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

Modelling the structure and evolution of cultural information as quasispecies

We present a novel mode of cultural evolution whereby some forms of transmission may be modelled as quasispecies. The model incorporates the effect of high rates of error in certain forms of communication; while also building on the structural similarities between biological molecules and written language. Firstly, both written language and key biological molecules, such as RNA and proteins, are modular. Within these molecules, structural domains may be recombined, while retaining their function. Likewise, sentences are structured as combinations of clauses, in which each clause contains a domain of information. The clausal structure permits the recombination of information to adopt different meanings, while allowing each unit to retain its identity. Secondly, by virtue of intrinsically-high error rates, we show that some, but not all, aspects of communicated culture information exists as rapidly evolving clouds within the population. These clouds of cultural information behave as quasispecies, which we model with varying mutation rates and suitable selection coefficients. We then integrate these ideas with the application of Shannon Diversity Index to produce a more holistic view of culture that is centred on the evolution of its information. Re-imagining culture, as evolving clouds of information, unifies the mode in which information is stored culturally and biologically, and opens up new avenues of comparative analysis.

The geologic history of primary productivity

The rate of primary productivity is a keystone variable in driving biogeochemical cycles today and has been throughout Earth's past.1 For example, it plays a critical role in determining nutrient stoichiometry in the oceans,2 the amount of global biomass,3 and the composition of Earth's atmosphere.4 Modern estimates suggest that terrestrial and marine realms contribute near-equal amounts to global gross primary productivity (GPP).5 However, this productivity balance has shifted significantly in both recent times6 and through deep time.7,8 Combining the marine and terrestrial components, modern GPP fixes ≈250 billion tonnes of carbon per year (Gt C year-1).5,9,10,11 A grand challenge in the study of the history of life on Earth has been to constrain the trajectory that connects present-day productivity to the origin of life. Here, we address this gap by piecing together estimates of primary productivity from the origin of life to the present day. We estimate that ∼1011-1012 Gt C has cumulatively been fixed through GPP (≈100 times greater than Earth's entire carbon stock). We further estimate that 1039-1040 cells have occupied the Earth to date, that more autotrophs than heterotrophs have ever existed, and that cyanobacteria likely account for a larger proportion than any other group in terms of the number of cells. We discuss implications for evolutionary trajectories and highlight the early Proterozoic, which encompasses the Great Oxidation Event (GOE), as the time where most uncertainty exists regarding the quantitative census presented here.

Innate immune pathways act synergistically to constrain RNA virus evolution in Drosophila melanogaster

Host-pathogen interactions impose recurrent selective pressures that lead to constant adaptation and counter-adaptation in both competing species. Here, we sought to study this evolutionary arms-race and assessed the impact of the innate immune system on viral population diversity and evolution, using Drosophila melanogaster as model host and its natural pathogen Drosophila C virus (DCV). We isogenized eight fly genotypes generating animals defective for RNAi, Imd and Toll innate immune pathways as well as pathogen sensing and gut renewal pathways. Wild-type or mutant flies were then orally infected with DCV, and the virus was serially passaged ten times via reinfection in naïve flies. Viral population diversity was studied after each viral passage by high-throughput sequencing, and infection phenotypes were assessed at the beginning and at the end of the evolution experiment. We found that the absence of any of the various immune pathways studied increased viral genetic diversity while attenuating virulence. Strikingly, these effects were observed in a range of host factors described as having mainly antiviral or antibacterial functions. Together, our results indicate that the innate immune system as a whole, and not specific antiviral defense pathways in isolation, generally constrains viral diversity and evolution.

Intra- and inter-host evolution of H9N2 influenza A virus in Japanese quail

Influenza A viruses (IAVs) are constantly evolving. Crucial steps in the infection cycle, such as sialic acid (SA) receptor binding on the host cell surface, can either promote or hamper the emergence of new variants. We previously assessed the relative fitness in Japanese quail of H9N2 variant viruses differing at a single amino acid position, residue 216 in the hemagglutinin (HA) viral surface protein. This site is known to modulate SA recognition. Our prior study generated a valuable set of longitudinal samples from quail transmission groups where the inoculum comprised different mixed populations of HA 216 variant viruses. Here, we leveraged these samples to examine the evolutionary dynamics of viral populations within and between inoculated and naïve contact quails. We found that positive selection dominated HA gene evolution, but fixation of the fittest variant depended on the competition mixture. Analysis of the whole genome revealed further evidence of positive selection acting both within and between hosts. Positive selection drove fixation of variants in non-HA segments within inoculated and contact quails. Importantly, transmission bottlenecks were modulated by the molecular signature at HA 216, revealing viral receptor usage as a determinant of transmitted diversity. Overall, we show that selection strongly shaped the evolutionary dynamics within and between quails. These findings support the notion that selective processes act effectively on IAV populations in poultry hosts, facilitating rapid viral evolution in this ecological niche.

