Viana, DS.; Gordo, I.; Sucena, E.; Moita, M.A.P.
Background: Game theory and the Prisoner's Dilemma (PD) game in particular, which captures the paradox of cooperative interactions that lead to benefits but entail costs to the interacting individuals, have constituted a powerful tool in the study of the mechanisms of reciprocity. However, in non-human animals most tests of reciprocity in PD games have resulted in sustained defection strategies. As a consequence, it has been suggested that under such stringent conditions as the PD game humans alone have evolved the necessary cognitive abilities to engage in reciprocity, namely, numerical discrimination, memory and control of temporal discounting.
Perfeito, L.; Fernandes, C.; Mota, G.; Isabel, G.
Evolution by natural selection is driven by the continuous generation of adaptive mutations. We measured the genomic mutation rate that generates beneficial mutations and their effects on fitness in Escherichia coli under conditions in which the effect of competition between lineages carrying different beneficial mutations is minimized. We found a rate on the order of 10(-5) per genome per generation, which is 1000 times as high as previous estimates, and a mean selective advantage of 1%. Such a high rate of adaptive evolution has implications for the evolution of antibiotic resistance and pathogenicity.
Gordo, I.; Charlesworth, B.
Gordo, I. and B. Charlesworth (2000) The degeneration of asexual haploid populations and the speed of Muller's ratchet. Genetics 154: 1379-87
Gordo, I.; Charlesworth, B.
Gordo, I. and B. Charlesworth (2000) On the speed of Muller's ratchet. Genetics 156: 2137-40
Gordo, I.; Charlesworth, B.
The rate of accumulation of deleterious mutations by Muller's ratchet is investigated in large asexual haploid populations, for a range of parameters with potential biological relevance. The rate of this process is studied by considering a very simple model in which mutations can have two types of effect: either strongly deleterious or mildly deleterious. It is shown that the rate of accumulation of mildly deleterious mutations can be greatly increased by the presence of strongly deleterious mutations, and that this can be predicted from the associated reduction in effective population size (the background selection effect). We also examine the rate...
Gordo, I.; Navarro, A.; Charlesworth, B.
For access the publication please visit the following link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1462134/
Knowledge of the mutational parameters that affect the evolution of organisms is of key importance
in understanding the evolution of several characteristics of many natural populations, including
recombination and mutation rates. In this study, we estimated the rate and mean effect of spontaneous
mutations that affect fitness in a mutator strain of Escherichia coli and review some of the
estimation methods associated with mutation accumulation (MA) experiments. We performed an
MA experiment where we followed the evolution of 50 independent mutator lines that were subjected
to repeated bottlenecks of a single individual for approximately 1150 generations. From
the decline in mean fitness and the increase in variance...
Gordo, I.; Sousa, A.
Mutation is the ultimate source of genetic variation. The
rate at whichnew mutations typically occurs, their effects
on fitness and the strength and type of genetic interactions
between different mutations are key for understanding
the evolution of any population. Estimates of
these parameters in organisms such as bacteria will have a
profound impact on our understanding of their biology,
diversity, rate of speciation and in our health. Experimental
evolution with bacteria presents us with the
opportunity to directly measure these parameters and to
test theoretical predictions about the genetic basis of
adaptive evolution. Evidence has been increasing to support
the view that bacterial adaptation can be extraordinary
fast, that competition between different
Bachtrog, D.; Gordo, I.
We study the population genetics of adaptation in nonequilibrium haploid asexual populations. We find
that the accumulation of deleterious mutations, due to the operation of Muller’s ratchet, can considerably reduce the
rate of fixation of advantageous alleles. Such reduction can be approximated reasonably well by a reduction in the
effective population size. In the absence of Muller’s ratchet, a beneficial mutation can only become fixed if it creates
the best possible genotype; if Muller’s ratchet operates, however, mutations initially arising in a nonoptimal genotype
can also become fixed in the population, since the loss of the least-loaded class implies that an initially nonoptimal
background can become...
Rosas, A.; Gordo, I.; Campos, P.R.A.
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...
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.
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...
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...
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...
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.
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....
Campos, P.R.A.; Gordo, I.
We introduce a model for assessing the levels and patterns of genetic
diversity in pathogen populations, whose epidemiology follows a susceptible–
infected–susceptible model. We assume a population which is structured
into many small subpopulations (hosts) that exchange migrants (transmission)
between their neighbours. We consider that the hosts are connected according to
a small-world network topology, and in this way our model interpolates between
two classical population genetics models: the stepping-stone and the island model.
We have observed that the level of diversity has a maximum at intermediate
values of the basic reproductive number R0. This result is independent of the
topology considered, but depends on the relation between parasite...
Gokaydin, D.; Oliveira-Martins, J.B.; Gordo, I.; Gomes, M.G.M.
For accessing the publication please visit the following link:
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...
Gordo, I.; Campos, P.R.A.
The analysis of genetic variation in populations of infectious agents may help us understand their epidemiology and evolution. Here we study a model for assessing the levels and patterns of genetic diversity in populations of infectious agents. The population is structured into many small subpopulations, which correspond to their hosts, that are connected according to a specific type of contact network. We considered different types of networks, including fully connected networks and scale free networks, which have been considered as a model that captures some properties of real contact networks. Infectious agents transmit between hosts, through migration, where they grow...