Dissertations / Theses on the topic 'Evolution of Cooperation - Mechanisms'
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1
Dong, Lu. "Behavioural mechanisms of cooperation and coordination." Thesis, University of Nottingham, 2017. http://eprints.nottingham.ac.uk/44618/.
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This thesis consists of three independent chapters investigating behavioural mechanisms of cooperation and coordination. In particular, chapter 1 analyses a voluntary contribution game and proposes a simple behavioural mechanism to achieve social efficiency. Specifically, in this mechanism, each player can costlessly assign a share of the pie to each of the other players, after observing the contributions, and the final distribution of the pie is determined by these assignments. In a controlled laboratory experiment, I find that participants assign the reward based on others' relative contributions in most cases and that the contribution rates improve substantially and almost immediately with 80 percent of players contribute fully. Chapter 2 studies the effects of costly monitoring and heterogeneous social identities on an equity principle of reward allocation. The investigation is based on the mechanism proposed in chapter 2. I hypothesised that the equity principle may be violated when participants bear a personal cost to monitor others' contributions, or when heterogeneous social identities are present in reward allocations. The experimental results show that almost half of the allocators are willing to sacrifice their own resources to enforce the social norm of equity principle. Likewise, with the presence of heterogeneous social identities, though a few participants give more to their in-group member, the majority of them still follow the equity principle to allocate. Chapter 3 explores the behavioural mechanism of communication and leadership in coordination problems. Specifically, I consider two types of leaders: cheap-talk leaders who suggest an effort level, and first-mover leaders who lead by example. I use experimental methods to show the limits of these two mechanisms in avoiding coordination failure in a challenging minimum effort game, with low benefits of coordination relative to the effort cost. The results suggest that both types of leadership have some ability to increase effort in groups with no history, but are insufficient in groups with a history of low effort.
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Wang, Tzai-Der. "The evolution of cooperation in artificial communities." Thesis, University of the West of Scotland, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.395688.
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El, Mouden Claire M. "The evolution of cooperation, especially in humans." Thesis, University of Oxford, 2011. http://ora.ox.ac.uk/objects/uuid:2ebc0b15-d745-48d8-bb5a-a4d83b3304ed.
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I develop social evolution theory to study the evolution of cooperation as follows: (1) Many organisms undergo a dispersal phase prior to breeding; I demonstrate that knowing ones dispersal status aids the evolution of helping (by non-dispersers) and harming (by dispersers). (2) Policing driven by group-benefits may be selected to enforce cooperation in human and animal societies. I extend existing theory to show that policing may be harder to evolve that previously thought, but that it is maintained more readily than it evolves. (3) Archeological and anthropological evidence suggests that warfare was prevalent during our evolution. I show that, contrary to previous suggestions, between-group competition can favour any social behaviour (pro-social or anti-social) so long as it helps the group compete, and that such traits can be altruistic or mutually beneficial. (4) Reproductive leveling is analogous to policing; in the human literature there is doubt as to whether it can evolve. I extend my previous work to consider the coevolution of culturally and genetically inherited traits for reproductive leveling and selfishness. I find that cooperation can evolve between non-kin if they share the same culture. (5) Monogamy is thought to favour the evolution of cooperative breeding. I show that in the simplest case, because of the cost of competition between non-dispersing siblings, the level of promiscuity has little or no effect on the evolution of cooperation. (6) Spatial structure (limited dispersal) is thought to favour the evolution of inter-specific mutualisms as it aligns the partners’ interests. I consider the case of plant-fungi mutualisms and show that spatial structure can disfavour cooperation if it limits the potential fungal partners available to the plant.
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O'Neill, Moira Patricia. "Evolution and Cooperation in the Youngstown Area." Kent State University / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=kent1564599603688389.
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Hooper, L. "International cooperation : A role for institutional mechanisms." Thesis, University of Essex, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.381237.
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LEWIS-ROBERTS, BRITTANY KIRSTEN. "COOPERATION AND ENFORCEMENT MECHANISMS: ASSESSING FOUR COUNTRIES." Thesis, The University of Arizona, 2008. http://hdl.handle.net/10150/190666.
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Kiers, Erica Tobyn. "Evolution of cooperation in the legume-rhizobium symbiosis /." For electronic version search Digital dissertations database. Restricted to UC campuses. Access is free to UC campus dissertations, 2005. http://uclibs.org/PID/11984.
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Eckert, Daniel, Wolfgang Janko, and Johann Mitlöhner. "Evolution of cooperation and discrimination in software development." Institut für Informationsverarbeitung und Informationswirtschaft, WU Vienna University of Economics and Business, 2004. http://epub.wu.ac.at/1672/1/document.pdf.
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Software development projects typically involve repeated interactions among several groups of people. This setting seems well suited for an analysis by means of the standard-model of the evolution of cooperation, the Iterated Prisoner's Dilemma. Computer simulations of a population of stochastic reactive strategies show that the existence of intergroup discrimination can be modeled endogeneously as a result of noise due to misperception of the opponent's move. (author's abstract)Series: Working Papers on Information Systems, Information Business and Operations
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Trubenova, Barbora. "Indirect genetic effects and the evolution of cooperation." Thesis, University of Manchester, 2014. https://www.research.manchester.ac.uk/portal/en/theses/indirect-genetic-effects-and-the-evolution-of-cooperation(cac253c8-500d-4f5e-91ff-878f6ead4c0e).html.
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The evolution of social behaviour has been studied using different frameworks based on game theory and quantitative genetics. While both approaches provide a conceptually clear explanation of evolution of social behaviour, both have been limited in their applicability to empirical systems, mainly due to difficulties in measuring model parameters. Here, I develop a new quantitative genetics approach to the study of the evolution of social behaviours based on indirect genetic effects (IGEs), which parameters can be readily determined by empirical studies. IGEs describe effects of an individual's genotype on phenotypes of social partners, which may indirectly affect their fitness. Unlike traditional quantitative genetics assuming a non-genetical, non-heritable environment, IGE models assume that part of the environment is social, provided by parents and other interacting partners, thus has a genetic basic and can be heritable. In this study I explore the effects of IGEs on the magnitude and range of phenotypic values in a focal individual. I show that social interactions may not only cause indirect genetic effects but can also modify direct genetic effects. I demonstrate that interactions can substantially alter group mean phenotype and variance. This may lead to scenarios in which between group phenotypic variation is much higher than within group variation despite similar underlying genetic properties of different groups. Further, I analyse how IGEs influence levels of selection and predictions about evolutionary trajectories. I show that IGEs can create selection pressure at the group level, leading to evolution of behaviours that would not evolve otherwise. Moreover, I demonstrate that IGEs may lead to differences in the direction of evolutionary response between genotypes and phenotypes. Building on these results, I show that IGE models can be translated to and are fully compatible with traditional kin and multilevel selection models. I express costs and benefits in IGE parameters and determine the conditions under which social interactions lead to the evolution of cooperative or harmful behaviours. Therefore, the model I propose combines the conceptual clarity of kin and multilevel selection models with the applicability of IGE models, which parameters can be empirically determined, facilitating the testing of model predictions. Finally, I show that the use of IGE models is strongly limited by the underlying assumption of linearity. I prove that the modelling of interaction dynamics leads to steady state solutions found by IGE models only under limited conditions. In this light, I discuss the relevance of results published previously and propose a solution of how this problem can be addressed.
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Lamba, S. "The evolution of large-scale cooperation in human populations." Thesis, University College London (University of London), 2011. http://discovery.ucl.ac.uk/1317770/.
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Large-scale cooperation between unrelated humans is a major evolutionary puzzle. Natural selection should favour traits benefiting the self, whereas cooperation entails a cost to self to benefit another. The work presented in this thesis makes an empirical contribution towards understanding the evolution of large-scale cooperation in humans. Theory posits that large-scale cooperation evolves via selection acting on populations amongst which variation is maintained by cultural transmission. While cross-cultural variation in cooperation is taken as evidence in support of this theory, most studies confound cultural and environmental differences between populations. I test and find support for the hypothesis that variation in levels of cooperation between populations is driven by differences in demography and ecology rather than culture. I use economic games and a new ‘real-world’ measure of cooperation to demonstrate significant variation in levels of cooperation across 21 villages of the same small-scale, forager society, the Pahari Korwa of central India. Demographic factors explain part of this variation. Variation between populations of the same cultural group in this study is comparable in magnitude to that found between different cultural groups in previous studies. Experiments conducted in 14 of the villages demonstrate that the majority of individuals do not employ social learning in the context of a cooperative dilemma. Frequency of social learning varies considerably across populations; I identify demographic factors associated with the learning strategy individuals employ. My findings empirically challenge cultural group selection models of large-scale cooperation; behavioural variation driven by demographic and ecological factors is unlikely to maintain stable differences essential for selection at the population-level. This calls for re-interpretation of cross-cultural data sampled from few populations per society; behavioural variation attributed to ‘cultural norms’ may reflect environmental variation. The work presented in this thesis emphasises the central role of demography and ecology in shaping human social behaviour.
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Walker, Lindsay. "The evolution and regulation of cooperation in the wild." Thesis, University of Exeter, 2015. http://hdl.handle.net/10871/21129.
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In cooperatively breeding societies, where individuals (termed ‘helpers’) provide care to young which are not their own, group members can vary substantially in their contributions to cooperative activities. Individuals are expected to exhibit higher levels of cooperative investment if the benefit of performing that behaviour greatly outweighs the cost of performing that behaviour. This may be achieved by directing investment towards kin (thereby maximising indirect fitness benefits) and/or attaining large direct fitness benefits. In this thesis, I explore whether direct fitness benefits shape patterns of helping behaviour in the cooperatively breeding white-browed sparrow weaver (Plocepasser mahali). White-browed sparrow weavers live in year round territorial groups with high reproductive skew, comprising a dominant pair and subordinates of both sexes. Although all group members contribute to a wide range of highly conspicuous cooperative activities, there is large inter-individual variation in investment. In chapter 2, I use simulated territorial intrusions to show that sexually-selected direct benefits shape the expression of sentinel behaviour. In chapter 4, I provide evidence that the direct benefits associated with either the pay-to-stay or social prestige hypotheses are unlikely to modulate patterns of provisioning in male white-browed sparrow weavers. Evidence of marked individual differences in contributions to offspring care in cooperative societies is also generating increased interest in the proximate causes of such variation. In chapter 5, I use within-individual measurements to demonstrate that variation in provisioning effort is not directly regulated by variation in circulating levels of prolactin (a pituitary hormone). The evidence does suggest, however, that provisioning behaviour may be induced by exceeding a threshold hormone level. Individual contributions to parental behaviours (as opposed to alloparental) may be shaped by constraints associated with life-history traits. In chapter 3, I show that parents in white-browed sparrow weaver societies perform different provisioning rates yet employ similar food allocation tactics, and that these patterns are expected in tropical living bird species. Combined, these findings provide insights into the selection pressures that may shape individual contributions to cooperative activities.
