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Additional file 1: Figure S1. Schematic of calcium cycling in a cardiac muscle cell (pink oblong). Unidirectional calcium transporters are indicated by orange or blue rectangles. Bidirectional calcium transporters are indicated by green circles. Orange transporters and arrows show direction of transport associated with influx of calcium into the cytosol (light pink shaded area) associated with contraction in myofilaments. Blue transporters and arrows show direction of transport associated with efflux of calcium from the cytosol into the sarcoplasmic reticulum (SR, white oblong) or extracellular space.

The kentia palm (Howea forsteriana) is endemic to a 12 km2 volcanic island in the Tasman Sea, Lord Howe Island. It is one of the most traded houseplants in the world. The typical kentia palm presents a dark green-coloured stem. Note that the stem is made of leaf rachis and petioles, which are intermingled towards the base. However, we discovered on Lord Howe Island a new biological variety that has a red stem. Red-stemmed palm species are known and highly demanded as decorative plants. However, these red palm horticultural varieties require tropical or subtropical conditions to grow, hence commercialization is limited. Thus, a red-stemmed variety of H. forsteriana may have tremendous market potential. Nonetheless, palm trees grow generally slowly and often reach maturity at 15–20 years old or later, which may make conventional strategies unsuitable for the propagation of a new variety. This difficulty needs to be addressed before commercialization can be achieved. Here, we found that anthocyanin is responsible for the red colouration of the stem in the new variety. Using RNA sequencing and quantitative PCR, we identified two gene isoforms displaying altered expression associated with this red colouration, encoding a cytochrome b561 and a chalcone synthase. The latter protein is known to be part of the anthocyanin biosynthesis pathway, which plays a central role in pigmentation in plants. The levels of cytochrome b561 transcripts accumulated were found to be well correlated with an increased anthocyanin concentration in the red stems.

Phylogenetic tree of sharks. Based on analyses of 1,197 genes (1,101,288 bp per species). Species are named along with the orders and families they belong to. ‘Lam.’ refers to Lamniformes order and ‘Tri.’ refers to Triakidae family. The non-placental species are shown in red. Each node is supported with a bootstrap value of 100 %. (PDF 25 kb)

DNA that survives in museum specimens, bones and other tissues recovered by archaeologists is invariably fragmented and chemically modified. The extent to which such modifications accumulate over time is largely unknown but could potentially be used to differentiate between endogenous old DNA and present-day DNA contaminating specimens and experiments. Here we examine mitochondrial DNA sequences from tissue remains that vary in age between 18 and 60,000 years with respect to three molecular features: fragment length, base composition at strand breaks, and apparent C to T substitutions. We find that fragment length does not decrease consistently over time and that strand breaks occur preferentially before purine residues by what may be at least two different molecular mechanisms that are not yet understood. In contrast, the frequency of apparent C to T substitutions towards the 59-ends of molecules tends to increase over time. These nucleotide misincorporations are thus a useful tool to distinguish recent from ancient DNA sources in specimens that have not been subjected to unusual or harsh treatments.

Sexual conflict arises when the fitness interests of males and females diverge, leading to genes and traits that have antagonistic fitness effects across the sexes. This thesis uses theoretical models to examine the causes and consequences of such conflict, focusing on the roles of population ecology and genetic architecture in shap- ing evolutionary responses to sex-specific selection. Chapter 1 investigates the demographic consequences of selection on males to harm or harass females in order to improve their own mating success. It shows that such male harassment traits readily evolve condition-dependence, whereby individuals in good condition, or of high genetic quality, express more harm. Consequently, intensified sexual conflict can lead high-condition populations to show reduced population size and greater extinction risk, contrary to the commonly held view that individual condition is positively correlated with population viability. Chapter 2 concerns the segregation of sexually antagonistic alleles, genetic variants beneficial to one sex but harmful to the other, in spatially subdivided populations. It shows that a species’ dispersal pattern modulates the evolutionary dynamics of such alleles due to the effects of kin selection. Thus, dispersal ecology can determine which sex is better adapted to its environment, and how much genetic variation is maintained in populations. Finally, Chapter 3 asks how frequently sexually antagonistic alleles arise from sex-specific selection on complex traits (those encoded by many interacting loci). It investigates how antagonism may be resolved through expression modifiers, showing that variation in genetic architecture (such as the number and distribution of fitness effects across trait loci) favours different patterns of sex-specific versus sex-limited gene expression, and that this can drive outbreeding depression in dispersal-limited populations. Together, the chapters of this thesis demonstrate that aspects of trait genetic architecture and a species’ population ecology that have been underappreciated in previous theory, are relevant to the outcomes of sexual conflict. Open Access

