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PubMed1983

Selection and evolution in macromolecular systems.

The notion of a quasi-species represents the ensemble of macromolecular sequences derived by the mechanism of mutation and replication from a single wild type. In Eigen (1971) and Eigen & Schuster (1979), the deterministic evolution of this ensemble under constant environmental conditions is given in terms of continuous models which describe the dynamics of the distribution of polynucleotides. This paper starts from a discrete model of macromolecular evolution and introduces the notion of a genealogy in order to study the dynamics of the quasi-species in constant and variable environments. We introduce, in terms of these genealogies, the notions of entropy and adaptive value of a quasi-species and the notion of capacity of the environment. We discuss the significance of these indices as measures of selective value and we analyse the conditions under which these measures coincide with the growth rate of the quasi-species.

Base Sequence↗

PubMed1997

Male-driven evolution of DNA sequences in birds.

Assuming that new mutations arise mainly during DNA replication, sequence evolution in mammals has been seen as 'male driven' (ref. 1) because of the many more cell divisions in spermatogenesis than in oogenesis. Molecular support for this idea has been obtained from the observation of higher substitution rates in genes on the Y than on the X chromosome of primates and rodents, which are species with male heterogamety, but has not been confirmed by the reciprocal analysis of organisms with female heterogamety. The recent suggestion that an intrinsic reduction in the X-chromosome mutation rate may be confounded with male effects in previous comparisons, and the paradoxical finding of low levels of polymorphism on the primate Y chromosome indicate that the idea of male-biased mutation rate needs to be re-examined. We have analysed the molecular evolution of the gene CHD, which is present on the Z and W sex chromosomes of birds. The substitution rate at synonymous positions, as well as in intron DNA, was considerably higher on the Z chromosome than on the female-specific W chromosome, with an estimated male-to-female bias in mutation rate (alpha m) of 3.9-6.5. Thus, evolution appears to be male driven in birds--a situation that supports a neutral model of molecular evolution.

Animals↗

PubMed2003

Food competition in captive female sooty mangabeys (Cercocebus torquatus atys).

We studied the social and foraging behavior of two captive groups of sooty mangabeys under two different spatial food situations. These food conditions were clumped (food was placed in a box) and dispersed (food was dispersed over the entire enclosure). In each group five adult females and two adult males were observed. As a criterion for food competition, individual differences in the relative food intake were used. Adult female mangabeys had a linear, stable, and unidirectional dominance hierarchy. Access to food was rank dependent among females only under clumped food distribution, as current models of the evolution of primate social systems predict. However, feeding success appeared to be mediated not by female but by male agonistic behavior toward females. High-ranking females received relatively less aggression from males and could, therefore, stay and feed longer in the feeding area. Male tolerance of higher-ranking females seems to mediate female feeding success under restricted food resources. The establishment of a special relationship with a high-ranking male might, therefore, be a strategy to get better access to food. This study demonstrates that female competition for access to food should not be analyzed separately from male influences on females and suggests that a more integral role of males in socioecological models of the evolution of primate social systems should be considered.

Animals↗

PubMed2002

Learning and the evolution of language: the role of cultural variation and learning costs in the Baldwin effect.

The Baldwin effect has been explicitly used by Pinker and Bloom as an explanation of the origins of language and the evolution of a language acquisition device. This article presents new simulations of an artificial life model for the evolution of compositional languages. It specifically addresses the role of cultural variation and of learning costs in the Baldwin effect for the evolution of language. Results show that when a high cost is associated with language learning, agents gradually assimilate in their genome some explicit features (e.g., lexical properties) of the specific language they are exposed to. When the structure of the language is allowed to vary through cultural transmission, Baldwinian processes cause, instead, the assimilation of a predisposition to learn, rather than any structural properties associated with a specific language. The analysis of the mechanisms underlying such a predisposition in terms of categorical perception supports Deacon's hypothesis regarding the Baldwinian inheritance of general underlying cognitive capabilities that serve language acquisition. This is in opposition to the thesis that argues for assimilation of structural properties needed for the specification of a full-blown language acquisition device.

Algorithms↗

PubMed2003

Maternal control of offspring sex and male morphology in the Otitesella fig wasps.

Models concerning the evolution of alternative mating tactics commonly assume that individuals determine their own strategies. Here we develop a computer-based ESS model that allows mothers, ovipositing in discrete patches, to choose both the sex and the male mating tactics (natal-patch mating or dispersing) of their offspring based only on how many other mothers have used the specific patch before them. Data for three species of nonpollinating fig wasps from the Otitesella genus agree quantitatively with the model's assumptions and predictions. This suggests that females respond to population densities at the level of individual figs. The alternative male tactics in the species we studied are probably a result of a conditional strategy exercised by the mother that laid them. In addition, as females were only allowed to lay one egg per patch, our results suggest a new mechanism that can skew population sex ratios towards a female bias.

