BACKGROUND:A hub protein is one that interacts with many functional partners. The annotation of hub proteins, or more generally the protein-protein interaction "degree" of each gene, requires quality genome-wide data. Data obtained using yeast two-hybrid methods contain many false positive interactions between proteins that rarely encounter each other in living cells, and such data have fallen out of favor.RESULTS:We find that protein "stickiness", measured as network degree in ostensibly low quality yeast two-hybrid data, is a more predictive genomic metric than the number of functional protein-protein interactions, as assessed by supposedly higher quality high throughput affinity capture mass spectrometry data. In the yeast Saccharomyces cerevisiae, a protein's high stickiness, but not its high number of functional interactions, predicts low stochastic noise in gene expression, low plasticity of gene expression across different environments, and high probability of forming a homo-oligomer. Our results are robust to a multiple regression analysis correcting for other known predictors including protein abundance, presence of a TATA box and whether a gene is essential. Once the higher stickiness of homo-oligomers is controlled for, we find that homo-oligomers have noisier and more plastic gene expression than other proteins, consistent with a role for homo-oligomerization in mediating robustness.CONCLUSIONS:Our work validates use of the number of yeast two-hybrid interactions as a metric for protein stickiness. Sticky proteins exhibit low stochastic noise in gene expression, and low plasticity in expression across different environments.

For vector-borne parasites such as malaria, how within- and between-host processes interact to shape transmission is poorly understood. In the host, malaria parasites replicate asexually but for transmission via mosquitoes to occur, specialized sexual stages (gametocytes) must be produced. Once inside the mosquito vector, gametocytes immediately differentiate into male and female gametes, and motile male gametes must swim through the hostile environment of the bloodmeal to find and fertilise female gametes. Despite the central role that gametocytes play in disease transmission, explanations of why parasites adjust gametocyte production in response to in-host factors remain controversial. Furthermore, surprisingly little is known about the mating behaviour of malaria parasites once inside the mosquito. Developing drugs and/or vaccines that prevent transmission by disrupting sexual stages are major goals of biomedicine, but understanding variation in gametocyte investment and male gamete behaviour is key to the success of any intervention. First, I propose that the evolutionary theory developed to explain variation in reproductive effort in multicellular organisms provides a framework to understand gametocyte investment strategies in malaria parasites. I then demonstrate that parasites appear to change their reproductive strategies in response to environmental cues and in a manner consistent with our predictions. Next, I show how digital holographic microscopy can be used to characterise the morphology and motility of male gametes. I then provide evidence for non-random movement of male gametes and that gamete interactions with red blood cells appear to hinder mating success in a bloodmeal. Finally, I discuss the variation in gametocyte differentiation and fertilisation success when exposed to a number of factors implicated in gametocyte activation. The data presented here provides important information on the basic biology of malaria parasite reproductive stages and demonstrates considerable variation in parasite traits and behaviours in response environmental changes; both in the host and in the mosquito vector.

Earth mean surface temperature has increased by 1 °C since the industrial revolution, and this has already had considerable effects on animal and plant species. Ecological responses to the warming climate – often facilitated via phenotypic plasticity – are ubiquitous. However, even though evolution can occur rapidly there are only few examples of genetic adaptation to climate change. In my thesis, I used a near-natural system to study if and how organisms have adapted to 30 years of warming, and how this has affected competitive species interactions. I investigated Baltic Sea populations of the aquatic snails Galba truncatula and Theodoxus fluviatilis, which had been subjected to cooling water discharge from power plants, resulting in water temperatures 4 to 10 °C higher than in the surrounding sea. G. truncatula had high upper thermal limits and large acclimation potential. This plasticity may have helped the species to survive under the new conditions, allowing evolution through natural selection to take place. I found that the populations of the two thermal origins had diverged in SNP markers associated with warmer temperature, whereas divergence in selectively neutral markers was mainly related to geographical distance. Adaptation occurred from standing genetic variation, emphasizing the importance of genetic diversity and population size in enabling the persistence of populations. Changes in thermal sensitivity of growth and survival were subtle yet significant, and complied with theoretical models of thermal adaptation in ectotherms. At the community level, pre-adaptation to warmer conditions aided the native T. fluviatilis when competing with the alien Potamopyrgus antipodarum. However, interspecific competition limited the snails most in those traits favored under warming, highlighting the challenge of adapting to different selecting forces during global change. The persistence of species and populations under climate change depends on several factors - plasticity allowing for initial survival, evolvability in allowing the genetic changes, and species interactions affecting the new ecological niches. The results of my thesis indicate that persistence under climate change is possible when these factors align, but the relative roles of ecology and plasticity may explain why there are so few observed instances of evolution in response to climate change.

