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  • ItemOpen Access
    Pangolin Exploitation and Wild Meat Hunting in Nigeria
    Emogor, Charles A; Emogor, Charles [0000-0002-9589-2931]
    Pangolins, eight species of scaly African and Asian mammals, are all threatened by overexploitation according to the International Union for the Conservation of Nature’s Red List of Threatened Species. The medicinal use of scales in traditional therapeutic medicines in Asia is considered the primary driver of population declines among Asian pangolins, with these dwindling numbers leading to increased trafficking of African species to supply Asian markets. This has in turn prompted research into the ecology and threats of African pangolins. However, there are fundamental knowledge gaps yet to be addressed, including a) quantifying the number of pangolins involved in the trade, b) understanding stakeholder preferences for interventions to reduce their decline, and c) determining the drivers of their exploitation. My thesis, containing six data chapters, addresses these gaps primarily by studying wild meat hunting and use, as pangolins frequently appear in hunting records. I focus on Nigeria, a hub in international pangolin trafficking. Most of my work uses data I collected during three years of fieldwork in the Cross River Forest landscape, one of the few remaining pangolin hotspots in West Africa. In Chapter 2, my first data chapter, I explore Nigeria’s role in global pangolin trafficking, analysing the dynamics of the trade and quantifying the number of pangolins involved in seizure events. I show that Nigeria-linked seizures (2010-Sept 2021) involved ~ 190,400 kg of pangolin specimens, mainly scales, from approximately 800,000 pangolins. Chapter 3 uses interviews across 15 locations with hunters, wild meat vendors, and staff of conservation organisations and the Nigeria Customs Service (NCS) to examine local perceptions of pangolins and stakeholder preferences for pangolin interventions in southeast Nigeria. Here I show that there is considerable local demand and consumption of pangolin meat. I also show that hunters and vendors favour community-focused interventions (such as community stewardship programs) to reduce exploitation, while NCS and conservation organisation staff prefer enforcement-centred interventions (anti-poaching patrols, for example). Chapter 4 draws on a three-year hunting dataset (1,008 hunter-months, including 54 records of pangolins) from two communities to determine the success of hunting trips. My results reveal that hunters are more likely to catch at least one animal during drier periods and on shorter hunting trips, although when assessing the successful trips, the number of animals caught increases with trip durations, indicating that hunters set a target of not returning empty-handed rather than optimising their efforts. In Chapter 5, I assess differences, across meat types, in their average palatability, as perceived by 190 hunters, 190 vendors, and adult members of 190 households in 15 communities. My results show comparability in the median palatability of domestic meat, fish, invertebrates, and wild meat. Furthermore, among mammals, ungulates, carnivores, primates, and rodents showed similar palatability. However, pangolins had higher palatability than all other orders, except rodents. Chapter 6 then looks at changes in hunting and use of wild meat during the COVID-19 lockdown (using data from Chapter 4). Here I show that the monthly rate of successful hunting trips and the number, mass, and value of animals caught increased during Nigeria’s lockdown compared to matched non-lockdown periods. Moreover, hunters consumed a larger proportion of wild meat and sold less during the lockdown, suggesting a reliance on wild meat to augment the reduced food and income posed by the lockdown. In my concluding chapter, I use interviews with 809 hunters and vendors in 25 locations to assess drivers and temporal trends in pangolin exploitation and characterise how far exploitation of scales is the primary motivation for pangolin hunting around Cross River. Perhaps surprisingly, but in line with my palatability results, results from Chapter 7 show that demand for meat, not exploitation for scales, is likely to be the primary driver of pangolin harvesting in southeast Nigeria. I also show that pangolins are not targeted in this landscape but harvested during general wild meat hunting trips. In conclusion, my thesis shows that pangolin harvesting in Southeast Nigeria is perhaps integral to wild meat hunting for food and income and that pangolins here are not targeted for scales but for meat, probably because of the meat’s exceptionally high palatability. Studies in Central and Western Africa also show the high palatability of pangolin meat, and with wild meat hunting being pervasive in these regions, it is likely that pangolins are also targeted for their meat in other African forest landscapes. Therefore, the survival of African pangolins may hinge on prioritising community-based interventions, particularly through behaviour change interventions and efforts to improve the food security of rural communities.