Animals↗

PubMed1998

Evolution of a transfer RNA gene through a point mutation in the anticodon.

The transfer RNA (tRNA) multigene family comprises 20 amino acid-accepting groups, many of which contain isoacceptors. The addition of isoacceptors to the tRNA repertoire was critical to establishing the genetic code, yet the origin of isoacceptors remains largely unexplored. A model of tRNA evolution, termed "tRNA gene recruitment," was formulated. It proposes that a tRNA gene can be recruited from one isoaccepting group to another by a point mutation that concurrently changes tRNA amino acid identity and messenger RNA coupling capacity. A test of the model showed that an Escherichia coli strain, in which the essential tRNAUGUThr gene was inactivated, was rendered viable when a tRNAArg with a point mutation that changed its anticodon from UCU to UGU (threonine) was expressed. Insertion of threonine at threonine codons by the "recruited" tRNAArg was corroborated by in vitro aminoacylation assays showing that its specificity had been changed from arginine to threonine. Therefore, the recruitment model may account for the evolution of some tRNA genes.

Anticodon↗

PubMed1998

Adaptive Walks by the Fittest among Finite Random Mutants on a Mt. Fuji-type Fitness Landscape.

Based on the theory of fitness distributions on a Mt. Fuji-type fitness landscape in a multivalued sequence space (Aita & Husimi, 1996 J. theor. Biol. 182, 469-485), we investigated the properties of adaptive walks on the ideal landscape in the case of a cloning-screening-type evolution experiment. We modeled that an adaptive walk is performed by repetition of the evolution cycle composed of the mutagenesis process generating random d-fold point mutants of population size N and the selection process looking for the fittest mutant among them. While an adaptive walk is described in a sequence space, we simplified the description as follows. We mapped the landscape in an x-y plane, where x and y represent a normalized Hamming distance from the global peak and a scaled fitness, respectively. An adaptive walk is described as a trajectory in the plane. The most certain step for a walker to move in a single evolution cycle is represented by a vector in the plane. Then, a walker moves along the streams in the vector field determined by d and N. The walker performs fast hill-climbing until a "trap-line", which traverses the plane. Subsequently, the walker is likely to get trapped in an "apparent local optimum". To continue the walk, apparent local optima must be eliminated by resetting d and N larger. Therefore, for the fastest walk, the optimal schedule of the d-values (initially large d, then small d) is effective, although the economical walk with high cost-performance is different. If a real landscape is just of the Mt. Fuji-type, the walk with the highest cost-performance will be performed by scanning site-directed optimization through all sites. However, in the case of the rough Mt. Fuji-type, which seems to be more realistic, the walking method we have examined will be effective for a walker to sidestep true local optima.Copyright 1998 Academic Press

Journal Article↗

PubMed1993

The D/H ratio and the evolution of water in the terrestrial planets.

The presence of liquid water at the surface of the Earth has played a major role in the biological evolution of the Earth. None of the other terrestrial planets--Mercury, Venus and Mars--has liquid water at its surface. However, it has been suggested, since the early seventies, from both geological and atmospheric arguments that, although Venus and Mars are presently devoid of liquid water, their surfaces could have been partially or completely covered by water at some time of their evolution. There are many possible diagnostics of the long-term evolution of the planets, either from the present characteristics of their surfaces or from their present atmospheric compositions. Among them, the present value of the D/H ratio is of particular interest, although its significance in terms of long term evolution has been challenged by some authors. Recent progress has been made in this field. We now have evidence for higher D/H ratios on Mars and Venus than on Earth, with an enrichment factor of the order of 5 on Mars, and about 100 on Venus. Any scenario for the evolution of these planets must take this into The most recent models on the evolution of Mars and Venus are reviewed in light of these new measurements.

Atmosphere↗

PubMed2005

Diffuse-interface model for rapid phase transformations in nonequilibrium systems.

A thermodynamic approach to rapid phase transformations within a diffuse interface in a binary system is developed. Assuming an extended set of independent thermodynamic variables formed by the union of the classic set of slow variables and the space of fast variables, we introduce finiteness of the heat and solute diffusive propagation at the finite speed of the interface advancing. To describe transformations within the diffuse interface, we use the phase-field model which allows us to follow steep but smooth changes of phase within the width of the diffuse interface. Governing equations of the phase-field model are derived for the hyperbolic model, a model with memory, and a model of nonlinear evolution of transformation within the diffuse interface. The consistency of the model is proved by the verification of the validity of the condition of positive entropy production and by outcomes of the fluctuation-dissipation theorem. A comparison with existing sharp-interface and diffuse-interface versions of the model is given.