For insects that develop inside discrete hosts both host size and host quality constrain offspring growth, influencing the evolution of body size and life history traits. This dissertation examines the effects of host size, host quality, and intraspecific competition on life history and associated traits of populations of the seed-feeding beetle S. limbatus adapted to different host plants, and quantifies population differences in phenotypic plasticity. Populations of the study correspond to divergent clades of the species phylogeography (Colombia and United States). Clades compared differ genetically for all traits when beetles were raised in a common garden. Contrary to expectations from the local adaptation hypothesis, beetles from all populations were larger, developed faster and had higher survivorship when reared in Acacia greggii, the larger host. Two host-plant mediated maternal effects were found: offspring matured sooner, regardless of their rearing host, when their mothers were reared on Pseudosamanea guachapele and females laid larger eggs on Ps. guachapele. These results also show that this species in addition to be a smaller is a low quality host. Females also laid more eggs and sooner on A. greggii than in Ps. guachapele and, laid more eggs on P. guachapele when A. greggii seeds were small than when they were large. Eggs were larger when laid on Ps. guachapele and Parkinsonia florida, two hosts that reduce survivorship in all populations. However, Colombia females laid eggs of similar size on Ps. guachapele and Pa. florida, while USA females laid the largest eggs on Pa. florida. Larger beetles were most affected when larval competition was increased and seed size decreased. The responses of different body sized females were asymmetrical showing significant variation in plasticity. Although differences between populations in growth and life history traits appear to be adaptations to the size and quality of their host plants, host-associated maternal effects, partly mediated by maternal egg size plasticity play an important role in the evolution of S. limbatus’ diet breadth. More generally, phenotypic plasticity mediates the fitness consequences of using novel hosts, likely facilitating colonization of new hosts but also buffering herbivores from selection post-colonization.

Cyrba algerina is a salticid (Salticidae) spider that lives on the undersides of stones. Two populations were studied, Sintra and Algarve (Portugal), and shown to have similar phenology but different dominant prey. Life cycle in the laboratory was similar for the two populations, but Sintra matured at larger size than Algarve individuals, with these differences potentially having a genetic basis. Sintra individuals used prey-specific prey-capture behaviour against allopatric (Oecobius amboseli) and sympatric (O. machadoi, Trachyzelotes bardiae) spider and insect (bristletails) species. In contrast, Algarve C. algerina only adopted specialised capture behaviour against bristletails. Sintra, but not Algarve, individuals responded to the odour of O. machadoi and T. bardiae, and showed preference for T. bardiae over O. machadoi. Interpopulation variation in the use of specific prey-capture behaviour and in sensitivity to odour cues from prey is directly related to the prey available to individuals from each population, suggesting local adaptation to local prey. Preference for oecobiids seems to be controlled by an experiencetriggered developmental switch. The optics and histology of C. algerina’s principal eye suggest that living in a microhabitat with dim ambient light has favoured sensitivity at the expense of spatial acuity. Short focal length, reduced power of the eye’s diverging lens, and wide, contiguous rhabdomeres, seem to minimise the visual constraints imposed by the low light levels in C. algerina’s microhabitat. While relying solely on vision, C. algerina can detect, identify and capture prey in dim-light conditions under which other salticids perform poorly. C. algerina’s behaviour suggest use of temporal summation to improve its visual performance in dim light.

