BACKGROUND
viruses are powerful and relevant models for understanding fundamental molecular biology, genetics and evolution  <cit> , and elucidating infectious-disease evolution  <cit> .
the typically short generation times, large population sizes, and high mutation rates of rna viruses make such studies highly efficient from an evolutionary standpoint  <cit> .
furthermore, the small genome sizes and disease importance of rna viruses make them particularly attractive for research in evolutionary genomics of virus-host interactions, such as molecular evolution of virus speciation events  <cit> , and divergence in viral genetic architectures due to host specialization versus generalization  <cit> .
previous experimental evolution studies with viral models generally used either individual populations or homogeneous spatially structured experimental design.
more complex demographics such as a phylogenetic tree structure have been studied but generally under a small set of selective conditions  <cit> .
here we examine how rna viruses evolve with demographic structure imposed by a phylogenetic tree, under selective conditions of novel host environments and parametrically varying population sizes.
viruses are exceedingly diverse in their evolved strategies to manipulate hosts for viral replication  <cit> .
despite this diversity, variable environments and fluctuating population sizes are two challenges often faced by virus populations.
first, viruses can be passively transmitted between hosts  and cannot evaluate host ‘habitat quality’ prior to infection  <cit> , creating the possibility that virus particles bind to less permissive target cells .
therefore, virus populations may unexpectedly encounter new environments, including intrahost changes brought on by immune function  <cit> .
second, virus population size naturally tends to fluctuate, sometimes by several orders of magnitude  <cit> ; e.g., virus population size will necessarily vary due to changing availability of susceptible host individuals, occurrence of transmission bottlenecks when initiating a new infection, and immunity-related fluctuations in within-host viral load.
these variable population sizes can lead to differing relative strengths of natural selection versus genetic drift acting in virus evolution  <cit> .
experimental overview
we examined the experimental evolution of rna bacteriophage  ϕ <dig> by tracking molecular and phenotypic changes in virus lineages experimentally evolved under environmental variation and fluctuating population sizes.
figure  <dig> shows our experimental design: a bifurcating deme structure that reflects lineage splitting that gives rise to demes with separated gene pools.
thus, we created a ‘known phylogeny’, allowing tests of the accuracy of phylogenetic algorithms  <cit> .
phage ϕ <dig> is typically grown in the laboratory on the plant pathogenic bacterium pseudomonas syringae pathovar phaseolicola, but prior work  <cit>  shows that the virus can adaptively improve on this host.
however, selection pressures differ and greater adaptive change occurs when phage ϕ <dig> is cultured on the novel host p. pseudoalcaligenes  <cit> , which is distantly related to p. phaseolicola  <cit> .
here we extended this work by contrasting phage ϕ <dig> evolution on the original and novel hosts and considering effects of host switching on virus evolution.
previous studies examined the effects of population size on mutational load and subsequent fitness recovery in phage ϕ <dig>  <cit> .
here we examined how constant versus variable population sizes impacted host-use adaptation in the virus.
overall, by combining whole-genome sequencing and measurements of host-use traits, we generated a very large dataset that fostered subsequent tests of inferred genotype-phenotype associations.
the known-phylogeny experiment, with additional independent confirmation using experimental evolution, demonstrated that host-use adaptation in phage ϕ <dig> involved an allelic switch in the viral assembly protein, a locus previously unknown to function in host-specific growth of the virus.
more generally, our combined genomic/phenotypic approach was used to show where molecular substitutions tended to cluster in the genomes of phage ϕ <dig> populations subjected to the host-use challenges.
last, we showed that several popular methods were unable to accurately resolve the true experimental phylogeny, due to a paucity of molecular substitutions separating the sequenced clones.
RESULTS
molecular evolution
phage ϕ <dig> has a ~ <dig> kb segmented tri-partite dsrna genome  <cit> .
the three genomic segments are denoted large , medium , and small .
the genome is organized such that polymerase functions are located on segment l, genes for host attachment proteins are on segment m, and genes for the nucleocapsid shell , the major membrane protein , the lytic enzyme , and the membrane assembly nonstructural protein  are on segment s  <cit> .
segment reassortment can occur when multiple ϕ <dig> viruses co-infect the same host cell and generate reassortant  progeny, which contain a mixture of the segments found in the co-infecting parents  <cit> .
however, recombination  is lacking or occurs at an extremely low rate in phage ϕ <dig>  <cit> , allowing its possible effects to be ignored in our study.
we challenged phage ϕ <dig> lineages to evolve on their typical host p. phaseolicola , and on the distantly-related novel host p. pseudoalcaligenes era , which poses a relatively greater opportunity for adaptive improvement  <cit> .
thus, we expected that the treatment populations evolving on pp and era hosts under large population sizes would experience positive selection  to fix adaptive mutations.
in addition, our experiment subjected some virus lineages to extreme population bottlenecking which should cause drift to overwhelm selection, allowing random fixation of non-lethal mutations of moderate effect  <cit> .
phage evolution occurred strictly through the ~ <dig> generations per day as plaques grew on bacterial lawns  <cit>  ; no phage infections occurred in liquid culture.
we used whole-genome sequencing to identify molecular changes that occurred in the experiment.
figures  <dig> and  <dig> summarize the observed mutations, and the time points and treatment regimes where they were identified; the indicated mutations are those separating a clone from the sequenced predecessor clone.
we founded the experiment with a wild type ϕ <dig> ancestor ; after  <dig> phage generations on pp we observed that this starting lineage contained no fixed mutations separating it from strain a <dig>  because this lineage was designed to give rise to a bifurcation where one of the two derived lineages would be propagated on host era , we chose a spontaneous host-range mutant able to grow on both pp and era, from the initial 50-gen. lineage.
this mutant, denoted clone b <dig>  contained a non-synonymous mutation  in gene p <dig> of the m segment, the locus for the host attachment protein  <cit> .
we note that this p <dig> mutation differs from the nine known non-synonymous substitutions in gene p <dig> which allow phage ϕ <dig> to infect the era host  <cit> .
by the end of the study, each of the  <dig> clones at the tips of the tree differed from the ancestor  by  <dig> to  <dig> substitutions , excluding reversions .
overall, we observed a total of  <dig> substitutions  at  <dig> sites across the  <dig> genomic segments, equivalent to ~ <dig> % of the sequenced genome .
reversion mutations
we observed that identical reversion mutations sometimes occurred in lineages evolved independently.
one case involved evolution under host switching, whereas the other did not.
the host-switching case was a substitution on segment s in gene p <dig> , which encodes an assembly protein used in viral membrane morphogenesis  <cit> .
