Theses - Zoology

Permanent URI for this collection

https://www.repository.cam.ac.uk/handle/1810/219489

Browse

Now showing 1 - 20 of 153

Open Access
Painting the Past: Uncovering Ancestral Contributions to Complex Human Phenotypes in Western Eurasia
Barrie, William
The high mutation load within and phenotypic differences between modern human populations remain poorly understood. Understanding these phenomena would lead to a better understanding of the origins of complex phenotypes, including genetically-influenced diseases, and their geographic distributions. The aim of this thesis is to uncover the genetic origins of complex human phenotypes, from the Last Glacial Maximum until the Bronze Age in western Eurasia. Specifically, it aims to assess the contributions of differentiated genetic ancestries which existed in this period, and link this to modern-day differences in disease susceptibility. To achieve this, methods were developed to infer local ancestry in a large modern panel, the UK Biobank, using new ancient reference genomes. Modern samples were selected based on a ‘typical ancestral profile’ for each country represented in the UK Biobank. This dataset was then used to infer the genome-wide ancestry components of modern populations, and the contribution of each ancestry to a polygenic phenotype using a new statistic analogous to a polygenic risk score based on local ancestry probabilities. An in-depth investigation into the origins of Multiple Sclerosis (MS) was performed. This project was the first to use ancient DNA to infer local ancestry in a very large modern panel to assess ancestral contributions to polygenic phenotypes. Simulations showed that the accuracy of ancestry assignment was good. Differences in average ancestry components were calculated per-country within Eurasia and north Africa, and per-county within Britain, reflecting past episodes of migration and admixture. Aggregate ancestral contributions to phenotypes known to be over-dispersed in ancient populations were then calculated, including height, BMI and some psychiatric traits. Finally, the origins of the genetic risk for MS were traced to the Bronze Age Steppe populations; positive selection drove these variants to higher frequency, likely in response to novel pathogen exposure resulting from lifestyles changes and leading to a heterogeneous risk profile across Europe today. These results demonstrate the power of combining large ancient and modern DNA panels, using local ancestry assignment methods, to investigate the histories of genetic variants and associate them with selection due to differing ancient lifestyles, or drift. This can explain geographic differences in genetic risk, and highlights the importance of the Bronze Age as a determinant of modern immune response. This may have clinical implications for the treatment of auto-immune diseases, for example concerning childhood pathogen exposure.
Open Access
Population genomics and domestication of the Black Soldier Fly (Hermetia illucens L.)
Generalovic, Tomas; Generalovic, Tomas [0000-0002-8983-1024]
Our global food chain is under considerable threat from a growing human population and climate change. Improving food security requires an increase in sustainable agricultural practices to alleviate this threat. Recent development of an insect livestock industry has promoted a circular approach to producing food and feed through the bioremediation of organic wastes. Central to this novel industry, the black soldier fly, *Hermetia illucens*, an insect with a polyphagous diet, global distribution, and large population sizes has seen rapid uptake in agricultural activity. Improved knowledge of the evolutionary history, genetic diversity and potential for genetic improvement of this species will be fundamental to the success of this important industry. I investigate the role of domestication and its impact on the genome of *H. illucens*. I developed a suite of high-quality genomic resources for this novel agricultural system and used this to investigate the genomic landscape of an inbred *H. illucens* population. I obtained whole-genome sequences for a total of 54 *H. illucens* and an outgroup taxon, *Ptecticus aurifer*. Phylogenetic patterns provide evidence for previously undescribed cryptic diversity within *H. illucens*. Genome-wide insights into wild and captive populations revealed genomic signatures of domestication in captive populations across the globe. In addition, I identified several genomic regions associated with domestication which appear to converge in populations experiencing parallel selective pressures across the globe. After documenting genetic diversity, I performed phenotypic characterisation for several domesticated strains. This work revealed both genotype- and family-environment interactions which suggested a genetic and heritable basis for the high phenotypic variation observed within the species. I next carried out experimental evolution for increased pupal size in a replicated design. I achieved considerable genetic gain for this phenotype and identified complex trait interactions including a trade-off between pupal size and development time. I also optimised genetic modification using CRISPR/Cas9 to generate a transgenic line of *yellow H. illucens* mutants. I used this loss-of-function line to explore the role of *yellow* in mating behaviour in this novel system. This work combines genetic, phenotypic, behavioural and experimental evolution studies to lay the foundation for the advancement of *Hermetia illucens* as a globally important agricultural system.
Open Access
Understanding the impacts of land-use change and management decisions within oil palm on insect assemblages in Peninsular Malaysia and Borneo
Harianja, Martina Faika; Harianja, Martina [0000-0002-9607-6151]
Being one of the world’s biodiversity hotspots, Southeast Asia’s rainforest is home to an extremely high density of species. However, the region has lost a high proportion of its rainforest as a result of logging and conversion to agriculture since the early 1970s, causing declines in species diversity across wide-ranging taxa. Studies have found that this loss has been driven by changes in microclimatic conditions, resources (for feeding, breeding, protection against predators, and refuge during extreme weather events), and connectivity. Invertebrates, in particular, have been found to decline in richness, abundance, and biomass with land-use change (although logging seems to have much less of an impact than converting forest to agriculture), causing concerns over the various functions they support in the ecosystem, including nutrient recycling, pollination, and biological control. Despite an increasing number of studies, the effects of habitat change and alternative management options on many invertebrate taxa remain unknown, making studies assessing them a priority for informing targeted and successful conservation efforts. In this thesis, I investigated the impacts of rainforest logging and conversion to oil palm on semi-aquatic bugs (Gerromorpha, Hemiptera), representing aquatic communities, as well as management decisions by oil palm smallholders within existing plantations on butterflies (Rhopalocera, Lepidoptera), representing terrestrial communities. Studies took place in Sabah, Malaysian Borneo for semi-aquatic bugs (Chapters 2 – 4) and Selangor, Peninsular Malaysia for butterflies (Chapters 5 & 6). In Selangor, I also studied the effects of environmental conditions at a smaller scale, particularly how habitat structure and complexity within smallholder plantations affected the resource-use behaviour of butterflies. In Chapter 2, I developed length-biomass equations which can be used to predict the biomass of semi-aquatic bugs from their body lengths. Biomass can be a good indicator of ecosystem function but obtaining these data can be costly and difficult. I found that power regression equations gave the most accurate estimations of biomass across life stages, particularly when taking into account the body forms of semi-aquatic bugs. In Chapter 3, I investigated the impacts of forest conversion for logging and oil palm on semi-aquatic bug communities. Despite being sensitive to anthropogenic disturbance and ecologically important (they are predators of invertebrates and prey for some invertebrates and vertebrates), semi-aquatic bugs are little studied in the region. The abundance and species richness were lower following forest conversion, whilst total biomass was not affected, potentially indicating the robustness of prey availability for predators of semi-aquatic bugs. In Chapter 4, I assessed the effects of within-stream physical structure and maintaining forested margins around oil palm streams on semi-aquatic bugs. I found that, at the small-scale (along 10-meter transect), there was a significantly higher abundance of semi-aquatic bugs in oil palm streams with forested margins than those without, as well as significantly different community composition. However, species richness and total biomass remained unaffected. In Chapter 5, I investigated the effects of smallholder management decisions, in terms of replanting and crop choices after replanting (monoculture vs polyculture), on butterfly assemblages. I found that smallholders managed their plantations in widely different ways, resulting in differing habitat structure and complexity across plantations, but that broad management decisions (immature monoculture, immature polyculture, and mature monoculture plantations) did not significantly impact the density or species richness of butterflies. Despite this, finer scale differences, such as more understory vegetation, including nectar sources for adult butterflies, as well as polyculture farming, increased the density of butterflies. In Chapter 6, I studied the impacts of habitat structure and complexity, associated with management decisions, on the resource-use behaviour of butterflies. Although data were limited, I found that the novel methods developed for this chapter are promising and can provide detailed information at a small scale, which could be applied in other habitat types. In conclusion, this thesis found that semi-aquatic bugs are sensitive to rainforest logging and conversion to oil palm. I also demonstrated that conservation management around streams (by maintaining forested margins) and within plantations (by maintaining understory vegetation including hostplants and nectar sources, as well as polyculture farming) can increase the abundance of semi-aquatic bugs and butterflies, respectively. I also demonstrated that agricultural habitats do not support forest-dependent species, at least within the two taxa studied here. Therefore, in addition to the evident negative impacts on many other taxa that existing studies have found, this confirms that preventing further forest conversion remains a priority for biodiversity conservation. Nevertheless, conservation management options I have identified open up opportunities to better support persisting species within altered habitats, particularly oil palm systems, potentially increasing biodiversity and associated ecosystem processes across the wider landscape.
