equally suitable habitat area remained vacant. Using an individual based modelling approach, I then test the effect of different dispersal strategies on the rate of range expansion for biologically realistic mating systems. Mating finding requirements lead to slower expansion, though avoiding high density patches and mate-searching reduced these lags. Lags may emerge from processes across a range of spatial scales, though species translocations may offer a potential tool for mitigating these lags, and prevent substantial declines in geographical distributions.

Rocky plateaus are globally threatened ecosystems and the lateritic plateaus in northern section of the Indian Western Ghats/Sri Lanka Biodiversity Hotspot (NWG) are notable landscape features. The NWG are geologically distinct from and biologically isolated from the other two sections of the Western Ghats. The NWG is known to possess elevated levels of endemic flora their biotic relationships remain poorly understood. We present here the first quantitative multi-taxa comparative study of plateau fauna in the northern Western Ghats. Ants, water beetles and amphibians were selected for the comparison as they use different ecological resources from each other and at various times of year therefore may provide a wider representation of plateau usage. Distribution and endemism were expected to reflect distribution and isolation by plateau and inter-plateau environment related to elevational, latitudinal, climatic and land-use clines. The study explored patterns of amphibian, water beetle, ant and fungal distribution and sampling seasonal pools and terrestrial surfaces of 13 representative plateaus in western Maharashtra, with sites ranging from 67-1179 m and across 2° of (sub) tropical latitude. Distribution of all taxonomic groups was spatially non-random at all levels of organisation and across all spatial scales. At the macroscale assemblages differed significantly with climate related to elevation, latitude but at a local scale land-use and microhabitat availably had an impact. Ants displayed a large seasonal assemblage variation, responding to seed availability. Water beetles the ants (combined survey data) were the best surrogates for all taxa data with amphibians the weakest representatives. Infection by the fungal pathogen, Batrachochytrium dendrobatidis, was extensive but less intense below the escarpment. We report the first records of infection in 13 endangered and data deficient amphibian species in the Western Ghats. The plateaus of western Maharashtra have recently been recognised as fragile and threatened ecosystems most still lack adequate statutory protection. In the absence of peer reviewed comparative data, the importance of individual sites is difficult to demonstrate hampering evidence-based conservation decisions.

How long has the extant flora been present in the Antarctic? Glaciological reconstructions propose that most areas in Antarctica were covered by thick ice sheets throughout the Last Glacial Maximum (LGM; ~22-18 kya) as well as previous glaciations, suggesting terrestrial life must have been extremely limited during these periods. In contrast, recent biogeographic and genetic studies support most extant groups of Antarctic terrestrial fauna having survived past glaciations in situ. However, studies on the origin and age of the Antarctic flora remain sparse. Applying population genetic, phylogeographic and divergence time analyses I assessed the global biogeography, origin and age of several abundant Antarctic moss species, including: four Polytrichaceae mosses, characterised by having bipolar distributions, the most common (~45% of species) distribution pattern amongst Antarctic mosses; the globally widespread moss Ceratodon purpureus; the bank-forming moss Chorisodontium aciphyllum, also known for its old sub-fossils in Antarctica and long-term viability from revival experiments; and, lastly, the genus Schistidium, the most species-rich moss genus in Antarctica, including many endemic species. Genetic analyses revealed evidence of long-term (multi-million year) survival of plants in Antarctica (several species of Schistidium, Ceratodon purpureus, and possibly Polytrichum juniperinum). However, evidence for a likely more recent (< 100 ky) arrival of Chorisodontium aciphyllum was also found. Some species revealed multiple separate dispersal events to the Antarctic, suggesting the region may be less isolated for spore-dispersed organisms than previously thought. Evidence for increased genetic diversity in the northern maritime Antarctic compared to other regions point at it including potential refugial areas. Furthermore, genetic patterns revealed geographic features that enable and limit the connectivity of bryophytes globally as well as in Antarctica. This study suggests that, despite the harsh polar climate during glaciation periods, many bryophytes have had a much longer presence in Antarctica than previously thought.

Understanding the processes that have affected the diversification of herbaceous plants is fundamental to understand how flowering plants evolve, how ecosystems form and to predict the effect of climate change and geological events in plant communities. Aiming to create a strong phylogenetic framework where biogeographic and morphological hypothesis can be tested a higher level dated phylogeny of Gesneriaceae was produced. Gesneriaceae is a good study group as it has variable floral morphology, a broad distribution throughout the tropics and subtropics - represented in all non-arid tropical and subtropical hotspots of biodiversity. There are evident differences between lineages in the numbers of species, and it is comparatively well studied compared with other asterid families. In this study a consolidated taxonomic hypothesis of Gesneriaceae is suggested based on a genus level phylogeny, the ages of the main lineages of the family are presented, the effect of geological events are explored, the geographic origin of lineages are suggested and an insight into the effect of floral morphology on the evolution of the family is given. Limiting the taxonomic scope and focusing on a single family should help us better understand how flowering plants diversify.

The island of Sri Lanka’s exceptional biodiversity and enigmatic biogeography begs investigation, as the island is key in understanding the evolution of the Asian tropical flora. Since the Jurassic, Sri Lanka has been subjected to remarkable tectonic changes, thus its flora could have been influenced by that of a number of nearby landmasses, as well giving Sri Lanka the potential to have played a wider role in the assemblage of floras elsewhere. Firstly, as Sri Lanka originated as a fragment of the supercontinent Gondwana, part of its flora may contain Gondwanan relict lineages. There is also the potential for immigration from Laurasia after the Deccan Plate collided with it 45-50 Mya. Further, Sri Lanka may harbour floristic elements from nearby land masses such as Africa and Southeast Asia as a result of long distance dispersals, and in situ speciation has the potential to have played an important role in enhancing the endemic Sri Lankan flora. I tested the relative contributions of the above hypotheses for the possible origins of the Sri Lankan flora using three representative families, Begoniaceae, Sapotaceae and Zingiberaceae. These families represent both herbaceous and woody elements, and have high diversity across the tropics. Dated molecular phylogenies were constructed for each family. I used recent analytical developments in geographic range evolution modelling and ancestral area reconstruction, incorporating a parameter J to test for founder event speciation. A fine scale area coding was used in order to obtain a better picture of the biogeography of continental Asia. Amongst all the models compared, a dispersal-extinction cladogenesis model incorporating founder event speciation proved to be the best fit for the data for all three families. The dates of origin for Sri Lankan lineages considerably post-date the Gondwanan break up, instead suggesting a geologically more recent entry followed by diversification of endemics within the island. The majority of Sri Lankan lineages have an origin in the Sunda Shelf (53%). Persistence of warm temperate and perhumid climate conditions in southwestern Sri Lanka resembling those of Peninsular Malaysia and Sumatra could have facilitated suitable habitats for these massive dispersals from the Sunda Shelf region. Some trans-oceanic long distance dispersals from Africa (11%) are also evidenced, again these are too young to accept a hypothesis of dispersal during the Deccan Plate’s migration close to the African coast during the late Cretaceous, but occurred later during the Miocene. Further, some lineages of Laurasian origin (20%) are evidenced in the Zingiberaceae with ancestral areas of China and Indochina, which is congruent with a post collision invasion. Among the families tested, dispersals have occurred stochastically, one during the Eocene, six during the Oligocene, seven during the Miocene, two during the Pliocene and one during the Pleistocene. The highest number of dispersals occurred during the Miocene when a warm climate was prevailing during the Miocene thermal maximum. My results confirm that in situ speciation is an important contributor to the Sri Lankan flora. More rapid radiation of endemics has occurred during Pliocene-Pleistocene; two endemics in Begoniaceae, ten endemics in Sapotaceae and ten endemics in Zingiberaceae have evolved in situ during this period. Sri Lanka will have been subjected to expansion and contraction of climatic and vegetation zones within the island during glacial and interglacial periods, potentially resulting in allopatric speciation. As a conclusion, long distance dispersals have played a prominent role in the evolution of the Sri Lankan flora. The young ages challenge the vicariant paradigm for the origin and current disjunct distributions of the world’s tropical lineages and provide strong evidence for a youthful tropics at the species level. The thesis contains six chapters; first two are introductory chapters, then there are three analytical chapters, one for each family, and finally a summary chapter is provided. Each analytical chapter is written as a stand-alone scientific publication, thus there is some repetition of relevant content in each.

