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PubMed2000

Is Echo a complex adaptive system?

We evaluate whether John Holland's Echo model exemplifies his theory of complex adaptive systems. After reviewing Holland's theory of complex adaptive systems and describing his Escho model, we describe and explain the characteristic evolutionary behavior observed in a series of Echo model runs. We conclude that Echo lacks the diversity of hierarchically organized aggregates that typify complex adaptive systems, and we explore possible explanations for this failure.

Algorithms↗
PubMed1987

Comparison of solvent-inaccessible cores of homologous proteins: definitions useful for protein modelling.

The three-dimensional structures of 41 homologous proteins (belonging to eight families) were compared by pairwise superposition. A subset of 'core' residues was defined as those whose side chains have less than 7% of their surface exposed to solvent. This subset has significantly higher sequence identity and lower root mean square (RMS) alpha carbon separation than for all topologically equivalent residues in the structure, when members of a protein family are superposed. For such superpositions the relationship between RMS distance and percentage sequence identity of this subset of residues is similar to that for all equivalent residues, although some variation is observed between families of proteins which are predominantly beta sheet and those which are mainly alpha helix. The definition of a structurally more conserved core may be useful in model building proteins from an homologous family. The RMS differences of coordinates of structures of proteins with identical sequences are found to be related to the resolutions of the structures.

Biological Evolution↗
PubMed1998

Quasispecies and the implications for virus persistence and escape.

BACKGROUND: In the 1970s Manfred Eigen and colleagues proposed a new model of molecular evolution to explain adaptability and rapid evolution of simple replicons, as those that probably populated the earth at the onset of life. This model of evolution placed emphasis on mutant generation, to the point of invalidating the concept of wild-type genomes as a defined sequence of nucleotides. In striking similarity with the proposals for such early replicons, present-day RNA viruses consist of complex distributions of nonidentical but closely related genomes termed quasispecies. OBJECTIVES: To discuss indeterminations inherent to a quasispecies structure and to the analytical procedures to define it, biological implications of quasispecies, and the need to take into account this type of population structure, in order to design effective strategies to prevent and control diseases caused by highly variable viruses. RESULTS: Quasispecies have many biological implications, extending from viral pathogenesis to the emergence of new pathogens, rapid antigenic variation, and alterations in cell tropism, virulence, host range and viral gene expression. CONCLUSIONS: Diseases caused by highly variable RNA viruses prove very difficult to control and vaccine development against such viruses are largely unsuccessful. It is important to understand quasispecies composition and dynamics, as quasispecies are an important step in the natural history of RNA viruses.

Animals↗
PubMed1998

Rose: generating sequence families.

MOTIVATION: We present a new probabilistic model of the evolution of RNA-, DNA-, or protein-like sequences and a software tool, Rose, that implements this model. Guided by an evolutionary tree, a family of related sequences is created from a common ancestor sequence by insertion, deletion and substitution of characters. During this artificial evolutionary process, the 'true' history is logged and the 'correct' multiple sequence alignment is created simultaneously. The model also allows for varying rates of mutation within the sequences, making it possible to establish so-called sequence motifs. RESULTS: The data created by Rose are suitable for the evaluation of methods in multiple sequence alignment computation and the prediction of phylogenetic relationships. It can also be useful when teaching courses in or developing models of sequence evolution and in the study of evolutionary processes. AVAILABILITY: Rose is available on the Bielefeld Bioinformatics WebServer under the following URL: http://bibiserv.TechFak.Uni-Bielefeld.DE/rose/ The source code is available upon request. CONTACT: folker@TechFak.Uni-Bielefeld.DE

Algorithms↗
PubMed2001

Necessary and sufficient conditions for evolutionary suicide.