Embargo
Signatures and forgeries: optimality in a coevolutionary arms race
Dixit, Tanmay; Dixit, Tanmay [0000-0001-5604-7965]
When species interact antagonistically, ‘arms races’ played out on coevolutionary battlegrounds can drive the rapid evolution of intricate and complex adaptations in each species. However, evolution in one species may prevent optimality in these adaptations from being realised in the other. In the Choma District of southern Zambia, the brood-parasitic cuckoo finch *Anomalospiza imberbis* parasitises four species of cisticolid warbler. In response to parasitic egg mimicry, these four hosts have evolved inter-individual variation in egg colours and patterns: so-called egg signatures. Such individual signatures, used to convey identity, are in many ways analogous to human signatures, passwords, and codes. This means we can use principles from fields such as computer science and cryptography to ask (1) how could signature traits be optimised in principle; and (2) do we observe such optimality in nature? The aim of this thesis, alongside arguing for a broader definition of coevolution (Chapter 2), is to answer these two questions using a combination of theoretical perspectives from the physical sciences, and field experiments. In Chapter 3, I generate hypotheses about how different forms of perception influence coevolution. In Chapter 4, I test these ideas in my study system. Using an optimisation algorithm and field experiments, I show that egg pattern complexity predicts egg rejection, determine how complexity is perceived, and predict its evolutionary trajectory. In Chapter 5, I show that while this evolutionary trajectory has been followed, traits in hosts and parasites are nevertheless suboptimal. In Chapters 6 and 7, I use mathematical tools to quantify phenotypes in hosts and parasites, showing that hosts do not use traits optimally, likely due to perceptual constraints or inherent trade-offs in signature production. Finally, in Chapter 8 I show that whether host signature variation is categorically or continuously distributed has important consequences for hosts. Overall, I conclude that while rapid evolution can occur due to the strong selection pressures inherent to arms races, mechanistic factors may constrain the evolution of optimal traits. Even under strong coevolutionary selection pressures, animals may not exhibit traits as optimal as an engineer might design them.
Open Access
The Palaeogenomics of Arctic and Sub-Arctic Peoples: A Study of Population Genetics, Adaptations, and Pathogen Incidence
Sutherland, Alison
The northeastern regions of Siberia and the North American Arctic are some of the last regions of the world to be inhabited by humans; there, sophisticated technologies were developed for hunting marine mammals. Continued migration waves of ancient Western Eurasians and ancient East Asians into northeastern Siberia led to the early formation of the “Palaeo-Siberians'' in the Late Pleistocene and the “Neo-Siberians'' in the Holocene, the latter being genetically continuous with present-day groups in the region. The North American Arctic was populated by two genetically distinct, archaeologically-defined cultural traditions of Neo-Siberian-related peoples: the Palaeo-Inuit (entering ~5.5 thousand years ago) and the Neo-Inuit (entering ~1 thousand years ago). Limited archaeological and palaeogenomic findings into prehistoric contacts and admixture between ancient Siberian and Arctic groups leave a knowledge gap in the demographic histories of these regions. This thesis comprises palaeogenomic, radiocarbon, and stable carbon and nitrogen isotope datasets of unmatched quality and scale, generated from 217 sets of human remains from northeastern Siberia and North America to investigate population histories, evidence of adaptations to the Arctic environment, and pathogen incidence. Using allele-frequency based methods, the population genetics analyses in this thesis investigate three main research questions pertaining to Palaeo-Siberian, Palaeo-Inuit, and Neo-Inuit groups. Genetic similarity within and between these groups was determined, adding insight into ancient migrations and population interactions. Adaptations associated with fat metabolism and cold were examined in the ancient Arctic and sub-Arctic groups, at genetic *loci* that have been proposed to be under selection in present-day populations from the region. Ancient pathogens were identified from the sequencing data of the ancient individuals, expanding the catalogue of human pathogens in these regions over time. The findings from this thesis elucidate the population histories of Arctic and sub-Arctic groups over time. Importantly, through continued community engagement and knowledge exchange with Indigenous peoples, this interdisciplinary project tells a more complete history of the peopling of the Siberian and North American Arctic.