this non-synonymous substitution was a thymine to cytosine transition , observed in clone c <dig> isolated following the first experimental bifurcation, in the ‘host shift’ lineage that had evolved for  <dig> generations on novel host era .
the p <dig> substitution persisted in descendent lineages propagated at constant large population sizes on era, and in lineages bottlenecked at constant small population sizes regardless of host .
however, in all cases where descendent lineages were grown at constant large or initially large population sizes on pp, the p <dig> mutation underwent a reversion: l176f .
the combined influences of host type and population size  on forward/back mutation suggested that these alleles governed host-specific growth performance.
below we describe additional evolution experiments that further examined this finding .
the reversion unrelated to host-switching was also a mutation on the s segment:  <dig> a → g in gene p <dig>  which codes for a membrane protein essential for virion membrane formation  <cit> .
the mutation occurred in a lineage experiencing selection at constant large population sizes on pp, which gave rise to one of the third set of experimental bifurcations .
the substitution then reverted in the two immediately descendent lineages, which were either bottlenecked at constant small population sizes on alternating hosts, or further evolved at constant large population sizes on pp.
one possibility is that the mutation in gene p <dig> is antagonistic for growth on host era, explaining why it was selected against in the alternating pp/era bottlenecking; although the bottlenecking method caused drift to overwhelm selection, some positive selection necessarily occurred during plaque formation .
the reversion that occurred under continued pp-selection at large population size suggests that the mutation may also be antagonistic with additional mutations fostering growth on the normal host.
in particular, the reversion was observed alongside two synonymous mutations on segments m and s ; although these were synonymous mutations they could potentially affect membrane formation properties of protein p <dig> and/or protein-protein interactions with other viral proteins that affect performance on the pp host.
this suggestion is highly speculative, however, and further experiments are warranted to confirm the idea.
accounting for low rates of molecular change
the spontaneous mutation rate in phage ϕ <dig> is estimated to be 2 × 10- <dig> mutations/base/round of replication  <cit> ; this rate provides the genetic variation potentially useful for adaptation, but it is relatively low compared to the typical error-prone replication rates associated with rna viruses  <cit> .
one possible explanation is that the inferred ‘stamping machine’ model of rna segment replication in phage ϕ <dig> should lead to fewer mutations generated per infected cell, compared to a geometric mode of replication occurring in other rna viruses  <cit> .
regardless of the mechanistic explanation, one key result from our study was that molecular evolutionary changes were rather modest after  <dig> viral generations ; clones isolated at the tree tips sometimes contained only  <dig> substitutions separating them from the wildtype ancestor.
although phage ϕ <dig> experiments on the order of  <dig> to  <dig> generations can produce profound phenotypic changes under strong directional selection  <cit> , previous work and the current study suggest that few underlying genetic substitutions may fix during such timeframes  <cit>  perhaps owing to strong clonal interference among mutations of similar magnitude in their beneficial effects.
severe bottlenecking increases mutational load in phage ϕ <dig> populations through effects of drift  <cit> .
however, we estimate that  <dig> days of consecutive bottlenecking should be required to fix roughly one mutation, on average.
the logic is the following.
the estimated genomic mutation rate in phage ϕ <dig> is gauged to be  <dig>  deleterious mutations per generation  <cit> , causing one mutation on average to fix in a lineage after  <dig> bottlenecks , where the majority of spontaneous mutations are assumed to be deleterious.
thus, the 20-day bottlenecking treatments may have caused fitness declines, but they were unexpected to cause large numbers of mutations to accumulate.
in addition, to impose the conditions which fostered drift over selection, we used the reliable method of randomly choosing a single plaque  to propagate the evolving virus lineage  <cit> .
however, this method allows for considerable within-plaque selection; despite the tight bottleneck, the ~ <dig> generations of virus growth needed to produce a visible plaque allow for positive selection occurring during this process  <cit> .
for these reasons, our bottlenecking method was unlikely to cause large numbers of fixed molecular substitutions.
in the future, similar studies employing phage ϕ <dig> could use a mutagen to achieve higher mutation rates, and relatively greater occurrence of substitutions per unit time.
however, we caution that while the mutation rates of certain viruses can be manipulated by mutagens, the resulting artificial mutant spectrum compromises inferences drawn from a ‘known phylogeny’ experiment.
for instance, mutagenic deaminating agents cause substitution biases  that cannot be accurately modeled with reversible substitution models  <cit> .
two solutions for avoiding insufficient change in known-phylogeny experiments with viruses are to allow evolution to proceed for a relatively long time, and to evolve the phylogeny under conditions of continuous-growth  where very many generations can occur in a single day.
fitness evolution: growth on p. phaseolicola
for the ancestor and sequenced clones, we measured a phenotypic trait that was often a direct target of selection in our study: fitness  on the pp host.
we observed that all viruses retained the ability to infect the original pp host even when evolved solely on era; in contrast, duffy et al.
<cit>  showed that strict era selection can sometimes lead to fixation of a non-synonymous mutation in p <dig>  that prevents phage ϕ <dig> entry into pp host cells.
thus, for all  <dig> sequenced viruses we conducted fitness assays on pp against a genetically-marked common competitor that contained a host-range mutation on segment m, and an inserted x-gal mutation on segment l .
assays were performed with six-fold replication, yielding  <dig> total measures .
these measures were log-transformed to improve normality.
because pp is the typical lab host for phage ϕ <dig>  the a priori prediction was that viruses evolved at large population sizes on this host should show equal or higher fitness relative to the ancestor .
table  <dig> shows mean lnw for each virus on pp.
the mean lnw of the ancestral clone a <dig> was determined to be significantly greater than  <dig>  , indicating that the ancestor was more fit on pp than the common competitor.
we then conducted independent t-tests to gauge whether the mean lnw of a test virus differed from that of the ancestor; because these tests involved  <dig> comparisons versus the ancestor dataset we conservatively gauged significance using a bonferroni correction of α =  <dig>  .
we observed that fitness on pp statistically differed from the ancestor in a majority of these comparisons , and most of these outcomes showed fitness significantly lower than the ancestor .
consistent with our prediction, close inspection of these data and the experimental design revealed that all clones which had recently experienced constant selection on pp at large population size  did not suffer a decrease in fitness on pp .
in contrast,  <dig> of  <dig> clones which had recently undergone constant selection on era at large size  suffered a decline in fitness on pp.
these data suggested that selection for fitness improvement on era tended to trade off with performance on pp see also  <cit> .
1values are means  of six log fitness estimates; ↑ and ↓ indicate significantly higher and lower fitness relative to ancestor or to immediate predecessor clone; open cells indicate no statistical difference; --- indicates test could not be performed.
2tested relative to bonferroni corrected probability of  <dig> .
