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PubMed2005

Selective advantage for conservative viruses.

In this article we study the full semiconservative treatment of a model for the coevolution of a virus and an adaptive immune system. Regions of viability are calculated for both conservatively and semiconservatively replicating viruses interacting with a realistic semiconservatively replicating immune system. The conservative virus is found to have a selective advantage in the form of an ability to survive in regions with a wider range of mutation rates than its semiconservative counterpart, as well as an increased replication rate where both species can survive. This may help explain the existence of a rich range of viruses with conservatively replicating genomes, a trait that is found nowhere else in nature.

Adaptation, Physiological↗

PubMed2005

Coevolutionary dynamics on scale-free networks.

We investigate Bak-Sneppen coevolution models on scale-free networks with various degree exponents gamma including random networks. For gamma>3 , the critical fitness value f(c) approaches a nonzero finite value in the limit N --> infinity, whereas f(c) approaches zero as 2 (N) on the networks with size N. The avalanche size distribution P (s) shows the normal power-law behavior for gamma>3. In contrast, P (s) for 2 tau(2) ). The origin of the two power regimes is explained by the dynamics on an artificially made star-linked network.

Journal Article↗

PubMed2005

Epidemic spreading and cooperation dynamics on homogeneous small-world networks.

We introduce a class of small-world networks--homogeneous small-worlds--which, in contrast with the well-known Watts-Strogatz small-worlds, exhibit a homogeneous connectivity distribution, in the sense that all nodes have the same number of connections. This feature allows the investigation of pure small-world effects, detached from any associated heterogeneity. Furthermore, we use at profit the remarkable similarity between the properties of homogeneous small worlds and the heterogeneous small-worlds of Watts-Strogatz to assess the separate roles of heterogeneity and small-world effects. We investigate the dependence on these two mechanisms of the threshold for epidemic outbreaks and also of the coevolution of cooperators and defectors under natural selection. With respect to the well-studied regular homogeneous limits, we find a subtle interplay between these mechanisms. While they both contribute to reduce the threshold for an epidemic outburst, they exhibit opposite behavior in the evolution of cooperation, such that the overall results mask the true nature of their individual contribution to this process.

Journal Article↗

PubMed1996

The Arabidopsis profilin gene family. Evidence for an ancient split between constitutive and pollen-specific profilin genes.

Profilin is a ubiquitous eukaryotic protein that regulates the actin cytoskeleton and recently has been identified as a potent allergen in pollen. We examined the profilin gene family in the model plant, Arabidopsis thaliana, and found that it contained approximately 8 to 10 members. Four distinct profilin sequences, three cDNAs, PRF1, PRF2, and PRF3, and two genomic clones, PRF1 and PRF4, were isolated and characterized. These genes encoded four distinct profilin isoforms of 131 to 134 amino acids. Northern and reverse-transcriptase polymerase chain reaction analyses demonstrated that Arabidopsis PRF1 was expressed in all major plant organs, whereas PRF4 was specifically expressed in mature pollen. Gene trees constructed from amino acid sequence data revealed the presence of two ancient, distinct profilin gene classes in plants. PRF4 was in a class with previously identified pollen-specific profilins from monocot and dicot species. PRF1, PRF2, PRF3, and a distant dicot sequence formed a separate novel class, suggesting an ancient separation of plant profilins based on regulation and perhaps function. The coevolution of plant actin and profilin classes with similar patterns of expression is discussed. The similarity of plant, fungal, protist, insect, and nematode profilins and their extreme divergence from the vertebrate profilins has striking implications for the evolution of fungal-spore- and plant-pollen-profilins as allergens.

Allergens↗

PubMed2005

Visual learning by coevolutionary feature synthesis.

In this paper, a novel genetically inspired visual learning method is proposed. Given the training raster images, this general approach induces a sophisticated feature-based recognition system. It employs the paradigm of cooperative coevolution to handle the computational difficulty of this task. To represent the feature extraction agents, the linear genetic programming is used. The paper describes the learning algorithm and provides a firm rationale for its design. Different architectures of recognition systems are considered that employ the proposed feature synthesis method. An extensive experimental evaluation on the demanding real-world task of object recognition in synthetic aperture radar (SAR) imagery shows the ability of the proposed approach to attain high recognition performance in different operating conditions.

Algorithms↗

PubMed2004

The folding landscape of Streptomyces griseus protease B reveals the energetic costs and benefits associated with evolving kinetic stability.

