Evolution of host specificity drives reproductive isolation among RNA viruses

Host specificity determinants as a genetic continuum

Host specificity is an important concept that underlies the interaction of all clinically and agriculturally relevant microbes with their hosts. Changes in the host specificity of animal pathogens, in particular, are often of greatest concern due to their immediate and unexpected impact on human health. Host switching or host jumps can often be traced to modification of key microbial pathogenicity factors that facilitate the formation of particular host associations. An increase in the number of genome-level studies has begun revealing that almost any type of change, from the simplest to the most complex, can potentially impact host specificity. This review highlights examples of host specificity determinants of viruses, bacteria and fungi, and presents them from within a genetic continuum that spans from the single residue through to entire genomic islands.

Host phylogeny determines viral persistence and replication in novel hosts

Pathogens switching to new hosts can result in the emergence of new infectious diseases, and determining which species are likely to be sources of such host shifts is essential to understanding disease threats to both humans and wildlife. However, the factors that determine whether a pathogen can infect a novel host are poorly understood. We have examined the ability of three host-specific RNA-viruses (Drosophila sigma viruses from the family Rhabdoviridae) to persist and replicate in 51 different species of Drosophilidae. Using a novel analytical approach we found that the host phylogeny could explain most of the variation in viral replication and persistence between different host species. This effect is partly driven by viruses reaching a higher titre in those novel hosts most closely related to the original host. However, there is also a strong effect of host phylogeny that is independent of the distance from the original host, with viral titres being similar in groups of related hosts. Most of this effect could be explained by variation in general susceptibility to all three sigma viruses, as there is a strong phylogenetic correlation in the titres of the three viruses. These results suggest that the source of new emerging diseases may often be predictable from the host phylogeny, but that the effect may be more complex than simply causing most host shifts to occur between closely related hosts.

Emerging infectious diseases such as SARS, HIV and swine-origin influenza have all been recently acquired by humans from other species. Understanding the reasons why parasites jump between different host species is essential to allow us to predict future threats and understand the causes of disease emergence. Here we ask how host-relatedness might determine when host-shifts can occur in the most important group of emerging diseases—RNA viruses. We show that the relationship between host species is the primary factor in determining a virus's ability to persist and replicate in a novel host following exposure. This can be broken down into two components. Firstly, species closely related to the virus's natural host are more susceptible than distantly related species. Secondly, independent of the distance effect, groups of closely related host species have similar levels of susceptibility. This has important implications for our understanding of disease-emergence, and until now the only large-scale studies of viruses have been correlative rather than experimental. We also found groups of related species that are susceptible to these viruses but are distantly related to the natural hosts, which may explain why viruses sometimes jump between distantly related species.

Population genetic structure and phylogeographical pattern of rice grasshopper, Oxya hyla intricata, across Southeast Asia

The rice grasshopper, Oxya hyla intricata, is a rice pest in Southeast Asia. In this study, population genetic diversity and structure of this Oxya species was examined using both DNA sequences and AFLP technology. The samples of 12 populations were collected from four Southeast Asian countries, among which 175 individuals were analysed using mitochondrial DNA cytochrome c oxidase subunit I (COI) sequences, and 232 individuals were examined using amplified fragment length polymorphisms (AFLP) to test whether the phylogeographical pattern and population genetics of this species are related to past geological events and/or climatic oscillations. No obvious trend of genetic diversity was found along a latitude/longitude gradient among different geographical groups. Phylogenetic analysis indicated three deep monophyletic clades that approximately correspond to three geographical regions separated by high mountains and a deep strait, and TCS analysis also revealed three disconnected networks, suggesting that spatial and temporal separations by vicariance, which were also supported by AMOVA as a source of the molecular variance presented among groups. Gene flow analysis showed that there had been frequent historical gene flow among local populations in different regions, but the networks exhibited no shared haplotype among populations. In conclusion, the past geological events and climatic fluctuations are the most important factor on the phylogeographical structure and genetic patterns of O. hyla intricata in Southeast Asia. Habitat, vegetation, and anthropogenic effect may also contribute to gene flow and introgression of this species. Moreover, temperature, abundant rainfall and a diversity of graminaceous species are beneficial for the migration of O. hyla intricata. High haplotype diversity, deep phylogenetic division, negative Fu's F (s) values and unimodal and multimodal distribution shapes all suggest a complicated demographic expansion pattern of these O. hyla intricata populations, which might have been caused by climatic oscillations during glacial periods in the Quaternary.