Regional endothermy, where metabolically-derived heat is used to maintain elevated temperatures in parts of the body, has independently evolved in several lineages of pelagic, predatory fish, including billfish, tuna, lamnid sharks and the opah. The lamnid sharks and tunas demonstrate a striking phenotypic convergence, despite 450 million years of independent evolution. This is characterised by a distinctive muscle morphology, which has enabled them to utilise a unique stiff-bodied swimming style and maintain elevated muscular temperatures and metabolic capacities. This has facilitated expansions in thermal niche and increases in swimming speed and exercise recovery rate. We find selection has acted on one gene independently in both groups, glycogenin-1, which is associated with post-exercise glycogen replenishment. Different metabolic pathways have been targeted by selection in either group. Amongst the endothermic fish, there is considerable variability between species in endothermic capacity and cold-tolerance. By investigating diversification among the eight Thunnus tuna species, we find that the three highly cold-tolerant and endothermic bluefin tuna species are paraphyletic. We infer that parallel selection on ancestral genetic variation is likely to have enabled their evolution. This includes selection for variants in genes associated with metabolism and thermogenesis in other animals. Adaptations in the cardiac system of bluefin tuna are crucial to their ability to tolerate cold-water, as their heart operates at ambient temperature yet must supply oxygen for metabolically demanding warm muscle. We show that this elevated cardiac capacity is associated with increased expression of a key sarcoplasmic reticulum calcium-cycling gene, SERCA2b, in the atrium. Tuna muscle has a thermal gradient, with temperatures highest in the centre of the body. We found no upregulation of metabolic or thermogenesis genes in regions of warm muscle, indicating that intrinsic muscular contraction is sufficient for heat production. Our results provide insight into the genomic basis of endothermy in fish. Open Access

As global landscapes and habitats become increasingly fragmented under pressure imposed by anthropogenic development, it is essential that we gain a better understanding of species functional responses to such change and the degree of connectivity between populations. I use African lions (Panthera leo) as model species and ask how natural and anthropogenic barriers affect lion dispersal across the multiple geopolitical boundaries of the Kavango-Zambezi Transfrontier Conservation Area (KAZA-TFCA). A better understanding of inbreeding depression, gene flow, loss of genetic diversity and the implications of genetic supplementation are all highlighted by the IUCN Cat Specialist Group as important for guiding future conservation plans. This research will give conservation stakeholders an insight into how these genetic factors can be influenced by the management of landscapes and populations with a view to improving the chances of long-term conservation success. Using genetics to assess functional connectivity, I determine the important isolating mechanisms across the landscape, testing both environmental and anthropogenic drivers, with a view to guiding future management of this mammal. I demonstrate how genetics can reveal unexpected cryptic patterns of gene flow that more traditional methods may miss. Furthermore, I identify patterns of gene flow and dispersal across the landscape to assess the feasibility of the KAZA TFCA to successfully conserve the species. Incorporating DNA from 19th century museum collections, I develop an assessment of how population genetic diversity has changed over time, with respect to human activities, and its relevance to conservation status. The results of the genetic analysis are finally incorporated into a population viability assessment to predict how potential future management actions are likely to affect the persistence of this lion population, one of the last remaining lion strongholds in Africa. The results demonstrate that the lion population is differentiated into two distinct genetic groups, one inhabiting the wetland Okavango Delta and the other inhabiting the surrounding dryland Kalahari. Further genetic substructure divides the population into distinct units, largely corresponding to the Wildlife management zones of the KAZA protected area network and likely a consequence of fragmentation, but which could realistically be reconnected given appropriate management of the intervening habitat matrix. Analysis of the historical samples identifies a considerable decline in the genetic diversity of this lion stronghold corresponding with the arrival of European settlers to the region, and a likely increase in persecution of the species and landscape alteration. Finally, modelling of future management scenarios suggests that continued fragmentation of the area, through increased habitat encroachment or even intensive management interventions such as fencing, will likely lead to a dramatic decline in the population due to the effects of inbreeding depression. Conversely, given the reconnection of the protected area network and therefore the promotion of low-level dispersal, my analysis predicts the long-term persistence of the lion population in this region. Open Access