Hieracium lepidulum is an invasive weed in New Zealand. It colonises a wide range of habitats including pine plantations, scrubland, native Nothofagus forest, and mid-altitude to alpine tussock grassland, where it is competing with indigenous species. Understanding the breeding systems and population genetic structure of H. lepidulum is important for biocontrol, and aids in the understanding of evolutionary colonisation processes. H. lepidulum is a triploid, diplosporous, obligate apomict. This type of reproduction through clonal seed does not involve meiosis or fertilisation, and theoretically populations should contain very low levels of genetic variation, the only source being somatic mutation. Common garden experiments and microsatellite markers were used to determine the population genetic structure of H. lepidulum populations in the Craigieburn Range, Canterbury. Both experiments revealed that populations, sampled from three replicate altitudes within three geographically-separated locations, contained no genetic variation; individuals all possessed the same microsatellite genotype. These results strongly suggest that the Craigieburn Range H. lepidulum individuals reproduce solely by apomixis and populations belong to the same clonal lineage. Populations were also examined for their response to two abiotic environmental ‘stresses’, drought and shade. H. lepidulum populations’ exhibited high drought tolerance, yet appeared to be shade-intolerant. Low levels of reproduction in light-limiting habitats will prevent the invasion of H. lepidulum into closed-canopy forest habitats. H. lepidulum appears to have overcome the reduction in fitness associated with apomictic reproduction by phenotypic plasticity, fixed heterozygosity and polyploidy – all associated with increased vigour, fitness, and the ability to occupy broader ecological niches. This study’s results are hopeful for the development of biocontrol programs involving genotype-specific pathogens but suggest that grazing management may not succeed. The data will be useful for future comparisons of genetic structure during the course of H. lepidulum invasions and will contribute to the management of this invasive weed.

Thesis (MSc)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: To predict the influence of temperature increases on organisms, and their capacity to respond to climate change, information on the upper thermal tolerance of organisms and its plasticity is required. However, various factors, such as rate of temperature change, may influence basal thermal tolerance and plastic responses, and consequently the vulnerability of organisms to temperature change. Although slower rates of temperature change might be more ecologically relevant, the majority of thermal tolerance studies feature rates of temperature change that are faster than those experienced by organisms in nature. Additionally, studies using slower rates of temperature change have been criticized as factors such as changes in body condition and accumulation of stress over time may confound results. This study determined the influence of fast and slow rates of temperature change and plasticity, induced by acclimation to different temperature conditions for 5 – 15 days, on the upper thermal tolerance of marine amphipod and isopod species from sub-Antarctic Marion Island and South Africa. Using congeners, intra- and inter-specific comparisons of the upper thermal tolerance and plasticity of these organisms were made across geographical regions (South Africa vs. Marion Island), across sites within regions (West coast vs. South coast of South Africa) and between tidal zones. Overall, lower rates of temperature change were found to be associated with lower values of upper thermal tolerance. At fast rates of temperature change, acclimation at high temperatures was associated with an increase in thermal tolerance, whereas at slow rates, acclimation to higher temperatures either had no effect or caused a decrease in thermal tolerance. Furthermore, microclimate recordings suggest that these organisms likely experience rates of temperature increase that are intermediate between the fast and slow rates employed in this study. Thus, in nature these marine invertebrates have upper thermal tolerances that are higher than mean environmental temperature and can likely mount plastic responses during short-term temperature variation. At slow rates of temperature change, however, the upper thermal tolerance of these organisms approximates environmental temperature and plasticity is reduced, likely increasing vulnerability to high temperatures. At the intra-specific level, upper thermal tolerance and plasticity response varied based on mass and sex, however, these effects were species-specific. Isopods inhabiting cooler but more variable microsites on the West coast of South Africa had a higher upper thermal tolerance, but similar magnitude of plasticity, than a population of the same species from the warmer, less variable South coast. Generally, Marion Island species had a lower upper thermal tolerance but higher magnitude of plasticity than South African species. The variability reported here at different hierarchical and geographical scales could be linked to the distinct thermal