Browsing by Author "Dionisio, F."
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- Controlling excludability in the evolution of cooperationPublication . Dionisio, F.; Gordo, I.Background: A tragedy of the commons arises if individuals cannot protect their future use of a depletable resource, and individual fitness increases if individuals exploit the resource at rates beyond sustainability. Natural selection then forces the individuals to diminish, perhaps even to destroy, their resource. One way to protect future use is privatization - that is, locally excluding rivals from the resource. Another is to reduce rivalry among individuals by restricting exploitation rates.
- Nonequilibrium model for estimating parameters of deleterious mutationsPublication . Gordo, I.; Dionisio, F.Deleterious mutations are of extreme evolutionary importance because, even though they are eliminated by natural selection, their continuous pressure creates a pool of variability in natural populations. They are of potential relevance for the existence of several features in evolution, such as sexual reproduction, and pose a risk to small asexual populations. Despite their extreme importance, the deleterious mutation rate and the effects of each mutation on fitness are poorly known quantities. Here we analyze a simple model that can be applied to simple experiments, in microorganisms, aiming at the quantification of these values.
- Positive Epistasis Drives the Acquisition of Multidrug ResistancePublication . Trindade, S.; Sousa, A.; Xavier, KB.; Dionisio, F.; Ferreira, MG.; Gordo, I.The evolution of multiple antibiotic resistance is an increasing global problem. Resistance mutations are known to impair fitness, and the evolution of resistance to multiple drugs depends both on their costs individually and on how they interact-epistasis. Information on the level of epistasis between antibiotic resistance mutations is of key importance to understanding epistasis amongst deleterious alleles, a key theoretical question, and to improving public health measures. Here we show that in an antibiotic-free environment the cost of multiple resistance is smaller than expected, a signature of pervasive positive epistasis among alleles that confer resistance to antibiotics. Competition assays reveal that the cost of resistance to a given antibiotic is dependent on the presence of resistance alleles for other antibiotics.
- Positive Epistasis Drives the Acquisition of Multidrug ResistancePublication . Trindade, S.; Sousa, A.; Xavier, KB.; Dionisio, F.; Ferreira, MG.; Gordo, I.The evolution of multiple antibiotic resistance is an increasing global problem. Resistance mutations are known to impair fitness, and the evolution of resistance to multiple drugs depends both on their costs individually and on how they interact-epistasis. Information on the level of epistasis between antibiotic resistance mutations is of key importance to understanding epistasis amongst deleterious alleles, a key theoretical question, and to improving public health measures. Here we show that in an antibiotic-free environment the cost of multiple resistance is smaller than expected, a signature of pervasive positive epistasis among alleles that confer resistance to antibiotics. Competition assays reveal that the cost of resistance to a given antibiotic is dependent on the presence of resistance alleles for other antibiotics. Surprisingly we find that a significant fraction of resistant mutations can be beneficial in certain resistant genetic backgrounds, that some double resistances entail no measurable cost, and that some allelic combinations are hotspots for rapid compensation. These results provide additional insight as to why multi-resistant bacteria are so prevalent and reveal an extra layer of complexity on epistatic patterns previously unrecognized, since it is hidden in genome-wide studies of genetic interactions using gene knockouts.
- Small-word networks decrease the speed of Muller's ratchetPublication . Combadão, J.; Dionisio, F.; Campos, P.R.A.; Gordo, I.; Gomes, M.G.M.Muller's ratchet is an evolutionary process that has been implicated in the extinction of asexual species, the evolution of non-recombining genomes, such as the mitochondria, the degeneration of the Y chromosome, and the evolution of sex and recombination. Here we study the speed of Muller's ratchet in a spatially structured population which is subdivided into many small populations (demes) connected by migration, and distributed on a graph. We studied different types of networks: regular networks (similar to the stepping-stone model), small-world networks and completely random graphs. We show that at the onset of the small-world network - which is characterized by high local connectivity among the demes but low average path length - the speed of the ratchet starts to decrease dramatically. This result is independent of the number of demes considered, but is more pronounced the larger the network and the stronger the deleterious effect of mutations. Furthermore, although the ratchet slows down with increasing migration between demes, the observed decrease in speed is smaller in the stepping-stone model than in small-world networks. As migration rate increases, the structured populations approach, but never reach, the result in the corresponding panmictic population with the same number of individuals. Since small-world networks have been shown to describe well the real contact networks among people, we discuss our results in the light of the evolution of microbes and disease epidemics
- The evolution of a conjugative plasmid and its ability to increase bacterial fitness.Publication . Dionisio, F.; Conceição, I.C.; Marques, A.C.R.; Fernandes, L.; Gordo, I.Conjugative plasmids are extra-chromosomal DNA elements that are capable of horizontal transmission and are found in many natural isolated bacteria. Although plasmids may carry beneficial genes to their bacterial host, they may also cause a fitness cost. In this work, we studied the evolution of the R1 plasmid and we found that, in spite of the R1 plasmid conferring an initial cost to its host, after 420 generations the cost disappeared in all five independent evolution experiments. In fact, in two of these five experiments evolved conjugative plasmids actually conferred a fitness advantage to their hosts. Furthermore, the relative fitness of the ancestral clone bearing one of the evolved plasmids is significantly higher than both the plasmid-free ancestral cells and the evolved cells carrying the evolved plasmid. Given that the R1 plasmid may spread among different species of enterobacteria, we wondered what the effect of the evolved plasmid would be inside Salmonella enterica cells. We found that the evolved plasmid is also able to dramatically increase the relative fitness of these cells. Our results suggest that even if general usage of antibiotics is halted, conjugative plasmids that have been selected with antibiotics in previous years can still persist among bacterial populations or even invade new strains.
- 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.