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PubMed2006

Inferring evolutionary signals from ecological data in a plant-pathogen metapopulation.

We followed the dynamics of local epidemics in three populations of a natural plant-pathogen system for four sequential years. We characterize the overwintering process with spatial statistics and use a stochastic, spatially explicit, modeling approach with Bayesian parameter estimation to study the spread of the infection during the growing season. Our modeling approach allows us to infer coevolutionary signals from spatiotemporal data on pathogen prevalence. Most importantly, we are able to assess the distribution of resistant hosts within the distribution of all host plants. We show that resistant hosts occur in areas with high pathogen encounter rates, and that the occurrence of resistance correlates with overwintering probability of the pathogen. The estimates for essentially all model parameters are characterized by a large amount of variation over the years and the populations. While the variation in the fraction of resistant hosts and in the force of infection is to a large extent explained by the population, the other model parameters (two parameters describing the shape of the dispersal kernel) vary essentially in an unpredictable manner, suggesting that much of the variation may occur at very fine spatial and temporal scales.

Bayes Theorem↗
PubMed1992

[Changes in the dynamics of viral infectious diseases].

Modern methods of molecular biology are suitable to analyse evolutionary processes in the area of infectious diseases. Visible expression of this evolution is the emergence of "new" infectious agents, e.g., canine parvovirus, the agent of the porcine reproductive and respiratory syndrome and phocine distemper virus. In addition a gradual change of disease syndromes may be observed, e.g., classical and African swine fever and myxoma. These processes are based on genomic changes of the respective infectious agents, i.e., point mutations and recombinations. Especially RNA viruses are prone to genomic change, and the plasticity of their genomes enables them to adapt to varying selective pressures. Human activities in agriculture, global commerce and tourism may enhance and precipitate microbial evolution.

Animals↗
PubMed2003

Construction of genetic network using evolutionary algorithm and combined fitness function.

This paper proposes a method to capture the dynamics in gene expression data using S-system formalism and construct genetic network models. Our purposed method exploits the probabilistic heuristic search and divide-and-conquer approach to estimate the network structure. In evaluating the network structure, we attempt a primitive integration of other knowledge to the statistical criterion. The Z-score is used to analyze the robust and significant parameters from stochastic search results. We evaluated the proposed method on artificially generated data and E.coli mRNA expression data.

Algorithms↗
PubMed2005

Evolutionary autonomous agents and the nature of apraxia.

BACKGROUND: Evolutionary autonomous agents are robots or robot simulations whose controller is a dynamical neural network and whose evolution occurs autonomously under the guidance of a fitness function without the detailed or explicit direction of an external programmer. They are embodied agents with a simple neural network controller and as such they provide the optimal forum by which sensorimotor interactions in a specified environment can be studied without the computational assumptions inherent in standard neuroscience. METHODS: Evolutionary autonomous agents were evolved that were able to perform identical movements under two different contexts, one which represented an automatic movement and one which had a symbolic context. In an attempt to model the automatic-voluntary dissociation frequently seen in ideomotor apraxia, lesions were introduced into the neural network controllers resulting in a behavioral dissociation with loss of the ability to perform the movement which had a symbolic context and preservation of the simpler, automatic movement. RESULTS: Analysis of the changes in the hierarchical organization of the networks in the apractic EAAs demonstrated consistent changes in the network dynamics across all agents with loss of longer duration time scales in the network dynamics. CONCLUSION: The concepts of determinate motor programs and perceptual representations that are implicit in the present day understanding of ideomotor apraxia are assumptions inherent in the computational understanding of brain function. The strength of the present study using EAAs to model one aspect of ideomotor apraxia is the absence of these assumptions and a grounding of all sensorimotor interactions in an embodied, autonomous agent. The consistency of the hierarchical changes in the network dynamics across all apractic agents demonstrates that this technique is tenable and will be a valuable adjunct to a computational formalism in the understanding of the physical basis of neurological disorders.

Apraxias↗
PubMed2026

Microrna Expression in Aurelia aurita Metamorphosis.