3tested relative to bonferroni corrected probability of  <dig> .
4tested relative to bonferroni corrected probability of  <dig> .
fitness declines on pp were also observed for clones which were bottlenecked on either pp, era or alternating pp/era, and whose immediate predecessor clone showed significantly lower fitness on pp ; these data were consistent with predicted effects of bottlenecking that cause drift to overwhelm positive selection  <cit> , preventing the lineages from regaining fitness.
for a detailed summary of the inferred effects of population size on observed evolution of clone fitness on pp, see the additional file  <dig>
fitness evolution: growth on p. pseudoalcaligenes era
we also determined how the fitness of viruses on era changed in our study.
clone b <dig> was a direct descendent of the ancestor, and contained a spontaneous host-range mutation  in gene p <dig> on the m segment, allowing infection of novel host era .
we sought to examine fitness on era for the  <dig> clones derived from clone b <dig>  but assays on era were not possible for a subset of these viruses because they were never directly exposed to era and therefore had experienced a reverse mutation  preventing infection of era .
thus, fitness assays against the common competitor on era were conducted for only  <dig> clones, yielding a total of  <dig> measures , which were log-transformed to improve normality.
our a priori prediction was that evolution on era at large population size should lead to strong performance on this host.
table  <dig> shows mean lnw for the  <dig> viruses assayed on era.
the mean lnw of clone b <dig> was determined to be significantly lower than  <dig>  , indicating that clone b <dig> was less fit on era than the common competitor.
independent t-tests gauged whether mean lnw of a test virus differed from that of clone b1; because these tests involved  <dig> comparisons versus b <dig> we employed a bonferroni correction of α =  <dig>  .
we observed that fitness on era was significantly greater than that of clone b <dig> in every comparison.
this outcome was consistent with the predicted improvement on era for clones recently experiencing evolution on era at large population size .
interestingly, clones e <dig> thru e <dig> were direct descendents of strong performers on era and maintained high fitness on this host despite bottlenecking.
the e <dig> clone, by chance did not experience any mutations from its d <dig> ancestor.
for e <dig> and e <dig>  the result suggested that era performance was less affected by drift occurring during the 20-day bottlenecks, compared with typical debilitating effects of 20-day bottlenecking on pp fitness  <cit> ; related to the above suggestion, one possibility is that within-plaque growth/selection more easily counters the effects of drift when phage ϕ <dig> is bottlenecked on era, compared to identical propagation on pp.
the phenomenon may also explain why clone e <dig> showed high fitness on era despite being subjected to bottlenecks on this host.
for additional discussion of era performance shown by individual clones, see the additional file  <dig>  figure 5b summarizes the fitness values observed on era, in relation to our experimental design.
it is obvious that the clade containing lineages mostly selected on era tended to show high fitness values on era.
fitness evolution relative to immediate predecessors
to examine fitness changes on selected and unselected hosts over evolutionary time, we compared the phenotype of a virus clone to that of its immediate predecessor clone: the virus used to initiate a bifurcation that gave rise to the descendant clone.
this effort yielded up to  <dig> statistical comparisons for each of the three measured traits, where we employed a bonferroni correction of α =  <dig>  for determining significant differences in t-tests where two clones were tested relative to their common progenitor.
we observed that mean lnw of a virus clone on the typical host pp did not always statistically differ from that of its predecessor virus .
fitness on pp tended to be equal for clones isolated from lineages successively evolved on pp at constant large size ; a linear regression showed that this trajectory of lnw through time had positive slope but did not differ from zero .
however, fitness on era showed a significantly positive increase through time  for clones from lineages successively evolved on era .
we found some evidence that the viruses constantly evolved on era suffered a tradeoff in performance on pp; the regression of differential performance across hosts  versus time was a decreasing function, but did not differ statistically from zero .
a similar analysis was not possible for differential performance of pp-evolved viruses across hosts, because most of these clones could not infect era .
additional discussion of individual clone performance on pp and/or era relative to the immediate predecessor is contained in the additional file  <dig>
limitations to inferring genotype-phenotype associations
we note one important caveat in interpreting the phenotypic consequences of the molecular substitutions stems from our acquisition of clones from each population to conduct whole-genome sequencing.
at the end of each treatment period, as detailed in the methods, a single clone was chosen and this clone was then subjected to sequencing.
for example, we began a selective regime with a clone whose sequence was known, the clone was expanded into a population and that population underwent a particular selective regime for a period of time.
subsequently, an individual clone was selected at random from the population, sequenced and measured phenotypically.
we then inferred from the changes separating the starting clone and the endpoint clone how the virus population responded to selection.
through this method, there was a chance that the clone we chose was not representative of the parent population.
thus, the molecular changes we observed were not necessarily reflective of measurable performance changes in the parent population; see also  <cit>  for related discussion.
however, given the overall low number of observed changes in the experimental evolution, we are confident that a discrepancy between clone-level changes and majority alleles in the parent population should occur with low probability, in turn suggesting that the above-described associations should be generally robust interpretations.
evolution under host switching
the importance of the p <dig> protein in host switching events in phage ϕ <dig> has been previously established  <cit> .
this study confirmed this observation, but additionally brought to light the importance of the p <dig> protein in host switching events.
this non-structural protein controls the liberation of mature ϕ <dig> particles from the host cytoplasmic membrane, but is not incorporated into the virion  <cit> .
like many eukaryotic viruses, cystoviridae have envelopes comprised of both viral proteins and host lipids.
different hosts may have different lipid constituents which are contributed to the viral envelope and thus may require slightly altered p <dig> proteins for efficient envelope assembly.
we have already shown that phage ϕ <dig> maturation in era affects fitness when the virion infects pp, and vice versa <cit> .
we assume this epigenetic effect is mediated by the lipids taken from these very different hosts, and we speculate that our current results may relate to the importance of host lipid incorporation for multiple host-use in phage ϕ <dig>
as described above, we observed that non-synonymous mutation f176l in gene p <dig> on the s segment was associated with a host switch to the novel host era.
this mutation seemed to revert when a virus lineage was subsequently allowed to evolve on the typical host pp, as long as population size was constantly large or decreased from large size to small size .
we hypothesized that the f176l mutation was beneficial for era infection, but that the l176f reversion was beneficial for growth on pp.
to confirm the hypothesized functional significance of the allelic switch for growth on pp and era, we conducted follow-up experimental evolution to test whether population size and host type affected allele fixation in test populations.
the design for this experiment is shown in additional file  <dig>  we isolated a single plaque-purified copy of clone c <dig> that had evolved on era at large population sizes; sequencing confirmed that this clone contained the f176l mutation presumably beneficial for era infection.