  • ItemEmbargo
    Bivalve molluscs as environmental monitors and tools for sustainable water management
    Vereycken, James
    Freshwater environments are capable of providing a wide range of vital ecosystem services, from basic provision of drinking water to energy production, waste removal to recreation. Well-managed water resources allow such precious services to be preserved. However, anthropogenic influences have led to the widespread degradation of freshwater environments, resulting in extensive decline in freshwater organisms. With growing pressures on water resources, there is an increasing need for change: sustainable water management regimes are needed, to allow the water requirements of society to be met as far as is feasible both at the current time, and in the future. The improvement of monitoring capacity affords an effective tool for the protection and conservation of waterways, which represent key components of sustainable water management strategies. In situ physical and chemical sensing has allowed improved temporal and spatial resolution of water monitoring, yet the information they provide is limited, and key ecological information is lacking. This has encouraged the use of aquatic biota to provide direct information on the ecological state of a waterway. Such monitoring is beneficial, both to the protection of the health of aquatic ecosystems, and the human populations that rely upon them. Bivalve molluscs offer particular promise for the biomonitoring of aquatic systems. This thesis seeks to progress understanding and enable wider study of prominent means by which bivalves can, or may yet, provide insights into their environments. Production of a review explained the key behaviours of bivalves used in biosensing of water quality, and suggested means to enhance the informativeness of systems employing them, as well as other potential behaviours that could be valuable in biosensing, and future directions. Subsequently, a novel system was developed, demonstrating how the key behaviours used in biosensing, valve movements and cardiac activity, may both be simultaneously measured. With extensive detail and explanation of a sophisticated yet simple, inexpensive, scalable and adaptable set-up, this work encourages and facilitates the widespread implementation of bivalve-based monitoring. The system was then demonstrated in experimental work through simple testing of stressor responses with specimens of Duck Mussel (Anodonta anatina), which highlighted the potential benefits of integration of behaviours (a key suggestion of the review), and helped address practical concerns regarding their simultaneous use. Within the review, vertical and horizontal movements of mobile bivalve species were suggested as an alternative biosensing behaviour. Harnessing advances in artificial intelligence, a proof-of-concept system was therefore developed for tracking these movements in specimens of Painter’s Mussel (Unio pictorum) and Duck Mussel, in an entirely natural mode of life, and their responses to different stressors were tested. There was high variability between individual mussels, which indicated that future approaches using artificial intelligence to monitor movements should control for individual variation by monitoring deviations from baselines. The viability of the approach is proven and should prompt further study. Finally, examination of external and (novel) internal anatomical features across very small distances in space (microhabitats), revealed significant morphological responses in specimens of the Swollen River Mussel (Unio tumidus), highlighting the sensitivity of morphology to intricacies of a bivalve’s environment. The knowledge gained in the current work expands understanding of the various ways by which bivalve molluscs can provide tools for monitoring the environment and, through prototype and proof-of-concept studies, helps to demonstrate and encourage more widespread implementation of study. While providing further water monitoring tools, this work enables a greater understanding of bivalve ecology; this is valuable for informing their conservation. Furthermore, freshwater mussels are prominent ecosystem engineers and shape the aquatic community around them. Hence, their conservation facilitates the conservation of the whole freshwater ecosystem. Therefore, the work here demonstrates that bivalves are effective tools in sustainable water management strategies, through enabling protection of freshwater resources, and aiding their conservation.