Open Access
The potential of green space in schools to enhance biodiversity, ecological knowledge and student wellbeing
Howlett, Katherine; Howlett, Kate [0000-0002-1020-9161]
Children in the UK are increasingly disconnected from the natural world, a trend often attributed to rapid urbanisation and reduced daily contact with nature. Spending time in the presence of biodiversity is known to benefit mental health, physical health and wellbeing, and increase awareness of the natural world and conservation, yet there are concerns that direct experiences in nature are being replaced by indirect, technology-mediated experiences, such as through television programmes. However, there is little understanding of how the natural world is portrayed within these media, or how new types of nature experience contribute to the development of a connection with nature, ecological knowledge or the wellbeing benefits of biodiversity. There is also concern that an increasing disconnect between children and the natural world could lead to the attrition of ecological knowledge, reducing awareness of biodiversity loss and eroding support for conservation. In this context, the relationship between children and the natural world is of crucial importance to the future of conservation and children’s wellbeing. In this thesis, I use school grounds in the UK as a focal point for studying the relationship between children and the natural world, and nature-documentary content to assess portrayals of the natural world in the media, as well as exploring the effects of the COVID-19 lockdown in the UK on parental attitudes to green space. Chapter One: A wide range of disciplines are currently involved in research investigating people’s relationship with the natural world. I conducted a literature review and used an evidence-mapping approach to quantify existing research focused on human relationships with the natural world and to identify the extent of overlap between disciplines. I also quantified which disciplines use which terminology and to what extent terminology is discipline-specific. I found that research on people and nature is generally well integrated, with disparate disciplines citing each other fairly well. However, the communities of disciplines cited were significantly different between publishing disciplines, with research from psychology, education and public health being particularly distinct. There were also consistent differences between publishing disciplines in the terminology used to refer to nature, with a particularly broad range of terms used in psychology and public health research. This could act as a barrier to efficient knowledge exchange, potentially limiting both development of further research and the translation of findings into effective policy. Chapter Two: To assess the biodiversity that children are exposed to while at school, I conducted biodiversity surveys of 14 primary schools in England. I quantified the amount of green space and levels of associated biodiversity, surveying for invertebrates, birds, plant cover and trees. I assessed whether amount of green space, species abundance, species richness or community composition of taxa varied with school fee-paying status (state-funded, including state and academy, or non-state-funded). Non-state-funded schools had higher levels of vegetation than state-funded schools, and this translated into higher invertebrate abundance, higher species richness of plant cover and larger, more mature trees. My findings have implications for the development of nature connection in children from different socioeconomic backgrounds and provide a powerful case for increasing funding to state-funded schools to improve biodiversity-related management of school grounds. Chapter Three: During the COVID-19 lockdown in 2020, I designed and distributed an online survey for parents of primary school-aged children to investigate the importance of green space, the amount of time children spent outside and whether this changed as a result of lockdown. 83.3% of rural parents reported being happy with the amount of green space to which their children had access, in contrast with only 40.5% of urban parents. Lockdown restrictions affected parents' attitudes to the importance of green space, with 77.8% of urban parents saying their views had changed during lockdown, in contrast with 41.2% of rural parents. Further, most urban children spent more time inside during lockdown, while most rural children spent more time outside. These findings suggest that lockdown restrictions exacerbated pre-existing differences in nature access between urban and rural children. Chapter Four: To assess the current state of ecological awareness among UK children, I asked children (aged between seven and 11 years old) from 12 primary schools in England to draw the wildlife in their local green space. I quantified animal and plant species richness and community composition of drawings, as well as the taxonomic level to which terms used in the captions and labels could be identified. I assessed whether there were differences in these metrics between state-funded and non-state-funded school pupils, and whether the level of identification differed between taxa. Children’s awareness was skewed towards mammals and birds over invertebrates, reptiles and plants, and children were also better at identifying mammals and birds over other groups. These differences were consistent across the state and non-state education systems, suggesting these biases are cultural rather than educational in origin. Chapter Five: To investigate the level of information and coverage of the natural world provided by media portrayals, I analysed the content of wildlife documentaries to assess whether they provide an accurate reflection of the natural world and whether conservation messaging in documentaries has changed over time. Sampling an online film database showed that vertebrate groups, particularly mammals and birds, were overrepresented compared to their actual diversity in the natural world, while invertebrate groups and plants were underrepresented. This mirrored the precision with which these organisms were referred to, with mammals and birds being the most well identified and invertebrates and plants being the least identified. The frequency of conservation messaging increased over time, as did mentions of anthropogenic threats to biodiversity, which were not mentioned at all before 1970. Chapter Six: To assess potential wellbeing benefits of exposure to biodiversity in school children, I collaborated with a secondary school to establish an experiment within their grounds, which assessed species richness in three different settings within the school and quantified changes in student anxiety and pulse rate after walking through different settings. I found that species richness differed significantly between settings, with a restored area of the school grounds having more species of both plants and butterflies. Both state anxiety and pulse rate showed a greater reduction in children who had walked through the most biodiverse setting. This case study has important implications for long-term wellbeing in children and highlights the value of green space in schools for enhancing biodiversity and wellbeing, as well as the role of university-school collaborations in helping ecology come alive in schools. My findings show that there are differences in children’s exposure to biodiversity between school types and that current inequalities in nature access in the UK may have been exacerbated by lockdown restrictions, with implications for children’s exposure to nature during key, formative years for nature connection. The patchiness in interactions between children and nature across socioeconomic groups and regions in the UK has long-term implications for which species and ecosystems attract conservation funding and continue to feature prominently in collective cultural memory. While media portrayals of nature are diverse, there are limitations in the coverage afforded to different taxa, which is reflected in children’s awareness of nature in their local green spaces. Taken together, my results highlight the need for more concerted work to engage children with the natural world, both in natural environments and through other media, to foster a better understanding of biodiversity and threats the natural world faces. Only by doing so can we successfully engage the next generation with nature conservation, fostering the skills and motivation necessary to halt and reverse biodiversity declines.
Embargo
The social environment and the evolution of morphology in the burying beetle, Nicrophorus vespilloides
Smith, Jack Marcus
Social interactions within species are ubiquitous in nature, and cause animals to exist in a social environment. In this thesis, I investigate how the social environment can influence morphological evolution, using a combination of observation and experiments on burying beetles *Nicrophorus vespilloides*. This species exhibits a set of social interactions at all life stages that centre around the acquisition and use of small carrion during reproduction. Larvae grow and develop on an edible carrion nest fashioned from a corpse by their parents. Here they interact with siblings and caring parents as they acquire resources from the carrion to grow and develop. Later, as sexually mature adults, they themselves compete with conspecifics of their own sex for carrion to breed upon. I investigate how these various social interactions influence morphology at these different lifestages. I start by investigating how the social environment influences morphological evolution of offspring, by collecting data from replicate experimental populations that had been evolving for 39 generations in different social environments when I began work. In two populations, parents were able to supply care (‘Full Care’ populations), whereas in two other populations parents were prevented from supplying any post-hatching care (‘No Care’ populations). In Chapter 2, I show that hatchling morphology evolves divergently in these two different social environments. In the Full Care populations, first-hatched larvae have relatively larger head morphology and body size compared with last-hatched larvae. In the No Care populations, by contrast, first- and last-hatched larvae are significantly more uniform in their head morphology and body size throughout the entire brood. In Chapter 3, I show that third instar larval morphology also diverges between the ‘Full Care’ and ‘No Care’ environments. In general, larvae from the Full Care populations have disproportionately larger heads, compared to larvae from the No Care populations. In each case, I suggest that this divergence in the evolution of larval morphology between populations is due to the selection pressures of sibling competition that materialises only in the presence of parents. Next, I investigate how the social environment contributes to morphological change in adult beetles. In Chapter 4, I discover a new form of sexual dimorphism in burying beetles: male burying beetles exhibit disproportionately larger heads than females. I show that this head morphology is directly linked to biting performance, and that beetles with larger heads exert a greater bite force. I then link this to the burying beetle’s natural history and show that head size predicts the outcome of contests over carrion, in both males and females. Finally, in Chapter 5, I investigate how head morphology functions in the preparation of the carrion nest. Males typically invest more than females in nest preparation, though females can prepare a nest singlehandedly if widowed. I use an experimental approach in the laboratory to investigate how parental division of labour influences the evolution of adult morphology; taking advantage of ongoing experimental evolution in a different set of experimental populations, in which females were induced to prepare a carrion nest without any help from the male. I show that females evolve a relatively larger head in response to this additional parental responsibility, whereas males evolve smaller head morphology. In Chapter 6, I discuss how these different results together show that key morphological traits do evolve in response to divergent social environments, whilst highlighting the role of constraints in morphological evolution.