Prior evolution in stochastic versus constant temperatures affects RNA virus evolvability at a thermal extreme

It is unclear how historical adaptation versus maladaptation in a prior environment affects population evolvability in a novel habitat. Prior work showed that vesicular stomatitis virus (VSV) populations evolved at constant 37°C improved in cellular infection at both 29°C and 37°C; in contrast, those evolved under random changing temperatures between 29°C and 37°C failed to improve. Here, we tested whether prior evolution affected the rate of adaptation at the thermal-niche edge: 40°C. After 40 virus generations in the new environment, we observed that populations historically evolved at random temperatures showed greater adaptability. Deep sequencing revealed that most of the newly evolved mutations were de novo. Also, two novel evolved mutations in the VSV glycoprotein and replicase genes tended to co-occur in the populations previously evolved at constant 37°C, whereas this parallelism was not seen in populations with prior random temperature evolution. These results suggest that prior adaptation under constant versus random temperatures constrained the mutation landscape that could improve fitness in the novel 40°C environment, perhaps owing to differing epistatic effects of new mutations entering genetic architectures that earlier diverged. We concluded that RNA viruses maladapted to their previous environment could "leapfrog" over counterparts of higher fitness, to achieve faster adaptability in a novel environment.

Experimental evolution for niche breadth in bacteriophage T4 highlights the importance of structural genes

Ecologists have long studied the evolution of niche breadth, including how variability in environments can drive the evolution of specialism and generalism. This concept is of particular interest in viruses, where niche breadth evolution may explain viral disease emergence, or underlie the potential for therapeutic measures like phage therapy. Despite the significance and potential applications of virus-host interactions, the genetic determinants of niche breadth evolution remain underexplored in many bacteriophages. In this study, we present the results of an evolution experiment with a model bacteriophage system, Escherichia virus T4, in several host environments: exposure to Escherichia coli C, exposure to E. coli K-12, and exposure to both E. coli C and E. coli K-12. This experimental framework allowed us to investigate the phenotypic and molecular manifestations of niche breadth evolution. First, we show that selection on different hosts led to measurable changes in phage productivity in all experimental populations. Second, whole-genome sequencing of experimental populations revealed signatures of selection. Finally, clear and consistent patterns emerged across the host environments, especially the presence of new mutations in phage structural genes-genes encoding proteins that provide morphological and biophysical integrity to a virus. A comparison of mutations found across functional gene categories revealed that structural genes acquired significantly more mutations than other categories. Our findings suggest that structural genes are central determinants in bacteriophage niche breadth.

Experimental Studies of Evolutionary Dynamics in Microbes

Evolutionary dynamics in laboratory microbial evolution experiments can be surprisingly complex. In the past two decades, observations of these dynamics have challenged simple models of adaptation and have shown that clonal interference, hitchhiking, ecological diversification, and contingency are widespread. In recent years, advances in high-throughput strain maintenance and phenotypic assays, the dramatically reduced cost of genome sequencing, and emerging methods for lineage barcoding have made it possible to observe evolutionary dynamics at unprecedented resolution. These new methods can now begin to provide detailed measurements of key aspects of fitness landscapes and of evolutionary outcomes across a range of systems. These measurements can highlight challenges to existing theoretical models and guide new theoretical work towards the complications that are most widely important.

Deep-sequencing of Marburg virus genome during sequential mouse passaging and cell-culture adaptation reveals extensive changes over time

Marburg virus (MARV) has caused outbreaks of filoviral hemorrhagic fever since its discovery in 1967. The largest and deadliest outbreak occurred in Angola in 2005, with 252 cases and 227 deaths. In 2014, we developed a mouse-adapted MARV, Angola variant through serial passaging in mice. The mouse-adapted MARV exhibits many of the hallmarks of MARV disease in humans. By applying deep-sequencing to every passage of the virus, we are able to study virus evolution in this host with surprising precision. We show that two regions go through substantial changes: the intergenic region between NP and VP35, as well as the first 100 amino acids of the VP40 protein. Our results also reveal that there were profound changes during the production of the final virus stock in cell culture. Overall, our results show that a handful of regions carry most of the mutations acquired during the adaptation of the virus to a new host and that many mutations become fixed very early during the adaptation process.