The plant family Gesneriaceae is represented in Sri Lanka by six genera: Aeschynanthus, Epithema, Championia, Henckelia, Rhynchoglossum and Rhynchotechum, with 13 species (plus one subspecies/variety) of which ten are endemic including the monotypic genus Championia, according to the last revision in 1981. They are exclusively distributed in undisturbed habitats, and some have high ornamental value. The species are morphologically diverse, but face a problem of taxonomic delineation, which is further complicated by the presence of putative hybrids. Sri Lanka and Indian Peninsula, represent the Deccan plate of the ancient Gondwanan supercontinent. The presence of a relict flora may indicate the significance of the geological history of the Deccan plate for the evolution of angiosperms. The high degree of endemism here, along with their affinities to the global angiosperm flora paints a complex picture, but its biogeographic history is still unclear. The pantropical family Gesneriaceae distributed in Sri Lanka and South India is therefore an appropriate study group in this context. Besides, the family itself has a complex but largely unresolved biogeographical history especially concerning the origin and diversification of Old World Gesneriaceae. Modern approaches for the taxonomic studies were applied, integrating morphological and molecular data. Multiple samples were collected for each species across their geographical distribution. Nuclear ITS and chloroplast trnL-F sequences for the taxa from Sri Lanka were used to generate regional genus phylogenies of all six genera, using maximum parsimony. The rate of evolution of the nuclear ITS region versus chloroplast trnL-F was varied greatly across the six genera studied. Molecular delimitations were mostly congruent with the classical taxonomy. Over 65 taxonomic characters were studied in detail to recognize synapomorphies for clades and taxa. A complete taxonomic revision of Gesneriaceae in Sri Lanka, including lectotypification, was conducted based on both, the molecular and morphological data. This resulted in the recognition of 14 species in the six genera, including one newly described species H. wijesundarae Ranasinghe and Mich. Möller. Henckelia communis and H. angusta were not supported molecularly as two separate entities but are recognized as two species because of consistent morphological differences between them. Henckelia humboldtiana is proposed to represent a species complex due to its highly variable and inconsistent molecular and morphological diversity and overlap with H. incana and H. floccosa; more research is needed here. National conservation assessments were conducted, and all 14 species were recognized as threatened. Biogeographic affinities of Sri Lankan Gesneriaceae were elucidated, generating a dated phylogeny using an existing matrix of four plastid gene regions; trnL-F, matK, rps16 and ndhF, amended by sequences generated in this study. The final combined matrix included 175 taxa including newly generated sequences for the 13 Sri Lankan taxa. Phylogenetic trees were generated using parsimony, maximum likelihood and Bayesian inference. Molecular dating was carried out using BEAST and ancestral area reconstruction using BioGeoBears. These analyses indicated that the six genera of Gesneriaceae arrived in Sri Lanka separately and sometimes different time periods. One lineage dated back to the early diversification of the subfamily Didymocarpoideae (generally regarded as the Old World Gesneriaceae), which occurred around the KT boundary, before the Deccan plate was connected to Asia.

Whilst the geographical range of species is a fundamental unit of macroecology and a leading predictor of extinction risk, the evolutionary dynamics of species’ ranges remain poorly understood. In some aquatic beetles, thermal niche has been shown to be related to both the relative range size and position of congeners but whether other physiological niche parameters play a role is unknown. Here, immunocompetence and metabolic plasticity were related to biogeography in these insects. Immunocompetence was first compared within a rare-common pair of Hydroporus species, finding species-specific immunity, which was affected by sex and acclimation time in the laboratory, with no clear relationship with rarity. This relationship was explored further in Deronectes species, whilst controlling for sex and acclimation time. Southern, narrow-ranging species had higher phenoloxidase (PO) activity, lower parasite load and antimicrobial peptide (AMP) activity that was stronger against Gram-negative Bacteria but weaker against Gram-positive Bacteria than their wider-ranging counterparts. As both of these studies found that PO activity did not positively correlate with encapsulation or AMP activity as reported in the literature, the pathway was investigated further in Tribolium castaneum. The data showed that the assumptions of the widely-used PO assay were violated, with differential activity between PO-driven reactions in melanin synthesis and different substrates used by larvae and adults. Future work should be wary of using the PO assay as a marker of potential melanin production and take into account the developmental requirements for melanin at different life stages. The relationship between metabolic plasticity and range was then assessed in Deronectes, finding that southerly species had more marked changes in glucose and protein content under elevated temperature stress than their northerly counterparts. Glucose content was also significantly positively correlated to lipid content, indicating that the energetics of species exhibiting differing range sizes may warrant future study. As the results from Hydroporus suggested that there may be trade-offs between immune defence and metabolism, the data on metabolic plasticity and immunocompetence in a sub-sample of Deronectes species were combined with thermal physiology, dispersal ability, body size and phylogenetic relatedness to assess which of these best explained variation in range size and position. Whilst variation in range extent and position were explained in part by thermal physiology, aspects of metabolic plasticity and immunocompetence also appeared to be important. This thesis provides one of the first indications that immunocompetence and metabolic plasticity may be related to geographical range and suggests parameters that may be worthy of exploration in other taxa.

Sandy beaches are often highly allochthonous, depending on external subsidies of carbon and nutrients. Despite this, sandy beach macrofaunal assemblages have received little attention regarding their response to enhanced primary productivity generated from coastal upwelling. This thesis investigates the influence of upwelling on macrofaunal assemblages over a variety of spatial and temporal scales. Spatially, four regions were examined across two biogeographic provinces to remove temperature as a confounding factor, and limit biogeography-specific effects. A nested hierarchical design enabled both large and small scales to be examined and generalities about upwelling effects across multiple areas to be considered. Sampling was conducted in two seasons, and over two years, to test the persistence of any effects. Biogeography and region had the strongest influences on macrofaunal biodiversity. Upwelling influenced macrofaunal assemblages in every region when analyses were conducted at the species level. However, the particular effect, positive or negative, differed among regions depending on local factors, and between the response variables, abundance and biomass. Coarser scales of taxonomy, feeding guild and developmental mode were investigated; however, the influence of upwelling generally became weaker and more varied, and occasionally disappeared. Seasonality was greater on the South Coast but was still important in some analyses on the West Coast. At the small-scale, variation within-beaches was lower than between beaches, assemblage structure remained stable over time, and consistent zonation was not present. The influence of temperature on filtration rate and oxygen consumption of Donax serra was investigated to test a driving mechanism for assemblage responses to upwelling. Feeding ability was significantly reduced at colder temperatures indicating an important factor which may be involved in determining assemblage structure. These results suggest that alterations to upwelling regimes predicted under climate change scenarios will impact sandy beach macrofauna, however the specific outcome will depend on multiple contextual factors.

Species diversity varies dramatically across the surface of the Earth. A key step in the accumulation of species diversity is the ability of species to coexist in biological communities. Thus, identifying the mechanisms underlying community assembly is a major challenge for ecologists seeking to explain patterns in species diversity and composition. Recently some consensus has been reached on the set of processes that influence community assembly: speciation, demographic stochasticity, niche-based fitness trade-offs among species and dispersal. However, it is unclear how the importance of a particular process changes with spatial scale, which interactions exist among processes at large spatial scales and the extent to which niche-based resource partitioning among species explains differences in diversity among communities. Neotropical birds offer an ideal opportunity to address these uncertainties because of their high diversity and the existence of detailed information on their evolutionary history and ecology. In this thesis, I first use trait and phylogenetic metrics of community structure to show that both habitat filtering and interspecific competition shape community composition at the scale of individual bird territories (~1-2 ha). Second, I use simulations of community assembly to show that trait-based metrics of community structure outperform phylogenetic metrics for detecting niche-based community assembly, and that both sets of metrics often have low power when multiple processes influence community composition. Third, taking a trait-based, species-level approach, I show that both habitat filtering and interspecific competition influence species occurrence at regional scales (~75000 km2), and interact with dispersal ability so that their effect on species occurrence is increased for species with greater dispersal ability. Finally, using a combination of trait- and isotope-based methods to quantify resource partitioning, I show that species' niche widths do not change and niche overlap is reduced at high compared to low species richness. Taken together, these results suggest that both habitat filtering and interspecific competition (i.e. niche-based processes) influence community assembly from local to regional scales. However, at least at regional scales, the degree to which these processes are important for determining the occurrence of any given species depends on that species's dispersal ability. They also suggest, based on niche-based interspecific competition influencing community composition, that differences in species richness among communities are in part explained by differences among sites in the breadth of available niche space, not by increased ecological specialisation or niche overlap.

