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PubMed1995

Arboreal clambering and the evolution of self-conception.

A fundamentally new psychology related to the ability to conceive of limited aspects of the self may have evolved in the ancestor of the great ape/human clade. Existing models of the evolution of primate intelligence do not provide an adequate explanation of the apparent restriction of this phenomenon. We propose that the capacity for self-conception evolved as a psychological mechanism enabling large-bodied, highly arboreal apes to cope with problems posed by the need to negotiate their way through a habitat that was fragile due to their body size. First, we briefly outline the case for believing that a new psychology related to self-conception evolved during the Miocene in the ancestor of the great ape/human clade. Next, we examine the existing models of the evolution of primate intelligence and assess their ability to account for the evolution of self-conception. Finally, we offer details of our alternative model, along with a series of predictions that can be derived from it.

Animals↗
PubMed1988

[Host-parasite interaction as a factor in the evolution of genetic recombination].

A model of the rec-system evolution determined by species interactions of the host-parasite type has been studied. In contrast to known formalizations, the genetic structure of both populations is clearly represented in our model, which makes it possible to set the mode of their interrelations in a more natural and biologically consistent way. The numerical analysis has revealed the situations, where nondecreasing oscillations of the linkage disequilibrium coefficient and, consequently, the selection favourable for higher recombination occur in a system. The evolutionary advantage of recombination has been demonstrated both in terms of population mean fitness and in the models with locus modifier of recombination.

Animals↗
PubMed2004

The paradox of T-cell-mediated antitumor immunity in spite of poor clinical outcome in human melanoma.

Human melanoma is hardly ever curable at an advanced stage, but overwhelming evidence from untreated or vaccinated patients indicates that this tumor is highly antigenic and frequently immunogenic. Here, we review recent results indicating that CD8(+) T cell-mediated antitumor immunity is activated at the systemic and tumor level in the early clinical stages (AJCC stages I and II) and continues to be promoted, in a fraction of patients, even in metastatic disease (stages III and IV). This evidence was obtained by looking at frequency, differentiation phenotype, and function of antitumor T cells in periphery and tumor site of melanoma patients. On the other hand, the paradox of immunity in spite of poor clinical evolution of the disease, points toward a model of concurrent evolution of immunity and tumor escape. As melanoma progresses to metastatic disease, powerful mechanisms of tumor evasion from immune recognition, and of immunosuppression, are activated, thus tilting the balance between immunity and escape in favor of tumor resistance to host defense. Nevertheless, recent developments in our understanding of regulation of T cell-mediated immunity can provide clues to the prospects for improved immunotherapy approaches. By integrating the information from basic research in immunology, from murine tumor models, and from trials of immunotherapy, we discuss how the most relevant steps of the antitumor response should be manipulated with greater efficacy by future clinical trials.

Antigens, Differentiation↗
PubMed1998

High apparent rate of simultaneous compensatory base-pair substitutions in ribosomal RNA.

We present a model for the evolution of paired bases in RNA sequences. The new model allows for the instantaneous rate of substitution of both members of a base pair in a compensatory substitution (e.g., A-U-->G-C) and expands our previous work by allowing for unpaired bases or noncanonical pairs. We implemented the model with distance and maximum likelihood methods to estimate the rates of simultaneous substitution of both bases, alphad, vs. rates of substitution of individual bases, alphas in rRNA. In the rapidly evolving D2 expansion segments of Drosophila large subunit rRNA, we estimate a low ratio of alphad/alphas, indicating that most compensatory substitutions involve a G-U intermediate. In contrast, we find a surprisingly high ratio of alphad/alphas in the core small subunit rRNA, indicating that the evolution of the slowly evolving rRNA sequences is modeled much more accurately if simultaneous substitution of both members of a base pair is allowed to occur approximately as often as substitution of individual bases. Using simulations, we have ruled out several potential sources of error in the estimation of alphad/alphas. We conclude that in the core rRNA sequences compensatory substitutions can be fixed so rapidly as to appear to be instantaneous.

Animals↗
PubMed2000

Modeling DNA mutation and recombination for directed evolution experiments.

