The Sea is the Limit: Foraging Ecology of Breeding Antarctic Procellariiformes Bentley, Lily In the dynamic marine environment, highly mobile predators are expected to select profitable foraging areas, especially when provisioning young in addition to meeting their own energy needs. Knowing how and where animals choose to forage is not only important to advance ecological theory, but also to assess and mitigate the impact of anthropogenic threats. In this thesis I examine the breeding-season foraging behaviour of several of the Procellariiformes, a wide-ranging, long-lived group of seabirds, many of which have experienced steep population declines since the mid-20th century. Advances in biologging technologies over the last four decades have made it possible not only to accurately track individual movements, but also to identify important behaviours at sea. In my first data chapter (Chapter 2), I combine data from multiple tag types to describe diving behaviour in three albatross species, and discuss the implications for both foraging ecology and bycatch susceptibility. Moving from foraging capability of the individual to foraging preferences at the level of genus, in Chapter 3 I analyse the divergent niches of a summer- and a winter- breeding species of Procellaria petrel. Here I compare the habitat preferences of Grey Petrels and White-chinned Petrels breeding at Gough Island and South Georgia, respectively. Using high-resolution remote sensing environmental data, I identify divergent foraging preferences in dynamic habitats. Finally, in Chapter 4, I compare habitat preferences and accessibility between the two species of Phoebetria albatrosses across six colonies. While most studies of habitat preference consider only a single species or site, here I investigate whether closely- related species inhabit the same ecological niche at sympatric and allopatric colonies throughout their range. I show that Light-mantled Albatrosses have a consistent foraging niche, whereas Sooty Albatrosses select different habitats in sympatry and allopatry. I then discuss the impact of interspecific competition on plasticity in habitat preferences in general. Overall, my thesis examines diverse aspects of seabird foraging ecology from the individual to community level, discusses habitat preferences (and their potential flexibility) in relation to species' evolutionary history and as drivers of community structure, and considers the implications for conservation planning.

Research data supporting 'Pollen-feeding delays reproductive senescence and maintains toxicity of Heliconius butterflies' Pinheiro De Castro, Erika; McPherson, Josie; Julian, Glennis; Mattila, Anniina; Bak, Søren; Montgomery, Stephen; Jiggins, Chris The dataset has information about Heliconius erato demophoon butterflies fed for 14d (young) and 45d (old) on three different diets: sugar only (N); sugar + supplement (C) ; sugar + pollen from flowers (F). These experiments were set up with 8 males and 8 females of similar size (~3 cm of forewing radius) per treatment (diet/age). At the end of the experiment, females were individually assay for fertility: number of laid eggs recorded and the total eggs per females collected for quantification of cyanogenic glucosides (CG) using target-metabolomic (HPLC-MS/MS). Recently ecloded butterflies (0d, unfed) was also collected as a baseline. All butterflies were also weighted and collected for target metabolomics at the end of the experiment.

Fossoriality In Snakes: Perspectives From Morphology And The Fossil Record Howard, Alexandra Snakes are a speciose clade of squamates that have diversified into almost all habitats, all with the same elongate limbless body plan. This thesis aims to improve scientific understanding of snake evolution by focusing on novel perspectives using both extant snakes and the fossil record. 1. Alternate phylogenetic positions of fossils affects body size estimates in snakes Body size is a readily available metric for both extant and extinct snakes. The competing hypothesis of ecological snake origins also predict different outcomes for the evolution of body size in snakes. I used a combination of ancestral state reconstructions, body size estimates of fossils from regression models, and evolutionary rate modelling to examine the evolution of body size in snakes, with a particular focus on early snake evolution. This project showed that snakes achieve a wide range of diversity of body size during the Cretaceous, trends that are not observed when using data from extant taxa. 2. Cranial osteology of Typhlopidae (Serpentes: Scolecophidia) Scolecophidia are a distinctive group of snakes that occupy the basal most diverging branches of the snake phylogeny. However, due to the small overall size of many taxa, they have been relatively understudied in regards to comparative anatomy. In this project I examined segmented CT scans of 10 different species of Typhlopoidea, the largest clade of Scolecophidia. Using these comparisons I identified variability in several morphological characters not previously thought to be variable in Scolecophidia, as well as the identification of features in large typhlopids such as the lateral wings of the basisphenoid, which were previously thought to be limited only to Alethinophidia. 3. Morphometrics provide evidence for the fossorial origin of snakes The problem of homoplasy, particularly in relation to adaptation to fossoriality, is potentially responsible for the incongruences between phylogenetic hypothesis of snakes that use either morphological or molecular data. In this project I used CT scans of 73 species of alethinophidian snake and geometric morphometrics to examine morphological correlates to fossoriality. I found that there is a clear morphological signal between the parietal of alethinophidian snakes and ecology. In general, the parietal of fossorial snakes is more elongate with a deep u or v shaped fronto-parietal suture, with an elongated posterior shelf that overlaps the braincase. These projects show how integrative research using both extant and palaeontological data can inform questions about the early evolution of clades, particularly the heavily debated ecological origin of snakes.