Experimental evolution, loss-of-function mutations, and "the first rule of adaptive evolution"

Adaptive evolution can cause a species to gain, lose, or modify a function; therefore, it is of basic interest to determine whether any of these modes dominates the evolutionary process under particular circumstances. Because mutation occurs at the molecular level, it is necessary to examine the molecular changes produced by the underlying mutation in order to assess whether a given adaptation is best considered as a gain, loss, or modification of function. Although that was once impossible, the advance of molecular biology in the past half century has made it feasible. In this paper, I review molecular changes underlying some adaptations, with a particular emphasis on evolutionary experiments with microbes conducted over the past four decades. I show that by far the most common adaptive changes seen in those examples are due to the loss or modification of a pre-existing molecular function, and I discuss the possible reasons for the prominence of such mutations.

Character displacement and the origins of diversity

In The Origin of Species, Darwin proposed his principle of divergence of character (a process now termed "character displacement") to explain how new species arise and why they differ from each other phenotypically. Darwin maintained that the origin of species and the evolution of differences between them is ultimately caused by divergent selection acting to minimize competitive interactions between initially similar individuals, populations, and species. Here, we examine the empirical support for the various claims that constitute Darwin's principle, specifically that (1) competition promotes divergent trait evolution, (2) the strength of competitively mediated divergent selection increases with increasing phenotypic similarity between competitors, (3) divergence can occur within species, and (4) competitively mediated divergence can trigger speciation. We also explore aspects that Darwin failed to consider. In particular, we describe how (1) divergence can arise from selection acting to lessen reproductive interactions, (2) divergence is fueled by the intersection of character displacement and sexual selection, and (3) phenotypic plasticity may play a key role in promoting character displacement. Generally, character displacement is well supported empirically, and it remains a vital explanation for how new species arise and diversify.

Maladaptation in wild populations of the generalist plant pathogen Pseudomonas syringae

Multihost pathogens occur widely on both natural and agriculturally managed hosts. Despite the importance of such generalists, evolutionary studies of host-pathogen interactions have largely focused on tightly coupled interactions between species pairs. We characterized resistance in a collection of Arabidopsis thaliana hosts, including 24 accessions collected from the Midwest USA and 24 from around the world, and patterns of virulence in a collection of Pseudomonas syringae strains, including 24 strains collected from wild Midwest populations of A. thaliana (residents) and 18 from an array of cultivated species (nonresidents). All of the nonresident strains and half of the resident strains elicited a resistance response on one or more A. thaliana accessions. The resident strains that failed to elicit any resistance response possessed an alternative type III secretion system (T3SS) that is unable to deliver effectors into plant host cells; as a result, these seemingly nonpathogenic strains are incapable of engaging in gene for gene interactions with A. thaliana. The remaining resident strains triggered greater resistance compared to nonresident strains, consistent with maladaptation of the resident bacterial population. We weigh the plausibility of two explanations: general maladaptation of pathogen strains and a more novel hypothesis whereby community level epidemiological dynamics result in adaptive dynamics favoring ephemeral hosts like A. thaliana.

