Clonal interference and the evolution of RNA viruses

Following the very initial growth of biological RNA viral clones

Due to their extremely high genetic diversity, which is a direct consequence of high mutation rates, RNA viruses are often described as molecular quasispecies. According to this theory, RNA virus populations cannot be understood in terms of individual viral clones, as they are clouds of interconnected mutants, but this prediction has not yet been demonstrated experimentally. The goal of this study was to determine the fitness of individual clones sampled from a given RNA virus population, a necessary previous step to test the above prediction. To do so, limiting dilutions of a vesicular stomatitis virus population were employed to isolate single viral clones and their initial growth dynamics were followed, corresponding to the release of the first few hundred viral particles. This technique is useful for estimating basic fitness parameters, such as intracellular growth rate, viral yield per cell, rate at which cells are infected and time spent in cell-to-cell transmission. A combination of these parameters allows estimation of the fitness of individual clones, which seems to be determined mainly by their ability to complete infection cycles more quickly. Interestingly, fitness was systematically higher for initial clones than for their derived populations. In addition to environmental changes, such as cellular defence mechanisms, these differences are attributable to high RNA virus mutation rates.

Validating viral quasispecies with digital organisms: a re-examination of the critical mutation rate

Background

In this report we re-examine some recent experiments with digital organisms to test some predictions of quasispecies theory. These experiments revealed that under high mutation rates populations of less fit organisms previously adapted to such high mutation rates were able to outcompete organisms with higher average fitness but adapted to low mutation rates.

Results

We have verified that these results do hold in the original conditions and, by extending the set of initial parameters, we have also detected that the critical mutation rate was independent of population size, a result that we have found to be dependent on a different, contingent factor, the initial fitness vector. Furthermore, in all but one case, the critical mutation rate is higher than the error threshold, a key parameter in quasispecies theory, which prevents its extrapolation to natural viral populations.

Conclusion

From these results we conclude that digital organisms are useful tools for investigating evolutionary patterns and processes including some predictions from the quasispecies theory.

Functional divergence in tandemly duplicated Arabidopsis thaliana trypsin inhibitor genes

In multigene families, variation among loci and alleles can contribute to trait evolution. We explored patterns of functional and genetic variation in six duplicated Arabidopsis thaliana trypsin inhibitor (ATTI) loci. We demonstrate significant variation in constitutive and herbivore-induced transcription among ATTI loci that show, on average, 65% sequence divergence. Significant variation in ATTI expression was also found between two molecularly defined haplotype classes. Population genetic analyses for 17 accessions of A. thaliana showed that six ATTI loci arranged in tandem within 10 kb varied 10-fold in nucleotide diversity, from 0.0009 to 0.0110, and identified a minimum of six recombination events throughout the tandem array. We observed a significant peak in nucleotide and indel polymorphism spanning ATTI loci in the interior of the array, due primarily to divergence between the two haplotype classes. Significant deviation from the neutral equilibrium model for individual genes was interpreted within the context of intergene linkage disequilibrium and correlated patterns of functional differentiation. In contrast to the outcrosser Arabidopsis lyrata for which recombination is observed even within ATTI loci, our data suggest that response to selection was slowed in the inbreeding, annual A. thaliana because of interference among functionally divergent ATTI loci.

The contribution of epistasis to the architecture of fitness in an RNA virus

The tendency for genetic architectures to exhibit epistasis among mutations plays a central role in the modern synthesis of evolutionary biology and in theoretical descriptions of many evolutionary processes. Nevertheless, few studies unquestionably show whether, and how, mutations typically interact. Beneficial mutations are especially difficult to identify because of their scarcity. Consequently, epistasis among pairs of this important class of mutations has, to our knowledge, never before been explored. Interactions among genome components should be of special relevance in compacted genomes such as those of RNA viruses. To tackle these issues, we first generated 47 genotypes of vesicular stomatitis virus carrying pairs of nucleotide substitution mutations whose separated and combined deleterious effects on fitness were determined. Several pairs exhibited significant interactions for fitness, including antagonistic and synergistic epistasis. Synthetic lethals represented 50% of the latter. In a second set of experiments, 15 genotypes carrying pairs of beneficial mutations were also created. In this case, all significant interactions were antagonistic. Our results show that the architecture of the fitness depends on complex interactions among genome components.

Mutational effects on the clonal interference phenomenon

We study the process of fixation of beneficial mutations in an asexual population by means of a theoretical model. Particularly, we wish to investigate how the supply of deleterious and beneficial mutations influences the dynamics of the adaptive process of an evolving population. It is well known that the deleterious mutations drastically affect the fate of beneficial mutations. In addition, an increasing supply of favorable mutations, to compensate the decay of the fitness due to the accumulation of deleterious mutations, produces the clonal interference phenomenon where advantageous mutations in distinct lineages compete to reach fixation. This competition imposes a limit to the speed of adaptation of the population. Intuitively, we would expect that the interplay of the two mechanisms would conspire to ensure fixation of only large-effect beneficial mutations. Our results, however, show that beneficial mutations of small effect have an increased probability of fixation when both beneficial and deleterious mutations rates are increased.