INTRODUCTION: In animal taxa and jellyfish, the same genome encodes for the different phenotypes that characterize life stages that follow each other during ontogeny. This situation underscores the existence of profound regulation of genomic information at the epigenetic level. MicroRNAs are fundamental epigenetic regulators. The aim of this study is to evaluate the role of microRNA regulation during jellyfish metamorphosis and to explore the existence of evolutionarily conserved microRNAs. METHODS: Specimens belonging to the 4-metamorphosis stages of A. aurita (polyps, ephyra, young, and adult jellyfish) were bred and collected. The expression of 2,549 miRNAs for each stage was tested using microarray technology. The comparison of microRNA expression for each phase was performed using line plot analysis and Principal Component Analysis of variance (PCA), while the identification of microRNA clusters was performed via volcano plot analysis. RESULTS: A remarkable number of A. aurita miRNAs specifically hybridize with a human miRNA library. Each metamorphosis stage is characterized by a different level of expression of miRNAs: 1) Polyp vs. Ephyra stage: 128 upregulated, 2 downregulated; 2) Ephyra vs. Young stage: 2 upregulated, 135 downregulated; 3) Young vs. Adult stage: 69 upregulated, 6 downregulated. Specific functions inferred from known activities of corresponding miRNAs in higher animals (PubMed database) appear to be coherent with the correlated experimental model. DISCUSSION: Present results reveal that microRNAs with human homologs undergo specific expression changes throughout Aurelia aurita metamorphosis. This observation reinforces the hypothesis of a shared evolutionary origin of certain miRNA families between Cnidaria and Bilateria. The dynamic and stage-specific regulation pattern observed suggests that miRNAs play a key role in orchestrating the complex transitions involved in jellyfish development. These findings point to a broader conservation of epigenetic mechanisms, such as miRNA-mediated gene silencing, which may have emerged early in metazoan evolution and contributed to the regulation of cell differentiation and phenotype modulation. CONCLUSION: The present study highlights the importance of Aurelia aurita as a model for investigating miRNA-driven epigenetic regulation in non-bilaterian animals. The identification of human-homologous miRNAs provides novel insights into the evolutionary stability of the epigenetic machinery and suggests conserved regulatory functions across distant taxa. Although limited by the use of a human-based microarray platform, the data presented here lay a solid foundation for future studies employing sequencing and functional assays to further explore the role of miRNAs in cnidarian development and evolution.

Animals↗
PubMed2006

Active linking in evolutionary games.

In the traditional approach to evolutionary game theory, the individuals of a population meet each other at random, and they have no control over the frequency or duration of interactions. Here we remove these simplifying assumptions. We introduce a new model, where individuals differ in the rate at which they seek new interactions. Once a link between two individuals has formed, the productivity of this link is evaluated. Links can be broken off at different rates. In a limiting case, the linking dynamics introduces a simple transformation of the payoff matrix. We outline conditions for evolutionary stability. As a specific example, we study the interaction between cooperators and defectors. We find a simple relationship that characterizes those linking dynamics which allow natural selection to favour cooperation over defection.

Animals↗
PubMed2006

Hybrid grammar-based approach to nonlinear dynamical system identification from biological time series.

We introduce a grammar-based hybrid approach to reverse engineering nonlinear ordinary differential equation models from observed time series. This hybrid approach combines a genetic algorithm to search the space of model architectures with a Kalman filter to estimate the model parameters. Domain-specific knowledge is used in a context-free grammar to restrict the search space for the functional form of the target model. We find that the hybrid approach outperforms a pure evolutionary algorithm method, and we observe features in the evolution of the dynamical models that correspond with the emergence of favorable model components. We apply the hybrid method to both artificially generated time series and experimentally observed protein levels from subjects who received the smallpox vaccine. From the observed data, we infer a cytokine protein interaction network for an individual's response to the smallpox vaccine.

Algorithms↗
PubMed2006

High conservation of the differentially amplified MPA2 satellite DNA family in parthenogenetic root-knot nematodes.

