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PubMed2003

In silico protein recombination: enhancing template and sequence alignment selection for comparative protein modelling.

Comparative modelling of proteins is a predictive technique to build an atomic model for a given amino acid sequence, on the basis of the structures of other proteins (templates) that have been determined experimentally. Critical problems arise in this procedure: selecting the correct templates, aligning the query sequence with them and building the non-conserved surface loops. In this work, we apply a genetic algorithm, with crossover and mutation, as a new tool to overcome the first two. In silico protein recombination proves to be an effective way to exploit the variability of templates and sequence alignments to produce populations of optimized models by artificial selection. Despite some limitations, the procedure is shown to be robust to alignment errors, while simplifying the task of selecting templates, making it a good candidate for automatic building of reliable protein models.

Algorithms↗

PubMed1975

Genetic change and rates of cladogenesis.

Models are introduced which predict ratios of mean levels of genetic divergence in species-rich versus species-poor phylads under two competing assumptions: (1) genetic differentiation is a function of time, unrelated to the number of cladogenetic events and (2) genetic differentiation is proportional to the number of speciation events in the group. The models are simple, general, and biologically real, but not precise. They lead to qualitatively distinct predictions about levels of genetic divergence depending upon the relationship between rates of speciation and amount of genetic change. When genetic distance between species is a function of time, mean genetic distances in speciose and depauperate phylads of equal evolutionary age are very similar. On the contrary, when genetic distance is a function of the number of speciations in the history of a phylad, the ratio of mean genetic distances separating species in speciose versus depauperate phylads is greater than one, and increases rapidly as the frequency of speciations in one group relative to the other increases. The models may be tested with data from natural populations to assess (1) possible correlations between rates of anagenesis and cladogenesis and (2) the amount of genetic differentiation accompanying the speciation process. The data collected in electrophoretic surveys and other kinds of studies can be used to test the predictions of the models. For this purpose genetic distances need to be measured in speciose and depauperate phylads of equal evolutionary age. The limited information presently available agrees better with the model predicting that genetic change is primarily a function of time, and is not correlated with rates of speciation. Further testing of the models is, however, required before firm conclusions can be drawn.

Biological Evolution↗

PubMedDate not supplied

Capuchin monkey tool use and Léon Croizat's ideas on the evolution of human behavior.

This note reviews Léon Croizat's ideas about the evolution of human behavior, based on his evaluation of the tool use capabilities of a capuchin monkey. Croizat theorized mainly on his orthogenetic view to explain such behavior. Interesting enough is the timeframe (1962) and context of his statement and the monkey's model used for such explanation. In this direction, some comments are provided considering the current knowledge of capuchin tool using and its potential implications for modeling hominid evolution.

Animals↗

PubMed2003

Waddington's widget: Hsp90 and the inheritance of acquired characters.

Conrad Waddington published an influential model for evolution in his 1942 paper, Canalization of Development and Inheritance of Acquired Characters. In this classic, albeit controversial, paper, he proposed that an unknown mechanism exists that conceals phenotypic variation until the organism is stressed. Recent studies have proposed that the highly conserved chaperone Hsp90 could function as a "capacitor," or an "adaptively inducible canalizer," that masks silent phenotypic variation of either genetic or epigenetic origin. This review will discuss evidence for, and arguments against, the role of Hsp90 as a capacitor for morphological evolution, and as a key component of what we call "Waddington's widget."

Animals↗

PubMed1997

The meaning of near-neutrality at coding and non-coding regions.

The nature of weak selection differs between coding and non-coding regions. Coding regions contain genetic information, whereas most non-coding regions do not have any information. Genetic information may be regarded as interaction systems, and the NK model of Kauffman was analysed. This model assumes that each amino acid makes a fitness contribution that depends on the amino acid and on K other amino acids among the N that make the protein. Through simulations, it was found that there are numerous nearly-neutral mutations under this model. Therefore, evolution is rapid in small populations, and slow in large populations. The variance of the evolutionary rate is not quite as large as data indicate under the model, and additional factors, such as environmental change or population-size fluctuation, need to be considered. Weak selection at non-coding regions may come from chromosome organization, and may be regional in character, which differs from that at coding regions. The problem of genetic load is thought to disappear in these circumstances.