The Nonstationary Dynamics of Fitness Distributions: Asexual Model with Epistasis and Standing Variation

Various models describe asexual evolution by mutation, selection, and drift. Some focus directly on fitness, typically modeling drift but ignoring or simplifying both epistasis and the distribution of mutation effects (traveling wave models). Others follow the dynamics of quantitative traits determining fitness (Fisher's geometric model), imposing a complex but fixed form of mutation effects and epistasis, and often ignoring drift. In all cases, predictions are typically obtained in high or low mutation rate limits and for long-term stationary regimes, thus losing information on transient behaviors and the effect of initial conditions. Here, we connect fitness-based and trait-based models into a single framework, and seek explicit solutions even away from stationarity. The expected fitness distribution is followed over time via its cumulant generating function, using a deterministic approximation that neglects drift. In several cases, explicit trajectories for the full fitness distribution are obtained for arbitrary mutation rates and standing variance. For nonepistatic mutations, especially with beneficial mutations, this approximation fails over the long term but captures the early dynamics, thus complementing stationary stochastic predictions. The approximation also handles several diminishing returns epistasis models (e.g., with an optimal genotype); it can be applied at and away from equilibrium. General results arise at equilibrium, where fitness distributions display a "phase transition" with mutation rate. Beyond this phase transition, in Fisher's geometric model, the full trajectory of fitness and trait distributions takes a simple form; robust to the details of the mutant phenotype distribution. Analytical arguments are explored regarding why and when the deterministic approximation applies.

Experimental evolution of an RNA virus in cells with innate immunity defects

Experimental evolution studies have shown that RNA viruses respond rapidly to directional selection and thus can adapt efficiently to changes in host cell tropism, antiviral drugs, or other imposed selective pressures. However, the evolution of RNA viruses under relaxed selection has been less extensively explored. Here, we evolved vesicular stomatitis virus in mouse embryonic fibroblasts knocked-out for PKR, a protein with a central role in antiviral innate immunity. Vesicular stomatitis virus adapted to PKR-negative mouse embryonic fibroblasts in a gene-specific manner, since the evolved viruses exhibited little or no fitness improvement in PKR-positive cells. Full-length sequencing revealed the presence of multiple parallel nucleotide substitutions arising in independent evolution lines. However, site-directed mutagenesis showed that the effects of these substitutions were not PKR dependent. In contrast, we found evidence for sign epistasis, such that a given substitution which was positively selected was strongly deleterious when tested as a single mutation. Our results suggest that virus evolution in cells with specific innate immunity defects may drive viral specialization. However, this process is not deterministic at the molecular level, probably because the fixation of mutations which are tolerated under a relaxed selection regime is governed mainly by random genetic drift.

Temporal dynamics of intrahost molecular evolution for a plant RNA virus

Populations of plant RNA viruses are highly polymorphic in infected plants, which may allow rapid within-host evolution. To understand tobacco etch potyvirus (TEV) evolution, longitudinal samples from experimentally evolved populations in the natural host tobacco and from the alternative host pepper were phenotypically characterized and genetically analyzed. Temporal and compartmental variabilities of TEV populations were quantified using high throughput Illumina sequencing and population genetic approaches. Of the two viral phenotypic traits measured, virulence increased in the novel host but decreased in the original one, and viral load decreased in both hosts, though to a lesser extent in the novel one. Dynamics of population genetic diversity were also markedly different among hosts. Population heterozygosity increased in the ancestral host, with a dominance of synonymous mutations fixed, whereas it did not change or even decreased in the new host, with an excess of nonsynonymous mutations. All together, these observations suggest that directional selection is the dominant evolutionary force in TEV populations evolving in a novel host whereas either diversifying selection or random genetic drift may play a fundamental role in the natural host. To better understand these evolutionary dynamics, we developed a computer simulation model that incorporates the effects of mutation, selection, and drift. Upon parameterization with empirical data from previous studies, model predictions matched the observed patterns, thus reinforcing our idea that the empirical patterns of mutation accumulation represent adaptive evolution.

Genome rearrangement affects RNA virus adaptability on prostate cancer cells

Gene order is often highly conserved within taxonomic groups, such that organisms with rearranged genomes tend to be less fit than wild type gene orders, and suggesting natural selection favors genome architectures that maximize fitness. But it is unclear whether rearranged genomes hinder adaptability: capacity to evolutionarily improve in a new environment. Negative-sense non-segmented RNA viruses (order Mononegavirales) have specific genome architecture: 3' UTR - core protein genes - envelope protein genes - RNA-dependent RNA-polymerase gene - 5' UTR. To test how genome architecture affects RNA virus evolution, we examined vesicular stomatitis virus (VSV) variants with the nucleocapsid (N) gene moved sequentially downstream in the genome. Because RNA polymerase stuttering in VSV replication causes greater mRNA production in upstream genes, N gene translocation toward the 5' end leads to stepwise decreases in N transcription, viral replication and progeny production, and also impacts the activation of type 1 interferon mediated antiviral responses. We evolved VSV gene-order variants in two prostate cancer cell lines: LNCap cells deficient in innate immune response to viral infection, and PC-3 cells that mount an IFN stimulated anti-viral response to infection. We observed that gene order affects phenotypic adaptability (reproductive growth; viral suppression of immune function), especially on PC-3 cells that strongly select against virus infection. Overall, populations derived from the least-fit ancestor (most-altered N position architecture) adapted fastest, consistent with theory predicting populations with low initial fitness should improve faster in evolutionary time. Also, we observed correlated responses to selection, where viruses improved across both hosts, rather than suffer fitness trade-offs on unselected hosts. Whole genomics revealed multiple mutations in evolved variants, some of which were conserved across selective environments for a given gene order.