this clone was used to found four additional virus lineages that were evolved on pp for  <dig> days  at population bottlenecks of either  <dig>   <dig>   <dig>  or  <dig> pfu .
after the evolution experiment, we used targeted consensus sequencing of each test population to examine changes in the p <dig> gene.
we observed that the l176f reversion was the dominant allele  in the experimental populations evolved at population sizes of  <dig> and  <dig> pfu.
in contrast, the allelic reversion did not fix  in the test populations evolved at bottleneck sizes of  <dig> and  <dig> pfu.
we then conducted a repeat of this evolution experiment in a separate block , and observed qualitatively identical results.
these data strongly supported the idea that the non-synonymous p <dig> mutation was beneficial for growth on era and deleterious for performance on pp, whereas the reversion produced the opposite function.
we concluded that population sizes of  <dig> and larger were sufficient for selection to efficiently drive the reversion to high frequencies within  <dig> generations, when viruses were cultured on the original pp host see also  <cit> .
why does fixation or dominance of reversion mutation happen at some population sizes and not others?
current literature emphasizes that waiting time for selective sweeps does not necessarily explain what happens in clonal microbial populations.
rather, there is more likely genetic variation present at any one time and selection draws upon this variation to produce change; there is thus an importance of clonal interference among variants of similar magnitude.
in our lineages where population size started large and became small, we observed that the reversion fixed .
likely such lineages of initially large size already had the needed revertant present within their existing variation, and it was able to spread through time even though population size diminished.
in contrast, the lineages where population size started small and increased had to wait for the revertant to appear, because the initially small size made it unlikely that the needed genotype was initially present.
the result was that the revertant never fixed because enough time did not elapse at large size for that revertant to exist within the standing genetic variation.
but when population size was sufficiently large enough for a lineage subsequently evolved on pp, the beneficial revertant was able to spontaneously arise and fix in the population.
because era and pp are distantly related  <cit> , one possible explanation is that the substitution in the p <dig> assembly protein enables more effective incorporation of era membrane lipids into the virus envelope at the expense of effectively incorporating pp membrane lipids.
phylogenetic reconstruction
the bifurcating-deme structure we imposed in our experiment afforded the possibility to test whether phylogenetic methods could successfully reconstruct the tree topology using genetic data alone.
all methods returned the same phylogeny with similar assessment of uncertainty by bootstrap or posterior probability .
the lineage containing descendants of c <dig> , were reconstructed with no false positive clades and one false negative clade .
the reconstructions for the descendants of c <dig>  were more mixed with several false negatives and one false positive.
the false negatives involved failure to identify the clades descended from d <dig> while the false positive involved placing the f <dig> line together with f9-f <dig>  creating an erroneous clade of {f <dig>  f <dig>  f <dig>  f <dig>  f13}.
the false negatives, that is, the failure to resolve certain branches, is due to the small number of polymorphic sites within our dataset.
purifying and directional selection over linked loci seems to have greatly reduced the phylogenetically informative sites in our study.
some of the problems with the reconstruction can be traced to particular mutational history.
as noted, the clade {f <dig>  f <dig>  f <dig>  f16} is unresolved in the estimated tree.
the clade descendant from d <dig> is delineated by q8q  mutation in the p <dig> gene on segment s. however, in both e <dig> and e <dig>  direct descendants of d <dig>  there was a reversal synonymous q8q  mutation that erased the evolutionary history .
a parallel mutation of a143a  in m-p <dig> gene in both the e <dig> and f <dig> lineages seems to be the main signature that caused f <dig> to erroneously fall into the clade that contains f <dig>  f <dig>  f <dig>  and f <dig>  finally, we used maximum likelihood ancestral state estimation in paup to reconstruct the ancestral sequences.
all ancestral states were correctly reconstructed with the exception of two sites.
the first site was the q8q site, which as described, reverted back to the ancestral state in two descendent lineages, in effect completely hiding the mutation in the terminal lineages.
no algorithm is expected to reconstruct such exact reversions.
the second site is the highly variable f176l mutation in p <dig> gene of segment s discussed above, which showed parallel changes in four terminal lineages.
the terminal mutations were all c to t changes in the terminal lineages, which are reversions to state t of the common ancestor to all lineages, following an early t to c change in the “era” clade.
therefore, the true ancestral state was c but was incorrectly estimated to the t state, reflecting the shared t state in the “pp” clade as well as the t’s in the other terminal lineage of the “era” clade.
the high degree of parallel terminal mutations is highly unlikely by standard probabilistic models, as well as by the parsimony criterion and the ancestral states of such singular events are not expected to be estimated correctly.
in sum, complex evolutionary history, especially with selective pressures that can cause parallel or reversal of specific loci, can cause difficulties with phylogenetic reconstruction even when the whole sequenced genome is available.
regarding use of our dataset to investigate how environmental complexities  impact the ability for phylogenetic methods to accurately infer historical relationships, we observed that none of the investigated methods could accurately reconstruct the true phylogeny.
this result is similar to the observations of bull et al.
<cit>  in a previous known phylogeny study.
in the prior experiment, the failure was due to the effects of convergence of the phylogenetic topography.
however, in the current study we showed that the failure could occur due to a paucity of observed molecular changes.
for example, two of the sixteen endpoint lineages presented exactly the same genetic sequence, rendering it impossible to distinguish them, regardless of the method employed.
thus, we could not effectively assess how variable selection impacted the usefulness of various methods of phylogenetic reconstruction.
overall, the results of our dataset were not useful for evaluating the relative effectiveness of the various methods due to the paucity of changes in some lineages.
however, when examining how well the methods performed on the clade produced from the initial switch to era, we observed that the methods were more accurate in inferring the actual phylogeny; in particular, ml again proved to be the most effective method for accurately regenerating the actual clade.
CONCLUSIONS
phylogenetic methods can often fail to resolve deep relationships with saturated molecular data; here we showed a similar difficulty in using the methods to resolve the simple bifurcating design implemented in this ~ <dig> generation known phylogeny experiment.
using the natural mutation rate of this rna virus and environments similar to the selective pressures and population size changes experienced by many viruses in nature, we were able to demonstrate several aspects of viral evolution that can confound the usefulness of phylogenetic algorithms: few informative sites, and parallel and reversion mutations.
because these complications will often occur when tracking the evolution of emerging viruses, our work implies that phylogenetic trees encompassing molecular epidemiology over short timescales may tend to be inaccurate.
specific to the study system, we identified that the protein-coding gene p <dig> on the s segment of phage ϕ <dig> is important for host-use selection in the virus.
our study demonstrated that experimental evolution involving a large number of increasingly diverged lineages is a useful tool for testing evolutionary theory , as well as for discovering novel traits  in evolving populations that more narrowly-focused studies would omit.