  • ItemOpen Access
    The biodiversity and climate impacts of alternative approaches to meeting demands for tropical timber and forest restoration
    Cerullo, Gianluca
    Alongside agricultural expansion, two other major forces will determine biodiversity and ecosystem services within tropical landscapes of the future. First is timber production, which already exerts substantial impacts on forest species and the climate through selective logging and the development of intensive tree plantations. Second is the restoration of large tracts of degraded lands in order to recover ecosystem services and biodiversity and support livelihoods. Both timber production and restoration will grow dramatically in the near future, as global wood demand grows up to 54% by 2050, and as major restoration agendas gather pace under the UN Decade on Restoration and Bonn Challenge to restore 350 Mha of degraded lands by 2030. Understanding how timber production and restoration can be implemented to navigate trade-offs between competing objectives is critical. In this thesis I consider these trade-offs at different spatial scales, from local to pan-tropical. I do so firstly by advancing the land sparing-sharing framework developed in agriculture to consider the production of wood. I create and evaluate production-matched scenarios that generate timber within a fully forested logging concession, and then across a wider landscape which encompasses the potential for sourcing timber from purpose-grown plantations. Next, I consider how timber production and restoration objectives might intersect over large spatial scales. I predict spatial variation in where tree plantations are likely to expand across Brazil between 2020 and 2030, and evaluate how this expansion may impact areas where ecological restoration would most benefit terrestrial vertebrates. I conclude by considering how restoration can be scaled up across tropical landscapes in ways that are socially and ecologically responsible, and which avoid severe unintended consequences. In Chapter 2, I use previously collected field data to characterise how the abundance of 57 dung beetle species changes with yield along a harvest intensity gradient in a 50,000 ha Brazilian Amazon logging concession. I then use these abundance-yield relationships, combined with company-reported logging rates, to evaluate the biodiversity performance of >8000 hypothetical scenarios, each delivering a fixed volume of wood across the concession. These scenarios follow the sparing-sharing paradigm as originally conceived for farming, but also consider a wide array of mixed approaches. I find that logging approaches that maximise the sparing of old-growth forest (‘extreme sparing’), in exchange for intensifying logging, deliver the highest concession-wide species abundances and population sizes for species negatively affected by harvests. Sparing-style logging also has improved functional diversity outcomes. Just 3% of mixed approaches outperform ‘extreme sparing’ when considering all species, but still involve considerable sparing of old-growth stands combined with higher yields elsewhere than under business-as-usual logging. Yet I also reveal that such concentrated logging is up to 90% less profitable than business-as-usual practices since it limits harvesting of highly-valuable but scattered trees. In Chapter 3, I develop this analytical approach to consider a wider variety of outcomes and harvesting regimes across a 1 Mha landscape in Sabah, Malaysia. I present results from extensive new fieldwork surveys of dung beetles and birds, plus carbon, ‘megatrees’, timber yields, and profits across seven contrasting land uses, including plantations, and spanning >25,000 landscape-level scenarios. I also extend previous analysis by: (i) more comprehensively incorporating post-harvesting trajectories of species’ abundance, and (ii) evaluating how near-optimal harvesting approaches might depend on the composition and degradation status of the starting landscapes. For a wide variety of production targets, biodiversity and climate outcomes would be greatest under production approaches that focus production in plantations alongside reducing logging within either primary or already-logged rainforest ecosystems. This finding holds even as starting landscapes become more degraded, though benefits are greatest within less-degraded landscapes and at higher production targets. However, I again find financial hurdles to sparing-style production: plantation-focused scenarios have much lower harvest profits and also incur greater protection costs in order to conserve forests nolonger falling within active logging concessions. In Chapter 4, I investigate the potential risk of expanding tree plantations into high-value lands forecological restoration in a national-level analysis for Brazil - a timber production powerhouse and restoration hotspot. Using remote-sensing data showing historic patterns of tree plantation expansion, I develop random forest models which use biophysical, economic and spatial-contagion predictor variables to forecast national plantation expansion probability between 2020 and 2030. I then consider the magnitude and extent of potential overlap between areas where future tree plantation expansion is most likely and areas that would deliver the highest restoration benefits for terrestrial vertebrates, if returned to natural habitat cover. I forecast that of 2.8 Mha of future plantation expansion (equivalent to the expansion observed 2010-2020), roughly 1.3 Mha (46%) will occur in the top 30% of restoration priority areas for vertebrates, with the first 1 Mha of expansion