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PubMed1989

Selection and evolution of bacteriophages in cellstat.

Objectives of this work were as follows: 1. to establish a laboratory experimental system utilizable in a biophysical approach to molecular evolution; and 2. to provide real world parameters to theories of molecular evolution, especially to Eigen's theory of quasi-species. Secretion type bacteriophage fd of E. coli, closely related phages and artificial chimera phages of fd, and a virulent phage Q beta of E. coli were cultured continuously in a specially designed fermenter called a "cellstat". A phage is cultured in a flow of host bacterial cells. Due to its high dilution rate, the mutant cell could not be selected in the cellstat. It was therefore recognized that the cellstat is suitable for study of the selection and evolution process of a bacteriophage under well-defined environmental conditions without interference from host cell mutations. Population dynamics of bacteriophages of various types in the cellstat were studied theoretically by computer simulation and experimentally. A genetically invariable pure population of phage behaves like an open non-linear chemical reaction system. An invariable mixed population shows a selection process, while a variable population generates an evolution process. Kinetic constants describing the dynamics were determined by curve fitting between the theoretical and the experimental curve obtained from competition experiments and from biological relaxation experiments. One of the most important kinetic parameters thus obtained was the selection coefficient, and its dependence on the base sequence of phage DNA. We drew a local landscape of the selection coefficient near the fd sequence on the base sequence space. From this landscape we were able to confirm the importance of slightly deleterious mutants in molecular evolution. We also confirmed the possibility of developing an evolutionary molecular engineering using a cellstat as an evolution reactor and fd phage as a working replicon. Novelties of this work were as follows: 1. the first stable continuous culture of a bacteriophage was achieved with a cellstat; 2. a local landscape of selection coefficient near the fd sequence on the sequence space was the first experimental drawing of such a map; 3. a biological relaxation method was realized to measure kinetic constants of a biological kinetic process, or molecular evolution; and 4. a practical engineering process of evolutionary molecular engineering was proposed.

Bacteriophages↗

PubMed2024

Interspecific transfer of genetic information through polyploid bridges.

Hybridization blurs species boundaries and leads to intertwined lineages resulting in reticulate evolution. Polyploidy, the outcome of whole genome duplication (WGD), has more recently been implicated in promoting and facilitating hybridization between polyploid species, potentially leading to adaptive introgression. However, because polyploid lineages are usually ephemeral states in the evolutionary history of life it is unclear whether WGD-potentiated hybridization has any appreciable effect on their diploid counterparts. Here, we develop a model of cytotype dynamics within mixed-ploidy populations to demonstrate that polyploidy can in fact serve as a bridge for gene flow between diploid lineages, where introgression is fully or partially hampered by the species barrier. Polyploid bridges emerge in the presence of triploid organisms, which despite critically low levels of fitness, can still allow the transfer of alleles between diploid states of independently evolving mixed-ploidy species. Notably, while marked genetic divergence prevents polyploid-mediated interspecific gene flow, we show that increased recombination rates can offset these evolutionary constraints, allowing a more efficient sorting of alleles at higher-ploidy levels before introgression into diploid gene pools. Additionally, we derive an analytical approximation for the rate of gene flow at the tetraploid level necessary to supersede introgression between diploids with nonzero introgression rates, which is especially relevant for plant species complexes, where interspecific gene flow is ubiquitous. Altogether, our results illustrate the potential impact of polyploid bridges on the (re)distribution of genetic material across ecological communities during evolution, representing a potential force behind reticulation.

Polyploidy↗

PubMed2026

Predictive evolutionary genomics: principles, validation, and practice.