 viruses are powerful and relevant models for understanding fundamental molecular biology, genetics and evolution, and elucidating infectious-disease evolution. the typically short generation times, large population sizes, and high mutation rates of rna viruses make such studies highly efficient from an evolutionary standpoint. furthermore, the small genome sizes and disease importance of rna viruses make them particularly attractive for research in evolutionary genomics of virus-host interactions, such as molecular evolution of virus speciation events, and divergence in viral genetic architectures due to host specialization versus generalization. previous experimental evolution studies with viral models generally used either individual populations or homogeneous spatially structured experimental design. more complex demographics such as a phylogenetic tree structure have been studied but generally under a small set of selective conditions. here we examine how rna viruses evolve with demographic structure imposed by a phylogenetic tree, under selective conditions of novel host environments and parametrically varying population sizes. viruses are exceedingly diverse in their evolved strategies to manipulate hosts for viral replication. despite this diversity, variable environments and fluctuating population sizes are two challenges often faced by virus populations. first, viruses can be passively transmitted between hosts and cannot evaluate host ‘habitat quality’ prior to infection, creating the possibility that virus particles bind to less permissive target cells. therefore, virus populations may unexpectedly encounter new environments, including intrahost changes brought on by immune function. second, virus population size naturally tends to fluctuate, sometimes by several orders of magnitude; e.g., virus population size will necessarily vary due to changing availability of susceptible host individuals, occurrence of transmission bottlenecks when initiating a new infection, and immunity-related fluctuations in within-host viral load. these variable population sizes can lead to differing relative strengths of natural selection versus genetic drift acting in virus evolution. experimental overview we examined the experimental evolution of rna bacteriophage ϕ by tracking molecular and phenotypic changes in virus lineages experimentally evolved under environmental variation and fluctuating population sizes. figure shows our experimental design: a bifurcating deme structure that reflects lineage splitting that gives rise to demes with separated gene pools. thus, we created a ‘known phylogeny’, allowing tests of the accuracy of phylogenetic algorithms. phage ϕ is typically grown in the laboratory on the plant pathogenic bacterium pseudomonas syringae pathovar phaseolicola, but prior work shows that the virus can adaptively improve on this host. however, selection pressures differ and greater adaptive change occurs when phage ϕ is cultured on the novel host p. pseudoalcaligenes, which is distantly related to p. phaseolicola. here we extended this work by contrasting phage ϕ evolution on the original and novel hosts and considering effects of host switching on virus evolution. previous studies examined the effects of population size on mutational load and subsequent fitness recovery in phage ϕ. here we examined how constant versus variable population sizes impacted host-use adaptation in the virus. overall, by combining whole-genome sequencing and measurements of host-use traits, we generated a very large dataset that fostered subsequent tests of inferred genotype-phenotype associations. the known-phylogeny experiment, with additional independent confirmation using experimental evolution, demonstrated that host-use adaptation in phage ϕ involved an allelic switch in the viral assembly protein, a locus previously unknown to function in host-specific growth of the virus. more generally, our combined genomic/phenotypic approach was used to show where molecular substitutions tended to cluster in the genomes of phage ϕ populations subjected to the host-use challenges. last, we showed that several popular methods were unable to accurately resolve the true experimental phylogeny, due to a paucity of molecular substitutions separating the sequenced clones.  molecular evolution phage ϕ has a ~ kb segmented tri-partite dsrna genome. the three genomic segments are denoted large, medium, and small. the genome is organized such that polymerase functions are located on segment l, genes for host attachment proteins are on segment m, and genes for the nucleocapsid shell, the major membrane protein, the lytic enzyme, and the membrane assembly nonstructural protein are on segment s. segment reassortment can occur when multiple ϕ viruses co-infect the same host cell and generate reassortant progeny, which contain a mixture of the segments found in the co-infecting parents. however, recombination is lacking or occurs at an extremely low rate in phage ϕ, allowing its possible effects to be ignored in our study. we challenged phage ϕ lineages to evolve on their typical host p. phaseolicola, and on the distantly-related novel host p. pseudoalcaligenes era, which poses a relatively greater opportunity for adaptive improvement. thus, we expected that the treatment populations evolving on pp and era hosts under large population sizes would experience positive selection to fix adaptive mutations. in addition, our experiment subjected some virus lineages to extreme population bottlenecking which should cause drift to overwhelm selection, allowing random fixation of non-lethal mutations of moderate effect. phage evolution occurred strictly through the ~ generations per day as plaques grew on bacterial lawns; no phage infections occurred in liquid culture. we used whole-genome sequencing to identify molecular changes that occurred in the experiment. figures  and summarize the observed mutations, and the time points and treatment regimes where they were identified; the indicated mutations are those separating a clone from the sequenced predecessor clone. we founded the experiment with a wild type ϕ ancestor; after phage generations on pp we observed that this starting lineage contained no fixed mutations separating it from strain a because this lineage was designed to give rise to a bifurcation where one of the two derived lineages would be propagated on host era, we chose a spontaneous host-range mutant able to grow on both pp and era, from the initial 50-gen. lineage. this mutant, denoted clone b contained a non-synonymous mutation in gene p of the m segment, the locus for the host attachment protein. we note that this p mutation differs from the nine known non-synonymous substitutions in gene p which allow phage ϕ to infect the era host. by the end of the study, each of the clones at the tips of the tree differed from the ancestor by to substitutions, excluding reversions. overall, we observed a total of substitutions at sites across the genomic segments, equivalent to ~ % of the sequenced genome. reversion mutations we observed that identical reversion mutations sometimes occurred in lineages evolved independently. one case involved evolution under host switching, whereas the other did not. the host-switching case was a substitution on segment s in gene p, which encodes an assembly protein used in viral membrane morphogenesis. this non-synonymous substitution was a thymine to cytosine transition, observed in clone c isolated following the first experimental bifurcation, in the ‘host shift’ lineage that had evolved for generations on novel host era. the p substitution persisted in descendent lineages propagated at constant large population sizes on era, and in lineages bottlenecked at constant small population sizes regardless of host. however, in all cases where descendent lineages were grown at constant large or initially large population sizes on pp, the p mutation underwent a reversion: l176f. the combined influences of host type and population size on forward/back mutation suggested that these alleles governed host-specific growth performance. below we describe additional evolution experiments that further examined this finding. the reversion unrelated to host-switching was also a mutation on the s segment: a → g in gene p which codes for a membrane protein essential for virion membrane formation. the mutation occurred in a lineage experiencing selection at constant large population sizes on pp, which gave rise to one of the third set of experimental bifurcations. the substitution then reverted in the two immediately descendent lineages, which were either bottlenecked at constant small population sizes on alternating hosts, or further evolved at constant large population sizes on pp. one possibility is that the mutation in gene p is antagonistic for growth on host era, explaining why it was