Populations of cells live in uncertain environments, where they encounter large variations in nutrients, oxygen and toxic compounds. In the fluctuating environment, cells can sense their surroundings and express proteins to protect themselves against harmful substances. However, if the stressor appears infrequently or abruptly, sensing can be too costly or too slow, and cells cannot rely solely on it. To hedge against the sudden appearance of a stressor, cell populations can also rely on phenotypic diversification through bet-hedging. In bet-hedging, cells exploit noise in gene expression or use multistable genetic networks to produce an heterogeneous distribution of resistance-conferring protein levels. In this thesis, we analyze novel roles of noise in biological systems. Through a combination of modeling and stochastic simulations, we find that noise can coordinate multi-component stress response mechanisms in a subset of the population with no extra cost. In addition, we use evolutionary algorithms to analyze the conditions where the benefits provided by noise in gene expression are equivalent to those of a more complicated, bistable distribution of protein levels. Our results show that for cells living in noisy fluctuating environments, both noise in gene expression and bistability show similar growth rates, meaning that noise in gene expression can be an effective bet-hedging strategy.

Most theoretical models predict an optimal offspring size that maximises parental fitness. Variation in the quality of the offspring environment can result in multiple offspring size optima and therefore variation of offspring provisioning can evolve. Variation in offspring provisioning is common and found across a variety of taxa. It can be defined as between populations, explained by optimality models, or between and within individuals, neither so easily explained by optimality models. My research focused on the evolution of variable offspring provisioning by testing theoretical models relating to variation in offspring provisioning between and within individuals. Using comparative methods, I found a positive relationship between intraclutch variation in offspring provisioning and variation in the quality of the offspring environment in a suite of pond breeding frogs. This positive relationship provided evidence that patterns of variable offspring provisioning are related to the offspring environment. This study also identified a species (Crinia georgiana) with high variation in offspring provisioning on which to focus further investigations. High variation in offspring provisioning occured between and within individuals of this species independent of female phenotype and a trade-off in offspring size and number existed. In laboratory studies, increased yolk per offspring led to increased fitness per offspring. Parental fitness calculations revealed that in high quality conditions production of small more numerous offspring resulted in higher parental fitness, but in lower quality conditions the production of large offspring resulted in the highest parental fitness. This was confirmed in field experiments under natural conditions using molecular markers to trace offspring to clutches of known provisioning, allowing me to measure exact parental fitness. The strategy of high variation in offspring size within clutches can be of benefit when the future of the offspring environment is not known to the parents: as a form of bet-hedging. Further study of the offspring environment revealed that conditions such as density dependent fitness loss, spatial variation in habitat quality, and non-random offspring dispersal, can combine to create the conditions predicted by theoretical models to maintain a strategy of variable offspring provisioning in the population. My research provides a comprehensive empirical test of the theory of variable offspring provisioning

Human health is increasingly threatened by the emergence of multiply drug resistant malignant organisms. Yet, our understanding of the numerous ways by which such resistance arises is modest. Here, we present evidence of a bet hedging strategy in the budding yeast, Saccharomyces cerevisiae, to counter the effects of cytotoxic drugs through the action of Pdr5, an ATP-binding cassette transporter. We have employed flow cytometry and fluorescent activated cell sorting to probe the expression levels of a GFP-tagged version of PDR5 in individual cells. The results obtained from these experiments demonstrate that each yeast population is variable in the levels of Pdr5 production, and a small subpopulation of cells produces this efflux pump at much higher quantities than the population average. Consequently, cells with high and low levels of Pdr5 grow differentially in presence and absence of cycloheximide, a cytotoxic drug. These properties are highly suggestive of a bet hedging strategy mediated by Pdr5 levels. We further link this bet hedging strategy to the transcriptional regulatory network of PDR5 consisting of two major transcription factors, Pdr1 and Pdr3. Our analysis suggests that a self-activating feedback loop acting on Pdr3 plays an important role in generation of the aforementioned subpopulation. Furthermore, our results point to a large difference in the activity of these two regulators wherein Pdr3 is notably stronger than Pdr1. The disparity in their activity could indicate a mechanism for generation of the observed proportions of subpopulations with regards to the level of Pdr5.

