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PubMed2005

A model-based approach for detecting coevolving positions in a molecule.

We present a new method for detecting coevolving sites in molecules. The method relies on a set of aligned sequences (nucleic acid or protein) and uses Markov models of evolution to map the substitutions that occurred at each site onto the branches of the underlying phylogenetic tree. This mapping takes into account the uncertainty over ancestral states and among-site rate variation. We then build, for each site, a "substitution vector" containing the posterior estimates of the number of substitutions in each branch. The amount of coevolution for a pair of sites is then measured as the Pearson correlation coefficient between the two corresponding substitution vectors and compared to the expectation under the null hypothesis of independence. We applied the method to a 79-species bacterial ribosomal RNA data set, for which extensive structural characterization has been done over the last 30 years. More than 95% of the intramolecular predicted pairs of sites correspond to known interacting site pairs.

Base Sequence↗
PubMed1994

The reconstructed evolutionary process.

Phylogenies reconstructed from contemporary taxa do not contain information about lineages that have gone extinct. We derive probability models for such phylogenies, allowing real data to be compared with specified null models of evolution, and lineage birth and death rates to be estimated.

Animals↗
PubMed1996

Evolutionary perspective on a composite Shigella flexneri 2a virulence plasmid-borne locus comprising three distinct genetic elements.

Nucleotide sequence analysis of a Shigella flexneri 2a virulence plasmid-borne locus revealed that it comprised three distinct genetic elements: a stretch of colicin 1a/1b-linked sequence, a truncated IS911 element, and a third element containing two ORFs that shared a high level of similarity to a Salmonella-specific chromosomal sequence. Examination of other known IS911-like sequences showed that these sequences also were frequently associated with other accessory elements and appeared to be prone to partial deletion events. Analysis of the data led to a model of the evolution of this unusual composite locus.

Amino Acid Sequence↗
PubMed2003

Towards identifying lateral gene transfer events.

This paper is concerned with evaluating the performance of the model and algorithm in 5 for detecting lateral gene transfers events. Using a Poisson process to describe arrival times of transfer events, a simulation is used to generate "synthetic" gene and species trees. An implementation of an efficient algorithm in 5 is used to estimate the minimum number of transfers necessary to explain disagreements between the generated gene and species trees. Our first result suggests that the algorithm can solve realistic size instances of the problem. Our second result suggests that the mean error and variance are low when saturation does not occur. Additionally, certain plausible evolutionary events allowed by our model of evolution used to generate gene and species trees but not detectable by the algorithm occur rarely implying the framework should work well in practice. Our third, surprising result suggests that the number of optimal scenarios is on average low for realistic input sizes.

Algorithms↗
PubMed1992

Amino acid substitution of proteins coded for in mitochondrial DNA during mammalian evolution.

Three Markov models (Dayhoff, Proportional and Poisson models; Hasegawa et al., 1992a) for amino acid substitution during evolution were used for maximum likelihood analyses of proteins coded for in mitochondrial DNA in estimating a phylogenetic tree among human, bovine and murids (mouse and rat) with chicken as an outgroup. It turned out that Dayhoff model is the most appropriate model among the alternatives in approximating the amino acid substitutions of proteins coded for in mitochondrial DNA. In spite of the presence of the complete sequence data of mitochondrial genomes, we could not resolve the trichotomy among human, bovine and murids, probably because the time length separating two branching events among these three lines was short and because chicken is too distant from mammals to be used as an outgroup. It was suggested that the average substitution rate of amino acids coded for in mitochondrial DNA is lower along the bovine line than those along the human or murid lines. Advantages of amino acid sequence analysis over nucleotide sequence analysis in phylogenetic study were discussed.

Amino Acid Sequence↗
PubMedDate not supplied

Is the "small world" effect relevant to evolution?

Mutations and selection are the driving forces of biological evolution. We model here the simplest case: an evolving population of asexual organisms. We consider two kinds of mutations: point mutations, corresponding to local displacements in the genotypic space, and all the other genotypic rearrangements, equivalent to long-range jumps. We show that a small-world effect is present in evolution: even a small fraction of quenched long-range jumps makes the results indistinguishable from those obtained by assuming all mutations equiprobable. We apply this result to the evolution of a population on a smooth fitness landscape, showing that the equilibrium distribution is a Boltzmann one, in which the fitness plays the role of an energy, and mutations that of a temperature.

Evolution, Molecular↗
PubMed2001

The Baldwin effect: a neglected influence on C. G. Jung's evolutionary thinking.