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Barker, John. "Driving mechanisms for cataclysmic variable evolution." Thesis, Open University, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.289006.
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Hearns, Glen Spencer. "Analysis of process mechanisms promoting cooperation in transboundary waters." Thesis, University of British Columbia, 2010. http://hdl.handle.net/2429/28367.
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International water basins are experiencing increasingly rapid changes. Climate change, increased pressure from population growth and development, and shifting societal values are converging making water availability increasingly precarious in many areas. Where management structures do exist, change is often exceeding their capacities to address issues escalating the potential for conflict. Particularly urgent therefore, is the development of effective and adaptive governance regimes in the majority of the 263 international basins where management is inadequate. Effective and adaptive regimes require high levels of cooperation and interdependence.
This thesis focuses on actions or process mechanisms available to states to enhance cooperation and regime effectiveness. Through case study analysis, five mechanisms are identified to be important factors in the formation of international transboundary water regimes. They are; (i) balancing and creating incentives, (ii) information exchange, (iii) cooperating in a stepwise process, (iv) neutral party involvement, and (v) adequate stakeholder engagement. An analytical framework is developed, based on case survey methodology, to assess the impact of the process mechanisms on existing regimes. Practitioners and academics applied the framework to the Columbia, Mekong, Danube, Mahakali Rivers and the West Bank Aquifers through a series of interviews. The framework proved versatile in describing all scenarios, showed consistency in responses from practitioners and was sufficiently comprehensive to reflect important singularities of basins.
Analysis indicated that high levels of balancing and creating incentives, information exchange, and neutral party involvement were required for regime effectiveness in all situations. All process mechanisms appeared to be needed when development goals of the parties differed, or when initial relations between the parties were poor. Stepwise cooperation and stakeholder engagement were not seen to be requisites for developing cooperative regimes when relationships between basin states were good and they shared common development goals.
The framework is able to combine quantitative analysis in parallel to quantitative analysis in a manner that until now has not been achieved in the study of transboundary waters. Major elements of the framework are already being applied in a three-year program to analyse marine, groundwater and river systems, and develop training tools to enhance regime effectiveness.
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Buchta, Claire Marie. "Mechanisms of TLR signaling and cooperation in B lymphocytes." Diss., University of Iowa, 2014. https://ir.uiowa.edu/etd/4584.
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B lymphocytes play important roles in antibody production, cytokine production, and antigen presentation to T cells. Ligation of Toll-like receptors (TLRs) on B cells stimulates cellular activation and B cell effector functions. Synergistic activation of other receptors such as CD40 or the B cell receptor (BCR) with TLR ligation further enhances B cell activation and effector functions. The tumor necrosis factor receptor associated factor (TRAF) family of proteins act as cytoplasmic signaling adaptor molecules and moderate downstream signaling from both the tumor necrosis factor receptor (TNFR) superfamily of proteins, including CD40, and the IL-1R/TLR superfamily of proteins.
To date, only TRAFs 3 and 6 have been shown to be involved in TLR signaling, with TRAF6 providing positive regulation and TRAF3 providing negative regulation of TLR signaling in B cells. Deficiency in another TRAF family member, TRAF5, has been implicated in the development of atherosclerosis, a disease developed in part due to TLR dysregulation. Here, we addressed the hypothesis that TRAF5 is a negative regulator of TLR signaling.
We found that TRAF5 negatively regulated TLR-mediated cytokine and antibody production in B lymphocytes. The enhanced cytokine production seen in TLR-stimulated TRAF5 KO B cells was not attributable to altered cellular survival or proliferation, but instead more cytokine was produced on a per-cell basis, likely due to enhanced MAPK pathways after TLR ligation. Additionally, TRAF5 deficiency did not dramatically affect cytokine production in TLR-stimulated bone marrow-derived macrophages or dendritic cells, suggesting that TRAF5 plays a greater role in TLR signaling in lymphoid versus myeloid cells. TRAF5 associated with the TLR signaling proteins MyD88 and TAB2, and negatively regulated the association of TAB2 with its binding partner TRAF6.
Furthermore, we manipulated B cell activation via ligation of various TLRs, CD40, and/or the BCR in order to activate the cells to effectively present antigen. Activated B cells pulsed with antigen served as an effective cellular vaccine and offered protection against both an infectious pathogen (Listeria monocytogenes) and a model of murine melanoma. We identified two candidate activation criteria for B cell vaccines (Bvacs): stimulation through the BCR and TLR7, and stimulation through CD40 and TLR4. Additionally, we found that high IL-6 production by the activated Bvac was essential for inducing optimal CD8+ T cell memory. These B cell activation protocols offer significant advantages over those currently being tested for clinical use. Understanding B cell activation through TLRs is a critical step in developing new therapies against cancer and infectious disease.
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Molin, Filippo <1995>. "Epidemic diseases: between cooperation and competition The evolution of the international sanitary cooperation and new challenges." Master's Degree Thesis, Università Ca' Foscari Venezia, 2022. http://hdl.handle.net/10579/20718.
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L’elaborato analizza le origini e l’evoluzione della cooperazione sanitaria internazionale come risposta alla lotta contro le malattie infettive. Per meglio capire le complesse relazioni tra malattie infettive, cooperazione sanitaria, diplomazia e commercio è necessario capire il contesto storico in cui queste relazioni si sono sviluppate. Partendo dall'età moderna, questo studio analizza la nascita dell'idea che una risposta internazionale è desiderabile per affrontare crisi sanitarie a carattere epidemico, e come quest'ultima si sia sviluppata fino ad oggi. Per raggiungere lo scopo prefissato, la prima parte della tesi si concentra sulla definizione di termini chiave legati alle epidemie del passato il cui significato si è evoluto nel corso dei secoli, a cui segue un’analisi storica delle principali teorie legate alla diffusione delle malattie e come quest’ultime venivano considerate. Successivamente, viene presa in considerazione l’introduzione del vaiolo nel continente americano, gli effetti demografici sulla popolazione locale, le misure di contenimento adottate e il suo uso come strumento bellico. Lo studio procede prendendo in esame le reti d’informazione in epoca moderna, tra notizie vere e notizie false. Seguono le politiche sanitarie della Repubblica di Venezia ed il loro ruolo come modello internazionale, usate non solo come strumento di tutela della salute pubblica ma anche come strumento di politica estera. Viene poi esplorato il network delle stazioni di quarantena e le patenti di sanità ed in che modo hanno contribuito a mantenere attivi gli scambi commerciali. Viene inoltre trattato l’importante passo verso una maggiore globalizzazione della lotta contro le malattie infettive dato delle numerose campagne di vaccinazione transnazionale fino a raggiungere la prima pietra miliare della cooperazione sanitaria: la Conferenza di Parigi del 1851 a cui fanno seguito le successive conferenze sanitarie. La parte finale dell’elaborato si concentra su eventi più recenti con particolare attenzione al periodo della guerra fredda con la campagna vaccinale contro il vaiolo, portata avanti con sforzo congiunto tra Stati Uniti e Unione Sovietica nonostante le tensioni geopolitiche. Tuttavia, viene discussa anche la campagna di disinformazione sovietica degli anni ’80 sull’HIV. La tesi prosegue con le origini e lo sviluppo dell’Organizzazione Mondiale della Sanità e il programma COVAX contro il COVID-19. L’elaborato si conclude con una riflessione sul futuro della cooperazione sanitaria internazionale e i possibili pericoli che quest’ultima potrebbe essere chiamata ad affrontare: la minaccia del bioterrorismo e le nuove malattie infettive dovute al salto di specie e al cambio climatico.
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Sylwester, Karolina. "The role of reputations in the evolution of human cooperation." Thesis, University of Newcastle Upon Tyne, 2011. http://hdl.handle.net/10443/1154.
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In human societies, cooperation between strangers flourishes despite the risk of being exploited. Correct evaluation of others‟ cooperative intentions aids in selecting partners for profitable interactions. Assessment of intentions can be made by (a) considering individuals‟ reputations gained through observed interactions with others and third-party information (gossip) or (b) interpreting immediate cues such as facial expressions and body language. I empirically investigated the role reputations play in human economic decisions. More specifically, I addressed research questions such as (1) how and why people manage cooperative reputations, (2) what role reputations play in partner choice, (3) whether reputations can stabilize cooperation in groups, (4) whether people have a memory bias for specific reputations and (5) whether the ability to assess trustworthiness in faces relates to mind reading skills known as Theory of Mind (ToM). Student participants were recruited for five experiments, all involving the use of economic games to a greater or lesser extent. Depending on the study, participants either played social dilemma games in groups under various experimental conditions or performed individual tasks e.g. recalled information previously presented in different contexts or assessed photographed faces with regard to their cooperativeness and completed ToM tasks. The results provide evidence for the existence of reputation-based partner choice („competitive altruism‟). Participants strategically invested in reputations and reaped benefits from such investments in the form of profitable interactions with the most desired partners. By varying endowments I demonstrated that resource inequalities affect the way people invest in reputation with low-resource individuals behaving in a relatively more generous way than their high-resource counterparts. Moreover, I showed that cooperation in social dilemmas can be stabilized by introducing reputational incentives in the form of partner choice. My results also suggest that people have a memory bias for information about uncooperative acts which is independent of the cooperativeness of the environment they are exposed to. I found no relationship between the ability to identify cooperative intentions in faces and ToM skills. In summary, by unravelling the mechanisms behind reputational cooperation my thesis sheds light on the reasons for extensive cooperation among strangers observed in humans.
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Hodge, S. "The evolution of cooperation in the communal breeding banded mongoose." Thesis, University of Cambridge, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.604118.