Climate change and habitat loss are driving rapid evolutionary responses in populations world-wide, which creates an urgent need for evolutionary forecasting in conservation and agriculture. Such forecasting can be categorized into three time scales: trait-based models that use multivariate quantitative genetic equations to project correlated phenotypic responses up to c. 20 generations, allele-based analyses that model allele frequency dynamics up to 100 generations, and composite adaptation scores that aggregate many small effects to yield predictions across longer horizons. However, these approaches have remained largely disconnected. Here, we present a Bayesian framework that integrates these three complementary approaches for evolutionary prediction. Our framework combines genomic, phenotypic, and environmental data to yield probabilistic predictions with explicit uncertainty. We show how predictive evolutionary forecasts can be validated with experimental evolution, field experimentation, historical specimens, and reciprocal transplants. These validated forecasts can help advance conservation and agricultural programmes by helping predict which populations are at risk of future extinction, optimizing breeding programmes for future climates, and planning ecosystem management under environmental change. By supporting a shift towards more predictive approaches in evolutionary biology, this framework may help improve our ability to manage biodiversity and food security in a changing world.

Genomics↗

PubMed1984

The dynamics of quantifiable homeostasis. V: Homeostasis of higher order.

The properties are explored of a cybernetic process with lag L and force of restoration equal to the size of displacement one lag unit earlier, raised to any arbitrary positive power (w greater than 1), multiplied by the restoration constant b, the sign being opposite to that of the displacement at that time. No closed-form solution is available, but a converging Taylor series expansion is presented that gives a solution of arbitrary precision. Unlike the linear system previously discussed, the amplitude of the displacement (A) is germane, and it is shown that the criterion that the effect of a perturbation be damped out is whether or not LbAw-1 exceeds a constant, kw, that depends only on w. The counterpart of this pattern of higher-order homeostasis is closer to the biological behavior of many forms of homeostasis than the scaled invariance characteristic of the linear process. kw is shown to be bounded between pi/2 and 2, and increases monotonically with w. Exactly computed values and large-sample approximations are given for the critical values below which no overshoot at all occurs. It is shown that where it does not, the minimum expected cost decreases with increasing w and reaches a minimum at infinite w. However, this evolutionary gain is vitiated where large displacements are involved, and may need to be redressed by a change in the restoration constant. Thus, the dynamic balance becomes much more subtle than with lower-order processes. Several brief clinical illustrations of these ideas are presented.

Biological Evolution↗

PubMed2003

Prophage contribution to bacterial population dynamics.

Cocultures of Salmonella strains carrying or lacking specific prophages undergo swift composition changes as a result of phage-mediated killing of sensitive bacteria and lysogenic conversion of survivors. Thus, spontaneous prophage induction in a few lysogenic cells enhances the competitive fitness of the lysogen population as a whole, setting a selection regime that forces maintenance and spread of viral DNA. This is likely to account for the profusion of prophage sequences in bacterial genomes and may contribute to the evolutionary success of certain phylogenetic lineages.

Biological Evolution↗

PubMed2004

Diversity and specificity in the interaction between Caenorhabditis elegans and the pathogen Serratia marcescens.

BACKGROUND: Co-evolutionary arms races between parasites and hosts are considered to be of immense importance in the evolution of living organisms, potentially leading to highly dynamic life-history changes. The outcome of such arms races is in many cases thought to be determined by frequency dependent selection, which relies on genetic variation in host susceptibility and parasite virulence, and also genotype-specific interactions between host and parasite. Empirical evidence for these two prerequisites is scarce, however, especially for invertebrate hosts. We addressed this topic by analysing the interaction between natural isolates of the soil nematode Caenorhabditis elegans and the pathogenic soil bacterium Serratia marcescens. RESULTS: Our analysis reveals the presence of i) significant variation in host susceptibility, ii) significant variation in pathogen virulence, and iii) significant strain- and genotype-specific interactions between the two species. CONCLUSIONS: The results obtained support the previous notion that highly specific interactions between parasites and animal hosts are generally widespread. At least for C. elegans, the high specificity is observed among isolates from the same population, such that it may provide a basis for and/or represent the outcome of co-evolutionary adaptations under natural conditions. Since both C. elegans and S. marcescens permit comprehensive molecular analyses, these two species provide a promising model system for inference of the molecular basis of such highly specific interactions, which are as yet unexplored in invertebrate hosts.

Animals↗

PubMed2002

Thermodynamics and kinetics of protein folding: an evolutionary perspective.