The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus

Little is known about the mutational fitness effects associated with single-nucleotide substitutions on RNA viral genomes. Here, we used site-directed mutagenesis to create 91 single mutant clones of vesicular stomatitis virus derived from a common ancestral cDNA and performed competition experiments to measure the relative fitness of each mutant. The distribution of nonlethal deleterious effects was highly skewed and had a long, flat tail. As expected, fitness effects depended on whether mutations were chosen at random or reproduced previously described ones. The effect of random deleterious mutations was well described by a log-normal distribution, with -19% reduction of average fitness; the effects distribution of preobserved deleterious mutations was better explained by a beta model. The fit of both models was improved when combined with a uniform distribution. Up to 40% of random mutations were lethal. The proportion of beneficial mutations was unexpectedly high. Beneficial effects followed a gamma distribution, with expected fitness increases of 1% for random mutations and 5% for preobserved mutations.

The population genetics and evolutionary epidemiology of RNA viruses

RNA viruses are ubiquitous intracellular parasites that are responsible for many emerging diseases, including AIDS and SARS. Here, we discuss the principal mechanisms of RNA virus evolution and highlight areas where future research is required. The rapidity of sequence change in RNA viruses means that they are useful experimental models for the study of evolution in general and it enables us to watch them change in 'real time', and retrace the spread through populations with molecular phylogenies. An understanding of the mechanisms of RNA virus sequence change is also crucial to predicting important aspects of their emergence and long-term evolution.

Evolutionary potential of an RNA virus

RNA viruses are remarkably adaptable to changing environments. This is medically important because it enables pathogenic viruses to escape the immune response and chemotherapy and is of considerable theoretical interest since it allows the investigation of evolutionary processes within convenient time scales. A number of earlier studies have addressed the dynamics of adapting RNA virus populations. However, it has been difficult to monitor the trajectory of molecular changes in RNA genomes in response to selective pressures. To address the problem, we developed a novel in vitro evolution system based on a recombinant double-stranded RNA bacteriophage, phi 6, containing a beta-lactamase (bla) gene marker. Carrier-state bacterial cells are resistant to ampicillin, and after several passages, they become resistant to high concentrations of another beta-lactam antibiotic, cefotaxime, due to mutations in the virus-borne bla gene. We monitored the changes in bla cDNAs induced by cefotaxime selection and observed an initial explosion in sequence variants with multiple mutations throughout the gene. After four passages, a stable, homogeneous population of bla sequences containing three specific nonsynonymous mutations was established. Of these, two mutations (E104K and G238S) have been previously reported for beta-lactamases from cefotaxime-resistant bacterial isolates. These results extend our understanding of the molecular mechanisms of viral adaptation and also demonstrate the possibility of using an RNA virus as a vehicle for directed evolution of heterologous proteins.

Unifying the epidemiological and evolutionary dynamics of pathogens

A key priority for infectious disease research is to clarify how pathogen genetic variation, modulated by host immunity, transmission bottlenecks, and epidemic dynamics, determines the wide variety of pathogen phylogenies observed at scales that range from individual host to population. We call the melding of immunodynamics, epidemiology, and evolutionary biology required to achieve this synthesis pathogen "phylodynamics." We introduce a phylodynamic framework for the dissection of dynamic forces that determine the diversity of epidemiological and phylogenetic patterns observed in RNA viruses of vertebrates. A central pillar of this model is the Evolutionary Infectivity Profile, which captures the relationship between immune selection and pathogen transmission.

Contributions of vesicular stomatitis virus to the understanding of RNA virus evolution

Vesicular stomatitis virus has been a preferred system to study evolution for several decades. New approaches to antiviral treatment, such as lethal mutagenesis, stem from investigations done with VSV. Recent work has shed new light in the way we view neutrality, a fundamental concept to understand the evolutionary history of RNA viruses.

Quasispecies and the development of new antiviral strategies

RNA virus populations consist of complex and dynamic mutant distributions, rather than defined genomic sequences. This feature confers great adaptability on viruses and is partly responsible for current difficulties of viral disease prevention and control. Mutant distributions, also termed mutant swarms or mutant clouds, were first proposed in a theory of molecular evolution termed quasispecies theory. The theoretical formulation of quasispecies and its links to present day RNA viruses are discussed. The need to accommodate antiviral strategies to the dynamic nature of viral populations is emphasized. In particular, recent results on viral extinction associated with enhanced mutagenesis (virus entry into error catastrophe) are reviewed and presented as an example of how the understanding of viruses as quasispecies could lead to a potential practical application in medicine.

