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PubMed2006

Phenomenological models of socioeconomic network dynamics.

We study a general set of models of social network evolution and dynamics. The models consist of both a dynamics on the network and evolution of the network. Links are formed preferentially between "similar" nodes, where the similarity is defined by the particular process taking place on the network. The interplay between the two processes produces phase transitions and hysteresis, as seen using numerical simulations for three specific processes. We obtain analytic results using mean-field approximations, and for a particular case we derive an exact solution for the network. In common with real-world social networks, we find coexistence of high and low connectivity phases and history dependence.

Journal Article↗

PubMed1999

Modeling DNA shuffling.

In vitro evolution is a new, important laboratory method to evolve molecules with desired properties. It has been used in a variety of biological studies and drug development. In this paper, we study one important mutagenesis method used in in vitro evolution experiments called DNA shuffling. We construct a mathematical model for DNA shuffling and study the properties of molecules after DNA shuffling experiments based on this model. The model for DNA shuffling consists of two parts. First we apply the Lander-Waterman model for physical mapping by fingerprinting random clones to model the distribution of regions that can be reassembled through DNA shuffling. Then we present a model for recombination between different DNA species with different mutations. We compare our theoretical results with experimental data. Finally we propose novel applications of the theoretical results to the optimal design of DNA shuffling experiments and to physical mapping using DNA shuffling.

Base Sequence↗

PubMed2002

Purifying selection and birth-and-death evolution in the histone H4 gene family.

Histones are small basic proteins encoded by a multigene family and are responsible for the nucleosomal organization of chromatin in eukaryotes. Because of the high degree of protein sequence conservation, it is generally believed that histone genes are subject to concerted evolution. However, purifying selection can also generate a high degree of sequence homogeneity. In this study, we examined the long-term evolution of histone H4 genes to determine whether concerted evolution or purifying selection was the major factor for maintaining sequence homogeneity. We analyzed the proportion (p(S)) of synonymous nucleotide differences between the H4 genes from 59 species of fungi, plants, animals, and protists and found that p(S) is generally very high and often close to the saturation level (p(S) ranging from 0.3 to 0.6) even though protein sequences are virtually identical for all H4 genes. A small proportion of genes showed a low level of p(S) values, but this appeared to be caused by recent gene duplication. Our findings suggest that the members of this gene family evolve according to the birth-and-death model of evolution under strong purifying selection. Using histone-like genes in archaebacteria as outgroups, we also showed that H1, H2A, H2B, H3, and H4 histone genes in eukaryotes form separate clusters and that these classes of genes diverged nearly at the same time, before the eukaryotic kingdoms diverged.

Animals↗

PubMed1994

Conservation and prediction of solvent accessibility in protein families.

Currently, the prediction of three-dimensional (3D) protein structure from sequence alone is an exceedingly difficult task. As an intermediate step, a much simpler task has been pursued extensively: predicting 1D strings of secondary structure. Here, we present an analysis of another 1D projection from 3D structure: the relative solvent accessibility of each residue. We show that solvent accessibility is less conserved in 3D homologues than is secondary structure, and hence is predicted less accurately from automatic homology modeling; the correlation coefficient of relative solvent accessibility between 3D homologues is only 0.77, and the average accuracy of predictions based on sequence alignments is only 0.68. The latter number provides an effective upper limit on the accuracy of predicting accessibility from sequence when homology modeling is not possible. We introduce a neural network system that predicts relative solvent accessibility (projected onto ten discrete states) using evolutionary profiles of amino acid substitutions derived from multiple sequence alignments. Evaluated in a cross-validation test on 238 unique proteins, the correlation between predicted and observed relative accessibility is 0.54. Interpreted in terms of a three-state (buried, intermediate, exposed) description of relative accessibility, the fraction of correctly predicted residue states is about 58%. In absolute terms this accuracy appears poor, but given the relatively low conservation of accessibility in 3D families, the network system is not far from its likely optimal performance. The most reliably predicted fraction of the residues (50%) is predicted as accurately as by automatic homology modeling. Prediction is best for buried residues, e.g., 86% of the completely buried sites are correctly predicted as having 0% relative accessibility.

Biological Evolution↗

PubMed1979

Complementary carrier peptide synthesis: general strategy and implications for prebiotic origin of peptide synthesis.

