This thesis explores the far-reaching impacts of sexual conflict over care on a suite of traits in the penduline tit family (Remizidae), further confirming the intricate relationships between parental care, mating systems and sexual selection. The results reveal the first genetic phylogeny of this family and suggest that uniparental care evolved once in this group. The transition to uniparental care is associated with rapid evolution of male plumage ornaments most likely driven by increased sexual selection. The results also suggest a relationship between male care and the likelihood of paternity on an evolutionary time-scale, as the biparental species exhibit much lower levels of promiscuity than the uniparental European penduline tit. Increased promiscuity was also found to impact sperm morphology in the penduline tits and allies with greater sperm length uniformity in more promiscuous species. This sperm trait was also discovered to co-vary with a sexually selected plumage trait in the European penduline tit suggesting potential interactions between female mate choice and male fertility. An investigation into genetic diversity within the Sylvioidea super-family finds large variation but does not suggest any link between promiscuity and genetic diversity as predicted if promiscuity maintains a higher effective population size in these passerines. The work highlights the interlinked relationships between parental care, mating systems and sexually selected traits, which are increasingly studied in concert. The consequences of sexual conflict over care appear to be far-reaching in the penduline tits, however the degree to which they feedback upon each other and the effect that it has on speciation remains to be seen. The penduline tits further prove their ability to provide valuable insight into the evolution of sexual conflict.

Growth rates are highly variable, both within and among genotypes and populations. The resolution of the trade-off between size and age at maturity has been the study of extensive research by life historians. The fitness advantages of large body size and rapid development time are well supported, leading to two predictions. First, realized growth rates should be maximized. Second, growth rate will be subject to strong stabilizing or directional selection, and consequently, low genetic variability. In real populations, despite the advantages of rapid growth, animals often, in fact, grow at rates lower than the maximum rate that is physiologically possible, even in the absence of external constraints on growth rate (e.g. resource restriction or risk of predation while foraging). This implies that growth may have direct fitness consequences that are independent of the size and age of maturity, thereby lowering the optimal rate of growth. In addition to inducing plastic declines in growth rate, such costs may also select for lower intrinsic rates of growth. Despite the strong fitness effects arising from attaining a large body size quickly, variation in growth rate persists at both the phenotypic and genetic levels. The evolutionary and ecological factors contributing to this variation in growth rate are the focus of this thesis. Growth rate variation in insect model species was produced by the manipulation of resource levels during development. By comparing fitness-associated traits and body composition of adults from different treatment groups, I identify direct costs of rapid growth that could explain why animals benefit from growth at submaximal rates. In the second part of the thesis, the relationship between environmental variation and genetic variance in growth rate is investigated by quantitative genetic analysis of body size at different ages and in different growth environments. The results of this analysis suggest that environmental stress can lead to increased genetic variance via decanalization. This has consequences for the evolvability of growth rates in changing environments.

Growth rates are highly variable, both within and among genotypes and populations. The resolution of the trade-off between size and age at maturity has been the study of extensive research by life historians. The fitness advantages of large body size and rapid development time are well supported, leading to two predictions. First, realized growth rates should be maximized. Second, growth rate will be subject to strong stabilizing or directional selection, and consequently, low genetic variability. In real populations, despite the advantages of rapid growth, animals often, in fact, grow at rates lower than the maximum rate that is physiologically possible, even in the absence of external constraints on growth rate (e.g. resource restriction or risk of predation while foraging). This implies that growth may have direct fitness consequences that are independent of the size and age of maturity, thereby lowering the optimal rate of growth. In addition to inducing plastic declines in growth rate, such costs may also select for lower intrinsic rates of growth. Despite the strong fitness effects arising from attaining a large body size quickly, variation in growth rate persists at both the phenotypic and genetic levels. The evolutionary and ecological factors contributing to this variation in growth rate are the focus of this thesis. Growth rate variation in insect model species was produced by the manipulation of resource levels during development. By comparing fitness-associated traits and body composition of adults from different treatment groups, I identify direct costs of rapid growth that could explain why animals benefit from growth at submaximal rates. In the second part of the thesis, the relationship between environmental variation and genetic variance in growth rate is investigated by quantitative genetic analysis of body size at different ages and in different growth environments. The results of this analysis suggest that environmental stress can lead to increased genetic variance via decanalization. This has consequences for the evolvability of growth rates in changing environments.