Directed evolution experiments rely on the cyclical application of mutagenesis, screening and amplification in a test tube. They have led to the creation of novel proteins for a wide range of applications. However, directed evolution currently requires an uncertain, typically large, number of labor intensive and expensive experimental cycles before proteins with improved function are identified. This paper introduces predictive models for quantifying the outcome of the experiments aiding in the setup of directed evolution for maximizing the chances of obtaining DNA sequences encoding enzymes with improved activities. Two methods of DNA manipulation are analysed: error-prone PCR and DNA recombination. Error-prone PCR is a DNA replication process that intentionally introduces copying errors by imposing mutagenic reaction conditions. The proposed model calculates the probability of producing a specific nucleotide sequence after a number of PCR cycles. DNA recombination methods rely on the mixing and concatenation of genetic material from a number of parent sequences. This paper focuses on modeling a specific DNA recombination protocol, DNA shuffling. Three aspects of the DNA shuffling procedure are modeled: the fragment size distribution after random fragmentation by DNase I, the assembly of DNA fragments, and the probability of assembling specific sequences or combinations of mutations. Results obtained with the proposed models compare favorably with experimental data.

Animals↗
PubMed2005

Evolution of the spermatozoon in muroid rodents.

In the rodent superfamily Muroidea, a model for the evolution of sperm form has been proposed in which it is suggested that a hook-shaped sperm head and long tail evolved from a more simple, nonhooked head and short tail in several different subfamilies. To test this model the shape of the sperm head, with particular emphasis on its apical region, and length of sperm tail were matched to a recent phylogeny based on the nucleotide sequence of several protein-coding nuclear genes from 3 families and 10 subfamilies of muroid rodents. Data from the two other myomorph superfamilies, the Dipodoidea and kangaroo rats in the Geomyoidea, were used for an outgroup comparison. In most species in all 10 muroid subfamilies, apart from in the Murinae, the sperm head has a long rostral hook largely composed of acrosomal material, although its length and cross-sectional shape vary across the various subfamilies. Nevertheless, in a few species of various lineages a very different sperm morphology occurs in which an apical hook is lacking. In the outgroups the three species of dipodid rodents have a sperm head that lacks a hook, whereas in the heteromyids an acrosome-containing apical hook is present. It is concluded that, as the hook-shaped sperm head and long sperm tail occur across the muroid subfamilies, as well as in the heteromyid rodents, it is likely to be the ancestral condition within each of the subfamilies with the various forms of nonhooked sperm heads, that are sometimes associated with short tails, being highly derived states. These findings thus argue against a repeated evolution in various muroid lineages of a complex, hook-shaped sperm head and long sperm tail from a more simple, nonhooked sperm head and short tail. An alternative proposal for the evolution of sperm form within the Muroidea is presented in the light of these data.

Animals↗
PubMed2004

The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model.

We investigated the gene coexpression network in Saccharomyces cerevisiae, in which genes are linked when they are coregulated. This network is shown to have a scale-free, small-world architecture. Such architecture is typical of biological networks in which the nodes are connected when they are involved in the same biological process. Current models for the evolution of intracellular networks do not adequately reproduce the features that we observe in the network. We therefore derive a new model for its evolution based on the observation that there is a positive correlation between the sequence similarity of paralogues and their probability of coexpression or sharing of transcription factor binding sites (TFBSs). The simple, neutralist's model consists of (1) coduplication of genes with their TFBSs, (2) deletion and duplication of individual TFBSs and (3) gene loss. A network is constructed by connecting genes that share multiple TFBSs. Our model reproduces the scale-free, small-world architecture of the coregulation network and the homology relations between coregulated genes without the need for selection either at the level of the network structure or at the level of gene regulation.

Binding Sites↗
PubMed2005

Consideration of RNA secondary structure significantly improves likelihood-based estimates of phylogeny: examples from the bilateria.

Sequences from ribosomal RNA (rRNA) genes have made a huge contribution to our current understanding of metazoan phylogeny and indeed the phylogeny of all of life. That said, some parts of this rRNA-based phylogeny remain unresolved. One approach to increase the resolution of these trees would be to use more appropriate models of sequence evolution in phylogenetic analysis. RNAs transcribed from rRNA genes have a complex secondary structure mediated by base pairing between sometimes distant regions of the rRNA molecule. The pairing between the stem nucleotides has important consequences for their evolution which differs from that of unpaired loop nucleotides. These differences in evolution should ideally be accounted for when using rRNA sequences for phylogeny estimation. We use a novel permutation approach to demonstrate the significant superiority of models of sequence evolution that allow stem and loop regions to evolve according to separate models and, in common with previous studies, we show that 16-state models that take base pairing of stems into account are significantly better than simpler, 4-state, single-nucleotide models. One of these 16-state models has been applied to the phylogeny of the Bilateria using small subunit rRNA (SSU) sequences. Our optimal tree largely echoes previous results based on SSU in particular supporting the tripartite Bilaterian tree of deuterostomes, lophotrochozoans, and ecdysozoans. There are also a number of differences, however, perhaps most important of which is the observation of a clade consisting of the gastrotrichs plus platyheminthes that is basal to all other lophotrochozoan taxa. Use of 16-state models also appears to reduce the Bayesian support given to certain biologically improbable groups found using standard 4-state models.

