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PubMed2005

Evolutionary suicide.

The great majority of species that lived on this earth have gone extinct. These extinctions are often explained by invoking changes in the environment, to which the species has been unable to adapt. Evolutionary suicide is an alternative explanation to such extinctions. It is an evolutionary process in which a viable population adapts in such a way that it can no longer persist. In this paper different models, where evolutionary suicide occurs are discussed, and the theory behind the phenomenon is reviewed.

Adaptation, Biological↗
PubMed1990

The 18S ribosomal RNA sequence of the sea anemone Anemonia sulcata and its evolutionary position among other eukaryotes.

Evolutionary trees based on partial small ribosomal subunit RNA sequences of 22 metazoa species have been published [(1988) Science 239, 748-753]. In these trees, cnidarians (Radiata) seemed to have evolved independently from the Bilateria, which is in contradiction with the general evolutionary view. In order to further investigate this problem, the complete srRNA sequence of the sea anemone Anemonia sulcata was determined and evolutionary trees were constructed using a matrix optimization method. In the tree thus obtained the sea anemone and Bilateria together form a monophyletic cluster, with the sea anemone forming the first line of the metazoan group.

Animals↗
PubMed1996

Inconsistency of evolutionary tree topology reconstruction methods when substitution rates vary across characters.

A fundamental problem in reconstructing the evolutionary history of a set of species is to infer the topology of the evolutionary tree that relates those species. A statistical method for estimating such a topology from character data is called consistent if, given data from more and more characters, the method is sure to converge to the true topology. A number of popular methods are based on modeling the evolution of each character as a Markov process along the evolutionary tree. The standard models further assume that each character has in fact evolved according to the same Markov process. This homogeneity assumption is unrealistic; for example, different types of characters are known to experience substitutions at different rates. Certain distance and maximum likelihood methods for topology estimation have been shown to be consistent under the homogeneity assumption. Here we give examples showing that these methods can fail to be consistent when the homogeneity assumption is relaxed. The examples are very simple, requiring only four taxa, binary characters, and characters that evolve at two different rates.

Animals↗
PubMedDate not supplied

Prospective and retrospective tests of evolutionary theories of senescence.

Retrospective and prospective methods in the study of the evolution of longevity and senescence are compared. Retrospective studies can provide tests of evolutionary theories of senescence through the interpretation of evolutionary pattern demonstrated by species in nature. Patterns in longevity displayed by African rivulin fishes provide a clear and incisive example of the evolution of longevity and associated life history characters, but such tests are often difficult to find or unclear in the a posteriori interpretation of evolution that they offer. Far more experimentation of the prospective kind has been applied to testing theories of life span. Though prospective tests of evolutionary theory are compromised to a degree by the artificiality of the laboratory environment, experiments performed there are not necessarily invalid. In addition, prospective tests offer the added impetus that theoretical predictions are tested a priori. The use of Drosophila melanogaster as a laboratory model for the study of longevity has provided a number of particularly enlightening recent advances describing the number and distribution of genes controlling longevity, the metabolic pathways by which other characters are physiologically associated with life span, and even the controlling genetic elements affecting those traits. Improvements in longevity shown under programs of selective breeding may be the result of adaptations in the glycolytic pathway altering the ability to utilize the sugar sucrose as a food source.

Journal Article↗
PubMed1995

A comparison of methods for self-adaptation in evolutionary algorithms.

Evolutionary algorithms, including evolutionary programming and evolution strategies, have often been applied to real-valued function optimization problems. These algorithms generally operate directly on the real values to be optimized, in contrast with genetic algorithms which usually operate on a separately coded transformation of the objective variables. Evolutionary algorithms often rely on a second-level optimization of strategy parameters, tunable variables that in part determine how each parent will generate offspring. Two alternative methods for performing this second-level optimization have been proposed and are compared across a series of function optimization tasks. The results appear to favor the approach offered originally in evolution strategies, although the applicability of the findings may be limited to the case where each parameter of a parent solution is perturbed independently of all others.

Algorithms↗
PubMed1996

Evolutionary stability in the n-person iterated prisoner's dilemma.