A method for peptide synthesis is proposed based on a template-directed scheme that parallels that of the native ribosomal mechanism. In this procedure, peptide bond formation is facilitated by the juxtaposition of aminoacyl and peptidyl oligonucleotide carriers bound adjacent to one another on an oligonucleotide template. The general strategy of the synthesis and relevant model studies are described. The scheme provides an intrinsic mechanism by which oligonucleotides can direct the synthesis of polypeptides in the absence of protein or ribosomal machinery and, as such, suggests a model for the origin of prebiotic protein synthesis.

Biological Evolution↗

PubMed1999

Dynamical renormalization group calculation of a two-phase sharp interface model.

The temporal evolution of an interface separating two phases is studied using renormalization group and scaling theory and exact calculation of a sharp interface model incorporating surface tension and kinetic undercooling. Under conditions favoring rapid solidification the characteristic length, R(t), varies as t(1/2) while the total surface area of the interface, S(t), varies as t((d-1)/2). This complements the results of Jasnow and Vinals who found R(t) approximately t in the quasistatic regime. The transition in exponents from R(t) approximately t to R(t) approximately t(1/2), as solidification proceeds from the quasistatic to the rapid solidification regime, suggests a complex evolution toward a self-similar late stage growth.

Journal Article↗

PubMed2000

Male killing can select for male mate choice: a novel solution to the paradox of the lek.

In lekking species, intense directional selection is applied to aspects of the male genotype by female choice. Under conventional quantitative genetics theory, the expectation is that this will lead to a rapid loss in additive genetic variance for the trait in question. However, despite female choice, male variation is maintained and hence it pays females to continue choosing. This has been termed the 'paradox of the lek'. Here we present a theoretical analysis of a putative sex-role-reversed lek in the butterfly Acraea encedon. Sex-role reversal appears to have come about because of infection with a male-killing Wolbachia. The bacterium is highly prevalent in some populations, such that there is a dearth of males. Receptive females form dense aggregations, and it has been suggested that males preferentially select females uninfected with the bacterium. As with more conventional systems, this presents a theoretical problem exactly analogous to the lek paradox, namely what maintains female variation and hence why do males continue to choose? We model the evolution of a male choice gene that allows discrimination between infected and uninfected females, and show that the stable maintenance of both female variation and male choice is likely, so long as males make mistakes when discriminating between females. Furthermore, our model allows the maintenance, in a panmictic population, of a male killer that is perfectly transmitted. This is the first model to allow this result, and may explain the long-term persistence of a male killer in Hypolimnas bolina.

Animals↗

PubMed2005

Games among cannibals: competition to cannibalize and parent-offspring conflict lead to increased sibling cannibalism.

Sibling cannibalism occurs in many species, yet understanding of sibling cannibalism as an adaptation currently lags behind understanding of other antagonistic interactions among siblings. Observed sibling cannibalism phenotypes likely reflect the interaction between competitive games among siblings and parent-offspring conflict. Using a game-theoretic approach, we derive optimal offspring cannibalism behaviour and parental modifiers that limit or facilitate cannibalism. The results are compared to contemporary frequency-independent analysis. With the addition of game interactions among siblings or parent-offspring co-evolution, our model predicts increased cannibalism (compared to the frequency-independent prediction), as offspring compete to eat siblings. When infertile eggs are present--strengthening competition--offspring risk eating viable siblings in order to gain access to infertile eggs, intensifying parent-offspring conflict. We use the results to make new predictions about the occurrence of sibling cannibalism. Additionally, we demonstrate the utility of trophic egg laying as a maternal mechanism to promote egg eating.

Animals↗

PubMed2003

Concerted and nonconcerted evolution of the Hsp70 gene superfamily in two sibling species of nematodes.

We have identified the Hsp70 gene superfamily of the nematode Caenorhabditis briggsae and investigated the evolution of these genes in comparison with Hsp70 genes from C. elegans, Drosophila, and yeast. The Hsp70 genes are classified into three monophyletic groups according to their subcellular localization, namely, cytoplasm (CYT), endoplasmic reticulum (ER), and mitochondria (MT). The Hsp110 genes can be classified into the polyphyletic CYT group and the monophyletic ER group. The different Hsp70 and Hsp110 groups appeared to evolve following the model of divergent evolution. This model can also explain the evolution of the ER and MT genes. On the other hand, the CYT genes are divided into heat-inducible and constitutively expressed genes. The constitutively expressed genes have evolved more or less following the birth-and-death process, and the rates of gene birth and gene death are different between the two nematode species. By contrast, some heat-inducible genes show an intraspecies phylogenetic clustering. This suggests that they are subject to sequence homogenization resulting from gene conversion-like events. In addition, the heat-inducible genes show high levels of sequence conservation in both intra-species and inter-species comparisons, and in most cases, amino acid sequence similarity is higher than nucleotide sequence similarity. This indicates that purifying selection also plays an important role in maintaining high sequence similarity among paralogous Hsp70 genes. Therefore, we suggest that the CYT heat-inducible genes have been subjected to a combination of purifying selection, birth-and-death process, and gene conversion-like events.