Sequence variability and distribution of a newly characterized MPA2 satellite DNA family are described in five root-knot nematode species of the genus Meloidogyne, the mitotic parthenogens M. paranaensis, M. incognita, M. arenaria and M. javanica, and the meiotic/mitotic M. hapla (isolates A and B, respectively). The lack of distinctive mutations and the considerable contribution (40.8%) of ancestral changes disclose an ancient satellite DNA which existed in the common ancestor of extant parthenogenetic species in the same or similar form and remained preserved for a period of at least 43 My. Nonuniformly distributed polymorphic sites along the satellite monomer suggest differences in constraints acting on particular sequence segments. Sequence diversity is clearly unaffected by significant differences in genomic abundance of the MPA2 satellite DNA in the examined species. Observed results suggest that the dynamics of this satellite DNA family might be in the first instance a consequence of characteristics of its nucleotide sequence and possible constraints imposed on it. Under conditions of mitotic and meiotic parthenogenesis, slow accumulation of mutations and slow replacement of old MPA2 sequence variants with new ones may be equivalent to the dynamics of some satellite DNA sequences conserved for extremely long evolutionary periods in sexual species.

Animals↗
PubMed2026

Control of foreign DNA: emerging roles of xenogeneic silencers.

Bacteria continuously acquire foreign DNA through horizontal gene transfer, yet its successful integration depends on regulatory mechanisms that balance genome protection with evolutionary innovation. Xenogeneic silencers are central to this process: they preferentially bind AT-rich DNA, a common feature of many horizontally acquired genetic elements, and repress its transcription. Recent studies, however, reveal a much broader regulatory repertoire. Beyond transcriptional repression, these proteins contribute to chromosome organization by forming higher-order nucleoprotein complexes and phase-separated condensates that shape bacterial nucleoid architecture. Furthermore, they play roles in regulating bacteriophage infection cycles, including mechanisms by which phages hijack host silencing activities for their own benefit. Their extensive regulatory reach, spanning virulence genes, biofilm formation, specialized metabolite production, and mobile genetic elements (MGEs), underscores their central role in connecting environmental signals, including fluctuations in the second messenger c-di-GMP, with gene expression, and genome organization. The diversification of xenogeneic silencers across bacterial chromosomes, plasmids, phages, and other MGEs highlights their evolutionary significance. Together, these recent findings position xenogeneic silencers as dynamic regulatory modules that shape the fate of foreign DNA across the horizontal gene transfer network.

Gene Transfer, Horizontal↗
PubMed2003

Effects of pathological mutations on the stability of a conserved amino acid triad in retinoschisin.

A three-dimensional model has been calculated for the discoidin domain of retinoschisin (RS1), the protein involved in the X-linked juvenile retinoschisis. The model allows for a mapping of the pathological retinoschisis missense mutations and a rationale for the structural effects of an evolutionary conserved surface exposed triad (W122-R200-W163). Molecular dynamics simulations of the triad mutants models, together with ab initio energy calculations of the complexes corresponding to the triad show that the observed pathological mutations sensibly destabilize local interactions and the entire fold. Moreover the presented model reveals evidence of a putative site for membrane association.

Amino Acid Sequence↗
PubMed2003

Modeling high-resolution broadband discourse in complex adaptive systems.

Numerous researchers and practitioners have turned to complexity science to better understand human systems. Simulation can be used to observe how the microlevel actions of many human agents create emergent structures and novel behavior in complex adaptive systems. In such simulations, communication between human agents is often modeled simply as message passing, where a message or text may transfer data, trigger action, or inform context. Human communication involves more than the transmission of texts and messages, however. Such a perspective is likely to limit the effectiveness and insight that we can gain from simulations, and complexity science itself. In this paper, we propose a model of how close analysis of discursive processes between individuals (high-resolution), which occur simultaneously across a human system (broadband), dynamically evolve. We propose six different processes that describe how evolutionary variation can occur in texts-recontextualization, pruning, chunking, merging, appropriation, and mutation. These process models can facilitate the simulation of high-resolution, broadband discourse processes, and can aid in the analysis of data from such processes. Examples are used to illustrate each process. We make the tentative suggestion that discourse may evolve to the "edge of chaos." We conclude with a discussion concerning how high-resolution, broadband discourse data could actually be collected.

Adaptation, Psychological↗
PubMed2004

Population structure and strong divergent selection shape phenotypic diversification in maize landraces.