having disproportionate impacts. In Chapter 5, I consider how forest restoration can be scaled up and applied effectively in tropicallandscapes across large spatial scales. I review the potential of alternative approaches to restoration in logged forests, abandoned agricultural lands, plantations and farms. I also consider synergies and trade-offs in delivering different restoration objectives. Key environmental challenges to restoration include the risk of displacing agricultural production, the impacts of inappropriate planting in rangelands and savanna woodlands, and the need to embed resilience to climate change and unlock sustainable financing. Overall, I suggest that successful restoration will require addressing issues of poor governance and sociocultural disparities in benefits and costs at landscape levels. In sum, I find that spatially concentrating the production of timber by restricting logging or sourcing more wood from purpose-grown plantations has the potential to substantially improve the biodiversity and climate impacts of meeting future timber demand. However, in order to mitigate the extinction and climate crises this way we need to develop new approaches to supporting such production because it is typically less profitable for harvesters and can also increase overall forest protection costs. When considering the potential benefits of plantations, I also identify the clear need for joined-up approaches to tree plantation expansion which consider alternative land-use options, including the potential to recover species’ populations via targeted ecosystem restoration. More broadly, I find that the potential value of restoration in tropical landscapes is substantial, in part due to the enduring damage caused by historic timber harvests. However, we need integrated, system-level approaches to production and restoration that maximise benefits of different strategies, which avoid interventions that may appear promising locally but cause wider-scale harm to biodiversity and the climate, and which ensure that broadly beneficial landscape-wide management regimes are financially attractive to forestry and plantation enterprises.
  • ItemOpen Access
    Sea sparing, sea sharing, and production at least cost to the planet
    Erm, Philip; Erm, Philip [0000-0003-1642-9808]
    Fisheries are the most direct threat to marine biodiversity. However, fisheries are also vital for food security, with over 3.2 billion people relying on fish for a significant part of their diet. With growing international support for protecting 30% of the planet by 2030, no-take marine protected areas (MPAs) that exclude fishing from certain areas entirely have emerged as a popular tool for conserving biodiversity and ensuring fisheries sustainability. But some argue that the benefits of no-take MPAs may be limited in seascapes that are already ‘well-regulated’ by other forms of fisheries management, particularly if they only displace fishing effort to other areas for no net biodiversity gain. In this thesis, I aimed to evaluate the conservation benefits of no-take MPAs in such seascapes through the creation of a sea sparing and sharing framework. With it, I posed and attempted to answer the following question: for any sustainable level of fishery harvest, what proportion of a seascape – if any – ought to be spared from fishing to maximise seascape-wide biodiversity? By fixing catch targets across management scenarios, this framing ensured that the biodiversity impacts of fishing effort displacement from no-take MPAs would not be overlooked. In Chapter 2, I outline the framework and adapt it to a modelled archetypal trawl fishery using empirically informed estimates of species’ sensitivities to fishing. I find that a strategy with no-take MPAs is best for biodiversity when avoiding the local extinction of sensitive species is a priority, but that a strategy without no-take MPAs is best for the abundance of more resilient species and reducing fishing effort. I also extend these findings to crustacean trawl fisheries globally, where I find that biodiversity in 72% of fisheries could potentially benefit from no-take MPAs. In Chapter 3, I develop a more complex model that also includes differences in species’ ranges and the impacts of fishing-induced habitat damage. When habitat damage is absent, I find that no-take MPAs provide a net biodiversity benefit so long as there are significant range overlaps between fishing grounds and bycatch species. When habitat damage is instead present, I find that no-take MPAs generally benefit biodiversity regardless of range overlap, but that this is diminished if the carrying capacities of deliberately fished species also decline due to damage. However, as in Chapter 2, no-take MPAs still increase the total fishing effort required to reach catch targets in the seascape. Finally, in Chapter 4, I integrate the insights from Chapters 2 and 3 with previous work from agriculture and forestry to present a general theory of how conservation operates within production systems. Through it I argue that almost all conservation interventions in production systems act upon just three domains: area-use allocation, the direct impacts of production on biodiversity, and supply and demand. I also outline how these domains interact with one another, and in so doing show how many otherwise well-intentioned conservation interventions can actually risk increasing biodiversity loss by causing knock-on effects in other domains. Additionally, in the Chapter 4 Supplementary Material, I illustrate how these domains and their interactions can be modelled to identify ideal conservation