Animals↗

PubMed1985

Evolution of replicators playing a strategic game.

A mathematical model of replicator evolution is considered. Replicators are words of a formal language specifying a strategy for a parlour game. They replicate with mutations and are selected according to their pay-off against other replicators.

Biological Evolution↗

PubMed1999

Selection, evolution of behavior and animal models in behavioral neuroscience.

We investigated whether genetic differences in various forms of intraspecific aggression and anxiety in four different genetic lines of mice (i.e. wild, outbred Swiss-CD1, inbred DBA/2 and inbred C57/BL6N) may reflect modifications in behavioral strategy. Experiments 1 and 2 used ethologically based paradigms to analyze aggressive and anxiety responses both in social (i.e. aggression) and non-social (i.e. novel environment exploration) contexts. In Experiment 3, an anxiolytic drug (chlordiazepoxide (CDP)) was used to examine possible differences in proximal mechanisms underlying anxiety-related behaviors. The data show that intrasexual aggression, infanticide and maternal aggressions are related and covarying. Genetic lines with the highest levels of intermale attack (i.e. Wild and Swiss-CD1) also have highest levels of infanticide, interfemale attack and maternal aggression but, interestingly, the lowest levels of anxiety. In fact, exploratory behavior is lower and risk assessment behavior markedly higher in DBA/2 and C57/BL6N mice (i.e. the less aggressive strains) compared to Swiss and Wild genetic lines. Although reproductive status influences anxiety levels in female mice, our findings show that (contrary to previous studies) lactating mice are more anxious than virgin females in terms of risk assessment activities. These data demonstrate the importance of studying behavior in a more ecologically-relevant context which emphasizes the function of behavior in a specific situation. Moreover, differential strain sensitivity to the behavioral effects of CDP suggests that genetic lines of mice may differ in the underlying mechanisms mediating behavior. It is therefore possible that artificial selection of different genotypes has resulted in differences in proximate mechanisms modulating the levels of aggression and anxiety, thereby leading to modification of social behavior. Overall, the results presented here suggest that subtle genetic alterations in specific underlying neural mechanisms are likely to cause profound effects on behavioral responses and their adaptive significance. Implications for behavioral neuroscience research that seeks to understand both the proximal and ultimate mechanisms of behavior are discussed.

Animals↗

PubMed1988

Evolution of cancer genes as a mutation-driven process.

Cancer is primarily a somatic genetic disease resulting from the accumulation of several precancerous mutations in a cell lineage. The evolution of highly oncogenic retroviruses has been used as a model for the evolution of a cancer cell. The properties of intermediates between one set of replication-competent retrovirus and protooncogene progenitors and the homologous highly oncogenic retrovirus were analyzed to differentiate between selection-driven and mutation-driven models of this evolution. In this case and in some other cases where sufficient data are available, it appears that the intermediates in the evolution of highly oncogenic retroviruses are not transforming, indicating that they were not formed in a purely selection-driven process. Furthermore, analysis of retrovirus mutation rates indicates that there is a high rate of mutation in retrovirus replication such that the evolution of highly oncogenic retroviruses could be mutation-driven. Other evidence is mentioned suggesting that oncogenesis in general is at least partially mutation-driven, although mutational mechanisms are involved that are different from those involved in the evolution of highly oncogenic retroviruses.

Biological Evolution↗

PubMed2005

Evolution of phenotypic plasticity: where are we going now?

The study of phenotypic plasticity has progressed significantly over the past few decades. We have moved from variation for plasticity being considered as a nuisance in evolutionary studies to it being the primary target of investigations that use an array of methods, including quantitative and molecular genetics, as well as of several approaches that model the evolution of plastic responses. Here, I consider some of the major aspects of research on phenotypic plasticity, assessing where progress has been made and where additional effort is required. I suggest that some areas of research, such the study of the quantitative genetic underpinning of plasticity, have been either settled in broad outline or superseded by new approaches and questions. Other issues, such as the costs of plasticity are currently at the forefront of research in this field, and are likely to be areas of major future development.