The destruction and fragmentation of natural habitat is the leading driver of the current extinction crisis. As a result, a research area has emerged focused on studying ecology in islands of natural habitat surrounded by a sea of anthropogenic land uses, so called ‘habitat islands’. However, this research has largely been undertaken on small-medium scales, generally in single systems. Furthermore, many habitat island studies have used previous results and theory derived in the context of oceanic island research. Thus, this thesis aims to examine a variety of macroecological and biogeographical patterns using a large number of purely habitat datasets sourced from both the literature and my own sampling, with the objective of teasing out any general statistical patterns. The various macroecological and biogeographical patterns can be grouped under four broad headings: 1) species–area relationships (SAR), 2) nestedness, 3) species abundance distributions (SADs), and 4) species incidence functions (function of area). Overall, it was found that there were few hard macroecological generalities that hold in all cases across habitat island systems. This is because most habitat island systems are highly disturbed environments, with a variety of confounding variables and undesirable species (e.g. species associated with human land uses) acting to modulate the patterns of interest. Nonetheless, some clear patterns did emerge. In particular, it was found that the power model was by the far the best general SAR model for habitat islands. The slope of the island species–area relationship (ISAR) was related to the matrix type surrounding archipelagos, such that habitat island ISARs were shallower than true island ISARs. Significant compositional and functional nestedness was rare in habitat island datasets, although island area was seemingly responsible for what nestedness was observed. Species abundance distribution models were found to provide useful information for conservation in fragmented landscape, but the presence of undesirable species substantially affected the shape of the SAD. Species incidence function curves were found to vary across space for a given species, but not in any systematic manner. In conclusion, this thesis finds that the application of standard island biogeography theory to habitat islands is too simplistic. It is hoped that the results of this thesis will act as a catalyst for a more macroecological approach to habitat island research, and a starting point for the development of an integrated theory of habitat islands.

Understanding the evolutionary processes shaping species distributions in both marine and terrestrial environments has been a central interest among evolutionary biologists, biogeographers, and ecologists. Species richness in a given region is directly influenced by three key processes: speciation, extinction, and dispersal. Variations in the rates and timing of these processes are responsible for shaping diversity gradients such as those observed along latitudinal, longitudinal, elevation, and depth gradients. These variations arise from a complex interplay of biotic and abiotic factors, encompassing climatic stability, geographical barriers, trophic specializations, productivity, competition, and predation. Macroevolutionary studies using phylogenies can illuminate these evolutionary patterns and processes over extensive timescales and diverse taxonomic groups. Specifically, integration of comprehensive phylogenetic trees, derived from extensive taxonomic sampling of both extinct and extant species, with thorough genetic analysis, and supplemented by ecological and morphological datasets, can facilitate identifying factors influencing diversification and biogeographic trends across taxa. The overarching goal of my dissertation is to understand how extrinsic (e.g., formation of historical barriers, temperature) and intrinsic (e.g., life history processes such as feeding mode, dispersal ability) factors may have shaped the evolution of two charismatic groups of marine reef fishes. The first two chapters aim at examining Syngnatharia, an extraordinarily diverse clade (>660 species) that includes trumpetfishes, goatfishes, dragonets, seahorses, pipefishes, and allies. The third chapter focuses on fishes in the order Acanthuriformes, which comprises surgeonfishes, the louvar, and the moorish idol (87 species). Despite progress made in unravelling the relationships of these and other clades of disparate marine fish groups based on a handful of genetic markers sequenced from a few representative lineages, the vast majority of the species lack phylogenetic placement. Additionally, very few studies have looked at genes associated with phenotypic or ecological changes in reef fishes from a macroevolutionary perspective. To fill in these gaps, my research aims to examine the evolutionary history of these groups using state-of-the-art approaches, including phylogenomics, phylogenetic comparative methods, and phylogenetically-informed genotype-to-phenotype (PhyloG2P) comparative genomic approaches based on whole genomes. In my first chapter, I applied an integrative phylogenomic approach to elucidate the evolutionary history and biogeography of Syngnatharia. I collected genome-wide DNA sequence and geographic distribution data for 169 species to cover ~25% of the species diversity and all 10 families in the group, and complemented these datasets with paleontological and geological information. With these datasets I inferred a set of time-calibrated trees and reconstructed the ancestral ranges of the group. I then examined the sensitivity of biogeographic analyses to phylogenetic uncertainty (estimated from multiple genomic subsets), area delimitation, and biogeographic models. After accounting for these uncertainties, my results reveal that syngnatharians originated in the ancient Tethys Sea at the Late Cretaceous, 87 million years ago (Ma) and subsequently occupied the Indo-Pacific Ocean. Throughout syngnatharian history, multiple independent lineages colonized the Eastern Pacific (6–8 times) and the Atlantic (6–14 times) from their center of origin, with most events taking place following an east-to-west route prior to the closure of the Tethys Seaway between 12–18 Ma. These colonizations were facilitated by the long-distance dispersal ability of syngnatharians during their pelagic larval stages or through rafting, such as with sargassum-associated species, aided by oceanic currents. For my second chapter, I examined factors driving syngnatharians species richness along the longitudinal diversity gradient across oceans and assessed whether patterns of morphological diversity are congruent with this gradient. I increased the taxonomic sampling of syngnatharians from my first chapter to 323 species (50% of the species diversity) to test three non-mutually exclusive evolutionary hypotheses proposed to explain the longitudinal diversity gradient: time-for-speciation, center of accumulation, and in situ diversification rates. I estimated diversification rates and body shape disparity broadly across the group, considering biogeographic regions within all three major oceanic realms (Indo-Pacific, Atlantic, and eastern Pacific), as well as within the Indo-Pacific region. The analyses showed that the extensive diversity of syngnatharian species in the Indo-Pacific region primarily stems from ancient colonizations, leading to in situ speciation during the Palaeogene, shortly after the Paleocene-Eocene Thermal Maximum (PETM), and subsequent lineage accumulation during the Miocene coinciding with the initiation of the Indo-Australian Archipelago (IAA) rearrangement. Conversely, the eastern Pacific and Atlantic regions exhibit lower regional diversities, largely due to more recent colonization events and the onset of diversification, with most lineages in these areas emerging during the Miocene. These findings strongly support the time for speciation and center of accumulation hypotheses. My study also reveals that a significant portion of syngnatharian morphological diversity originated early in their evolutionary history within the Tethys Sea, followed by a gradual decline in subclade disparity marked by the emergence of multiple adaptive peaks, particularly in head morphology. This suggests that while high species richness exists, it does not necessarily correlate with high morphological disparity across various biogeographic contexts. All in all, colonization dynamics explain the longitudinal diversity patterns of syngnatharian fishes across marine realms while morphological similarities persist among them. In my third chapter, I examined the ecological drivers of trophic transitions among fossil and extant acanthuriforms as well as the genomic basis of these transitions. By combining genomic data for 80 extant species (~93% of total diversity) with morphological characters for 32 fossil taxa, I inferred total evidence time-calibrated phylogenies. Using these phylogenies, I reconstructed the diet of acanthuriforms and investigated the number of times the planktivory lifestyle evolved, along with the geographic location and timing of these transitions. The analyses indicate an origin of acanthuriforms approximately 64 Ma following the K-Pg mass extinction event, with at least seven documented transitions to planktivory from non-planktivorous lineages, followed by at least four reversals to non-planktivorous diets. While the earliest transitions occurred in the ancient Tethys Sea, the most recent ones happened within the Indo-Pacific region. I then evaluated the effect of the convergently evolved diets on acanthuriforms’ diversification, finding no significant effect as diversification rates remain constant across trophic guilds. However, transition rates are higher from planktivores to non-planktivores compared to the opposite direction. Diversification of planktivore species does appear to be influenced by cool past climatic temperatures, although there is also a confounding effect from phylogenetic signal. Despite ecological and morphological factors commonly driving this trophic specialization, the extent to which this adaptive convergence is caused by convergent changes at the molecular level remains understudied in reef fishes. Therefore, in this study I performed PhyloG2P analyses, using newly-generated chromosome-level (Acanthurus chirurgus) and short-read (45 species) genomes to identify genes under positive selection across planktivore lineages and along branches where a transition to planktivory occurred. We identified a total of 91 genes that underwent convergent positive selection in planktivorous lineages, along with three genes unique to planktivores. These genes are implicated in metabolic processes and adaptations in body shape, consistent with the repeated instances of convergence towards a pelagic environment, which are associated with planktivory and specialized morphological traits. In summary, my dissertation explores the evolutionary processes shaping the distributions of marine fish species, highlighting the pivotal roles of speciation, extinction, and dispersal in driving diversity across oceans. My research also underscores the importance of integrating data from both fossil and living species to obtain a more comprehensive picture of the evolutionary history of groups. Through comprehensive analyses based on genomic, ecological, and morphological data, I emphasize the need to address various factors generating uncertainty in macroevolutionary and biogeographic inferences. Furthermore, my findings contribute to our understanding of the evolutionary dynamics as well as genetic underpinnings of trophic transitions in marine fishes, shedding light on the adaptive mechanisms driving diversification. Overall, my thesis represents an important step towards understanding the evolutionary history of marine fishes by disentangling their diversification patterns in space and time.

