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PubMed1983

Interspecific cytoplasmic gene flow in the absence of nuclear gene flow: evidence from Drosophila.

mtDNA polymorphism has been studied by restriction endonuclease site variation in Drosophila pseudoobscura and its sibling species D. persimilis. Eight enzymes have been used to study 54 isofemale strains from areas where the two species are sympatric and D. pseudoobscura is allopatric. Where sympatric, 75-80% of the strains have mitochondrial genomes found in both species. Where allopatric, D. pseudoobscura has diverged to the point where none of the strains have mtDNA in common with D. persimilis. The most likely explanation for this observation is that where sympatric the two species hybridize frequently enough to keep their mtDNA from diverging. However, hybridization has not prevented their nuclear genomes from diverging, perhaps due to selection against nuclear gene introgression contrasted with little or no selection against mtDNA introgression. These observations suggest that nuclear and cytoplasmic genomes have different evolutionary dynamics.

Animals↗
PubMed1985

Interaction of selection and biased gene conversion in a multigene family.

A model of the evolutionary dynamics of a multigene family in a finite population under the joint effects of selection and (possibly biased) gene conversion is analyzed. It is assumed that the loss or fixation of a polymorphism at any particular locus in the gene family occurs on a much faster time scale than the introduction of new alleles to a monomorphic locus by gene conversion. A general formula for the fixation of a new allele throughout a multigene family for a wide class of selection functions with biased gene conversion is given for this assumption. Analysis for the case of additive selection shows that (i) unless selection is extremely weak or bias is exceptionally strong, selection usually dominates the fixation dynamics, (ii) if selection is very weak, then even a slight conversion bias can greatly alter the fixation probabilities, and (iii) if both selection and conversion bias are sufficiently small, the substitution rate of new alleles throughout a multigene family is approximately the single locus mutation rate, the same result as for neutral alleles at a single-copy gene. Finally, I analyze a fairly general class of underdominant speciation models involving multigene families, concluding for these models under weak conversion that although the probability of fixation may be relatively high, the expected time to fixation is extremely long, so that speciation by "molecular drive" is unlikely. Furthermore, speciation occurs faster by fixing underdominant alleles of the same effect at single-copy genes than by fixing the same number of loci in a single multigene family under the joint effects of selection, conversion, and drift.

Alleles↗
PubMed1985

Expected time for random genetic drift of a population between stable phenotypic states.

Natural selection and random genetic drift are modeled by using diffusion equations for the mean phenotype of a quantitative (polygenic) character in a finite population with two available adaptive zones or ecological niches. When there is appreciable selection, the population is likely to spend a very long time drifting around the peak in its original adaptive zone. With the mean phenotype initially anywhere near the local optimum, the expected time until a shift between phenotypic adaptive peaks increases approximately exponentially with the effective population size. In comparison, the expected duration of intermediate forms in the actual transition between adaptive peaks is extremely short, generally below the level of resolution in the fossil record, and increases approximately logarithmically with the effective population size. The evolutionary dynamics of this model conform to the pattern of current paleontological concepts of morphological "stasis" and "punctuated equilibria."

Biological Evolution↗
PubMed1988

A fundamental division in the Alu family of repeated sequences.

The Alu family of repeated sequences from the human genome contains two distinct subfamilies. This division is based on different base preferences in a number of diagnostic sequence positions. One subfamily of the sequences, referred to as the Alu-J subfamily, is very similar to 7SL DNA in these positions. The other subfamily, Alu-S, can be divided further into well-defined branches of sequences. These findings revise the previous picture of the Alu family and expose their complex evolutionary dynamics. They reveal sequence variations of potential importance for the proliferation of Alu repeats and relate them to their structural features. In addition, they open the possibility of using different types of Alu sequences as natural markers for studying genetic rearrangements in the genome.

Base Sequence↗
PubMed1988

An epistatic mating system model can produce permanent cytonuclear disequilibria in a hybrid zone.

