Combining experimental evolution and field population assays to study the evolution of host range breadth

Adapting to specific hosts often involves trade‐offs that limit performance on other hosts. These constraints may either lead to narrow host ranges (i.e. specialists, able to exploit only one host type) or wide host ranges often leading to lower performance on each host (i.e. generalists). Here, we combined laboratory experiments on field populations with experimental evolution to investigate the impact of adaptation to the host on host range evolution and associated performance over this range. We used the two‐spotted spider mite, Tetranychus urticae, a model organism for studies on the evolution of specialization. Field mite populations were sampled on three host plant species: tomato, citrus tree and rosebay (Nerium oleander). Testing these populations in the laboratory revealed that tomato populations of mites could exploit tomato only, citrus populations could exploit citrus and tomato whereas Nerium populations could exploit all three hosts. Besides, the wider niche ranges of citrus and Nerium populations came at the cost of low performance on their non‐native hosts. Experimental lines selected to live on the same three host species exhibited similar patterns of host range and relative performance. This result suggests that adaptation to a new host species may lead to wider host ranges but at the expense of decreased performance on other hosts. We conclude that experimental evolution may reliably inform on evolution in the field.     

Evolution of host specificity drives reproductive isolation among RNA viruses

Ecological speciation hypotheses claim that assortative mating evolves as a consequence of divergent natural selection for ecologically important traits. Reproductive isolation is expected to be particularly likely to evolve by this mechanism in species such as phytophagous insects that mate in the habitats in which they eat. We tested this expectation by monitoring the evolution of reproductive isolation in laboratory populations of an RNA virus that undergoes genetic exchange only when multiple virus genotypes coinfect the same host. We subjected four populations of the RNA bacteriophage phi6 to 150 generations of natural selection on a novel host. Although there was no direct selection acting on host range in our experiment, three of the four populations lost the ability to infect one or more alternative hosts. In the most extreme case, one of the populations evolved a host range that does not contain any of the hosts infectible by the wild-type phi6. Whole genome sequencing confirmed that the resulting reproductive isolation was due to a single nucleotide change, highlighting the ease with which an emerging RNA virus can decouple its evolutionary fate from that of its ancestor. Our results uniquely demonstrate the evolution of reproductive isolation in allopatric experimental populations. Furthermore, our data confirm the biological credibility of simple "no-gene" mechanisms of assortative mating, in which this trait arises as a pleiotropic effect of genes responsible for ecological adaptation.     

Delayed transmission selects for increased survival of vesicular stomatitis virus

Life-history theory predicts that traits for survival and reproduction cannot be simultaneously maximized in evolving populations. For this reason, in obligate parasites such as infectious viruses, selection for improved between-host survival during transmission may lead to evolution of decreased within-host reproduction. We tested this idea using experimental evolution of RNA virus populations, passaged under differing transmission times in the laboratory. A single ancestral genotype of vesicular stomatitis virus (VSV), a negative-sense RNA Rhabdovirus, was used to found multiple virus lineages evolved in either ordinary 24-h cell-culture passage, or in delayed passages of 48 h. After 30 passages (120 generations of viral evolution), we observed that delayed transmission selected for improved extracellular survival, which traded-off with lowered viral fecundity (slower exponential population growth and smaller mean plaque size). To further examine the confirmed evolutionary trade-off, we obtained consensus whole-genome sequences of evolved virus populations, to infer phenotype–genotype associations. Results implied that increased virus survival did not occur via convergence; rather, improved virion stability was gained via independent mutations in various VSV structural proteins. Our study suggests that RNA viruses can evolve different molecular solutions for enhanced survival despite their limited genetic architecture, but suffer generalized reproductive trade-offs that limit overall fitness gains.     