This project used a variety of genetic markers to investigate the evolution and population genetics of hydrothermal vent fauna that were recovered from the Scotia Sea, in the Atlantic sector of the Southern Ocean. The origins of one of these species, an undescribed species of Kiwa sp. found on the East Scotia Ridge (ESR) and its constituent family Kiwaidae, a group of vent and seep-associated decapod squat lobsters (infraorder Anomura) was investigated using a concatenated nine-gene dataset and key divergences were dated using fossil calibrations. These results confirm earlier research showing Kiwaidae reside in the superfamily Chirostyloidea, but form a monophyletic clade with the non-chemosynthetic family Chirostylidae and not Eumunididae. Chirostyloid families diverged in the Cretaceous, although extant Kiwaidae radiated in the Eocene, consistent with many other chemosynthetic taxa that appear recently derived. The basal tree position of Pacific species (and the Alaska location of a likely stem-lineage kiwaid fossil) suggests kiwaids originated in the East Pacific. Within a Southern Hemisphere clade, the divergence between the southeastern Pacific K. hirsuta and a non-Pacific lineage (Kiwa sp. ESR and Southwest Indian Ridge kiwaids) is no earlier than 25.9 Ma, consistent with a spread from the Pacific into the Scotia Sea and beyond via now-extinct active ridge connections or mediated by a Miocene onset of the Antarctic Circumpolar Current (ACC) through a newly-opened Drake Passage. This project also investigated the population genetics of three undescribed species found at two vent fields ~ 440 km apart at either end of the ESR: Kiwa sp., a peltospirid gastropod and Lepetodrilus sp. limpets. Lepetodrilus sp. was also found at the Kemp Caldera, a submerged part of the South Sandwich Islands (SSI). Analyses of cytochrome c oxidase subunit 1 (COI) as well as microsatellite loci developed from Roche 454 sequence libraries revealed no differentiation along the ESR for all three species consistent with panmixia, or the dominance of non-equilibrium processes between vent field colonies within a metapopulation, possibly enhanced further by cold-induced arrested larval development. Despite apparent connectivity along the ESR, both COI and microsatellites revealed differentiation between ESR limpets and Kemp Caldera limpets ~ 95 km to the east, possibly owing to the hydrographic isolation of the caldera. Both COI and microsatellite diversity patterns were consistent with recent (< 1 Ma) demographic expansions for all three species (although the influence of selection sweeps on COI cannot be discounted); a pattern observed worldwide at vent communities and may reflect demographic instability over time as a consequence of the stochastic birth and death of vent colonies within a metapopulation. Different COI bottleneck ages between the three species (excluding the influence of possible selection) as well as the absence of kiwaids and peltospirids at Kemp, have been attributed to differences in life history, in particular larval morphology and presumed dispersal strategy. These results highlight the role of larval dispersal of vent fauna along active spreading ridges, both in maintaining vent metapopulations across vent colonies prone to stochastic birth and extinction in the short term, but also in the spread of taxa globally and the formation of biogeographic provinces. The likelihood that the three species presented here exist at vents east of the ESR and SSI, prompts further exploration along ridges in the South Atlantic, in order to investigate the effect of the ACC in enhancing gene flow and delineating biogeographic provinces.

The Cretaceous Period was a time of extreme greenhouse warmth and a time of major global events. Hence, the Cretaceous represents an interesting geologic time to study a biota that lived under a very different evolutionary context and climate dynamics compared to the present. This thesis examines the geographic patterns of plant biomes based on a global quantitative analysis of palaeobotanical evidence. The distribution, ecology, and composition of Cretaceous floras are assessed through the analysis of databases built from information found in museums, collections, electronic resources and literature published since the 1800s. Biogeographic analyses of Cretaceous woods reveal that araucarioid and podocarpoid conifers were globally codominant in equatorial regions during Early Cretaceous times while cupressoid conifers were most common in midlatitude. The analysis of pinoid wood reveals these conifers were mainly distributed at high latitudes and exclusively restricted to the Northern Hemisphere since the Cretaceous. Spatial analysis suggests that the loss of conifer forests was linked to the rise of co-occurring angiosperms, which spread and dominated high latitudes until the Late Cretaceous, somewhat latter than indicated by palynological studies. Biogeographic analyses of Cheirolepid conifers show a significant spatial correlation between the distribution of arid climate-sensitive sediments (evaporites and calcrete) and cheirolepid occurrences during the Early Cretaceous. In contrast, Late Cretaceous cheirolepids show a stronger correlation with sediments that indicate humid tropical environments (coal, kaolinite, and bauxite). This finding adds evidence to the fact that the presence of cheirolepid fossil does not exclusively indicate arid environments as previously thought. Biogeographic analyses of Cretaceous plants improve the knowledge of Cretaceous vegetation biomes and allow to investigate possible macroevolutionary patterns over extended spatiotemporal scales, offering a valuable quantitative comparison to integrate with computer climate models proposed for the Cretaceous. Furthermore, two putative Cretaceous woods were examined to clarify their age, provenance and affinity. Results show the valuable use of biogeography, taphonomy, wood anatomy and morphometrics as an essential tool for taxonomic revision of Cretaceous fossil material. An extensive taxonomic re-examination of problematic fossil samples is recommended in order to improve data quality to develop more accurate biome reconstructions.