Open Access
Understanding and improving the cost-effectiveness of biodiversity conservation
White, Thomas; White, Thomas [0000-0002-0536-6162]
Biodiversity conservation is currently facing extraordinary challenges but remains severely limited by funding. Thus, the importance of cost-effective conservation is being increasingly realised – requiring information on both the effects and costs of actions taken to conserve biodiversity. Yet, despite progress in collating and using evidence on the effectiveness of conservation in decision-making, the recording and use of cost data has received far less attention. This PhD aims to help bridge this gap by investigating the collection and use of economic data for conservation decision making, as part of wider research into evidence-based conservation. The research presented is structured into several stages: i) investigate the current state of cost reporting and the use of evidence (including costs) in conservation decision making, ii) develop frameworks and approaches to help improve the reporting of the economic costs and benefits of conservation actions, and the use of evidence in decision-making around biodiversity impact mitigation. Lastly, I then apply this thinking to two detailed case studies where I assess the costs and cost-effectiveness of different conservation interventions. Reviewing the published literature on conservation interventions, I identified low rates of detailed cost reporting. Reported costs often lacked important contextual detail necessary to interpret the data and apply it in different contexts. Where detailed costs were provided, they showed considerable variation, with differences in how costs were reported likely to explain much of this variance. I then conducted an interview-based study investigating the use of evidence in business-biodiversity decision making. This revealed a wide range of themes including the high reliance of professionals on experts, policy and guidance as a stamp of cost-effective, evidence-based practice. Several challenges to integrating biodiversity in the private sector were also noted, including the need for better understanding the economic costs and benefits of mitigation action. Building on these studies, I then developed i) a step-by-step framework for the standardised reporting of economic costs and benefits of conservation action, and ii) a set of principles for the use of evidence (including data on costs) to guide actions that businesses and consultants can take to minimize and compensate for their impacts on biodiversity. To demonstrate the complexities and importance of using cost data in decision-making, I then provide two case studies. The first of these studies assesses the costs and cost-effectiveness of actions to avoid and minimize the impacts of power lines on at-risk bird species in Spain. The study identified large variations in the effectiveness and cost-effectiveness of different actions to prevent collisions with at-risk bird species. Changing how cost is measured, by including the costs associated with negative impacts, can improve the apparent cost-effectiveness of mitigation measures, particularly those more effective measures which avoid impact at the outset. In the second case study, I used a dataset of field-level costs of commonly applied agri-environment interventions in the UK to investigate actions to protect and restore biodiversity in farmland. I identified a high variation in costs both between and within different conservation actions. Costs and cost-effectiveness varied depending on the inclusion of several inputs (e.g., fertilizer, pesticide) during implementation, field size, as well as the types of cost and benefit included. Understanding the variability in costs within actions, and how costs and cost-effectiveness are calculated, are critical considerations when assessing the feasibility of different actions to protect and restore biodiversity.
Embargo
Variation in neural crest development contributes to phenotypic diversification of East African cichlid fishes
Marconi, Aleksandra
The cichlid fishes comprise the largest extant vertebrate family and are the quintessential example of rapid “explosive” adaptive radiations and phenotypic diversification. Despite low genetic divergence, East African cichlids harbour a spectacular intra- and interspecific morphological diversity. Akin to other vertebrates, a considerable proportion of hyper-diverse cichlid traits, such as craniofacial morphologies and pigmentation patterns, originates from a common embryonic migratory progenitor cell population, the neural crest (NC). Although the genetic and developmental basis of these phenotypes has been investigated, understanding of how and when, specifically how early, in ontogeny species-specific differences emerge, remains limited. In this PhD thesis, I present a multispecies comparative analysis of the developmental basis of NC-derived phenotypic diversity in Lake Malawi cichlids, focusing on the variation in development of the embryo, NC, and its derivatives. First, I demonstrate fundamental differences in multiple aspects of cichlid embryogenesis, including variation in morphology and timing, duration, and rate of developmental events (heterochrony) concomitant with NC development. Interspecific differences were also identified at the onset of overt formation of craniofacial skeleton and body pigmentation, irrespective of the developmental heterochronies. Second, I characterise the developmental and cellular basis of divergent pigmentation patterns among cichlids, including in the underexplored context of sexual dimorphism in this NC-derived trait. Among the abundant differences between species in many aspects of body colouration, I show that, in contrast to zebrafish, divergent cellular mechanisms underlie formation of analogous phenotypes among closely related cichlids. These results provide a novel perspective on the developmental basis and evolution of vertebrate pigmentation beyond traditional model systems. Finally, I examine the temporal and spatial variation in NC genetic and developmental programme in two divergent cichlids. In addition to spatial-temporal differences in migratory pathways of the NC cells, I identified novel NC subpopulations based on the differential expression of canonical marker of migratory NC sox10 and its duplicate sox10-like. The variation in the spatial distribution of these NC subpopulations implicates neo- and subfunctionalisation as well as partial redundancy between sox10 duplicates, one of which has been lost in the well-studied zebrafish lineage, and thus entirely unexplored role in NC and teleost evolution. The results I present in this thesis offer an integrated perspective on the complex genetic and developmental basis of cichlid morphological variation, spanning from the fundamental processes of embryogenesis to development of the NC and its derivatives. In particular, my work provides compelling evidence of the unprecedented variability in the NC developmental programme between closely related species and therefore contributes to our understanding of the role of this remarkable cell population in evolution of vertebrate morphological diversity.