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Recent attempts to understand the evolutionary origins of cooperative breeding systems have focused on finding the answers to two questions; (1) when do subordinates help? and (2) when do subordinates breed? In this thesis, I investigate these questions in the banded mongoose, one of the few cooperative species where multiple females regularly breed. I show that helpers benefit the offspring that they care for; pups that receive a lot of care grow faster, survive better and have better future reproductive success than their littermates. Pups compete aggressively for access to good helpers, and larger offspring have a competitive advantage. Larger, more dominant females produce larger pups that can outcompete their subordinate littermates. As a result, the costs of allowing subordinates to breed are likely to be low, because the offspring of more dominant females will be buffered against resource shortages by their superior ability to compete for helpers. As a consequence, suppression of subordinate reproduction is likely to be unnecessary in the banded mongoose, providing an explanation for why reproductive skew among females is low. However, if the communal litter size exceeds the level that is optimal, females employ behavioural tactics to interfere with the reproductive attempts of subordinates Female reproductive success is strongly correlated with body condition, which may explain why helper contributions in the banded mongoose are male-biased, as male helpers are better able to bear the short-term weight loss associated with providing care. These results highlight the importance of understanding how patterns of reproductive skew influence contributions to helping in cooperative societies.
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Jin, Xin, and 靳鑫. "Peer-to-peer system design: incentives and evolution of cooperation." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2013. http://hub.hku.hk/bib/B50662235.
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The persistence of cooperation is a longstanding problem in the social and biological sciences. Recent advances of peer-to-peer (P2P) networks manifest as a promising platform to experiment and contribute to theories and algorithms on cooperation. In this thesis, by and large, we view P2P systems as an economy in which incentives are critical to stimulate contribution. Indeed, a P2P system can be considered as a society where different behaviors can emerge, and an empirical platform to understand cooperation and mimic evolving population. Specifically, we consider the problem of cooperation from two perspectives.
First and foremost, autonomous nodes are strategic and selfish, who are reluctant to cooperate solely for public good. We investigate incentive scheme design for cooperation in P2P live media streaming networks. The general approach of protocol decomposition shows that practical incentives can only be guaranteed by efficient peer selection, due to stringent playback deadlines. Striker strategy is then proposed so as to align the optimal peer selection of heterogeneous nodes with social welfare maximization, the efficiency of which is validated by repeated game modeling and extensive simulations. The hidden philosophy is to coerce non-cooperative peers into cooperation by collectively implementing punishment threats. This is analogous to strikes and coercion implemented by organizations like unions in human society.
On the other hand, just as node selfishness, competition and struggle for survival raise another problem for cooperation. Similar to human society and biological systems, we envision that diverse strategies—some are more exploitative, while others more altruistic—could be deployed by selfish participants to compete against interacting nodes and gain performance advantages. In such a variegated environment, our coevolutionary perspective aims to understand cooperation and rationalize the coexistence and success of diverse behaviors. Population games and evolutionary game theory provide analytical tractability, while learning and evolutionary dynamics are proposed to evolve strategies.published_or_final_version
Electrical and Electronic Engineering
Doctoral
Doctor of Philosophy
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Horii, Satoko. "Frontex and the evolution of cooperation on European border controls." Thesis, University of Sussex, 2015. http://sro.sussex.ac.uk/id/eprint/58522/.
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This dissertation explores the role of the EU agency Frontex in the EU border regime. Contrary to the mainstream formulation in academic research which views that Frontex is a mere tool of EU member states and did not change the intergovernmental cooperation, this dissertation has pursued the agency's potential in bringing integrative effect on the regime. To this aim, this dissertation has used the sociological institutionalist approach as it provides a theoretical basis for defining the EU border regime and explaining the nature and mechanisms that Frontex has exercised to influence the regime. By looking at Frontex's activities in mobilisation of state border agencies, promotion of common standards and producing risk analysis at external borders, this research has found that Frontex has had integrative effects on the regime with certain limitations. Empirical analyses have shown that a set of procedures and mechanisms that Frontex has developed have increased the participation of state border agencies in EU's border guard activities, which implies the shift of the initial intergovernmental cooperation to a more structured form of cooperation. It has also found that, although the outcome has been unevenly spread in Europe, Frontex has acted as an agent of transfer in promoting common standards for border guard training curriculums and automated border control systems. Moreover, Frontex has effectively transformed the politically defined “risks” at the EU's external border to measureable terms at an operational level, which has enabled the classification of the EU member states. This dissertation has observed the effect of the agency's risk analysis in the policy makers' decisions. These findings conclude that, although it is still of a hybrid nature that has derived from contradicting elements between state-centric and supranational forces, Frontex has certainly changed the regime towards integration. In this context, this dissertation has enriched the understanding of institutional and organisational dynamics in a EU policy field and the role that EU agencies can play in it.
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Arranz, Jordi. "Selective pressures towards the evolution of cooperation, communication and cognition." Thesis, University of Southampton, 2015. https://eprints.soton.ac.uk/383620/.
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One of the main problems in studying human origins from an evolutionary perspective is uniqueness: we have evolved to fill a social and cognitive niche that is so distinctive it renders useless the usual investigative tool of careful comparison with other, similar species. Features such as cognition, communication and cooperation reached, in humans, unprecedented levels of sophistication and complexity. These features not only converge to the social dimension but they also lack a clear function outside it, a fact that makes epiphenomenal explanations unlikely. The main goal of this thesis is to shed light on the conditions that led to the evolution of modern humans through the development of computational models. Our research hypothesis is based on the assumption that the human “primeval niche” lies in the intersection of three fundamental phenomena: cooperation, communication and cognition. We argue that these three elements are intimately connected and that their intersection is the ideal spot to explore the so called human cognitive explosion. The new internal selective pressures that arise from any cooperative environment trigger asymmetric competitive co-evolutionary arms races that can pull the population in the opposing directions of altruism and selfishness. Co evolutionary feedback loops usually stagnate due to their increasing biological cost, however, in the human case, the invention of communication and language as a tool for social cohesion opened up a new “medium”, where both co operators and defectors can play their own personal “battle” at a lower cost and at a faster pace. Following this, we re-implement and develop several models of the evolution of communication and cooperation. As this thesis progresses, the scope of our modelling efforts is narrowed towards the study of the emergence of the simplest cooperative mechanism that explicitly relies on communication and important cognitive abilities: indirect reciprocity. Our findings strongly suggest that primitive communication could have evolved in order to sustain cooperation through indirect reciprocity and therefore communication and, eventually, language could have evolved as a tool for social cohesion. Moreover, our results indicate that there are two different evolutionary paths towards this goal. The first includes low levels of gossip in a trusting environment governed by a moderately heterogeneous moral system. The second consists of high levels of gossip in a suspicious context governed by a homogeneous moral system. The main contribution of this thesis is a plausible evolutionary outline of the primeval niche that early humans occupied and its depiction through the interactions and interdependence of the three cornerstones of human nature: cognition, communication and cooperation.
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Quinn, Alexander E., and n/a. "EVOLUTION OF SEX-DETERMINING MECHANISMS IN REPTILES." University of Canberra. Institute for Applied Ecology, 2008. http://erl.canberra.edu.au./public/adt-AUC20090311.120346.
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Reptiles exhibit marked diversity in sex-determining mechanisms. Many species exhibit
genotypic sex determination (GSD) with male heterogamety (XX females/XY males),
others have GSD with female heterogamety (ZW females/ZZ males), and still others
exhibit temperature-dependent sex determination (TSD). The distribution of these
mechanisms throughout the reptile phylogeny implies evolutionary lability in sex
determination, and in some lineages there has been a number of transitions between
GSD and TSD. Despite this diversity, GSD and TSD have traditionally been viewed as
mutually-exclusive mechanisms of sex determination in reptiles, since there is little
evidence for their co-occurrence. Considerable empirical and theoretical effort has been
directed towards understanding the adaptive significance of TSD in reptiles. In
comparison, there has been little focus on understanding how evolutionary transitions
between GSD and TSD occur at a genetic and mechanistic level. I addressed this
question by applying both empirical and theoretical approaches to investigate
interaction of genotypic and temperature influences in the sex determination of two
endemic species of Australian lizards.
The three-lined skink, Bassiana duperreyi, has XX/XY chromosomal sex
determination, yet a previous investigation reported a significant male bias in the sex
ratio of eggs incubated at low temperatures. To enable an explicit test for temperature induced
sex reversal in this species, a 185 bp Y chromosome marker was isolated by
Amplified Fragment Length Polymorphism (AFLP) analysis. The marker was
subsequently converted into a duplex PCR assay that co-amplified a 185 bp (or 92 bp)
Y chromosome fragment and a 356 bp fragment of the single-copy nuclear gene C-mos
(from both sexes) as a positive control. The accuracy of the PCR sex assay was tested
on 78 individuals for which sex reversal was not expected. PCR genotype and sex
phenotype were concordant for 96% of the animals. This is one of the very few sex tests
developed for a reptile, and the first report of Y chromosome sequence from a reptile.
The PCR assay was subsequently applied to genotype hatchlings from both cool
(16-7.5C) and warm (22-7.5C) cyclical incubation temperature treatments, and
identified sex reversal in 15% of genotypically female (XX) embryos (n=26) from the
cool treatment, but no sex reversal in eggs from the warmer treatment (n=35). Thus, low
incubation temperatures can over-ride genotypic sex determination in B. duperreyi,
indicating that GSD and TSD co-occur in this species.
The Central bearded dragon, Pogona vitticeps (Agamidae), has ZZ/ZW chromosomal
sex determination, and is a member of a lizard family in which GSD and TSD are both
widespread, indicating evolutionary lability in sex determination. AFLP analysis was
applied to isolate homologous Z and W chromosome-linked markers (71 bp and 72 bp,
respectively) from this species. The AFLP sequences were subsequently extended into
larger genomic fragments by a reiterated genome walking procedure, producing three
non-overlapping contigs of 1.7 kb, 2.2 kb and 4.5 kb. The latter two fragments were
verified as distinct, homologous Z/W chromosome fragments by PCR analyses. An
amplified 3 kb fragment of the 4.5 kb contig was physically mapped to metaphase
spreads, identifying the W microchromosome, and for the first time in this species, the
Z microchromosome. PCR analyses indicated the presence of homologous sequences in
other Australian agamid species, including both GSD and TSD species. The isolated
sequences should therefore prove useful as a comparative genomic tool for investigating
the genomic changes that have occurred in evolutionary transitions between sexdetermining
mechanisms in agamids, by enabling the identification of chromosomes in
TSD species that are homologous to the sex chromosomes of P. vitticeps. The isolated
sequences were further converted into a duplex DNA sex assay that co-amplified a 224
bp W chromosome fragment and a 963 bp positive control fragment in both sexes. This
PCR assay diagnosed chromosomal sex in three Pogona species, but was not effective
outside the genus.