Tradeoffs and co-benefits among impacts of contrasting livestock systems Bartlett, Harriet Livestock farming generates some striking externalities; whilst it provides 30% of human dietary protein, it occupies 75% of agricultural land, emits 14-17% of anthropogenic greenhouse gas emissions, and uses more antimicrobials than human medicine. Demand for livestock products is high and rising, especially for pork which has quadrupled in the past 50 years. Livestock farming systems vary considerably in the scale of their externalities, but our understanding of how multiple externalities co-vary across contrasting production systems is limited. Research typically focuses on impacts in isolation, and the synergies or tradeoffs among them are assumed. To identify and promote the types of systems that best limit impacts or even carry co-benefits we need to explicitly consider multiple externalities and evaluate them across a wide range of alternative production systems. The main aim of my thesis was to do this for pig production. I recruited, visited, and evaluated over 100 pig farms in the UK and Brazil from those considered to be the most “intensive” through to those certified as Organic. My analyses treat a breed-to-finish system as a datapoint, which may consist of one or several farms (e.g. breeding, rearing and finishing farms). I developed metrics which advanced the quantitative characterisation of farm animal welfare to be compatible with life cycle assessments and to account for both quality of life and the quantity of life years required to produce a unit of product (Chapter 2). I systematically evaluated two externality costs that are commonly perceived to trade off against one another: land use and antimicrobial use (Chapter 3). I found weak evidence of a tradeoff between these externalities but importantly also found several systems characterised by low externality costs in both domains. These systems were spread across different label and husbandry types, and no type was an indicator of systems that performed well in both domains. I built upon these assessments of one or two costs by systematically contrasting the land use, greenhouse gas emissions, antimicrobial use and animal welfare of as many of my UK and Brazilian pig systems as possible (Chapter 4). I found evidence of positive associations between land use and greenhouse gas emissions, and antimicrobial use and poor animal welfare, but tradeoffs between these pairs of externalities - systems with low land use generally had low greenhouse gas emissions, but high antimicrobial use and poor welfare. Again however, I found systems that carried relatively low externality costs in all domains. I 6 conclude that contrary to prevailing wisdom, tradeoffs among these externalities are not inevitable. In parallel with this detailed work on pig production, I explored the viral zoonotic emerging infectious disease risks of contrasting ways of meeting livestock product demand (Chapter 5). Analyses to date typically ignore how land use affects emerging infectious disease risks. I created a framework that considered risk factors associated with livestock management and land use. I identified significant knowledge gaps and argued these shortfalls in understanding mean we cannot currently determine whether lower- or higher-yielding systems would better limit the risk of future pandemics. My findings challenge many commonly held perceptions about the externalities of farming systems and have important implications for mitigation strategies. My work illustrates the importance of using empirical evidence rather than relying on patchily supported assumptions. I believe that this warrants the systematic testing of other assumed relationships among externalities. I addressed some important knowledge gaps for the pork sector, and more broadly for emerging infectious disease risks, but the same must be done on a much larger scale, spanning other externalities and sectors.

Code supporting: pastclim 1.2: an R package to easily access and use paleoclimatic reconstructions Leonardi, Michela; Manica, Andrea; Hallett, Emily Y This supplementary material contains code (in R) to run the examples. $$ \ $$ Associated data. These are examples that can be used to familiarise with pastclim, an R package to easily access and use palaeoclimatic reconstructions. While the code for the examples is self-explanatory, more information on the software can be found on the following pages: $$ \ $$ Website: https://evolecolgroup.github.io/pastclim/ Github: https://github.com/EvolEcolGroup/pastclim Manual: https://rdrr.io/github/EvolEcolGroup/pastclim/ Vignette (general overview): https://evolecolgroup.github.io/pastclim/articles/a0_pastclim_overview.html Cheatsheet: https://evolecolgroup.github.io/pastclim/pastclim_cheatsheet.pdf $$ \ $$ Please cite the article and the source of the climatic data if using the package.