actions using the historic case of the endangered Australian sea lion. In all, I find that no-take MPAs are generally able to deliver biodiversity benefits in ‘well-regulated’ fisheries when accounting for the impacts of fishing effort displacement, but that this can change where seascapes lack sensitive species or fishing-induced habitat damage. No-take MPAs also always increase the total fishing effort required to maintain fixed catch targets. The best strategy in a given seascape is thus likely to depend on its ecology and the management priorities of its stakeholders, although no-take MPAs are likely to be useful if biodiversity conservation is deemed important. When considering conservation in production systems more broadly, I identify how just three domains – area-use allocation, production’s direct impacts, and supply and demand – characterise the conservation interventions available to managers, and show how these can interact to limit the effectiveness of certain actions. The latter in particular suggests that many single-domain conservation interventions may be far less beneficial than commonly supposed.
  • ItemOpen Access
    Cross-species single-cell transcriptomics and its applications in evolutionary and translational research
    Keitley, Daniel
    Single-cell transcriptomics has emerged as a powerful technology to characterise gene expression within individual cells. Over the last 5 years, as the technology has matured, single-cell techniques have been used to profile cells in species across the tree of life. The availability of single-cell data from a rich diversity of species presents an opportunity to compare gene expression, cell types and developmental programmes across organisms and interpret these transcriptomic observations within a phylogenetic framework. This opens up new possibilities to study the evolution of cell types and infer molecular properties of organisms inaccessible to experimental research. In this thesis, I explore these two applications in the context of early mammalian development and vertebrate brain evolution. I first detail efforts to construct a single-cell atlas of rabbit gastrulation, which offers a new window into human embryogenesis and provides a resource for validating therapeutic targets, or observations from mice, in a non-rodent system. I then present three new approaches to visualise and compare single-cell transcriptomics data from multiple species. These methods overcome challenges of relating gene features and cell types, which may be applicable to contexts beyond the cross-species setting. Finally, I apply comparative single-cell analyses to trace networks of neural development across deuterostomes. This reveals a conserved molecular signature present in the sea urchin, amphioxus and zebrafish embryo and offers a template for future studies to compare vertebrate and invertebrate nervous systems with single-cell approaches.
  • ItemOpen Access
    The social and management factors that contribute to the ecological sustainability of oil palm plantations
    Reiss-Woolever, Valentine; Reiss-Woolever, Valentine [0000-0002-6905-4387]
    Over the past century, oil palm has developed from a sustenance crop in West Africa to the world’s most traded vegetable oil. Although the oil palm industry contributes to local and national economies across the tropics, its cultivation has also been linked to severe negative impacts on biodiversity, ecosystem functioning, and the wellbeing of local communities. While there is a growing awareness of the need to manage such agricultural landscapes more sustainably, there remains a lack of interdisciplinary research focused on tractable solutions to do so. In this thesis, I conducted social, ecological, and interdisciplinary studies of both smallholder and industrial plantations in two key oil palm countries, aiming to provide a more holistic understanding of the social factors influencing plantation management, and the ecological effects of alternative management options. My first chapter reviews the global relevance of agriculture and acts as an introduction to this thesis. In my second chapter I carried out a systematic mapping exercise to quantify social, ecological, and interdisciplinary research on oil palm cultivation, assess trends in publication focus, and identify priority knowledge gaps in the literature. I found a global increase in oil palm research over the past three decades, with over 70% of research focused on ecological outcomes, but only 20% on social and less than 10% on interdisciplinary. The majority of studies were conducted within industrial plantations and compared oil palm to non-modified habitats, such as forests. The most pressing knowledge gaps included a lack of studies on the effects of plantation inputs on pollination and herbivory, the relationship between ecological factors and human health and wellbeing, and comparisons of different management practices within oil palm plantations. I argue that these gaps should become the focus of future research attention, as they lie in identified priority research areas and their outcomes are critical for informing the development of more sustainable palm oil production. Through the rest of my thesis, I present research which begins to address these topics. In my third chapter, I conducted social surveys in collaboration with smallholder farmers in Riau, Indonesia, and Perak, Malaysia. These farmers varied in the extent to which they followed management-assistance programs led by an industrial palm oil company (in Indonesia) and a conservation focused NGO (in Malaysia). These groups acted as examples of the