Experimental evolution of an oncolytic vesicular stomatitis virus with increased selectivity for p53-deficient cells

Experimental evolution has been used for various biotechnological applications including protein and microbial cell engineering, but less commonly in the field of oncolytic virotherapy. Here, we sought to adapt a rapidly evolving RNA virus to cells deficient for the tumor suppressor gene p53, a hallmark of cancer cells. To achieve this goal, we established four independent evolution lines of the vesicular stomatitis virus (VSV) in p53-knockout mouse embryonic fibroblasts (p53-/- MEFs) under conditions favoring the action of natural selection. We found that some evolved viruses showed increased fitness and cytotoxicity in p53-/- cells but not in isogenic p53+/+ cells, indicating gene-specific adaptation. However, full-length sequencing revealed no obvious or previously described genetic changes associated with oncolytic activity. Half-maximal effective dose (EC50) assays in mouse p53-positive colon cancer (CT26) and p53-deficient breast cancer (4T1) cells indicated that the evolved viruses were more effective against 4T1 cells than the parental virus or a reference oncolytic VSV (MΔ51), but showed no increased efficacy against CT26 cells. In vivo assays using 4T1 syngeneic tumor models showed that one of the evolved lines significantly delayed tumor growth compared to mice treated with the parental virus or untreated controls, and was able to induce transient tumor suppression. Our results show that RNA viruses can be specifically adapted typical cancer features such as p53 inactivation, and illustrate the usefulness of experimental evolution for oncolytic virotherapy.

Intrahost mechanisms governing emergence of resistance-breaking variants of Potato virus Y

The emergence of resistance breaking (RB) variants starting from the avirulent Potato virus Y NN strain (PVY(NN)) was analyzed after imposing different selective host constraints. Tobacco resistance to PVY(NN) is conferred by va in both NC745 and VAM genotypes, but VAM carries an extra resistance gene, va2. RB-variants emerged only in NC745 and unexpectedly accumulated higher in the original host, tobacco B21, than the parental PVY(NN). However, the recovery of RB-variants was interfered by PVY(NN) in mixed infections. Further analysis indicated that RB-variants also arose in tobacco VAM, but they were limited to subliminal local infections. Their inability to breakout was associated with absence of a mutational adaptation in the viral VPg gene, which implied a loss of fitness in tobacco B21. Altogether, the emergence of RB-variants was conditioned by inherited host constraints, interference by co-infecting avirulent virus genotypes, and fitness tradeoff of virus adaptations.

Stochastic temperatures impede RNA virus adaptation

Constant environments are often assumed to favor the evolution of specialization whereas exposure to changing environments may favor the evolution of generalists. Here we explored the phenotypic and molecular changes associated with evolving an RNA virus in constant versus fluctuating temperature environments. We used vesicular stomatitis virus (VSV) to determine whether selection at a constant temperature entails a performance trade-off at an unselected temperature, whether virus populations evolve to be generalists when selected in deterministically changing temperature environments, and whether selection under stochastically changing temperatures prevents evolved generalization, such as by constraining the ability for viruses to adaptively improve. We observed that all VSV lineages evolved at constant temperatures showed fitness gains in their selected temperature with little evidence for trade-offs in performance in the unselected environment. Evolution in deterministically and stochastically changing temperatures led to populations with the highest and lowest overall fitness gains, respectively. Sequence analysis revealed little evidence for convergent molecular evolution among lineages within the same treatment. Across all temperature treatments, the majority of genome substitutions occurred in the G (glycoprotein) gene, suggesting that this locus for the cell-binding protein plays a key role in dictating VSV performance under changing temperature.

Mechanisms of GII.4 norovirus evolution

Since the late 1990s norovirus (NoV) strains belonging to a single genotype (GII.4) have caused at least four global epidemics. To date, the higher epidemiological fitness of the GII.4 strains has been attributed to a faster rate of evolution within the virus capsid, resulting in the ability to escape herd immunity. Four key factors have been proposed to influence the rate of evolution in NoV. These include host receptor recognition, sequence space, duration of herd immunity, and replication kinetics. In this review we discuss recent advancements in our understanding of these four mechanisms in relation to GII.4 evolution.