Every organism needs to survive and successfully reproduce in the face of changing environmental conditions in which variation in resource availability can seriously limit performance. Organisms can respond to the variation in quality or availability of food resources with behavioural and physiological accommodations going from the baseline physiological response to environmental stressors to complex life-history strategies like migration and diapause. In insects, one avenue to cope with the resources’ variation is to plastically tune the reproductive system to the environmental conditions in order to shift resources away from reproduction during unfavourable periods but maximize it when resources are abundant. I studied the role of reproductive physiology in both males and females in mediating a response to challenging conditions determined by a lack of food resources or the presence of qualitatively different diets using the milkweed bug, Oncopeltus fasciatus, as model species. I studied the role of oosorption, a plastic physiological response through which resources can be recovered and redirected to body maintenance and survival, in shaping behavioural strategies to cope with challenging environments. I also studied the effects of diet quality on male’s sexual behaviour and how these modulate the trade-offs between reproduction and survival. I then investigated how the effects of diet quality, sexual maturation and rearing conditions influence the occurrence of reproductive diapause in both males and females. I found that females exposed to different diets plastically adapt their schedule of reproduction depending on diet quality: this also influences the occurrence of oosorption in the ovary mediating the amount of resources that are directed to reproduction or survival. Diet quality influences males’ sexual behaviour so that even after a long-term adaptation on an alternative artificial diet, they invest more in reproduction at the expenses of survival when fed on an ancestral high quality diet; this is achieved with a shift in the trade-off between reproduction and survival. The occurrence of reproductive diapause in both males and females is a function of several factors: the quality of food resources ultimately modulates sexual maturation in adult individuals determining the occurrence of diapause or reproduction. Finally, oosorption may be involved in the evolution of alternative condition-dependent strategies as an adaptive physiological mechanism to cope with stressful environments; thus females from different populations may be able either to migrate in favourable areas where they can exploit abundant food resources or remain residents and perform high levels of oosorption to cope with the seasonal shortage of food.

While there is increasing interest in the evolutionary consequences of species invasions on native plant communities, the connection between the phylogenetic relatedness of invaders and natives, and its evolutionary consequences, has not yet received much attention. One way to examine the role of relatedness on the impact of species invasions is through the use of meta-analytical techniques combined with a phylogenetic framework. I apply this technique and expand on a prior meta-analysis by Oduor (2013), in order to compare how native plant species that either have prior experience coexisting with an invasive (‘experienced’) or do not (‘naïve'), differ in terms of their growth and reproduction in the presence of the invasive for evidence of a phylogenetic signal in their response to plan invasions. My results suggest that the effects of a species invasion on native growth and reproductive traits may be greater when the native and invasive species are distantly related, and/or when the invasive species is allelopathic, but only in the presence on the invader. I also found that the negative effect of competition with an invader on native growth traits tended to be greatest when the native and invasive species were closely related, suggesting that the strength of competition and the evolutionary response of native plants to invasive plants may not be as closely associated as it is often assumed. Overall, my analysis suggests that future studies may benefit from integrating phylogenetic relatedness when exploring native evolutionary responses to invasions, but that considerable work need sot be done to tease apart the roles of relatedness and competition.