The iterated prisoner's dilemma game has been used extensively in the study of the evolution of cooperative behaviours in social and biological systems. The concept of evolutionary stability provides a useful tool to analyse strategies for playing the game. Most results on evolutionary stability, however, are based on the 2-person iterated prisoner's dilemma game. This paper extends the results in the 2-person game and shows that no finite mixture of pure strategies in the n-person iterated prisoner's dilemma game can be evolutionarily stable, where n > 2. The paper also shows that evolutionary stability can be achieved if mistakes are allowed in the n-person game.

Animals↗
PubMedDate not supplied

Environmental quality induced predicted by evolutionary theory.

The use of evolutionary theory to understand and predict environmental quality indices has been described. Three specific examples concerning the environmental health implications of black skin, heat stress adaptation, and G-6-PD deficiency have been discussed in which evolutionary theory provides the conceptual framework for novel insights and reasonable predictions of environment, pollutant and human interactions. The use of the evolutionary paradigm in the development of environmental quality indices offers a clear alternative to trial and error research efforts.

Biological Evolution↗
PubMed1990

An evolutionary perspective of endotoxin: a signal for a well-adapted defense system.

In the evolutionary view of endotoxin presented here, endotoxin is the primary signal animals use to detect gram negative (Gr-) bacteria. Since endotoxin, or lipopolysaccharide (LPS), is an integral part of the surface of all Gr- bacteria, it was excellent evolutionary 'choice' for the signal. The concept of an 'endotoxin response system' (ERS) is introduced. The ERS protects against Gr- bacteria by employing many of the body's defenses to both detect and react against LPS. The intensity of the response has evolved to maximize protection while minimizing the biological cost and self-damaging effects. The setting of the response, here termed the 'endostat', is programmed by natural selection and fine tuned by feedback mechanisms. Other potentially invasive organisms are detected by different signals, but the effector components of the defenses are similar. This evolutionary view of LPS offers a framework for the seemingly contradictory findings on endotoxin and suggests new avenues of productive research.

Adaptation, Physiological↗
PubMedDate not supplied

Menopause: an evolutionary perspective.

Evolutionary biologists classify theories of menopause as either: 1) adaptive, suggesting that female reproductive cessation results from its selective advantage, in that the increased risk of personal reproduction late in life makes it biologically more advantageous to rechannel reproductive energy into helping existing descendents, or 2) nonadaptive, indicating menopause is an artifact of the relatively recent dramatic increase in human longevity. With the possible exception of pilot whales, no mammals studied to date are known to commonly exhibit reproductive cessation in nature. To demonstrate adaptive menopause, one would need to establish both that the longevity of preagricultural humans commonly allowed them to exhibit menopause, and that postreproductive females could assist their descendents sufficiently to compensate for the loss of personal reproduction. The data on longevity of preagricultural humans with respect to the adaptive menopause hypothesis are mixed. Evolutionary models evaluated with data from modern hunting-gathering or agricultural humans fail to find that humans can assist their descendents sufficiently to offset the evolutionary cost of ceasing reproduction. However, assuming the human body has been physiologically adapted to the conditions extant during the vast majority of human history, it may be well worth pursuing how the signs and symptoms of menopause are affected by dietary, exercise, and reproductive hormone regimes mimicking those of the late Paleolithic era.

Animals↗
PubMedDate not supplied

Evolutionary patterns among measures of aging.

Maximum lifespan has been one of the most common aging measures in comparative studies, while the Gompertz model has recently attracted both proponents and critics of its capacity to adequately describe the acceleration of mortality in the oldest age classes. The Gompertz demographic model describes age-dependent mortality rate acceleration and age-independent mortality using the parameters alpha and A, respectively. Evolutionary biologists have predominantly used average longevity in studies of aging. Little is known about the evolutionary relationships of these measures on the microevolutionary time scale. We have simultaneously compared Gompertz parameters, average longevity, and maximum longevity in 50 related populations of Drosophila melanogaster, many of which have been selected for postponed aging. Overall, these populations have differentiated significantly for the A and alpha parameter of the Gompertz equation, as well as average and maximum longevity. These indices of aging appear to measure the same genetic changes in aging. However, in some specific population comparisons, the relationships among these measures are more complex. In a second experiment, environmental manipulation of longevity had substantially different effects from genetic differentiation, with the A parameter accounting for changes in overall mortality. The adequacy of the maximum lifespan and the Gompertz equation as indices of aging in evolutionary studies is discussed.

