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PubMed2001

Modelling the closure-related geochemical evolution of groundwater at a former uranium mine.

A newly developed reactive transport model was used to evaluate the potential effects of mine closure on the geochemical evolution in the aquifer downgradient from a mine site. The simulations were conducted for the Königstein uranium mine located in Saxony, Germany. During decades of operation, uranium at the former mine site had been extracted by in situ acid leaching of the ore underground, while the mine was maintained in a dewatered condition. One option for decommissioning is to allow the groundwater level to rise to its natural level, flooding the mine workings. As a result, pore water containing high concentrations of dissolved metals, radionuclides, and sulfate may be released. Additional contamination may arise due to the dissolution of minerals contained in the aquifer downgradient of the mine. On the other hand, dissolved metals may be attenuated by reactions within the aquifer. The geochemical processes and interactions involved are highly non-linear and their impact on the quality of the groundwater and surface water downstream of the mine is not always intuitive. The multicomponent reactive transport model MIN3P, which can describe mineral dissolution-precipitation reactions, aqueous complexation, and oxidation-reduction reactions, is shown to be a powerful tool for investigating these processes. The predictive capabilities of the model are, however, limited by the availability of key geochemical parameters such as the presence and quantities of primary and secondary mineral phases. Under these conditions, the model can provide valuable insight by means of sensitivity analyses.

Forecasting↗

PubMed2006

Catching a 'hopeful monster': shepherd's purse (Capsella bursa-pastoris) as a model system to study the evolution of flower development.

Capsella is a small genus within the mustard family (Brassicaceae). Its three species, however, show many evolutionary trends also observed in other Brassicaceae (including Arabidopsis) and far beyond, including transitions from a diploid, self-incompatible, obligatory outcrossing species with comparatively large and attractive flowers but a restricted distribution to a polyploid, self-compatible, predominantly selfing, invasive species with floral reductions. All these evolutionary transitions may have contributed to the fact that Capsella bursa-pastoris (shepherd's purse) has become one of the most widely distributed flowering plants on our planet. In addition, Capsella bursa-pastoris shows a phenomenon that, although rare, could be of great evolutionary importance, specifically the occurrence of a homeotic variety found in relatively stable populations in the wild. Several lines of evidence suggest that homeotic changes played a considerable role in floral evolution, but how floral homeotic varieties are established in natural populations has remained a highly controversial topic among evolutionary biologists. Due to its close relationship with the model plant Arabidopsis thaliana, numerous experimental tools are available for studying the genus Capsella, and further tools are currently being developed. Hence, Capsella provides great opportunities to investigate the evolution of flower development from molecular developmental genetics to field ecology and biogeography, and from morphological refinements to major structural transitions.

Biological Evolution↗

PubMed1998

Male courtship song frequency as an indicator of male genetic quality in an insect species, Drosophila montana.

Most theoretical models on evolution of male secondary sexual characters and female preferences for these characters suggest that the male characters evolve in response to female preferences that may themselves evolve in response to direct or indirect benefits of choice. In Drosophila montana (a species of the D. virilis group), females use male song in their mate choice, preferring males that produce songs with short sound pulses and a high carrier frequency. We demonstrate here that the females get indirect benefits from their choice: in our data the frequency of the male song correlated with the survival rate of the male's progeny from egg to adulthood (indirect benefit for the female), but not with the fecundity of his mating partner (no direct benefit for the female). Male wing centroid asymmetry did not correlate with male wing song characters, nor with female egg production nor the fitness of her progeny, suggesting that fluctuating asymmetry in male wings does not play a major role in sexual signalling. The fact that the male song gives the female information on the male's condition/genetic quality in D. montana suggests that in this species the evolution of female preferences for male song characters could have evolved through condition-dependent viability selection presented in some 'good genes' models.

Animals↗

PubMed2006

Invasion and persistence of a selfish gene in the Cnidaria.

