Fixation Of Beneficial Mutations Research Articles

A Model for Designing Adaptive Laboratory Evolution Experiments.

The occurrence of mutations is a cornerstone of the evolutionary theory of adaptation, capitalizing on the rare chance that a mutation confers a fitness benefit. Natural selection is increasingly being leveraged in laboratory settings for industrial and basic science applications. Despite increasing deployment, there are no standardized procedures available for designing and performing adaptive laboratory evolution (ALE) experiments. Thus, there is a need to optimize the experimental design, specifically for determining when to consider an experiment complete and for balancing outcomes with available resources (i.e., laboratory supplies, personnel, and time). To design and to better understand ALE experiments, a simulator, ALEsim, was developed, validated, and applied to the optimization of ALE experiments. The effects of various passage sizes were experimentally determined and subsequently evaluated with ALEsim, to explain differences in experimental outcomes. Furthermore, a beneficial mutation rate of 10-6.9 to 10-8.4 mutations per cell division was derived. A retrospective analysis of ALE experiments revealed that passage sizes typically employed in serial passage batch culture ALE experiments led to inefficient production and fixation of beneficial mutations. ALEsim and the results described here will aid in the design of ALE experiments to fit the exact needs of a project while taking into account the resources required and will lower the barriers to entry for this experimental technique.IMPORTANCE ALE is a widely used scientific technique to increase scientific understanding, as well as to create industrially relevant organisms. The manner in which ALE experiments are conducted is highly manual and uniform, with little optimization for efficiency. Such inefficiencies result in suboptimal experiments that can take multiple months to complete. With the availability of automation and computer simulations, we can now perform these experiments in an optimized fashion and can design experiments to generate greater fitness in an accelerated time frame, thereby pushing the limits of what adaptive laboratory evolution can achieve.

Simple phenotypic sweeps hide complex genetic changes in populations.

Changes in allele frequencies and the fixation of beneficial mutations are central to evolution. The precise relationship between mutational and phenotypic sweeps is poorly described however, especially when multiple alleles are involved. Here, we investigate these relationships in a bacterial population over 60 days in a glucose-limited chemostat in a large population. High coverage metagenomic analysis revealed a disconnection between smooth phenotypic sweeps and the complexity of genetic changes in the population. Phenotypic adaptation was due to convergent evolution and involved soft sweeps by 7–26 highly represented alleles of several genes in different combinations. Allele combinations spread from undetectably low baselines, indicating that minor subpopulations provide the basis of most innovations. A hard sweep was also observed, involving a single combination of rpoS, mglD, malE, sdhC, and malT mutations sweeping to greater than 95% of the population. Other mutant genes persisted but at lower abundance, including hfq, consistent with its demonstrated frequency-dependent fitness under glucose limitation. Other persistent, newly identified low-frequency mutations were in the aceF, galF, ribD and asm genes, in noncoding regulatory regions, three large indels and a tandem duplication; these were less affected by fluctuations involving more dominant mutations indicating separate evolutionary paths. Our results indicate a dynamic subpopulation structure with a minimum of 42 detectable mutations maintained over 60 days. We also conclude that the massive population-level mutation supply in combination with clonal interference leads to the soft sweeps observed, but not to the exclusion of an occasional hard sweep.

Population Dynamics of Metastable Growth-Rate Phenotypes

Neo-Darwinian evolution has presented a paradigm for population dynamics built on random mutations and selection with a clear separation of time-scales between single-cell mutation rates and the rate of reproduction. Laboratory experiments on evolving populations until now have concentrated on the fixation of beneficial mutations. Following the Darwinian paradigm, these experiments probed populations at low temporal resolution dictated by the rate of rare mutations, ignoring the intermediate evolving phenotypes. Selection however, works on phenotypes rather than genotypes. Research in recent years has uncovered the complexity of genotype-to-phenotype transformation and a wealth of intracellular processes including epigenetic inheritance, which operate on a wide range of time-scales. Here, by studying the adaptation dynamics of genetically rewired yeast cells, we show a novel type of population dynamics in which the intracellular processes intervene in shaping the population structure. Under constant environmental conditions, we measure a wide distribution of growth rates that coexist in the population for very long durations (>100 generations). Remarkably, the fastest growing cells do not take over the population on the time-scale dictated by the width of the growth-rate distributions and simple selection. Additionally, we measure significant fluctuations in the population distribution of various phenotypes: the fraction of exponentially-growing cells, the distributions of single-cell growth-rates and protein content. The observed fluctuations relax on time-scales of many generations and thus do not reflect noisy processes. Rather, our data show that the phenotypic state of the cells, including the growth-rate, for large populations in a constant environment is metastable and varies on time-scales that reflect the importance of long-term intracellular processes in shaping the population structure. This lack of time-scale separation between the intracellular and population processes calls for a new framework for population dynamics which is likely to be significant in a wide range of biological contexts, from evolution to cancer.