Embargo
Evolution in a fragmented world: Phenotypic and genetic divergence amongst neighbouring populations of the burying beetle Nicrophorus vespilloides
Catherall-Ostler, Andrew
Habitat fragmentation is a leading cause of biodiversity loss, but relatively little is known about its long-term evolutionary consequences. I addressed this problem using neighbouring wild populations of burying beetles (*Nicrophorus* spp.), insects which fight to secure carrion upon which they breed. My work focused on the *Nicrophorus* populations inhabiting a cluster of seven ancient woods west of Cambridge. Whilst the criteria used to identify ancient woods are increasingly controversial, I combined new and existing approaches to show there is strong evidence that these woods have been physically separated for at least a thousand years. I carried out three years of fieldwork in each of the seven woods and found that four different species of burying beetle compete over carrion. The carrion niche is partitioned among burying beetles by size: but despite overlapping spatially and temporally with its larger competitors, the smallest species *N. vespilloides* is the most abundant in each wood. Notwithstanding their similarity in age, ecology and geographic location, I found that the community structure and density of burying beetles varied between the seven woods. I argue that these differences likely cause differences in the intensity of competition between the woods. If this is true, then selection could then favour different levels of investment in competition-related phenotypes between the populations. I tested this hypothesis by establishing seven laboratory populations of *N. vespilloides*, each derived from a different woodland population. I then measured relevant phenotypes from each population in common garden experiments. I found that the contests between burying beetles over carcasses are fought primarily with their mandibles but that there is also a behavioural component of individual fighting ability. Females from woods with more diverse community structures were found to be better fighters. A second set of experiments revealed between-population variation in the behaviour of larvae and adults when breeding on a carcass. In woods that had more diverse community structures, larvae arrived at the carcass sooner after oviposition than did larvae from woods with less diverse community structures. I also found that larval arrival time at the carcass causes a sudden drop in the motivation of potential usurpers to take over a carcass. Together, these results suggest that a quicker larval arrival time might provide a mechanism for evading intense interspecific competition for carrion. Finally, I found that males from woods which support a high density of burying beetles had a shorter duration of parental care, presumably because males departed earlier to secure additional off-carcass mating opportunities. After working with collaborators to obtain pooled whole genome sequencing for the populations, I measured the extent of between population genetic differentiation. I found that the extent of genetic differentiation correlates strongly with the extent of dissimilarity in their community structures. These results suggest that the populations are undergoing divergent adaptation despite gene flow. Together with recent work on other species, the emerging picture is that even populations living in closely-connected habitat fragments can be genetically distinct from one another, at least at some loci. The spatial grain of biodiversity may be far finer than previously believed.
Open Access
Social Evolution in Action: Causes and Consequences
Bladon, Eleanor
Across the animal kingdom, social behaviour has been shown to be both a driver of and a response to selection. The question of how social interactions within the family contribute to evolutionary change has received much attention from behavioural ecologists and evolutionary biologists alike, with the former largely focussing on how these interactions are adaptive, and how they impose selection on each member of the partnership, and the latter focussing more on the specific mechanisms of inheritance and how social behaviours of one partner induce the evolution of traits in others. The aim of this thesis is to unite these approaches by asking how adaptive social behaviour (i.e. parental care) can potentially influence evolution: by providing a mechanism for non-genetic inheritance, by constructing the environment in which further social interactions play out, and by influencing trait loss and trait evolvability. The burying beetle *Nicrophorus vespilloides* represents an excellent system for investigating these consequences of parental care. This species exhibits elaborate but variable biparental care, whereby both parents prepare an edible nest for their young from a small vertebrate carcass. They then defend the larvae from predators and competitors and feed them trophallactically with oral fluids. Larvae can survive without any post-hatching care – in the lab at least. I begin in Chapter 2, by examining how burying beetles inherit their gut microbiome, in collaboration with Dr Rahia Mashoodh and Dr Helen Leggett at the University of Cambridge. Previous work suggests this is achieved by two routes: directly from the parents via oral trophallaxis and indirectly via the carcass, through the deposition by parents of oral and anal exudates, which larvae then consume. I eliminated the former mechanism of inheritance, by breeding beetles with and without post-hatching care for two generations, and analysed the resulting gut bacteria of grand-offspring using 16S sequencing. I found that different bacteria are inherited by each route but that gut bacterial communities are just as diverse when vertical transmission happens via the carcass alone. In future work it would be interesting to determine whether beetles have reduced fitness when vertical transmission of the gut bacterial community during post-hatching is prevented. In Chapters 3-6, I extended this approach of comparing populations that had and had not experienced post-hatching care. I analysed replicate experimental burying beetle populations that had evolved for 40 or more generations in the Kilner lab either with or without post-hatching care, respectively the ‘Full Care’ and ‘No Care’ populations. In Chapters 3 and 4, I focused on traits linked to the preparation of the carrion nest. In Chapter 3, I conducted breeding experiments that investigated whether nest construction had evolved divergently between the Full Care and No Care populations. I found that faster nest building in the No Care populations did not compensate for poorer post-hatching care. There was evidence of within-family co-adaptation for nest construction, but the extent of co-adaptation did not diverge between ‘Full Care’ and ‘No Care’ populations. In Chapter 4, in collaboration with Prof. Adria LeBoeuf at the University of Fribourg, Switzerland, I analysed the proteins in oral fluids produced by parents and offspring, which are deposited on the carrion nest. We found that No Care parents had evolved to deposit proteins that could assist their larvae in their absence, but found no evidence of equivalent change in the No Care larvae. Finally, to look at the longer-term evolutionary consequences of parental care, in Chapter 5 I investigated whether traits for supplying and receiving care can persist when they are no longer expressed (as experienced by the No Care populations). I found that No Care fathers and larvae had lower expression of post-hatching care-related traits than their Full Care counterparts, but similar trait loss was not found in mothers. In Chapter 6, I investigated whether evolving with or without care conferred greater resilience when beetles were exposed to increased temperatures during sexual maturation. I found that founder effects were a far better predictor of a population’s resilience than social evolutionary history. I conclude that long-term consequences of social evolution are unpredictable and that the resilience of a population will largely be predicted by the standing genetic variation of its founders.