RIG-I family RNA helicases: cytoplasmic sensor for antiviral innate immunity

Viral infection is detected by cellular sensors as foreign nucleic acid and initiates innate antiviral responses, including the activation of type I interferon (IFN) and proinflammatory cytokines. Recent advances in cytoplasmic virus sensors highlight their essential role in the induction of innate immunity. Moreover, it is intriguing to understand how they can discriminate innate RNA from viral foreign RNA. In this mini-review, we focus on these cytoplasmic virus sensors, termed retinoic acid inducible gene-I (RIG-I)-like receptors (RLRs), and discuss their function in the innate immune system.     

Restrictions to RNA virus adaptation: an experimental approach

Some basic properties of RNA viruses are their high mutation rate, their enormous population sizes and their short generation time. These properties allow RNA virus populations to quickly explore fitness landscapes. A great adaptability has been amply demonstrated in experimental, as well as in natural, populations of RNA viruses. However, at least from a theoretical point of view, a limit to the extent of viral adaptation may exist as a consequence of adaptive trade-offs arising during evolution in changing environmental conditions. Here, I review previously published results searching for such fitness trade-offs. The following scenario has been explored: the cost of host-range expansion, the cost of resistance to antiviral drugs, and the adaptation to different population densities. Despite the environmental conditions tested, results show a common pattern: whenever a virus adapt to a simple environmental situation it pays a cost in terms of adaptation to alternative situations. However, in those cases where the virus has been simultaneously adapted to different environmental conditions, this cost disappears or, at least, is greatly reduced. Finally, and as another factor imposing a limit to their speed of adaptation, I review results showing that clonal interference also plays an important role during viral evolution. This revised version was published online in August 2006 with corrections to the Cover Date.     

Parasite host range and the evolution of host resistance

Parasite host range plays a pivotal role in the evolution and ecology of hosts and the emergence of infectious disease. Although the factors that promote host range and the epidemiological consequences of variation in host range are relatively well characterized, the effect of parasite host range on host resistance evolution is less well understood. In this study, we tested the impact of parasite host range on host resistance evolution. To do so, we used the host bacterium Pseudomonas fluorescens SBW25 and a diverse suite of coevolved viral parasites (lytic bacteriophage Φ2) with variable host ranges (defined here as the number of host genotypes that can be infected) as our experimental model organisms. Our results show that resistance evolution to coevolved phages occurred at a much lower rate than to ancestral phage (approximately 50% vs. 100%), but the host range of coevolved phages did not influence the likelihood of resistance evolution. We also show that the host range of both single parasites and populations of parasites does not affect the breadth of the resulting resistance range in a naïve host but that hosts that evolve resistance to single parasites are more likely to resist other (genetically) more closely related parasites as a correlated response. These findings have important implications for our understanding of resistance evolution in natural populations of bacteria and viruses and other host–parasite combinations with similar underlying infection genetics, as well as the development of phage therapy.     

Specialized avian Haemosporida trade reduced host breadth for increased prevalence

Parasite specialization on one or a few host species leads to a reduction in the total number of available host individuals, which may decrease transmission. However, specialists are thought to be able to compensate by increased prevalence in the host population and increased success in each individual host. Here, we use variation in host breadth among a community of avian Haemosporida to investigate consequences of generalist and specialist strategies on prevalence across hosts. We show that specialist parasites are more prevalent than generalist parasites in host populations that are shared between them. Moreover, the total number of infections of generalist and specialist parasites within the study area did not vary significantly with host breadth. This suggests that specialists can infect a similar number of host individuals as generalists, thus compensating for a reduction in host availability by achieving higher prevalence in a single host species. Specialist parasites also tended to infect older hosts, whereas infections by generalists were biased towards younger hosts. We suggest that this reflects different abilities of generalists and specialists to persist in hosts following infection. Higher abundance and increased persistence in hosts suggest that specialists are more effective parasites than generalists, supporting the existence of a trade‐off between host breadth and average host use among these parasites.     