Journal Article↗

PubMed2005

DNA sequence polymorphism and divergence at the erect wing and suppressor of sable loci of Drosophila melanogaster and D. simulans.

Several evolutionary models of linked selection (e.g., genetic hitchhiking, background selection, and random environment) predict a reduction in polymorphism relative to divergence in genomic regions where the rate of crossing over per physical distance is restricted. We tested this prediction near the telomere of the Drosophila melanogaster and D. simulans X chromosome at two loci, erect wing (ewg) and suppressor of sable [su(s)]. Consistent with this prediction, polymorphism is reduced at both loci, while divergence is normal. The reduction is greater at ewg, the more distal of the two regions. Two models can be discriminated by comparing the observed site frequency spectra with those predicted by the models. The hitchhiking model predicts a skew toward rare variants in a sample, while the spectra under the background-selection model are similar to those of the neutral model of molecular evolution. Statistical tests of the fit to the predictions of these models require many sampled alleles and segregating sites. Thus we used SSCP and stratified DNA sequencing to cover a large number of randomly sampled alleles (approximately 50) from each of three populations. The result is a clear trend toward negative values of Tajima's D, indicating an excess of rare variants at ewg, the more distal of the two loci. One fixed difference among the populations and high FST values indicate strong population subdivision among the three populations at ewg. These results indicate genetic hitchhiking at ewg, in particular, geographically localized hitchhiking events within Africa. The reduction of polymorphism at su(s) combined with the excess of high-frequency variants in D. simulans is inconsistent with the hitchhiking and background-selection models.

Animals↗

PubMed1992

The hu-PBL-SCID mouse model. Long-term human serologic evolution associated with the xenogeneic transfer of human peripheral blood leukocytes into SCID mice.

We present a 2-year serologic analysis of severe combined immune deficiency (SCID) mice populated with human peripheral blood leukocytes (PBL, hu-PBL-SCID mice). After 10-20 x 10(6) PBL transfer, human IgG serum levels generally increased in the SCID mouse recipient for 2 months, and thereafter decreased without returning to zero for at least 2 years. Great variability existed between different hu-PBL-SCID mice with regard to Ig serum levels even when derived from the same donor's PBL aliquot. The ratio of IgM to IgG serum levels was lower in hu-PBL-SCID mice than in the donors. The half-life of human IgG in the SCID mouse is shorter than in the human (8 days vs 23 days), suggesting a much higher production of IgG than expected from serum levels. The majority of hu-PBL-SCID mouse sera analyzed by high resolution electrophoresis had a smear appearance suggestive of diverse human Ig, generally with superimposed multiple faint mIg. Few mice developed strong human mIg, associated with lymphoproliferative diseases. In the hu-PBL-SCID mouse model, the transfer of cells from donors making antibody with defined specificity against TT and nuclear antigen resulted in the appearance of these antibodies in only a minority of the recipients.

Animals↗

PubMed2004

Different versions of the Dayhoff rate matrix.

Many phylogenetic inference methods are based on Markov models of sequence evolution. These are usually expressed in terms of a matrix (Q) of instantaneous rates of change but some models of amino acid replacement, most notably the PAM model of Dayhoff and colleagues, were originally published only in terms of time-dependent probability matrices (P(t)). Previously published methods for deriving Q have used eigen-decomposition of an approximation to P(t). We show that the commonly used value of t is too large to ensure convergence of the estimates of elements of Q. We describe two simpler alternative methods for deriving Q from information such as that published by Dayhoff and colleagues. Neither of these methods requires approximation or eigen-decomposition. We identify the methods used to derive various different versions of the Dayhoff model in current software, perform a comparison of existing and new implementations, and, to facilitate agreement among scientists using supposedly identical models, recommend that one of the new methods be used as a standard.

Animals↗

PubMed1995

Evolution of the Enterococcus faecalis sex pheromone system.

In this article we present data that form the basis of a model of the evolution of the unique Enterococcus faecalis sex pheromone system. The data indicate tht sex pheromone plasmid-encoded genes/functions, which are essential for this highly efficient plasmid collection system, are common among all sex pheromone plasmids; pAM373 seems to be only distantly related to all other pheromone plasmids. These genes appear to be restricted to sex pheromone plasmids (but see below for possible exceptions). However, the ability to produce sex pheromone-like peptides is not restricted to E. faecalis. We argue that the sex pheromone system of E. faecalis developed only once--but into at least 19 different variants--to form a system which is highly specific for this bacterium and is related to virulence.