Combining mathematics and empirical data to predict emergence of RNA viruses that differ in reservoir use

RNA viruses may be particularly capable of contributing to the increasing biomedical problem of infectious disease emergence. Empirical studies and epidemiological models are informative for the understanding of evolutionary processes that promote pathogen emergence, but rarely are these approaches combined in the same study. Here, we used an epidemiology model containing observations of pathogen productivity in reservoirs, as a means to predict which pathogens should be most prone to emerge in a primary host such as humans. We employed as a model system a collection of vesicular stomatitis virus populations that had previously diverged in host-use strategy: specialists, directly selected generalists and indirectly selected (fortuitous) generalists. Using data from experiments where these viral strategists were challenged to grow on unencountered novel hosts in vitro, logistic growth models determined that the directly selected generalist viruses tended to grow best on model reservoirs. Furthermore, when we used the growth data to estimate average reproductive rate across secondary reservoirs, we showed that the combined approach could be used to estimate relative success of the differing virus strategists when encountering a primary host. Our study suggests that synergistic approaches combining epidemiological modelling with empirical data from experimental evolution may be useful for developing efforts to predict which types of pathogens pose the greatest probability of emerging in the future.

Geographic differences in sexual reassortment in RNA phage

The genetic structure of natural bacteriophage populations is poorly understood. Recent metagenomic studies suggest that phage biogeography is characterized by frequent migration. Using virus samples mostly isolated in Southern California, we recently showed that very little population structure exists in segmented RNA phage of the Cystoviridae family due to frequent segment reassortment (sexual genetic mixis) between unrelated virus individuals. Here we use a larger genetic dataset to examine the structure of Cystoviridae phage isolated from three geographic locations in Southern New England. We document extensive natural variation in the physical sizes of RNA genome segments for these viruses. In addition, consistent with earlier findings, our phylogenetic analyses and calculations of linkage disequilibrium (LD) show no evidence of within-segment recombination in wild populations. However, in contrast to the prior study, our analysis finds that reassortment of segments between individual phage plays a lesser role among cystoviruses sampled in New England, suggesting that the evolutionary importance of genetic mixis in Cystoviridae phage may vary according to geography. We discuss possible explanations for these conflicting results across the studies, such as differing local ecology and its impact on phage growth, and geographic differences in selection against hybrid phage genotypes.

Phenotypic plasticity's impacts on diversification and speciation

Phenotypic plasticity (the ability of a single genotype to produce multiple phenotypes in response to variation in the environment) is commonplace. Yet its evolutionary significance remains controversial, especially in regard to whether and how it impacts diversification and speciation. Here, we review recent theory on how plasticity promotes: (i) the origin of novel phenotypes, (ii) divergence among populations and species, (iii) the formation of new species and (iv) adaptive radiation. We also discuss the latest empirical support for each of these evolutionary pathways to diversification and identify potentially profitable areas for future research. Generally, phenotypic plasticity can play a largely underappreciated role in driving diversification and speciation.

Speciation genetics: current status and evolving approaches

The view of species as entities subjected to natural selection and amenable to change put forth by Charles Darwin and Alfred Wallace laid the conceptual foundation for understanding speciation. Initially marred by a rudimental understanding of hereditary principles, evolutionists gained appreciation of the mechanistic underpinnings of speciation following the merger of Mendelian genetic principles with Darwinian evolution. Only recently have we entered an era where deciphering the molecular basis of speciation is within reach. Much focus has been devoted to the genetic basis of intrinsic postzygotic isolation in model organisms and several hybrid incompatibility genes have been successfully identified. However, concomitant with the recent technological advancements in genome analysis and a newfound interest in the role of ecology in the differentiation process, speciation genetic research is becoming increasingly open to non-model organisms. This development will expand speciation research beyond the traditional boundaries and unveil the genetic basis of speciation from manifold perspectives and at various stages of the splitting process. This review aims at providing an extensive overview of speciation genetics. Starting from key historical developments and core concepts of speciation genetics, we focus much of our attention on evolving approaches and introduce promising methodological approaches for future research venues.