Thesis (PhD)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: How organisms respond to unpredictable environments is a fundamental question in evolutionary ecology. For example, plants may reduce the risk of reproductive failure by spreading their reproductive effort in space (dispersal) or in time (dormancy, iteroparity). Similarly, different plant breeding systems, (for example the ability to autonomously self-fertilise) may reduce the risk of reproductive failure in environments where pollination in particular is unreliable. Each of these strategies may be affected by selective pressures exerted by heterogeneous abiotic and biotic environments (e.g. unreliable rainfall patterns or range edge habitats). However, there is little theoretical or empirical consensus on how these strategies are related. In Chapter 2, I explore the association between dispersal and breeding system traits and range edge proximity. I show that annual daisies from Namaqualand, South Africa, are characterised by two discreet syndromes: high selfing ability associated with good dispersal and obligate outcrossing associated with lower dispersal, regardless of range position. This chapter illustrates that selection on both breeding system and dispersal traits may act consistently across distribution ranges. Because co-flowering plants often share pollinators, their fecundity is likely affected by changes in pollinator visitation rates or the transfer of conspecific relative to heterospecific pollen. In Chapter 3 I experimentally investigate the effects of con- and heterospecific density and spatial distribution pattern on pollination and fecundity in annual Namaqualand daisies. I show that increasing conspecific density and aggregation enhanced fecundity through increased mate availability and reduced heterospecific interference, independent of pollinator visitation rates. Moreover, I demonstrate the benefits of autonomous selfing when mates are limited and the potential for interspecific pollen transfer is high. In Chapter 4, I examine relative investment in dispersal vs. dormancy in seed heteromorphic Dimorphotheca (Asteraceae) species in relation to life history, rainfall unpredictability and range edge proximity. I show annuals and perennials differ significantly in the relative investment in different dispersal strategies. However, my findings provide little support for theoretical predictions of bet-hedging strategies in unpredictable or range edge habitats. This chapter emphasises the role of local environmental factors on fruit set that may obscure expected patterns across broad climatic gradients. Because of different costs and benefits of dispersal in space and time, we may expect negative patterns of covariation among dispersal and dormancy as alternative risk-reducing strategies. In Chapter 5, I provide evidence for a trade-off between these traits across 27 wind- dispersed daisy species from South Africa. This trade-off did not depend on life history effects, but was inconsistent at different levels of biological organisation. I also show that the effects of life history on spatial and temporal dispersal were inconsistent. Taken together, my research illustrates the importance of simultaneously investigating different risk-reducing strategies, because associations among them are clearly complex and often contradict theoretical expectations. Moreover I show that the effects of life history and phylogenetic relatedness cannot be disregarded. My findings underscore the importance of dispersal in space and time as well as autonomous selfing as risk-reducing responses to unreliable environments.

Herbivory by Western Flower Thrips (Frankliniella occidentalis Pergande) (WFT) and drought-stress due to limited water availability are currently two major factors that can severely impact cotton (Gossypium hirsutum L.) production. This dissertation examines the effects of drought-stress on cotton and host-plant resistance (HPR) to WFT in laboratory conditions, and seeks to identify the physiological and morphological mechanisms that underlie drought-tolerance and HPR. A life-history systems-approach was developed that provides a new level of detail for understanding how environmental variation impacts adult female WFT. The approach was illustrated by investigating the combined effects of cotton genotype, periodic drought-stress, and prey availability on the adult female omnivorous thrips using a factorial design. Three treatment conditions were significantly different, none of which were predicted based on prevailing ecological-hypotheses. At the same time, the approach produced three novel insights about WFT life-history and reproductive strategy. The roles of negative photo-taxis and leaf biomechanical properties were investigated as potential mechanisms that influence WFT foraging-decisions on individual cotyledons. Results showed that WFT foraging-decisions could be considered adaptive, but there was limited support for either of the mechanisms investigated. The physiological responses to drought stress and drought recovery were investigated for three transgenic cotton cultivars and an untransformed wild-type (WT). At peak drought, ABA levels, stomatal area, and stomatal apertures in the transgenic isolone, AtRAV1-1 were 48% lower, 27.7%, and 16.3% smaller than WT. These results suggest that AtRAV1-1 was the most drought-tolerant and support the hypothesis that changes in stomatal morphology may have functionally contributed to drought-tolerance. Lastly, I investigated whether changes in phytohormone concentrations associated with periodic-drought stress in four cotton cultivars (three transgenic and WT) were correlated with WFT feeding, fitness and state-dependent reproductive responses (i.e., the relationship between initial weight and reproduction). Results showed that JA-Ile and JA were positively correlated with state-dependent egg viability and fecundity, respectively, and negatively correlated with total egg viability and fecundity, respectively, supporting the hypothesis that JA and JA-Ile underlie the negative effects on WFT reproduction and the associated shift to state-dependent reproduction.

Previous studies of the relationship between egg size and the embryonic development time showed a positive correlation between the two variables at interspecies level, thus offering the idea that the evolution of the latter could be a limiting factor for enlarging the size of eggs during evolution. Some research into interspecies and intraspecific level of reptiles doesn't confirm this correlation. At the same time, the relationship between the development time and egg size is influenced by many factors, such as shifts in ontogenetic stages of the embryo at the time of ablation of eggs, due to temperature and humidity, the presence of embryonic diapause during embryogenesis or synchronization of hatching time, of which the authors of previous studies took no account or filtered out inaccurately. I think that most of these factors can be well controlled in intraspecific studies, but, variation in egg size within species also tends to be small, which prevents a reliable test for correlation. The solution can be to compare closely related species with high variability in the size of the eggs, in our case the geckos of the genus Paroedura and family Eublepharidae. I eliminated temperature effects by comparing the time of incubation in two equal constant temperatures. The results show that, in this...