This article appeals to an evolutionary model which postulates that primordial proteins were described by small polypeptide chains which (i) lack disulfide bridges, and (ii) display slow folding rates with multi-state kinetics, to determine relations between structural properties of proteins and their folding kinetics. We parameterize the energy landscape of proteins in terms of thermodynamic activation variables. The model studies evolutionary changes in these thermodynamic parameters, and we invoke relations between these activation variables and structural properties of the protein to predict the following correspondence between protein structure and folding kinetics. 1. Proteins with inter- and intra-chain disulfide bridges: large variability in both folding rates and stability of intermediates, multi-state kinetics. 2. Proteins which lack inter and intra-chain disulfide bridges. 2.1 Single-domain chains: fast folding rates; unstable intermediates; two-state kinetics. 2.2 Multi-domain monomers: intermediate rates; metastable intermediates; multi-state kinetics. 2.3 Multi-domain oligomers: slow rates; metastable intermediates; multi-state kinetics. The evolutionary model thus provides a kinetic characterization of one important subfamily of proteins which we describe by the following properties: Folding dynamics of single-domain proteins which lack disulfide bridges are described by two-state kinetics. Folding rate of this class of proteins is positively correlated with the thermodynamic stability of the folded state.

Disulfides↗

PubMed1998

Evolutionary Stable Strategies and Trade-Offs in Generalized Beverton and Holt Growth Models.

A generalized Beverton-Holt model is considered in which a parameter gamma characterizes the onset of density dependence. An evolutionary stable strategy analysis of this parameter, reported in Getz (1996), is developed further here, using invasion exponents and the strategy dynamics of Vincent et al. (1993). The parameter gamma is also allowed to be density dependent, and it is shown that the most successful strategies of this type are those for which gamma is large for low densities and close to its minimum for high densities. A biological interpretation is given in the context of mobile females depositing their relatively sessile young on patches of resource, namely, females should overdisperse their young on resources when adult densities are high and underdisperse them when these densities are low. Finally the per capita growth rate parameter is also allowed to depend on gamma. It is shown that this dependence provides a mechanism by which periodic or chaotic attractor dynamics could evolve towards equilibrium attractor dynamics. Copyright 1998 Academic Press.

Journal Article↗

PubMed2000

The cytonuclear effects of facultative apomixis. I. Disequilibrium dynamics in diploid populations.

We comprehensively analyze the cytonuclear effects of generalized mixed mating, including all combinations of selfing, outcrossing, and apomixis, the asexual production of seeds. After first deriving the time-dependent solutions for nonrandom associations (disequilibria) between a diallelic cytoplasmic marker and the alleles and genotypes at a diploid nuclear locus, we delimit all possible dynamical behaviors and the conditions under which each occurs. As in standard mixed mating systems, all disequilibria ultimately decay to zero except when outcrossing is absent, in which case permanent disequilibria result if the allelic association is initially nonzero. When at least some outcrossing is present, any initial allelic association decays at a constant geometric rate, whereas genotypic disequilibria may first increase in magnitude or change sign. Although selfing and apomixis tend to retard the decay of disequilibria (or approach to equilibrium) and often to the same extent, apomixis can have a stronger effect under some conditions. We also determine the dynamics of cytonuclear disequilibria in specific examples that may be of particular interest for empirical studies of hybrid zones. The results suggest several practical guidelines for experimental design and data analysis and show how the cytonuclear disequilibrium dynamics under mating system alone furnish a quantitative baseline for null hypotheses against which to test for the presence of other evolutionary forces.

Data Interpretation, Statistical↗

PubMed1985

Constructional morphology: the analysis of constraints in evolution dedicated to A. Seilacher in honour of his 60. birthday.

Evolutionary change is opportunistic, but its course is strongly constrained in several fundamental ways. These constraints (historical/phylogenetic, functional/adaptive, constructional/morphogenetic) and their dynamic relationships are discussed here and shown to constitute the conceptual framework of Constructional Morphology. Notwithstanding recent published opinions which claim that the "discovery" of constraints renders Neodarwinian selection theory obsolete, we regard the insights of Constructional Morphology as being entirely consistent with this theory. As is shown here in the case of the Hyracoidea, formal analysis of the constraints which have framed the evolution of various characters extends our understanding of the evolution of a taxon.