Members of the annual killifish genus Austrolebias live in temporary ponds across South America and possess a remarkable life cycle. These fish live in small ponds that dry out completely; killing the adults but not before they have laid eggs in the substrate of their pond. The desiccation-resistant eggs develop during the dry season, going through multiple stages of diapause until the next wet season rains trigger hatching and the cycle is repeated. There is considerable variation in size in Austrolebias, the largest species can reach up to 150mm in length while the typical size is just 40mm. Phylogenetic trees and species distribution models were built and used together to identify the factors that influence patterns of co-occurrence within this genus. Differences in growth and morphology among Austrolebias species were examined to quantify how differences in growth pattern can lead to the large variation in size and shape seen within the genus. Genomic data was generated for hybrid offspring of two species of Austrolebias using double-digest RAD sequencing. These data were then used to build linkage maps that were in turn used to identify any regions associated with sex determination and potential chromosomal rearrangements. At a broader scale, a generic-level tree for the order Cyprinodontiformes was constructed. Austrolebias is a member of this order, as well as many model fish genera such as Fundulus, Nothobranchius and Poecilia. Two extraordinary reproductive life-history adaptations have evolved in this order; viviparity and annualism. The new tree was used to determine whether the evolution of viviparity or annualism lead to increased rates of diversification. Finally this generic-level tree was used to examine patterns of positive selection in the low-light vision gene, rhodopsin and whether sites under selection were linked to functional changes. Open Access

Deer have been introduced outside their native ranges numerous times worldwide, causing significant economic and environmental impacts. The scale of problems caused by some introduced deer species is expected to increase, while others are relatively harmless and may be important for conservation as their numbers decline in native regions. This thesis examines the factors promoting invasion in non-native deer, and investigates the population genetics of two deer species introduced to Great Britain. Factors hypothesised to predict invasion success were tested using a comparative analysis of the outcomes of introductions of non-native deer populations. Two modelling approaches were taken to account for confounding effects in species-level and population-level analyses, and different factors were found to explain success at different stages of the invasion process. Populations of roe deer expanding from refugia and reintroductions were examined, and differences in genetic diversity between core and peripheral populations, alongside a decline in diversity with rate of expansion from the core were found. High levels of differentiation between and among core and peripheral populations suggest that genetic drift is the major factor causing these patterns. Using a genome scan of British and European roe deer, loci potentially under selection were identified. Association between some of these loci and environmental variables suggests that climatic extremes may have a role in exerting selective pressures on roe populations. The Chinese water deer is severely declining in range and number in its native habitat, but rapidly expanding after being introduced to Great Britain. Relatively high levels of diversity in native Chinese populations, and significant differentiation between the Chinese and British populations were found. The source population of the British deer is likely to be extinct, and the level of genetic structuring indicates that conserving populations across both ranges is important to maintaining their diversity. Open Access

Lord Howe Island (LHI) is an ideal location for researching the speciation process. The diversity of unique species, its isolation and minute size offer a rare opportunity to investigate the contribution that speciation has made to the entire flora of an ecosystem. On LHI, speciation in sympatry has been documented previously in Howea palms and this project sought to investigate whether this divergence was an exceptional occurrence or if the process is more general. A phylogenetic approach was used to acquire the first estimates of the frequency of sympatric speciation and speciation with gene flow in a community of island plants. The results indicate that speciation with gene flow may be relatively common on LHI. Biogeographic patterns show that Australia is a major source of species for LHI and that, for a given region, the number of immigrants that can establish and speciate is dependent on dispersal limitation and niche conservatism. Speciation events in two genera (Metrosideros and Coprosma) were examined in greater detail to determine whether ecological divergent selection may have promoted the evolution of reproductive isolation. In both cases, evidence is presented demonstrating that natural selection, habitat isolation and competitive exclusion may have played vital roles in these speciation events. Closer examination of speciation in Coprosma revealed that six species have evolved following a single colonisation of LHI, the first documented evidence for a sympatric radiation in plants. Four of these species have evolved via speciation with gene flow and two species are derived from hybrid speciation events; supporting theories that speciation with gene flow and hybrid speciation may be integral to the onset of an adaptive radiation. Together with speciation in Howea, these new cases show that ecologically driven speciation with gene flow is an important source of biodiversity on LHI and potentially in other botanical communities.