Beneficial mutations and the dynamics of adaptation in asexual populations

We discuss the dynamics of adaptive evolution in asexual (clonal) populations. The classical 'periodic selection' model of clonal evolution assumed that beneficial mutations are very rare and therefore substitute unfettered into populations as occasional, isolated events. Newer models allow for the possibility that beneficial mutations are sufficiently common to coexist and compete for fixation within populations. Experimental evolution studies in microbes provide empirical support for stochastic models in which both selection and mutation are strong effects and clones compete for fixation; however, the relative importance of competition among clones bearing mutations of different selective effects versus competition among clones bearing multiple mutations remains unresolved. We provide some new theoretical results, moreover, suggesting that population dynamics consistent with the periodic selection model can arise even in a deterministic model that can accommodate a very high beneficial mutation rate.

Adaptation of experimental yeast populations to stressful conditions in relation to population size

The purpose of this experiment was to find out how a population becomes adapted to extremely stressful conditions as its environment deteriorates. We created a deteriorating environment for experimental selection lines of yeast by a stepwise increase in the concentration of salt in the growth medium. After each step, we tested the ability of the lines to grow at a high concentration of salt near the lethal limit for the ancestral strain. We found that mutations enhancing growth in this highly stressful environment began to spread at intermediate salt concentrations. The degree of enhancement was related to effective population size by a power law with a small exponent. The effect size of these mutations also increased with the population size in a similar fashion. From these results, we interpret adaptation to lethal stress as an indirect response to selection for resistance to previous lower levels of stress in a deteriorating environment. This suggests that the pattern of genetic correlation between successively higher levels of stress is an important factor in facilitating evolutionary rescue.

Small effective population sizes and rare nonsynonymous variants in potyviruses

Analysis of nucleotide sequence polymorphism in complete genomes of 12 species of potyviruses (single-stranded, positive-sense RNA viruses, family Potyviridae) revealed evidence that long-term effective population sizes of these viruses are on the order of 10(4). Comparison of nucleotide diversity in non-coding regions and at synonymous and nonsynonymous sites in coding regions showed that purifying selection has acted to eliminate numerous deleterious mutations both at nonsynonymous sites and in non-coding regions. The ratio of nonsynonymous to synonymous polymorphic sites increased as a function of the number of genomes sampled, whereas mean gene diversity at nonsynonymous polymorphic sites decreased with increasing sample size at a substantially faster rate than does mean gene diversity at synonymous polymorphic sites. Very similar relationships were observed both in available genomic sequences of 12 potyvirus species and in subsets created by randomly sampling from among 98 TuMV genomes. Taken together, these observations imply that a greater proportion of nonsynonymous than of synonymous variants are relatively rare as the result of ongoing purifying selection, and thus many nonsynonymous variants are unlikely to be discovered without extensive sampling.

A linear relationship between fitness and the logarithm of the critical bottleneck size in vesicular stomatitis virus populations

We explored the relationship between fitness change and population size during transmission in vesicular stomatitis populations of very high fitness. The results show a linear correlation between the logarithm of the critical bottleneck size (population size at which there are no significant fitness changes after 20 passages) and the initial fitness of the population. In addition, limits to fitness increases during large-population passages of very-high-fitness strains were abolished by increasing the population size during transmission, indicating that beneficial variation is still available in these populations.

Enhanced adaptation of vesicular stomatitis virus in cells infected with vaccinia virus

Infections involving different viruses (multiple infections) are common in nature and can take place between different strains of the same virus or between different virus species, including DNA and RNA viruses. The influence of multiple infections on viral evolution has been previously studied using different populations of the same virus. Here, we took a step forward by studying the evolution of an RNA virus (vesicular stomatitis virus, VSV) in the presence of a resident DNA virus (vaccinia virus, VV). Cell cultures were infected with a constant amount of VV, and VSV was added at four different post-VV-inoculation times and four different population sizes. The results showed that the presence of VV accelerates the adaptation of VSV to a cellular environment, especially at high population sizes. The effect of VV on VSV evolution was stronger when cells were incubated for longer times with VV prior to the addition of VSV. Our results suggest that cooperation between the two viruses rather than competition might be responsible for the enhanced rate of adaptation of VSV. Further studies are needed to discern whether infections involving different viruses could have an increased ability to escape antiviral strategies.

Experimental evolution and genome sequencing reveal variation in levels of clonal interference in large populations of bacteriophage phiX174

Background

In large asexual populations where beneficial mutations may co-occur and recombination is absent, the fate of beneficial mutations can be significantly affected by competition (i.e., clonal interference). Theoretical models predict that clonal interference (CI) can slow adaptation, alter the distribution of fixed beneficial mutations, and affect disease progression by impacting within-host evolution of pathogens. While phenotypic data support that CI is a significant determinant of adaptive outcome, genetic data are needed to verify the patterns and to inform evolutionary models. We adapted replicate populations of the bacteriophage φX174 under two levels of CaCl₂ to create benign and harsh environments. Genomic sequences of multiple individuals from evolved populations were used to detect competing beneficial mutations.