A genetic background with low mutational robustness is associated with increased adaptability to a novel host in an RNA virus

Although mutational robustness is central to many evolutionary processes, its relationship to evolvability remains poorly understood and has been very rarely tested experimentally. Here, we measure the evolvability of Vesicular stomatitis virus in two genetic backgrounds with different levels of mutational robustness. We passaged the viruses into a novel cell type to model a host‐jump episode, quantified changes in infectivity and fitness in the new host, evaluated the cost of adaptation in the original host and analyzed the genetic basis of this adaptation. Lineages evolved from the less robust genetic background demonstrated increased adaptability, paid similar costs of adaptation to the new host and fixed approximately the same number of mutations as their more robust counterparts. Theory predicts that robustness can promote evolvability only in systems where large sets of genotypes are connected by effectively neutral mutations. We argue that this condition might not be fulfilled generally in RNA viruses.     

Evolution of RNA virus in spatially structured heterogeneous environments

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

Rate of novel host invasion affects adaptability of evolving RNA virus lineages

Although differing rates of environmental turnover should be consequential for the dynamics of adaptive change, this idea has been rarely examined outside of theory. In particular, the importance of RNA viruses in disease emergence warrants experiments testing how differing rates of novel host invasion may impact the ability of viruses to adaptively shift onto a novel host. To test whether the rate of environmental turnover influences adaptation, we experimentally evolved 144 Sindbis virus lineages in replicated tissue-culture environments, which transitioned from being dominated by a permissive host cell type to a novel host cell type. The rate at which the novel host ‘invaded’ the environment varied by treatment. The fitness (growth rate) of evolved virus populations was measured on each host type, and molecular substitutions were mapped via whole genome consensus sequencing. Results showed that virus populations more consistently reached high fitness levels on the novel host when the novel host ‘invaded’ the environment more gradually, and gradual invasion resulted in less variable genomic outcomes. Moreover, virus populations that experienced a rapid shift onto the novel host converged upon different genotypes than populations that experienced a gradual shift onto the novel host, suggesting a strong effect of historical contingency.     

Differences in host plant selection among three Athalia sawflies feeding on crucifers in Japan

Abstract 1. The ways of using host plants were compared among the three Athalia sawflies [ A. japonica (Klug), A. rosae ruficornis Jakovlev, and A. infumata (Marlatt)] feeding on crucifers in Japan to determine whether host specialisation can explain the difference in their life-history traits. The occurrence of their larvae was examined on each crucifer species in the field, and the suitability of each crucifer species for the three successive steps of host use by the sawflies was evaluated: microhabitat selection by adult females, female oviposition, and larval growth.
2. There were 11 species of crucifer in the study area, and A. japonica , A. rosae , and A. infumata used nine, seven, and eight species respectively. Thus, sawfly host ranges overlapped.
3. Adult females of A. japonica , A. rosae , and A. infumata preferred shady clumps of crucifers, sunny clumps of crucifers, and disturbed areas respectively.
4. Unsuitable hosts for larval performance such as Brassica oleracea and Arabis plants were eliminated from the host ranges of the three sawflies.
5. Once they chose microhabitats, the suitability of each host plant for female oviposition and larval growth was similar.
6. Because of the divergent preferences for microhabitats, the host plants that were suitable for all the three steps were restricted to different sets of plants among the sawflies: Cardamine for A. japonica , cultivated crucifers ( Raphanus and Brassica ) for A. rosae , and Rorippa for A. infumata . These plants could be recognised as the respective primary host plants.
7. The spatio-temporal distributions of primary hosts were consistent with and explained the pattern of diapause and migration of each sawfly, suggesting that host specialisation caused their life-history traits to differentiate.     

Upper-limit mutation rate estimation for a plant RNA virus

It is generally accepted that mutation rates of RNA viruses are inherently high due to the lack of proofreading mechanisms. However, direct estimates of mutation rate are surprisingly scarce, in particular for plant viruses. Here, based on the analysis of in vivo mutation frequencies in tobacco etch virus, we calculate an upper-bound mutation rate estimation of 3×10⁻⁵ per site and per round of replication; a value which turns out to be undistinguishable from the methodological error. Nonetheless, the value is barely on the lower side of the range accepted for RNA viruses, although in good agreement with the only direct estimate obtained for other plant viruses. These observations suggest that, perhaps, differences in the selective pressures operating during plant virus evolution may have driven their mutation rates towards values lower than those characteristic of other RNA viruses infecting bacteria or animals.     