environments experienced, and the differing physiological and behavioural responses of populations and species to their thermal environments. This variation in thermal tolerance might be critical during environmental change and suggests that species composition may be altered in the future. / AFRIKAANSE OPSOMMING: Om die invloed van temperatuur verhogings op organismes, en hul vermoë om te reageer op hierdie verandering, te voorspel, word inligting oor hoë temperatuur verdraagsaamheid van organismes en die plastisiteit hiervan, benodig. Verskeie faktore, soos die tempo van verandering, kan egter basale termiese verdraagsaamheid en plastiese reaksies beïnvloed. Dus, mag dit die tasbaarheid vir temperatuur verandering beïnvloed. Alhoewel stadiger tempo van verandering meer ekologies relevant kan wees, fokus die meerderheid van warm verdraagsaamheid studies op temperatuur veranderinge wat vinniger gebeur as wat ervaar word deur organismes in die natuur. Boonop word studies wat fokus op stadige veranderinge in temperatuur, gekritiseer omdat faktore soos ‘n verandering in liggaamstoestand en die opeenhoping van stres, potentieël die resultate kan belemmer. Hierdie studie ondersoek die invloed van vinnige en stadige temperatuur veranderinge en die plastisiteit, geïnduseer deur akklimasie, met betrekking tot verskeie temperature vir 5-15 dae. Ons fokus spesifiek op die hoë temperatuur verdraagsaamheid van mariene amphipod- en isopod spesies van sub-Antarktiese Marion Island en Suid Afrika. Deur gebruik te maak van spesies wat aan dieselfde genus behoort, is vergelykings getrek tussen intra- en inter-spesies verbande met betrekking tot hul termiese verdraagsaamheid en plastisiteit. Die studie is oor geografiese streke (Suid Afrika vs. Marion Island), tussen areas binne ‘n geografiese streek (Weskus vs. Suidkus van Suid Afrika) en tussen gety sones voltooi. Oor die algemeen was stadige temperatuur veranderinge geassosieër met ‘n laer termiese verdraagsaamheid vir hoë temperature. Met vinnige veranderinge in klimaat, was akklimasie by hoë temperature geassosieër met ‘n hoër temperatuur limiet, maar by stadige temperatuur veranderinge het akklimasie by hoë temperature geen effek gehad nie, of het ‘n afname in termiese verdraagsaamheid veroorsaak. Verder het mikroklimaat opnames aangedui dat hierdie organismes waarskynlik temperatuur verhogings ondervind in hul natuurlike habitat, wat intermediêre is van die vinnige en stadige veranderinge wat in hierdie studie gebruik is. Dus, in die natuur, het hierdie mariene invertebrate `n boonste termiese toleransies wat hoër is as die gemiddelde omgewingstemperatuur en kan hulle waarskynlik van platiese reaksies gebruik maak tydens kort-termyn temperatuur variasie. Gedurende stadige temperatuur veranderinge toon hulle alhoewel hoë termiese verdraagsaamheid teenoor die omgewingstemperature en plastisiteit is verminder, wat heel waarskynlik toenemende kwesbaarheid vir hoë temperature tot gevolg het. Op die intra-spesifieke vlak was wisseling in hoë termiese verdraagsaamheid gebaseer op liggaams massa en geslag, maar hierdie veskille was spesie-spesifiek. Isopoda wat koeler areas bewoon, met meer variasie in hul mikroklimaat, soos ondervind in die Weskus van Suid Afrika, het `n hoër termiese verdraagsaamheid. Maar, soortgelyke mate van plastisiteit, as 'n populasie van dieselfde spesie van die warmer, minder veranderlike Suidkus. Oor die algemeen het Marion-eiland spesies 'n laer termiese verdraagsaamheid, maar hoër grootte van plastisiteit as Suid-Afrikaanse spesies. Die veranderlikheid wat hier geraporteer is, kan op verskeie hiërargiese en geografiese vlakke gekoppel wees aan die unieke termiese omgewings wat hierdie organismes ervaar en aan die verskillende fisiologiese- en gedrags reaksies van populasies en spesies tot hulle termiese omgewings. Die variasie in termiese verdraagsaamheid kan krities wees tydens omgewingsverandering en dui daarop dat spesie-samestelling kan verander in die toekoms. / The British Antarctic Survey for funding

It is widely documented that non-human organisms express individual differences in behavioural patterns. For example individuals can be categorised as bold or shy and when these individual behavioural differences are consistent through time, they are termed behavioural types (BTs). In recent years research has identified that BTs often correlate across contexts/situations and these correlations are referred to as behavioural syndromes. Behavioural types and syndromes (i.e. personality) have also been implicated as major factors shaping population dynamics and the ability to buffer environmental disturbance. Recent theoretical predictions have proposed that BT variation may be underpinned by life-history strategies; however, these predictions have been little studied to date. Moreover, little research has focused upon environmental influences and the ontogeny of personality. In this thesis I use the Mangrove killifish (Kryptolebias marmoratus), a naturally occurring clonal vertebrate, as a model organism. This species presents a powerful tool providing the ability to replicate within and between isogenic genotypes in a controlled manner. Moreover the natural clonality expressed by this species permits environmental effects upon BT plasticity