To conserve the long-term selection potential of maize, it is necessary to investigate past and present evolutionary processes that have shaped quantitative trait variation. Understanding the dynamics of quantitative trait evolution is crucial to future crop breeding. We characterized population differentiation of maize landraces from the State of Oaxaca, Mexico for quantitative traits and molecular markers. Qst values were much higher than Fst values obtained for molecular markers. While low values of Fst (0.011 within-village and 0.003 among-villages) suggest that considerable gene flow occurred among the studied populations, high levels of population differentiation for quantitative traits were observed (ie an among-village Qst value of 0.535 for kernel weight). Our results suggest that although quantitative traits appear to be under strong divergent selection, a considerable amount of gene flow occurs among populations. Furthermore, we characterized nonproportional changes in the G matrix structure both within and among villages that are consequences of farmer selection. As a consequence of these differences in the G matrix structure, the response to multivariate selection will be different from one population to another. Large changes in the G matrix structure could indicate that farmers select for genes of major and pleiotropic effect. Farmers' decision and selection strategies have a great impact on phenotypic diversification in maize landraces.

Agriculture↗
PubMed1988

Control of pollen hydration in Brassica requires continued protein synthesis, and glycosylation in necessary for intraspecific incompatibility.

Pollen hydration and self-incompatibility (SI) in Brassica have been studied by using a combination of in vivo video-microscopy and experiments with metabolic inhibitors. Experiments with cycloheximide confirm earlier observations that pollen hydration is regulated through protein synthesis. No protein or glycoprotein has positively been identified with this event; however, it is unlikely that the total pool of any particular glycoprotein is involved, but rather a newly synthesized or otherwise activated fraction. Micromanipulation of pollen on the stigmatic papillae suggests that access to this hydration regulation system is limited to members of the Brassicaceae: pollen grains of other species-even those possessing dry stigmas-fail to hydrate. It is proposed that an interaction between enzymes of the stigma surface and the superficial layer of the pollen grain coating creates continuity between the content of the papillar wall and the grain protoplast. Inhibition of protein synthesis also overcomes SI, and since the advent of regulated hydration and synthesis of the so-called S-gene glycoproteins coincide with the acquisition of the SI system, there is strong circumstantial evidence that the same molecular species is involved in both processes. Experiments with tunicamycin, which prevents glycosylation of glycoproteins, indicate that the glycosyl groups of the S-gene glycoprotein are required for the operation of the SI system but not for the regulation of hydration. Further experiments suggest that pollen is positively inhibited on incompatible papillae but that this inhibition is biostatic. Recovery from the effects of the SI system appears to involve the metabolism of an inhibitor by the pollen. SI in Brassica thus emerges as a sophisticated process under dynamic control in both the female and male partners. The evolutionary advantages of such a system are discussed.

Journal Article↗
PubMed1999

Genomic evolution during a 10,000-generation experiment with bacteria.

Molecular methods are used widely to measure genetic diversity within populations and determine relationships among species. However, it is difficult to observe genomic evolution in action because these dynamics are too slow in most organisms. To overcome this limitation, we sampled genomes from populations of Escherichia coli evolving in the laboratory for 10,000 generations. We analyzed the genomes for restriction fragment length polymorphisms (RFLP) using seven insertion sequences (IS) as probes; most polymorphisms detected by this approach reflect rearrangements (including transpositions) rather than point mutations. The evolving genomes became increasingly different from their ancestor over time. Moreover, tremendous diversity accumulated within each population, such that almost every individual had a different genetic fingerprint after 10,000 generations. As has been often suggested, but not previously shown by experiment, the rates of phenotypic and genomic change were discordant, both across replicate populations and over time within a population. Certain pivotal mutations were shared by all descendants in a population, and these are candidates for beneficial mutations, which are rare and difficult to find. More generally, these data show that the genome is highly dynamic even over a time scale that is, from an evolutionary perspective, very brief.

Biological Evolution↗
PubMed2001

Heterologous, splicing-dependent RNA editing in chloroplasts: allotetraploidy provides trans-factors.