Divergence in host use ability of a marine herbivore from two habitat types

We studied ecological divergence of host use ability in a generalist marine herbivore living in two distinct host plant assemblages. We collected Idotea balthica isopods from three populations dominated by the brown alga Fucus vesiculosus and three dominated by the seagrass Zostera marina. In two reciprocal common garden feeding experiments for adult and laboratory‐born juvenile isopods, we found that isopods from both assemblages performed better with their sympatric dominant host species than did isopods allopatric to this host. This indicates parallel divergence of populations according to the sympatric host plant assemblage. Furthermore, initial body size and body size‐dependent mortality differed between populations from the two assemblages. In nature, this may result in lower fitness of immigrants compared with that of residents and consequently reinforce divergence of the populations. Finally, we discuss how phenotypic plasticity and maternal and random effects may associate with the results.     

Evolution of host acceptance and its reversibility in a seed beetle

1. Adapting to a low‐quality plant may require modification of an insect's digestive physiology, oviposition behaviour, or other host‐use traits. If colonising a marginal host entails a cost, a decay in adaptation would be expected after selection is relaxed, i.e. if populations on a novel host are reverted to their high‐quality ancestral host. 2. Replicate lines of the seed beetle Callosobruchus maculatus (F.) rapidly adapted to lentil seeds; larval survival rose from approximately 1 to ≥ 90%, and oviposition on lentil increased more than two‐fold. This study compared egg‐laying behaviour in lines that either remained on lentil or were reverted to the ancestral host, mung bean, for 22–62 generations. 3. Consistent with the trade‐off hypothesis, females from two reverted sublines showed decreased oviposition on lentil (estimated as lifetime fecundity), but host acceptance in a third subline was unchanged. In a short‐term assay, acceptance of lentil by newly emerged females was lower in each reverted subline than in the corresponding non‐reverted one. Because effective population sizes (determined from genome resequencing) were large throughout the experiment, this decline in host acceptance is unlikely to be explained solely by genetic drift. 4. Variation among replicates in the magnitude of the reversion effect was also observed in a previous study of larval survival. However, the pattern of variation for survival was not congruent with the pattern of variation for host acceptance in this study. Thus, genes mediating improved performance on lentil appear to be largely independent of those responsible for increased oviposition.     

The evolution of parasite host range in heterogeneous host populations

Theory on the evolution of niche width argues that resource heterogeneity selects for niche breadth. For parasites, this theory predicts that parasite populations will evolve, or maintain, broader host ranges when selected in genetically diverse host populations relative to homogeneous host populations. To test this prediction, we selected the bacterial parasite Serratia marcescens to kill Caenorhabditis elegans in populations that were genetically heterogeneous (50% mix of two experimental genotypes) or homogeneous (100% of either genotype). After 20 rounds of selection, we compared the host range of selected parasites by measuring parasite fitness (i.e. virulence, the selected fitness trait) on the two focal host genotypes and on a novel host genotype. As predicted, heterogeneous host populations selected for parasites with a broader host range: these parasite populations gained or maintained virulence on all host genotypes. This result contrasted with selection in homogeneous populations of one host genotype. Here, host range contracted, with parasite populations gaining virulence on the focal host genotype and losing virulence on the novel host genotype. This pattern was not, however, repeated with selection in homogeneous populations of the second host genotype: these parasite populations did not gain virulence on the focal host genotype, nor did they lose virulence on the novel host genotype. Our results indicate that host heterogeneity can maintain broader host ranges in parasite populations. Individual host genotypes, however, vary in the degree to which they select for specialization in parasite populations.     