Incubation treatment of P. vitticeps eggs revealed a strong and increasing female bias at
high constant temperatures (34-36C), but an unbiased sex ratio between 22-32C.
Hatchlings from three clutches split between 28C and 34 or 36C incubation treatments
were genotyped with the W chromosome AFLP marker. At 28C, the sex ratio was 1:1
but the high temperature treatments produced 2 males and 33 females. All but one of the
30 lizards (97%) incubated at 28C had concordant sex phenotype and genotype, but
only 18 of 35 animals (51%) from the high temperature treatment were concordant. All
discordant animals were genotypic males (ZZ) that developed as females. Thus,
temperature and genotypic influences can interact to determine sex in P. vitticeps.
These empirical findings for B. duperreyi and P. vitticeps were extended into a novel
theory for the evolution of sex-determining mechanisms in reptiles, working within the
framework that species with temperature-induced reversal of chromosomal sex
determination are a window to transitional stages of evolution between GSD and TSD.
A model was derived from the observation that in both lizards, an extreme of incubation
temperature causes sex reversal of the homogametic genotype. In this model, the
strength of a genetic regulatory signal for sex determination must exceed a threshold for
development of the homogametic sex to occur (male in Pogona, female in Bassiana).
The strength of this signal is also temperature-sensitive, so diminishes at extremes of
temperature. Simulation modelling demonstrated that increasing the relative magnitude
of the threshold for sexual development can cause evolutionary transitions between
GSD and TSD. Even more remarkably, decreasing the relative magnitude of the
threshold value causes an evolutionary transition between female and male
heterogametic GSD. Quantitative adjustment of a single model parameter (the threshold
value) thus charts a continuous evolutionary pathway between the three principal
mechanisms of sex determination in reptiles (XX/XY-ZZ/ZW-TSD), which were
previously considered to be qualitatively distinct mechanisms.
The experimental demonstration of temperature-induced reversal of chromosomal sex
determination in both B. duperreyi and P. vitticeps presents a challenge to the traditional
view that reptilian sex determination is strictly dichotomous (GSD or TSD), and
suggests instead that sex determination in reptiles consists of a continuum of systems of
interaction between genotypic and temperature influences. Simulation modelling
provided solid theoretical support for this proposition, demonstrating that transitions
along this continuum are effected simply through shifts in the mean population value for
the sex-determining threshold, without requiring substantial genotypic innovation. An
important implication of this theory is that transitions between XX/XY and ZZ/ZW
modes of GSD may retain the same sex chromosome pair, and the same primary sexdetermining
gene, in contrast to previous models for heterogametic transitions. A more
immediate implication of these findings is that many reptile species believed to have
strict TSD (in particular, lizards and crocodilians), may in fact have a sex-determining
system of GSD-TSD interaction, where there is an equilibrium between GSD and TSD
individuals within the population.
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Boxall, Nicola. "The mechanisms and processes of microsatellite evolution." Thesis, University of Reading, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.430923.
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Kulkarni, Saurabh S. "Endocrine Mechanisms Underlying Phenotypic Evolution in Frogs." University of Cincinnati / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1342106009.
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Blockus, Heike. "Evolution and molecular mechanisms of commissure formation." Thesis, Paris 6, 2015. http://www.theses.fr/2015PA066255.
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Chez les espèces ayant une symétrie morphologique bilatérale, les connections entre la gauche et la droite au sein du système nerveux sont appelées commissures. Le développement de nouveaux circuits commissuraux et la modification des circuits existants ont accompagné l’émergence de caractéristiques neurobiologiques essentielles. D’un point de vue moléculaire, le guidage des commissures dépend de couplage ligand-récepteur tels que Netrin-1/DCC, responsable de l’attraction des axones commissuraux, et tel que Slit/Robo3, responsable de la répulsion des axones ayant traversé la ligne médiane. Plusieurs commissures ne se développent pas en absence d’un unique récepteur, le Robo3, contestant ainsi une présumée redondance moléculaire. Tout d’abord, il est impérial de caractériser le mécanisme moléculaire sous-jacent à cette fonction unique de Robo3 chez les mammifères et au cours de l’évolution. Ensuite, nous visons à extrapoler vers une indentification de nouvelles molécules impliquées dans le développement commissural. Nos travaux ouvrent la voie à une réévaluation du contrôle développemental assuré par Robo3 au sein du système commissural des mammifères. Par biochimie fonctionnelle, nous avons observé que Robo3 du mammifère ni se lie, ni ne réagit aux slits. Par ailleurs, Robo3 interagit avec DCC, ce qui produit une phosphorylation intracellulaire sélective de Robo3 par l’entremise de la Nétrine-1. Cette dernière n’a pas d’effet attractif sur les neurones pontiques dépourvus de Robo3; phénomène qui peut être rétabli chez des souris Robo3 -/- par l’expression de Robo3 mammifère, mais non par l’expression de Robo3 non-mammifère. En conclusion, nous démontrons que la fonction de Robo3 a été spécifiquement convertie lors de l’évolution des mammifères. Une telle diversification mécanistique dérivée de l’évolution moléculaire d’un gène spécifique est susceptible d’être à la base de la précision du contrôle des mouvements volontaires chez les mammifèresIn species with bilateral morphological symmetry, connections between left and right in the nervous system are called commissures. The development of novel commissural circuits and modification of existing ones have accompanied the emergence of key neurobiological features in vertebrate evolution. Molecularly, guidance of commissures relies on ligand-receptor pairs such as Netrin-1/DCC mediating attraction of commissural axons to, and Slit/Robo mediated repulsion of post-crossing axons away from the midline. Arguing against assumed molecular redundancy, many commissures fail to develop in absence of a single receptor, Robo3. The objective of the current work is threefold: first, it sets out to characterize the molecular mechanisms underlying this unique function of Robo3 in mammals and evolutionarily across species. Secondly, we aim to extrapolate towards the identification of new molecules important for commissure development to lastly functionally evaluate some of these putative novel commissural signaling pathways. Our work paves the way to a complete reevaluation of Robo3-mediated developmental control in mammalian commissural systems. Using functional biochemistry, we find that mammalian Robo3 does neither bind nor respond to Slits. Moreover, Robo3 interacts with DCC and Netrin-1 selectively triggers intracellular phosphorylation of mammalian Robo3. Netrin-1 fails to attract pontine neurons lacking Robo3 and attraction can be restored in Robo3-/- mice by expression of mammalian, but not nonmammalian, Robo3. Conclusively, we show that Robo3 function has been uniquely converted during mammalian evolution. Such mechanistic diversification through molecular evolution in one specific gene likely underlies fine-tuning of mammalian voluntary movement control
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Allen, Richard Charles. "Secreted virulence factors : evolution, ecology and therapeutic manipulation." Thesis, University of Edinburgh, 2016. http://hdl.handle.net/1842/25789.
Full textAbstract:
Bacterial infections are an increasing cause for concern as resistance spreads to the majority of our front line antibiotics. To counter antibiotic resistance, new treatment regimens and drug targets are being investigated, including directly targeting bacterial virulence (pathogen-induced harm to the host), and therapies which target resistance mechanisms. The outcome of successful treatment with these compounds is not always killing or halting growth of bacteria, therefore selection for resistance to these types of therapeutics is complex. This complexity is increased by the secretion of many virulence factors, meaning their effects are shared with neighbouring individuals. In addition virulence factors show high phenotypic plasticity due to regulation by processes like quorum sensing (QS), which further complicates treatments targeting virulence, or the regulatory processes themselves. Using the example of quorum sensing inhibitors this study shows the importance of understanding the function and ecology of targeted virulence factors, to predict the selection for resistance to anti-virulence drugs. Later chapters elaborate on this to show how quorum sensing control affects selection on secreted virulence factors. The use of anti-virulence drugs as adjuvants is discussed, with a study showing that the interaction between QS inhibition and translation inhibitors is dependent on the environment. The selection for resistance to combinations of antibiotics and adjuvants is investigated using co-amoxiclav as an example, showing that treatment with high doses of adjuvant are robust to the evolution of resistance.
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Vichitsorasatra, Natee. "The evolution of cooperation between the European community and East Asia." Thesis, Loughborough University, 2007. https://dspace.lboro.ac.uk/2134/8113.
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This thesis focuses on the problem of cooperation within the international political economy, with special reference to the European Union's relations with key partners in East Asia. In pursuing this focus, the thesis probes a number of central issues in international cooperation, which thus far have not been applied in detail to inter-regional cooperation. In particular, the argument focuses on the reasons for cooperation and defection, the balance between material interests, institutions and ideas in shaping cooperation, and the shifting balance between bilateral and multilateral modes of cooperation. This research makes use of three bodies of conceptual literature related to IPE and interregionalism. It firstly makes use of existing thoughts on cooperation inherent in modern IPE theory, especially with regard to neorealism, neoliberal institutionalism, and social constructivism, to analyse the balance between bilateralism and multilateralism as well as between material interest, institutions and ideas. Secondly, Robert Axelrod's findings concerning the 'evolution of cooperation' are integrated into the work, making use of ideas which support as well as clarify various means of understanding the global political economy already presented by IPE theories. Thirdly, in the respective chapters, comparisons are drawn between IPE's propositions on cooperation and Axelrod's notions of cooperation in relation to literature on regionalism and interregionalism. These insights are finally combined to set the foundations for a set of questions and propositions on interregional cooperation. These questions and propositions are subsequently analysed through four empirical cases focused on the European Community's political-economic relationship with East Asia. The bilateral cases are observed through a material, institutional, and ideational analysis of the EC's interregional relationships with Japan, the Republic of Korea, and the People's Republic of China. A similar analysis focusing on the multilateral dimension is conducted with the EC's interregional relationship with East Asia as seen through the Asia Europe Meeting (ASEM). The observations in both cases include an analysis of trade, institutional development, and the EC's strategic documents. These observations are designed to draw out comparisons of how an evolution of cooperation occurs based on primary values and interests, cooperative modes, the development of accepted codes of conduct, and progressive institutionalisation. It is argued that this material, institutional, and ideational analysis provides insights which are not possible in a more parsimonious or dichotomous approach. The thesis contends that the evolution of cooperation between the EC and East Asia has taken on a strongly material form and that the preferred cooperative mode has been 'active bilateralism', strongly stimulated by the predominantly important issue of trade but with some characteristics of a maturing dialogue and bilateral institutionalisation. The ASEM multilateral forum, suffering increasing indifference, can be seen as 'passive multilateralism' and strongly based on values and ideas, albeit possibly conflicting and incompatible ones. On the basis of the evidence assembled, the empirical cases provide further insight into the initial research questions and suggest that bilateral interregionalism in the EC-East Asia relationship is more grounded in material interests while multilateral interregionalism as seen in ASEM is based more strongly on ideas and values. The research also confirms the coexistence and confluence between bilateralism and multilateralism, the binding role of institutions, the importance of policy areas, and acknowledges the possible effect that a combination of endogenous and exogenous factors may have on the evolution of interregional cooperation.