This paper considers the claim that C. G. Jung used a Lamarckian model of evolution to underwrite his theory of archetypes. This claim is challenged on the basis of Jung's familiarity with and use of the writings of James Mark Baldwin and Conway Lloyd Morgan, both of whom were noted and forceful opponents of neo-Lamarckian theory from within a neo-Darwinian framework. The paper then outlines the evolutionary model proposed by Baldwin and Lloyd Morgan, which has come to be known as Baldwinian evolution or the Baldwin effect. This model explicitly views psychological factors as central to the evolutionary process. Finally, the use of Baldwinian thinking in contemporary theorizing regarding language and other symbolic systems is reviewed and suggestions are made regarding the implications of Baldwinian models for theory building in analytical psychology.

Animals↗
PubMed2006

Class prediction from time series gene expression profiles using dynamical systems kernels.

We present a kernel-based approach to the classification of time series of gene expression profiles. Our method takes into account the dynamic evolution over time as well as the temporal characteristics of the data. More specifically, we model the evolution of the gene expression profiles as a Linear Time Invariant (LTI) dynamical system and estimate its model parameters. A kernel on dynamical systems is then used to classify these time series. We successfully test our approach on a published dataset to predict response to drug therapy in Multiple Sclerosis patients. For pharmacogenomics, our method offers a huge potential for advanced computational tools in disease diagnosis, and disease and drug therapy outcome prognosis.

Artificial Intelligence↗
PubMed1996

Full reconstruction of Markov models on evolutionary trees: identifiability and consistency.

A Markov model of evolution of characters on a phylogenetic tree consists of a tree topology together with a specification of probability transition matrices on the edges of the tree. Previous work has shown that, under mild conditions, the tree topology may be reconstructed, in the sense that the topology is identifiable from knowledge of the joint distribution of character states at pairs of terminal nodes of the tree. Also, the method of maximum likelihood is statistically consistent for inferring the tree topology. In this article we answer the analogous questions for reconstructing the full model, including the edge transition matrices. Under mild conditions, such full reconstruction is achievable, not by using pairs of terminal nodes, but rather by using triples of terminal nodes. The identifiability result generalizes previous results that were restricted either to characters having two states or to transition matrices having special structure. The proof develops matrix relationships that may be exploited to identify the model. We also use the identifiability result to prove that the method of maximum likelihood is consistent for reconstructing the full model.

Animals↗
PubMed2006

Divergent outcomes of reinforcement speciation: the relative importance of assortative mating and migration modification.

Most studies of reinforcement speciation focus on the evolution of assortative mating, but R. A. Fisher argued that migration modification is likely to be a common alternative mechanism. Despite previous models showing that assortative mating and migration modification may both be involved in reinforcement, no one has determined their relative evolutionary importance. This is surprising because understanding the biological conditions favoring these mechanisms may explain why certain pairs of species exhibit abutting, nonoverlapping geographical ranges with habitat fidelity while other pairs coexist in sympatry with sexual isolation. In this article, we explicitly model the evolution of both mechanisms simultaneously. First, we explore how these mechanisms differ in their evolutionary dynamics. Second, we ask how they affect each other's evolution and whether the interaction alters their relative importance in reinforcement. Our results reveal that assortative mating may evolve faster and under a broader range of biological conditions than migration modification. However, direct evolutionary interactions favor migration modification when populations experience strong divergent selection. Depending on the nature of postmating isolation, these mechanisms may either interfere with each other's evolution or coevolve in the same system. These results illustrate the importance of studying multiple mechanisms of speciation simultaneously in future speciation models.

Animal Migration↗
PubMed1992

Reconstructing recent human evolution.

The two most distinct models of recent human evolution, the multiregional and the recent African origin models, have different retrodictions concerning specific archaic-recent population relationships. The former model infers multiple regional archaic-modern connections and the ancient establishment of regional characteristics, whereas the latter model implies only an African archaic-all modern relationship, with recent (late Pleistocene) development of regionality. In this paper, four late archaic groups from Europe, southwest Asia, Africa and East Asia are compared with various fossil and recent Homo sapiens crania or cranial samples. The results of Penrose shape comparisons narrowly favour a late archaic African-modern special relationship over an East Asian-modern one, with European and southwest Asian Neanderthal groups much more distant. No specific archaic-recent regional relationships are indicated in the shape analyses, nor in separate examinations of patterns of regionality, which indicate a recent origin for present day regionality. The Skhul-Qafzeh sample provides an excellent shape intermediate between the archaic and recent samples.

Animals↗
PubMed2004

Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae.

Whole-genome duplication followed by massive gene loss and specialization has long been postulated as a powerful mechanism of evolutionary innovation. Recently, it has become possible to test this notion by searching complete genome sequence for signs of ancient duplication. Here, we show that the yeast Saccharomyces cerevisiae arose from ancient whole-genome duplication, by sequencing and analysing Kluyveromyces waltii, a related yeast species that diverged before the duplication. The two genomes are related by a 1:2 mapping, with each region of K. waltii corresponding to two regions of S. cerevisiae, as expected for whole-genome duplication. This resolves the long-standing controversy on the ancestry of the yeast genome, and makes it possible to study the fate of duplicated genes directly. Strikingly, 95% of cases of accelerated evolution involve only one member of a gene pair, providing strong support for a specific model of evolution, and allowing us to distinguish ancestral and derived functions.