Adaptation, Physiological↗

PubMed1987

Dynamics and stability in coevolutionary ecological systems. I. Community stability and coevolutionarily stable states.

An extension of J. Roughgarden's [1979, Theor. Pop. Biol. 9, 388; 1979, "An Introduction to Evolutionary Ecology and Population Genetic Theory," Macmillan, New York] formalism for investigating the effects of coevolution on community structure is presented. The extension assumes the result that a coevolved community is asymptotically stable when coevolution takes place at a genetically noninvasible boundary. This is proved for the general case of n interacting species. From this a community persistence function, phi (P), is defined that allows measuring the domain of attraction for the community as well as the resilience time, that is, the time taken for a perturbation to decay to 1-1/e (63%) of its initial value.

Animals↗

PubMed2006

A question of timing: emerging links between transcription and replication.

The coordination of transcription and timing of DNA replication during the S phase of the cell cycle has recently been studied chromosome-wide in high resolution. This revealed that in the complex genome of higher eukaryotes actively transcribed genes are more likely to replicate early in S phase. Dynamic changes in chromatin structure and nuclear organization appear to provide the underlying mechanism to link transcription and replication. A possible evolutionary benefit for this connection might result from differential replication fidelity during S phase, and comparisons of the human and chimpanzee genomes are compatible with this hypothesis.

Animals↗

PubMedDate not supplied

Exploring the local conformational space of a membrane protein by site-directed spin labeling.

Molecular modeling based on a hybrid evolutionary optimization and an information condensation algorithm, called GHOST, of spin label ESR spectra was applied to study the structure and dynamics of membrane proteins. The new method is capable of providing detailed molecular information about the conformational space of the spin-labeled segment of the protein in a membrane system. The method is applied to spin-labeled bacteriophage M13 major coat protein, which is used as a model membrane protein. Single cysteine mutants of the coat protein were labeled with nitroxide spin labels and incorporated in 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) bilayers. The new computational method allows us to monitor distributions of local spatial constraints and molecular mobility, in addition to information about the location of the protein in a membrane. Furthermore, the results suggest that different local conformations may coexist in the membrane protein. The knowledge of different local conformations may help us to better understand the function-structure relationship of membrane proteins.

Algorithms↗

PubMed2005

Species lifetime distribution for simple models of ecologies.

Interpretation of empirical results based on a taxa's lifetime distribution shows apparently conflicting results. Species' lifetime is reported to be exponentially distributed, whereas higher-order taxa, such as families or genera, follow a broader distribution, compatible with power-law decay. We show that both forms of evidence are consistent with a simple evolutionary model that does not require specific assumptions on species interaction. The model provides a zero-order description of the dynamics of ecological communities, and its species lifetime distribution can be computed exactly. Different behaviors are found as follows: an initial t(-3/2) power law, emerging from a random walk type of dynamics, which crosses over to a steeper t(-2) branching process-like regime and finally is cut off by an exponential decay that becomes weaker and weaker as the total population increases. Sampling effects also can be taken into account and shown to be relevant. If species in the fossil record were sampled according to the Fisher log-series distribution, lifetime should be distributed according to a t(-1) power law. Such variability of behaviors in a simple model, combined with the scarcity of data available, casts serious doubt on the possibility of validating theories of evolution on the basis of species lifetime data.

Animals↗

PubMed1996

Dynamics of repeat polymorphisms under a forward-backward mutation model: within- and between-population variability at microsatellite loci.

Suggested molecular mechanisms for the generation of new tandem repeats of simple sequences indicate that the microsatellite loci evolve via some of forward-backward mutation. We provide a mathematical basis for suggesting a measure of genetic distance between populations based on microsatellite variation. Our results indicate that such a genetic distance measure can remain proportional to the divergence time of populations even when the forward-backward mutations produce variable and/or directionally biased alleles size changes. If the population size and the rate of mutation remain constant, then the measure will be proportional to the time of divergence of populations. This genetic distance is expressed in terms of a ratio of components of variance of allele sizes, based on expressions developed for studying population dynamics of quantitative traits. Application of this measure to data on 18 microsatellite loci in the nine human populations leads to evolutionary trees consistent with the known ethnohistory of the populations.