Frankia est une actinobactérie capable d'établir une symbiose racinaire avec les plantes actinorhiziennes dont le genre Alnus. Seulement certaines souches de Frankia sont capables de sporuler in planta, ce qui est illustré par la présence (Sp+) ou l'absence (Sp–) de sporanges dans les cellules végétales de la nodosité. C’est à notre connaissance un cas unique de sporulation endophyte. Cependant la description et l’interprétation écologique de ce trait d’histoire de vie (THV) original étaient incomplètes. Notre contribution à l’étude de la sporulation in planta des Frankia infectives de l’aulne intègre des approches théorique, descriptive et expérimentale, pour préciser (i) l’influence relative de la souche bactérienne, de l’espèce de la plante-hôte et des conditions pédoclimatiques sur ce THV, (ii) le rôle de la variabilité environnementale sur la distribution, la diversité et la sélection du trait, ainsi que (iii) les coûts et bénéfices associés pour les deux partenaires. Nous avons démontré pour la première fois que la sporulation in planta est un THV (i) spécifique de certaines lignées de Frankia, (ii) majeur pour en comprendre l'histoire évolutive et (iii) significativement corrélé à des caractéristiques génétiques des souches. Nous avons également confirmé que l’occurrence du trait varie selon l’environnement. Nous avons enfin établi un modèle de l'évolution du trait abordant sa valeur adaptative. L’ensemble des réflexions menées et des résultats obtenus nous permet de discuter de la sporulation in planta dans le cadre d’un continuum de stratégies symbiotiques, et plus généralement de discuter de l’écologie évolutive des symbioses entre microorganismes et plantes / Frankia sp. is a telluric actinobacteria able to establish a root symbiosis with actinorhizal plant such as Alnus sp. Only some Frankia strains are able to sporulate in-planta, as spores can be present in (Sp+) or absent from (Sp–) the vegetal cells of the root nodule. It is to our knowledge a unique case of endophytic sporulation. However, the description and the ecological interpretation of this original life-history trait (LHT) were scarce. Our contribution to the study of the in-planta sporulation of Alnus-infective Frankia sp. combines theoretical, descriptive and experimental approaches to precise (i) the relative effect of the bacterial strain, the host-plant species and the pedoclimatic conditions on this LHT, (ii) the effect of the of the environmental variability on the distribution, diversity and selection of the trait, and (iii) the associated costs and benefits for the two symbiotic partners. We demonstrated for the first time that the in-planta sporulation is a LHT (i) specific to some Frankia lineages, (ii) major to understand their evolutionary history and (iii) significantly correlated to particular genetic features. We also shown that the occurrence of the trait varies according to the environment We also proposed a model of the evolution of the trait taking its fitness into account. We bring all the previous considerations and results to discuss the inplanta sporulation trait within a continuum of symbiotic strategies and more generally to discuss the evolutionary ecology of plant-microbe symbioses

This thesis aims to find general principles governing the behaviour of biological systems, with a particular emphasis in the communicational (social) aspect of these systems. Communication between biological entities plays a major role in their evolution, enabling them to exchange information about their environment and thereby improving their chances of survival. Communication also plays a pivotal role in the organisation of populations of organisms, clearly observed in social insects, but present also at least in bacteria, plants, fungi, animals and humans. It is also theorised that the genetic code is a by-product of the establishment of an innovation-sharing protocol between primitive cells [Vetsigian et al., 2006]. This thesis is mainly concerned with identifying necessary conditions for the emergence of communicational codes, and the problems that arise with their establishment. For this purpose, we introduce an information-theoretic framework where species maximise their growth rate by following a Kelly-gambling strategy to bet on environmental conditions. Information theory provides a powerful tool for abstracting away mechanisms and for focusing on hard limits of a system's dynamics which cannot be circumvented. We begin by exploring the relation between information exchange and limited resources. We show that a transition from cooperation to antagonism in the exchange of environmental information follows from a change in the availability of resources, from abundant to scarce. We then assume a non-competitive scenario with abundance of resources, where conflicts in a population occur only at a communicational (informational) level, rather than on the physical level, such as competing for (physical) resources. However, traditional Shannon communication is non-semantic, as opposed to the semantic communication observed in biological systems, which is necessary for capturing conflicts in communication. In the traditional use of information theory, it is assumed that every organism knows how to \interpret" the information offered by other organisms. However, this assumes that one \knows" which other organisms one observes, and thus which code they use. In our model, however, we wish to preclude that: namely, we will do away with the assumption that the identity of the organisms who send the messages and those who receive them is known, and the resulting usable information is therefore influenced by the universality of the code used and by which organisms an organism is \listening" to. We introduce a model which captures semantic communication in information-theoretic terms, where organisms talk to each other in a communication network. We show that, for particular population structures, when organisms cannot identify which other organisms they talk to, the adoption of a universal code emerges as a solution for full interpretation of the shared information. However, the evolution and establishment of universal codes for communication introduces vulnerabilities: organisms can be exploited by parasites. We de ne two types of parasites whose strategies have different levels of complexity and study the co-evolution of a host (the population) and a parasite by optimising their respective objective functions in stages. First, we consider a disruptive parasite (a troll) that inflicts harm in a host by minimising a population's mutual understanding, and then a more complex parasite, which manipulates the members of the population via their codes (the puppetmaster). We show emergent characterisations of both parasites, as well as which host configurations are robust against parasites and show adaptive properties. This thesis introduces a framework which allows the study of informational properties in the host-parasite co-evolution, where the rules of the parasite's habitat, the host, are the outcome of an evolutionary process, and where these very same rules are those that allow the parasite to exploit the host.