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Lee, William. "The evolution of cooperation and diversity in public good producing organisms." Thesis, Royal Holloway, University of London, 2013. http://repository.royalholloway.ac.uk/items/57a5032b-ce0d-1e40-a7da-3d85a0df5d57/6/.
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In a population of altruists, all individuals thrive. But altruists are exploited by cheating individuals which do not perform altruistic acts but still benefit from those. In these conditions cooperation cannot easily evolve. This issue is resolved by kin recognition: altruists recognise each other through the use of a conspicuous tag. These altruists do well until cheaters acquire the signalling tag and disrupt the cooperation. But altruists using a different tag can then invade the population, followed by new cheaters. This mechanism can lead to a diversity of tags coexisting in the population. However it has not yet been applied in realistic biological systems. In this thesis, I formulated mathematical and simulation models to investigate the effect of diversity on the evolutionary dynamics in systems where different altruists compete with cheaters. In particular, I focused on organisms producing public goods, i.e. goods that can profit to the whole population. I considered two biological systems models: gynodioecious populations of plants, where hermaphrodites produce pollen that can be used by female-only individuals, and bacteria producing an iron-chelating molecule, called siderophore, that can be exploited by both producers and non-producers. I found that diversity in gynodioecious plants is dependent on population structure. In particular, I found that the maximal level of diversity occurs when the population structure does not favour altruists or cheaters. Next, I found a number of important results in siderophore-producing bacteria. By considering a detailed ecological model, I derived Hamilton's rule in a metapopulation and found that the level of cooperation in a population depends on the length of interaction between strains. Finally, I discovered a novel evolutionary mechanism generating and maintaining diversity and showed that it results from non-equilibrium mechanisms. These findings explain why cheaters appear readily in experiments but are rare in natural populations. My results demonstrate the importance of integrating ecological details in order to understand the mechanisms leading to cooperation and diversity, and will provide a basis and framework for future studies on the emergence and maintenance of diversity.
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Miller, Steven. "Network fluctuation as an explanatory factor in the evolution of cooperation." Thesis, University of Manchester, 2017. https://www.research.manchester.ac.uk/portal/en/theses/network-fluctuation-as-an-explanatory-factor-in-the-evolution-of-cooperation(56d08050-ce8d-408d-89b9-5cbe1f70f25d).html.
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Network reciprocity describes the emergence of cooperative behaviour where interactions are constrained by incomplete network connectivity. It has been widely studied as an enabling mechanism for the emergence of cooperation and may be of particular interest in explaining cooperative behaviours amongst unrelated individuals or in organisms of lower cognitive abilities. Research in this area has been galvanised by the finding that heterogeneous topology promotes cooperation. Consequently there has been a strong focus on scale-free networks; however, such networks typically presuppose formative mechanisms based on preferential attachment, a process which has no general explanation. This assumption may give rise to models of cooperation that implicitly encode capabilities only generally found in more complex forms of life, thus constraining their relevance with regards to the real world. By considering the connectivity of populations to be dynamic, rather than fixed, cooperation can exist at lower levels of heterogeneity. This thesis demonstrates that a model of network fluctuation, based on random rather than preferential growth, supports cooperative behaviour in simulated social networks of only moderate heterogeneity, thus overcoming difficulties associated with explanations based on scale-free networks. In addition to illustrating the emergence and persistence of cooperation in existing networks, we also demonstrate how cooperation may evolve in networks during their growth. In particular our model supports the emergence of cooperation in populations where it is originally absent. The combined impact of our findings increases the generality of reciprocity as an explanation for cooperation in networks.
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Han, The Anh. "Intention recognition, commitment and their roles in the evolution of cooperation." Doctoral thesis, Faculdade de Ciências e Tecnologia, 2012. http://hdl.handle.net/10362/8784.
Full textAbstract:
Dissertação para obtenção do Grau de Doutor em
InformáticaThe goal of this thesis is twofold. First, intention recognition is studied from an Arti cial Intelligence (AI) modeling perspective. We present a novel and e cient intention recognition method that possesses several important features: (i) The method is context-dependent and incremental, enabled by incrementally constructing a three-layer Bayesian network model as more actions are observed, and in a context-dependent manner, relying on a logic programming knowledge base concerning the context; (ii) The Bayesian network is composed from a knowledge base of readily speci ed and readily maintained Bayesian network fragments with simple structures, enabling an e cient acquisition of the corresponding knowledge base (either from domain experts or else automatically from a plan corpus); and, (iii) The method addresses the issue of intention change and abandonment, and can appropriately resolve the issue of multiple intentions recognition. Several aspects of the method are evaluated experimentally, achieving some de nite success. Furthermore, on top of the intention recognition method, a novel framework for intention-based decision making is provided, illustrating several ways in which an ability to recognize intentions of others can enhance a decision making process. A second subgoal of the thesis concerns that, whereas intention recognition has been extensively studied in small scale interactive settings, there is a major shortage of modeling research with respect to large scale social contexts, namely evolutionary roles and aspects of intention recognition. Employing our intention recognition method and the tools of evolutionary game theory, this thesis explicitly addresses the roles played by intention recognition in the nal outcome of cooperation in large populations of self-regarding individuals. By equipping individuals with the capacity for assessing intentions of others in the course of social dilemmas, we show how intention recognition is selected by natural selection, opening a window of opportunity for cooperation to thrive, even in hard cooperation prone games like the Prisoner's Dilemma. In addition, there are cases where it is di cult, if not impossible, to recognize the intentions of another agent. In such cases, the strategy of proposing commitment, or of intention manifestation, can help to impose or clarify the intentions of others. Again using the tools of evolutionary game theory, we show that a simple form of commitment can lead to the emergence of cooperation; furthermore, the combination of commitment with intention recognition leads to a strategy better than either one by itself. How the thesis should be read? We recommend that the thesis be read sequentially, chapter by chapter [1-2-3-4-5-6-7-8]. However, for those more interested in intention recognition from the AI modeling perspective, i.e. the rst subgoal of the thesis, Chapters 6 and 7 can be omitted and Chapters 4 and 5 are optional [1-2-3-(4)-(5)-8]. In addition, for those more keen on the problem of the evolution of cooperation, i.e. the second subgoal of thesis, Chapter 3 and even Chapter 2, can be omitted [1-(2)-4-5-6-7-8].
Fundação para a Ciência e Tecnologia - PhD grant (ref. SFRH/BD/62373/2009)
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Hanley, James E. "The role of non-cooperative games in the evolution of cooperation /." view abstract or download file of text, 2000. http://wwwlib.umi.com/cr/uoregon/fullcit?p9986740.
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Thesis (Ph. D.)--University of Oregon, 2000.Typescript. Includes vita and abstract. Includes bibliographical references (leaves 115-123). Also available for download via the World Wide Web; free to University of Oregon users.
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Levando, Dmitry <1966>. "Essays on trade and cooperation." Doctoral thesis, Università Ca' Foscari Venezia, 2012. http://hdl.handle.net/10579/1177.
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In this dissertation, we study two questions of strategic behavior. One is related to the trade in strategic market games.
The paper studies strategic market games with wash sales. This class of games posses best response correspondences that in turn generate non-uniqueness of pure strategy equilibria. We introduce a mixed strategy equilibrium that resolves the aforementioned indeterminacy, therefore, results into a unique equilibrium. Finally we provide an example that illustrates our equilibrium concept.
Another paper offers non-cooperative mechanism for coalition formation. It includes a special non-cooperative game and a self-financed enforcement. Enforcement is performed by an external central planner. The enforcement operates as a reallocation between all players in the game. In order to support stability of the induced coalition partition the central planner distorts payoffs in an equilibrium ("a carrot") and outside the equilibrium ("a stick"). Induced cores of the distorted game can not exist without the enforcement. If the enforcement exists, then the corresponding induced equilibrium has the properties of a strong Nash equilibrium. Credibility of the enforcement is supported by the balance of used resources from one side and reallocations and punishments from another.
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Sun, Song. "Dynamics and Mechanisms of Adaptive Evolution in Bacteria." Doctoral thesis, Uppsala universitet, Institutionen för medicinsk biokemi och mikrobiologi, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-172786.
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Determining the properties of mutations is fundamental to understanding the mechanisms of adaptive evolution. The major goal of this thesis is to investigate the mechanisms of bacterial adaptation to new environments using experimental evolution. Different types of mutations were under investigations with a particular focus on genome rearrangements. Adaptive evolution experiments were focused on the development of bacterial resistance to antibiotics. In paper I, we performed stochastic simulations to examine the role of gene amplification in promoting the establishment of new gene functions. The results show that gene amplification can contribute to creation of new gene functions in nature. In paper II, the evolution of β-lactam resistance was studied by evolving S. typhimurium carrying a β-lactamase gene towards increased resistance against cephalosporins. Our results suggest that gene amplification is likely to provide an immediate solution at the early stage of adaptive evolution and subsequently facilitate further stable adaptation. In paper III, we isolated spontaneous deletion mutants with increased competitive fitness, which indicated that genome reduction could be driven by selection. To test this hypothesis, independent lineages of wild type S. typhimurium were serially passaged for 1000 generations and we observed fixation of deletions that significantly increased bacterial fitness when reconstructed in wild type genetic background. In paper IV, we developed a new strategy combining 454 pyrosequencing technology and a ‘split mapping’ computational method to identify unique junction sequences formed by spontaneous genome rearrangements. A high steady-state frequency of rearrangements in unselected bacterial populations was suggested from our results. In paper V, the rates, mechanisms and fitness effects of colistin resistance in S. typhimurium were determined. The high mutation rate and low fitness costs suggest that colistin resistance could develop in clinical settings. In paper VI, a novel Metallo-β-lactamase (MBL) with low resistance against β-lactam antibiotics was employed as the ancestral protein in a directed evolution experiment to examine how an enzyme evolves towards increased resistance. For most isolated mutants, in spite of their significantly increased resistance, both mRNA and protein levels were decreased as compared with the parental protein, suggesting that the catalytic activity had increased.