Unseen sex in ancient virgin fungi

Unseen sex in ancient virgin fungi

Nucleotide substitutions in dengue virus serotypes from Asian and American countries: insights into intracodon recombination and purifying selection

BackgroundDengue virus (DENV) infection represents a significant public health problem in many subtropical and tropical countries. Although genetically closely related, the four serotypes of DENV differ in antigenicity for which cross protection among serotypes is limited. It is also believed that both multi-serotype infection as well as the evolution of viral antigenicity may have confounding effects in increased dengue epidemics. Numerous studies have been performed that investigated genetic diversity of DENV, but the precise mechanism(s) of dengue virus evolution are not well understood.ResultsWe investigated genome-wide genetic diversity and nucleotide substitution patterns in the four serotypes among samples collected from different countries in Asia and Central and South America and sequenced as part of the Genome Sequencing Center for Infectious Diseases at the Broad Institute. We applied bioinformatics, statistical and coalescent simulation methods to investigate diversity of codon sequences of DENV samples representing the four serotypes. We show that fixation of nucleotide substitutions is more prominent among the inter-continental isolates (Asian and American) of serotypes 1, 2 and 3 compared to serotype 4 isolates (South and Central America) and are distributed in a non-random manner among the genes encoded by the virus. Nearly one third of the negatively selected sites are associated with fixed mutation sites within serotypes. Our results further show that of all the sites showing evidence of recombination, the majority (~84%) correspond to sites under purifying selection in the four serotypes. The analysis further shows that genetic recombination occurs within specific codons, albeit with low frequency (< 5% of all recombination sites) throughout the DENV genome of the four serotypes and reveals significant enrichment (p < 0.05) among sites under purifying selection in the virus.ConclusionThe study provides the first evidence for intracodon recombination in DENV and suggests that within codons, genetic recombination has a significant role in maintaining extensive purifying selection of DENV in natural populations. Our study also suggests that fixation of beneficial mutations may lead to virus evolution via translational selection of specific sites in the DENV genome.

Rate of fixation of beneficial mutations in sexual populations

We have investigated the rate of substitution of advantageous mutations in populations of haploid organisms where the rate of recombination can be controlled. We have verified that in all the situations recombination speeds up adaptation through recombination of beneficial mutations from distinct lineages in a single individual, and so reducing the intensity of clonal interference. The advantage of sex for adaptation is even stronger when deleterious mutations occur since now recombination can also restore genetic background free of deleterious mutations. However, our simulation results demonstrate that evidence of clonal interference, as increased mean selective effect of fixed mutations and reduced likelihood of fixation of small-effect mutations, are also present in sexual populations. What we see is that this evidence is delayed when compared to asexual populations.

The Genetic Basis of Phenotypic Adaptation I: Fixation of Beneficial Mutations in the Moving Optimum Model

We study the genetic basis of adaptation in a moving optimum model, in which the optimal value for a quantitative trait increases over time at a constant rate. We first analyze a one-locus two-allele model with recurrent mutation, for which we derive accurate analytical approximations for (i) the time at which a previously deleterious allele becomes beneficial, (ii) the waiting time for a successful new mutation, and (iii) the time the mutant allele needs to reach fixation. On the basis of these results, we show that the shortest total time to fixation is for alleles with intermediate phenotypic effect. We derive an approximation for this "optimal" effect, and we show that it depends in a simple way on a composite parameter, which integrates the ecological parameters and the genetic architecture of the trait. In a second step, we use stochastic computer simulations of a multilocus model to study the order in which mutant alleles with different effects go to fixation. In agreement with the one-locus results, alleles with intermediate effect tend to become fixed earlier than those with either small or large effects. However, the effect size of the fastest mutations differs from the one predicted in the one-locus model. We show how these differences can be explained by two specific effects of multilocus genetics. Finally, we discuss our results in the light of three relevant timescales acting in the system-the environmental, mutation, and fixation timescales-which define three parameter regimes leading to qualitative differences in the adaptive substitution pattern.