Experimental evidence that source genetic variation drives pathogen emergence

A pathogen can readily mutate to infect new host types, but this does not guarantee successful establishment in the new habitat. What factors, then, dictate emergence success? One possibility is that the pathogen population cannot sustain itself on the new host type (i.e. host is a sink), but migration from a source population allows adaptive sustainability and eventual emergence by delivering beneficial mutations sampled from the source's standing genetic variation. This idea is relevant regardless of whether the sink host is truly novel (host shift) or whether the sink is an existing or related, similar host population thriving under conditions unfavourable to pathogen persistence (range expansion). We predicted that sink adaptation should occur faster under range expansion than during a host shift owing to the effects of source genetic variation on pathogen adaptability in the sink. Under range expansion, source migration should benefit emergence in the sink because selection acting on source and sink populations is likely to be congruent. By contrast, during host shifts, source migration is likely to disrupt emergence in the sink owing to uncorrelated selection or performance tradeoffs across host types. We tested this hypothesis by evolving bacteriophage populations on novel host bacteria under sink conditions, while manipulating emergence via host shift versus range expansion. Controls examined sink adaptation when unevolved founding genotypes served as migrants. As predicted, adaptability was fastest under range expansion, and controls did not adapt. Large, similar and similarly timed increases in fitness were observed in the host-shift populations, despite declines in mean fitness of immigrants through time. These results suggest that source populations are the origin of mutations that drive adaptive emergence at the edge of a pathogen's ecological or geographical range.

Linking the emergence of fungal plant diseases with ecological speciation

Emerging diseases represent a growing worldwide problem accompanying global environmental changes. There is tremendous interest in identifying the factors controlling the appearance and spread of these diseases. Here, we discuss emerging fungal plant diseases, and argue that they often result from host shift speciation (a particular case of ecological speciation). We consider the factors controlling local adaptation and ecological speciation, and show that certain life-history traits of many fungal plant pathogens are conducive for rapid ecological speciation, thus favoring the emergence of novel pathogen species adapted to new hosts. We argue that placing the problem of emerging fungal diseases of plants within the context of ecological speciation can significantly improve our understanding of the biological mechanisms governing the emergence of such diseases.

Adaptation rates of lytic viruses depend critically on whether host cells survive the bottleneck

We use a branching process approach to estimate the substitution rate, the rate at which beneficial mutations occur and fix, in populations of lytic viruses whose growth is controlled by periodic population bottlenecks. Our model predicts that substitution rates, and by extension adaptation rates, are profoundly affected by the survival of infected host cells at the bottleneck. In particular, we find that direct transfer (or environmental) bottlenecks, in which some fraction of both free virus and host cells are preserved, are associated with relatively slow adaptation rates for the virus. In contrast, viruses can adapt much more quickly when only free virus is transferred to a new host population, as is typical in an epidemiological setting. Finally, when premature lysis of the host-cell population is induced at the bottleneck, we predict that adaptation rates for the virus will, in general, be faster still. These results hold irrespective of the life-history trait affected by the beneficial mutation. The substitution rates in the presence of environmental bottlenecks are predicted to be as much as an order of magnitude lower than in the other two cases.

Continua of specificity and virulence in plant host-pathogen interactions: causes and consequences

Ecological, evolutionary and molecular models of interactions between plant hosts and microbial pathogens are largely based around a concept of tightly coupled interactions between species pairs. However, highly pathogenic and obligate associations between host and pathogen species represent only a fraction of the diversity encountered in natural and managed systems. Instead, many pathogens can infect a wide range of hosts, and most hosts are exposed to more than one pathogen species, often simultaneously. Furthermore, outcomes of pathogen infection vary widely because host plants vary in resistance and tolerance to infection, while pathogens are also variable in their ability to grow on or within hosts. Environmental heterogeneity further increases the potential for variation in plant host-pathogen interactions by influencing the degree and fitness consequences of infection. Here, we describe these continua of specificity and virulence inherent within plant host-pathogen interactions. Using this framework, we describe and contrast the genetic and environmental mechanisms that underlie this variation, outline consequences for epidemiology and community structure, explore likely ecological and evolutionary drivers, and highlight several key areas for future research.