Results

There were several competing genotypes in most of the populations where CaCl₂ was abundant, but no evidence of CI where CaCl₂ was scarce, even though rates of adaptation and population sizes among the treatments were similar. The sequence data revealed that observed mutations were limited to a single portion of one gene in the harsh treatment, but spanned a different and larger region of the genome under the benign treatments, suggesting that there were more adaptive solutions to the benign treatment.

Conclusion

Beneficial mutations with relatively large selection coefficients can be excluded by CI. CI may commonly determine the fate of beneficial mutations in large microbial populations, but its occurrence depends on selective conditions. CI was more frequent in benign selective conditions possibly due to a greater number of adaptive targets under this treatment. Additionally, the genomic sequence data showed that selection can target different types and numbers of phenotypes in environments that differ by only a single continuous variable.

Heterogeneous adaptive trajectories of small populations on complex fitness landscapes

Background

Small populations are thought to be adaptively handicapped, not only because they suffer more from deleterious mutations but also because they have limited access to new beneficial mutations, particularly those conferring large benefits.

Methodology/Principal Findings

Here, we test this widely held conjecture using both simulations and experiments with small and large bacterial populations evolving in either a simple or a complex nutrient environment. Consistent with expectations, we find that small populations are adaptively constrained in the simple environment; however, in the complex environment small populations not only follow more heterogeneous adaptive trajectories, but can also attain higher fitness than the large populations. Large populations are constrained to near deterministic fixation of rare large-benefit mutations. While such determinism speeds adaptation on the smooth adaptive landscape represented by the simple environment, it can limit the ability of large populations from effectively exploring the underlying topography of rugged adaptive landscapes characterized by complex environments.

Conclusions

Our results show that adaptive constraints often faced by small populations can be circumvented during evolution on rugged adaptive landscapes.

Beneficial mutation selection balance and the effect of linkage on positive selection

When beneficial mutations are rare, they accumulate by a series of selective sweeps. But when they are common, many beneficial mutations will occur before any can fix, so there will be many different mutant lineages in the population concurrently. In an asexual population, these different mutant lineages interfere and not all can fix simultaneously. In addition, further beneficial mutations can accumulate in mutant lineages while these are still a minority of the population. In this article, we analyze the dynamics of such multiple mutations and the interplay between multiple mutations and interference between clones. These result in substantial variation in fitness accumulating within a single asexual population. The amount of variation is determined by a balance between selection, which destroys variation, and beneficial mutations, which create more. The behavior depends in a subtle way on the population parameters: the population size, the beneficial mutation rate, and the distribution of the fitness increments of the potential beneficial mutations. The mutation-selection balance leads to a continually evolving population with a steady-state fitness variation. This variation increases logarithmically with both population size and mutation rate and sets the rate at which the population accumulates beneficial mutations, which thus also grows only logarithmically with population size and mutation rate. These results imply that mutator phenotypes are less effective in larger asexual populations. They also have consequences for the advantages (or disadvantages) of sex via the Fisher-Muller effect; these are discussed briefly.

Selection for robustness in mutagenized RNA viruses

Mutational robustness is defined as the constancy of a phenotype in the face of deleterious mutations. Whether robustness can be directly favored by natural selection remains controversial. Theory and in silico experiments predict that, at high mutation rates, slow-replicating genotypes can potentially outcompete faster counterparts if they benefit from a higher robustness. Here, we experimentally validate this hypothesis, dubbed the "survival of the flattest," using two populations of the vesicular stomatitis RNA virus. Characterization of fitness distributions and genetic variability indicated that one population showed a higher replication rate, whereas the other was more robust to mutation. The faster replicator outgrew its robust counterpart in standard competition assays, but the outcome was reversed in the presence of chemical mutagens. These results show that selection can directly favor mutational robustness and reveal a novel viral resistance mechanism against treatment by lethal mutagenesis.

The speed of evolution and maintenance of variation in asexual populations

BACKGROUND

The rate at which beneficial mutations accumulate determines how fast asexual populations evolve, but this is only partially understood. Some recent clonal-interference models suggest that evolution in large asexual populations is limited because smaller beneficial mutations are outcompeted by larger beneficial mutations that occur in different lineages within the same population. This analysis assumes that the important mutations fix one at a time; it ignores multiple beneficial mutations that occur in the lineage of an earlier beneficial mutation, before the first mutation in the series can fix. We focus on the effects of such multiple mutations.

RESULTS

Our analysis predicts that the variation in fitness maintained by a continuously evolving population increases as the logarithm of the population size and logarithm of the mutation rate and thus yields a similar logarithmic increase in the speed of evolution. To test these predictions, we evolved asexual budding yeast in glucose-limited media at a range of population sizes and mutation rates.