Animals↗
PubMed1995

Selection, mutations and codon usage in a bacterial model.

We present a statistical model of bacterial evolution based on the coupling between codon usage and tRNA abundance. Such a model interprets this aspect of the evolutionary process as a balance between the codon homogenization effect due to mutation process and the improvement of the translation phase due to natural selection. We develop a thermodynamical description of the asymptotic state of the model. The analysis of naturally occurring sequences shows that the effect of natural selection on codon bias affects genes whose products are largely required at maximal growth rate conditions or undergo rapid transient increases.

Bacteria↗
PubMed2005

Hormone signaling in evolution and development: a non-model system approach.

Cooption and modularity are informative concepts in evolutionary developmental biology. Genes function within complex networks that act as modules in development. These modules can then be coopted in various functional and evolutionary contexts. Hormonal signaling, the main focus of this review, has a modular character. By regulating the activities of genes, proteins and other cellular molecules, a hormonal signal can have major effects on physiological and ontogenetic processes within and across tissues over a wide spatial and temporal scale. Because of this property, we argue that hormones are frequently involved in the coordination of life history transitions (LHTs) and their evolution (LHE). Finally, we promote the usefulness of a comparative, non-model system approach towards understanding how hormones function and guide development and evolution, highlighting thyroid hormone function in echinoids as an example.

Animals↗
PubMed1995

Speculations on the evolution of the genetic code IV. The evolution of the aminoacyl-tRNA synthetases.

An evolutionary scheme is postulated in which a primitive code, involving only guanine and cytosine, would code for glycine(GG.), alanine(GC.), arginine(CG.) and proline(CC.). There evolves from this primitive code families of related amino acids as the code expands. The evolution of the aminoacyl-tRNA synthetases are considered to be indicators for the evolution of the genetic code. The postulated model for the evolution of the genetic code is used to give an evolutionary interpretation to the recent work on the structure and sequences of the aminoacyl-tRNA synthetases.

Amino Acid Sequence↗
PubMed1981

Two-enzyme active transport in vitro with pH induced asymmetrical functional structures. III. Discussions based on numerical treatments of the time-dependent evolutions.

Three complementary models have been considered in which pH gradients (step function, linear pH or linear H+) impose asymmetry on a two-enzyme mixture. If the "combined pH dependences" of enzymes is pro-asymmetrical, the pH gradient induces an asymmetrical distribution of potential activities ("latent" asymmetry of functional structure). When substrate is added, "developed" asymmetry of effective activities appears which results in "substrate space wave" and pumping when the catalysed reaction couple is "inversible". It is shown that only one steady state exists for a given boundary condition and is attained when the "combined effective activity" of enzymes is nil; the stationary flux with symmetrical boundaries or the stationary load with moving boundaries is proportional to "effective global activities" of enzymes. "Equivalent square models" could be proposed that would be able to describe "functional" or "permanent" structure pumps as well. These models belong to the thermodynamic branch and the asymmetrical "space wave" substrate concentration profiles obtained must be distinguished from dissipative structures. It appears that such primary active transport pumps are chemical equivalents of heat pumps.

Biological Transport, Active↗
PubMed1999

Dynamics of disease resistance polymorphism at the Rpm1 locus of Arabidopsis.

The co-evolutionary 'arms race' is a widely accepted model for the evolution of host-pathogen interactions. This model predicts that variation for disease resistance will be transient, and that host populations generally will be monomorphic at disease-resistance (R-gene) loci. However, plant populations show considerable polymorphism at R-gene loci involved in pathogen recognition. Here we have tested the arms-race model in Arabidopsis thaliana by analysing sequences flanking Rpm1, a gene conferring the ability to recognize Pseudomonas pathogens carrying AvrRpm1 or AvrB. We reject the arms-race hypothesis: resistance and susceptibility alleles at this locus have co-existed for millions of years. To account for the age of alleles and the relative levels of polymorphism within allelic classes, we use coalescence theory to model the long-term accumulation of nucleotide polymorphism in the context of the short-term ecological dynamics of disease resistance. This analysis supports a 'trench warfare' hypothesis, in which advances and retreats of resistance-allele frequency maintain variation for disease resistance as a dynamic polymorphism.

Arabidopsis↗
PubMed2002

Genetic events in the evolution of thyroid cancer.