We examine the evolutionary dynamics of gametic and genotypic disequilibria between a cytoplasmic gene and a nuclear gene under two mating system models relevant to hybrid zones. In the first model, in which female mating preference is determined by an epistatic interaction between the two loci, permanent nonzero cytonuclear disequilibria are possible for a variety of initial genotype frequencies, particularly when rates of assortative mating for the two parental species are high. In contrast, when mating preference is effectively determined by interaction between a cytoplasmic gene and the multilocus nuclear genotypes characteristic of the parental species, all cytonuclear disequilibria, as well as frequencies of pure parentals, rapidly decay to zero unless assortative mating is nearly perfect. Results of the models are applied to the interpretation of observed cytonuclear associations in a hybrid population of Hyla tree frogs.

Algorithms↗
PubMed1992

Gene-culture coevolution: toward a general theory of vertical transmission.

A general formulation of cultural and genetic transmission is developed. The cultural transmission is vertical and the genetics may involve multiple loci. Each individual is represented by a phenogenotype, and conditions are given under which the evolutionary dynamics of phenogenotype frequencies are reducible to phenogametic or phenoallelic frequencies. The interaction between genes and culture is specified by an association measure, and results on the order of magnitude of this association at equilibrium are presented.

Biological Evolution↗
PubMed2000

Interpreting the universal phylogenetic tree.

The universal phylogenetic tree not only spans all extant life, but its root and earliest branchings represent stages in the evolutionary process before modern cell types had come into being. The evolution of the cell is an interplay between vertically derived and horizontally acquired variation. Primitive cellular entities were necessarily simpler and more modular in design than are modern cells. Consequently, horizontal gene transfer early on was pervasive, dominating the evolutionary dynamic. The root of the universal phylogenetic tree represents the first stage in cellular evolution when the evolving cell became sufficiently integrated and stable to the erosive effects of horizontal gene transfer that true organismal lineages could exist.

Cell Size↗
PubMed2000

Evolution of the recombination signal sequences in the Ig heavy-chain variable region locus of mammals.

The Ig and T cell receptor (TCR) loci have an exceptionally dynamic evolutionary history, but the mechanisms responsible remain a subject of speculation. Ig and TCR genes are unique in vertebrates in that they are assembled from V, D, and J segments by site-specific recombination in developing lymphocytes. Here we examine the extent to which the V(D)J recombination in germline cells may have been responsible for remodeling Ig and TCR loci in mammals by asking whether gene segments have evolved as a unit, or whether, instead, recombination signal sequences (RSSs) and coding sequences have different phylogenies. Four distinct types of RSS have been defined in the human Ig heavy-chain variable region (Vh) locus, namely H1, H2, H3, and H5, and no other RSS type has been detected in other mammalian species. There is a well-supported discrepancy between the evolutionary history of the RSSs as compared with the Vh coding sequences: the RSS type H2 of one Vh gene segment has clearly become replaced by a RSS type H3 during mammalian evolution, between 115 and 65 million years ago. Two general models might explain the RSS swap: the first involves an unequal crossing over, and the second implicates germline activation of V(D)J recombination. The Vh-H2/RSS-H3 recombination product has likely been selected during the evolution of mammals because it provides better V(D)J recombination efficiency.

Base Sequence↗
PubMed2001

Directed evolution of ampicillin-resistant activity from a functionally unrelated DNA fragment: A laboratory model of molecular evolution.

To establish an experimental system to directly observe molecular evolution, a DNA fragment that confers ampicillin resistance on Escherichia coli was cloned from an archaeal genomic DNA. The activity of this clone was enhanced by 50 rounds of directed evolution by using DNA shuffling. Analysis of the evolved DNA fragments shows that two genetic regions have coevolved: One region, which has no obvious ORF, is essential for the activity, whereas the other, which appears to encode a protein, is not essential but enhances the activity of the former region. Analysis of the evolutionary intermediates shows that negative mutations are effectively removed while beneficial mutations accumulate and illustrates how a protein has evolved over the course of the evolution experiments. Although the mechanism of the activity remains unclear, the evolved DNA fragments also confer resistance to other drugs that inhibit bacterial cell-wall synthesis. The present system would serve as an experimental model to study evolutionary dynamics in the laboratory and provide the concept of screening natural libraries to obtain starting materials for directed evolution.