Aging↗
PubMed1992

A statistical method for detecting regions with different evolutionary dynamics in multialigned sequences.

We describe a stochastic method for tracing the evolutionary pattern of multialigned sequences. This method allows us to detect gene regions with distinct evolutionary dynamics, e.g., regions that significantly deviate from the expected behavior. Accurate detection of hypervariable or hyperconstrained regions may provide useful information on the structure/function relationship of biosequences. This information can help localize functional constraints. In addition, the selection of distinct evolutionary dynamics may assist in the correct use of biosequences as reliable molecular clocks.

Animals↗
PubMed2006

Metazoan OXPHOS gene families: evolutionary forces at the level of mitochondrial and nuclear genomes.

Mitochondrial and nuclear DNAs contribute to encode the whole mitochondrial protein complement. The two genomes possess highly divergent features and properties, but the forces influencing their evolution, even if different, require strong coordination. The gene content of mitochondrial genome in all Metazoa is in a frozen state with only few exceptions and thus mitochondrial genome plasticity especially concerns some molecular features, i.e. base composition, codon usage, evolutionary rates. In contrast the high plasticity of nuclear genomes is particularly evident at the macroscopic level, since its redundancy represents the main feature able to introduce genetic material for evolutionary innovations. In this context, genes involved in oxidative phosphorylation (OXPHOS) represent a classical example of the different evolutionary behaviour of mitochondrial and nuclear genomes. The simple DNA sequence of Cytochrome c oxidase I (encoded by the mitochondrial genome) seems to be able to distinguish intra- and inter-species relations between organisms (DNA Barcode). Some OXPHOS subunits (cytochrome c, subunit c of ATP synthase and MLRQ) are encoded by several nuclear duplicated genes which still represent the trace of an ancient segmental/genome duplication event at the origin of vertebrates.

Animals↗
PubMed2004

Evolutionary dynamics of cellular automata-based self-replicators in hostile environments.

In this paper we investigate population dynamics, genealogy and complexity-increase of locally interacting populations of cellular automata-based evolving self-replicating loops (evoloops). We outline experiments indicating that the evolutionary growth in complexity, known to be achievable in principle given the complete genetic accessibility granted by universal construction, may be achievable in practice using much simpler replicating structures. By introducing evoloop populations to hostile environments, we demonstrate that selection pressures toward smaller species can be mediated to enable evolutionary accessibility to larger species, which themselves roam a much more vast portion of genetic state-space. We show that this growth in size results from intrinsically biased genealogy inherent in the rules of the evoloop CA, normally suppressed by selection pressures from direct competition favouring the smallest species. This shows that, in populations of simple self-replicating structures, a limited form of complexity-increase may result from a process which is driven by biased genealogical connectivity--a purely emergent property arising out of bottom-up evolutionary dynamics--and not just by adaptation . Implications of this result are discussed and contrasted with other self-replication studies in Artificial Life and Biology.

Cells↗
PubMed2005

On the use of multi-objective evolutionary algorithms for the induction of fuzzy classification rule systems.

Extracting comprehensible and general classifiers from data in the form of rule systems is an important task in many problem domains. This study investigates the utility of a multi-objective evolutionary algorithm (MOEA) for this task. Multi-objective evolutionary algorithms are capable of finding several trade-off solutions between different objectives in a single run. In the context of the present study, the objectives to be optimised are the complexity of the rule systems, and their fit to the data. Complex rule systems are required to fit the data well. However, overly complex rule systems often generalise poorly on new data. In addition they tend to be incomprehensible. It is, therefore, important to obtain trade-off solutions that achieve the best possible fit to the data with the lowest possible complexity. The rule systems produced by the proposed multi-objective evolutionary algorithm are compared with those produced by several other existing approaches for a number of benchmark datasets. It is shown that the algorithm produces less complex classifiers that perform well on unseen data.

Algorithms↗
PubMed2006

On the use of multi-objective evolutionary algorithms for survival analysis.