selected against in the alternating pp/era bottlenecking; although the bottlenecking method caused drift to overwhelm selection, some positive selection necessarily occurred during plaque formation. the reversion that occurred under continued pp-selection at large population size suggests that the mutation may also be antagonistic with additional mutations fostering growth on the normal host. in particular, the reversion was observed alongside two synonymous mutations on segments m and s; although these were synonymous mutations they could potentially affect membrane formation properties of protein p and/or protein-protein interactions with other viral proteins that affect performance on the pp host. this suggestion is highly speculative, however, and further experiments are warranted to confirm the idea. accounting for low rates of molecular change the spontaneous mutation rate in phage ϕ is estimated to be 2 × 10- mutations/base/round of replication; this rate provides the genetic variation potentially useful for adaptation, but it is relatively low compared to the typical error-prone replication rates associated with rna viruses. one possible explanation is that the inferred ‘stamping machine’ model of rna segment replication in phage ϕ should lead to fewer mutations generated per infected cell, compared to a geometric mode of replication occurring in other rna viruses. regardless of the mechanistic explanation, one key result from our study was that molecular evolutionary changes were rather modest after viral generations; clones isolated at the tree tips sometimes contained only substitutions separating them from the wildtype ancestor. although phage ϕ experiments on the order of to generations can produce profound phenotypic changes under strong directional selection, previous work and the current study suggest that few underlying genetic substitutions may fix during such timeframes perhaps owing to strong clonal interference among mutations of similar magnitude in their beneficial effects. severe bottlenecking increases mutational load in phage ϕ populations through effects of drift. however, we estimate that days of consecutive bottlenecking should be required to fix roughly one mutation, on average. the logic is the following. the estimated genomic mutation rate in phage ϕ is gauged to be deleterious mutations per generation, causing one mutation on average to fix in a lineage after bottlenecks, where the majority of spontaneous mutations are assumed to be deleterious. thus, the 20-day bottlenecking treatments may have caused fitness declines, but they were unexpected to cause large numbers of mutations to accumulate. in addition, to impose the conditions which fostered drift over selection, we used the reliable method of randomly choosing a single plaque to propagate the evolving virus lineage. however, this method allows for considerable within-plaque selection; despite the tight bottleneck, the ~ generations of virus growth needed to produce a visible plaque allow for positive selection occurring during this process. for these reasons, our bottlenecking method was unlikely to cause large numbers of fixed molecular substitutions. in the future, similar studies employing phage ϕ could use a mutagen to achieve higher mutation rates, and relatively greater occurrence of substitutions per unit time. however, we caution that while the mutation rates of certain viruses can be manipulated by mutagens, the resulting artificial mutant spectrum compromises inferences drawn from a ‘known phylogeny’ experiment. for instance, mutagenic deaminating agents cause substitution biases that cannot be accurately modeled with reversible substitution models. two solutions for avoiding insufficient change in known-phylogeny experiments with viruses are to allow evolution to proceed for a relatively long time, and to evolve the phylogeny under conditions of continuous-growth where very many generations can occur in a single day. fitness evolution: growth on p. phaseolicola for the ancestor and sequenced clones, we measured a phenotypic trait that was often a direct target of selection in our study: fitness on the pp host. we observed that all viruses retained the ability to infect the original pp host even when evolved solely on era; in contrast, duffy et al. showed that strict era selection can sometimes lead to fixation of a non-synonymous mutation in p that prevents phage ϕ entry into pp host cells. thus, for all sequenced viruses we conducted fitness assays on pp against a genetically-marked common competitor that contained a host-range mutation on segment m, and an inserted x-gal mutation on segment l. assays were performed with six-fold replication, yielding total measures. these measures were log-transformed to improve normality. because pp is the typical lab host for phage ϕ the a priori prediction was that viruses evolved at large population sizes on this host should show equal or higher fitness relative to the ancestor. table  shows mean lnw for each virus on pp. the mean lnw of the ancestral clone a was determined to be significantly greater than, indicating that the ancestor was more fit on pp than the common competitor. we then conducted independent t-tests to gauge whether the mean lnw of a test virus differed from that of the ancestor; because these tests involved comparisons versus the ancestor dataset we conservatively gauged significance using a bonferroni correction of α = . we observed that fitness on pp statistically differed from the ancestor in a majority of these comparisons, and most of these outcomes showed fitness significantly lower than the ancestor. consistent with our prediction, close inspection of these data and the experimental design revealed that all clones which had recently experienced constant selection on pp at large population size did not suffer a decrease in fitness on pp. in contrast, of clones which had recently undergone constant selection on era at large size suffered a decline in fitness on pp. these data suggested that selection for fitness improvement on era tended to trade off with performance on pp see also. 1values are means of six log fitness estimates; ↑ and ↓ indicate significantly higher and lower fitness relative to ancestor or to immediate predecessor clone; open cells indicate no statistical difference; --- indicates test could not be performed. 2tested relative to bonferroni corrected probability of. 3tested relative to bonferroni corrected probability of. 4tested relative to bonferroni corrected probability of. fitness declines on pp were also observed for clones which were bottlenecked on either pp, era or alternating pp/era, and whose immediate predecessor clone showed significantly lower fitness on pp; these data were consistent with predicted effects of bottlenecking that cause drift to overwhelm positive selection, preventing the lineages from regaining fitness. for a detailed summary of the inferred effects of population size on observed evolution of clone fitness on pp, see the additional file fitness evolution: growth on p. pseudoalcaligenes era we also determined how the fitness of viruses on era changed in our study. clone b was a direct descendent of the ancestor, and contained a spontaneous host-range mutation in gene p on the m segment, allowing infection of novel host era. we sought to examine fitness on era for the clones derived from clone b but assays on era were not possible for a subset of these viruses because they were never directly exposed to era and therefore had experienced a reverse mutation preventing infection of era. thus, fitness assays against the common competitor on era were conducted for only clones, yielding a total of measures, which were log-transformed to improve normality. our a priori prediction was that evolution on era at large population size should lead to strong performance on this host. table  shows mean lnw for the viruses assayed on era. the mean lnw of clone b was determined to be significantly lower than, indicating that clone b was less fit on era than the common competitor. independent t-tests gauged whether mean lnw of a test virus differed from that of clone b1; because these tests involved comparisons versus b we employed a bonferroni correction of α = . we observed that fitness on era was significantly greater than that of clone b in every comparison. this outcome was consistent with the predicted improvement on era for clones recently experiencing evolution on era at large population size. interestingly, clones e thru e were direct descendents of strong performers on era and maintained high fitness on this host despite bottlenecking. the e clone, by chance did not experience any mutations from its d ancestor. for e and e the result suggested that era performance was less affected by drift occurring during the 20-day bottlenecks, compared with typical debilitating