BACKGROUND: Homing endonuclease genes (HEGs) are superfluous, but are capable of invading populations that mix alleles by biasing their inheritance patterns through gene conversion. One model suggests that their long-term persistence is achieved through recurrent invasion. This circumvents evolutionary degeneration, but requires reasonable rates of transfer between species to maintain purifying selection. Although HEGs are found in a variety of microbes, we found the previous discovery of this type of selfish genetic element in the mitochondria of a sea anemone surprising. METHODS/PRINCIPAL FINDINGS: We surveyed 29 species of Cnidaria for the presence of the COXI HEG. Statistical analyses provided evidence for HEG invasion. We also found that 96 individuals of Metridium senile, from five different locations in the UK, had identical HEG sequences. This lack of sequence divergence illustrates the stable nature of Anthozoan mitochondria. Our data suggests this HEG conforms to the recurrent invasion model of evolution. CONCLUSIONS: Ordinarily such low rates of HEG transfer would likely be insufficient to enable major invasion. However, the slow rate of Anthozoan mitochondrial change lengthens greatly the time to HEG degeneration: this significantly extends the periodicity of the HEG life-cycle. We suggest that a combination of very low substitution rates and rare transfers facilitated metazoan HEG invasion.

Animals↗

PubMed2006

Segmentation of focal cortical dysplasia lesions on MRI using level set evolution.

Focal cortical dysplasia (FCD) is the most frequent malformation of cortical development in patients with medically intractable epilepsy. On MRI, FCD lesions are not easily differentiable from the normal cortex and defining their spatial extent is challenging. In this paper, we introduce a method to segment FCD lesions on T1-weighted MRI. It relies on two successive three-dimensional deformable models, whose evolutions are based on the level set framework. The first deformable model is driven by probability maps obtained from three MRI features: cortical thickness, relative intensity and gradient. These features correspond to the visual characteristics of FCD and allow discriminating lesions and normal tissues. In a second stage, the previous result is expanded towards the underlying and overlying cortical boundaries, throughout the whole cortical section. The method was quantitatively evaluated by comparison with manually traced labels in 18 patients with FCD. The automated segmentations achieved a strong agreement with the manuals labels, demonstrating the applicability of the method to assist the delineation of FCD lesions on MRI. This new approach may become a useful tool for the presurgical evaluation of patients with intractable epilepsy related to cortical dysplasia.

Adult↗

PubMed2006

Evolution of dispersal in a structured metapopulation model in discrete time.

In this article, a structured metapopulation model in discrete time with catastrophes and density-dependent local growth is introduced. The fitness of a rare mutant in an environment set by the resident is defined, and an efficient method to calculate fitness is presented. With this fitness measure evolutionary analysis of this model becomes feasible. This article concentrates on the evolution of dispersal. The effect of catastrophes, dispersal cost, and local dynamics on the evolution of dispersal is investigated. It is proved that without catastrophes, if all population-dynamical attractors are fixed points, there will be selection for no dispersal. A new mechanism for evolutionary branching is also found: Even though local population sizes approach fixed points, catastrophes can cause enough temporal variability, so that evolutionary branching becomes possible.

Algorithms↗

PubMed1994

Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation.

Using real sequence data, we evaluate the adequacy of assumptions made in evolutionary models of nucleotide substitution and the effects that these assumptions have on estimation of evolutionary trees. Two aspects of the assumptions are evaluated. The first concerns the pattern of nucleotide substitution, including equilibrium base frequencies and the transition/transversion-rate ratio. The second concerns the variation of substitution rates over sites. The maximum-likelihood estimate of tree topology appears quite robust to both these aspects of the assumptions of the models, but evaluation of the reliability of the estimated tree by using simpler, less realistic models can be misleading. Branch lengths are underestimated when simpler models of substitution are used, but the underestimation caused by ignoring rate variation over nucleotide sites is much more serious. The goodness of fit of a model is reduced by ignoring spatial rate variation, but unrealistic assumptions about the pattern of nucleotide substitution can lead to an extraordinary reduction in the likelihood. It seems that evolutionary biologists can obtain accurate estimates of certain evolutionary parameters even with an incorrect phylogeny, while systematists cannot get the right tree with confidence even when a realistic, and more complex, model of evolution is assumed.

Computer Simulation↗

PubMed2005

Application of spectrofluorometry to the prediction of PHB concentrations in a fed-batch process.