Evolutionary suicide is an evolutionary process where a viable population adapts in such a way that it can no longer persist. It has already been found that a discontinuous transition to extinction is a necessary condition for suicide. Here we present necessary and sufficient conditions, concerning the bifurcation point, for suicide to occur. Evolutionary suicide has been found in structured metapopulation models. Here we show that suicide can occur also in unstructured population models. Moreover, a structured model does not guarantee the possibility of suicide: we show that suicide cannot occur in age-structured population models of the Gurtin-MacCamy type. The point is that the mutant's fitness must explicitly depend not only on the environmental interaction variable, but also on the resident strategy.

Adaptation, Biological↗
PubMed1987

Darwinian evolution in games with perfect information.

We consider a model of Darwinian evolution in games with perfect information like chess or checkers. The evolution is viewed as a sequence of strategies, each of which wins over its immediate predecessor. We argue that the intelligence level of strategies need not necessarily increase during this type of evolution.

Algorithms↗
PubMed2005

Food choices at lunch during the third year of life: increase in energy intake but decrease in variety.

AIM: Modelling the evolution between the ages of 2 and 3 y of the energy intake and the variety of free food choices at lunch time in relation to children's and context variables. METHODS: One-year follow-up from 2 to 3 y old. In a nursery canteen, food choices at lunch were recorded by trained assistants who monitored portion size. Energy intake and food variety were estimated. Three hundred and ninety-five children were studied, for 112 meals and over 10 mo on average. Mixed models of analysis of variance were used to take into account the longitudinal character of the data. RESULTS: From 2 to 3 y, energy intake increased. Variety decreased during the first 7 mo and then remained constant. The individual variability in mean values and in evolution was high for both variables. Energy was positively linked to BMI at 2 y. Variety was slightly higher for girls and increased with duration of breastfeeding. Energy was higher in September to November than in December-January. Variety was maximal in December-January and in June-July. CONCLUSION: During the third year of life, while energy intake increases, the restriction of food variety appears to be a normal transition phase. Long duration of breastfeeding is associated with higher food variety.

Age Factors↗
PubMed1995

Molecular evolution of the genes encoding receptor tyrosine kinase with immunoglobulinlike domains.

Receptor tyrosine kinases (RTK) with five, three, or seven immunoglobulinlike domains in their extracellular regions are classified as subclasses III, IV, and V, respectively. Conservation of the exon/intron structure of the downstream part of the human KIT, FMS, and FLT3 genes that encode RTK of subclass III together with the particular chromosomal localization of these genes suggests that RTKIII genes have evolved from a common ancestor by cis and trans duplications. To strengthen this model of evolution and to determine if it can be extended to RTKIV and V genes, we constructed a phylogenetic tree of RTKIII, IV, and V on the basis of a multiple alignment of their catalytic tyrosine kinase domain sequences and determined the exon/intron structure of PDGFRA (subclass III), FGFR4 (subclass IV), and FLT4 (subclass V) genes in their downstream part. Phylogenetic analyses with amino acid or nucleotide sequences both resulted in one most parsimonious tree. The phylogenetic trees obtained indicate that all three subclasses are well individuated and that RTKIII and RTKV are closer to each other than RTKIV. Furthermore, RTKIII and FLT4 (subclass V) genes possess the same exon/intron structure in their downstream part while the structure of the RTKIV genes is very similar to that of RTKIII and FLT4. Both approaches are in complete agreement and indicate that RTKIII, IV, and V genes most probably evolved from a common ancestor already "in pieces" by successive duplications involving entire genes.

Alternative Splicing↗
PubMed2003

Play and the evolution of fairness: a game theory model.

Bekoff [J. Consci. Stud. 8 (2001) 81] argued that mammalian social play is a useful behavioral phenotype on which to concentrate in order to learn more about the evolution of fairness. Here, we build a game theoretical model designed to formalize some of the ideas laid out by Bekoff, and to examine whether 'fair' strategies can in fact be evolutionarily stable. The models we present examine fairness at two different developmental stages during an individual's ontogeny, and hence we create four strategies-fair at time 1/fair at time 2, not fair at time 1/not fair at time 2, fair at time 1/not fair at time 2, not fair at time 1/fair at time 2. Our results suggest that when considering species where fairness can be expressed during two different developmental stages, acting fairly should be more common than never acting fairly. In addition, when no one strategy was evolutionarily stable, we found that all four strategies we model can coexist at evolutionary equilibrium. Even in the absence of an overwhelming database from which to test our model, the general predictions we make have significant implications for the evolution of fairness.