Like most extracellular bacterial proteases, Streptomyces griseus protease B (SGPB) and alpha-lytic protease (alphaLP) are synthesized with covalently attached pro regions necessary for their folding. In this article, we characterize the folding free energy landscape of SGPB and compare it to the folding landscapes of alphaLP and trypsin, a mammalian homolog that folds independently of its zymogen peptide. In contrast to the thermodynamically stable native state of trypsin, SGPB and alphaLP fold to native states that are thermodynamically marginally stable or unstable, respectively. Instead, their apparent stability arises kinetically, from unfolding free energy barriers that are both large and highly cooperative. The unique unfolding transitions of SGPB and alphaLP extend their functional lifetimes under highly degradatory conditions beyond that seen for trypsin; however, the penalty for evolving kinetic stability is remarkably large in that each factor of 2.4-8 in protease resistance is accompanied by a cost of ~10(5) in the spontaneous folding rate and ~5-9 kcal/mole in thermodynamic stability. These penalties have been overcome by the coevolution of increasingly effective pro regions to facilitate folding. Despite these costs, kinetic stability appears to be a potent mechanism for developing native-state properties that maximize protease longevity.

Amino Acid Sequence↗

PubMed2004

Disabling the folding catalyst is the last critical step in alpha-lytic protease folding.

Alpha-Lytic protease (alphaLP) is an extracellular bacterial pro-protease marked by extraordinary conformational rigidity and a highly cooperative barrier to unfolding. Although these properties successfully limit its proteolytic destruction, thereby extending the functional lifetime of the protease, they come at the expense of foldability (t(1/2) = 1800 yr) and thermodynamic stability (native alphaLP is less stable than the unfolded species). Efficient folding has required the coevolution of a large N-terminal pro region (Pro) that rapidly catalyzes alphaLP folding (t(1/2) = 23 sec) and shifts the thermodynamic equilibrium in favor of folded protease through tight native-state binding. Release of active alphaLP from this stabilizing, but strongly inhibitory, complex requires the proteolytic destruction of Pro. alphaLP is capable of initiating Pro degradation via cleavage of a flexible loop within the Pro C-terminal domain. This single cleavage event abolishes Pro catalysis while maintaining strong native-state binding. Thus, the loop acts as an Achilles' heel by which the Pro foldase machinery can be safely dismantled, preventing Pro-catalyzed unfolding, without compromising alphaLP native-state stability. Once the loop is cleaved, Pro is rapidly degraded, releasing active alphaLP.

Binding Sites↗

PubMed2000

Disease, frequency-dependent selection, and genetic polymorphisms: experiments with stripe rust and wheat.

Pathogens have the potential to maintain genetic polymorphisms by creating frequency-dependent selection on their host. This can occur when a rare host genotype is less likely to be attacked by a pathogen (frequency-dependent disease attack) and has higher fitness at low frequency (negative frequency-dependent selection). In this study, we used wheat genotypes that were susceptible to different races of the pathogen Puccinia striiformis to test whether disease created frequency-selection on its host and whether such selection could maintain polymorphisms for resistance genes in the wheat populations. Four different two-way mixtures of wheat genotypes were planted at different frequencies in both the presence and absence of disease. Disease created frequency-dependent selection on its host in some populations. Unknown factors other than disease also created frequency-dependent selection in this system because, in some instances, rare genotype advantage was observed in the absence of disease. Although the pathogen created frequency-dependent selection on its host, this selection was not sufficient to maintain genetic polymorphism in the host populations. In all cases where frequency-dependent selection occurred only in the diseased plots, one of the two genotypes was predicted to dominate in the population and the same genotype was predicted to dominate in both the presence and absence of disease. Only in cases where frequency-dependent selection was not caused by disease was there evidence that genetic polymorphisms would be maintained in the population. The frequency-dependent selection described in this study is a consequence of epidemiological effects of disease and differs from the time-lagged frequency-dependent selection resulting from coevolution between hosts and parasites. The impact of this direct frequency-dependent selection on the maintenance of genetic polymorphisms in the host population is discussed.

Fungi↗

PubMed2000

Local adaptation, resistance, and virulence in a hemiparasitic plant-host plant interaction.