Gene Frequency↗

PubMed1997

A likelihood approach to populations samples of microsatellite alleles.

This paper presents a likelihood approach to population samples of microsatellite alleles. A Markov chain recursion method previously published by GRIFFITHS and TAVARE is applied to estimate the likelihood function under different models of microsatellite evolution. The method presented can be applied to estimate a fundamental population genetics parameter theta as well as parameters of the mutational model. The new likelihood estimator provides a better estimator of theta in terms of the mean square error than previous approaches. Furthermore, it is demonstrated how the method may easily be applied to test models of microsatellite evolution. In particular it is shown how to compare a one-step model of microsatellite evolution to a multi-step model by a likelihood ratio test.

Alleles↗

PubMed2003

Streamer initiation in atmospheric pressure gas discharges by direct particle simulation.

A two-dimensional particle code that simulates electrical breakdown of gases by modeling avalanche evolution from the initial ion-electron pair up to the development of a streamer is presented. Trajectories of individual particles are followed, the self-field is included consistently and collision processes are accurately modeled using experimentally determined cross sections. It is emphasized that the tadpolelike structure of well-formed streamer heads is present throughout the avalanche phase, and that the transition to the self-similar evolution characteristic of the streamer phase merely reflects the continued development of this structure. The importance of this for conventional fluid simulations of streamers, where the initial conditions for the streamer are taken to be a structureless Gaussian concentration of neutral plasma with significant density, is discussed. In the (realistic) situation where several avalanches are present simultaneously the large self-fields that rapidly develop lead to a strong interaction between them, in accord with the standard "cartoon" of streamer evolution.

Journal Article↗

PubMed2002

"Living" under the challenge of information decay: the stochastic corrector model vs. hypercycles.

The combined problem of having a large genome size when the accuracy of replication was a limiting factor is probably the most difficult transition to explain at the late stages of RNA world. One solution has been to suggest the existence of a cyclically coupled system of autocatalytic and cross-catalytic molecular mutualists, where each member helps the following member and receives help from the preceding one (i.e., a "hypercycle"). However, such a system is evolutionarily unstable when mutations are taken into account because it lacks individuality. In time, the cooperating networks of genes should have been encapsulated in a cell-like structure. But once the cell was invented, it closely aligned genes' common interests and helped to reduce gene selfishness, so there was no need for hypercycles. A simple package of competing genes, described by the "stochastic corrector model" (SCM), could have provided the solution. Until now, there is no clear demonstration that the proposed mechanisms (compartmentalized hypercycles and the stochastic corrector model) do in fact solve the error threshold problem. Here, we present a Monte Carlo model to test the viability of protocell populations that enclose a hypercyclic (HPC) or a non-hypercyclic (SCM) system when faced with realistic mutation rates before the evolution of efficient enzymic machinery for replication. The numerical results indicate that both systems are efficient information integrators and are able to overcome the danger of information decay in the absence of accurate replication. However, a population of SCM protocells can tolerate higher deleterious mutation rates and reaches an equilibrium mutational load lower than that in a population of HPC protocells.

Animals↗

PubMed2004

The biopsychosocial model in medical research: the evolution of the health concept over the last two decades.