Journal Article↗
PubMed2002

Coexistence of sexual and asexual conspecifics: a cellular automaton model.

Most previous models of populations mixed for reproductive mode have omitted important local interactions between sexual and asexual individuals. We propose a cellular automaton model where local rules focus on fertilization and colonization. This model produces rich sets of data which are then studied by means of spatial statistics. Results point to the fixation of one of the two reproductive modes in the landscape. However, some examples of coexistence of sexual and asexual conspecifics over long periods of time are also found. This model is an example of a CA that diverges from its mean field approximation. The formation of sexual and asexual clusters reduces effective colonization rate in the CA and may account for this behaviour.

Biological Evolution↗
PubMed2006

The unified neutral theory of biodiversity: do the numbers add up?

Hubbell's unified neutral theory is a zero-sum ecological drift model in which population sizes change at random in a process resembling genetic drift, eventually leading to extinction. Diversity is maintained within the community by speciation. Hubbell's model makes predictions about the distribution of species abundances within communities and the turnover of species from place to place (beta diversity). However, ecological drift cannot be tested adequately against these predictions without independent estimates of speciation rates, population sizes, and dispersal distances. A more practical prediction from ecological drift is that time to extinction of a population of size N is approximately 2N generations. I test this prediction here using data for passerine birds (Passeriformes). Waiting times to speciation and extinction were estimated from genetic divergence between sister populations and a lineage-through-time plot for endemic South American suboscine passerines. Population sizes were estimated from local counts of birds in two large forest plots extrapolated to the area of wet tropical forest in South America and from atlas data on European passerines. Waiting times to extinction (ca. 2 Ma) are much less than twice the product of average population size (4.0 and 14.4 x 10(6) individuals in South America and Europe) and generation length (five and three years) for songbirds, that is, 40 and 86 Ma, respectively. Thus, drift is too slow to account for turnover in regional avifaunas. Presumably, other processes, involving external drivers, such as climate and physiographic change, and internal drivers, such as evolutionary change in antagonistic interactions, predominate. Hubbell's model is historical and geographic, and his perspective importantly links local and regional process and pattern. Ecological reality can be added to the mix while retaining Hubbell's concept of continuity of communities in space and time.

Biodiversity↗
PubMed2004

Interhemispheric interaction and beliefs on our origin: degree of handedness predicts beliefs in creationism versus evolution.

It has been suggested that strongly handed individuals have attenuated systems for updating beliefs compared to mixed handers (Niebauer, Aselage, & Schutte, 2002). The current research extended this theory to individual differences in updating beliefs concerning our origins. Although the theory of evolution has gained overwhelming success in the sciences, a significant percentage of the population believes in biblical creationist accounts of human origins that are inconsistent with accepted, contemporary scientific views. If strongly handed individuals possess attenuated systems for updating beliefs, they might be more likely to believe in creationism. In two studies, strongly handed participants were more likely to believe in creationism while mixed-handed participants were more likely to believe in evolution. A model of how interhemispheric interaction functions in maintaining and updating beliefs is discussed. Specifically, mixed-handedness seems to be associated with a lower threshold for updating beliefs.

Adolescent↗
PubMed2003

Mathematical models of cell colonization of uniformly growing domains.