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Tholander, Fredrik Otto. "Catalytic mechanisms and evolution of leukotriene A₄ hydrolyse /." Stockholm, 2006. http://diss.kib.ki.se/2006/91-7140-952-1/.
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Stilwell, Peter Robert. "The ecology and evolution of diversity and cooperation in bacterial public-goods." Thesis, University of Exeter, 2017. http://hdl.handle.net/10871/33191.
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Explaining why cooperation exists despite the persistent advantage of cheats has been the focus of much theoretical and empirical attention in biology. Using the bacterium Pseudomonas aeruginosa as a model system for the evolution of cooperation, I investigate two distinct phenomena which may develop our understanding of how cooperation is maintained; 1) tag-based cooperation and diversity; and 2) environmental heterogeneity. The first investigates how diversity in cooperative systems may be a response to the selective pressure exerted by cheating, and how cheats may then regulate communities to maintain diversity: I demonstrate that in competition, tag-based cooperation is able to evade parasitism, provided the public-good is only accessible to producer strains, i.e., the cheat possesses the “wrong” tag. I also demonstrate that cheats can have a marked influence on diversity: In a community of two producer strains with different tags, if a third cheater strain is introduced, it will drive both its own producer and itself extinct. I do not find that the presence of cheats maintains diversity in either structured or unstructured environments, and discuss the possible causes of this. In the second topic of this thesis, I investigate the effect of environmental heterogeneity in resource availability, through space and time, on the evolution of cooperation. Environmental heterogeneity is a ubiquitous feature of natural landscapes, yet its effect on the evolution of cooperation has not been extensively studied. I demonstrate that resource availability heterogeneity, in both time and space, acts to maintain cooperation at higher levels than homogeneous environments of the same total resource value. This effect is due to the covariance between productivity and the cost of cooperation: high resource availability periods and spaces are highly productive, and also incur a relatively lower cost of cooperation.
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Crosby, Garth Valentine. "Trust Based Security Mechanisms for Wireless Sensor Networks." FIU Digital Commons, 2007. http://digitalcommons.fiu.edu/etd/61.
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Wireless sensor networks are emerging as effective tools in the gathering and dissemination of data. They can be applied in many fields including health, environmental monitoring, home automation and the military. Like all other computing systems it is necessary to include security features, so that security sensitive data traversing the network is protected. However, traditional security techniques cannot be applied to wireless sensor networks. This is due to the constraints of battery power, memory, and the computational capacities of the miniature wireless sensor nodes. Therefore, to address this need, it becomes necessary to develop new lightweight security protocols. This dissertation focuses on designing a suite of lightweight trust-based security mechanisms and a cooperation enforcement protocol for wireless sensor networks. This dissertation presents a trust-based cluster head election mechanism used to elect new cluster heads. This solution prevents a major security breach against the routing protocol, namely, the election of malicious or compromised cluster heads. This dissertation also describes a location-aware, trust-based, compromise node detection, and isolation mechanism. Both of these mechanisms rely on the ability of a node to monitor its neighbors. Using neighbor monitoring techniques, the nodes are able to determine their neighbors’ reputation and trust level through probabilistic modeling. The mechanisms were designed to mitigate internal attacks within wireless sensor networks. The feasibility of the approach is demonstrated through extensive simulations. The dissertation also addresses non-cooperation problems in multi-user wireless sensor networks. A scalable lightweight enforcement algorithm using evolutionary game theory is also designed. The effectiveness of this cooperation enforcement algorithm is validated through mathematical analysis and simulation. This research has advanced the knowledge of wireless sensor network security and cooperation by developing new techniques based on mathematical models. By doing this, we have enabled others to build on our work towards the creation of highly trusted wireless sensor networks. This would facilitate its full utilization in many fields ranging from civilian to military applications.
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Plunket, Anne. "Evolution de la cooperation : contribution a l'etude des determinants des processus d'evolution et de selection de la cooperation technologique." Paris 11, 1999. http://www.theses.fr/1999PA111002.
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Cette these propose une analyse theorique de l'evolution de la cooperation technologique interfirmes. Pour ce faire, elle applique directement la notion evolutionniste de selection (lamarckienne et darwinienne) a l'etude des accords interfirmes. L'evolution de la cooperation est presentee comme le resultat de processus d'adaptation et de selection agissant sur trois unites de selection (la structure de gouvemance, les competences-routines, les projetsstrategies). Ces unites sont sanctionnees par deux environnements de selection : d'une part, l'environnement interne resulte d'une double dynamique : l'evolution de la cooperation comme input (arrangements contractuels et incitations a la cooperation regissant la mise en commun d'actifs) et l'evolution de la cooperation comme output (les produits de la cooperation tels que l'institutionnalisation de la relation et la creation de ressources), d'autre part, l'environnement externe (contexte economique et institutionnel). Ces environnements sanctionnent les trois unites de selection precitees, i. E. Respectivement, les dimensions contractuelle (potentiel de coordination regissant l'arbitrage marche, hierarchie et partenariat), cognitive (la capacite a engendrer de nouveaux produits et savoir-faire) et economique (profitabilite, i. E. La capacite a generer des revenus pour les partenaires). Les deux premieres dimensions rendent compte des changements endogenes, alors que le dernier decoule de changements exogenes. Ainsi, l'evolution et la survie de la cooperation ne suivent pas une logique de selection reposant sur un critere defini mais sur une ensemble de criteres, qui conjugues, determinent la poursuite ou l'arret de l'accord. Les criteres de selection expliquent le renforcement (i. E. Le maintien) ou l'arret (rupture ou passage a une autre structure de gouvemance) de l'accord, alors que les mecanismes de selection rendent compte du biais par lequel l'adaptation et la selection expliquent l'evolution de la cooperation. Sur un plan empirique, la these s'appuie sur 25 etudes de cas d'accords eureka dans le domaine des biotechnologies et des nouveaux materiauxThis thesis proposes a theoretical framework to study the evolution of technological interfirm agreements. It applies directly evolutionary notions, namely the selection principle (lamarckian and darwinian) to the dynamics of agreements. The evolution of cooperation appears as the result of processes of adaptation and selection acting on three units of selection (the governance structure, the competencies-routines, the projects-strategies). These units depend on two selection environments: an internal environment determined by two interrelated dynamics : the evolution of cooperation as an input (contractuel arrangements and incentives to allocate ressources to the agreement) and as an output (products of cooperation such as the institutionalization process and the creation of ressources), and an external environment (institutional and economic context). These environments act on the three units of selection, i. E. On, respectively, the contractual (coordination potential, i. E. The market, hierarchy, cooperation trade-off), the cognitive (capacity to create new products and know how) and the economic dimension (capacity to generate profits) of the agreement. Thus, the evolution and survival of cooperation do not depend on a single selection criterion but on a set of selection criteria which jointly determine the reinforcement (i. E. Continuity) or the breach of the agreement. The mecanisms of selection explain the evolution of cooperation through adaptation and selection processes. The thesis is based on 25 case stydies of eureka agreements in the field of biotechnologies and new materials
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Roydan, Alexa. "Legitimacy and international public authority : the evolution of IAEA safeguards." Thesis, University of St Andrews, 2010. http://hdl.handle.net/10023/984.
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Using the IAEA as a case for focused study, this thesis argues that the construction and reconstruction of the Secretariat’s legitimacy has been dependant upon several different legitimating influences at different stages in the IAEA’s evolution. In brief, it will be demonstrated that early on, in the absence of clear non-proliferation norms, power wielded by critical and self-interested actors functioned as the primary legitimator – promoting early development and insulating the organization from outside pressures. However, based upon this particular case, I will also argue that state power alone is insufficient to guarantee legitimacy and the exercise of international public authority, especially in light of the degree to which these institutions are increasingly expected to challenge the territorial sovereignty of member states. In order for an organization to acquire adequate legitimacy to exercise public authority over the long term, it must develop beyond the point at which state power is instrumental, and assume a degree of organizational autonomy. This happened with the evolution of organizational expertise recognizing the IAEA’s bureaucracy as an authority, development of specific nonproliferation rules and norms that placed the IAEA in authority, and “right” processes within the bureaucracy that reinforced these and other substantive norms, positioning the Secretariat as a trusted agent within international society. Thus, the development of a professional identity, successful norms and rules, and the elaboration of a “right” process were key to the creation of legitimacy, and as a consequence, the Secretariat’s exercise of public authority in support of the safeguards regime.
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Jolly, Jennifer Elaine. "The evolution and development of international health collaboration." Thesis, University of British Columbia, 1987. http://hdl.handle.net/2429/26847.
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The goal of this thesis is to document and explain the evolution and development of international health collaboration. Utilizing international relations theory, the initial development of the health regulatory regime is traced through the early sanitary conferences. The establishment of international health organizations is then documented, along with the transformation this entailed in international health collaboration. The resulting effect the institutionalization of the international health regime had upon international health collaboration is finally presented.
It is determined that states initial interest in international health collaboration grew out of a concern for reducing the impediments to international trade and commerce that quarantine measures imposed. States were, at first, reluctant to collaborate, but as scientific knowledge increased, international cooperation in this area expanded. Realizing the benefits of joint technical cooperation, states formed international organizations. The special characteristics of international health under the guiding influence of medical specialists were to cause an evolution within this regime.
Collaboration in this area has greatly increased. The primary concern of the international health regime is no longer the containment of pestilent diseases without significant interference to international commerce. This regime is now concerned with improving the level of health care to all states, regardless of the effects this might have on the interests of the developed states. Technical cooperation and aid to developing countries is now the central focus of the World Health Organization. This evolution has not occurred without some degree of conflict, however, as it is the developing states and the medical elites of the organization have forced the evolution of the previous norms of this regime. The developing states have a clear interest in securing assistance in developing their health infrastructures, and the elites of the WHO are committed by nature of their scientific training to work towards this ideal. The developed states are not in favour of this change as it threatens their interests and power within this regime. Although it initially appeared that collaboration in this area would be relatively easy to secure as an improvement in health would be to every state's benefit, this has not always been the case. International relations theory is utilized in this thesis to explain the origins, the obstacles, and the evolution that has occurred within this regime.Arts, Faculty of
Political Science, Department of
Graduate
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Gale, J. L. H. "Nature's secret art : the evolution of conventions, cooperation and customary international law." Thesis, University of Cambridge, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.599274.