Adhesins, Bacterial↗

PubMed1999

Using protein structural information in evolutionary inference: transmembrane proteins.

We present a model of amino acid sequence evolution based on a hidden Markov model that extends to transmembrane proteins previous methods that incorporate protein structural information into phylogenetics. Our model aims to give a better understanding of processes of molecular evolution and to extract structural information from multiple alignments of transmembrane sequences and use such information to improve phylogenetic analyses. This should be of value in phylogenetic studies of transmembrane proteins: for example, mitochondrial proteins have acquired a special importance in phylogenetics and are mostly transmembrane proteins. The improvement in fit to example data sets of our new model relative to less complex models of amino acid sequence evolution is statistically tested. To further illustrate the potential utility of our method, phylogeny estimation is performed on primate CCR5 receptor sequences, sequences of l and m subunits of the light reaction center in purple bacteria, guinea pig sequences with respect to lagomorph and rodent sequences of calcitonin receptor and K-substance receptor, and cetacean sequences of cytochrome b.

Animals↗

PubMed1990

Analysis of the inheritance, selection and evolution of growth trajectories.

We present methods for estimating the parameters of inheritance and selection that appear in a quantitative genetic model for the evolution growth trajectories and other "infinite-dimensional" traits that we recently introduced. Two methods for estimating the additive genetic covariance function are developed, a "full" model that fully fits the data and a "reduced" model that generates a smoothed estimate consistent with the sampling errors in the data. By decomposing the covariance function into its eigenvalues and eigenfunctions, it is possible to identify potential evolutionary changes in the population's mean growth trajectory for which there is (and those for which there is not) genetic variation. Algorithms for estimating these quantities, their confidence intervals, and for testing hypotheses about them are developed. These techniques are illustrated by an analysis of early growth in mice. Compatible methods for estimating the selection gradient function acting on growth trajectories in natural or domesticated populations are presented. We show how the estimates for the additive genetic covariance function and the selection gradient function can be used to predict the evolutionary change in a population's mean growth trajectory.

Animals↗

PubMed1995

The multiregional and single origin hypotheses of the evolution of modern man: a reconciliation.

A current debate opposes two theories of the origin of modern man. One view is that modern Homo sapiens emerged from Africa relatively recently, most probably within the last two or three hundred thousand years (Wilson & Cann, 1992, Sci. Am. 266(4), 22-27). The opposing view is that modern man has resulted from parallel evolution in different regions, producing convergent modernization of local populations over the last million years or so--the multiregional model (Frayer et al., 1993, Am. Anthrop. 95, 14-50). Proponents of both views believe that their interpretations are irreconcilable. The object of the present paper is to describe a genetic mechanism--mitochondrial exclusion--which offers a basis for a model of human evolution that is compatible with the evidence adduced for both contemporary views. The model proposes a mechanism by which complete replacement of archaic mitochondrial DNA may have occurred in a population produced by recent admixture of archaic and modern types of man.

Animals↗

PubMed1984

Emergence of adaptable systems and evolution of a translation device.

An over-all organizational framework for the origin of life is outlined and attempts for realization are given. Evolution can be described as a process resulting in an increase of "knowledge" where knowledge is the number of carriers of genetic information discarded, on the average, until the evolutionary state under consideration is reached. A model for the evolution of a translation device, a crucial event in the origin of life, is described in detail. Aggregates of short polynucleotide strands in a hairpin conformation play a major role in this model. Experimental evidence for the selectivity of aggregation supports the idea of aggregates as error filters. Chromatographic separation as selection process during chemical evolution supports the model of the early translation device leading to the origin of the genetic code.

Amino Acids↗

PubMed1998

Evolution by nearly-neutral mutations.

Genetic systems are complex and interact at various levels; among amino acids or nucleotide sites, among gene products, and among regulatory regions and proteins. Patterns of synonymous and nonsynonymous substitutions of mammalian genes indicate that nonsynonymous substitutions are nearly neutral, coming from interactions among amino acids. As an interactive system, the NK model of Kauffman was analysed. This model assumes that each amino acid makes a fitness contribution that depends upon the amino acid and upon K other amino acids among the N that make the protein. Through simulations, it was found that there are numerous nearly-neutral mutations in this model, and that evolution is rapid in small populations and slow in large ones. The system moves on the rugged fitness landscape by mutation, random genetic drift and selection. Small populations have more chance to attain novel genetic systems than large ones because of larger effects of random drift, but the chance of extinction becomes greater.

Animals↗