On-line estimation of biopolymer production during fermentation would be a useful adjunct to the development of strategies for process control and optimization. This study examined the applicability of spectrofluorometry, along with other on-line measurements, for the prediction of poly-beta-hydroxybutyric acid (PHB) concentrations in a high-cell density fed-batch fermentation of Ralstonia eutropha. Models previously used for modelling PHB evolution with time are not sufficiently accurate for situations where transient intermediate accumulations or PHB degradation occur. Thus, the mass balance in the model was modified to account for these situations. An estimation algorithm was developed that is based on a hybrid model consisting of a dynamic mass balance of PHB where the main reaction coefficient was regressed with respect to spectrofluorometric data. The regression between the kinetic parameter and the spectrofluorometric data was accomplished using partial least squares (PLS) regression to avoid high sensitivity to noise expected from highly correlated data, such as the spectrofluorometric readings. The model accounts for dynamics of intermediates and in this way allows the prediction of dynamic behaviour in PHB concentrations that cannot be predicted with other reported mathematical models.

Algorithms↗

PubMed2005

Modelling the spatio-temporal evolution of 3H in the waters of the River Tagus.

Measurements of tritium specific activity levels and of temperatures in waters of the Torrejón-Tagus reservoir (Spain) showed that their radioactive characteristics were basically influenced by the radioactive liquid effluent from the Almaraz Nuclear Power Plant. This enters the Torrejón-Tagus reservoir via the Arrocampo cooling reservoir, which exchanges water with the first. We studied the temporal and spatial (in two dimensions) evolution of the mentioned parameters for years 1997 and 1998. The tritium levels were found to be significantly correlated with temperature. Two numerical models were constructed for a quantitative study of the tritium levels along Torrejón reservoir: a 1D model was used for the dispersion of tritium along the whole length of the reservoir, and a 2D depth-averaged model was used for a detailed study of the area where tritium is released into the reservoir. Both models solve the hydrodynamic equations, to obtain the currents induced by the exchanges of water between the reservoirs in the River Tagus and Arrocampo, and the advection/diffusion equation to calculate the dispersion of tritium. In general, the model results were in agreement with the experimental observations.

Environmental Monitoring↗

PubMed2004

On inconsistency of the neighbor-joining, least squares, and minimum evolution estimation when substitution processes are incorrectly modeled.

Using analytical methods, we show that under a variety of model misspecifications, Neighbor-Joining, minimum evolution, and least squares estimation procedures are statistically inconsistent. Failure to correctly account for differing rates-across-sites processes, failure to correctly model rate matrix parameters, and failure to adjust for parallel rates-across-sites changes (a rates-across-subtrees process) are all shown to lead to a "long branch attraction" form of inconsistency. In addition, failure to account for rates-across-sites processes is also shown to result in underestimation of evolutionary distances for a wide variety of substitution models, generalizing an earlier analytical result for the Jukes-Cantor model reported in Golding and a similar bias result for the GTR or REV model in Kelly and Rice (1996). Although standard rates-across-sites models can be employed in many of these cases to restore consistency, current models cannot account for other kinds of misspecification. We examine an idealized but biologically relevant case, where parallel changes in rates at sites across subtrees is shown to give rise to inconsistency. This changing rates-across-subtrees type model misspecification cannot be adjusted for with conventional methods or without carefully considering the rate variation in the larger tree. The results are presented for four-taxon trees, but the expectation is that they have implications for larger trees as well. To illustrate this, a simulated 42-taxon example is given in which the microsporidia, an enigmatic group of eukaryotes, are incorrectly placed at the archaebacteria-eukaryotes split because of incorrectly specified pairwise distances. The analytical nature of the results lend insight into the reasons that long branch attraction tends to be a common form of inconsistency and reasons that other forms of inconsistency like "long branches repel" can arise in some settings. In many of the cases of inconsistency presented, a particular incorrect topology is estimated with probability converging to one, the implication being that measures of uncertainty like bootstrap support will be unable to detect that there is a problem with the estimation. The focus is on distance methods, but previous simulation results suggest that the zones of inconsistency for distance methods contain the zones of inconsistency for maximum likelihood methods as well.

Archaea↗

PubMed2006

Application of the secondary structure model of rRNA for phylogeny: D2-D3 expansion segments of the LSU gene of plant-parasitic nematodes from the family Hoplolaimidae Filipjev, 1934.