Mechanisms for the generation of biodiversity in species-rich biomes such as rain forests remain unclear. Molecular phylogenies using DNA sequence data, calibrated with a temporal dimension offer a means of addressing this question, enabling the testing of different hypotheses on biogeographic histories and causes of diversification. Manilkara is a genus of trees in the Sapotaceae consisting of ~79 species distributed throughout the tropics (30 South and Central American, 35 African and 14 Southeast Asian). This species diversity in all major tropical regions of the globe makes it an ideal candidate for in-depth biogeographic studies. Maximum parsimony and Bayesian analyses of nuclear (ITS) and chloroplast (rpl32-trnL, rps16-trnK and trnS-trnFM) sequences were used to reconstruct a species level phylogeny of Manilkara and related genera in the tribe Mimusopeae. Manilkara, as currently defined, is not monophyletic due to the placement of three Asian taxa (M. fasciculata, M. dissecta and M. udoido), which are more closely related to the Madagascan genera Labourdonnaisia and Faucherea than to Manilkara s.s. and need to be re-circumscribed in a new genus. Letestua is nested in Manilkara and the genera Faucherea and Labourdonnaisia are not monophyletic. Nuclear and chloroplast datasets were mostly congruent, however, three instances of hard incongruence were demonstrated, suggesting chloroplast capture events. Bayesian analyses of ITS sequences using a relaxed molecular clock calibrated with fossils, focused on testing biogeographical hypotheses on the origin of Manilkara’s pantropical disjunct distribution and spatio-temporal diversification patterns on each continent. Mimusopeae, originated during the Eocene ~46-57 Ma and fossil evidence supports its existence in the boreotopical region of the northern hemisphere during this time. This suggests that the tribe may have evolved there and found refuge in Africa when Oligocene climatic cooling made higher latitudes uninhabitable for megathermal taxa. The subtribe Manilkarinae was resolved as ~42-36 Myo. These ages fall on the Eocene-Oligocene boundary and the crown node age coincides with the onset of Oligocene cooling and the closing of the boreotropical route. The genus Manilkara is estimated to have evolved ~36-33 Ma. The current distribution of the genus could not, therefore, have been the result of Gondwanan vicariance or migration through the boreotropics, but results instead support long distance dispersal as an important factor influencing the distribution of the group. Resolution along the backbone of the phylogeny is weak and the area of origin is, therefore, difficult to determine. However, all sister taxa to Manilkara are African and this suggests that the most likely explanation is an African origin for the genus with subsequent inter-continental dispersal during the Miocene. Manilkara spread from Africa to the Neotropics and Asia via at least three separate long distance dispersal events. A single lineage dispersed to the Neotropics ~27-21 Ma and spread across the Isthmus of Panama before its closure. Another lineage dispersed to Southeast Asia ~30-25 Ma from mainland Africa and subsequently diversified throughout the region. A third dispersal from Madagascar to the Sahul Shelf, occurred ~31-16 Ma in the M. fasciculata/dissecta/udoido lineage. In South America, diversification is consistent with both aridification and the rearrangement of drainage patterns in the Amazon basin as a result of Andean orogeny. The Atlantic coastal forest clade and the Amazonian clade of Manilkara split from one another ~14 Ma, at approximately the same time as the dry biomes of the Cerrado and Caatinga were forming between them. In Africa diversification coincides with Tertiary cycles of aridification and uplift of the east African plateaux. In Southeast Asia Wallace’s Line did not affect the dispersal of Manilkara. Instead, the limiting factor was the appearance of land in New Guinea ~10 Ma, which coincides with the dispersal and establishment of new taxa east of Wallace’s Line. Spatio-temporal patterns of diversification in Manilkara were compared to those of 34 other wet tropical genera which have intercontinental disjunctions. Ages of disjunctions ranged from the Eocene to the Pliocene, indicating that compilation of the tropical rain forest biome is a dynamic process which has been occurring throughout the Tertiary. Recent migration via long distance dispersal is a significant phenomenon in biome construction. Geo-climatic events have also been shown to be important drivers of diversification in all continental regions.

Molecular phylogenetic analyses of subtribe Senecioninae, based on combining sequenced ITS and trnL-F fragments from specimens collected in the field with sequences collected from GenBank, suggest the subtribe is monophyletic, as is Senecio s.str. (including Robinsonia), and suggest an expanded monophyletic section Senecio. Many Senecio species should be removed from the genus, as they are only distantly related to it, emphasising the para- or polyphyletic nature of Senecio as it is currently circumscribed. Area optimisation suggests southern Africa as a possible geographical origin for the genus and section. Harvey’s (1865) sectional classification of South African Senecio species (the only attempt to date to impose infrageneric groupings on these taxa), was tested for monophyly which, however, was not seen in the sections tested. A number of southern African species from Harvey’s sections are suggested for inclusion in an expanded section Senecio. A clade suggested as basal to sect. Senecio, consisting of Senecio engleranus and Senecio flavus, was found to be only distantly related to the section. Resolution of the two species within the clade was not evident; a comparative study was therefore made employing RAPDs, morphometrics and breeding experiments. The two proved to be distinct entities, both genetically and morphologically, although they remain interfertile, suggesting that intrinsic postzygotic barriers between them are weak, and that hybridisation – not found in the wild - is mainly prevented by prezygotic barriers. F1 hybrids created between the two were seen to have intermediate morphologies and RAPD profiles. A single F1 individual self-pollinated to produce a vigorous F2 generation, allowing preliminary surveys of pollen number, pollen fertility and pappus type. Pappus type is seen to be under the control of allelic variations in a single major gene, while pollen numbers and pollen fertility are seen to be under more complex genetic control.

Two molecular phylogenetic studies were undertaken to examine relationships within Myricaceae. Analyses of DNA sequences of the plastid rbcL gene, trnL-Fregion and nuclear ITS region showed the family to be monophyletic. In all analyses Canacomyrica, a monotypic genus endemic to New Caledonian that bears several distinctive features such as staminodes in the female flowers, fell into a well- supported clade sister to the rest of Myricaceae. Phylogenetic analyses of ITS and trnL-F sequence data, representing all genera and subgeneric groups, were undertaken using maximum parsimony and Bayesian methods. The following relationships were strongly supported: (Canacomyrica (Comptonia (Myrica, Morella))). The clade containing all species formerly considered to comprise Myrica s.l. was split into two strongly supported clades corresponding to Myrica s.s. and Morella; this finding strengthens the argument for recognition of these as separate genera. Within Morella, two clades corresponded to previously recognized subgenera. Molecular dating analyses were performed using Penalized Likelihood. Close correlations between lineage-specific diversification and major orogenic or climatic events were inferred. This study suggests that much of the diversity in Morella arose during the Neogene and seed-dispersal by birds has been a significant factor in determining the modem distribution. A study of the conservation status of Canacomyrica was conducted using field observations and data from herbarium specimens. This species was found to occur in just eleven fragmented localities: six outside protected areas and three threatened by mining or bush fires. IUCN Red List status of Endangered was recommended. The morphology and ecology of Canacomyrica was studied to enhance knowledge of this poorly known species and provide comparative data for use in a study of the morphology of the entire family. A new classification scheme with keys was presented including, for the first time, Canacomyrica. New combinations in Morella were recommended.

The Andean uplift is arguably the most important geologic event that led to the diversification of the richest biota in the planet. By the end of the Miocene, the Andes reached almost half their current elevation and their eastern slopes intercepted, condensed, and precipitated enough westward-moving moist air from the Amazon to cause the formation of montane forests. Later, climatic oscillations during the Pleistocene heavily affected the distribution of upper montane forests. Today, the upper belt of these forests, also known as cloud forest, possesses the highest levels of endemism in the world, however, the processes that drove this diversification are still poorly understood. To investigate these processes, I selected the blueberry tribe, Vaccinieae, that contains ~1,760 species mostly concentrated in the Neotropics and particularly abundant in the montane forests of the eastern Andean slopes. In chapter 1, I focus on a group of five endemic genera (Demosthenesia, Pellegrinia, Polyclita, Rusbya, and Siphonandra) that inhabit the cloud forest up to timberline at ~3000-3500 masl. I investigate if they share a single or multiple evolutionary origins by constructing the largest and most robust time-calibrated phylogeny of the tribe to date and performing diversification and historical biogeographic analyses. In chapter 2, I use a phylogenomic approach seeking to further resolve the relationships of the most recently diverged groups, Demosthenesia and Rusbya. Finally, in chapter 3, I explore the effects of Pleistocene climatic oscillations on the present geographic and genetic structure of the widespread blueberry species Demosthenesia mandonii, and attempt to locate areas that might have served as Pleistocene refugia. My results indicate that the five genera do not share a single origin, however their divergence dates are contemporaneous at ~6 Ma. At a larger scale, the Neotropical blueberries have multiple evolutionary origins, with a main radiation influenced by both the uplift of the Andes and Cenozoic temperatures. Lastly, the population analysis of D. mandonii, suggests a severe contraction of its range during the last glacial maximum followed by re-expansion towards the present, this species most likely survived the las glaciation in a single Pleistocene refugium located in the Urubamba valley (Cusco, Peru).