The object of this study was to assess the change towards a biopsychosocial health concept among medical researchers in the last two decades, after the explicit criticism of the biomedical model in the late 1970s because of its somatic reductionism. The concepts of 'health' or 'healthy status of an individual' as reported as variable in empirical articles published in the journal The Lancet over the years 1978-1982 (period a) and 1996-2000 (period b) were searched by means of Medline and compared for their definition of these variables. None of the 52 examined papers set out a positive and replicable definition of 'health' (seven papers) or 'healthy status' (45). No difference was found between the two periods studied except for the failure of reports to describe 'healthy status' at all (65.5% in a, 19% in b). Most articles do it in an indirect way, namely through exclusion conditions of subjects taking part in treatment or control groups. Only three studies include psychological dimensions in their measures of 'healthy status' (two in a, one in b). Concerning 'health', all seven examined papers include psychological or both psychological and social dimensions. Although a change towards a more holistic concept of health has occurred in academic and institutional contexts over the last few decades, there does not appear to have been a parallel change in the practical domains of medicine. Possible reasons are discussed, specially the difficulty of applying the biopsychosocial model in medical care and the difficulty of competing with the traditional biomedical concept of health, which has proved fruitful and dominant in medicine over the past three centuries.

Attitude of Health Personnel↗

PubMed2005

In silico analysis of disease-association mapping strategies using the coalescent process and incorporating ascertainment and selection.

We present a new method for simulating samples of marker haplotypes, genotypes, or diplotypes in case-control studies in which the markers are linked to a disease locus in any specified region of the genome. The method allows realistic features to be incorporated into the simulations, including selection acting on disease alleles, sample ascertainment of disease chromosomes and polymorphic markers, a genetic dominance model of disease expression that allows incomplete penetrance and phenocopies, and an accurate genetic map of recombination rates and hotspots for recombination in the human genome (or, alternatively, an improved method for simulating the distribution of hotspots). The new method uses an approach that combines simulation of the coalescent process for the sampled chromosomes with a diffusion process used to model the evolution of the disease-mutation frequency over time. Examples illustrate how the method may be used to study the expected power of a marker-disease association study.

Alleles↗

PubMed2006

Phylogenomics and molecular evolution of polyomaviruses.

We provide in this chapter an overview of the basic steps to reconstruct evolutionary relationships through standard phylogeny estimation approaches as well as network approaches for sequences more closely related. We discuss the importance of sequence alignment, selecting models of evolution, and confidence assessment in phylogenetic inference. We also introduce the reader to a variety of software packages used for such studies. Finally, we demonstrate these approaches throughout using a data set of 33 whole genomes of polyomaviruses. A robust phylogeny of these genomes is estimated and phylogenetic relationships among the polyomaviruses determined using Bayesian and maximum likelihood approaches. Furthermore, population samples of SV40 are used to demonstrate the utility of network approaches for closely related sequences. The phylogenetic analysis suggested a close relationship among the BK viruses, JC viruses, and SV40 with a more distant association with mouse polyomavirus, monkey polymavirus (LPV) and then avian polyomavirus (BFDV).

Computational Biology↗

PubMed1984

Evolution of multigene families under interchromosomal gene conversion.

A model for the evolution of the probabilities of genetic identity within and between loci of a multigene family in a finite population is formulated and investigated. Unbiased interchromosomal gene conversion, equal crossing-over between tandemly repeated genes, random genetic drift, and mutation to new alleles are incorporated. Generations are discrete and nonoverlapping; the diploid, monoecious population mates at random. Formulae for the equilibrium values of the probabilities of identity and for the rate of convergence are deduced. At equilibrium, the amount of intralocus homology, f, always exceeds the amount of interlocus homology, ĝ. The equilibrium homologies f and ĝ and the characteristic convergence time T are independent of the crossover rate. As the population size and the number of repeats increase, f and ĝ decrease and T increases; as the rate of gene conversion increases, f and T decrease whereas ĝ increases. The time T can be sufficiently short to imply that interchromosomal gene conversion may be an important mechanism for maintaining sequence homogeneity among repeated genes.

Biological Evolution↗

PubMed2006

Modeling of pattern regulation in melanophores.