Two peaks of eclosion dates, about 15 days apart, occur in the same batch of fertilized eggs in the marine midge, Pontomyia oceana. Two hypotheses, the variable adaptive peaks and the bet-hedging hypotheses, were proposed as the ultimate factor of the polymorphic phenomenon. They were tested by experiments controlling feeding amount and photoperiod, as well as selective breeding experiments. The offspring eclosing in the two peaks do not differ in fecundities, egg diameters, thorax and head lengths of males; this is not compatible with the variable adaptive peaks hypothesis. Both peaks exist under various feeding and photoperiods, although peak ratios differed in the former. The results in the first peak lineage did not support there is genetic component in peak ratio determination. The experiments in the second peak lineage had much lower success rates, although the results seemed to suggest a genetic component. The results in a more extreme selection experiment did not support that there is genetic component either. The present results are more compatible with the bet-hedging hypothesis. Wind velocity may be a factor hard to predict by the midges, and it may cause reproductive failure of them. Whereas high emergence synchronization, a prominent feature of the marine midge, may have advantages in many aspects, it also concentrates the risk of total reproductive failure. Spreading offspring to more than one suitable eclosion peak, the midge may have sacrificed short-term reproductive rate for long-term fitness.

The multidisciplinary field of microfluidics has shown great promise for research at the interface of biology, chemistry, engineering, and physics. Laminar flow, versatile fabrication, and small length scales have made microfluidics especially well-suited for single-cell characterization. In particular, the evaluation of single-cell growth rates is of fundamental interest for studying the cell cycle and the effects of environmental factors, such as drugs, on cellular growth. This work presents aspects in the development of a microfluidic cell impedance sensor for measuring the volumetric growth rate of single cells and covers its application in the investigation of a new discovery relating to multidrug resistance in S. cerevisiae. While there are many avenues for the utilization and interpretation of growth rates, this application focused on the quantitative assessment of biological fitness—an important parameter in population genetics and mathematical biology. Through a combination of growth measurements and optics, this work concludes a novel case of bet-hedging in yeast, as well as the first ever case of bet-hedging in eukaryotic multidrug resistance.

Diapause is often an adaptation for survival during periods of harsh environmental conditions. Some diapausing stages do not terminate the dormancy once the favourable conditions are restored. Such prolonged diapause may be enforced by environment if a diapausing stage cannot be reached by the cues inducing termination of dormancy. However, it may also be an advantageous bet-hedging strategy to allow only a fraction of dormant stages produced in any given season to hatch the next time conditions become favourable. I tested whether such strategy can be observed in hatching patterns of dormant eggs of Daphnia obtusa - a cladoceran occurring in small Central European temporary waters. I investigated the influence of intensity of illumination on hatching success, and effect of isolating the eggs encased in ephippia from the sediment. Fraction of eggs terminating diapause, fraction of embryos successfully leaving the egg membranes, and timing of the response were assessed at 15 ˚C under four intensities of illumination (100% = 35µmol.m2 .s-1 , 75%, 50%, 25%; photoperiod 12h light: 12h dark) and in complete darkness for 21 days. My results support previous suggestions that there is no genetically-fixed bet-hedging strategy in D. obtusa. I observed high proportion of eggs which terminated diapause in all...