This thesis aims to reconstruct the phylogenetic and biogeographic history of gibbons, genus Hylobates. Phylogenetic relationships among gibbons are controversial. This study uses molecular and morphological data to resolve some of these controversies, and provides a new phylogeny for the genus. The estimate of gibbon phylogeny is combined with distribution data to reconstruct the biogeographic history of gibbons. In the first part of the study, original mitochondrial control region sequence data and published cytochrome b gene sequence data are analysed using maximum likelihood, parsimony and bootstrapping methods. Results of these analyses indicate a gibbon phylogeny which shows the following subgeneric relationships: Nomascus, Symphalangus and Bunopithecus are successively more closely related to Hylobates. A molecular clock is employed which suggests that the gibbon radiation dates to about 10.5 million years ago (Ma). In the second part of the study, craniodental and postcranial metric variables are analysed using multivariate statistical methods to investigate interspecific morphological variability. Multivariate statistical analyses across the gibbon skeleton show that the eleven currently recognised species form five distinct morphological groups. The metric data are further employed to investigate phylogenetic interrelationships among gibbons. These data are converted into discrete character states using segment and range coding. The re-coded data are analysed using parsimony and bootstrapping methods. These analyses indicate that gibbon skeletal metric data is phylogenetically uninformative at the species or subgenus level. In the third part of the study, three alternative methods of biogeographic reconstruction are employed: ancestral area analysis using irreversible parsimony, ancestral area analysis using reversible parsimony and dispersal-vicariance analysis (DIVA). Results of the DIVA analysis are combined with estimates of divergence dates, to propose a new pattern of radiation for the genus Hylobates. This analysis indicates that the gibbon radiation may have begun in Indochina around 10.5 Ma. Between 10.5 and 8.6 Ma gibbons radiated southwards to Sumatra. Subsequently, they differentiated into two types of gibbon on Sumatra, representing the subgenera Symphalangus and Hylobates. A third radiation approximately 7-8 Ma saw the dispersal of Bunopithecus into Burma, Assam, and Bangladesh. At around 3-5 Ma there was a second radiation of subgenus Hylobates, involving dispersal onto the islands of Borneo, Mentawai and Java. Between 0.3 and 1.8 Ma taxa in the subgenus Nomascus differentiated into Cambodia and Hainan Island. This study provides a novel reconstruction of the historical biogeography of gibbons. In addition, parsimony and likelihood analyses of molecular and morphological data sheds light on the controversial topic of hylobatid phylogeny.

Patterns in the distributions of species result from numerous ecological and evolutionary processes, including competitive interactions, evolved physiological tolerances, and the historical environmental fluctuations that have caused ranges to shift, expand, or contract over long time periods. For some groups of species, these processes have resulted in an elaborate diversification of traits. For other groups, however, such as woodland salamanders (genus Plethodon), closely related species may be phenotypically similar or even identical. It is less clear what drives the formation of such species, whether and how they maintain their identities and interact after initial divergence, and how such similar species might have evolved ecologically in subtle ways to differentially utilize the landscape. The Eastern Red-backed Salamander (Plethodon cinereus) is a small, fully terrestrial woodland salamander notable for its wide distribution and high phylogeographic diversity in the eastern United States and southeastern Canada. Most of its current distribution, however, was covered by ice sheets at the end of the Pleistocene, suggesting recent and rapid post-glacial expansion. It is not yet clear how P. cinereus colonized these landscapes, and what ecological characteristics made P. cinereus so successful in its range expansion compared to other species. Some studies comparing narrowly-distributed montane Plethodon to their lowland counterparts have suggested a combination of physiological specialization and competitive superiority of montane species relative to generalist lowland species such as P. cinereus, but it is unknown if this asymmetry applies to sets of lowland species outside of montane systems. In this dissertation, I explore the biogeography of woodland salamanders, with special attention to P. cinereus, at ecological and evolutionary time scales to uncover the processes that shape genetic diversity and species distributions. Chapters 1 and 2 concern the historical biogeography and evolution of P. cinereus, while Chapters 3 and 4 compare the habitat use of P. cinereus to two of its more broadly distributed relatives, the Northern Ravine Salamander (P. electromorphus) and the Southern Ravine Salamander (P. richmondi), to test if they have diverged ecologically, including multiple ecological scales. In Chapter 1, I used next-generation DNA sequencing to explore the phylogeographic structure and demographic history of P. cinereus, using the species as a model for the formation of incipient lineages of Plethodon. I identified several groups that diverged within the Pleistocene, yet I also found numerous and sometimes extensive regions of admixture between groups, suggesting a model of range fragmentation and fusion during incipient species formation. In Chapter 2, I focus on the most recent post-glacial expansion of P. cinereus, using DNA sequencing from range-wide samples to uncover the origins and routes of colonization. Results generally supported a southeastern coastal origin that expanded northward, westward into the Great Lakes region, and then a novel colonization route southward back into unglaciated areas. In Chapter 3, I used ecological niche modeling to test if niche differentiation between P. cinereus, P. electromorphus, and P. richmondi explains their broad distributional patterns. All species had estimated niches that were more different than expected by chance, and historical habitat suitability has fluctuated dramatically in the Holocene epoch, although I did not find strong evidence that climatic or topographic variables differentiated occurrences of P. cinereus and P. electromorphus within their overlapping distribution. Finally, in Chapter 4, I explore microhabitat differentiation between P. cinereus and P. electromorphus where they occur and interact at fine spatial scales. Plethodon cinereus greatly outnumbered P. electromorphus, and P. electromorphus used cooler, wetter microhabitats that were also occupied by P. cinereus, with no evidence for a negative correlation in their occupancies or abundances. Taken together, my work suggests that current distributions, including patterns within and between species, are shaped by historical range expansion and contractions, as well as subtle differences in habitat use at multiple spatial scales.

Roads are one of the most recognizable artifacts of human habitation and development. They cross various landscapes and expand with the increasing density of human settlements. While these structures are vital in facilitating vehicular transportation, they can also have unintended negative consequences for natural ecosystems, such as road-related wildlife mortality. To examine the negative impacts of roads on wildlife at a local level, I quantified the frequency and patterns of road mortality across a yearlong study period in a study area within Montgomery and Giles Counties in southwest Virginia. I also examined relationships between roadkill patterns and several land and road variables, hoping to close a current literature gap by focusing specifically on small and meso-mammals weighing less than 15kg. I recorded the location and species of carcasses found along predetermined routes, including roads with variable speed limits, road infrastructure, and adjacent land cover. I used government-provided data sets, satellite imagery, and field verification to characterize our study routes. I recorded 294 carcasses and identified 221, of which 84% were small or meso-mammals, including 11 taxa. The most frequent roadkill taxa were tree squirrels (Sciurus sp.), opossums (Didelphis virginiana), striped skunks (Mephitus mephitis), and raccoons (Procyon lotor). I found three roadkill hotspots, all along a major highway, and a high frequency of roadkill in spring, autumn, and early winter. High posted speed limits, the presence of artificial road lighting, and high proportions of forest and early successional growth cover (often present in pastures) were associated with an increased frequency of wildlife-vehicle collisions.

Paleoecological analyses of six shallow marine bivalves were conducted to test the Abundant Center Hypothesis using data from the fossil record of the Pleistocene through modern day. This hypothesis predicts the highest abundance of a species is at the center of the geographic or environmental range, decreasing toward the edges. In geographic space, distances to a centerline within a geographic range were variably correlated with population abundances, and some species displayed a sharp drop-off in abundance as distance increased. In environmental space, bivalve species showed moderate correlations between abundance and centrality when measured using cumulative data across the last 2.8 Ma. Shorter time bins across that duration show no consistent patterns, potentially indicative of an abundance-centrality pattern apparent only in the species’ fundamental niche, which is best measured cumulatively over geologic time. These results suggest caution should be taken when interpreting modeled environmental preferences, particularly over short durations.