The spread of a beneficial mutation in experimental bacterial populations: the influence of the environment and genotype on the fixation of rpoS mutations

The spread of beneficial mutations through populations is at the core of evolutionary change. A long-standing hindrance to understanding mutational sweeps was that beneficial mutations have been slow to be identified, even in commonly studied experimental populations. The lack of information on what constitutes a beneficial mutation has led to many uncertainties about the frequency, fitness benefit and fixation of beneficial mutations. A more complete picture is currently emerging for a limited set of identified mutations in bacterial populations. In turn, this will allow quantitation of several features of mutational sweeps. Most importantly, the 'benefit' of beneficial mutations can now be explained in terms of physiological function and how variations in the environment change the selectability of mutations. Here, the sweep of rpoS mutations in Escherichia coli, in both experimental and natural populations, is described in detail. These studies reveal the subtleties of physiology and regulation that strongly influence the benefit of a mutation and explain differences in sweeps between strains and between various environments.

Speed of adaptation in structured populations

Adaptation of populations takes place with the occurrence and subsequent fixation of mutations that confer some selective advantage to the individuals which acquire it. For this reason, the study of the process of fixation of advantageous mutations has a long history in the population genetics literature. Particularly, the previous investigations aimed to find out the main evolutionary forces affecting the strength of natural selection in the populations. In the current work, we investigate the dynamics of fixation of beneficial mutations in a subdivided population. The subpopulations (demes) can exchange migrants among their neighbors, in a migration network which is assumed to have either a random graph or a scale-free topology. We have observed that the migration rate drastically affects the dynamics of mutation fixation, despite of the fact that the probability of fixation is invariant on the migration rate, accordingly to Maruyama's conjecture. In addition, we have noticed a topological dependence of the adaptive evolution of the population when clonal interference becomes effective.

Fixation of beneficial mutations in the presence of epistatic interactions

We investigate the effect of deleterious mutations on the process of fixation of new advantageous mutants in an asexual population. In particular we wish to study the dependence of the process on the strength of the deleterious mutations. We suppose the existence of epistatic interaction between the genes. We study the model by means of branching process theory and also by numerical simulations. Our results show the occurrence of two distinct regimes of behavior for the probability of fixation of these variants. The occurrence of either regime depends on the ratio between the selective advantage of the beneficial mutation s b and on the selective parameter for deleterious mutations s d . In the former, which takes place for s b / s d ≲1, the probability of fixation increases with the epistasis parameter α, whereas for s b / s d ≫1 the probability of fixation is a complex function of α and the mutation rate U. Surprisingly, we find that for the multiplicative landscape ( α=1) the probability of fixation P fix is given by P fix= π( s b ) e − U/ s d where π( s b ) is the probability of fixation for the two-allele model in the absence of mutations as calculated by Haldane (1927, Proc. Camb. Phil. Soc., 26, 220–230) and Kimura (1962, Genetics, 47, 713–719).

Natural selection at linked sites in humans

Theoretical and empirical work indicates that patterns of neutral polymorphism can be affected by linked, selected mutations. Under background selection, deleterious mutations removed from a population by purifying selection cause a reduction in linked neutral diversity. Under genetic hitchhiking, the rise in frequency and fixation of beneficial mutations also reduces the level of linked neutral polymorphism. Here we review the evidence that levels of neutral polymorphism in humans are affected by selection at linked sites. We then discuss four approaches for distinguishing between background selection and genetic hitchhiking based on (i) the relationship between polymorphism level and recombination rate for neutral loci with high mutation rates, (ii) relative levels of variation on the X chromosome and the autosomes, (iii) the frequency distribution of neutral polymorphisms, and (iv) population-specific patterns of genetic variation. Although the evidence for selection at linked sites in humans is clear, current methods and data do not allow us to clearly assess the relative importance of background selection and genetic hitchhiking in humans. These results contrast with those obtained for Drosophila, where the signals of positive selection are stronger.