Ampicillin↗
PubMed1997

The concept of affect logic: an integrative psycho-socio-biological approach to understanding and treatment of schizophrenia.

In this article, the psycho-socio-biologically integrative concept of affect-logic, and its relevance for a comprehensive understanding and therapy of schizophrenia, is briefly presented. This concept has been developed by the author over the past 20 years, on the basis of the literature, of clinical experience and his own research into long-term evolution, rehabilitation, effects of milieu-therapy, and nonlinear evolutionary dynamics of the illness. It postulates, basically, that fundamental affective states (or emotions, feelings, moods) are continuously and inseparably linked to all cognitive functioning (or "thinking" and "logic" in a broad sense), and that affects have essential organizing and integrating effects on cognition. Schizophrenia is understood as an altered mode of affective-cognitive interaction based, possibly, on disturbed (loosened) affective-cognitive connections. This hypothesis leads to: 1) an integrative psycho-socio-biological model of long-term evolution of the illness; 2) a new understanding of psychopathological core phenomena such as ambivalence, incoherence, and emotional flattening; 3) an innovative therapeutic approach based on an emotion-relaxing milieu and style of care; and 4) the hypothesis that schizophrenia could basically be an affective (and not a cognitive) disease, of another kind than mania or melancholia, however.

Affect↗
PubMed2003

Comparison of likelihood and Bayesian methods for estimating divergence times using multiple gene Loci and calibration points, with application to a radiation of cute-looking mouse lemur species.

Divergence time and substitution rate are seriously confounded in phylogenetic analysis, making it difficult to estimate divergence times when the molecular clock (rate constancy among lineages) is violated. This problem can be alleviated to some extent by analyzing multiple gene loci simultaneously and by using multiple calibration points. While different genes may have different patterns of evolutionary rate change, they share the same divergence times. Indeed, the fact that each gene may violate the molecular clock differently leads to the advantage of simultaneous analysis of multiple loci. Multiple calibration points provide the means for characterizing the local evolutionary rates on the phylogeny. In this paper, we extend previous likelihood models of local molecular clock for estimating species divergence times to accommodate multiple calibration points and multiple genes. Heterogeneity among different genes in evolutionary rate and in substitution process is accounted for by the models. We apply the likelihood models to analyze two mitochondrial protein-coding genes, cytochrome oxidase II and cytochrome b, to estimate divergence times of Malagasy mouse lemurs and related outgroups. The likelihood method is compared with the Bayes method of Thorne et al. (1998, Mol. Biol. Evol. 15:1647-1657), which uses a probabilistic model to describe the change in evolutionary rate over time and uses the Markov chain Monte Carlo procedure to derive the posterior distribution of rates and times. Our likelihood implementation has the drawbacks of failing to accommodate uncertainties in fossil calibrations and of requiring the researcher to classify branches on the tree into different rate groups. Both problems are avoided in the Bayes method. Despite the differences in the two methods, however, data partitions and model assumptions had the greatest impact on date estimation. The three codon positions have very different substitution rates and evolutionary dynamics, and assumptions in the substitution model affect date estimation in both likelihood and Bayes analyses. The results demonstrate that the separate analysis is unreliable, with dates variable among codon positions and between methods, and that the combined analysis is much more reliable. When the three codon positions were analyzed simultaneously under the most realistic models using all available calibration information, the two methods produced similar results. The divergence of the mouse lemurs is dated to be around 7-10 million years ago, indicating a surprisingly early species radiation for such a morphologically uniform group of primates.

Animals↗
PubMed2005

An empirical examination of the utility of codon-substitution models in phylogeny reconstruction.

