Browsing by Issue Date, starting with "2006"
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- The tragedy of the commons, the public goods dilemma, and the meaning of rivalry and excludability in evolutionary biologyPublication . Dionisio, F.; Gordo, I.Problem: In the study of conflicts, both economists and evolutionary biologists use the concepts ‘tragedy of the commons’ and ‘public goods dilemma’. What is the relationship between the economist and evolutionist views of these concepts? Model features: The economics literature defines the tragedy of the commons and the public goods dilemma in terms of rivalry and excludability of the good. In contrast, evolutionists define these conflicts based on fitness functions with two components: individual and group components of fitness. Mathematical method: Evolutionary game theory and the calculation of evolutionarily stable strategy trait values by standard optimization techniques and by replacing slopes of group phenotype on individual genotype by coefficients of relatedness. Conclusion: There is a direct relationship between rivalry and the individual component of fitness and between excludability and the group component of fitness. Moreover, although the prisoner’s dilemma constitutes a suitable metaphor to analyse both the public goods dilemma and the tragedy of the commons, it gives the false idea that the two conflicts are symmetric since they refer to situations in which individuals consume a common resource – tragedy of the commons – or contribute to a collective action or common good – public goods dilemma. However, the two situations are clearly not symmetric: from the economical point of view they differ by rivalry, and from the evolutionary biology point of view the two conflicts differ by the significance of the within-group competition in the fitness function.
- Modularity: Understanding the Development and Evolution of Natural Complex SystemsPublication . Pereira-Leal, J.B.
- Localized contacts between hosts reduce pathogen diversityPublication . Nunes, A.; da Gama, M. M. T.; Gomes, M. G. M.We investigate the dynamics of a simple epidemiological model for the invasion by a pathogen strain of a population where another strain circulates. We assume that reinfection by the same strain is possible but occurs at a reduced rate due to acquired immunity. The rate of reinfection by a distinct strain is also reduced due to cross-immunity. Individual based simulations of this model on a 'small-world' network show that the proportion of local contacts in the host contact network structure significantly affects the outcome of such an invasion, and as a consequence will affect the patterns of pathogen evolution. In particular, hosts interacting through a 'small-world' network of contacts support lower prevalence of infection than well-mixed populations, and the region in parameter space for which an invading strain can become endemic and coexist with the circulating strain is smaller, reducing the potential to accommodate pathogen diversity. We discuss the underlying mechanisms for the reported effects, and we propose an effective mean-field model to account for the contact structure of the host population in 'small-world' networks
- Did Germinal Centers evolve under differential effects of diversity vs affinity?Publication . Faro, J.; Combadão, J.; Gordo, I.The classical view on the process of mutation and affinity maturation that occurs in GCs assumes that their major role is to generate high affinity levels of serum Abs, as well as a dominant pool of high affinity memory B cells, through a very efficient selection process. Here we present a model that considers different types of structures where a mutation selection process occurs, with the aim at discussing the evolution of Germinal Center reactions. Based on the results of this model, we suggest that in addition to affinity maturation, the diversity generated during the GC reaction may have also been important in the evolution towards the presently observed highly organized structure of GC in higher vertebrates.
- Pertussis: increasing disease as a consequence of reducing transmissionPublication . Gomes, Maria Gabriela Miranda; Águas, R.; Gonçalves, G.Since the 1980s, the occurrence of pertussis cases in developed countries has increased and shifted towards older age groups. This resurgence follows 30 years of intense mass vaccination, and has been attributed primarily to three factors: (1) more effective diagnosis of the disease, (2) waning of vaccine-induced immunity, and (3) loss of vaccine efficacy due to the emergence of new Bordetella pertussis strains. Here we develop and analyse a mathematical model to assess the plausibility of these hypotheses. We consider that exposure to B pertussis through natural infection or vaccination induces an immune response that prevents severe disease but does not fully prevent mild infections. We also assume that these protective effects are temporary due to waning of immunity. These assumptions, describing the mode of action of adaptive immunity, are combined with a standard transmission model. Two distinct epidemiological scenarios are detected: under low transmission, most infections lead to severe disease; under high transmission, mild infections are frequent, boosting clinical immunity and maintaining low levels of severe disease. The two behaviours are separated by a reinfection threshold in transmission. As a result, the highest incidence of severe disease is expected to occur at intermediate transmission intensities--near the reinfection threshold--suggesting that pertussis resurgence may be induced by a reduction in transmission, independently of vaccination. The model is extended to interpret the outcomes of current control measures and explore scenarios for future interventions
- The effect of spatial structure in adaptive evolutionPublication . Perfeito, L.; Gordo, I.; Campos, P.R.A.We study the dynamics of adaptation in a spatially structured population. The model assumes local competition for replication, where each organism interacts only with its nearest neighbors and is inspired by experimental methods that can be used to study the process of adaptive evolution in microbes. In such experiments microbial populations are grown on petri dishes and allowed to adapt by serial passage. We compare the rate of adaptation in a structured population where the structure is maintained intact to those where movement of individuals can occur. We observe that the rate of adaptive evolution is higher and the mean effect of fixed beneficial mutations is lower in intact structures than in structures with mixing.