range of farmer socio-demographics, attitudes, and management decisions that exist, and allowed me to assess the alignment between the intentions of partnership programs and the current realities of smallholder plantations on the ground. Field work was conducted remotely with partner organisations in Malaysia and Indonesia, owing to the impacts of COVID. I found that farmers most closely partnered with the private sector were highly variable in their socio-demographics and attitudes, but showed little variation in management inputs. In contrast, farmers most closely partnered with an NGO were highly varied in all survey sections, and deviated from the intended management regime. Income, herbicide usage, and vegetation management were consistently among the most important factors determining differences between groups, and could be a fruitful focus of further study on smallholder management. My findings demonstrate the wide variety of farmers found within the most productive oil palm regions in the world, indicating that a ‘one-size-fits-all’ approach to sustainability is unlikely to be effective in a smallholder context. In my fourth chapter, I conducted social and ecological surveys with independent smallholders in Peninsular Malaysia to investigate which social factors affected smallholder farmer decisions to replant oil palm as a mono versus polyculture crop, and how such systems differed in management inputs and environmental features. I found no significant differences in socio-demographics or attitudes between farmers deciding to replant with a monoculture or a polyculture, suggesting there is no “typical” polyculture farmer. I also found no significant differences in management inputs, such as herbicide or fertiliser application, between plantation types, suggesting that farmers are not tailoring management strategies towards their unique plantation needs. However, plantations did differ in environmental features, suggesting that intercropping influences the ecosystem, regardless of inputs. In particular, soil conditions, understory vegetation, and key pests present differed between plantation types, with more abundant understory vegetation and higher herbivory found in polyculture plantations. In my fifth chapter, I investigated the impact of landscape scale plantation heterogeneity on biodiversity in industrial oil palm plantations in Sumatra, Indonesia. I assessed whether density and behaviour of day-flying Lepidoptera varied between different habitats within plantations (Edge habitats bordered by plantation roads on one side, and Core habitats in the centre of oil palm planting blocks) and across seasons (March and September). I found significantly higher total density of Lepidoptera in Edge than in Core habitats. There was an interaction between season and habitat, with density increasing more markedly in Edge than Core areas in September. There was also a significant effect of habitat and season on behaviour, with more active behaviours, such as foraging and mating, recorded more frequently in Edge than Core habitats, and more commonly in September than March. My findings indicate that Lepidoptera abundance is affected by habitat characteristics and can be influenced by plantation management. In particular, increasing non-crop vegetation in plantations through reduced clearing practices or planting of flowering plants could foster more abundant and active butterfly communities within oil palm. In the following chapter I investigated this hypothesis. In my sixth chapter and final data chapter, I assessed the long- and short-term effects of varying vegetation management regimes on the abundance, richness, and diversity of day-flying Lepidoptera, again based in mature industrial oil palm plantations in Sumatra, Indonesia. Over the long-term, less intensive understory vegetation clearing resulted in significantly more abundant and diverse Lepidoptera communities, with limited differences between plots with restricted herbicide application and plots where no herbicide was used. In contrast, Lepidoptera communities were little affected by vegetation management over the short-term, suggesting that manual removal of vegetation may be equally as damaging to butterfly and moth communities as removal by intermediate levels of herbicide spraying. My findings substantiate calls to limit understory clearing in oil palm and maintain habitat heterogeneity, while also indicating that a hard ‘no-spray’ guideline may not be the only option for developing more butterfly-friendly plantations. My findings relate directly to key areas of research (namely understory vegetation treatment and herbicide application) identified in my social and interdisciplinary data chapters (Chapters 2, 3 & 4). My seventh chapter is a discussion of my thesis findings as a whole, and its implications for socio-ecological research and the oil palm industry. Results of my thesis identified priority areas for oil palm research and management in both industrial and smallholder contexts, and have begun to close gaps in knowledge on tractable and effective methods to manage oil palm plantations more sustainably. I have demonstrated the linkage between social and ecological factors, and shown that social factors affect management inputs, which directly affect biodiversity and ecosystem functioning. Altogether, my thesis demonstrates that both small- and large-scale oil palm plantations can, and must, develop tailored management strategies to support biodiversity, ecosystem functioning, yield, and farmer socioeconomics, in order to preserve tropical habitats and livelihoods while meeting growing global demand.