Coevolution may lead to local adaptation of parasites to their sympatric hosts. Locally adapted parasites are, on average, more infectious to sympatric hosts than to allopatric hosts of the same species or their fitness on the sympatric hosts is superior to that on allopatric hosts. We tested local adaptation of a hemiparasitic plant, Rhinanthus serotinus (Scrophulariaceae), to its host plant, the grass Agrostis capillaris. Using a reciprocal cross-infection experiment, we exposed host plants from four sites to hemiparasites originating from the same four sites in a common environment. The parasites were equally able to establish haustorial connections to sympatric and allopatric hosts, and their performance was similar on both host types. Therefore, these results do not indicate local adaptation of the parasites to their sympatric hosts. However, the parasite populations differed in average biomass and number of flowers per plant and in their effect on host biomass. These results indicate that the virulence of the parasite varied among populations, suggesting genetic variation. Theoretical models suggest that local adaptation is likely to be detected if the host and the parasite have different evolutionary potentials, different migration rates, and the parasite is highly virulent. In the interaction between R. serotinus and A. capillaris all the theoretical prerequisites for local adaptation may not be fulfilled.

Adaptation, Physiological↗

PubMed2001

Viability of cytochrome c genotypes depends on cytoplasmic backgrounds in Tigriopus californicus.

Because of their extensive functional interaction, mitochondrial DNA (mtDNA) and nuclear genes may evolve to form coadapted complexes within reproductively isolated populations. As a consequence of coadaptation, the fitness of particular nuclear alleles may depend on mtDNA genotype. Among populations of the copepod Tigriopus californicus, there are high levels of amino acid substitutions in both the mtDNA genes encoding subunits of cytochrome c oxidase (COX) and the nuclear gene encoding cytochrome c (CYC), the substrate for COX. Because of the functional interaction between enzyme and substrate proteins, we hypothesized that the fitness of CYC genotypes would depend on mtDNA genotype. To test this hypothesis, segregation ratios for CYC and a second nuclear marker (histone H1) unrelated to mitochondrial function were scored in F2 progeny of several reciprocal interpopulation crosses. Genotypic ratios at the CYC locus (but not the H1 locus) differed between reciprocal crosses and differed from expected Mendelian ratios, suggesting that CYC genotypic fitnesses were strongly influenced by cytoplasmic (including mtDNA) background. However, in most cases the nature of the deviations from Mendelian ratios and differences between reciprocal crosses are not consistent with simple coevolution between CYC and mtDNA background. In a cross in which both newly hatched larvae and adults were sampled, only the adult sample showed deviations from Mendelian ratios, indicating that genotypic viabilities differed. In two of six crosses, large genotypic ratio differences for CYC were observed between the sexes. These results suggest that significant variation in nuclear-mtDNA coadaptation may exist between T. californicus populations and that the relative viability of specific cytonuclear allelic combinations is somehow affected by sex.

Animals↗

PubMed2001

Colony structure of a slavemaking ant. II. Frequency of slave raids and impact on the host population.

The parasite pressure exerted by the slavemaker ant Protomognathus americanus on its host species Leptothorax longispinosus was analyzed demographically and genetically. The origin of slaves found in colonies of the obligate slavemaker was examined with nuclear and mitochondrial DNA markers to make inferences about the frequency and severity of slave raids. Relatedness of enslaved L. longispinosus workers in the same nest was very low, and our data suggest that, on average, each slavemaker nest raids six host colonies per season. Therefore, the influence of slavemaker species on their hosts is much stronger than simple numerical ratios suggest. We also found that slave relatedness was higher in small than in large slavemaker nests; thus, larger nests wield a much stronger influence on the host. We estimated that in the study population, on average, a host nest has a 50% chance of being attacked by a slavemaker colony per year. Free-living Leptothorax colonies in the vicinity of slavemaker nests did not represent the source of slaves working in P. americanus colonies, which suggests that raided nests either do not survive or migrate after being raided. Colony composition and intranest relatedness of free-living L. longispinosus colonies differed markedly between areas with slavemakers and those that are parasite-free. In the presence of slavemakers, host colonies were less likely to be polygynous and had fewer workers and a higher relatedness among worker brood. Host nests with slavemaker neighbors allocated more resources into sexuals, possibly caused by these shifts in nest demography. Finally, enslaved Leptothorax workers in P. americanus nests appeared to be less efficient than their counterparts in free-living colonies. Thus, slavemakers exert a much stronger impact on their hosts than had previously been suspected and represent an unique system to study parasite-host coevolution.

Animals↗

PubMed2001

Positive genetic correlation between parasite resistance and body size in a free-living ungulate population.