Embargo
Avian brood parasitism as a model system for studying multispecies interactions
Kennerley, James; Kennerley, James [0000-0002-9129-0976]
The relationships between avian brood parasites and their hosts are widely recognised as model systems for studying coevolution. Through the examination of tractable interactions between one species of brood parasite and one species of host, important insights have been gained on the processes that shape and regulate the world’s biodiversity. While research has favoured the examination of simpler pairwise interactions, the examination of multispecies interactions remains rare despite most brood parasites being known to parasitise multiple species of host and hosts often subject to parasitism by multiple brood parasite species. With little attention paid to these more complex interactions, important opportunities to understand multispecies interactions go unrealised. In this thesis, I begin by establishing the extent of the opportunities offered by avian brood parasitism as a system for studying multispecies interactions. By compiling data on all known brood parasite–host relationships, I demonstrate that complex interactions are the global norm but most research has focused on pairwise interactions, especially in regions with low brood parasite–host network complexity. I argue that despite brood parasitism’s rich research pedigree, the study of multispecies interactions represents an almost entirely new frontier for the examination of the ecology and evolution of multispecies interactions. Through the following two chapters, I demonstrate how brood parasitism can address questions on multispecies interactions which have important implications for our understanding of the natural world. To understand why some species are targeted by brood parasites while others are not, I assemble a dataset on phenotype and life-history information for all species belonging to the passerine superradiation to examine the behavioural and ecological characteristics associated with host status. I find that brood parasites target species that, in addition to being biologically compatible, are the most conspicuous members of the community and discuss how evolutionary pressures may have facilitated convergence on the same host species by sympatric brood parasites contributing to increased network complexity. Next, I investigate the role and evolutionary origins of the whining vocalisation which is produced in response to observing a brood parasite by a group of distantly related host species found around the world. I find that the whining vocalisation plays an important role in communicating the threat of brood parasitism between species and that the pressure imposed on hosts by multiple species of brood parasites has selected for global convergence on a functionally referential vocalisation that sympatric and allopatric hosts respond to innately but are only able to produce once learned from others. Together, these findings highlight the important role that brood parasite–host networks have had in shaping host phenotypes. Overall, this thesis reveals avian brood parasitism to be a complex global network of interactions rather than a series of pairwise relationships as it has been traditionally treated. Furthermore, by showcasing its applications for addressing longstanding questions in evolutionary ecology, I make the case for avian brood parasitism to be looked at from new perspectives in recognition of its suitability as a model system for studying multispecies interactions.
Open Access
Calcium and actin coordinate egg activation and the metaphase-anaphase transition in Drosophila oocytes
Wood, Benjamin
Egg activation is the process through which the mature oocyte is prepared for embryogenesis, consisting of key cellular changes including, but not limited to: i) Physical and chemical changes to the oocyte’s outer covering; ii) The release of meiotic arrest, enabling the formation of a haploid oocyte; iii) Large-scale changes in the translational landscape; iv) Cytoskeletal rearrangements for regulating downstream events of egg activation and supporting further growth of the zygote. Preceding these events in Drosophila is a single calcium transient observed in the form of a polar wave upon hydration and swelling of the oocyte. A model outlining how the initiation of such a wave is regulated and how it then enacts these downstream effects is not yet fully outlined. The original working model supported by previous research suggested that mechanical triggers during ovulation initiate calcium entry. How this mechanical stimulus is transduced into a calcium wave and what this then means for the source of calcium has not been explored. I first provide an in depth analysis of calcium entry dynamics at egg activation, exploring the significance of seemingly less regulated calcium events. I then investigate the source of calcium and identify an ion channel that is required for calcium entry. By utilising a combination of pharmacological and genetic analysis, I highlight the requirement of Trpm for calcium entry at egg activation. Taken together I demonstrate that calcium enters the oocyte from the peri- vitelline space (between the oolemma and vitelline membrane) through Trpm in the form of a wave. I next ask what mechanisms regulate calcium entry through Trpm channels. I provide detailed visualisation of the actin population in the mature oocyte both before and after egg activation, focusing on the cortical actin. I reveal a clear relationship between calcium entry and the cortical actin- In particular, reduction of the cortical actin density or level of cross-linking promotes the entry of calcium. In the mature oocyte I show that the Arp2/3 machinery and tandem-actin binding domain nucleators are required for maintenance of the cortical actin. I further demonstrate that actin-binding proteins (ABPs) play a role in regulating calcium entry, likely via mediation of cross-linking and density of the cortical actin. This data therefore supports a model in which polar waves are in part a result of a reduced cortical actin density at the poles of the oocyte. I then explore a specific downstream event of egg activation; the resumption of meiosis. I demonstrate the presence of a novel population of actin within the Drosophila oocyte that forms a spindle-like structure. Given this is such a recent discovery, key questions are highlighted: 1) What is the role of this spindle-like apparatus?; 2) How does the spindle-like actin regulate meiosis?; 3) Is there conservation of this population? I first highlight the requirement of Formins in production of this population. I further reveal that the spindle-like actin is required for regulating the formation and morphology of the spindle and therefore the accurate movement of chromosomes during meiosis, demonstrating remarkable conservation with mammals. Finally, I bring together concepts of calcium and actin signalling explored in the previous chapters, revealing an essential interplay between the two at the metaphase-arrested spindle.
Open Access
Comparative ecology of the endemic Cyprus Warbler and the congeneric Sardinian Warbler: Implications of recent coexistence
Jones, Victoria Ruth
In 1992 the Sardinian Warbler was first recorded breeding in Cyprus. Since then, survey results from Paphos District suggest that the endemic Cyprus Warbler population has declined, while the Sardinian Warbler breeding population has increased and expanded in Paphos District. Colour-ringed Cyprus and Sardinian Warblers were observed during 2003 to 2005 breeding seasons on seven scrub study plots located across Paphos District. Both species appeared to establish home-ranges without reference to the other species, resulting in considerable interspecific home-range overlap. A playback experiment indicated that Cyprus Warblers reacted equally strongly to conspecific and congeneric song in areas where the two species coexist, but less strongly to congeneric than conspecific song in areas where Sardinian Warblers did not yet breed. The vegetation composition of Cyprus and Sardinian Warbler home-ranges was very similar. There was no indication that the species competed for nest sites. Cyprus and Sardinian Warbler have similar breeding biology; they laid similar sized first clutches and had similar chick output per pair for first nesting attempts. However Sardinian Warblers had a higher frequency of second nesting attempts and this resulted in a higher chick output per pair per year than was achieved by Cyprus Warblers. In both species total chick output per year was higher for pairs that nested early. Nest survival was similar for the two species. Cyprus and Sardinian Warbler diets were very similar. Body condition of both species’ chicks was higher earlier in the breeding season. Cyprus Warblers had higher productivity but lower chick body condition in the zone where their population has declined than in the zone with fewest breeding Sardinian Warblers. Productivity was positively related to arthropod biomass available on different plots for Sardinian Warbler, but not for Cyprus Warbler. There was no evidence of a negative impact of either species on the number or condition of nestlings produced by the congener.