effects of 20-day bottlenecking on pp fitness; related to the above suggestion, one possibility is that within-plaque growth/selection more easily counters the effects of drift when phage ϕ is bottlenecked on era, compared to identical propagation on pp. the phenomenon may also explain why clone e showed high fitness on era despite being subjected to bottlenecks on this host. for additional discussion of era performance shown by individual clones, see the additional file figure 5b summarizes the fitness values observed on era, in relation to our experimental design. it is obvious that the clade containing lineages mostly selected on era tended to show high fitness values on era. fitness evolution relative to immediate predecessors to examine fitness changes on selected and unselected hosts over evolutionary time, we compared the phenotype of a virus clone to that of its immediate predecessor clone: the virus used to initiate a bifurcation that gave rise to the descendant clone. this effort yielded up to statistical comparisons for each of the three measured traits, where we employed a bonferroni correction of α =  for determining significant differences in t-tests where two clones were tested relative to their common progenitor. we observed that mean lnw of a virus clone on the typical host pp did not always statistically differ from that of its predecessor virus. fitness on pp tended to be equal for clones isolated from lineages successively evolved on pp at constant large size; a linear regression showed that this trajectory of lnw through time had positive slope but did not differ from zero. however, fitness on era showed a significantly positive increase through time for clones from lineages successively evolved on era. we found some evidence that the viruses constantly evolved on era suffered a tradeoff in performance on pp; the regression of differential performance across hosts versus time was a decreasing function, but did not differ statistically from zero. a similar analysis was not possible for differential performance of pp-evolved viruses across hosts, because most of these clones could not infect era. additional discussion of individual clone performance on pp and/or era relative to the immediate predecessor is contained in the additional file limitations to inferring genotype-phenotype associations we note one important caveat in interpreting the phenotypic consequences of the molecular substitutions stems from our acquisition of clones from each population to conduct whole-genome sequencing. at the end of each treatment period, as detailed in the methods, a single clone was chosen and this clone was then subjected to sequencing. for example, we began a selective regime with a clone whose sequence was known, the clone was expanded into a population and that population underwent a particular selective regime for a period of time. subsequently, an individual clone was selected at random from the population, sequenced and measured phenotypically. we then inferred from the changes separating the starting clone and the endpoint clone how the virus population responded to selection. through this method, there was a chance that the clone we chose was not representative of the parent population. thus, the molecular changes we observed were not necessarily reflective of measurable performance changes in the parent population; see also for related discussion. however, given the overall low number of observed changes in the experimental evolution, we are confident that a discrepancy between clone-level changes and majority alleles in the parent population should occur with low probability, in turn suggesting that the above-described associations should be generally robust interpretations. evolution under host switching the importance of the p protein in host switching events in phage ϕ has been previously established. this study confirmed this observation, but additionally brought to light the importance of the p protein in host switching events. this non-structural protein controls the liberation of mature ϕ particles from the host cytoplasmic membrane, but is not incorporated into the virion. like many eukaryotic viruses, cystoviridae have envelopes comprised of both viral proteins and host lipids. different hosts may have different lipid constituents which are contributed to the viral envelope and thus may require slightly altered p proteins for efficient envelope assembly. we have already shown that phage ϕ maturation in era affects fitness when the virion infects pp, and vice versa. we assume this epigenetic effect is mediated by the lipids taken from these very different hosts, and we speculate that our current results may relate to the importance of host lipid incorporation for multiple host-use in phage ϕ as described above, we observed that non-synonymous mutation f176l in gene p on the s segment was associated with a host switch to the novel host era. this mutation seemed to revert when a virus lineage was subsequently allowed to evolve on the typical host pp, as long as population size was constantly large or decreased from large size to small size. we hypothesized that the f176l mutation was beneficial for era infection, but that the l176f reversion was beneficial for growth on pp. to confirm the hypothesized functional significance of the allelic switch for growth on pp and era, we conducted follow-up experimental evolution to test whether population size and host type affected allele fixation in test populations. the design for this experiment is shown in additional file we isolated a single plaque-purified copy of clone c that had evolved on era at large population sizes; sequencing confirmed that this clone contained the f176l mutation presumably beneficial for era infection. this clone was used to found four additional virus lineages that were evolved on pp for days at population bottlenecks of either or pfu. after the evolution experiment, we used targeted consensus sequencing of each test population to examine changes in the p gene. we observed that the l176f reversion was the dominant allele in the experimental populations evolved at population sizes of and pfu. in contrast, the allelic reversion did not fix in the test populations evolved at bottleneck sizes of and pfu. we then conducted a repeat of this evolution experiment in a separate block, and observed qualitatively identical results. these data strongly supported the idea that the non-synonymous p mutation was beneficial for growth on era and deleterious for performance on pp, whereas the reversion produced the opposite function. we concluded that population sizes of and larger were sufficient for selection to efficiently drive the reversion to high frequencies within generations, when viruses were cultured on the original pp host see also. why does fixation or dominance of reversion mutation happen at some population sizes and not others? current literature emphasizes that waiting time for selective sweeps does not necessarily explain what happens in clonal microbial populations. rather, there is more likely genetic variation present at any one time and selection draws upon this variation to produce change; there is thus an importance of clonal interference among variants of similar magnitude. in our lineages where population size started large and became small, we observed that the reversion fixed. likely such lineages of initially large size already had the needed revertant present within their existing variation, and it was able to spread through time even though population size diminished. in contrast, the lineages where population size started small and increased had to wait for the revertant to appear, because the initially small size made it unlikely that the needed genotype was initially present. the result was that the revertant never fixed because enough time did not elapse at large size for that revertant to exist within the standing genetic variation. but when population size was sufficiently large enough for a lineage subsequently evolved on pp, the beneficial revertant was able to spontaneously arise and fix in the population. because era and pp are distantly related, one possible explanation is that the substitution in the p assembly protein enables more effective incorporation of era membrane lipids into the virus envelope at the expense of effectively incorporating pp membrane lipids. phylogenetic reconstruction the bifurcating-deme structure we imposed in our experiment afforded the possibility to test whether phylogenetic methods could successfully reconstruct the tree topology using genetic data alone. all methods returned the same phylogeny with similar assessment of uncertainty by bootstrap or posterior probability. the lineage containing descendants of c, were reconstructed with no false positive clades and one false negative clade. the reconstructions for