Genomic evolution in a virus under specific selection for host recognition

Genetic variation in viral structural proteins is often explained by evolutionary escape of strong host defenses through processes such as immune evasion, host switching, and tissue tropism. An understanding of the mechanisms driving evolutionary change in virus surface proteins is key to designing effective intervention strategies to disease emergence. This study investigated the predictability of virus genomic evolution in response to highly specific differences in host receptor structure. The bacteriophage PhiX174 was evolved on three E. coli mutant hosts, each differing only by a single sugar group in the lipopolysaccharides, used for phage attachment. Large phage populations were used in order to maximize the amount of sequence space explored by mutation, and thus the potential for parallel evolution. Repeatability was assessed by genome sequencing of multiple isolates from endpoint populations and by fitness of the endpoint population relative to its ancestor. Evolutionary lines showed similar magnitudes of fitness increase between treatments. Only one mutation, occurring in the internal DNA pilot protein H, was completely repeatable, and it appeared to be a necessary stepping stone toward further adaptive change. Substitutions in the surface accessible major capsid protein F appeared to be involved in capsid stability rather than specific interactions with host receptors, suggesting that non-specific alterations to capsid structure could be an important component of adaptation to novel hosts. 33% of mutations were synonymous and showed evidence of selection on codon usage. Lastly, results supported previous findings that evolving populations of small ssDNA viruses may maintain relatively high levels of genetic variation.

Robustness promotes evolvability of thermotolerance in an RNA virus

BACKGROUND

The ability for an evolving population to adapt to a novel environment is achieved through a balance of robustness and evolvability. Robustness is the invariance of phenotype in the face of perturbation and evolvability is the capacity to adapt in response to selection. Genetic robustness has been posited, depending on the underlying mechanism, to either decrease the efficacy of selection, or increase the possibility of future adaptation. However, the true effect of genetic robustness on evolvability in biological systems remains uncertain.

RESULTS

Here we demonstrate that genetic robustness increases evolvability of thermotolerance in laboratory populations of the RNA virus phi6. We observed that populations founded by robust clones evolved greater resistance to heat shock, relative to populations founded by brittle (less-robust) clones. Thus, we provide empirical evidence for the idea that robustness can promote evolvability in this environment, and further suggest that evolvability can arise indirectly via selection for robustness, rather than through direct selective action.

CONCLUSION

Our data imply that greater tolerance of mutational change is associated with virus adaptability in a new niche, a finding generally relevant to evolutionary biology, and informative for elucidating how viruses might evolve to emerge in new habitats and/or overcome novel therapies.

On the scent of speciation: the chemosensory system and its role in premating isolation

Chemosensory speciation is characterized by the evolution of barriers to genetic exchange that involve chemosensory systems and chemical signals. Here, we review some representative studies documenting chemosensory speciation in an attempt to evaluate the importance and the different aspects of the process in nature and to gain insights into the genetic basis and the evolutionary mechanisms of chemosensory trait divergence. Although most studies of chemosensory speciation concern sexual isolation mediated by pheromone divergence, especially in Drosophila and moth species, other chemically based behaviours (habitat choice, pollinator attraction) can also play an important role in speciation and are likely to do so in a wide range of invertebrate and vertebrate species. Adaptive divergence of chemosensory traits in response to factors such as pollinators, hosts and conspecifics commonly drives the evolution of chemical prezygotic barriers. Although the genetic basis of chemosensory speciation remains largely unknown, genomic approaches to chemosensory gene families and to enzymes involved in biosynthetic pathways of signal compounds now provide new opportunities to dissect the genetic basis of these complex traits and of their divergence among taxa.

