A coevolutionary arms race causes ecological speciation in crossbills

We examined three ecological factors potentially causing premating reproductive isolation to determine whether divergent selection as a result of coevolution between South Hills crossbills (Loxia curvirostra complex) and Rocky Mountain lodgepole pine (Pinus contorta latifolia) promotes ecological speciation. One factor was habitat isolation arising because of enhanced seed defenses of lodgepole pine in the South Hills. This caused the crossbill call types (morphologically and vocally differentiated forms) adapted to alternative resources to be rare. Another occurred when crossbills of other call types moved into the South Hills late in the breeding season and feeding conditions were deteriorating so that relatively few non-South Hills crossbills bred ("immigrant infecundity"). Finally, among those crossbills that bred, pairing was strongly assortative by call type (behavioral isolation). Total reproductive isolation between South Hills crossbills and the two other crossbills most common in the South Hills (call types 2 and 5) summed to .9975 and .9998, respectively, on a scale of 0 (no reproductive isolation) to 1 (complete reproductive isolation). These extremely high levels of reproductive isolation indicate that the divergent selection resulting from the coevolutionary arms race between crossbills and lodgepole pine is causing the South Hills crossbill to speciate.     

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.     

The role of female investment in a sexual arms race

Forced copulations are common among waterfowl species (Anatidae), a group with relatively large eggs and very precocial young. They can be viewed as the outcome of an overt sexual conflict, and an evolutionary arms race between the sexes. We examined the female choice hypothesis suggested, but not properly tested by Briskie and Montgomerie (1997) and Montgomerie and Briskie (2007), that penis size in male ducks might correlate with female investment in eggs, predicting that in species where females lay larger eggs, penis size might be larger, because females would be more reluctant to abandon their eggs if forced to copulate. A larger data set than in earlier studies enabled us to test that hypothesis in a comparative way. Our results compelled us to reject the female choice hypothesis since egg size is negatively correlated with penis length and the number of vaginal spirals, both being seen as adaptations to frequent forced copulations. The apparent trade-off between egg size and morphological defences (vaginal spirals) is strong particularly among monogamous species. Overall, we conclude that factors that set a lower limit for egg size constrain the morphological defences of females and the arms race between the sexes in waterfowl.     

A genetic interaction network model of a complex neurological disease

Absence epilepsy (AE) is a complex, heritable disease characterized by a brief disruption of normal behavior and accompanying spike‐wave discharges (SWD) on the electroencephalogram. Only a handful of genes has been definitively associated with AE in humans and rodent models. Most studies suggest that genetic interactions play a large role in the etiology and severity of AE, but mapping and understanding their architecture remains a challenge, requiring new computational approaches. Here we use combined analysis of pleiotropy and epistasis (CAPE) to detect and interpret genetic interactions in a meta‐population derived from three C3H × B6J strain crosses, each of which is fixed for a different SWD‐causing mutation. Although each mutation causes SWD through a different molecular mechanism, the phenotypes caused by each mutation are exacerbated on the C3H genetic background compared with B6J, suggesting common modifiers. By combining information across two phenotypic measures – SWD duration and frequency – CAPE showed a large, directed genetic network consisting of suppressive and enhancing interactions between loci on 10 chromosomes. These results illustrate the power of CAPE in identifying novel modifier loci and interactions in a complex neurological disease, toward a more comprehensive view of its underlying genetic architecture.     

Direct evidence for the cell surface location of a protease-inhibitor complex on intact leukaemia cells

The interaction of a protease with two fluorescent inhibitors has been studied using intact fixed leukaemia cells as the source of the membrane bound enzyme. Fresh rat leukaemia cells were disrupted and the cytosol collected; this extract was known to contain a protein inhibitor of guanidinobenzoatase (GB) associated with leukaemia cells. All the cytosolic proteins were derivatised with Texas red acid chloride. Leukaemia cells with latent GB failed to bind the Texas red inhibitor protein but did so after activation of GB. Competition experiments with 9-amino acridine (a fluorescent marker for the active site of GB) demonstrated that the Texas red-inhibitor protein could only bind to intact leukaemia cells when the active centre of GB was not already occupied by 9-amino acridine. This competition between these two fluorescent inhibitors demonstrated their specificity for GB. The use of intact leukaemia cells and the high molecular weight of the inhibitor protein precludes the possibility of any interaction between GB and inhibitor within the cells. It is concluded that GB and the GB-inhibitor complex of latent GB are located on the external surface of intact leukaemia cells.     

Melittin-GM1 interaction: a model for a side-by-side complex

We report here the interaction of melittin with ganglioside GM1 by steady-state fluorescence, one-dimensional (1)H NMR spectroscopy and molecular modeling. In the presence of GM1 the emission maximum of melittin is blue shifted and fluorescence quenching efficiencies of iodide and acrylamide are substantially reduced, indicating a shielding of tryptophan of melittin from aqueous environment. Significant line broadening of NMR resonances of melittin, suggestive of motional restriction, is observed. Molecular modeling indicates a melittin-GM1 complex with N-terminal hydrophobic stretch of melittin associating with the ceramide tail and C-terminal hydrophilic end of melittin having favorable electrostatic interaction with the carbohydrate head group of GM1.     