Atlantic White Cedar (AWC), a coniferous evergreen species, is an important indicator of change along the eastern coast. This species is vulnerable and sensitive to environmental changes such as increasing salinity levels and water levels. This species can be found along the New Jersey coast and this area experienced a major disturbance in 2012, Hurricane Sandy. In response to these disturbances and environmental changes, there has been increased AWC mortality in this region. It is imperative to identify the locations of Atlantic White Cedar stands in this area to help protect this species moving forward. To identify the locations of AWC, a species distribution model was created using Random Forests and a combination of abiotic and remotely sensed variables. This work created a binary map of Atlantic White Cedar presence and identified 149 km2 of AWC throughout the study area. The model performed with high accuracy, with an AUC of 0.97. The most important predictor of AWC presence was NDVI during the leaf off period, indicating the importance of including remotely sensed variables in species distribution models. The spectral signature of AWC was also identified to help provide further insight into vegetation dynamics for this species with remote sensing. This work created a transferable, open-source framework to map Atlantic White Cedar throughout southern New Jersey which could provide necessary information to natural resource managers for the protection of this species.

Paleoecology relies on understanding relationships between modern animals and their environment. Animals are adapted to niches in their environments, and those physical adaptations, or functional traits, are utilized as proxies to interpret aspects of paleo-ecosystems. Much is known about individual functional traits in extant mammals and their relationship to the environment. Less is known about how multiple functional traits across a community can be utilized for paleoecological interpretations. I develop models utilizing traits in mammalian communities at the biome level. For Chapter 1, I build a model for North American regional biomes using mammalian trait frequencies. I quantify changes in trait frequency distributions from historical (1832-1899) to modern (2008-2020) times across twelve regional biomes. Results indicate broad species loss across all taxonomic levels and decreased trait frequencies in all biomes due to widespread range contractions. For Chapter 2, I develop models of North American and African mammalian trait distributions. Additionally, I use the models to make paleoecological interpretations of a middle Miocene (late Barstovian; Ba2) Great Plains fauna. Many established paleoecological proxies use African data, even for North American environments. I compare and evaluate these models to determine which is most appropriate for North American paleoecological interpretations. North American and African trait distributions of similar biomes are distinctly different. The African model provides a paleoecological interpretation of the Ba2 Great Plains fauna consistent with past interpretations. For Chapter 3, I apply trait distributions from three Miocene Nebraskan mammalian assemblages to the paleoecological North American and African models developed in Chapter 2. Miocene assemblages are more similar to each other than to modern communities, representing fundamental underlying differences in trait distributions. Both models appear unsuited to make interpretations of local assemblages. Species richness and geographic scale contribute to differences in trait distributions of local assemblages, as does sampling and taphonomic biases against small mammals. However, the African model is the best option for making paleoecological interpretations of Miocene assemblages, though differences still remain. Advisor: Ross Secord

The Southeastern United States is home to exceptionally high fish diversity among temperate latitudes. Species richness and endemism in this region is commonly attributed to historic biogeographic processes dating back to the Pliocene or earlier, and influences of sea levels through a relatively old though stochastic landscape and drainage basins. Specific and subspecific differentiation within the Southeastern United States occurs over a small geographic area and is well documented, though several species of lowland fishes seemingly defy biogeographic and phylogeographic models and expand well beyond other species ranges without any hypotheses for dispersal. Pirate Perches, Aphredoderus, are a widespread lowland freshwater fish native to the Eastern half of the United States. Aphredoderus was thought to contain a single species divided into an Eastern and Western subspecies on either side of the Appalachian Mountains with a widespread intergrade zone through much of the Eastern Gulf of Mexico and Southern Atlantic drainages. I use morphology and ddRADseq from specimens spanning the entire range of the genus to determine species limits within Aphredoderus. I find evidence of five species, four of which exhibit widespread sympatry in the Southeastern United States. I elevate A. sayanus sayanus and A. sayanus gibbosus to species, supplement previous descriptions, and describe three new species, A breviopercularis sp. nov., A. retrodorsalis sp. nov., and A. ornatus sp. nov. This research suggests that expansion through the Pliocene and Pleistocene was differential and several different historic refugia existed to facilitate allopatric speciation similar to what is proposed in earlier biogeographic and phylogeographic studies.

Observations of environmental degradation, ecosystem change, fisheries collapses, and biodiversity loss have raised concerns over our ability to preserve marine communities. Knowledge plays a key role in any attempt to preserve these ecosystems. However, the basic natural history knowledge necessary to understand these systems has also degraded as the discipline of ecology has evolved in response to technological pressure and changing funding priorities within science. To make matters worse significant species losses occurred before many ecosystems were monitored making it difficult to determine the nature of undisturbed systems. This thesis analyzes the data currently being produced by the marine ecologists and conservationists in order to describe to librarians and information scientists what efforts can be taken to preserve data critical for ongoing conservation efforts. Description of data generated for the purposes of aquatic ecology was obtained through a domain analysis of the journal Aquatic Conservation: Marine and Freshwater Ecosystems. Three years of data generation was recorded for all full-length research articles published between 2016-2018. The data is heterogeneous; however, important trends were uncovered. There is a large amount of geographic data being produced within the context of determining biodiversity. Physical sampling of the environment means that adequate data preservation requires museum resources play a part in preserving specimens. Accessibility of data will determine its utility to ongoing studies, and online resources can easily facilitate needed accessibility.

The nine-banded armadillo (Dasypus novemcinctus L.) is currently considered an invasive species in parts of its range in the United States. As it continues to expand its range, more states may begin to consider armadillos an invasive or nuisance species and will need to make management decisions regarding this species as (1) a pest for landowners or land managers, (2) a possible threat to other species of conservation concern, and (3) a vector for Hansen’s disease (leprosy). Although research funds are scarce for a species that is currently not seen as a threat or an endangered animal, there are ways to use limited resources and community science to assist in filling knowledge gaps, which can then provide a baseline for where to begin research efforts. My research used community science and roadkill surveys to study habitat preferences across the state of Tennessee and tested roadkill for Hansen’s disease prevalence.

Riverine fishes are confined by the hydrology of their river systems and their populations and communities are consequently modeled based on a dendritic network architecture. However, distinct river basins are known to become connected to one another through network-independent erosional processes and through flooding. The connections between adjacent river basins have been shown to allow out-of-network fish dispersal both contemporarily and over evolutionary time, and this is hypothesized to be an important mechanism shaping the diversity of riverine species. However, out-of-network fish dispersal violates the assumed longitudinal within-network dispersal of models, and remains poorly studied, making it a priority in better characterizing intra-network fish population structure and inter-network biogeographic patterns. The Guiana Shield of South America, as a region dominated by river systems, rich fish biodiversity, and a deep history of drainage rearrangements, is an ideal region in which to better understand the influences of inter-basin connections and out-of-network fish dispersal at several scales. In Chapter II of this dissertation, I analyzed the biogeography of Geophagus sensu stricto (Subfamily: Cichlinae) across the Guiana Shield to detect the influences of largescale drainage rearrangements in shaping its evolution. Using a reduced-representation genomic dataset, I produced a resolved phylogeny of Geophagus, prioritizing thorough representation from within the Guianas. Using the Geophagus phylogeny, I estimated ancestral ranges, and evaluated the importance of hypothesized inter-basin corridors in shaping the diversity of Geophagus. Since the mid-Miocene, drainage rearrangements have allowed Geophagus to move (i) into the lower Amazon, (ii) from western tributaries of the Amazon into the Guianas, and (iii) from the Rio Negro to the Orinoco River basin. Inter-basin corridors shaped the relationships of 31 lineages of Geophagus identified in this study. Chapter II showcases a spectrum of diversification outcomes for Geophagus, including various range expansion events across the Guiana Shield that highlight the importance of drainage rearrangement in shaping biogeography and diversification processes. In Chapter III, I further investigated out-of-network dispersal in structuring the populations of an upland fish species, Krobia potaroensis, in the Pakaraima Mountains of Guyana. Using the same genomic approach as in Chapter II, I determined the genetic relationships of K. potaroensis between several interdigitating river systems. The results highlight admixture in the uppermost riverine tributaries, suggesting a recent history connection. Dispersals between the river systems in the Pakaraima Mountains are discussed in the context of current models of riverine population genetics. I conclude existing models of dendritic network population structure should be extended to consider out-of-network dispersal conduits. Chapter IV further explores out-of-network fish dispersal in the Rupununi Portal of southern Guyana. The Portal has been observed to seasonally flood and allow for inter-basin fish dispersal of some species, while others remain isolated within one system or the other. I determined the genetic population structure of two fishes (Geophagus sp. and Guianacara dacrya) across the Rupununi Portal and observed inter-basin admixture that corroborates previous observations of fish dispersal. The results indicate that dispersal through ecological corridors shapes population genetic structure and generates recognizable phylogeographic patterns across corridors. Taken together my dissertation supports the importance of out-of-network dispersal in shaping fish population structure and biogeography on several spatial and temporal scales. A comprehensive understanding of the evolutionary and ecological processes that shape the freshwater biodiversity of the Guiana Shield, and across river systems more broadly, requires further consideration of out-of-network dispersal