Melanosomes, pigment granules in melanophores, play a principal role in physiological color adaptation of fish and frog. Melanophores regulate melanosome trafficking on cytoskeletal filaments to generate a range of spatiotemporal patterns. Here, we present the first comprehensive model of spatiotemporal evolution of melanosome patterns. The model encompasses both physical and biochemical aspects of melanosome dynamics. It consists of (i) a kinetic description of biochemical reactions involved in intracellular signaling, (ii) a system of macroscopic reaction-diffusion-convection equations for melanosome concentration, and (iii) a set of constitutive relationships for coupling transport with the biochemical network. The model relates molecular-level regulatory actions to cell-level melanosome distribution, allowing unification of existing experimental observations and qualitative hypotheses into an integrated, consistent framework. The model reproduces salient features of melanosome patterns, both during transient and steady state. It gives useful insights into how cells coordinate motor-assisted transport to maintain and adapt spatial organization of intracellular organelles. In particular, we calculate the optimal transition paths from aggregation to dispersion in fish melanophores. The calculations suggest that fish melanophores optimally control intracellular signaling to maximize the efficiency of motor-assisted transport during dispersion.

Adaptation, Physiological↗

PubMed2002

Genomic biodiversity, phylogenetics and coevolution in proteins.

Comprehensive sampling of genomic biodiversity is fast becoming a reality for some genomic regions and complete organelle genomes. Genomic biodiversity is defined as large genomic sequences from many species, and here some recent work is reviewed that demonstrates the potential benefits of genomic biodiversity for molecular evolutionary analysis and phylogenetic reconstruction. This work shows that using likelihood-based approaches, taxon addition can dramatically improve phylogenetic reconstruction. Features or dynamics of the evolutionary process are much more easily inferred with large numbers of taxa, and large numbers are essential for discriminating differences in evolutionary patterns between sites. Accurate prediction of site-specific patterns can improve phylogenetic reconstruction by an amount equivalent to quadrupling sequence length. Genomic biodiversity is particularly central to research relating patterns of evolution, adaptation and coevolution to structural and functional features of proteins. Research on detecting coevolution between amino acid residues in proteins demonstrates a clear need for much greater numbers of closely related taxa to better discriminate site-specific patterns of interaction, and to allow more detailed analysis of coevolutionary interactions between subunits in protein complexes. It is argued that parsing out coevolutionary and other context-dependent substitution probabilities is essential for discriminating between coevolution and adaptation, and for more realistically modelling the evolution of proteins. Also reviewed is research that argues for increasing the efficiency of acquiring genomic biodiversity, and suggests that this might be done by simultaneously shotgun cloning and sequencing genomic mixtures from many species. Increased efficiency is a prerequisite if genomic biodiversity levels are to rapidly increase by orders of magnitude, and thus lead to dramatically improved understanding of interactions between protein structure, function and sequence evolution.

Biodiversity↗

PubMed2000

Variation in modes and rates of evolution in nuclear and mitochondrial ribosomal DNA in the mushroom genus Amanita (Agaricales, Basidiomycota): phylogenetic implications.

Modes and rates of molecular evolution, and congruence and combinability for phylogenetic reconstruction, of portions of the nuclear large ribosomal subunit (nLSU-rDNA) and mitochondrial small subunit (mtSSU-rDNA) genes were investigated in the mushroom genus Amanita. The AT content was higher in the mtSSU-rDNA than in the nLSU-rDNA. A transition bias in which AT substitutions were as frequent as transitions was present in the mtSSU-rDNA but not in the nLSU-rDNA. Among-sites rate variation in nucleotide substitutions at variable sites was present in the nLSU-rDNA but not in the mtSSU-rDNA. Likelihood ratio tests indicated very different models of evolution for the two molecules. A molecular clock could be rejected for both data sets. Rates of molecular evolution in the two molecules were uncoupled: faster evolutionary rates in the mtSSU-rDNA and nLSU-rDNA were not observed for the same taxa. In separate phylogenetic analyses, the nLSU-rDNA data set had higher phylogenetic resolution. The partition homogeneity test and statistical bootstrap support for branches indicated absence of conflict in the phylogenetic signal in the two data sets; however, tree topologies produced from the separate data sets were not congruent. Heterogeneity in modes and rates of evolution in the two molecules pose difficulties for a combined analysis of the two data sets: the use of equally weighted parsimony is not fully satisfactory when rate heterogeneity is present, and it is impractical to determine a model for maximum-likelihood analysis that fits simultaneously two heterogeneous data sets. Overall topologies produced from either the separated or the combined analyses using various tree reconstruction methods were identical for nearly all statistically significant branches.