Open Access
A comparison of the costs of delivering conservation through land sharing and land sparing
Collas, Lydia
Globally, drastic biodiversity declines and the worsening climate crisis demand overhaul of existing land use policies which have failed to reconcile food production and environmental conservation. In Europe, most existing policies compensate farmers to voluntarily implement land-sharing measures, commonly referred to as wildlife-friendly farming, which seeks to deliver conservation benefits on the farmed land through agri-environment schemes (AES) offering a fixed price per hectare. Investment into sharing has continued despite the accumulation of evidence showing that, for the same amount of lost food production, substantially more would be delivered for conservation and climate change mitigation with the contrasting approach of land sparing, where high-yield farming allows large areas to be spared elsewhere in the landscape as (semi-)natural habitat. Following Brexit, the UK has the opportunity to rethink this approach; but until now policy decisions have had to be made without estimates of the relative taxpayer costs of using sharing and sparing to deliver target conservation outcomes. Addressing this critical research gap was the primary aim of this thesis, as follows. In this thesis, I sought to uncover the taxpayer and food production costs of delivering meaningful conservation outcomes with land sharing and sparing. First, I conducted a novel comparison of the costs of monitoring sharing and sparing schemes for compliance and effectiveness. Monitoring is a fundamental, though often overlooked, taxpayer cost. In terms of effectiveness monitoring, I found current monitoring levels to be insufficient to precisely determine the effects on wild species of sharing schemes; in contrast, the same effort could deliver relatively precise estimates of the much larger effects of sparing. Furthermore, turning to compliance monitoring, I found the cost-effectiveness of existing English AES could be vastly improved with more compliance monitoring; however, this may be politically unpopular with farmers. It is therefore notable that I also found relatively less money was wasted when monitoring sparing at a sub-optimal rate compared to sharing. Second, I used a discrete choice experiment involving 118 arable farmers to establish their willingness to accept (WTA) payment to participate in sharing and sparing schemes that delivered the same biodiversity and carbon outcomes. I found that all but the most farmland-tolerant outcomes were delivered at less taxpayer expense with sparing. Third, combining this assessment of farmer WTA with knowledge of how much schemes must be monitored, I compared the taxpayer costs of delivering the same environmental outcomes with fixed-price sharing and sparing schemes which paid all recruits at the WTA of the least-willing farmer required in the scheme to deliver the target outcome. I found that sparing delivered the same outcomes at less than half the taxpayer cost of sharing; and, importantly, sparing saw only 79% of the food production lost under sharing. Fourth, I examined the distribution of farmer stated WTA, finding that variation in responses was mostly driven by factors other than lost gross margin. Given marked inter-farmer variation in their stated WTA, variable-price schemes, which pay farmers their stated WTA rather than the rate required by the least-willing participant, offered savings to both sharing and sparing schemes. However, even under variable pricing, sharing was not cheaper than sparing in delivering our more farmland-sensitive outcomes. Finally, I examined whether a land-purchase strategy, where the government purchases land and then contracts organisations to manage and create habitat on it, would deliver sparing at less expense than a farm-subsidy approach. I found land purchase was more cost effective than the farm-subsidy approach if long timeframes, low discount rates and large budgets were considered; however the impacts on farming communities of largescale ownership changes warrant further consideration. To conclude, I found overwhelming evidence for UK arable farming that land sparing can deliver biodiversity and carbon outcomes at substantially lower cost than land sharing both in terms of taxpayer costs and lost food production. The relative costs of sharing would increase even more with consideration of species that do not tolerate farmland, in a country with a shorter history of agriculture where fewer habitat specialists have gone extinct compared the UK, and if the production required elsewhere to compensate greater volume of food production lost under sharing was taken into account. Furthermore, the effects of sharing may be near-impossible to precisely determine with current monitoring efforts and continued sub-optimal compliance monitoring would increase the costs of sharing-like options relatively more than the more sparing-like options of existing AES. Whilst variable pricing and land purchase may further reduce the costs of sparing, the costs of delivering meaningful environmental outcomes are most substantially reduced by pursuing a land-sparing, rather than land-sharing, approach. This work is of considerable significance to the UK government, given that prevailing land-sharing policy approaches can at best deliver less than half the environmental outcomes delivered by the same budget spent on land sparing.
Embargo
Ancient origins of the chordate forebrain: Conserved patterning of the anterior neuroectoderm in amphioxus
Gattoni, Giacomo
While the general organization of the chordate central nervous system (CNS) is highly conserved and consists of a dorsal neural tube with an anterior brain, the evolutionary origin of this key aspect of the chordate body plan remains obscure. In recent years, a conserved anterior gene regulatory network (aGRN) has been shown to pattern the larval anterior nervous system of several invertebrates, including the two non-chordate deuterostome phyla (echinoderms and hemichordates), in which the aGRN controls the development of the apical organ. Although clear homologs of the apical organ are not present in chordates, most aGRN genes are expressed in the vertebrate forebrain. In this PhD thesis I trace the evolution of the aGRN across deuterostomes using the cephalochordate amphioxus as the main model organism. I first show that during amphioxus development aGRN genes are expressed in a similar pattern to the one found in echinoderms and hemichordates, are regulated by Wnt/b-catenin signalling and are active in the anterior neuroectoderm that forms the larval brain. As a comparative system, I also characterize the development of the apical organ in an understudied group of echinoderms, the crinoids. To follow the fate of the amphioxus anterior neuroectoderm, I next investigate neurogenesis, proliferation and cell type differentiation in larval and adult brains. I demonstrate the presence of a hypothalamic-like region in the anterior cerebral vesicle, which derives from the region where the aGRN is active during development. Finally, I explore how changes in the specification of the body axes and in the expression of one of the upstream aGRN genes, FoxQ2, might have underlined the evolution of the complex vertebrate brain. Taken together, the results presented in this thesis support the conservation across deuterostome evolution of an aGRN that controls the development of the anterior neuroectoderm. In the chordate lineage, the network was integrated to the neurulation program to specify retinal and hypothalamic areas of the forebrain. Furthermore, this work provides a comprehensive characterization of neuroarchitecture and cell type composition across the amphioxus life cycle, facilitating the comparison with other chordate taxa to reconstruct the evolution of the chordate nervous system.
Open Access
The genomics of adaptive colouration in Hypolimnas butterflies and the wood tiger moth, Arctia plantaginis
Farré I Orteu, Anna; Farré I Orteu, Anna [0000-0002-3911-0747]
Wing phenotypes in butterflies and moths are a striking example of adaptive evolution and are a tractable trait to dissect the genetic mechanisms underlying adaptations. Studies of Lepidoptera, mainly mimetic species from the tropics, have led to two general patterns. First, a limited set of genes have been re-used multiple times in controlling the evolution of wing phenotypes, and second, structural variation often underlies such traits. Clarifying the generality of these two patterns requires the dissection of the genetic architecture of wing phenotypes in a wider variety of species. In this thesis, I explore the genetic basis of wing mimicry in Hypolimnas butterflies and of aposematism in the wood tiger moth using a range of genomics and transcriptomics methods. First, I produce genome assemblies of two Hypolimnas species and investigate the evolution of W chromosomes in Lepidoptera. By comparing the H. misippus genome assembly to multiple Lepidoptera species, I provide evidence that suggests that the W chromosome has a shared origin across the Lepidoptera. Second, I identify the genetic basis of forewing mimicry in H. misippus using a dataset of 335 individuals sequenced using haplotagging, a linked read sequencing technique. To analyse these data, I develop a method called Wrath for the visualisation and exploration of candidate structural variants. I find that transposable element insertions are associated with forewing phenotype and present evidence for the usefulness of Wrath to explore haplotagging data. Third, I examine the evolution of mimicry in the Hypolimnas genus by identifying and comparing the genetic basis of wing phenotypes in H. misippus and H. bolina. Using a dataset of 214 whole genome sequences of H. bolina individuals together with my H. misippus data, I show that cortex, a gene involved in wing colour in many Lepidoptera, is the most likely candidate for the control of white colour elements in the two species. Furthermore, I present evidence that the regulatory elements controlling the presence of hindwing white are likely not homologous between the two species. Additionally, I show that a region close to optix, another well-known colour gene, is associated with orange elements in H. bolina. Finally, I explore the genetic basis of a complex phenotype involving aposematism and behavioural and physiological traits in the wood tiger moth, Arctia plantaginis, and show that this trait is associated with the duplication of a yellow family gene. This work contributes to our understanding of the evolution of wing phenotypes in the Lepidoptera. Overall, my results highlight the importance of structural variation in the evolution of wing colouration while also emphasising the repeatability of the genetic basis of adaptive traits.