and BT-life-history interactions to be investigated within a developmental framework. In chapter 2, I present microsatellite genotyping results which show that the founding individuals used to propagate a laboratory population at The University of Exeter represent 20 genetically distinct homozygous genotypes. I additionally address five research questions exploring genotypic, environmental, and developmental effects upon three commonly studied BTs (exploration, boldness and aggression): Firstly; I ask do adult hermaphrodite and secondary males exhibit personality i.e. repeatable BT expression? In chapter 3, I present results showing that both of the sexes express short term personality. Moreover, I show that that genotype is an important factor influencing BTs expressed, regardless of sex, indicating underlying genetic control. Secondly I ask; does genotype level life-history variation underpin personality trait variation during ontogeny? In chapter 4, I show considerable developmental plasticity in behavioural expression between genotypes but not life-history and I find limited behaviour-life-history relationships during development. Thirdly I ask; does the rearing environment influence life-history and behavioural plasticity? In chapter 5, I show that in comparison to a control treatment, the presence of conspecifics during ontogeny results in an average reduction in behavioural scores; however, life-history was unaffected. In addition, I show that development in a low food environment lowered average exploration and growth rate but had no effect on boldness or aggression. Furthermore, fish exposed to a predation risk simulation during ontogeny exhibited similar behavioural scores as the control, yet this treatment generated BTs i.e. personality. My fourth question asks; does the parental rearing environment (utilised in chapter 5) influence behavioural expression in the next generation? In chapter 6, I show that transgeneratonal effects of each parental rearing environment influenced life-history but had a minimal effect upon behaviour in the next generation. Finally I ask; does kin or familiarity influence plasticity in associations and aggression? In chapter 7, I show that genotypes have the ability to discriminate kin and familiars and modulate aggression and association accordingly. These results support the concept that developmental and environmental induced plasticity may be more important than life-history in shaping behaviour. Furthermore, although adults exhibit personality and genotypic effects appear important, genotype interacts with environmental/experiential influences to differentially shape behavioural plasticity during ontogeny. I suggest that theoretical predictions regarding life-history may be insufficient to explain the complexity of animal personality in this species. I discuss these results within developmental and epigenetic frameworks with reference to the ecological significance of these patterns within this species and the animal kingdom as a whole.

Dans le contexte des changements climatiques, la capacité d’adaptation à la contrainte hydrique des arbres de plantation devient un enjeu majeur pour le maintien de leur productivité. La plasticité phénotypique des génotypes, facteur majeur de l’adaptation aux changements environnementaux, reste encore insuffisamment décrite chez les arbres forestiers, plantes pérennes à long cycle de révolution. Cette thèse se propose i / de caractériser la plasticité phénotypique pour deux clones commerciaux d’eucalyptus soumis à une contrainte hydrique au champ, ii/ d’identifier les caractères potentiellement adaptatifs (i.e. ceux présentant de l’interaction GxE) et iii/ de mettre en évidence les mécanismes moléculaires sous-jacents. Un dispositif expérimental mis en place en république du Congo a permis de comparer, à travers une approche intégrant différents caractères allant de l'expression de gènes à la production de biomasse, la réponse de deux génotypes d’eucalyptus soumis à des régimes hydriques différents au cours de la saison sèche sur les deux 1ères années de croissance. Les résultats montrent que si l’effet de la saison sèche est relativement similaire pour les deux génotypes (réduction des accroissements relatifs), le clone plus productif présente des accroissements très élevés en saison des pluies, et semble donc mieux optimiser des conditions environnementales favorables. La capacité d’ajustement physiologique, anatomique et moléculaire au niveau foliaire de ce génotype semble être un atout au maintien de ses capacités photosynthétiques.Cette thèse a permis de mettre en évidence certains critères (surface foliaire spécifique, accumulation de phénols, épaisseur de collenchyme dans les feuilles), qui pourraient permettre d’évaluer le potentiel adaptatif des populations d’eucalyptus, nécessaire à leur gestion durable des plantations. D’autre part, certains gènes impliqués dans la photosynthèse et le métabolisme secondaire, dont l’expression pourrait être liée à la variation de caractères phénotypiques ont été mis en évidence. L’identification de ces gènes constitue une première étape vers la compréhension des mécanismes moléculaires sous-jacents à la plasticité phénotypique chez l’eucalyptus. / In the context of climate