CRISPR-mediated phage resistance and the ghost of coevolution past

The past is never dead. It''s not even pastWilliam Faulkner (1951)

Bacteria can acquire heritable immunity to viral (phage) enemies by incorporating phage DNA into their own genome. This mechanism of anti-viral defence, known by the acronym CRISPR, simultaneously stores detailed information about current and past enemies and the evolved resistance to them. As a high-resolution genetic marker that is intimately tied with the host–pathogen interaction, the CRISPR system offers a unique, and relatively untapped, opportunity to study epidemiological and coevolutionary dynamics in microbial communities that were previously neglected because they could not be cultured in the laboratory. We briefly review the molecular mechanisms of CRISPR-mediated host–pathogen resistance, before assessing their potential importance for coevolution in nature, and their utility as a means of studying coevolutionary dynamics through metagenomics and laboratory experimentation.     

Virus-host arms race at the joint origin of multicellularity and programmed cell death

Unicellular eukaryotes and most prokaryotes possess distinct mechanisms of programmed cell death (PCD). How an “altruistic” trait, such as PCD, could evolve in unicellular organisms? To address this question, we developed a mathematical model of the virus-host co-evolution that involves interaction between immunity, PCD and cellular aggregation. Analysis of the parameter space of this model shows that under high virus load and imperfect immunity, joint evolution of cell aggregation and PCD is the optimal evolutionary strategy. Given the abundance of viruses in diverse habitats and the wide spread of PCD in most organisms, these findings imply that multiple instances of the emergence of multicellularity and its essential attribute, PCD, could have been driven, at least in part, by the virus-host arms race.     

Modelling the evolution of common cuckoo host‐races: speciation or genetic swamping?

Co‐evolutionary arms races have provided clear evidence for evolutionary change, especially in host–parasite systems. The evolution of host‐specific races in the common cuckoo (Cuculus canorus), however, is also an example where sexual conflict influences the outcome. Cuckoo females benefit from better adaptation to overcome host defences, whereas cuckoo males face a trade‐off between the benefits of better adaptation to a host and the benefits of multiple mating with females from other host‐races. The outcome of this trade‐off might be genetic differentiation or prevention of it by genetic swamping. We use a simulation model to test which outcome is more likely with three sympatric cuckoo host‐races. We assume a cost for cuckoo chicks that express a host adaptation allele not suited to their foster host species and that cuckoo males that switch to another host‐race experience either a fitness benefit or cost. Over most of the parameter space, cuckoo male host‐race fidelity increases significantly with time, and gene flow between host‐races ceases within a few thousand to a hundred thousand generations. Our results hence support the idea that common cuckoo host‐races might be in the incipient stages of speciation.     

Abiotic heterogeneity drives parasite local adaptation in coevolving bacteria and phages

Spatial abiotic heterogeneity can result in divergent selection, hence might increase the magnitude of host-parasite local adaptation (the mean difference in fitness of sympatric vs. allopatric host-parasite combinations). We explicitly tested this hypothesis by measuring local adaptation in experimentally coevolved populations of bacteria and viruses evolved in the same or different nutrient media. Consistent with previous work, we found that mean levels of evolved phage infectivity and bacteria resistance varied with nutrient concentration, with maximal levels at nutrient concentrations that supported the greatest densities of bacteria. Despite this variation in evolved mean infectivity and resistance between treatments, we found that parasite local adaptation was greatly increased when measured between populations evolved in different, compared with the same, media. This pattern is likely to have resulted from different media imposing divergent selection on bacterial hosts, and phages in turn adapting to their local hosts. These results demonstrate that the abiotic environment can play a strong and predictable role in driving patterns of local adaptation.     