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This central aim of this thesis is to provide sound foundations for understanding two persistent and closely related questions within international relations and international legal theory. First, can genuine cooperation arise in a world of self-interested states that recognise no political superior? And second, can we defend the reality of international law as a force for shaping state behaviour in a decentralised world? Most pertinently, building on international relations scholarship regarding the problem of cooperation, a profound redirection in our thinking about international law has gained momentum in recent years. This approach, based on game theory, emphasises the centrally of state interest and rationality as the basis concepts of international affairs; so far as state behaviour can be understood as the product of the rational pursuit of self-interest, it is argued that law and genuine cooperation have no explanatory parts to play. Game-theoretic scepticism regarding the reality of law and cooperation requires a robust game-theoretic defence, and this is what this thesis attempts to provide. It is first argued that customary international law is the logical basis of international law. This is not a defect of international law, for any system of law is ultimately based on custom. Conventions, defined as stable regularities of cooperative behaviour ultimately founded on self-interest, are taken to provide the theoretic foundations of social customs. The central theoretic difficulty is then to explain how self-regarding agents, unrestrained by a prior social order, may form conventions that give rise to social customs. Kant hypothesises that ‘Nature’ may play her hand and extricate us from the antagonism that characterises our relations before social norms have evolved. Identifying Nature with the forces of evolutionary selection, the tools of evolutionary game theory are used to demonstrate how self-interested egoists may establish stable norms of international behaviour. International interaction is modelled by the repeated Prisoner’s Dilemma, and how a state behaves in any interaction is determined by its strategy. So long as states occasionally imitate the strategies of other better-performing states, and so long as states occasionally switch spontaneously to other strategies, the evolutionary game theory may be used to understand how conventions arise and persist: importantly, rationality need not be presumed. Three mechanisms for the genesis of social conventions are presented. These are reciprocity, punishment based on multi-level selection, and reputation. Each mechanism provides a basis for an idealised understanding of the genesis and persistence of social conventions, and consequently international cooperation and customary law. It is hoped that this preliminary attempt to introduce evolutionary thinking to international affairs will broaden our understanding of, and help to direct future research into, the perennial controversies over the potential for cooperation and effectiveness of legal norms in international affairs.
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Artemova, Tatiana. "The role of cooperation and dispersal in the evolution of antibiotic resistance." Thesis, Massachusetts Institute of Technology, 2015. http://hdl.handle.net/1721.1/99315.
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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Physics, 2015.Cataloged from PDF version of thesis.
Includes bibliographical references (pages 89-92).
Understanding mechanisms of evolution under in real biological systems is a fundamental problem. Natural selection is one of the mechanisms that drive evolution. Due to the natural selection, phenotypes with higher fitness than the rest of the population increase in frequency and eventually dominate the populations. In real biological systems due to interactions between individuals within a population, it is not always obvious how natural selection manifests itself. Here we consider two types of interactions cooperative antibiotic break down and spatially expanding populations. In each of the cases predicting which phenotype is the most fit and the patterns corresponding to selection of this phenotype could be not straightforward. (1) Bacterial antibiotic resistance is typically quantified by the minimum inhibitory concentration (MIC), which is defined as the minimal concentration of antibiotic that inhibits bacterial growth starting from a standard cell density. However, when antibiotic resistance is mediated by degradation, the collective inactivation of antibiotic by the bacterial population causes the measured MIC to depend strongly on the initial cell density. Given this dependence, the relationship between MIC and bacterial fitness in such cases is not well-defined. Here we demonstrate that the resistance of a single, isolated cell-which we call the single cell MIC (scMIC)-provides a superior metric for quantifying antibiotic resistance. Unlike the MIC, we find that the scMIC predicts the direction of selection and also specifies the antibiotic concentration at which selection begins to favor new mutants. Understanding the cooperative nature of bacterial growth in antibiotics is therefore essential in predicting the evolution of antibiotic resistance. (2) During the expansions of natural populations, new phenotype can emerge. If it is fitter than the rest of the population, it will take over. However, the exact spatial patterns of this process are unknown. Here we show that for a wide class of models the fraction of the fit mutant should increase exponentially. We also observe this pattern experimentally by observing bacterial populations expanding in soft agar, as well as connection between the steepness of the exponent to the fitness difference.
by Tatiana Artemova.
Ph. D.
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von, Lippke Ilonka S. "Ecology and evolution of cooperation in the Española Mockingbird Nesomimus macdonaldi, Galápagos." Diss., Restricted to subscribing institutions, 2008. http://proquest.umi.com/pqdweb?did=1619490561&sid=1&Fmt=2&clientId=1564&RQT=309&VName=PQD.
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Ye, Jong Young. "Cooperation beyond rivalry : world system evolution and U.S.-Japan relations since 1945 /." Thesis, Connect to this title online; UW restricted, 2001. http://hdl.handle.net/1773/10790.
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Okada, Isamu, Hitoshi Yamamoto, Fujio Toriumi, and Tatsuya Sasaki. "The Effect of Incentives and Meta-incentives on the Evolution of Cooperation." Public Library of Science, 2015. http://dx.doi.org/10.1371/journal.pcbi.1004232.
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Although positive incentives for cooperators and/or negative incentives for free-riders in social dilemmas play an important role in maintaining cooperation, there is still the outstanding issue of who should pay the cost of incentives. The second-order free-rider problem, in which players who do not provide the incentives dominate in a game, is a well-known academic challenge. In order to meet this challenge, we devise and analyze a meta-incentive game that integrates positive incentives (rewards) and negative incentives (punishments) with second-order incentives, which are incentives for other players' incentives. The critical assumption of our model is that players who tend to provide incentives to other players for their cooperative or non-cooperative behavior also tend to provide incentives to their incentive behaviors. In this paper, we solve the replicator dynamics for a simple version of the game and analytically categorize the game types into four groups. We find that the second-order free-rider problem is completely resolved without any third-order or higher (meta) incentive under the assumption. To do so, a second-order costly incentive, which is given individually (peer-to-peer) after playing donation games, is needed. The paper concludes that (1) second-order incentives for first-order reward are necessary for cooperative regimes, (2) a system without first-order rewards cannot maintain a cooperative regime, (3) a system with first-order rewards and no incentives for rewards is the worst because it never reaches cooperation, and (4) a system with rewards for incentives is more likely to be a cooperative regime than a system with punishments for incentives when the cost-effect ratio of incentives is sufficiently large. This solution is general and strong in the sense that the game does not need any centralized institution or proactive system for incentives. (authors' abstract)
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Eldakar, Omar Tonsi. "Explaining individual differences in cooperation, cheating and punishment." Diss., Online access via UMI:, 2005.
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Pawlowska, Bogna Julia. "Mathematical models of microbial evolution : cooperative systems." Thesis, University of Exeter, 2016. http://hdl.handle.net/10871/26819.
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Microbes usually live in large communities, where they interact with other organisms and species. These interactions include cooperation, when individuals facilitate each others growth and reproduction. Such cooperation has been for instance observed within pathogens in the process of infection. Therefore, given the number and the frequency of infectious diseases, understanding the nature and the dynamics of microbial cooperation may be a crucial step in modern medicine. Microbes often secrete costly enzymes which extracellularly metabolise resources available in the environment. This external metabolism is a form of ’public good cooperation’, in which individuals invest their energy in producing ’public goods’, available to other organisms. To study this phenomenon we deploy mathematical models which are based on biologically relevant assumptions. Our models not only aim to capture the dynamics of studied microbial communities, but also to remove the natural complexity arising in the empirical studies and thus to provide a mechanistic understanding of their results. We first recover and explain the recent empirical finding, about mixed strain infections, showing that an addition of a low virulent strain which does not produce public goods (termed ’cheat’) may counter-intuitively enhance the total population virulence. What drives this result turns out to be an interaction of two different cooperative traits and the presence of spatial structure. Next we study the competition between the strains that do and do not produce public goods. Our results depend on environmental conditions, such as resource concentration and population density, but they are also determined by the degree of spatial structure - the ecological trait which so far has been treated only as a binary variable. Finally, we identify some environmental threats for the external metabolism feeding strategy, and we examine its competitiveness in comparison to ’internal metabolism’, in which the costly enzymes are private.
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Poulshock, Joseph W. "Language and morality : evolution, altruism, and linguistic moral mechanisms." Thesis, University of Edinburgh, 2006. http://hdl.handle.net/1842/25094.
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This thesis inquires into how human language relates to morality – and shows the ways language enables, extends, and maintains human value systems. Though we ultimately need to view the relation between language and morality from many different perspectives – biological, psychological, sociological, and philosophical – the approach here is primarily a linguistic one informed by evolutionary theory. At first, this study shows how natural selection relates to the problem of altruism and how language serves human moral ontogeny. Subsequently, the argument demonstrates how language helps enable cultural group selection. Moreover, as language helps influence human behaviour in an altruistic direction beyond in-group non-kin (helping facilitate cultural group selection), we also consider how language can help facilitate altruistic behaviour towards out-group non-kin. This therefore raises the prospect of a limited moral realism in a world of evolutionary processes. With these issues and possibilities in mind, we consider and analyze the properties of language that help extend human morality. Specifically, discussion covers how recursion, linguistic creativity, naming ability, displacement, stimulus freedom, compositionality, cultural transmission, and categorization extend moral systems. Moreover, because language so broadly influences morality, the inquiry extends into how linguistic differences (specifically between English and Japanese) might also cause subtle differences in moral perception between Japanese and English speakers. Lastly, we consider how moral ideas might take on a life of their own, catalytically propagating in degrees dependent and independent of human intention.
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Mandic, Milica. "Mechanisms and evolution of hypoxia tolerance in family Cottidae." Thesis, University of British Columbia, 2008. http://hdl.handle.net/2429/2518.
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A comparative phylogenetically independent contrast (PIC) analysis was employed to investigate the adaptive role of traits involved in hypoxia tolerance in sculpins, a group of closely related fish species that live in the nearshore marine environment. I demonstrated that there was a tight correlation between critical oxygen (O₂) tension (P-crit) and the distribution of species across an environmental gradient. Species of sculpins with the lowest P-crit inhabit the 0₂ variable intertidal zone, while species with higher P-crit inhabit the O₂ stable subtidal zone. Low P-crit values in sculpins were associated with enhanced O₂ extraction capacity, with three principal traits accounting for 83% of the variation in P-crit: low routine O₂ consumption rate (MO2 ), high mass specific gill surface area and high whole cell hemoglobin-oxygen (Hb-0₂) binding affinity. Variation in whole cell Hb-O₂ binding affinity was strongly correlated with the intrinsic affinity of Hb for O₂ and not to differences in the concentration of the allosteric Hb modulators ATP and GTP.