Phenotypic mixing and hiding may contribute to memory in viral quasispecies

BACKGROUND

In a number of recent experiments with food-and-mouth disease virus, a deleterious mutant, RED, was found to avoid extinction and remain in the population for long periods of time. Since RED characterizes the past evolutionary history of the population, this observation was called quasispecies memory. While the quasispecies theory predicts the existence of these memory genomes, there is a disagreement between the expected and observed mutant frequency values. Therefore, the origin of quasispecies memory is not fully understood.

RESULTS

We propose and analyze a simple model of complementation between the wild type virus and a mutant that has an impaired ability of cell entry, the likely cause of fitness differences between wild type and RED mutants. The mutant will go extinct unless it is recreated from the wild type through mutations. However, under phenotypic mixing-and-hiding as a mechanism of complementation, the time to extinction in the absence of mutations increases with increasing multiplicity of infection (m.o.i.). If the RED mutant is constantly recreated by mutations, then its frequency at equilibrium under selection-mutation balance also increases with increasing m.o.i. At high m.o.i., a large fraction of mutant genomes are encapsidated with wild-type protein, which enables them to infect cells as efficiently as the wild type virions, and thus increases their fitness to the wild-type level. Moreover, even at low m.o.i. the equilibrium frequency of the mutant is higher than predicted by the standard quasispecies model, because a fraction of mutant virions generated from wild-type parents will also be encapsidated by wild-type protein.

CONCLUSIONS

Our model predicts that phenotypic hiding will strongly influence the population dynamics of viruses, particularly at high m.o.i., and will also have important effects on the mutation-selection balance at low m.o.i. The delay in mutant extinction and increase in mutant frequencies at equilibrium may, at least in part, explain memory in quasispecies populations.

Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation

Microorganisms have been mutating and evolving on Earth for billions of years. Now, a field of research has developed around the idea of using microorganisms to study evolution in action. Controlled and replicated experiments are using viruses, bacteria and yeast to investigate how their genomes and phenotypic properties evolve over hundreds and even thousands of generations. Here, we examine the dynamics of evolutionary adaptation, the genetic bases of adaptation, tradeoffs and the environmental specificity of adaptation, the origin and evolutionary consequences of mutators, and the process of drift decay in very small populations.

Coinfection and superinfection in RNA virus populations: a selection-mutation model

In this paper, we present a general selection-mutation model of evolution on a one-dimensional continuous fitness space. The formulation of our model includes both the classical diffusion approach to mutation process as well as an alternative approach based on an integral operator with a mutation kernel. We show that both approaches produce fundamentally equivalent results. To illustrate the suitability of our model, we focus its analytical study into its application to recent experimental studies of in vitro viral evolution. More specifically, these experiments were designed to test previous theoretical predictions regarding the effects of multiple infection dynamics (i.e., coinfection and superinfection) on the virulence of evolving viral populations. The results of these experiments, however, did not match with previous theory. By contrast, the model we present here helps to understand the underlying viral dynamics on these experiments and makes new testable predictions about the role of parameters such the time between successive infections and the growth rates of resident and invading populations.

Evolution of RNA virus in spatially structured heterogeneous environments

A hallmark of the infectious cycle for many RNA viruses parasitizing multicellular hosts is the need to invade and successfully replicate in tissues that comprise a variety of cell types. Thus, multicellular hosts represent a heterogeneous environment to evolving viral populations. To understand viral adaptation to multicellular hosts, we took a double approach. First, we developed a mathematical model that served to make predictions concerning the dynamics of viral populations evolving in heterogeneous environments. Second, the predictions were tested by evolving vesicular stomatitis virus in vitro on a spatially structured environment formed by three different cell types. In the absence of gene flow, adaptation was tissue-specific, but fitness in all tissues decreased with migration rate. The performance in a given tissue was negatively correlated with its distance to the tissue hosting the population. This correlation decreased with migration rate.

Probability of fixation of an advantageous mutant in a viral quasispecies

The probability that an advantageous mutant rises to fixation in a viral quasispecies is investigated in the framework of multitype branching processes. Whether fixation is possible depends on the overall growth rate of the quasispecies that will form if invasion is successful rather than on the individual fitness of the invading mutant. The exact fixation probability can be calculated only if the fitnesses of all potential members of the invading quasispecies are known. Quasispecies fixation has two important characteristics: First, a sequence with negative selection coefficient has a positive fixation probability as long as it has the potential to grow into a quasispecies with an overall growth rate that exceeds that of the established quasispecies. Second, the fixation probabilities of sequences with identical fitnesses can nevertheless vary over many orders of magnitudes. Two approximations for the probability of fixation are introduced. Both approximations require only partial knowledge about the potential members of the invading quasispecies. The performance of these two approximations is compared to the exact fixation probability on a network of RNA sequences with identical secondary structure.