Knowledge of rRNA structure is increasingly important to assist phylogenetic analysis through reconstructing optimal alignment, utilizing molecule features as an additional source of data and refining appropriate models of evolution of the molecule. We describe a procedure of optimization for alignment and a new coding method for nucleotide sequence data using secondary structure models of the D2 and D3 expansion fragments of the LSU-rRNA gene reconstructed for fifteen nematode species of the agriculturally important and diverse family Hoplolaimidae, order Tylenchida. Using secondary structure information we converted the original sequence data into twenty-eight symbol codes and submitted the transformed data to maximum parsimony analysis. We also applied the original sequence data set for Bayesian inference. This used the doublet model with sixteen states of nucleotide doublets for the stem region and the standard model of DNA substitution with four nucleotide states for loops and bulges. By this approach, we demonstrate that using structural information for phylogenetic analyses led to trees with lower resolved relationships between clades and likely eliminated some artefactual support for misinterpreted relationships, such as paraphyly of Helicotylenchus or Rotylenchus. This study as well as future phylogenetic analyses is herein supported by the development of an on-line database, NEMrRNA, for rRNA molecules in a structural format for nematodes. We also have developed a new computer program, RNAstat, for calculation of nucleotide statistics designed and proposed for phylogenetic studies.

Animals↗

PubMed2006

Frustration and hydrophobicity interplay in protein folding and protein evolution.

A lattice model is used to study mutations and compacting effects on protein folding rates and folding temperature. In the context of protein evolution, we address the question regarding the best scenario for a polypeptide chain to fold: either a fast nonspecific collapse followed by a slow rearrangement to form the native structure or a specific collapse from the unfolded state with the simultaneous formation of the native state. This question is investigated for optimized sequences, whose native state has no frustrated contacts between monomers, and also for mutated sequences, whose native state has some degree of frustration. It is found that the best scenario for folding may depend on the amount of frustration of the native structure. The implication of this result on protein evolution is discussed.

Algorithms↗

PubMed2005

Toric ideals of phylogenetic invariants.

Statistical models of evolution are algebraic varieties in the space of joint probability distributions on the leaf colorations of a phylogenetic tree. The phylogenetic invariants of a model are the polynomials which vanish on the variety. Several widely used models for biological sequences have transition matrices that can be diagonalized by means of the Fourier transform of an abelian group. Their phylogenetic invariants form a toric ideal in the Fourier coordinates. We determine generators and Gröbner bases for these toric ideals. For the Jukes-Cantor and Kimura models on a binary tree, our Gröbner bases consist of certain explicitly constructed polynomials of degree at most four.

Animals↗

PubMed1997

Bottleneck effect on evolutionary rate in the nearly neutral mutation model.

Variances of evolutionary rates among lineages in some proteins are larger than those expected from simple Poisson processes. This phenomenon is called overdispersion of the molecular clock. If population size N is constant, the overdispersion is observed only in a limited range of 2N sigma under the nearly neutral mutation model, where sigma represents the standard deviation of selection coefficients of new mutants. In this paper, we investigated effects of changing population size on the evolutionary rate by computer simulations assuming the nearly neutral mutation model. The size was changed cyclically between two numbers, N1 and N2 (N1 > N2), in the simulations. The overdispersion is observed if 2N2 sigma is less than two and the state of reduced size (bottleneck state) continues for more than approximately 0.1/u generations, where u is the mutation rate. The overdispersion results mainly because the average fitnesses of only a portion of populations go down when the population size is reduced and only in these populations subsequent advantageous substitutions occur after the population size becomes large. Since the fitness reduction after the bottleneck is stochastic, acceleration of the evolutionary rate does not necessarily occur uniformly among loci. From these results, we argue that the nearly neutral mutation model is a candidate mechanism to explain the overdispersed molecular clock.

Biological Evolution↗

PubMed2005

Do orthologous gene phylogenies really support tree-thinking?