Molecular evidence of a peripatric origin for two sympatric species of field crickets (Gryllus rubens and G. texensis) revealed from coalescent simulations and population genetic tests

Species pairs that differ primarily in characters involved in mating interactions and are largely sympatric raise intriguing questions about the mode of speciation. When species divergence is relatively recent, the footprint of the demographic history during speciation might be preserved and used to reconstruct the biogeography of species divergence. In this study, patterns of genetic variation were examined throughout the geographical range of two cryptic sister taxa of field crickets, Gryllus texensis and G. rubens; mitochondrial cytochrome oxidase I (COI) was sequenced in 365 individuals sampled from 48 localities. Despite significant molecular divergence between the species, they were not reciprocally monophyletic. We devised several analyses to statistically explore what historical processes might have given rise to this genealogical structure. The analyses indicated that the biogeographical pattern of genetic variation does not support a model of recent gene flow between species. Instead, coalescent simulations suggested that the genealogical structure within G. texensis, namely a deep split between two geographically overlapping clades, reflects historical substructure within G. texensis. Additional tests that consider the concentration of G. rubens haplotypes in one of the two G. texensis genetic clusters suggest a model of speciation in which G. rubens was derived from one lineage of a geographically subdivided ancestor. These results indicate that, despite the contemporary sympatry of G. texensis and G. rubens, the data are indicative of an peripatric origin in which G. rubens was derived from one of the two historical partitions in the species currently recognized as G. texensis. This proposed model of species divergence suggests how the interplay of geography and selection may give rise to new species, although this requires testing with multilocus data. Specifically, the model highlights how that geographical partitioning of ancestral variation in the past may augment the selectively driven divergence of characters involved in the reproductive isolation of the species today.

Fungal viral mutualism moderated by ploidy

Endosymbionts and their hosts have inherently ambiguous relationships as symbionts typically depend upon their hosts for shelter, nutrition, and reproduction. Endosymbionts can acquire these needs by two alternative strategies: exploitation and cooperation. Parasites exploit hosts to advance their own reproduction at the cost of host fitness. In contrast, mutualists increase their reproductive output by increasing host fitness. Very often the distinction between parasites and mutualists is not discrete but rather contingent on the environment in which the interaction occurs, and can shift along a continuous scale from parasitism to mutualism. The cost benefit dynamics at any point along this continuum are of particular interest as they establish the likelihood of an interaction persisting or breaking down. Here we show how the interaction between the yeast Saccharomyces cerevisiae and an endosymbiotic killer virus is strongly dependent on both host ploidy and environmental pH. Additionally we elucidate the mechanisms underlying the ploidy-dependent interaction. Understanding these dynamics in the short-term is key to understanding how genetic and environmental factors impact community diversity.

Adaptive plasmid evolution results in host-range expansion of a broad-host-range plasmid

Little is known about the range of hosts in which broad-host-range (BHR) plasmids can persist in the absence of selection for plasmid-encoded traits, and whether this "long-term host range" can evolve over time. Previously, the BHR multidrug resistance plasmid pB10 was shown to be highly unstable in Stenotrophomonas maltophilia P21 and Pseudomonas putida H2. To investigate whether this plasmid can adapt to such unfavorable hosts, we performed evolution experiments wherein pB10 was maintained in strain P21, strain H2, and alternatingly in P21 and H2. Plasmids that evolved in P21 and in both hosts showed increased stability and decreased cost in ancestral host P21. However, the latter group showed higher variability in stability patterns, suggesting that regular switching between distinct hosts hampered adaptive plasmid evolution. The plasmids evolved in P21 were also equally or more stable in other hosts compared to pB10, which suggested true host-range expansion. The complete genome sequences of four evolved plasmids with improved stability showed only one or two genetic changes. The stability of plasmids evolved in H2 improved only in their coevolved hosts, not in the ancestral host. Thus a BHR plasmid can adapt to an unfavorable host and thereby expand its long-term host range.