Sex releases the speed limit on evolution

Explaining the evolutionary maintenance of sex remains a key problem in evolutionary biology. One potential benefit of sex is that it may allow a more rapid adaptive response when environmental conditions change, by increasing the efficiency with which selection can fix beneficial mutations. Here I show that sex can increase the rate of adaptation in the facultatively sexual single-celled chlorophyte Chlamydomonas reinhardtii, but that the benefits of sex depend crucially on the size of the population that is adapting: sex has a marked effect in large populations but little effect in small populations. Several mechanisms have been proposed to explain the benefits of sex in a novel environment, including stochastic effects in small populations, clonal interference and epistasis between beneficial alleles. These results indicate that clonal interference is important in this system.

r- and K-selection in experimental populations of vesicular stomatitis virus

Here we explore the adaptation of vesicular stomatitis RNA virus to different population densities and the existence of a trade-off between r- and K-selection. Increasing population density represents a challenging special situation for viruses, since different selective pressures arise depending upon the number of available host cells per virus. Adaptation to low density represents a prototypical case of r-selection, where the optimal evolutionary solution should be a high replication rate. Adaptation to high density represents a case of K-selection. In this case, genotypes optimally exploiting the resources, instead of faster replicating ones, should be selected. Five independent populations were maintained in two environments, called r and K, for 100 generations. In the r environment, effective population size was small. In contrast, the effective population size in the K environment was large. Our results support the existence of the expected trade-offs between these two types of selections. Viral populations evolved at low density performed worse as population density increased. Similarly, viral populations evolved at high density showed reduced fitness at low density. Finally, we compare our results with those obtained for other RNA viruses.

Linkage limits the power of natural selection in Drosophila

Population genetic theory shows that the efficacy of natural selection is limited by linkage-selection at one site interferes with selection at linked sites. Such interference slows adaptation in asexual genomes and may explain the evolutionary advantage of sex. Here, we test for two signatures of constraint caused by linkage in a sexual genome, by using sequence data from 255 Drosophila melanogaster and Drosophila simulans loci. We find that (i) the rate of protein adaptation is reduced in regions of low recombination, and (ii) evolution at strongly selected amino acid sites interferes with optimal codon usage at weakly selected, tightly linked synonymous sites. Together these findings suggest that linkage limits the rate and degree of adaptation even in recombining genomes.

Molecular basis of adaptive convergence in experimental populations of RNA viruses

Characterizing the molecular basis of adaptation is one of the most important goals in modern evolutionary genetics. Here, we report a full-genome sequence analysis of 21 independent populations of vesicular stomatitis ribovirus evolved on the same cell type but under different demographic regimes. Each demographic regime differed in the effective viral population size. Evolutionary convergences are widespread both at synonymous and nonsynonymous replacements as well as in an intergenic region. We also found evidence for epistasis among sites of the same and different loci. We explain convergences as the consequence of four factors: (1) environmental homogeneity that supposes an identical challenge for each population, (2) structural constraints within the genome, (3) epistatic interactions among sites that create the observed pattern of covariation, and (4) the phenomenon of clonal interference among competing genotypes carrying different beneficial mutations. Using these convergences, we have been able to estimate the fitness contribution of the identified mutations and epistatic groups. Keeping in mind statistical uncertainties, these estimates suggest that along with several beneficial mutations of major effect, many other mutations got fixed as part of a group of epistatic mutations.

The Effect of Deleterious Alleles on Adaptation in Asexual Populations

We calculate the fixation probability of a beneficial allele that arises as the result of a unique mutation in an asexual population that is subject to recurrent deleterious mutation at rate U. Our analysis is an extension of previous works, which make a biologically restrictive assumption that selection against deleterious alleles is stronger than that on the beneficial allele of interest. We show that when selection against deleterious alleles is weak, beneficial alleles that confer a selective advantage that is small relative to U have greatly reduced probabilities of fixation. We discuss the consequences of this effect for the distribution of effects of alleles fixed during adaptation. We show that a selective sweep will increase the fixation probabilities of other beneficial mutations arising during some short interval afterward. We use the calculated fixation probabilities to estimate the expected rate of fitness improvement in an asexual population when beneficial alleles arise continually at some low rate proportional to U. We estimate the rate of mutation that is optimal in the sense that it maximizes this rate of fitness improvement. Again, this analysis relaxes the assumption made previously that selection against deleterious alleles is stronger than on beneficial alleles.