BACKGROUND: Since Darwin's Origin of Species, reconstructing the Tree of Life has been a goal of evolutionists, and tree-thinking has become a major concept of evolutionary biology. Practically, building the Tree of Life has proven to be tedious. Too few morphological characters are useful for conducting conclusive phylogenetic analyses at the highest taxonomic level. Consequently, molecular sequences (genes, proteins, and genomes) likely constitute the only useful characters for constructing a phylogeny of all life. For this reason, tree-makers expect a lot from gene comparisons. The simultaneous study of the largest number of molecular markers possible is sometimes considered to be one of the best solutions in reconstructing the genealogy of organisms. This conclusion is a direct consequence of tree-thinking: if gene inheritance conforms to a tree-like model of evolution, sampling more of these molecules will provide enough phylogenetic signal to build the Tree of Life. The selection of congruent markers is thus a fundamental step in simultaneous analysis of many genes. RESULTS: Heat map analyses were used to investigate the congruence of orthologues in four datasets (archaeal, bacterial, eukaryotic and alpha-proteobacterial). We conclude that we simply cannot determine if a large portion of the genes have a common history. In addition, none of these datasets can be considered free of lateral gene transfer. CONCLUSION: Our phylogenetic analyses do not support tree-thinking. These results have important conceptual and practical implications. We argue that representations other than a tree should be investigated in this case because a non-critical concatenation of markers could be highly misleading.

Algorithms↗

PubMed1976

The measure-unit of evolution.

A theoretical study on evolution has been carried out, with the aim of disproving some value judgements essentially represented by the idea that the degree of evolution can increase. Our conclusions are based upon the preliminary statement that efficiency of survival is directly related to regulative ability. On this ground our reasoning led us to conclude that: (i) actual fitness measure units derive from an anthropocentric bias, and they mainly evaluate similarity to man rather than some objective parameter; (ii) a complete and meaningful unit is, at present, impossible to achieve in practice; (iii) since the study of evolution is only descriptive, and since the evolutionary process is time dependent, every ecological dominant living today must be considered as the most fitted to its environment; (iv) the view we can have of evolution is simply a transection, so that many generalized phyletic trees are trivial and it is impossible to claim the persistence today of those "ancestor organisms" upon which such trees are constructed. Moreover, a functional definition of the term "organism" is given, following criteria drawn from bioenergetics and from biological hierarchization. The concluding step is the assemblage of a slightly heterodox model for evolution.

Base Sequence↗

PubMed1993

Evolution of a quality-based compensation model: the third generation.

U.S. Healthcare (USHC) contracts for care with primary care physicians who are compensated through capitation (i.e., a fixed payment at specific intervals per member for all care provided, irrespective of the number of services). The amount of capitation is dependent upon their quality assessment rating and their ability to manage the cost of care effectively. In January of 1992 USHC implemented its current, third-generation incentive model and significantly altered its Quality Care Compensation System. The evolution of this model is presented to demonstrate that this third-generation Quality Care Compensation Model is a fair and effective means of measuring and valuing the delivery of health care to a population. It rewards physicians who expend the extra effort to manage both quality and cost. The experience of USHC continues to demonstrate that it is possible to develop and monitor incentive mechanisms in a systematic fashion with quality improvement as the outcome.

Adult↗

PubMed2001

The evolution of medical technology: lessons from the Burgess Shale.

Many forthcoming medical advances-growth factors, tissue engineering, gene therapy, attachable prosthetic limbs, and implantable computers--are so new that as yet there is no clinical experience with them. Each therapeutic technique will evolve in an environment containing few guideposts to help judge its efficacy and safety. Recent developments in evolution theory (based on an analysis of Cambrian fossils in Canada's Burgess Shale quarry) suggest that evolution passes, at times, through innovative cycles of progress--when diversification of design leads to perfection of form--with the concomitant production of many unsuccessful models. The evolution of the total knee replacement is a perfect example of the process, because many of the early devices have proven to be dismal failures. However, modern knee replacements would not have been developed without them. Because the risk of unforeseen complications associated with new medical products cannot be discerned in advance, each patient-consumer should have the opportunity to intelligently weigh an innovative product's risk potential against its possible benefit. The proposal made here, for a temporary New Product status for new drugs and devices after a product is cleared by the Food and Drug Administration for general marketing, provides a mechanism for making such decisions.

Humans↗