change, the ability of industrial forest plantation to cope with water scarcity is becoming a challenge for productivity maintenance. The phenotypic plasticity of genotypes, a major factor of adaptation to environmental changes, is still insufficiently described for long-lived species such as trees. This thesis proposes i/ to characterize the phenotypic plasticity for two commercial eucalyptus clones that differ in terms of productivity, subjected to water stress in the field, ii/ to identify potentially adaptive traits (i.e. those revealing GxE interaction) and iii/ to highlight the underlying molecular mechanisms.A field trial installed in the Republic of Congo was used to compare, responses of two contrasted eucalyptus genotypes subjected to different watering regimes during the dry season on the first two years of growth. We used an integrative approach involving different traits from gene expression to biomass production.The results show that if the effects of the dry season were relatively similar for both clones (lower relative increments), the most productive clone displayed a higher growth increment during the rainy season, and seemed to take more benefits when environmental conditions become more favorable. The ability to adjust leaf physiological, anatomical and molecular traits of this genotype seems to be an asset to maintain its photosynthetic capacity.This thesis allowed to highlight some criteria (specific leaf area, carbon isotope discrimination, thickness of collenchyma and cuticle in leaves), which could help to assess the adaptive potential of Eucalyptus populations for sustainable management of planted stands. On the other hand, some genes whose expression may be related to variation in phenotypic characters were revealed. This set of genes is resource first step toward the understanding of the molecular mechanisms underlying phenotypic plasticity in eucalyptus.

Adaptive phenotypic plasticity is a key mechanism by which organisms deal with variation in many different aspects of their environment. Adaptive plasticity can occur in any trait, from aspects of biochemistry and morphology to behaviors. Because so many different traits can be plastic, organisms often respond plastically to a given change in their environment, such as an increase in temperature, with adaptive changes in multiple traits. Nevertheless, how these different plastic responses interact with each other and evolve together has received little attention. My research addresses these potential interactions among plastic traits and proposes new hypotheses regarding the causes and consequences of these interactions. It does so by focusing on heat avoidance in the caterpillars of Battus philenor (the pipevine swallowtail) which involves two distinct plastic mechanisms. First, the caterpillars can change color when they molt, a form of morphological plasticity in which they develop a red color under high temperatures which cools them by absorbing less solar radiation. Second, when the caterpillars become too hot, they will leave their host to seek cooler thermal refuges, a case of behavior as a form of plasticity. In terms of function, I demonstrated through field research that these two responses to high temperatures are largely redundant. Behavior provides a much stronger and faster response than color change, and red coloration provides little additional cooling when on a refuge. Instead, the primary benefit of color change is that it reduces the use of refuge seeking behavior, allowing the caterpillars to stay on their hosts longer. Using laboratory experiments, I demonstrated that this change in the use of refuge-seeking behavior with color occurs because color changes the cue for the behavior, body temperature, rather having any effect on how the caterpillar responds to that cue. Alternatively, similar experiments on caterpillars of varying sizes show that developmental size change lowers the body temperature at which caterpillars leave their host, demonstrating a change in the response to the cue (although larger caterpillars are also warmer, so both mechanisms are likely relevant for how size changes the expression of behavior). All of my research to this point was conducted on the local population in southern Arizona, which experiences quite high temperatures, but B. philenor is also found in much cooler environments, such as the Appalachian Mountains. Given this variation in their thermal environment, I used common garden experiments to compare the capacity for color change and refuge-seeking among B. philenor caterpillars from across the species range. Both color change and refuge seeking not only occurred in all populations, but also had the same reaction norms, occurring at the same temperatures and to the same degree. This is particularly notable for color change, which is not observed in the wild in northeastern populations, and thus has persisted despite minimal if any use. Overall, I have shown that studies of plasticity need to account for plasticity in different traits as well as the interactions between these forms of plasticity. My research on B. philenor provides a model for how to address these interactions, which future research can extend to additional organisms and environmental circumstances.