Understanding cancer as a formless phenomenon

Complex living organisms possess qualities that cannot be reduced to the simple addition of quantities. Among such qualities are a specific form and a specific organization. Thinking about morphological aspects is a prime example of the qualitative approach to biological matters. Such a morphogenetic perspective has been continuously developed, both theoretically and experimentally, along the past century, even though it is now rather marginal within a mainstream dominated by molecular biology. However, the morphogenetic outlook can be applied to the understanding of complex biological phenomena, such as cancer. This phenomenon is currently explained as a cellular problem caused by specific gene mutations and/or specific loss of gene regulation. Nevertheless, cancer is a problem that affects the whole organism. Contemporary research based on the genetic paradigm of cancer causation has led to paradoxes and anomalies that cannot be explained within such a reductionist paradigm. Here it is proposed that real, non-experimental, sporadic cancer may be understood as a conflict between an organized morphology (the organism) and a part of such a morphology that drifts towards an amorphous state (the tumour). Thus, rare, sporadic cancer in children can be the result of early disruption of the developmental constraints before the organism has achieved its morphological maturity. While common sporadic cancer in aged individuals may ensue as a result of the weakening or exhaustion of the developmental constraints that determine the morphological stability of the organism, once the organism is past its reproductive prime.

Fitness effects of fixed beneficial mutations in microbial populations

Beneficial mutations are intuitively relevant to understanding adaptation, yet not all beneficial mutations are of consequence to the long-term evolutionary outcome of adaptation. Many beneficial mutations-mostly those of small effect-are lost due either to (1) genetic drift or to (2) competition among clones carrying different beneficial mutations, a phenomenon called the "Hill-Robertson effect" for sexual populations and "clonal interference" for asexual populations. Competition among clones becomes more prevalent with increasing genetic linkage and increasing population size, and it is thus generally characteristic of microbial populations. Together, these two phenomena suggest that only those beneficial mutations of large fitness effect should achieve fixation, despite the fact that most beneficial mutations produced are predicted to have very small fitness effects. Here, we confirm this prediction-both empirically and theoretically-by showing that fitness effects of fixed beneficial mutations follow a distribution whose mode is positive.

Experimental tests of the adaptive significance of sexual recombination

Numerous theories have been proposed to explain the advantages of sexual recombination the exchange of hereditary material between different genomes or homologous chromosomes. Many of these candidate benefits have been evaluated in controlled laboratory experiments, which, collectively, strongly indicate that sexual recombination provides important long-term advantages.

In vitro analysis of human immunodeficiency virus type 1 resistance to nevirapine and fitness determination of resistant variants

Nevirapine-resistant variants were generated by serial passages in MT-2 cells in the presence of increasing drug concentrations. In passage 5, mutations V106A, Y181C and G190A were detected in the global population, associated with a 100-fold susceptibility decrease. Sequence analysis of biological clones obtained from passage 5 and subsequent passages showed that single mutants, detected in first passages, were progressively replaced in passage 15 by double mutants, correlating with a 500-fold increase in phenotypic resistance. Fitness determination of single mutants confirmed that, in the presence of nevirapine, every variant was more fit than wild-type with a fitness order Y181C>V106A>G190A>wild-type. Unexpectedly, in the absence of the drug, the Y181C resistant mutant was more fit than wild-type, with a fitness gradient Y181C>wild-type >G106A>or=V190A. Using a molecular clone in which the Y181C mutation was introduced by in vitro mutagenesis, the greater fitness of the Y181C mutant was confirmed in new competition cultures. These data exemplify the role of resistance mutations on virus phenotype but also on virus evolution leading, occasionally, to resistant variants fitter than the wild-type in the absence of the drug.

Evolutionary history conditions the timing of transmission in vesicular stomatitis virus

It has been postulated that early transmitted viruses would evolve to be more virulent than late transmitted ones. The reason for this prediction is that early transmission selects for rapid viral replication and, consequently, rapid host death, whereas late transmission would select for slow-replicating viruses that permit longer survival to the host. To test this prediction, experimental lineages of vesicular stomatitis virus (VSV) had been adapted to three different transmission dynamics during more than 100 generations. Transmission dynamic differed in the stage of infection at which transmission took place: early, intermediate or late. Regardless the timing of transmission imposed during the competition experiments done for estimating fitness, lineages adapted to an intermediate time of transmission reached higher fitness than viruses adapted to either early or late transmission. Viruses adapted to early and late transmission schedules showed a trade-off in their performance at other transmission times, with higher fitness at their own transmission time than at any other. The basis of fitness differences, in terms of growth parameters, have also been explored. Fitness correlated with the rate of growth and with the moment of maximum population density but not with the maximum density itself. In addition, a positive correlation between virus performance at late transmission and stability outside the cellular host has been detected.