Journal Article↗

PubMed2003

Birth of 'human-specific' genes during primate evolution.

Humans and other Anthropoids share very similar chromosome structure and genomic sequence as seen in the 98.5% homology at the DNA level between us and Great Apes. However, anatomical and behavioral traits distinguish Homo sapiens from his closest relatives. I review here several recent studies that address the issue by using different approaches: large-scale sequence comparison (first release) between human and chimpanzee, characterization of recent segmental duplications in the human genome and analysis of exemplary gene families. As a major breakthrough in the field, the heretical concept of 'human-specific' genes has recently received some supporting data. In addition, specific chromosomal regions have been mapped that display all the features of 'gene nurseries' and could have played a major role in gene innovation and speciation during primate evolution. A model is proposed that integrates all known molecular mechanisms that can create new genes in the human lineage.

Animals↗

PubMed2005

In silico sequence evolution with site-specific interactions along phylogenetic trees.

MOTIVATION: A biological sequence usually has many sites whose evolution depends on other positions of the sequence, but this is not accounted for by commonly used models of sequence evolution. Here we introduce a Markov model of nucleotide sequence evolution in which the instantaneous substitution rate at a site depends on the states of other sites. Based on the concept of neighbourhood systems, our model represents a universal description of arbitrarily complex dependencies among sites. RESULTS: We show how to define complex models for some illustrative examples and demonstrate that our method provides a versatile resource for simulations of sequence evolution with site-specific interactions along a tree. For example, we are able to simulate the evolution of RNA taking into account both secondary structure as well as pseudoknots and other tertiary interactions. To this end, we have developed a program Simulating Site-Specific Interactions (SISSI) that simulates evolution of a nucleotide sequence along a phylogenetic tree incorporating user defined site-specific interactions. Furthermore, our method allows to simulate more complex interactions among nucleotide and other character based sequences. AVAILABILITY: We implemented our method in an ANSI C program SISSI which runs on UNIX/Linux, Windows and Mac OS systems, including Mac OS X. SISSI is available at http://www.bi.uni-duesseldorf.de/software/sissi/

Algorithms↗

PubMed2006

New bioorganic reagents: evolved cyclohexanone monooxygenase--why is it more selective?

Four mutants of the cyclohexanone monooxygenase (CHMO) evolved as catalysts for Baeyer-Villiger oxidation of 4-hydroxycyclohexanone were investigated as catalysts for a variety of 4-substituted and 4,4-disubstituted cyclohexanones. Several excellent catalytic matches (mutant/substrate) were identified. The most important, however, is the finding that, in a number of cases, a mutant with a single exchange, Phe432Ser, was shown to be as robust and more selective as a catalyst than the wild-type CHMO. All biotransformations were performed on a laboratory scale, allowing full characterization of the products. The absolute configurations of two products were established. A model suggesting a possible role of the 432 serine residue in enantioselectivity control is proposed.

Amino Acid Substitution↗

PubMed1984

[Systems approach to adolescence. Refresher course of the Swiss Psychiatric Society, Zurich, May 1983].

The author summarizes contributions of General Systems Theory to the understanding of adolescence. GST, a metatheory that does not replace intermediary theories which are directly comparable to experience, has firstly attempted to describe hierarchical organizations. More recently, new models have focused on processes. One of these models, the evolutive paradigm, has specified essential conditions of interaction between environment and evolutive systems, called constancy and adjustment. It is applied here to data of a crisis within a non-clinical family with adolescents.

Adolescent↗

PubMed1995

Models of G-protein coupled receptors revised for family-wide compliance with experimental data. A new sequence accommodation suggested for helix G.

The G-protein coupled receptors form a vast superfamily. The hydrophobic sequences of the transmembrane regions can be consistently and unambiguously aligned for nearly all, even distantly related, members owing to striking conserved patterns. As the fold is highly conserved in evolution, a model of the structure of the transmembrane helix bundle built for any individual receptor will thus be of family-wide relevance. Consequently the model must comply with key results experimentally obtained for other individual receptors. Meeting this demand can greatly reduce the uncertainties in modelling G-protein coupled receptors. This present communication shows how our recent template model based on the backbone structure of bacteriorhodopsin is revised according to that demand. Although it turns out to be in accordance with the experimental data in most of its parts, this revision suggests a sequence accommodation to helix G that is different from all other published models.

Amino Acid Sequence↗