Open Access
Phylogenetic inference using ancient environmental DNA
De Sanctis, Bianca
Ancient environmental DNA (aeDNA) has revolutionized our ability to describe and analyze biological communities in space and time by allowing for joint sequencing of entire ecosystems across thousands of years. However, because samples contain damaged, short fragments from multiple individuals or taxa, the field has been so far limited in its scope, and aeDNA has only been applied to population and phylogenetic studies in the last few years. In this thesis, I first build a theoretical coalescent framework to analyze error in supervised binning algorithms, which assign reads from environmental samples to individual taxa in a reference database. Under this framework, I determine the expected error rate under a wide range of parameters and the degradation in assignment accuracy as samples diverge from their closest reference sequence, and with incompleteness of reference sequences. Second, I describe a phylogenetic placement algorithm for non-recombining sequences such as mitochondria or chloroplast DNA, and apply this method to Mammuthus or mammoth and Equus or horse samples from an Arctic-wide aeDNA dataset spanning the last 50,000 years. This analysis demonstrates the potential existence of a previously undiscovered clade of mammoths, and extends the survival of an existing clade. Next, I report one of the first whole genome ancient environmental DNA studies, using DNA extracted from 14-16,000 year old cave soil with material from two closely related species, Ursus arctos or the American black bear and Arctodus simus or the extinct giant short-faced bear. By comparing the ancient sequence against a modern reference panel of black bears and a high-quality fossil giant short-faced bear reference, I infer evolutionary relationships between the Late Pleistocene populations and their modern relatives. Lastly, I molecularly date an ancient environmental Betula or birch tree chloroplast sequence from Northern Greenland, confirming that it was approximately 2 million years old, the oldest DNA to be successfully sequenced so far. All together, this work demonstrates the ability to infer phylogenies and population histories of individual taxa from ancient environmental DNA.
Embargo
The Sea is the Limit: Foraging Ecology of Breeding Antarctic Procellariiformes
Bentley, Lily
In the dynamic marine environment, highly mobile predators are expected to select profitable foraging areas, especially when provisioning young in addition to meeting their own energy needs. Knowing how and where animals choose to forage is not only important to advance ecological theory, but also to assess and mitigate the impact of anthropogenic threats. In this thesis I examine the breeding-season foraging behaviour of several of the Procellariiformes, a wide-ranging, long-lived group of seabirds, many of which have experienced steep population declines since the mid-20th century. Advances in biologging technologies over the last four decades have made it possible not only to accurately track individual movements, but also to identify important behaviours at sea. In my first data chapter (Chapter 2), I combine data from multiple tag types to describe diving behaviour in three albatross species, and discuss the implications for both foraging ecology and bycatch susceptibility. Moving from foraging capability of the individual to foraging preferences at the level of genus, in Chapter 3 I analyse the divergent niches of a summer- and a winter- breeding species of Procellaria petrel. Here I compare the habitat preferences of Grey Petrels and White-chinned Petrels breeding at Gough Island and South Georgia, respectively. Using high-resolution remote sensing environmental data, I identify divergent foraging preferences in dynamic habitats. Finally, in Chapter 4, I compare habitat preferences and accessibility between the two species of Phoebetria albatrosses across six colonies. While most studies of habitat preference consider only a single species or site, here I investigate whether closely- related species inhabit the same ecological niche at sympatric and allopatric colonies throughout their range. I show that Light-mantled Albatrosses have a consistent foraging niche, whereas Sooty Albatrosses select different habitats in sympatry and allopatry. I then discuss the impact of interspecific competition on plasticity in habitat preferences in general. Overall, my thesis examines diverse aspects of seabird foraging ecology from the individual to community level, discusses habitat preferences (and their potential flexibility) in relation to species' evolutionary history and as drivers of community structure, and considers the implications for conservation planning.
Embargo
Fossoriality In Snakes: Perspectives From Morphology And The Fossil Record
Howard, Alexandra
Snakes are a speciose clade of squamates that have diversified into almost all habitats, all with the same elongate limbless body plan. This thesis aims to improve scientific understanding of snake evolution by focusing on novel perspectives using both extant snakes and the fossil record. 1. Alternate phylogenetic positions of fossils affects body size estimates in snakes Body size is a readily available metric for both extant and extinct snakes. The competing hypothesis of ecological snake origins also predict different outcomes for the evolution of body size in snakes. I used a combination of ancestral state reconstructions, body size estimates of fossils from regression models, and evolutionary rate modelling to examine the evolution of body size in snakes, with a particular focus on early snake evolution. This project showed that snakes achieve a wide range of diversity of body size during the Cretaceous, trends that are not observed when using data from extant taxa. 2. Cranial osteology of Typhlopidae (Serpentes: Scolecophidia) Scolecophidia are a distinctive group of snakes that occupy the basal most diverging branches of the snake phylogeny. However, due to the small overall size of many taxa, they have been relatively understudied in regards to comparative anatomy. In this project I examined segmented CT scans of 10 different species of Typhlopoidea, the largest clade of Scolecophidia. Using these comparisons I identified variability in several morphological characters not previously thought to be variable in Scolecophidia, as well as the identification of features in large typhlopids such as the lateral wings of the basisphenoid, which were previously thought to be limited only to Alethinophidia. 3. Morphometrics provide evidence for the fossorial origin of snakes The problem of homoplasy, particularly in relation to adaptation to fossoriality, is potentially responsible for the incongruences between phylogenetic hypothesis of snakes that use either morphological or molecular data. In this project I used CT scans of 73 species of alethinophidian snake and geometric morphometrics to examine morphological correlates to fossoriality. I found that there is a clear morphological signal between the parietal of alethinophidian snakes and ecology. In general, the parietal of fossorial snakes is more elongate with a deep u or v shaped fronto-parietal suture, with an elongated posterior shelf that overlaps the braincase. These projects show how integrative research using both extant and palaeontological data can inform questions about the early evolution of clades, particularly the heavily debated ecological origin of snakes.