Alleles↗

PubMed2004

Tracking the trajectories of evolution.

This article proposes a method of visualizing and measuring evolution in artificial life simulations. The evolving population of agents is treated as a dynamical system. The proposed method is inspired by the notion of trajectory. The article provides examples of tracking of trajectories of evolutionary systems in the spaces of genotypes, strategies, and some global characteristics. Visualization similar to a bifurcation diagram is used to represent results of a series of simulations.

Artificial Intelligence↗

PubMed2005

Evolutionary strategies and adaptations for survival between mosquito-parasitic microsporidia and their intermediate copepod hosts: a comparative examination of Amblyospora connecticus and Hyalinocysta chapmani (Microsporidia: Amblyosporidae).

The epizootiology, transmission dynamics, and survival strategies employed by two mosquito-parasitic microsporidia that utilize copepods as intermediate hosts are examined in relation to the biological attributes of their hosts and the environments in which they inhabit. Amblyospora connecticus Andreadis, 1988, a parasite of Ochlerotatus cantator (Coquillett) and Acanthocyclops vernalis (Fischer) is found in an unstable salt marsh environment that is subject to periodic flooding and drying. Both hosts have distinct non-overlapping generations. A. connecticus exhibits a well-defined seasonal transmission cycle that relies heavily on maternal-mediated transovarial transmission by female O. cantator during the summer, and horizontal transmission via the copepod host during the spring (copepod to mosquito) and fall (mosquito to copepod). Its survival strategies include: delayed virulence, low pathogenicity and high tissue specificity that allow for transstadial transmission of horizontally acquired infections and maximum spore production, reliance on living hosts throughout most of its life cycle with overwintering in the copepod, polymorphic development that is well synchronized with host physiology, and production and dissemination of infectious spores that are coincident with the seasonal occurrence of susceptible stages in each host. Hyalinocysta chapmani Hazard et Oldacre, 1975, a parasite of Culiseta melanura (Coquillett) and Orthocyclops modestus (Herrick) is found in a comparatively stable, subterranean habitat that is inundated with water throughout the year. Copepods are omnipresent and C. melanura has overlapping broods. H. chapmani is maintained in a continuous cycle of horizontal transmission between each host throughout the summer and fall but lacks a developmental sequence leading to transovarial transmission in the mosquito host. It relies on living hosts for most of its life cycle and overwinters in diapausing mosquito larvae. Transstadial transmission does not occur and there is no dimorphic development in the mosquito host. The spatial and temporal overlap of both mosquito and copepod hosts during the summer and fall affords abundant opportunity for continuous horizontal transmission and increases the likelihood that H. chapmani will find a target host, thus negating the need for a transovarial route. It is hypothesized that natural selection has favoured the production of meiospores in larval female mosquitoes rather than congenital transfer of infection to progeny via ovarian infection as a strategy for achieving greater transmission success. Analysis of the molecular phylogeny data suggest that (1) transovarial transmission and the developmental sequence leading to ovarian infection have been secondarily lost in H. chapmani, as they occur in all other closely related genera, (2) the ancestral state included complex life cycles involving transovarial transmission and an intermediate host, and (3) mosquito-parasitic microsporidia are adjusting their life cycles to accommodate host ecological conditions.

Adaptation, Biological↗

PubMed1992

Neurosurgical approaches to cerebrospinal fluid rhinorrhea.

The evolutionary concepts of pinpointing and treating cerebrospinal fluid (CSF) fistulas over the past few decades are reviewed taking into consideration the dynamic character of CSF circulation. The localization of the site of leakage is greatly facilitated by the judicious use of a variety of radioisotope and radiological techniques. The most recent are Metrizamide CT Cisternography and Magnetic Resonance Imaging. It is asserted that still the most challenging cases are those with intermittent liquorrheas, and those patients in which the site of the fistula is not easily defined. The authors will describe their personal experience with intracranial surgical repair of fistulas located in the anterior fossa.

Accidents↗