- Adaptive evolution in a spatially structured asexual populationPublication . Gordo, I.; Campos, P.R.A.We study the process of adaptation in a spatially structured asexual haploid population. The model assumes a local competition for replication, where each organism interacts only with its nearest neighbors. We observe that the substitution rate of beneficial mutations is smaller for a spatially structured population than that seen for populations without structure. The difference between structured and unstructured populations increases as the adaptive mutation rate increases. Furthermore, the substitution rate decreases as the number of neighbors for local competition is reduced. We have also studied the impact of structure on the distribution of adaptive mutations that fix during adaptation.
- Genetic variation for outcrossing among Caenorhabditis elegans isolatesPublication . Teotónio, H; Manoel, D; Phillips, PCThe evolution of breeding systems results from the existence of genetic variation and selective forces favoring different outcrossing rates. In this study we determine the extent of genetic variation for characters directly related to outcrossing, such as male frequency, male mating ability, and male reproductive success, in several wild isolates of the nematode Caenorhabditis elegans. This species is characterized by an androdioecious breeding system in which males occur with hermaphrodites that can either self-fertilize or outcross with males. We find genetic variation for all characters measured, but also find that environmental variation is a large fraction of the total phenotypic variance. We further determine the existence of substantial genetic variation for population competitive performance in several laboratory environments. However, these measures are uncorrelated with outcrossing characters. The data presented here contribute to an understanding of male maintenance in natural populations through their role in outcrossing.
- Clusters of cytokines determine malaria severity in Plasmodium falciparum - Infected patients from endemic areas of central IndiaPublication . Prakash, D.; Fesel, C.; Jain, R.; Cazenave, P.A.; Mishra, G.C.; Pied, S.We investigated the role of interferon (IFN)- gamma , interleukin (IL)-1 beta , IL-2, IL-4, IL-5, IL-6, IL-10, IL-12, tumor necrosis factor (TNF)- alpha , and transforming growth factor (TGF)- beta in clinically well-defined groups of Plasmodium falciparum-infected patients manifesting mild malaria (MM), severe noncerebral malaria (SM), or cerebral malaria (CM) and in control subjects from Gondia, a malaria-endemic site in India, as well as in healthy subjects from non-malaria-endemic areas. Two-way coupled cluster analysis revealed 2 clusters of cytokines relevant to clinical subgroups of disease. The first cluster was composed of IFN- gamma , IL-2, IL-5, IL-6, and IL-12, the levels of which were significantly increased during infection but were predominant in patients with MM and allowed us to distinguish them from patients with SM or CM. The second cluster was composed of TGF- beta , TNF- alpha , IL-10, and IL-1 beta , the levels of which were highly correlated with each other in the different clinical groups of patients and significantly increased with disease severity, particularly in CM. Discriminant analyses allowed us to propose a minimal model. Levels of cytokines such as IL-5, IL-1 beta , IL-10, and IL-2 increase with infection. Levels of IL-12, IL-5, and IL-6 discriminate severe forms of malaria from MM. Finally, levels of IL-1 beta , IL-12, and IFN- gamma are relevant for the discrimination of CM from SM: high IL-1 beta levels are associated with CM, and high IL-12 and IFN- gamma levels are associated with SM
- Muller's ratchet in random graphs and scale free networksPublication . Campos, P.R.A.; Combadão, J.; Dionísio, F.; Gordo, I.Muller's ratchet is an evolutionary process that has been implicated in the extinction of asexual species, the evolution of mitochondria, the degeneration of the Y chromosome, the evolution of sex and recombination and the evolution of microbes. Here we study the speed of Muller's ratchet in a population subdivided into many small subpopulations connected by migration, and distributed on a network. We compare the speed of the ratchet in two distinct types of topologies: scale free networks and random graphs. The difference between the topologies is noticeable when the average connectivity of the network and the migration rate is large. In this situation we observe that the ratchet clicks faster in scale free networks than in random graphs. So contrary to intuition, scale free networks are more prone to loss of genetic information than random graphs. On the other hand, we show that scale free networks are more robust to the random extinction than random graphs. Since these complex networks have been shown to describe well real-life systems, our results open a framework for studying the evolution of microbes and disease epidemics.