Doctor of Philosophy / Department of Biology / Michael Tobler / Extremophiles are organisms with the ability to survive in environments characterized by strong physicochemical stressors lethal to most other organisms, providing excellent models to further our understanding of life's capacities and limitations to deal with far-from-average conditions. I studied how physiological processes varied among fish residing in starkly different environmental conditions to understand how organisms cope with extreme environments and disentangle the roles of short-term plastic responses and evolved population differences in shaping physiological responses. I used the Poecilia mexicana model, a series of extremophile fish populations that has colonized toxic hydrogen sulfide (H₂S) rich springs and caves, to address three major objectives: (1) I investigated the energetic consequences of life in extreme environments and tested whether predicted reductions in organismal energy demands evolved repeatedly along replicated environmental gradients. (2) I characterized variation in gene expression among populations and organs to test for interactive effects between different stressors and identify potential physiological mechanisms underlying adaptation to H₂S and cave environments. (3) I conducted common garden and H₂S-exposure experiments to test how evolutionary change and plasticity interact to shape variation in gene expression observed in nature. To address these objectives, I measured variation in metabolic physiology and quantified variation in physiological processes through genome-wide gene expression analyses. I found that adaptation to extreme environments directly impacts energy metabolism, with fish living in extreme environments consistently expending less energy overall. Reductions in energy demand have evolved in convergence and were primarily mediated through a life history shift (reduction in body mass). The quantification of gene expression across divergent habitats and organs revealed organ-specific physiological responses in H₂S-rich and cave habitats. Gene expression variation in the relevant genes was primarily shaped by evolutionary change in gene regulation, and ancestral plastic responses play a minor role in causing the observed expression differences between replicated sulfidic and nonsulfidic populations in nature. Overall, my research has implications for understanding the capacities and constraints that shape life in extreme environments and aids in our understanding of modifications in physiological pathways mediating adaptation to elevated H₂S and perpetual darkness.

The evolution of disease resistance in plants occurs within a framework of interacting phenotypes, balancing natural selection for life-history traits along a continuum of fast-growing and poorly defended, or slow-growing and well-defended lifestyles. Plant populations connected by gene flow are physiologically limited to evolving along a single axis of the spectrum of the growth-defense trade-off, and strong local selection can purge phenotypic variance from a population or species, making it difficult to detect variation linked to the trade-off. Hybridization between two species that have evolved different growth-defense trade-off optima can reveal trade-offs hidden in either species by introducing phenotypic and genetic variance. Here, I investigated the phenotypic and genetic basis for variation of disease resistance in a set of naturally formed hybrid poplars. The focal species of this dissertation were the balsam poplar (Populus balsamifera), black balsam poplar (P. trichocarpa), narrowleaf cottonwood (P. angustifolia), and eastern cottonwood (P. deltoides). Vegetative cuttings of samples were collected from natural populations and clonally replicated in a common garden. Ecophysiology and stomata traits, and the severity of poplar leaf rust disease (Melampsora medusae) were collected. To overcome the methodological bottleneck of manually phenotyping stomata density for thousands of cuticle micrographs, I developed a publicly available tool to automatically identify and count stomata. To identify stomata, a deep con- volutional neural network was trained on over 4,000 cuticle images of over 700 plant species. The neural network had an accuracy of 94.2% when applied to new cuticle images and phenotyped hundreds of micrographs in a matter of minutes. To understand how disease severity, stomata, and ecophysiology traits changed as a result of hybridization, statistical models were fit that included the expected proportion of the genome from either parental species in a hybrid. These models in- dicated that the ratio of stomata on the upper surface of the leaf to the total number of stomata was strongly linked to disease, was highly heritable, and wass sensitive to hybridization. I further investigated the genomic basis of stomata-linked disease variation by performing an association genetic analysis that explicitly incorporated admixture. Positive selection in genes involved in guard cell regulation, immune sys- tem negative regulation, detoxification, lipid biosynthesis, and cell wall homeostasis were identified. Together, my dissertation incorporated advances in image-based phenotyping with evolutionary theory, directed at understanding how disease frequency changes when hybridization alters the genomes of a population.