the descendants of c were more mixed with several false negatives and one false positive. the false negatives involved failure to identify the clades descended from d while the false positive involved placing the f line together with f9-f creating an erroneous clade of {f f f f f13}. the false negatives, that is, the failure to resolve certain branches, is due to the small number of polymorphic sites within our dataset. purifying and directional selection over linked loci seems to have greatly reduced the phylogenetically informative sites in our study. some of the problems with the reconstruction can be traced to particular mutational history. as noted, the clade {f f f f16} is unresolved in the estimated tree. the clade descendant from d is delineated by q8q mutation in the p gene on segment s. however, in both e and e direct descendants of d there was a reversal synonymous q8q mutation that erased the evolutionary history. a parallel mutation of a143a in m-p gene in both the e and f lineages seems to be the main signature that caused f to erroneously fall into the clade that contains f f f and f finally, we used maximum likelihood ancestral state estimation in paup to reconstruct the ancestral sequences. all ancestral states were correctly reconstructed with the exception of two sites. the first site was the q8q site, which as described, reverted back to the ancestral state in two descendent lineages, in effect completely hiding the mutation in the terminal lineages. no algorithm is expected to reconstruct such exact reversions. the second site is the highly variable f176l mutation in p gene of segment s discussed above, which showed parallel changes in four terminal lineages. the terminal mutations were all c to t changes in the terminal lineages, which are reversions to state t of the common ancestor to all lineages, following an early t to c change in the “era” clade. therefore, the true ancestral state was c but was incorrectly estimated to the t state, reflecting the shared t state in the “pp” clade as well as the t’s in the other terminal lineage of the “era” clade. the high degree of parallel terminal mutations is highly unlikely by standard probabilistic models, as well as by the parsimony criterion and the ancestral states of such singular events are not expected to be estimated correctly. in sum, complex evolutionary history, especially with selective pressures that can cause parallel or reversal of specific loci, can cause difficulties with phylogenetic reconstruction even when the whole sequenced genome is available. regarding use of our dataset to investigate how environmental complexities impact the ability for phylogenetic methods to accurately infer historical relationships, we observed that none of the investigated methods could accurately reconstruct the true phylogeny. this result is similar to the observations of bull et al. in a previous known phylogeny study. in the prior experiment, the failure was due to the effects of convergence of the phylogenetic topography. however, in the current study we showed that the failure could occur due to a paucity of observed molecular changes. for example, two of the sixteen endpoint lineages presented exactly the same genetic sequence, rendering it impossible to distinguish them, regardless of the method employed. thus, we could not effectively assess how variable selection impacted the usefulness of various methods of phylogenetic reconstruction. overall, the results of our dataset were not useful for evaluating the relative effectiveness of the various methods due to the paucity of changes in some lineages. however, when examining how well the methods performed on the clade produced from the initial switch to era, we observed that the methods were more accurate in inferring the actual phylogeny; in particular, ml again proved to be the most effective method for accurately regenerating the actual clade.  phylogenetic methods can often fail to resolve deep relationships with saturated molecular data; here we showed a similar difficulty in using the methods to resolve the simple bifurcating design implemented in this ~ generation known phylogeny experiment. using the natural mutation rate of this rna virus and environments similar to the selective pressures and population size changes experienced by many viruses in nature, we were able to demonstrate several aspects of viral evolution that can confound the usefulness of phylogenetic algorithms: few informative sites, and parallel and reversion mutations. because these complications will often occur when tracking the evolution of emerging viruses, our work implies that phylogenetic trees encompassing molecular epidemiology over short timescales may tend to be inaccurate. specific to the study system, we identified that the protein-coding gene p on the s segment of phage ϕ is important for host-use selection in the virus. our study demonstrated that experimental evolution involving a large number of increasingly diverged lineages is a useful tool for testing evolutionary theory, as well as for discovering novel traits in evolving populations that more narrowly-focused studies would omit. 
our study yielded a very large molecular and phenotypic dataset, fostering possible inferences on genotype-phenotype associations. to do so, we created a bifurcating deme structure that reflected lineage splitting in natural populations, allowing us to test whether phylogenetic algorithms could accurately resolve this ‘known phylogeny’. using further experimental evolution, we confirmed an inference on the unanticipated role of an allelic switch in a viral assembly protein, which governed viral performance across host environments. our study demonstrated that varying complexities can be simultaneously incorporated into experimental evolution, to examine the combined effects of population size, and adaptation in novel environments. we observed that rna segment size was negatively correlated with the extent of molecular change in the imposed treatments; molecular substitutions tended to cluster on the small and medium rna chromosomes of the virus, and not on the large segment. the imposed bifurcating structure revealed that some methods for phylogenetic reconstruction failed to resolve the true phylogeny, owing to a paucity of molecular substitutions separating the rna viruses that evolved in our study. however, despite these differences, most virus populations will occasionally experience two commonly-encountered challenges: growth in variable host environments, and growth under fluctuating population sizes. we used the segmented rna bacteriophage ϕ as a model for studying the evolutionary genomics of virus adaptation in the face of host switches and parametrically varying population sizes. the resulting tree yielded clones at the tips and internal nodes; these strains were fully sequenced and measured for phenotypic changes in selected traits.
 viruses are exceedingly diverse in their evolved strategies to manipulate hosts for viral replication. however, despite these differences, most virus populations will occasionally experience two commonly-encountered challenges: growth in variable host environments, and growth under fluctuating population sizes. we used the segmented rna bacteriophage ϕ as a model for studying the evolutionary genomics of virus adaptation in the face of host switches and parametrically varying population sizes. to do so, we created a bifurcating deme structure that reflected lineage splitting in natural populations, allowing us to test whether phylogenetic algorithms could accurately resolve this ‘known phylogeny’. the resulting tree yielded clones at the tips and internal nodes; these strains were fully sequenced and measured for phenotypic changes in selected traits.  we observed that rna segment size was negatively correlated with the extent of molecular change in the imposed treatments; molecular substitutions tended to cluster on the small and medium rna chromosomes of the virus, and not on the large segment. our study yielded a very large molecular and phenotypic dataset, fostering possible inferences on genotype-phenotype associations. using further experimental evolution, we confirmed an inference on the unanticipated role of an allelic switch in a viral assembly protein, which governed viral performance across host environments.  our study demonstrated that varying complexities can be simultaneously incorporated into experimental evolution, to examine the combined effects of population size, and adaptation in novel environments. the imposed bifurcating structure revealed that some methods for phylogenetic reconstruction failed to resolve the true phylogeny, owing to a paucity of molecular substitutions separating the rna viruses that evolved in our study. adaptationbacteriabacteriophageexperimental evolutionknown phylogenypseudomonasvirus 