Adaptive molecular evolution for 13,000 phage generations: a possible arms race

Bacteriophage phiX174 was evolved on a continuous supply of sensitive hosts for 180 days ( approximately 13,000 phage generations). The average rate of nucleotide substitution was nearly 0.2% (11 substitutions)/20 days, and, surprisingly, substitutions accumulated in a clock-like manner throughout the study, except for a low rate during the first 20 days. Rates of silent and missense substitutions varied over time and among genes. Approximately 40% of the 71 missense changes and 25% of the 58 silent changes have been observed in previous adaptations; the rate of parallel substitution was highest in the early phase of the evolution, but 7% of the later changes had evolved in previous studies of much shorter duration. Several lines of evidence suggest that most of the changes were adaptive, even many of the silent substitutions. The sustained, high rate of adaptive evolution for 180 days defies a model of adaptation to a constant environment. We instead suggest that continuing molecular evolution reflects a potentially indefinite arms race, stemming from high levels of co-infection and the resulting conflict among genomes competing within the same cell.     

A coalescent model of recombination hotspots

Recent experimental findings suggest that the assumption of a homogeneous recombination rate along the human genome is too naive. These findings point to block-structured recombination rates; certain regions (called hotspots) are more prone than other regions to recombination. In this report a coalescent model incorporating hotspot or block-structured recombination is developed and investigated analytically as well as by simulation. Our main results can be summarized as follows: (1) The expected number of recombination events is much lower in a model with pure hotspot recombination than in a model with pure homogeneous recombination, (2) hotspots give rise to large variation in recombination rates along the genome as well as in the number of historical recombination events, and (3) the size of a (nonrecombining) block in the hotspot model is likely to be overestimated grossly when estimated from SNP data. The results are discussed with reference to the current debate about block-structured recombination and, in addition, the results are compared to genome-wide variation in recombination rates. A number of new analytical results about the model are derived.     

The phage-host arms race: shaping the evolution of microbes

Bacteria, the most abundant organisms on the planet, are outnumbered by a factor of 10 to 1 by phages that infect them. Faced with the rapid evolution and turnover of phage particles, bacteria have evolved various mechanisms to evade phage infection and killing, leading to an evolutionary arms race. The extensive co-evolution of both phage and host has resulted in considerable diversity on the part of both bacterial and phage defensive and offensive strategies. Here, we discuss the unique and common features of phage resistance mechanisms and their role in global biodiversity. The commonalities between defense mechanisms suggest avenues for the discovery of novel forms of these mechanisms based on their evolutionary traits.     

A proposed molecular model for the interaction of calcineurin with the cyclosporin A-cyclophilin A complex.

Cyclosporin A (CsA) and FK506 are potent natural product immunosuppressants that induce their biological effects by forming an initial complex with cytosolic proteins termed immunophilins. These drug immunophilin complexes then bind to and inhibit the serine/threonine protein phosphatase calcineurin (CN). Two classes of immunophilin have been identified with cyclophilins (CyP's) being proteins specifically binding CsA and FKBPs specifically binding FK506. Solution and crystal structures of various CsA-CyP and FK506-FKBP complexes have been determined and show no apparent structural similarity between the two classes of drug protein complexes. These findings raise the question as to how, given their structural differences, these two complexes can both inhibit CN. While the crystal structure of the FK506-FKBP12-CN complex has been reported, no structure for a CsA-CyP CN complex has been determined. Here are reported studies that use various modelling strategies to construct a model for the interaction of the cyclosporin A- cyclophilin A complex with calcineurin. The first stage of constructing this model consisted of using conformational comparison of CsA and FK506, GRID and GROUP analysis and restrained molecular dynamics to dock CsA into the FK506 binding site of the FK506-FKBP12-CN structure. An initial model for the CsA-CyPA-CN complex was then constructed by superimposing the structure of the CsA-CyPA complex onto the docked CsA molecule. This model was then optimised with molecular dynamics simulations run on sterically clashing regions. The validity of the model for the CsA-CyPA-CN complex was then examined with respect to the effect of chemical modifications to CsA and amino acid substitutions within CyPA on the ability of the drug-immunophilin complex to inhibit calcineurin.     

A model for the C5a receptor and for its interaction with the ligand [corrected]

A model of the C5a receptor was built based on the assumption that the seven membrane-spanning helices of known inward/outward direction are in an arrangement roughly similar to that in bacteriorhodopsin. Guidelines for the positioning of the helices were cysteine pairing, 'ridges into grooves' interdigitation of side chains and aromatic cluster formation. The chain segments protruding from the membrane are too short for folding into an independent ectodomain. The only longer segment (179-202) is tied down in its centre onto the membrane by a disulphide bridge and, thereby, made into two short loops as well. Ideas of the interaction of the C5a receptor with its ligand were derived mainly from the search for accommodation of the functionally essential arginine residues 40 and 74 of C5a. Asp82 is the only charged residue in a pocket approximately 20 A below the receptor surface and is conserved in the rhodopsin superfamily. It commends itself for binding Arg74 which is the tip of the flexible C-terminal chain of C5a, and rules out Arg40 in the structurally well-defined part of the molecule. The latter may bind to Glu180 at the bottom of a more shallow pocket which happens to resemble the substrate-binding site of trypsin.     