  • ItemOpen Access
    Cool as a caterpillar: Understanding the responses of butterflies to temperature across the life cycle
    Ashe-Jepson, Esme; Ashe-Jepson, Esme [0000-0003-3872-295X]
    Anthropogenic effects, including land-use and climate change, have had dramatic and wide-ranging impacts on the natural world. The impacts of these changes have already been detected in many systems, with global biodiversity and abundance of many taxa declining across spatial scales. The loss of biodiversity has knock on impacts to human society, which are only just beginning to be understood. Only with a detailed understanding of how species will respond to environmental changes, and with effective dissemination of this knowledge, can we hope to slow and halt biodiversity loss. In this thesis, I use butterflies as a model taxon to understand the responses of insects to changing habitat and microclimatic conditions. Insects are a diverse and globally distributed group of organisms that play fundamental roles in ecosystem processes, many of which are critical to human societies. Despite this, there is growing evidence that insects are declining at rapid rates around the world, and many of these declines have been attributed to anthropogenic change. Butterflies show detectable responses to environmental change, including spatial responses, such as range shifts, and temporal responses, such as changes to timing of life cycle events. They are diverse, wide-spread, and ecologically sensitive, with complex life cycles that differ in morphology, behaviour, and ecology, and therefore differ in their sensitivities and requirements. In my first data chapter, I use a systematic mapping method to screen, quantify and discuss current knowledge on butterfly responses to temperature. I found that Nymphalidae were the most studied family, likely owing to their high number of species, including large, charismatic and common species of cultural importance. In contrast, Riodinidae were rarely studied, likely due to their elusive nature and being concentrated in the tropics. The tropics were less studied than temperate regions, and more studies reported the responses of butterflies at the adult life stage compared to all other life stages combined. I found that of the responses recorded, behavioural responses were the least common. I found that *in situ* studies were more common than *ex situ*. Taken together, there is an incomplete understanding of butterfly responses to temperature, which may lead to ill-informed decisions. I make suggestions for how to resolve these knowledge gaps, including calling for an increased focus on the tropics, the establishment of more butterfly monitoring schemes, particularly in the global south and South America, incorporating non-adult life stages into butterfly monitoring schemes, and conducting more studies on species from under-represented families. In my second data chapter, I investigated the habitat associations of 11 species of day-flying Lepidoptera as larvae and their foodplants from four nature reserves in Bedfordshire, UK. These study sites were the focus of fieldwork for three data chapters (Chapters 3, 4, and 5). These associations were tested across two spatial scales relevant to both Lepidoptera and land-managers; the reserve-scale and the foodplant patch-scale. I also assessed whether these associations were related to ecological traits. At the reserve-scale, I found substantial variation across species, with a tendency for species that overwinter at non-adult life stages to have stronger habitat associations. The majority of species shared similar habitat associations as their foodplants, indicating that management that benefits foodplants will also benefit these Lepidoptera. However, there were notable exceptions to this, with some species (*Erynnis tages*, *Cupido minimus*, *Polyommatus coridon*, *Aglais urticae*) having conflicting habitat associations with their foodplants, and therefore requiring focused management. At the foodplant scale, four species were associated with specific foodplant characteristics; two with taller foodplants (*C. minimus*, *Anthocharis cardamines*), and two with dense foodplant patches (*Aglais io*, *A. urticae*). These habitat associations can be used to manage for these species and their foodplants. In my third data chapter, I use a single species approach to highlight how citizen science data from butterfly monitoring schemes can be used alongside habitat use data to provide a more complete picture of how species change over time, focusing on the small blue (*C. minimus*). I used 26 years of data from the national UK Butterfly Monitoring Scheme and four