The rhythm of microbial adaptation

The evolutionary biologist "studies the steps by which the miraculous adaptations so characteristic of every aspect of the organic world have evolved". But the general nature of such adaptive steps is still unclear. Evolution is often thought to be random and dependent on unpredictable events. In this light, one might expect the steps taken by adaptation to be completely random, both biologically and temporally. Here I present a mathematical derivation to show that, on the contrary, adaptive steps can have fairly strong rhythm. I find that the strength of the adaptive rhythm, that is its relative temporal regularity, is equal to a constant that is the same for all microbial populations. As a consequence, numbers of accumulated adaptations are predicted to have a universal variance/mean ratio. The theory derived here is potentially applicable to the study of molecular evolution.

Multiple infection dynamics has pronounced effects on the fitness of RNA viruses

Several factors play a role during the replication and transmission of RNA viruses. First, as a consequence of their enormous mutation rate, complex mixtures of genomes are generated immediately after infection of a new host. Secondly, differences in growth and competition rates drive the selection of certain genetic variants within an infected host. Thirdly, but not less important, a random sampling occurs at the moment of viral infectious passage from an infected to a healthy host. In addition, the availability of hosts also influences the fate of a given viral genotype. When new hosts are scarce, different viral genotypes might infect the same host, adding an extra complexity to the competition among genetic variants. We have employed a two-fold approach to analyse the role played by each of these factors in the evolution of RNA viruses. First, we have derived a model that takes into account all the preceding factors. This model employs the classic Lotka-Volterra competition equations but it also incorporates the effect of mutation during RNA replication, the effect of the stochastic sampling at the moment of infectious passage among hosts and, the effect of the type of infection (single, coinfection or superinfection). Secondly, the predictions of the model have been tested in an in vitro evolution experiment. Both theoretical and experimental results show that in infection passages with coinfection viral fitness increased more than in single infections. In contrast, infection passages with superinfection did not differ from the single infection. The coinfection frequency also affected the outcome: the larger the proportion of viruses coinfecting a host, the larger increase in fitness observed.

Transmission bottlenecks and the evolution of fitness in rapidly evolving RNA viruses

We explored the evolutionary importance of two factors in the adaptation of RNA viruses to their cellular hosts, size of viral inoculum used to initiate a new infection, and mode of transmission (horizontal versus vertical). Transmission bottlenecks should occur in natural populations of viruses and their profound effects on viral adaptation have been previously documented. However, the role of transmission mode has not received the same attention. Here we used a factorial experimental design to test the combined effects of inoculum (bottleneck) size and mode of transmission in evolution of vesicular stomatitis virus (VSV) in tissue culture, and compared our results to the predictions of a recent theoretical model. Our data were in accord with basic genetic principles concerning the balance between mutation, selection and genetic drift. In particular, attenuation of vertically transmitted viruses was a consequence of the random accumulation of deleterious mutations, whereas horizontally transmitted viruses experiencing similar bottlenecks did not suffer the same fitness losses because effective bottleneck size was actually determined by the number of host individuals. In addition, high levels of viral fitness in horizontally transmitted populations were explained by competition among viral variants.

Evidence for the Non-quasispecies Evolution of RNA Viruses

The quasispecies model of RNA virus evolution differs from those formulated in conventional population genetics in that neutral mutations do not lead to genetic drift of the population, and natural selection acts on the mutant distribution as a whole rather than on individual variants. By computer simulation, we show that this model could be inappropriate for many RNA viruses because the neutral sequence space may be too large to allow the formation of a quasispecies distribution. This view is supported by our analysis of gene sequences from vesicular stomatitis virus, which is considered a prototype RNA virus quasispecies. Our results are relevant to the evolution of RNA systems in general.

Both point mutation and RNA recombination contribute to the sequence diversity of citrus viroid III

Field-grown citrus trees often harbor complex mixtures of 4-5 different viroid species, and the presence of citrus viroid III (CVd-III) has been shown to reduce the rate of tree growth without inducing disease. To more fully define the structure of its quasi-species, we have examined nine citrus viroid complexes for the presence of previously undescribed sequence variants of CVd-III. Analysis of 86 full-length cDNAs generated from these nine viroid complexes by RT-PCR revealed the presence of 20 new CVd-III variants. Chain lengths ranged from 293-297 nucleotides, and sequence changes were confined largely to the lower portions of the central conserved region and variable domain. The previously described variants CVd-IIIa (297 nt) and CVd-IIIb (294 nt) were clearly predominant, but phylogenetic analysis indicated that certain isolates may contain representatives of two additional fitness peaks. At least one group of CVd-III variants appears to have arisen as a result of RNA recombination. Populations recovered from diseased/declining trees were the most diverse, but even dwarfing isolates originating from old line Shamouti trees showed considerable variability.