Parasite resistance and body size are subject to directional natural selection in a population of feral Soay sheep (Ovis aries) on the island of St. Kilda, Scotland. Classical evolutionary theory predicts that directional selection should erode additive genetic variation and favor the maintenance of alleles that have negative pleiotropic effects on other traits associated with fitness. Contrary to these predictions, in this study we show that there is considerable additive genetic variation for both parasite resistance, measured as fecal egg count (FEC), and body size, measured as weight and hindleg length, and that there are positive genetic correlations between parasite resistance and body size in both sexes. Body size traits had higher heritabilities than parasite resistance. This was not due to low levels of additive genetic variation for parasite resistance, but was a consequence of high levels of residual variance in FEC. Measured as coefficients of variation, levels of additive genetic variation for FEC were actually higher than for weight or hindleg length. High levels of additive genetic variation for parasite resistance may be maintained by a number of mechanisms including high mutational input, balancing selection, antagonistic pleiotropy, and host-parasite coevolution. The positive genetic correlation between parasite resistance and body size, a trait also subject to sexual selection in males, suggests that parasite resistance and growth are not traded off in Soay sheep, but rather that genetically resistant individuals also experience superior growth.

Alleles↗

PubMed2002

Outcrossing increases infection success and competitive ability: experimental evidence from a hermaphrodite parasite.

The maintenance of two genetically distinct reproductive modes such as outcrossing and selfing within a population of animals or plants is still a matter of considerable debate. Hermaphroditic parasites often reproduce either alone by selfing or in pairs by outcrossing. They can be used as a model to study potential benefits of outcrossing. Any advantage from outcrossing may be important, especially in host-parasite coevolution, but has not, to our knowledge, been studied yet in any parasite species. We studied the potential effect of outcrossing in a tapeworm, Schistocephalus solidus, on both infection success and growth in its first intermediate host, the copepod Macrocyclops albidus. Tapeworms that had been obtained from natural populations of three-spined sticklebacks (Gasterosteus aculeatus) were allowed to reproduce either alone or in pairs, in an in vitro system that replaced the final host's gut. This resulted in either selfed or outcrossed offspring, respectively. In one part of the experiment, copepods were exposed to either selfed or outcrossed parasites, in a second part to both types simultaneously, in order to study the effect of competition between them. To discriminate parasites of either origin within the same host, a novel method for fluorescent vital labeling was used. We show here for the first time that outcrossed parasites had a higher infection success and faster development in the host. This advantage of outcrossing became apparent only in the competitive situation, in which superior abilities of parasites to extract limiting resources from the host become crucial.

Animals↗

PubMed2002

Patterns of divergence in the effects of mating on female reproductive performance in flour beetles.

Sexual selection can lead to rapid divergence in reproductive characters. Recent studies have indicated that postmating events, such as sperm precedence, may play a key role in speciation. Here, we stress that other components of postmating sexual selection may be involved in the evolution of reproductive isolation. One of these is the reproductive investment made by females after mating (i.e., differential allocation). We performed an experiment designed to assess genetic divergence in the effects of mating on female reproductive performance in flour beetles, Tribolium castaneum. Females were mated to males of three different wild-type genotypes at two different frequencies, in all possible reciprocal combinations. Male genotype affected all aspects of female reproduction, through its effects on female longevity, total offspring production, reproductive rate, mating rate, and fertility. Moreover, male and female genotype interacted in their effects on offspring production and reproductive rate. We use the pattern of these interactions to discuss the evolutionary process of divergence and suggest that the pattern is most consistent with that expected if divergence was driven by sexually antagonistic coevolution. In particular, the fact that females exhibited a relatively weak response to males with which they were coevolved suggests that females have evolved resistance to male gonadotropic signals/stimuli.

Animals↗

PubMed2002

Ecological bistability and evolutionary reversals under asymmetrical competition.

How does the process of life-history evolution interplay with population dynamics? Almost all models that have addressed this question assume that any combination of phenotypic traits uniquely determine the ecological population state. Here we show that if multiple ecological equilibria can exist, the evolution of a trait that relates to competitive performance can undergo adaptive reversals that drive cyclic alternation between population equilibria. The occurrence of evolutionary reversals requires neither environmentally driven changes in selective forces nor the coevolution of interactions with other species. The mechanism inducing evolutionary reversals is twofold. First, there exist phenotypes near which mutants can invade and yet fail to become fixed; although these mutants are eventually eliminated, their transitory growth causes the resident population to switch to an alternative ecological equilibrium. Second, asymmetrical competition causes the direction of selection to revert between high and low density. When ecological conditions for evolutionary reversals are not satisfied, the population evolves toward a steady state of either low or high abundance, depending on the degree of competitive asymmetry and environmental parameters. A sharp evolutionary transition between evolutionary stasis and evolutionary reversals and cycling can occur in response to a smooth change in ecological parameters, and this may have implications for our understanding of size-abundance patterns.

Animals↗

PubMed2002

Evolution of morphological and behavioral ontogenies in females of a highly dimorphic clade of blennioid fishes.