Integration of the group c phage JCL1032 of Lactobacillus delbrueckii subsp. lactis and complex phage resistance of the host

AIMS: Sequences related to Lactobacillus delbrueckii phage JCL1032 genome integration, the maintenance of lysogeny and putative immunity genes were characterized. Phenotypic changes of the JCL1032 lysogens were investigated. METHODS AND RESULTS: Integration of JCL1032 DNA into the host genome and the location of phage and bacterial attachment sites were studied by standard molecular methods. The frequency of lysogenization was 10(-7), and stable lysogeny was an even rarer phenomenon. JCL1032 integrates its genome into two distinct host genes of unknown functions. According to EOP (efficiency of plating) and adsorption tests JCL1032 lysogens showed resistance against several virulent and temperate Lactobacillus phages at different steps of phage infection. CONCLUSIONS: Temperate JCL1032 integrates its genome into bacterial DNA with exceptionally low frequency. JCL1032 lysogens express a complex phage resistance against several Lact. delbrueckii phages. An antagonistic arms race between the temperate phage and its host is proposed. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first time that the genome integration of a group c Lact. delbrueckii phage has been described. The characterized lysogens could facilitate studies on Lact. delbrueckii phage receptors and phage resistance mechanisms. The genetic information gained from this study benefits the development of integration vectors and phage resistant starters.     

Modelling the arms race in avian brood parasitism

In brood parasitism, interactions between a parasite and its host lead to a co-evolutionary process called an arms race, in which evolutionary progress on one side provokes a further response on the other side. The host evolves defensive means to reduce the impact of parasitism, while the parasite evolves means to counter the host's defence. To gain insights into the co-evolutionary process of the arms race, a model is developed and analysed, in which the host's defence and the parasite's counterdefence are assumed to be genetically determined. First, the effect of parasite counterdefence on host defence is analysed. I show that parasite counterdefence can critically affect the establishment of host defence, giving rise to three situations in the equilibrium state: The host shows (1) no defence, (2) an intermediate level of defence or (3) perfect defence. Based on these results, the evolution of parasite counterdefence is considered in connection with host defence. It is suggested that the parasite can evolve counterdefence to a certain degree, but once it has established counterdefence beyond this, the host gives up its defence against parasitism provided the defence entails some cost to perform. Dynamic aspects of selection pressure are crucial for these results. Based on these results, I propose a hypothetical evolutionary sequence in the arms race, along which interactions between the host and parasite proceed.     

Replicator-dynamics models of sexual conflict

Evolutionary conflict between the sexes has been studied in various taxa and in various contexts. When the sexes are in conflict over mating rates, natural selection favors both males that induce higher mating rates and females that are more successful at resisting mating attempts. Such sexual conflict may result in an escalating coevolutionary arms race between males and females. In this article, we develop simple replicator-dynamics models of sexual conflict in order to investigate its evolutionary dynamics. Two specific models of the dependence of a female's fitness on her number of matings are considered: in model 1, female fitness decreases linearly with increasing number of matings and in model 2, there is an optimal number of matings that maximizes female fitness. For each of these models, we obtain the conditions for a coevolutionary process to establish costly male and female traits and examine under what circumstances polymorphism is maintained at equilibrium. Then we discuss how assumptions in previous models of sexual conflict are translated to fit to our model framework and compare our results with those of the previous studies. The simplicity of our models allows us to consider sexual conflict in various contexts within a single framework. In addition, we find that our model 2 shows more complicated evolutionary dynamics than model 1. In particular, the population exhibits bistability, where the evolutionary outcome depends on the initial state, only in model 2.     

Adaptation to Host-Specific Bacterial Pathogens Drives Rapid Evolution of a Human Innate Immune Receptor

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Hawkmoths produce anti-bat ultrasound

Bats and moths have been engaged in aerial warfare for nearly 65 Myr. This arms race has produced a suite of counter-adaptations in moths, including bat-detecting ears. One set of defensive strategies involves the active production of sound; tiger moths'' ultrasonic replies to bat attack have been shown to startle bats, warn the predators of bad taste and jam their biosonar. Here, we report that hawkmoths in the Choerocampina produce entirely ultrasonic sounds in response to tactile stimulation and the playback of biosonar attack sequences. Males do so by grating modified scraper scales on the outer surface of the genital valves against the inner margin of the last abdominal tergum. Preliminary data indicate that females also produce ultrasound to touch and playback of echolocation attack, but they do so with an entirely different mechanism. The anti-bat function of these sounds is unknown but might include startling, cross-family acoustic mimicry, warning of unprofitability or physical defence and/or jamming of echolocation. Hawkmoths present a novel and tractable system to study both the function and evolution of anti-bat defences.