years of targeted egg surveys across 14 years to investigate the effects of local temperature on small blue emergence date and total abundance, and whether foodplant characteristics predicted oviposition behaviour. I found that adult small blues were emerging earlier over time, which correlated with higher maximum temperatures in February. In contrast, total abundance was not related to temperature, or abundance in the previous year. Oviposition behaviour was broadly consistent across time, with females selecting foodplants that were tall and apparent, surrounded by taller vegetation, and in low density patches. These results imply that management for greater availability of tall foodplants surrounded by tall vegetation would encourage oviposition across a greater number of flowers, reducing competition and improving larval survival in this rare and declining species. In the fourth data chapter, I investigated the capacity of 14 species of day-flying Lepidoptera to thermoregulate, whether this was influenced by morphological or ecological traits, and whether this capacity differed between adults and larvae. I also investigated what mechanisms species used to thermoregulate, and whether this differed between life stages. I found that larvae were worse at thermoregulating than adults, and that thermoregulatory capacity differed between families, species, and with body length, whereby Pieridae were better at thermoregulating than Nymphalidae, and large larvae were better at thermoregulating than small larvae. I found that adults relied on behavioural thermoregulation, whereas larvae relied more on microclimate selection. This implies that larvae are more dependent on their immediate area to thermoregulate than adults, and that management should maintain or protect vegetation surrounding butterfly foodplants to allow larvae to thermoregulate effectively under climate change. Finally, in the last data chapter, I investigated the impacts of temperature on tropical butterflies. I collected field data on 54 butterfly species in Panama, and also conducted heat knockdown assays on a subset of these species (24) in the lab, to determine whether ecological traits influenced the ability of tropical butterflies to thermoregulate, whether similar ecological traits also influenced thermal tolerance, and whether there was an interaction between the capacity to thermoregulate and thermal tolerance. Thermoregulation and thermal tolerance were influenced by family, wing length, and wing colour, with Pieridae, and butterflies that were large or dark having the strongest ability to thermoregulate, but Hesperiidae, small and dark butterflies tolerating the highest temperatures. There was also an interaction between capacity to thermoregulate and thermal tolerance, whereby species better at thermoregulating had lower thermal tolerance, and vice versa. This implies that species with more stable body temperatures in the field may be more vulnerable to increases in ambient temperatures than previously thought, particularly extreme temperatures such as heatwaves. Butterflies make a valuable taxon to investigate responses to environmental change. Though there are gaps in our understanding, I have started to address these, and made suggestions for future research directions. I have identified species, life stages, and ecological traits that make some butterflies more vulnerable to change than others. I have demonstrated that sensitivity to change differs across the life cycle, and these differences will require different management strategies. Crucially, this highlights that butterfly responses to environmental change can be predictable, and therefore can be managed for to improve butterfly conservation.
  • ItemOpen 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.
  • ItemOpen 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.
  • ItemOpen 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.
  • ItemEmbargo
    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.
  • ItemOpen 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.
  • ItemOpen 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.
  • ItemEmbargo
    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.
  • ItemOpen 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.
  • ItemEmbargo
    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.
  • ItemEmbargo
    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.
  • ItemOpen 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.
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    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.
  • ItemOpen 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.