Les amibes sociales sont des organismes eucaryotes présents dans le sol de presque toutes les zones climatiques. Ils sont remarquables pour leur passage d'un état unicellulaire à un état multicellulaire en réponse à la carence en nutriments. En période de carence, des millions de cellules forment des agrégats qui constituent chacun un nouvel organisme multicellulaire, contenant des spores, cellules reproductives, et des cellules de tige, cellules mortes qui favorisent la dispersion des spores. Ce comportement, de par le coût payé par les cellules de tige, a permis d'utiliser les amibes sociales en tant que système-modèle pour aborder des questions majeures de l'évolution de la coopération et de la multicellularité. Dans cette étude, nous examinons trois aspects différents du comportement des amibes sociales; agrégation, non-agrégation et compétition, et nous analysons comment ces aspects contribuent à notre compréhension de la coopération chez les amibes et systèmes microbiens en général.Nous avons exploré le fait bien connu mais négligé qu'en phase de carence nutritive, une fraction des cellules ne participent pas à la formation des agrégats pas et ne sont pas engagées dans le développement multicellulaire. Nous décrivons les facteurs phénotypiques et génétiques qui déterminent la fraction de cellules hors-agrégats chez D. discoideum. Les deux stratégies, d'agrégation et de non-agrégation, sont coûteuses ou bénéfiques d'un point de vue évolutif selon la durée de la phase de carence. Nous avons développé un modèle pour simuler ce processus. Nous proposons que le partitionnement de la population dans des états unicellulaire et multicellulaire est adaptative dans des environnements fluctuants avec une durée imprévisible des périodes de carence nutritive. Les amibes sociales sont donc situées à l'intersection de deux thèmes émergents en évolution microbienne, la coopération et le "placement des paris".Dans la deuxième partie, nous proposons un nouveau cadre pour aborder les observations a priori contradictoires de la diversité génétique dans les populations naturelles d'amibes sociales et une faible diversité nécessaire pour la coopération. Nous proposons que le cycle de vie complexe des amibes sociales fournit plusieurs points de compétition qui peut servir à la fois comme stabilisateur de la diversité et de la coopération. Nous explorons cette hypothèse expérimentalement avec un modèle en analysant la compétition entre 6 isolats naturels de D. discoideum. Notre simulation-modèle indique que la compétition à différents stades du cycle de vie peut conduire à l'exclusion des "gagnants sociaux". Toutefois nous n'avons pas réussi à expliquer la coexistence à long terme de souches génétiquement distinctes. Bien que préliminaires, nos résultats soulignent l'importance d'intégrer l'écologie des espèces dans les études de coopération microbienne.Enfin, nous nous concentrons sur une nouvelle dynamique d'agrégation chez P. pallidum observée dans notre laboratoire. L'agrégation est un processus au niveau de la population au cours duquel la population se divise en nombreuses sous-populations (agrégats) qui font face à la sélection de manière indépendante. Un tel fractionnement de la population peut avoir de fortes conséquences évolutives du point de vue de la coopération qui n'ont pas encore été explorées expérimentalement. Nous décrivons la dynamique des populations qualitativement et proposons plusieurs mesures quantitatives de partitionnement de la population en agrégats. Nos résultats préliminaires suggèrent qu'il existe une préférence pour les agrégats d'une certaine taille, mais qu'il n'existe aucune organisation spatiale des agrégats. / Social amoebae are eukaryotic organisms that inhabit soil of almost every climate zone. They are remarkable for their switch from unicellularity to multicellularity as an adaptation to starvation. When starved, millions of single cells aggregate and form a multicellular fruiting body, which contains reproductive spore cells and dead stalk cells, which help in spore dispersion. This costly behavior made social amoebae a model system for addressing major questions of the evolution of cooperation and multicellularity. In this study we look at three different aspects of social amoebae behavior; aggregation, non-aggregation and competition, and ask how they contribute to our understanding of cooperation in social amoebae and microbial systems in general.We explored the known but neglected observation that, upon starvation, not all cells aggregate and engage in multicellular development. We describe phenotypically and genetically non-aggregating cell proportion in D. discoideum species. Both aggregating and non-aggregating strategy are costly or beneficial depending on duration of starvation. With our computational model we propose that partitioning the population into unicellular and multicellular states is adaptive in fluctuating environments with unpredicted duration of starvation periods. Social amoebae may therefore lie at the intersection of cooperation and bet-hedging. In the second part, we provide a new framework for addressing the contrasting observations of high genetic diversity in natural populations of social amoebae and experimentally suggested low diversity-high relatedness required for cooperation. We propose that complex life cycle of social amoebae provides multiple competition points that can possibly play an important role in maintaining diversity and cooperation. We explore this experimentally and computationally by looking at competition over the whole life cycle between 6 natural isolates of D. discoideum. Our simulation model indicates that competition at different stages of the life cycle can lead to exclusion of “social winners”. Though we failed to explain strain coexistence. Although preliminary, our results emphasize the importance of integrating species ecology in cooperative studies.Finally, we focus on a new aggregation dynamics in P. pallidum species observed in our lab. Aggregation is a population level process during which population gets divided into numerous subpopulations/aggregates that face selection independently. Such population partitioning can have strong evolutionary consequences on cooperation that have not yet been explored experimentally. We describe the population dynamics qualitatively and propose several quantitative measurements of population partitioning into aggregates. Our preliminary results suggest that there is a preference for aggregates of certain size, but there is no spatial organization of aggregates.

Site 38CH1693 is a coastal site located in Charleston County, South Carolina. Thom’s Creek ceramics place the site in the Late Archaic/Early Woodland Period and radiocarbon dating corroborates this, placing the features present between 3650 and 3950 BP. Faunal analysis was undertaken to assess seasonality in order to understand the occupations that occurred at the site. Faunal seasonality, botanical seasonality, and sedentariness indicators are used to determine the sedentariness of the site. The presence of certain marine fish species is one of the most important seasonality indicators used. It is determined from the available evidence that at least one short-duration, year-round occupation is represented by the materials recovered at 38CH1693. Site 38CH1693 does not fit into the current Late Archaic settlement pattern models for the coast, calling for a reevaluation of these settlement pattern models and the sedentary sites within them.