Models of codon substitution have been commonly used to compare protein-coding DNA sequences and are particularly effective in detecting signals of natural selection acting on the protein. Their utility in reconstructing molecular phylogenies and in dating species divergences has not been explored. Codon models naturally accommodate synonymous and nonsynonymous substitutions, which occur at very different rates and may be informative for recent and ancient divergences, respectively. Thus codon models may be expected to make an efficient use of phylogenetic information in protein-coding DNA sequences. Here we applied codon models to 106 protein-coding genes from eight yeast species to reconstruct phylogenies using the maximum likelihood method, in comparison with nucleotide- and amino acid-based analyses. The results appeared to confirm that expectation. Nucleotide-based analysis, under simplistic substitution models, were efficient in recovering recent divergences whereas amino acid-based analysis performed better at recovering deep divergences. Codon models appeared to combine the advantages of amino acid and nucleotide data and had good performance at recovering both recent and deep divergences. Estimation of relative species divergence times using amino acid and codon models suggested that translation of gene sequences into proteins led to information loss of from 30% for deep nodes to 66% for recent nodes. Although computational burden makes codon models unfeasible for tree search in large data sets, we suggest that they may be useful for comparing candidate trees. Nucleotide models that accommodate the differences in evolutionary dynamics at the three codon positions also performed well, at much less computational cost. We discuss the relationship between a model's fit to data and its utility in phylogeny reconstruction and caution against use of overly complex substitution models.

Classification↗
PubMed2005

Calculating the evolutionary rates of different genes: a fast, accurate estimator with applications to maximum likelihood phylogenetic analysis.

In phylogenetic analyses with combined multigene or multiprotein data sets, accounting for differing evolutionary dynamics at different loci is essential for accurate tree prediction. Existing maximum likelihood (ML) and Bayesian approaches are computationally intensive. We present an alternative approach that is orders of magnitude faster. The method, Distance Rates (DistR), estimates rates based upon distances derived from gene/protein sequence data. Simulation studies indicate that this technique is accurate compared with other methods and robust to missing sequence data. The DistR method was applied to a fungal mitochondrial data set, and the rate estimates compared well to those obtained using existing ML and Bayesian approaches. Inclusion of the protein rates estimated from the DistR method into the ML calculation of trees as a branch length multiplier resulted in a significantly improved fit as measured by the Akaike Information Criterion (AIC). Furthermore, bootstrap support for the ML topology was significantly greater when protein rates were used, and some evident errors in the concatenated ML tree topology (i.e., without protein rates) were corrected. [Bayesian credible intervals; DistR method; multigene phylogeny; PHYML; rate heterogeneity.].

Algorithms↗
PubMed2003

The evolution of empty flowers revisited.

The evolution of plants that provide no form of reward for their pollinators is puzzling because they receive low numbers of pollinator visits and so have low reproductive success. To predict the evolutionary dynamics of empty morphs within a plant population, we modeled different foraging strategies that pollinators could use to avoid them. We predicted that the optimal strategy was to visit empty inflorescences randomly when these were infrequent but to use strategies such as visiting fewer flowers per inflorescence to avoid wasting time on them. As the frequencies of empty inflorescences increased, discriminating directly against empty morphs was more likely to be an optimal strategy than was avoiding the species altogether and switching to an alternative one. An experimental test of this model using artificial inflorescences showed that bumblebees used a variety of strategies to minimize time wasted on empty inflorescences. They showed weak discrimination against empty inflorescences but switched to an alternative type of inflorescence as the frequency of empty inflorescences increased. We predicted that empty morphs would be at a visitation rate disadvantage even when at low frequencies in a plant population. Differences in outcrossing rates, or male function, may explain how rewardlessness spreads in a plant population.

Animals↗
PubMed2005

Evolution of sexual isolation during secondary contact: genotypic versus phenotypic changes in laboratory populations.