Fitness effects of advantageous mutations in evolving Escherichia coli populations

The central role of beneficial mutations for adaptive processes in natural populations is well established. Thus, there has been a long-standing interest to study the nature of beneficial mutations. Their low frequency, however, has made this class of mutations almost inaccessible for systematic studies. In the absence of experimental data, the distribution of the fitness effects of beneficial mutations was assumed to resemble that of deleterious mutations. For an experimental proof of this assumption, we used a novel marker system to trace adaptive events in an evolving Escherichia coli culture and to determine the selective advantage of those beneficial mutations. Ten parallel cultures were propagated for about 1,000 generations by serial transfer, and 66 adaptive events were identified. From this data set, we estimate the rate of beneficial mutations to be 4 x 10(-9) per cell and generation. Consistent with an exponential distribution of the fitness effects, we observed a large fraction of advantageous mutations with a small effect and only few with large effect. The mean selection coefficient of advantageous mutations in our experiment was 0.02.

Cost of host radiation in an RNA virus

Although host radiation allows a parasite to expand its ecological niche, traits governing the infection of multiple host types can decrease fitness in the original or alternate host environments. Reasons for this reduction in fitness include slower replication due to added genetic material or modifications, fitness trade-offs across host environments, and weaker selection resulting from simultaneous adaptation to multiple habitats. We examined the consequences of host radiation using vesicular stomatitis virus (VSV) and mammalian host cells in tissue culture. Replicate populations of VSV were allowed to evolve for 100 generations on the original host (BHK cells), on either of two novel hosts (HeLa and MDCK cells), or in environments where the availability of novel hosts fluctuated in a predictable or random way. As expected, each experimental population showed a substantial fitness gain in its own environment, but those evolved on new hosts (constant or fluctuating) suffered reduced competitiveness on the original host. However, whereas evolution on one novel host negatively correlated with performance on the unselected novel host, adaptation in fluctuating environments led to fitness improvements in both novel habitats.

Models of experimental evolution: the role of genetic chance and selective necessity

We present a theoretical framework within which to analyze the results of experimental evolution. Rapidly evolving organisms such as viruses, bacteria, and protozoa can be induced to adapt to laboratory conditions on very short human time scales. Artificial adaptive radiation is characterized by a list of common observations; we offer a framework in which many of these repeated questions and patterns can be characterized analytically. We allow for stochasticity by including rare mutations and bottleneck effects, demonstrating how these increase variability in the evolutionary trajectory. When the product Np, the population size times the per locus error rate, is small, the rate of evolution is limited by the chance occurrence of beneficial mutations; when Np is large and selective pressure is strong, the rate-limiting step is the waiting time while existing beneficial mutations sweep through the population. We derive the rate of divergence (substitution rate) and rate of fitness increase for the case when Np is large and illustrate our approach with an application to an experimental data set. A minimal assumption of independent additive fitness contributions provides a good fit to the experimental evolution of the bacteriophage phiX174.

Evolution of circulating wild poliovirus and of vaccine-derived poliovirus in an immunodeficient patient: a unifying model

We determined nucleotide sequences of the VP1 and 2AB genes and portions of the 2C and 3D genes of two evolving poliovirus lineages: circulating wild viruses of T geotype and Sabin vaccine-derived isolates from an immunodeficient patient. Different regions of the viral RNA were found to evolve nonsynchronously, and the rate of evolution of the 2AB region in the vaccine-derived population was not constant throughout its history. Synonymous replacements occurred not completely randomly, suggesting the need for conservation of certain rare codons (possibly to control translation elongation) and the existence of unidentified constraints in the viral RNA structure. Nevertheless the major contribution to the evolution of the two lineages came from linear accumulation of synonymous substitutions. Therefore, in agreement with current theories of viral evolution, we suggest that the majority of the mutations in both lineages were fixed as a result of successive sampling, from the heterogeneous populations, of random portions containing predominantly neutral and possibly adverse mutations. As a result of such a mode of evolution, the virus fitness may be maintained at a more or less constant level or may decrease unless more-fit variants are stochastically generated. The proposed unifying model of natural poliovirus evolution has important implications for the epidemiology of poliomyelitis.

Dengue viral infections; pathogenesis and epidemiology

Dengue viral infections affect up to 100 million individuals per year. Dengue haemorrhagic fever is a clinical form of disease characterised by intravascular fluid loss. There has been a marked increase in the incidence of this form of the disease over the last few decades, associated with significant mortality, particularly in the paediatric population. A number of theories relating to the pathogenesis of dengue haemorrhagic fever exist that have evolved from the analysis of the epidemiology of this disease. Virological and immunopathological factors are both important but the exact mechanisms for the disease are unknown.