A systems biology approach for detecting toxicity-related hotspots inside protein interaction networks

Drug-induced neutropenia can be fatal when severe and therefore requires an improved understanding of its mechanism(s) of toxicity. Systems biology provides an opportunity to understand adverse events after drug administration using analysis of biomolecular networks. In this study, a human protein interaction network was analyzed to identify proteins that are most central to topological paths connecting a drug's target proteins to hematopoiesis-related proteins. For a set of non-immune neutropenia inducing drugs, 9 proteins were found to be common to putative signaling paths across all drugs evaluated. All 9 proteins showed relevance to neutrophil biology. Geneset enrichment analysis showed that proteins associated with cancer-related processes such as apoptosis provide topological linkages between drug targets and proteins involved in neutrophil production. The algorithm can be applied towards analysis of any toxicity where the drugs and the physiological processes involved in the toxic mechanism are known.     

Metapopulation structure of a seed-predator weevil and its host plant in arms race coevolution

Although the importance of gene flow in the geographic structuring of host-parasite interactions has been well discussed, little is known about how dispersal drives the spatial dynamics of other types of coevolutionary interactions in nature. We evaluated the roles of gene flow in the geographically structured processes of a predator-prey arms race involving a seed-predatory weevil with a long mouthpart and its host camellia plant with a thick fruit coat. Molecular genetic analyses showed that both weevil and camellia populations were structured at a spatial scale of several kilometers. Importantly, the spatial pattern of the migration of weevils, but not that of camellias, imposed significant effects on the geographic configuration of the levels of coevolutionary escalation. This result suggests that even if migration is limited in one species (camellia), local coevolution with the other species that migrates between neighboring localities (weevil) can reduce the interpopulation difference in the local adaptive optima of the former species. Thus, gene flow of a species potentially homogenizes the local biological environments provided by the species and thereby promotes the evolutionary convergence of its coevolving counterparts. Consequently, by focusing on coevolutionary interactions in natural communities, "indirect" effects of gene flow on the adaptive divergence of organisms could be identified.     

A simple model for the dynamics of a host-parasite-hyperparasite interaction

Hyperparasites can play a crucial role in the control of a host-parasite interaction if they are successfully established in the community. We investigated the specific traits of the hyperparasite and those of the release event which allow a successful regulation of primary parasite populations. This study has been motivated by the case study of chestnut-Cryphonectria parasitica-Cryphonectria Hypovirus interaction. We use a model of SIR/SIS type which assumes a limited diffusion of the parasite. Our model emphasizes the thresholds for invasion linked to the ecological specificities of both the pathogen and the hyperparasite (transmission rates and virulence) and to the initial conditions of the system (population sizes of the different categories). The predictions are consistent with data on the observed spread of the virus. "Mild" strains of the hyperparasite, characterized by a high vertical transmission rate and low virulence, are more prone to establish than "severe" strains. It also demonstrates that the horizontal transmission of the virus, which is controlled by a vegetative incompatibility system in the fungus, is not the unique constraint for the virus establishment. This study may contribute to theoretical and practical aspects of the biological control of plant diseases with a hyperparasite and to the ecology of biological invasions.     

The limits of adaptation: humans and the predator-prey arms race

In the history of life, species have adapted to their consumers by evolving a wide variety of defenses. By contrast, animal species harvested in the wild by humans have not adapted structurally. Nonhuman predators have high failure rates at one or more stages of an attack, indicating that victim species have spatial refuges or phenotypic defenses that permit further functional improvement. A new compilation confirms that species in the wild cannot achieve immunity from human predation with structural defenses. The only remaining options are to become undesirable or to live in or escape to places where harvesting by people is curtailed. Escalation between prey defenses and predators' weapons may be restricted under human dominance to interactions involving those low-level predators that have benefited from human overexploitation of top consumers.     

A chemical level in the coevolutionary arms race between an ant social parasite and its hosts

Here we investigate the coevolutionary interactions between the slavemaking ant Protomognathus americanus and its Temnothorax hosts on a chemical level. We show that, although this social parasite is principally well-adapted to its hosts' cuticular hydrocarbon profile, there are pronounced differences in the fine-tuning of this adaptation. Between populations, chemical adaptation varies with host community composition, as the parasite faces a trade-off when confronted with more than one host species. In addition to adaptation of its own chemical signature, the slavemaker causes a reciprocal adjustment in its slaves' cuticular profile, the degree of which depends on the slave species. On the host side, successful parasite defence requires efficient enemy recognition, and in behavioural aggression trials, host colonies could indeed discriminate between invading slaves, which commonly accompany slavemakers on raids, and free-living conspecifics. Furthermore, hosts shifted their acceptance threshold over the seasons, presumably to reduce the costs of defence.