When environmental O₂ dropped below a species' P-crit, some species of sculpins behaviorally responded to the severe hypoxia by performing aquatic surface respiration (ASR) and aerial emergence. Although intertidal sculpins consistently performed these behaviors, the clustering of these species into a single phylogenetic Glade did not allow us to draw conclusions regarding the relationship between ASR, aerial emergence and P-crit using PIC analysis. Three species of sculpins, which were chosen because of their low, medium and high P-crit values, exhibited dramatically varied mortality rates when exposed to severe hypoxia equivalent to 40% of their respective P-crit. Although ATP turnover rates were similar between the three species in the initial two hours of hypoxia exposure, the differences in the ability of the three species to survive severe hypoxia appeared to be associated with the concentration of on-board liver glycogen and the degree of liver glycogen depletion. However, when liver glycogen was assessed in twelve species of sculpins at normoxia and compared with P-crit, there was nosignificant PIC correlation between P-crit and liver glycogen.
Overall, I have shown that there is a clear relationship between P-crit and the distribution of sculpins along the nearshore environment and that this is primarily related to differences in O₂ extraction capacity. When O₂ tensions are well below their P-crit, there are dramatic differences in behavioral, physiological and biochemical responses among these species of sculpins.
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Linkevičius, Marius. "Evolution and Mechanisms of Tigecycline Resistance in Escherichia coli." Doctoral thesis, Uppsala universitet, Institutionen för medicinsk biokemi och mikrobiologi, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-259226.
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Antibiotic resistance is an ongoing global medical crisis and we are in great need of new antibacterial agents to combat rapidly emerging resistant pathogens. Tigecycline is one of few drugs that have been introduced into medicine during the last two decades. It is a broad-spectrum third generation tetracycline that is active against multidrug-resistant bacteria that cause complicated infections. In this thesis I examined the development of tigecycline resistance in Escherichia coli and associated in vitro and in vivo fitness effects. Selections of spontaneous E. coli mutants revealed relatively high accumulation rates of changes in the multidrug efflux system AcrAB-TolC regulation network and in heptose biosynthesis and transport pathways important for lipopolysaccharide (LPS) synthesis. Both groups of mutations led to reduced susceptibility to tigecycline and slower growth compared to the wild-type bacteria. Additional in vitro fitness assays and in vivo competitions showed that LPS mutants were less fit than efflux mutants, providing a possible explanation for why up-regulation of multidrug efflux pumps is the main tigecycline resistance mechanism reported in clinical isolates. Tigecycline was designed to evade the two most common tetracycline resistance mechanisms conferred by Tet proteins, efflux and ribosomal protection. However, tigecycline is a substrate for the tetracycline modifying enzyme Tet(X). Screening of Tet protein mutant libraries showed that it is possible to select Tet mutants with minimal inhibitory concentrations of tigecycline that reach clinically relevant levels. Mutations in Tet proteins that permitted a better protection from tigecycline frequently exhibited reduced activity against earlier generations of tetracyclines, except for the Tet(X) enzyme mutants, which were better at inactivating all tested tetracyclines. This is particularly worrisome because different variants of Tet(X) have recently spread to multidrug-resistant pathogens through horizontal gene transfer. Therefore, Tet(X) mutants with improved activity threaten the medical future of tetracyclines. Multidrug resistance is easily disseminated through horizontally spreading conjugative plasmids. pUUH239.2 is an example of a successful conjugative plasmid that caused the first clonal outbreak of extended spectrum β-lactamase-producing Klebsiella pneumoniae in Scandinavia. This plasmid was formed after rearrangements between two different plasmid backbones and it carries resistance genes to multiple antibiotic classes, heavy metals, and detergents.
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McGranahan, N. L. "Mechanisms of cancer evolution and drivers of tumour heterogeneity." Thesis, University College London (University of London), 2015. http://discovery.ucl.ac.uk/1473445/.
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Cancer drug resistance is almost inevitable in the majority of patients with advanced metastatic tumours. Intra-tumour heterogeneity, facilitating rapid tumour evolution, is a main cause of resistance to cancer therapies. In this thesis, I explore how cancer genome sequencing data can shed light intratumour heterogeneity and the processes shaping cancer genome evolution over space and time. Multi-region and single-sample sequencing data was harnessed to temporally and clonally dissect mutations across 10 major cancer-types. The existence of branched tumour evolution and widespread heterogeneity was demonstrated. Although mutations in known cancer genes typically occurred early in cancer evolution, subclonal ‘actionable’ mutations, including BRAF (V600E), IDH1 (R132H), PIK3CA (E545K), and EGFR (L858R), were also identified. Temporal dissection of mutational signatures revealed that APOBEC-mediated mutagenesis is frequently a late event in cancer evolution and plays a key role in the acquisition of subclonal driver mutations. Copy number analysis suggested that genome doubling is prevalent across tumour types and that it frequently occurs early in tumour evolution in colorectal cancer. A cancer cell-line system was used to demonstrate that rare cells that survive genome-doubling display increased tolerance to chromosome aberrations and a genome-doubling event was found to be independently predictive of reduced relapse-free survival in two independent cohorts. Finally, the clinical impact of intra-tumour heterogeneity was explored in the context of cancer neo-antigens and immune-modulation. The number of clonal neoantigens was associated with survival outcome in lung adenocarcinoma patients and T cells reactive to clonal neo-antigens were identified. Sensitivity to anti-PD-1 therapy was dependent on neo-antigen clonal burden and intra-tumour heterogeneity. Thus, immunotherapeutic strategies targeting clonal neo-antigens in combination with checkpoint-blockade may provide a tractable approach to tackling lung adenocarcinomas. This thesis demonstrates how analyses of genomic data can shed light on the biology and clinical relevance of cancer evolution and intra-tumour heterogeneity.
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Freschi, Luca. "Post-translational modifications regulatory networks : evolution, mechanisms et implications." Doctoral thesis, Université Laval, 2015. http://hdl.handle.net/20.500.11794/25812.
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Les modifications post-traductionnelles (PTM) sont des modifications chimiques des protéines qui permettent à la cellule de réguler finement ses fonctions ainsi que de coder et d’intégrer des signaux environnementaux. Les progrès récents en ce qui a trait aux techniques expérimentales et bioinformatiques nous ont permis de determiner les profils de PTM pour des protéomes entiers ainsi que d’identifier les molécules qui sont responsables d’ « écrire » ou d’« effacer » ces PTM. Avec ces donnés, il a été possible de commencer à definir des réseaux de régulation cellulaire par PTM. Ici, nous avons étudié l’évolution de ces réseaux pour mieux comprendre comment ils peuvent contribuer à expliquer la complexité et la diversité des organismes ainsi que pour mieux comprendre leurs mecanismes d’action. Avant tout, nous avons abordé la question de comment les réseaux de régulation des PTM peuvent être recablés après un évenement de duplication des gènes en étudiant comment le réseau de phosphorégulation de la levure bourgeonnante a été récablé après un évenement de duplication complète du génome qui a eu lieu il y a 100 milions d’années. Nos résultats mettent en évidence le rôle de la duplication des gènes comme mécanisme clé pour l’innovation et la complexification des réseaux de régulation par PTM. Par la suite, nous avons abordé la question de comment les PTM peuvent contribuer à la diversité des organismes en comparant les profils de phosphorylation de l’homme et de la souris. Nous avons trouvé des différences substantielles dans les profils de PTM de ces deux espèces qui ont le potentiel d’expliquer, au moins en partie, les différences phénotypiques observées entre eux. Nous avons aussi trouvé des évidences qui supportent l’idée que les PTM peuvent « sauter » vers des nouvelles localisations et quand même réguler les mêmes fonctions biologiques. Ce phénomène doit être pris en considération dans les comparaisons des profils de PTM qui appartiennent à des espèces différentes, pour éviter de surestimer la divergence causée par la régulation par les PTM. Enfin, nous avons investigué comment plusieures PTM alternatives pour un même residu pouvent interagir pour réguler des fonctions cellulaires. Nous avons examiné deux des PTM les plus connus, la phosphorylation et la O-GlcNAcylation, qui modifient les sérines et les thréonines, et nous avons étudié les mécanismes potentiels d’interaction entre ces deux PTM. Nos résultats supportent l’hypothèse que ces deux PTM contrôlent plusieurs fonctions biologiques plutôt qu’une seule fonction. Globalement, les résultats présentés dans cette thèse permettent d’élucider les dynamiques évolutives, les mécanismes de fonctionnement et les implications biologiques des PTM.Post-translational modifications (PTMs) are chemical modification of proteins that allow the cell to finely tune its functions as well as to encode and integrate environmental signals. The recent advancements in the experimental and bioinformatic techniques have allowed us to determine the PTM profiles of entire proteomes as well as to identify the molecules that write or erase PTMs to/from each protein. This data have made possible to define cellular PTM regulatory networks. Here, we study the evolution of these networks to get new insights about how they may contribute to increase organismal complexity and diversity and to better understand their molecular mechanisms of functioning. We first address the question of how and to which extent a PTM network can be rewired after a gene duplication event, by studying how the budding yeast phosphoregulatory network was rewired after a whole genome duplication event that occurred 100 million years ago. Our results highlight the role of gene duplication as a key mechanism to innovate and complexify PTM regulatory networks. Then, we address the question of how PTM networks may contribute to organismal diversity by comparing the human and mouse phosphorylation profiles. We find that there are substantial differences in the PTM profiles of these two species that have the potential to explain, at least in part, the phenotypic differences observed between them. Moreover, we find evidence supporting the idea that PTMs can jump to new positions during evolution and still regulate the same biological functions. This phenomenon should be taken into account when comparing the PTM profiles of different species, in order to avoid overestimating the divergence in PTM regulation. Finally, we investigate how multiple and alternative PTMs that affect the same residues interact with each other to control proteins functions. We focus on two of the most studied PTMs, protein phosphorylation and O-GlcNAcylation, that affect serine and threonine residues and we study their potential mechanisms of interactions in human and mouse. Our results support the hypothesis that these two PTMs control multiple biological functions rather than a single one. Globally this work provides new findings that elucidate the evolutionary dynamics, the functional mechanisms and the biological implications of PTMs.