OBJECTIVE: To delineate the evolution of thyroid cancer using the Volgelstein model of cancer evolution and to demonstrate the genetic "hits" in the development of undifferentiated cancer from normal thyroid cells. METHOD: Immunohistochemical and molecular biologic techniques were used to delineate the prevalence of (1) the ras oncogene, (2) p53, and (3) the ret/PTC oncogene in the development of differentiated thyroid cancer from normal cells and hyperplasia. The evolution of differentiated thyroid cancer to the dedifferentiated or anaplastic type was also investigated. The methodology used was standard immunohistochemical staining techniques as well as polymerase chain reaction technology for the elucidation of these various oncogenes and tumour suppressor genes. RESULTS: We have demonstrated that there is a high preponderance of ras and ret/PTC oncogenes in the evolution of thyroid cancer. Further along the continuum, p53 has been demonstrated to be prevalent in the development of dedifferentiated thyroid cancer (i.e., tall cell and insular variety as well as anaplastic cancer). CONCLUSION: Several genetic hits have been demonstrated to be prevalent in the evolution of thyroid cancer. These are preliminary oncogenic maps, and further work in this area will help to establish a definite biologic pattern in the development of this malignancy.

Carcinoma, Papillary↗
PubMed2001

Evidence for the non-quasispecies evolution of RNA viruses [corrected].

The quasispecies model of RNA virus evolution differs from those formulated in conventional population genetics in that neutral mutations do not lead to genetic drift of the population, and natural selection acts on the mutant distribution as a whole rather than on individual variants. By computer simulation, we show that this model could be inappropriate for many RNA viruses because the neutral sequence space may be too large to allow the formation of a quasispecies distribution. This view is supported by our analysis of gene sequences from vesicular stomatitis virus, which is considered a prototype RNA virus quasispecies. Our results are relevant to the evolution of RNA systems in general.

Computer Simulation↗
PubMed1998

The path from the RNA world.

We describe a sequential (step by step) Darwinian model for the evolution of life from the late stages of the RNA world through to the emergence of eukaryotes and prokaryotes. The starting point is our model, derived from current RNA activity, of the RNA world just prior to the advent of genetically-encoded protein synthesis. By focusing on the function of the protoribosome we develop a plausible model for the evolution of a protein-synthesizing ribosome from a high-fidelity RNA polymerase that incorporated triplets of oligonucleotides. With the standard assumption that during the evolution of enzymatic activity, catalysis is transferred from RNA --> RNP --> protein, the first proteins in the "breakthrough organism" (the first to have encoded protein synthesis) would be nonspecific chaperone-like proteins rather than catalytic. Moreover, because some RNA molecules that pre-date protein synthesis under this model now occur as introns in some of the very earliest proteins, the model predicts these particular introns are older than the exons surrounding them, the "introns-first" theory. Many features of the model for the genome organization in the final RNA world ribo-organism are more prevalent in the eukaryotic genome and we suggest that the prokaryotic genome organization (a single, circular genome with one center of replication) was derived from a "eukaryotic-like" genome organization (a fragmented linear genome with multiple centers of replication). The steps from the proposed ribo-organism RNA genome --> eukaryotic-like DNA genome --> prokaryotic-like DNA genome are all relatively straightforward, whereas the transition prokaryotic-like genome --> eukaryotic-like genome appears impossible under a Darwinian mechanism of evolution, given the assumption of the transition RNA --> RNP --> protein. A likely molecular mechanism, "plasmid transfer," is available for the origin of prokaryotic-type genomes from an eukaryotic-like architecture. Under this model prokaryotes are considered specialized and derived with reduced dependence on ssRNA biochemistry. A functional explanation is that prokaryote ancestors underwent selection for thermophily (high temperature) and/or for rapid reproduction (r selection) at least once in their history.

Archaea↗
PubMed2005

Resource partitioning among flower visitors and evolution of nectar concealment in multi-species communities.

The plant community within which flower evolution takes place has largely been ignored. We develop two models for the evolution of nectar concealment when flowers are visited by legitimate pollinators and flower parasites. When there is a single plant species, no level of nectar concealment is evolutionarily stable: any population can be invaded by mutants exhibiting a higher level of nectar concealment. However, the presence of a second flower species with exposed nectar and not subject to evolution breaks the runaway process. In the presence of open flowers, depending on the fitness function there may be an evolutionarily stable level of nectar concealment, or more complex evolutionary dynamics, with nectar concealment fluctuating within a bounded range. Concealment of nectar from flower parasites can evolve even if it implies decreasing the accessibility of nectar to legitimate pollinators.

Animals↗