In vitro host range of the Hz-1 nonoccluded virus in insect cell lines

A total of 13 insect cell lines spanning 4 orders (Lepidoptera, Coleoptera, Diptera, and Homoptera) were tested for their ability to replicate the nonoccluded virus Hz-1. Only the Lepidopteran cell lines supported replication of the virus with TN-CL1 and BCIRL-HZ-AM1 producing the highest titers of 2.4 × 10⁸ tissue culture infective dose (TCID)₅₀/ml and 2.0 × 10⁸ TCID₅₀/ml, respectively. A codling moth cell line (CP-169) was the only Lepidopteran cell line that did not replicate the virus and transfection of this cell line with Hz-1 DNA failed to replicate the virus. Also, transfection with DNA from a recombinant baculovirus carrying the red fluorescent protein gene (AcMNPVhsp70 Red) was not expressed in CP-169 cells. The replication cycle of Hz-1 in BCIRL-HZ-AM1 cells showed that this virus replicated rapidly starting at 16 h postinoculation (p.i.) and reaching a peak titer of 1.0 × 10⁸ TCID₅₀/ml 56 h postinoculation. Hz-1 when compared with several other baculoviruses has the widest in vitro host spectrum.     

Positive selection of synonymous mutations in vesicular stomatitis virus

Prevailing evolutionary forces are typically deduced from the pattern of differences in synonymous and non-synonymous mutations, under the assumption of neutrality in the absence of amino acid change. We determined the complete sequence of ten vesicular stomatitis virus populations evolving under positive selection. A significant number of the mutations occurred independently in two or more strains, a process known as parallel evolution, and a substantial fraction of the parallel mutations were silent. Parallel evolution was also identified in non-coding regions. These results indicate that silent mutations can significantly contribute to adaptation in RNA viruses, and relative frequencies of synonymous and non-synonymous substitutions may not be useful to resolve their evolutionary history.     

Parasite diversity drives rapid host dynamics and evolution of resistance in a bacteria‐phage system

Host–parasite evolutionary interactions are typically considered in a pairwise species framework. However, natural infections frequently involve multiple parasites. Altering parasite diversity alters ecological and evolutionary dynamics as parasites compete and hosts resist multiple infection. We investigated the effects of parasite diversity on host–parasite population dynamics and evolution using the pathogen Pseudomonas aeruginosa and five lytic bacteriophage parasites. To manipulate parasite diversity, bacterial populations were exposed for 24 hours to either phage monocultures or diverse communities containing up to five phages. Phage communities suppressed host populations more rapidly but also showed reduced phage density, likely due to interphage competition. The evolution of resistance allowed rapid bacterial recovery that was greater in magnitude with increases in phage diversity. We observed no difference in the extent of resistance with increased parasite diversity, but there was a profound impact on the specificity of resistance; specialized resistance evolved to monocultures through mutations in a diverse set of genes. In summary, we demonstrate that parasite diversity has rapid effects on host–parasite population dynamics and evolution by selecting for different resistance mutations and affecting the magnitude of bacterial suppression and recovery. Finally, we discuss the implications of phage diversity for their use as biological control agents.     

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.     

Avoiding conflicts between insect and weed biological control: selection of non-target species to assess host specificity of cabbage seedpod weevil parasitoids

Abstract:  Classical biological control of insect pests and weeds may lead to potential conflicts, where insect pests are closely related to weed biological control agents. Such a conflict may occur in the classical biological control of the cabbage seedpod weevil, Ceutorhynchus obstrictus (Marsham) in North America, which belongs to the same subfamily, Ceutorhynchinae, as a number of agents introduced or proposed for introduction against non-indigenous invasive weed species. We propose a step-by-step procedure to select non-target species and thereby to develop a non-target species test list for screening candidate entomophagous biological control agents of a herbivore pest insect in a way that would simultaneously evaluate non-target potential on weed biological control agents and other non-target species. Using these recommendations, we developed a non-target test list for host specificity evaluations in the area of origin (Europe) and the area of introduction (North America) for cabbage seedpod weevil parasitoids. Scientifically based predictions on expected host–parasitoid interactions and ecological information about the ecological host range in the area of origin can help avoid conflicts, while still allowing the introduction of safe and effective agents against both insect pests and weeds.