This paper proposes and evaluates a multi-objective evolutionary algorithm for survival analysis. One aim of survival analysis is the extraction of models from data that approximate lifetime/failure time distributions. These models can be used to estimate the time that an event takes to happen to an object. To use of multi-objective evolutionary algorithms for survival analysis has several advantages. They can cope with feature interactions, noisy data, and are capable of optimising several objectives. This is important, as model extraction is a multi-objective problem. It has at least two objectives, which are the extraction of accurate and simple models. Accurate models are required to achieve good predictions. Simple models are important to prevent overfitting, improve the transparency of the models, and to save computational resources. Although there is a plethora of evolutionary approaches to extract models for classification and regression, the presented approach is one of the first applied to survival analysis. The approach is evaluated on several artificial datasets and one medical dataset. It is shown that the approach is capable of producing accurate models, even for problems that violate some of the assumptions made by classical approaches.

Algorithms↗
PubMed2005

Thermodynamical interpretation of evolutionary dynamics on a fitness landscape in an evolution reactor, II.

In our previous report [Aita, T., Morinaga, S., Hosimi, Y., 2004. Thermodynamical interpretation of evolutionary dynamics on a fitness landscape in an evolution reactor I. Bull. Math. Biol. 66, 1371-1403], an analogy between thermodynamics and adaptive walks on a Mt. Fuji-type fitness landscape in an artificial selection system was presented. Introducing the 'free fitness' as the sum of a fitness term and an entropy term and 'evolutionary force' as the gradient of free fitness on a fitness coordinate, we demonstrated that the adaptive walk (=evolution) is driven by the evolutionary force in the direction in which free fitness increases. In this report, we examine the effect of various modifications of the original model on the properties of the adaptive walk. The modifications were as follows: first, mutation distance d was distributed obeying binomial distribution; second, the selection process obeyed the natural selection protocol; third, ruggedness was introduced to the landscape according to the NK model; fourth, a noise was included in the fitness measurement. The effect of each modification was described in the same theoretical framework as the original model by introducing 'effective' quantities such as the effective mutation distance or the effective screening size.

Algorithms↗
PubMed2004

Evolutionary rate variation and RNA secondary structure prediction.

Predicting RNA secondary structure using evolutionary history can be carried out by using an alignment of related RNA sequences with conserved structure. Accurately determining evolutionary substitution rates for base pairs and single stranded nucleotides is a concern for methods based on this type of approach. Determining these rates can be hard to do reliably without a large and accurate initial alignment, which ideally also has structural annotation. Hence, one must often apply rates extracted from other RNA families with trusted alignments and structures. Here, we investigate this problem by applying rates derived from tRNA and rRNA to the prediction of the much more rapidly evolving 5'-region of HIV-1. We find that the HIV-1 prediction is in agreement with experimental data, even though the relative evolutionary rate between A and G is significantly increased, both in stem and loop regions. In addition we obtained an alignment of the 5' HIV-1 region that is more consistent with the structure than that currently in the database. We added randomized noise to the original values of the rates to investigate the stability of predictions to rate matrix deviations. We find that changes within a fairly large range still produce reliable predictions and conclude that using rates from a limited set of RNA sequences is valid over a broader range of sequences.

Algorithms↗
PubMed2004

The interaction among evolutionary forces in the pathogenic fungus Mycosphaerella graminicola.

The population genetic dynamic of a species is driven by interactions among mutation, migration, drift, mating system, and selection, but it is rare to have sufficient empirical data to estimate values for all of these forces and to allow comparison of the relative magnitudes of these evolutionary forces. We combined data from a mark-release-recapture experiment, extensive population surveys, and computer simulations to evaluate interactions among these evolutionary forces in the pathogenic fungus Mycosphaerella graminicola. The results from these studies showed that, on average, the immigration rate was 0.027, the fraction of outcrossing individuals was 0.035, and the selection coefficient associated with immigrants was 0.106 each generation. We also estimated that effective population sizes for this fungus were larger than 24,000 and the mutation rate for the RFLP markers used in surveys and field experiments was approximately 4 x 10(-5). Computer simulations based on these estimates indicate that, on average, the global population of M. graminicola has reached equilibrium. Population genetic parameters including number of alleles, gene diversity, and population subdivision estimated from the computer simulations were surprisingly close to empirical estimates. Simulations also revealed that random drift is the major evolutionary force decreasing genetic variation in this fungus, followed by natural selection. The major force adding to genetic variation was mutation, followed by gene flow and sexual recombination. Gene flow played the leading role in decreasing population subdivision while natural selection was the major factor increasing population subdivision.

Ascomycota↗