The Red Queen hypothesis proposes that coevolution of interacting species (such as hosts and parasites) should drive molecular evolution through continual natural selection for adaptation and counter-adaptation 1-3 . Although the divergence observed at some host-resistance 4-6 and parasiteinfectivity 7-9 genes is consistent with this, the long time periods typically required to study coevolution have so far prevented any direct empirical test. Here we show, using experimental populations of the bacterium Pseudomonas fluorescens SBW25 and its viral parasite, phage Φ2 (refs 10, 11), that the rate of molecular evolution in the phage was far higher when both bacterium and phage coevolved with each other than when phage evolved against a constant host genotype. Coevolution also resulted in far greater genetic divergence between replicate populations, which was correlated with the range of hosts that coevolved phage were able to infect. Consistent with this, the most rapidly evolving phage genes under coevolution were those involved in host infection. These results demonstrate, at both the genomic and phenotypic level, that antagonistic coevolution is a cause of rapid and divergent evolution, and is likely to be a major driver of evolutionary change within species.

Recent cases of emergent diseases have renewed interest in the evolutionary and ecological mechanisms that promote parasite adaptation to novel hosts [1-6]. Crucial to adaptation is the degree of mixing of original, susceptible hosts, and novel hosts. An increase in the frequency of the original host has two opposing effects on adaptation: an increase in the supply of mutant pathogens with improved performance on the novel host [7-9]; and reduced selection to infect novel hosts, caused by fitness costs commonly observed to be associated with host switching [10-17]. The probability of disease emergence will therefore peak at intermediate frequencies of the original host. We tested these predictions by following the evolution of a virus grown under a range of different frequencies of susceptible (original) and resistant (novel) host bacteria. Viruses that evolved to infect resistant hosts were only detected when susceptible hosts were at frequencies between 0.1% and 1%. Subsequent experiments supported the predictions that there was reduced selection and mutation supply at higher and lower frequencies, respectively. These results suggest that adaptation to novel hosts can occur only under very specific ecological conditions, and that small changes in contact rates between host species might help to mitigate disease emergence.

Coinfection of parasite genotypes can select for various changes in parasite life history strategies relative to single genotype infections, with consequences for disease dynamics and severity. However, even where coinfection is common, a parasite genotype is also likely to regularly experience single genotype infections over relatively short periods of evolutionary time, due to chance, changes in local disease transmission, and parasite population structuring. Such alternating conditions between single genotype and coinfections will impose conflicting pressures on parasites, potentially selecting for facultative responses to coinfection. Although such adaptive phenotypic plasticity in response to social environment has been observed in protozoan parasites and viruses, here we show it evolving in real time in response to coinfection under conditions in which both single infections and coinfections are common. We experimentally evolved an obligate-killing virus under conditions of single virus infections (single lines) or a mix of single infections and coinfections (mixed lines) and found mixed lines to evolve a plastic lysis time: they killed host cells more rapidly when coinfecting than when infecting alone. This behavior resulted in high fitness under both infection conditions. Such plasticity has important consequences for the epidemiology of infectious diseases and the evolution of cooperation.

Disturbance, productivity, and natural enemies are significant determinants of the evolution of diversity, but their interactive effect remains unresolved. We develop a simple, qualitative model assuming trade-offs between growth rate, competitive ability and parasite resistance, to address the interactive effects of these variables on the evolution of host diversity. Consistent with previous studies our model predicts maximum diversity at intermediate levels of disturbance and productivity in the absence of parasitism. However, parasites break down these unimodal diversity relationships with productivity and disturbance, as selection for parasite resistance reduces the importance of growth rate-competitive ability trade-offs. We tested these predictions using the bacterium Pseudomonas fluorescens, which undergoes an adaptive radiation into spatial niche specialists under laboratory conditions. This is the first study of adaptive radiation in response to experimental manipulation of the three-way interaction between productivity, disturbance, and natural enemies. As hypothesized, unimodal diversity relationships with disturbance and productivity were weakened or disappeared in the presence of parasitic phages. This was the result of phages increasing diversity at environmental extremes, by imposing selection for phage-resistant variants, but decreasing diversity in less stressful environments, probably through reductions in resource competition. Phages had a net effect of increasing host diversity. Parasites and other natural enemies are therefore likely to have a large effect in mitigating the influence of other environmental variables on the evolution and maintenance of diversity.

Summary1. The hypothesis that multiple infections might disrupt or alter the density-dependent processes regulating a host-pathogen interaction is explored using time series from a well-known laboratory insect-pathogen model system. 2. We compare the population dynamics of the same host ( Plodia interpunctella ) infected with a single (granulovirus) or multiple (granulovirus and nucleopolyhedrovirus) pathogens and show how the dynamical fluctuations are altered by the presence of this second pathogen. 3. Using a maximum likelihood-based approach, we explore the density-dependent mechanisms underpinning the host-pathogen interaction. These regulatory processes differ between single and multiple infections. In singly infected systems, the density-dependent mechanisms of regulation operate through birth rate while in doubly infected systems, density dependence is mediated through death rate. 4. Further, these deterministic dynamics are modulated by the effects of demographic stochasticity. This stochastic process, the overall sum of individual probabilities of births, deaths and infection influence the changes in population size. In the Plodiagranulovirus system, nonlinear density-dependent births coupled with demographic noise is the necessary prerequisite for the observed dynamics. In the multiple infection system, noise acts together with disease transmission and mortality to affect the population dynamics. 5. We discuss the implication of these differing regulatory processes in the different-sized species assemblages in the presence of noise for understanding the ecologies of host-pathogen interactions.