CONCLUSIONS

We find that their evolution is dominated by the accumulation of multiple mutations of moderate effect. Our results agree with our theoretical predictions and are inconsistent with the one-by-one fixation of mutants assumed by recent clonal-interference analysis.

Adaptation of HIV-1 depends on the host-cell environment

Many viruses have the ability to rapidly develop resistance against antiviral drugs and escape from the host immune system. To which extent the host environment affects this adaptive potential of viruses is largely unknown. Here we show that for HIV-1, the host-cell environment is key to the adaptive potential of the virus. We performed a large-scale selection experiment with two HIV-1 strains in two different T-cell lines (MT4 and C8166). Over 110 days of culture, both virus strains adapted rapidly to the MT4 T-cell line. In contrast, when cultured on the C8166 T-cell line, the same strains did not show any increase in fitness. By sequence analyses and infections with viruses expressing either yellow or cyan fluorescent protein, we were able to show that the absence of adaptation was linked to a lower recombination rate in the C8166 T-cell line. Our findings suggest that if we can manipulate the host-cellular factors that mediate viral evolution, we may be able to significantly retard viral adaptability.

The effect of co- and superinfection on the adaptive dynamics of vesicular stomatitis virus

In many infectious diseases, hosts are often simultaneously infected with several genotypes of the same pathogen. Much theoretical work has been done on modelling multiple infection dynamics, but empirical evidences are relatively scarce. Previous studies have demonstrated that coinfection allows faster adaptation than single infection in RNA viruses. Here, we use experimental populations of the vesicular stomatitis Indiana virus derived from an infectious cDNA, to show that superinfection dynamics promotes faster adaptation than single infection. In addition, we have analysed two different periodicities of multiple infection, daily and separated 5 days in time. Daily multiple infections allow higher fitness increases than multiple infections taking place every 5 days. We propose that the effect of superinfection on fitness is mainly influenced by the time elapsed between the first and the second infection, since shorter time intervals offer more opportunities to competition between resident and invading populations.

Virus fitness: concept, quantification, and application to HIV population dynamics

Viral fitness has been broadly studied during the past three decades, mainly to test evolutionary models and population theories difficult to analyze and interpret with more complex organisms. More recent studies, however, are focused in the role of fitness on viral transmission, pathogenesis, and drug resistance. Here, we used human immunodeficiency virus (HIV) as one of the most relevant models to evaluate the importance of viral quasispecies and fitness in HIV evolution, population dynamics, disease progression, and potential clinical implications.

Analytic approach to the evolutionary effects of genetic exchange

We present an approximate analytic study of our previously introduced model of evolution including the effects of genetic exchange. This model is motivated by the process of bacterial transformation. We solve for the velocity, the rate of increase of fitness, as a function of the fixed population size, N. We find the velocity increases with ln N, eventually saturating at an N which depends on the strength of the recombination process. The analytical treatment is seen to agree well with direct numerical simulations of our model equations.

The cost of replication fidelity in an RNA virus

It is often argued that high mutation rates are advantageous for RNA viruses, because they confer elevated rates of adaptation. However, there is no direct evidence showing a positive correlation between mutation and adaptation rates among RNA viruses. Moreover, theoretical work does not argue in favor of this prediction. We used a series of vesicular stomatitis virus clones harboring single amino acid substitutions in the RNA polymerase to demonstrate that changes inducing enhanced fidelity paid a fitness cost, but that there was no positive correlation between mutation an adaptation rates. We demonstrate that the observed mutation rate in vesicular stomatitis virus can be explained by a trade-off between replication rate and replication fidelity.

Epistasis and the adaptability of an RNA virus

We have explored the patterns of fitness recovery in the vesicular stomatitis RNA virus. We show that, in our experimental setting, reversions to the wild-type genotype were rare and fitness recovery was at least partially driven by compensatory mutations. We compared compensatory adaptation for genotypes carrying (1) mutations with varying deleterious fitness effects, (2) one or two deleterious mutations, and (3) pairs of mutations showing differences in the strength and sign of epistasis. In all cases, we found that the rate of fitness recovery and the proportion of reversions were positively affected by population size. Additionally, we observed that mutations with large fitness effect were always compensated faster than mutations with small fitness effect. Similarly, compensatory evolution was faster for genotypes carrying a single deleterious mutation than for those carrying pairs of mutations. Finally, for genotypes carrying two deleterious mutations, we found evidence of a negative correlation between the epistastic effect and the rate of compensatory evolution.