RNA editing is unique among post-transcriptional processes in plastids, as it exhibits extraordinary phylogenetic dynamics leading to species-specific editing site patterns. The evolutionary loss of a site is considered to entail the loss of the corresponding nuclear-encoded site-specific factor, which prevents the editing of foreign, i.e. heterologous, sites. We investigated the editing of short 'spliced' and 'unspliced' ndhA gene fragments from spinach in Nicotiana tabacum (tobacco) in vivo using biolistic transformation. Surprisingly, it turned out that the spinach site is edited in the heterologous nuclear background. Furthermore, only exon-exon fusions were edited, whereas intron-containing messages remained unprocessed. A homologue of the spinach site was found to be present and edited in Nicotiana tomentosiformis, representing the paternal parent, but absent from Nicotiana sylvestris, representing the maternal parent of tobacco. Our data show that: (i) the cis-determinants for ndhA editing are split by an intron; (ii) the editing capacity cannot be deduced from editing sites; and (iii) allopolyploidization can increase the editing capacity, which implies that it can influence speciation processes in evolution.

Base Sequence↗
PubMed2026

Evolution of virulence of a plant RNA virus in developmental stage-structured host populations.

Natural host populations are age-structured, and developmental stages differ in susceptibility and within-host pathogen dynamics, potentially imposing distinct selective pressures on viruses. However, the evolutionary consequences of host age structure remain poorly understood. We experimentally evolved turnip mosaic potyvirus for 5 passages in Arabidopsis thaliana populations spanning 7 demographic regimes, from juvenile- to mature-dominated cohorts. We quantified disease progression, symptom severity, and viral load, cross-inoculated evolved lineages across host stages to construct infection matrices, and performed whole-population sequencing at passages 1 and 5. Disease traits changed markedly with passage, demography, and their interaction. Disease progression evolved faster in older populations, whereas symptom severity was independent of median age, indicating demographic reweighting of virulence components. Viral load increased across passages and positively correlated with severity, linking within-host fitness to symptoms. Cross-inoculation assays revealed a modular infection network: juvenile-evolved lineages specialized on juvenile hosts, whereas lineages from intermediate and older populations were more generalist. Genomically, we detected both parallel and demography-specific adaptations, including recurrent changes in the viral protein VPg (involved in translation, replication, and host interactions) as well as synonymous variants showing consistent or opposing selection across host population stage structures. Overall, host age structure emerges as a major ecological driver of virulence evolution, shaping tradeoffs between disease progression and severity and determining specialization versus generalism. These results integrate phenotypic and genomic responses and suggest that manipulating crop age structure could steer virus evolution toward less damaging outcomes.

Virulence↗
PubMed2006

How effective are maternal effects at having effects?

The well studied trade-off between offspring size and offspring number assumes that offspring fitness increases with increasing per-offspring investment. Where mothers differ genetically or exhibit plastic variation in reproductive effort, there can be variation in per capita investment in offspring, and via this trade-off, variation in fecundity. Variation in per capita investment will affect juvenile performance directly--a classical maternal effect--while variation in fecundity will also affect offspring performance by altering the offsprings' competitive environment. The importance of this trade-off, while a focus of evolutionary research, is not often considered in discussions about population dynamics. Here, we use a factorial experiment to determine what proportion of variation in offspring performance can be ascribed to maternal effects and what proportion to the competitive environment linked to the size-number trade-off. Our results suggest that classical maternal effects are significant, but that in our system, the competitive environment, which is linked to maternal environments by fecundity, can be a far more substantial influence.

Acari↗
PubMed2005

Characterization of degree frequency distribution in protein interaction networks.

In this work, we analyze the degree frequency distribution in the yeast protein interaction network by studying a previously proposed duplication network model. This model correctly predicts the observed degree distribution (a power law for large degree values and a departure from this behavior for small degree). We numerically and analytically characterize this distribution as a mixture of random and power-law behavior, and make a comparative study of the robustness of the network model against realistic perturbations. We conclude that the particular distribution observed in both the model and the experimental data has many advantages in terms of dynamical and topological robustness and could have emerged in the evolutionary history as a sort of compromise between purely deterministic and random underlying mechanisms of network growth.

Computer Simulation↗