Despite the fundamental importance of parasites, relatively few studies have adequately mapped basic patterns of parasitism onto host geographic ranges. This knowledge gap hinders our ability to evaluate and understand species biogeographical distributions, including their determinants and consequences. In the context of a predictive theoretical framework, I quantified how parasitism by animal and protozoan parasites varies among latitudes within the geographical ranges of individual species. Chapter 1 shows how quantifying parasitism (1) at the single host (parasite infracommunity) level, (2) considering distinct parasitic consumer strategies, and (3) by using parasite diversity and biomass load as currencies permitted me to document novel biogeographical distributional patterns of parasitism of four estuarine fish species. Parasite diversity increased at lower latitudes and was largely driven by parasites using trophic transmission. These findings indicate a particularly strong role for trophically transmitted parasites and predation in community structure and dynamics at lower latitudes. In Chapter 2, I documented the latitudinal variation in parasitism throughout the contiguous geographical range of the striped shore crab, Pachygrapsus crassipes. This crab commonly uses two distinct habitats throughout its range—living on mud in low-energy estuarine habitats and on rock in the high-energy rocky intertidal zone—providing a striking opportunity to examine latitudinal variation in parasite diversity and load while simultaneously examining the influence of habitat on parasitism. I showed that P. crassipes appears to be affected by parasites (1) that are trophically transmitted, overall; (2) in estuaries than in the rocky intertidal zone; and (3) down south in each habitat. In Chapter 3, I quantified the latitudinal variation in the probability of being infected by parasites, parasite diversity, and biomass load for 13 species sampled throughout their entire range, four northern species sampled at their center and southern edge, and two southern species sampled at their northern edge. I documented three strong patterns of parasitism—peaking at mid, low, and high latitudes—were repeatable among different host species and explicable from the theoretical framework. These trends have overlapping and different implications for how parasitism may play a role in the ecology of host range shifts and setting species range limits.

The deep sea is the largest ecosystem on the planet, comprising more than 90% of the volume that life can inhabit, yet it is the least explored biome in the world. The deep sea includes the benthos, which makes up 91.5 % of all the seafloor globally, and the water column deeper than 200 meters. It hosts a wealth of ecosystems including deep-sea vents, seamount coral gardens, abyssal plains, high-productivity whale falls, and life even in the deepest trenches. We now understand that all of these ecosystems host a variety of habitats, each with their own ecology and unique species. These ecosystems and habitats- and their associated biodiversity- provide essential ecosystem services such as carbon sequestration, nutrient regeneration, microbial processes detoxification, fisheries provisioning, and many others. However, despite the uniqueness of these ecosystems and the importance of the services they provide, we still know far less about them than we do about their shallow water and terrestrial counterparts. In this dissertation, I contribute new insights about the patterns of biodiversity in the Pacific Ocean across a large geographic area, and across a wide range of depths. To that end, in Chapter 1, I have used one of the largest ocean exploration datasets to look for patterns of the abundance and diversity across the most common benthic invertebrate families found on Pacific seamounts: Anthozoa, Porifera, and Echinodermata across the Central and Western Pacific. In addition to quantifying the diversity and abundance of known taxa, I also documented patterns of as-of-yet unidentified taxa by region, depth, and deepwater feature (seamount shape). Building on patterns associated with seamount shape that were described in Chapter 2, I focused on the effect of seamount shape on the diversity and abundance of deep-sea coral communities in Chapter 3. The analysis presented in Chapter 3 provides strong support for the novel hypothesis that gross seamount morphology is a significant driver of community composition. In Chapter 4, I focused on a single seamount to investigate biodiversity and abundance of coral and sponge taxa on a finer spatial scale, examining the role of direction (N, S, E, W) on different flanks of a single equatorial seamount. This analysis yielded interesting consistent patterns of zonation on all sides of the seamount in terms of depth, but with differences in abundance patterns on each flank for individual taxa. Finally, in Chapter 5, I took a global perspective to investigate gaps in deepwater data, with the goal of determining what regions need further exploration to conclusively determine patterns of deep-sea biodiversity, which will be critical for determining the health of deepwater ecosystems under climate change conditions with increased exploitation pressure and cooccuring with increased conservation efforts. Merging Ocean Biogeographic Information System (OBIS) records with the largest collection of deep submergence dive records ever collected, I used proposed biogeographic provinces schema to identify areas with the least supporting data. Additionally, I coupled records from OBIS with climate change projections to identify the areas with the fewest number of biodiversity records that are likely to change the fastest under different IPCC projections. These areas of low number of records and high likelihood of change by the end of the century should become priority targets for future exploration. Taken together, this dissertation provides valuable insights and generates new hypotheses about patterns and drivers of deep-sea biodiversity, and puts forth recommendations for future research and exploration efforts.

Even as early as Darwin, biologists recognized that closely related species were likely to be more similar to one another than to more distantly related organisms. Modern phylogenetic community ecology has extended this framework to suggest that closely related species should be similar in functional traits, occupied niche space, and even geographic distributions. The extent to which this type of phylogenetic niche conservatism has shaped modern biodiversity patterns remains a contentious issue, with extreme views arguing that niche conservatism is either the sole driver of modern distributions or that abiotic filtering alone is responsible for explaining where contemporary species are found. In this dissertation, I investigate the degree to which phylogenetic niche conservatism is observed among American angiosperms. Notably, I adopt the perspective that both niche conservatism and niche shift are important, scale-dependent factors contributing to modern biodiversity patterns, and attempt to analyze the phylogenetic scale over which we can observe niche conservatism for different aspects of these organisms’ niches. In CHAPTER ONE, I investigate the phylogenetic scale over which variation in a multi-trait resource-acquisition strategy is best observed. I show that coordinated evolution of height, growth form, seed mass, and wood density is best observed among species from con-ordinal families. Outside this phylogenetic scale, quantitative, clade-specific, variation in trait values among different angiosperm orders, as well as convergent evolution to similar trait values obscure the ability to detect phylogenetic niche conservatism. In CHAPTER TWO, I develop novel niche characterization methods in order to quantify the degree of climatic and elevational niche similarity across the ranges of American seed plants at different phylogenetic scales. I find strong statistical support for phylogenetic niche conservatism as an important contributor to plant diversity patterns, corroborating the hypothesis that plants may tend to track favorable climate. In particular, I observed greater conservatism in precipitation niches and niche breadth compared to temperature or elevation, and niche conservatism was greater at smaller phylogenetic scales. Nevertheless, even among closely related species, differences in climatic niche were significantly greater than expected by chance and variance in niche similarity among close relatives was large, such that within-clade variation equaled or exceeded between-clade differences. In the remaining chapters, I focus on American alpine communities across different mountain systems. I demonstrate that contrasting patterns of phylogenetic diversity and degree of alpine specialization differentiate the alpine communities occurring at opposite ends of the American mountain range system, despite broad climatic similarities in these two regions, thus suggesting an important role for historical factors in the assembly of their floras (CHAPTER THREE). I also use continuous character niche reconstruction to show how alpine lineages arise primarily from montane species, indicating that a perspective which views niche conservatism and niche shift as occurring on a continuous spectrum may be a more productive framework for understanding how species enter novel niche space (CHAPTER FOUR). I CONCLUDE by discussing (1) the generality of an appropriate phylogenetic scale for observing niche conservatism among angiosperm lineages; (2) the degree to which process such as abiotic filtering, biogeographic history, and ecological dynamics have shaped different assemblages; and (3) how the age of “big data” can be used and abused to investigate big picture questions of community assembly and evolutionary history. This dissertation underscores the complex interplay of niche conservatism, abiotic filtering, and historical processes in shaping modern angiosperm biodiversity.