During the development of vertebrate embryos, cell migrations occur on an underlying tissue domain in response to some factor, such as nutrient. Over the time scale of days in which this cell migration occurs, the underlying tissue is itself growing. Consequently cell migration and colonization is strongly affected by the tissue domain growth. Numerical solutions for a mathematical model of chemotactic migration with no domain growth can lead to travelling waves of cells with constant velocity; the addition of domain growth can lead to travelling waves with nonconstant velocity. These observations suggest a mathematical approximation to the full system equations, allowing the method of characteristics to be applied to a simplified chemotactic migration model. The evolution of the leading front of the migrating cell wave is analysed. Linear, exponential and logistic uniform domain growths are considered. Successful colonization of a growing domain depends on the competition between cell migration velocity and the velocity and form of the domain growth, as well as the initial penetration distance of the cells. In some instances the cells will never successfully colonize the growing domain. These models provide an insight into cell migration during embryonic growth, and its dependence upon the form and timing of the domain growth.

Animals↗
PubMed2006

Cooperation should not be assumed.

Evolutionary game theory provides a framework for explaining social interactions, including those between males and females. In a recent article, Roughgarden et al. discuss a new approach to sexual selection based on cooperative game theory and argue that cooperation rather than competition is fundamental in interactions between the sexes. However, compelling reasons for adopting this approach are not given and the authors do not adopt it consistently. We argue that non-cooperative game theory provides an adequate basis for understanding sexual selection, but that further work is needed to produce realistic models. We agree with Roughgarden and colleagues that bargaining is an important aspect of social interactions, but this is not a novel claim. Bargaining does not require the assumption of cooperation and does not necessarily lead to it.

Biological Evolution↗
PubMed2000

Quasi-equilibrium theory for the distribution of rare alleles in a subdivided population: justification and implications.

This paper examines a quasi-equilibrium theory of rare alleles for subdivided populations that follow an island-model version of the Wright-Fisher model of evolution. All mutations are assumed to create new alleles. We present four results: (1) conditions for the theory to apply are formally established using properties of the moments of the binomial distribution; (2) approximations currently in the literature can be replaced with exact results that are in better agreement with our simulations; (3) a modified maximum likelihood estimator of migration rate exhibits the same good performance on island-model data or on data simulated from the multinomial mixed with the Dirichlet distribution, and (4) a connection between the rare-allele method and the Ewens Sampling Formula for the infinite-allele mutation model is made. This introduces a new and simpler proof for the expected number of alleles implied by the Ewens Sampling Formula.

Alleles↗
PubMed1983

Selective constraint in protein polymorphism: study of the effectively neutral mutation model by using an improved pseudosampling method.

To investigate the pattern of allelic distribution in enzyme polymorphism, with special reference to the relationship between the mean (H) and the variance (V(H)) of heterozygosity, we used the model of effectively neutral mutations involving multiple alleles in which selective disadvantage of mutant alleles follows a Gamma distribution. A simulation method was developed that enables us to study efficiently the process of random drift in a multiallelic genetic system and that saves a great deal of computer time. It is an improved version of the pseudosampling-variable (PSV) method [Kimura, M. (1980) Proc. Natl. Acad. Sci. USA 77, 522-526] previously used to simulate random drift in a diallelic system. This method will be useful for simulating many models of population genetics that involve behavior of multiple alleles in a finite population. By using this method, it was shown that, as compared with the model of strictly neutral mutations, the present model gives the reduction of both H and V(H) and an excess of rare variant alleles. The results were discussed in the light of recent observations on protein polymorphism with special reference to the functional constraint of proteins involved.

Alleles↗
PubMed1995

Disaggregation in population forecasting: do we need it? And how to do it simply.

"We have described a method for reducing the dimensionality of the forecasting problem by parsimoniously modeling the evolution over time of the age schedules of vital rates. This method steers a middle course between forecasting aggregates and forecasting individual age specific rates: we reduce the problem to forecasting a single parameter for fertility and another one for mortality. We have described a number of refinements and extensions of those basic methods, which preserve their underlying structure and simplicity. In particular, we show how one can fit the model more simply, incorporate lower bounds to the forecasts of rates, disaggregate by sex or race, and prepare integrated forecasts of rates for a collection of regions. We also discuss alternate approaches to forecasting the estimated indices of fertility and mortality, including state-space methods. These many versions of the basic method have yielded remarkably similar results." (SUMMARY IN FRE)

Age Distribution↗