Adaptive evolution in a spatially structured asexual population

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.The original version is available at www.springerlink.co

The tragedy of the commons, the public goods dilemma, and the meaning of rivalry and excludability in evolutionary biology

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

Nonequilibrium model for estimating parameters of deleterious mutations

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

Sex and deleterious mutations

For access the publication please visit the following link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2390638/The evolutionary advantage of sexual reproduction has been considered as one of the most pressing questions in evolutionary biology. While a pluralistic view of the evolution of sex and recombination has been suggested by some, here we take a simpler view and try to quantify the conditions under which sex can evolve given a set of minimal assumptions. Since real populations are finite and also subject to recurrent deleterious mutations, this minimal model should apply generally to all populations. We show that the maximum advantage of recombination occurs for an intermediate value of the deleterious effect of mutations. Furthermore we show that the conditions under which the biggest advantage of sex is achieved are those that produce the fastest fitness decline in the corresponding asexual population and are therefore the conditions for which Muller's ratchet has the strongest effect. We also show that the selective advantage of a modifier of the recombination rate depends on its strength. The quantification of the range of selective effects that favors recombination then leads us to suggest that, if in stressful environments the effect of deleterious mutations is enhanced, a connection between sex and stress could be expected, as it is found in several specie

Increased Survival of Antibiotic-Resistant Escherichia coli inside Macrophages

Mutations causing antibiotic resistance usually incur a fitness cost in the absence of antibiotics. The magnitude of such costs is known to vary with the environment. Little is known about the fitness effects of antibiotic resistance mutations when bacteria confront the host's immune system. Here, we study the fitness effects of mutations in the rpoB, rpsL, and gyrA genes, which confer resistance to rifampin, streptomycin, and nalidixic acid, respectively. These antibiotics are frequently used in the treatment of bacterial infections. We measured two important fitness traits-growth rate and survival ability-of 12 Escherichia coli K-12 strains, each carrying a single resistance mutation, in the presence of macrophages. Strikingly, we found that 67% of the mutants survived better than the susceptible bacteria in the intracellular niche of the phagocytic cells. In particular, all E. coli streptomycin-resistant mutants exhibited an intracellular advantage. On the other hand, 42% of the mutants incurred a high fitness cost when the bacteria were allowed to divide outside of macrophages. This study shows that single nonsynonymous changes affecting fundamental processes in the cell can contribute to prolonged survival of E. coli in the context of an infection.European Research Council, LAO/ITQB, FCT

Evolution of clonal populations approaching a fitness peak

Populations facing novel environments are expected to evolve through the accumulation of adaptive substitutions. The dynamics of adaptation depend on the fitness landscape and possibly on the genetic background on which new mutations arise. Here, we model the dynamics of adaptive evolution at the phenotypic and genotypic levels, focusing on a Fisherian landscape characterized by a single peak. We find that Fisher's geometrical model of adaptation, extended to allow for small random environmental variations, is able to explain several features made recently in experimentally evolved populations. Consistent with data on populations evolving under controlled conditions, the model predicts that mean population fitness increases rapidly when populations face novel environments and then achieves a dynamic plateau, the rate of molecular evolution is remarkably constant over long periods of evolution, mutators are expected to invade and patterns of epistasis vary along the adaptive walk. Negative epistasis is expected in the initial steps of adaptation but not at later steps, a prediction that remains to be tested. Furthermore, populations are expected to exhibit high levels of phenotypic diversity at all times during their evolution. This implies that populations are possibly able to adapt rapidly to novel abiotic environments.CAPES-IGC

The effect of spatial structure in adaptive evolution

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.The original version is available at www.springerlink.co

Scaling, genetic drift and clonal interference in the extinction pattern of asexual populations

We investigate the dynamics of loss of favorable mutations in an asexual haploid population. In the current work, we consider homogeneous as well as spatially structured population models. We focus our analysis on statistical measurements of the probability distribution of the maximum population size N(sb) achieved by those mutations that have not reached fixation. Our results show a crossover behavior which demonstrates the occurrence of two evolutionary regimes. In the first regime, which takes place for small N(sb) , the probability distribution is described by a power law with characteristic exponent theta(d) =1.8 +/- 0.01. This power law is not influenced by the rate of beneficial mutations. The second regime, which occurs for intermediate to large values of N(sb), has a characteristic exponent theta(c) which increases as the rate of beneficial mutations grows. These results establish where genetic drift and clonal interference become the main underlying mechanism in the extinction of advantageous mutations

Did Germinal Centers evolve under differential effects of diversity vs affinity?

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

Muller's ratchet in random graphs and scale free networks

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