Amanita↗

PubMed1996

State-dependent life history evolution in Soay sheep: dynamic modelling of reproductive scheduling.

Adaptive decisions concerning the scheduling of reproduction in an animal's lifetime, including age at maturity and clutch or litter size, should depend on an animal's body condition or state. In this state-dependent case, we are concerned with the optimization of sequences of actions and so dynamic optimization techniques are appropriate. Here we show how stochastic dynamic programming can be used to study the reproductive strategies and population dynamics of natural populations, assuming optimal decisions. As examples we describe models based upon field data from an island population of Soay sheep on St. Kilda. This population shows persistent instability, with cycles culminating in high mortality every three or four years. We explore different assumptions about the extent to which Soay ewes use information about the population cycle in making adaptive decisions. We compare the observed distributions of strategies and population dynamics with model predictions; the results indicate that Soay ewes make optimal reproductive decisions given that they have no information about the population cycle. This study represents the first use of a dynamic optimization life history model of realistic complexity in the study of a field population. The techniques we use are potentially applicable to many other populations, and we discuss their extension to other species and other life history questions.

Acclimatization↗

PubMed2004

The effect of gene conversion on the divergence between duplicated genes.

Nonindependent evolution of duplicated genes is called concerted evolution. In this article, we study the evolutionary process of duplicated regions that involves concerted evolution. The model incorporates mutation and gene conversion: the former increases d, the divergence between two duplicated regions, while the latter decreases d. It is demonstrated that the process consists of three phases. Phase I is the time until d reaches its equilibrium value, d(0). In phase II d fluctuates around d(0), and d increases again in phase III. Our simulation results demonstrate that the length of concerted evolution (i.e., phase II) is highly variable, while the lengths of the other two phases are relatively constant. It is also demonstrated that the length of phase II approximately follows an exponential distribution with mean tau, which is a function of many parameters including gene conversion rate and the length of gene conversion tract. On the basis of these findings, we obtain the probability distribution of the level of divergence between a pair of duplicated regions as a function of time, mutation rate, and tau. Finally, we discuss potential problems in genomic data analysis of duplicated genes when it is based on the molecular clock but concerted evolution is common.

Animals↗

PubMed1999

Population dynamics and the evolution of virulence in epidemiological models with discrete host generations

Chaos is the likely outcome of the interaction between a parasite and a host with discrete generations, if the parasite's virulence is high and if transmission from one generation to the next is held constant. We studied two alternative routes of transmission-vertical transmission from infecteds to their offspring, and transmission via long-lasting spores produced in those individuals that were killed by the infection-to investigate the influence of the transmission route on the system's evolution and population dynamics. The major results are: (1) vertical transmission often leads to low virulence, thus confirming most epidemiological models. However, if hosts can become super-infected, the evolutionary dynamics of virulence can have several equilibrium points, including 100% disease-induced mortality; (2) when parasites are transmitted with long-lasting spores, the evolutionary dynamics of virulence can become unstable, leading to the repeated bifurcation of two sub-populations with high and low virulence or to punctuated equilibria with sudden changes in the average level of virulence; (3) in general, the evolution of virulence moves the system to an area where the population dynamics are stable. When evolution leads to chaos, the system most often becomes extinct. Only for a restricted parameter space in the system where transmission from one generation to the next is via long-lasting spores do the dynamics become chaotic without extinction of the system. Copyright 1999 Academic Press.

Journal Article↗