Comparison of ontogenetic trajectories with those inferred for ancestors provides a powerful but underused tool for the study of the evolution of different types of phenotypic characters. This approach was used to study morphological and behavioral evolution of the highly dimorphic chaenopsid genus Coralliozetus (Teleostei: Blennioidei). All sexually dimorphic synapomorphies of Coralliozetus involved evolution in females only; one character evolved via terminal addition (peramorphosis), whereas six evolved via terminal deletion (paedomorphosis). Evolution of the ontogeny of two behavioral characters (microhabitat use and feeding rate), as inferred by focal animal observations of eight species of tube blennies, was also confined to females and conformed to terminal deletion. Both sexes of outgroups and males of all species of Coralliozetus exhibit an ontogenetic shift from the open as juveniles to shelters as adults. However, females of all species of Coralliozetus retain the juvenile behavior of residing in the open. Blennies residing in the open take significantly more feeding bites than conspecifics residing in shelters, consequently, female Coralliozetus retain the high feeding rate of juveniles. Several of the paedomorphic morphological features of Coralliozetus females are plausibly associated with their paedomorphosis in microhabitat use. These include their reduced conspicuousness and reduced robustness compared to conspecific males. In groups such as chaenopsids, which undergo significant ontogenetic changes in microhabitat, paedomorphosis provides a mechanism for rapid coevolution of behavior and morphology. This study, the first to document the evolution of sexual dimorphism via both behavioral and morphological paedomorphosis, demonstrates the unique insights to be gained from a multidimensional analysis of phenotypic evolution.

Animals↗

PubMed2003

Phylogenetic analysis of correlation structure in stalk-eyed flies (Diasemopsis, Diopsidae).

Morphological divergence among species may be constrained by the pattern of genetic variances and covariances among traits within species. Assessing the existence of such a relationship in nature requires information on the stability of intraspecific correlation and covariance structure and the correspondence of this structure to the pattern of evolutionary divergence within a lineage. Here, we investigate these issues for nine morphological traits and 15 species of stalk-eyed flies in the genus Diasemopsis. Within-species matrices for these traits were generated from phenotypic data for all the Diasemopsis species and from genetic data for a single Diasemopsis species, D. dubia. The among-species pattern of divergence was assessed by calculating the evolutionary correlations for all pairwise combinations of the morphological traits along the phylogeny of these species. Comparisons of intraspecific matrices reveal significant similarity among all species in the phenotypic correlations matrices but not the covariance matrices. In addition, the differences in correlation structure that do exist among species are not related to their phylogenetic placement or change in the means of the traits. Comparisons of the phenotypic and phylogenetic matrices suggest a strong relationship between the pattern of evolutionary change among species and both the intraspecific correlation structure and the stability of this structure among species. The phenotypic and the phylogenetic matrices are significantly similar, and pairs of traits whose intraspecific correlations are more stable across taxa exhibit stronger coevolution on the phylogeny. These results suggest either the existence of strong constraints on the pattern of evolutionary change or a consistent pattern of correlated selection shaping both the phenotypic and phylogenetic matrices. The genetic correlation structure for D. dubia, however, does not correspond with patterns found in the phenotypic and phylogenetic data. Possible reasons for this disagreement are discussed.

Animals↗

PubMed2003

Host-dependent genetic structure of parasite populations: differential dispersal of seabird tick host races.

Despite the fact that parasite dispersal is likely to be one of the most important processes influencing the dynamics and coevolution of host-parasite interactions, little information is available on the factors that affect it. In most cases, opportunities for parasite dispersal should be closely linked to host biology. Here we use microsatellite genetic markers to compare the population structure and dispersal of two host races of the seabird tick Ixodes uriae at the scale of the North Atlantic. Interestingly, tick populations showed high within-population genetic variation and relatively low population differentiation. However, gene flow at different spatial scales seemed to depend on the host species exploited. The black-legged kittiwake (Rissa tridactyla) had structured tick populations showing patterns of isolation by distance, whereas tick populations of the Atlantic puffin (Fratercula arctica) were only weakly structured at the largest scale considered. Host-dependent rates of tick dispersal between colonies will alter infestation probabilities and local dynamics and may thus modify the adaptation potential of ticks to local hosts. Moreover, as I. uriae is a vector of the Lyme disease agent Borrelia burgdorferi sensu lato in both hemispheres, the large-scale movements of birds and the subsequent dispersal of ticks will have important consequences for the dynamics and coevolutionary interactions of this microparasite with its different vertebrate and invertebrate hosts.

Alleles↗