An Analysis of Host Adaptation and Its Relationship with Virulence in Cucumber mosaic virus

ABSTRACT The host range of a pathogen can have special consequences on its evolution and the evolution of its virulence. For generalists, adaptation to different hosts may be conditioned by different trade-offs in the pathogen's life history and be affected by evolutionary processes that shape pathogen populations. We have examined adaptation of Cucumber mosaic virus (CMV) to different hosts, and analyzed the relationship between host adaptation and virulence. For this, six CMV isolates from central Spain from three different hosts were compared for the ability to multiply and to affect host growth. These analyses were done before and after an experimental evolution process consisting of 10 serial passages in the original host of the isolate. The differential capacity to infect different hosts was compatible with host adaptation. However, the capacity to multiply in different hosts did not provide evidence of host adaptation and was not improved after 10 passages, suggesting that fitness of the natural population of CMV was at, or near to, its maximum. No relationship was found between capacity of multiplication and virulence in any of the three different hosts. These results suggest that the "trade-off" model for the evolution of virulence may not apply to CMV.

Recombination dramatically speeds up evolution of finite populations

We study the role of recombination, in the form of bacterial transformation, in speeding up Darwinian evolution. This is done by adding a new process to a previously studied Markov model of evolution on a smooth fitness landscape; this new process allows alleles to be exchanged with those in the surrounding medium. Our results, both numerical and analytic, indicate that, for a wide range of intermediate population sizes, recombination dramatically speeds up the rate of evolutionary advance.

The speed of adaptation in large asexual populations

In large asexual populations, beneficial mutations have to compete with each other for fixation. Here, I derive explicit analytic expressions for the rate of substitution and the mean beneficial effect of fixed mutations, under the assumptions that the population size N is large, that the mean effect of new beneficial mutations is smaller than the mean effect of new deleterious mutations, and that new beneficial mutations are exponentially distributed. As N increases, the rate of substitution approaches a constant, which is equal to the mean effect of new beneficial mutations. The mean effect of fixed mutations continues to grow logarithmically with N. The speed of adaptation, measured as the change of log fitness over time, also grows logarithmically with N for moderately large N, and it grows double-logarithmically for extremely large N. Moreover, I derive a simple formula that determines whether at given N beneficial mutations are expected to compete with each other or go to fixation independently. Finally, I verify all results with numerical simulations.

RNA viruses as complex adaptive systems

RNA viruses have high mutation rates and so their populations exist as dynamic and complex mutant distributions. It has been consistently observed that when challenged with a new environment, viral populations adapt following hyperbolic-like kinetics: adaptation is initially very rapid, but then slows down as fitness reaches an asymptotic value. These adaptive dynamics have been explained in terms of populations moving towards the top of peaks on rugged fitness landscapes. Fitness fluctuations of varying magnitude are observed during adaptation. Often the presence of fluctuations in the evolution of physical systems indicates some form of self-organization, or where many components of the system are simultaneously involved. Here we analyze data from several in vitro evolution experiments carried out with vesicular stomatitis virus (VSV) looking for the signature of criticality and scaling. Long-range fitness correlations have been detected during the adaptive process. We also found that the magnitude of fitness fluctuations, far from being trivial, conform to a Weibull probability distribution function, suggesting that viral adaptation belongs to a broad category of phenomena previously documented in other fields and related with emergence.

The effects of mosquito transmission and population bottlenecking on virulence, multiplication rate and rosetting in rodent malaria

Malaria parasites vary in virulence, but the effects of mosquito transmission on virulence phenotypes have not been systematically analysed. Using six lines of malaria parasite that varied widely in virulence, three of which had been serially blood-stage passaged many times, we found that mosquito transmission led to a general reduction in malaria virulence. Despite that, the between-line variation in virulence remained. Forcing serially passaged lines through extreme population bottlenecks (<5 parasites) reduced virulence in only one of two lines. That reduction was to a level intermediate between that of the virulent parental and avirulent ancestral line. Mosquito transmission did not reverse the increased parasite replication rates that had accrued during serial passage, but it did increase rosetting frequencies. Re-setting of asexual stage genes during the sexual stages of the life cycle, coupled with stochastic sampling of parasites with variable virulence during population bottlenecks, could account for the virulence reductions and increased rosetting induced by mosquito transmission.

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.

Can mutation and selection explain virulence in human P. falciparum infections?

BACKGROUND

Parasites incur periodic mutations which must ultimately be eliminated to maintain their genetic integrity.

METHODS

It is hypothesised that these mutations are eliminated not by the conventional mechanisms of competition between parasites in different hosts but primarily by competition between parasites within the same infection.

RESULTS

This process is enhanced by the production of a large number of parasites within individual infections, and this may significantly contribute to parasitic virulence.

CONCLUSIONS

Several features of the most virulent human malaria parasite Plasmodium falciparum can usefully be re-interpreted in this light and lend support to this interpretation. More generally, it constitutes a novel explanation for the evolution of virulence in a wider range of microparasites.

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.

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.