The evolution of RNA viruses: A population genetics view

RNA viruses are excellent experimental models for studying evolution under the theoretical framework of population genetics. For a proper justification of this thesis we have introduced some properties of RNA viruses that are relevant for studying evolution. On the other hand, population genetics is a reductionistic theory of evolution. It does not consider or make simplistic assumptions on the transformation laws within and between genotypic and phenotypic spaces. However, such laws are minimized in the case of RNA viruses because the phenotypic space maps onto the genotypic space in a much more linear way than on higher DNA-based organisms. Under experimental conditions, we have tested the role of deleterious and beneficial mutations in the degree of adaptation of vesicular stomatitis virus (VSV), a nonsegmented virus of negative strand. We also have studied how effective population size, initial genetic variability in populations, and environmental heterogeneity shapes the impact of mutations in the evolution of vesicular stomatitis virus. Finally, in an integrative attempt, we discuss pros and cons of the quasispecies theory compared with classic population genetics models for haploid organisms to explain the evolution of RNA viruses.

The rate of adaptation in asexuals

I study the population genetics of adaptation in asexuals. I show that the rate of adaptive substitution in an asexual species or nonrecombining chromosome region is a bell-shaped function of the mutation rate: at some point, increasing the mutation rate decreases the rate of substitution. Curiously, the mutation rate that maximizes the rate of adaptation depends solely on the strength of selection against deleterious mutations. In particular, adaptation is fastest when the genomic rate of mutation, U, equals the harmonic mean of selection coefficients against deleterious mutations, where we assume that selection for favorable alleles is milder than that against deleterious ones. This simple result is independent of the shape of the distribution of effects among favorable and deleterious mutations, population size, and the action of clonal interference. In the course of this work, I derive an approximation to the probability of fixation of a favorable mutation in an asexual genome or nonrecombining chromosome region in which both favorable and deleterious mutations occur.

Big-benefit mutations in a bacteriophage inhibited with heat

High temperature inhibits the growth of the wild-type bacteriophage phiX174. Three different point mutations were identified that each recovered growth at high temperature. Two affected the major capsid protein (residues F188 and F242), and one affected the internal scaffolding protein (B114). One of the major capsid mutations (F242) is located in a beta strand that contacts B114 in the procapsid during viral maturation, whereas the other capsid mutation (F188) is involved in subunit interactions at the threefold axis of symmetry. Selective coefficients of these mutations ranged from 13.9 to 3.8 in the inhibitory, hot environment, but all mutations reduced fitness at normal temperature. The selective effect of one of the mutations (F242) was evaluated at high temperature in four different genetic backgrounds and exhibited epistasis of diminishing returns: as log fitness of the background genotype increased from -0.1 to 4.1, the fitness boost provided by the F242 mutation decreased from 3.9 to 0. 8. These results support a model in which viral fitness is bounded by an upper limit and the benefit of a mutation is scaled according to the remaining opportunity for fitness improvement in the genome.

Diminishing returns of population size in the rate of RNA virus adaptation

Whenever an asexual viral population evolves by adapting to new environmental conditions, beneficial mutations, the ultimate cause of adaptation, are randomly produced and then fixed in the population. The larger the population size and the higher the mutation rate, the more beneficial mutations can be produced per unit time. With the usually high mutation rate of RNA viruses and in a large enough population, several beneficial mutations could arise at the same time but in different genetic backgrounds, and if the virus is asexual, they will never be brought together through recombination. Thus, the best of these genotypes must outcompete each other on their way to fixation. This competition among beneficial mutations has the effect of slowing the overall rate of adaptation. This phenomenon is known as clonal interference. Clonal interference predicts a speed limit for adaptation as the population size increases. In the present report, by varying the size of evolving vesicular stomatitis virus populations, we found evidence clearly demonstrating this speed limit and thus indicating that clonal interference might be an important factor modulating the rate of adaptation to an in vitro cell system. Several evolutionary and epidemiological implications of the clonal interference model applied to RNA viruses are discussed.

Reproductive biotechnology and "big" biological questions

In recent decades, scientists have learned to manipulate that cardinal characteristic of life, reproduction, with powerful techniques like artificial insemination, contraception, embryo transfer, cryopreservation, and cloning by nuclear transfer. While these technologies often are used for practical applications and basic research, they have another profound intrinsic quality, which is to engender deep-seated thinking about important biological questions. Examples that stimulate such thinking include a goat's giving birth to her identical twin sister via splitting embryos, cryopreservation, and embryo transfer; that a parthenogenetic embryo can never become an animal but can become a genetic mother via an aggregation chimera; or that a somatic cell can become the sole genetic parent of a calf via cloning. In this paper, I illustrate this thought-stimulating quality by considering contributions of reproductive technologies to understanding, if not completely answering, several important biological questions.