We monitored the phenotypic and genotypic changes that occur when two behavioral races come into contact in laboratory populations. Drosophila melanogaster from Zimbabwe and nearby regions (Z type) show strong but asymmetric sexual isolation from their cosmopolitan counterparts (M type). Crosses of Z females and M males do not take place readily when other choices are available. At least 15 loci are known to control Z-type mating preferences and performance. By thoroughly mixing the genomes of the two types in laboratory populations, we artificially created maximum secondary contact. Despite the strength of sexual selection favoring Z-type male characters, Z-type behavior is eliminated or greatly diminished in all 12 hybrid populations after only 60 generations. This trend is consistent with the spread of the M-type behavior throughout the world as well as a detailed analysis of fitness components. Surprisingly, in contrast with the phenotypic convergence toward the M-type, genotypic samples broadly covering the genomic regions of mapped behavioral loci show no such trend. The genome appears to be "fine grained," with adjacent loci having different evolutionary dynamics and genealogical histories.

Alleles↗
PubMed2005

Elasticities in variable environments: properties and implications.

Elasticities in stochastic matrix models are used to understand both population and evolutionary dynamics. We examine three such elasticities: stochastic elasticity E(ij)(S) with respect to the (i, j) matrix element, the elasticity E(ij)(S mu) with respect to the mean mu(ij) of the matrix element, and the elasticity E(ij)(S sigma) with respect to the variability sigma(ij) of the matrix element. We show that the stochastic elasticity E(S) does not accurately describe the effect of variability; one should use E(S sigma) and E(S mu). We establish two general properties of these elasticities: a sum rule that connects them and a limit on the sum of the E(S sigma). We discuss the implications of these properties for the analysis of buffering and selection on the average rates versus the variability of rates.

Ecosystem↗
PubMed2006

Longitudinal population analysis of dual infection with recombination in two strains of HIV type 1 subtype B in an individual from a Phase 3 HIV vaccine efficacy trial.

This study documents a case of coinfection (simultaneous infection of an individual with two or more strains) of two HIV-1 subtype B strains in an individual from a Phase 3 HIV-1 vaccine efficacy trial, conducted in North American and the Netherlands. We examined 86 full-length gp120 (env) gene sequences from this individual collected from nine different time points over a 20-month period. We estimated evolutionary relationships using maximum likelihood and Bayesian methods and inferred recombination breakpoints and recombinant sequences using phylogenetic and substitutional methods. These analyses identified two strongly supported monophyletic clades (clades A and B) of 14 and 69 sequences each and a small paraphyletic recombinant clade of three sequences. We then studied the genetic characteristics of these lineages by comparing estimates of genetic diversity generated by mutation and recombination and adaptive selection within a coalescent and maximum likelihood framework. Our results suggest significant differences on the evolutionary dynamics of these strains. We then discuss the implications of these results for vaccine development.

AIDS Vaccines↗
PubMed2003

Simple stochastic birth and death models of genome evolution: was there enough time for us to evolve?

MOTIVATION: The distributions of many genome-associated quantities, including the membership of paralogous gene families can be approximated with power laws. We are interested in developing mathematical models of genome evolution that adequately account for the shape of these distributions and describe the evolutionary dynamics of their formation. RESULTS: We show that simple stochastic models of genome evolution lead to power-law asymptotics of protein domain family size distribution. These models, called Birth, Death and Innovation Models (BDIM), represent a special class of balanced birth-and-death processes, in which domain duplication and deletion rates are asymptotically equal up to the second order. The simplest, linear BDIM shows an excellent fit to the observed distributions of domain family size in diverse prokaryotic and eukaryotic genomes. However, the stochastic version of the linear BDIM explored here predicts that the actual size of large paralogous families is reached on an unrealistically long timescale. We show that introduction of non-linearity, which might be interpreted as interaction of a particular order between individual family members, allows the model to achieve genome evolution rates that are much better compatible with the current estimates of the rates of individual duplication/loss events.

Computer Simulation↗