Codon↗
PubMedDate not supplied

Organization and structure of wild rabbit kappa2 genes: implications for regulation of kappa expression.

In domestic populations, the rabbit kappa light chains are known to be encoded by two loci which are unequally expressed. The kappa1 chains account for the majority of total serum kappa chains, and display an unusual complex polymorphism. In order to study the evolution and the putative correlations between the expression, the organization and the structure of the kappa genes, we analysed the kappa loci in wild rabbit populations. The kappa genes of b95, b97 and b98 allotypes are organized in two loci similar to that of domestic rabbits. The structure of the constant region of the kappa2 locus was determined from a wild rabbit which expresses b95 allotype kappa1 chains. The Ckappa2bas2 of b95 displays a single silent mutation when compared to Ckappa2bas2 associated with b4 and one amino acid change relative to Ckappa2bas1 chain. Therefore, in contrast to the kappa1 locus, the constant regions of the kappa2 locus display strong conservation during evolution. A model based on conformation of the kappa chains is discussed to explain the evolution and expression of the two kappa loci.

Amino Acid Sequence↗
PubMed2025

Temperature and Pressure Shaped the Evolution of Antifreeze Proteins in Polar and Deep Sea Zoarcoid Fishes.

Antifreeze proteins (AFPs) have enabled teleost fishes to repeatedly colonize polar seas. Four AFP types have convergently evolved in several fish lineages. AFPs inhibit ice crystal growth and lower tissue freezing point. In lineages with AFPs, species inhabiting colder environments may possess more AFP copies. Elucidating how differences in AFP copy number evolve is challenging due to the genes' tandem array structure and consequently poor resolution of these repetitive regions. Here, we explore the evolution of type III AFPs (AFP III) in the globally distributed suborder Zoarcoidei, leveraging six new long-read genome assemblies. Zoarcoidei has fewer genomic resources relative to other polar fish clades while it is one of the few groups of fishes adapted to both the Arctic and Southern Oceans. Combining these new assemblies with additional long-read genomes available for Zoarcoidei, we conducted a comprehensive phylogenetic test of AFP III evolution and modeled the effects of thermal habitat and depth on AFP III gene family evolution. We confirm a single origin of AFP III via neofunctionalization of the enzyme sialic acid synthase B. We also show that AFP copy number increased under low temperature but decreased with depth, potentially because pressure lowers freezing point. Associations between the environment and AFP III copy number were driven by duplications of paralogs that were translocated out of the ancestral locus at which AFP III arose. Our results reveal novel environmental effects on AFP evolution and demonstrate the value of high-quality genomic resources for studying how structural genomic variation shapes convergent adaptation.

Animals↗
PubMedDate not supplied

[The Rosemary Rizzo Theory discusses "developing man" a phenomenologic approach to nursing].

The Authors discuss the "Human Becoming Theory" by R.R. Parse and main philosophical principles of theory are presented: man as open system in a continuum coostrascendental relationship with the universe. Health is the model of relationship experienced by man to which he gives values for the evolution of model itself. The theory is illustrated and discussed with its structure, research methodology and application for clinical practice.

Humans↗
PubMed1989

Protein evolution on rugged landscapes.

We analyze a mathematical model of protein evolution in which the evolutionary process is viewed as hill-climbing on a random fitness landscape. In studying the structure of such landscapes, we note that a large number of local optima exist, and we calculate the time and number of mutational changes until a protein gets trapped at a local optimum. Such a hill-climbing process may underlie the evolution of antibody molecules by somatic hypermutation.

Biological Evolution↗
PubMed1991

Variations in polymer fitness at elevated mutation rates.

Two series expressions were obtained that give the first and second order rates of change in population fitness during competitive replication at elevated mutation rates. At their zero-error limit, the respective power series reduces to the second (Fisher's theorem) and third moments of the fitness distribution. The first series maximized the variation in mean polymer fitness, for a given amount of population covariance. From experimental results reported by Spiegelman's group on evolution in vitro among Q beta RNA variants, it was demonstrated: (i) terms in the (second) series fall-off at a rate broadly equal to the replicase error (epsilon congruent to 10(-4); (ii) the rate of change in mean RNA fitness (polymer formation rate constant) corresponds to the variance in fitness; and (iii) agreement exists between second order rate changes in fitness and the third moment (skewness) regression line, extending over 20 successive replication reactions. The impact of these findings on the standard model of evolution has been discussed.

Biological Evolution↗