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PubMed2004

Mating system and population structure of the primitively eusocial wasp Ropalidia revolutionalis: a model system for the evolution of complex societies.

Mating systems are important determinants of genetic structure in cooperative groups, and their effects can influence profoundly the interactions of group members. The primitively eusocial wasp, Ropalidia revolutionalis, has an interesting genetic and social structure that makes it an excellent model system for examining the evolution of more complex societies. In particular, its colonies sometimes have multiple queens, a key characteristic of more advanced wasp societies. In this study, we have characterized the mating system of the social wasp Ropalidia revolutionalis to understand better its colony genetic structure. R. revolutionalis females nearly always mate singly and they are unrelated to their mates. However, different females in the same colony do mate with males, on average, who are related as cousins. Single mating will help to maintain high relatedness, which should be important for continued cooperation in multiple queen societies, but it creates potential conflicts in single queen colonies over the production of males as well as over the timing of male production. We have also characterized the population structure of R. revolutionalis from Townsville, in tropical north Queensland, to Brisbane in the subtropics. Even at such a large scale, the population is remarkably unstructured with an average F(ST) of 0.0546. There is weak isolation by distance, and evidence for subtle differentiation between a southern region with no dry season, which extends as far north as Rockhampton, and a northern region with a severe to moderate dry season. This may reflect historical effects of extreme aridity on the population structure.

Analysis of Variance↗

PubMed2005

"Winner takes it all": strongest node rule for evolution of scale-free networks.

We study a model for evolution of complex networks. We introduce information filtering for reduction of the number of available nodes to a randomly chosen sample, as a stochastic component of evolution. New nodes are attached to the nodes that have maximal degree in the sample. This is a deterministic component of network evolution process. This fact is unusual for evolution of scale-free networks and depicts a possible route for modeling network growth. We present both simulations and theoretical results for network evolution. The obtained degree distributions exhibit an obvious power-law behavior in the middle with the exponential cut off in the end. This highlights the essential characteristics of information filtering in the network growth mechanisms.

Algorithms↗

PubMed2004

Allee effects, immigration, and the evolution of species' niches.

Theoretical studies of adaptation to sink environments (with conditions outside the niche requirements of a species) have shown that immigration from source habitats can either facilitate or inhibit local adaptation. Here, we examine the influence of immigration on the evolution of local adaptation, given an Allee effect (i.e., at low densities, absolute fitness increases with population density). We consider a deterministic model for evolution at a haploid locus, and a stochastic individual-based model for evolution of a quantitative trait, and several kinds of Allee effects. We demonstrate that increased immigration can greatly facilitate adaptive evolution in the sink; with greater immigration, local population sizes rise, and because of the Allee effect, there is a positive indirect effect of immigration on local fitness. This makes it easier for alleles of modest effect to be captured by natural selection, transforming the sink into a locally adapted population that can persist without immigration.

Adaptation, Biological↗

PubMed1996

Computing marginal expectations for large compartmentalized models with application to AIDS evolution in a prison system.

The customary models for the AIDS epidemic are compartmentalized according to criteria such as risk factors, sexual habits, gender, race, age, and HIV status and stage. Hitherto, with very few exceptions, investigators have resorted to deterministic approximations or to simulation for the computational investigation of such models, which do not yield to purely analytic methods. The present paper describes a numerical technique, not dependent on Monte Carlo simulations, for such compartmentalized Markov population processes. Analytic error bounds and computational evidence suggest that this technique is quite accurate. The study is motivated and illustrated by a model for a prison system, with ten interrelated prisons, twenty compartments, and thousands of individuals. This model is of increasing interest in itself because the HIV/AIDS epidemic is particularly virulent among prison populations, where the environment offers special opportunities to investigate various prevention and educational programmes quantitatively. Our computational techniques are shown to be effective for the analysis of such a prison system, even though the resulting Markov process is an order of magnitude more complicated than other stochastic epidemic models currently being investigated. The modelling approach and numerical device appear to be applicable to a wide variety of population processes involving migration between population patches.

Acquired Immunodeficiency Syndrome↗

PubMed2005

Reproductive compensation in the evolution of plant mating systems.

Reproductive compensation, the replacement of dead embryos by potentially viable ones, is known to play a major role in the maintenance of deleterious mutations in mammalian populations. However, it has received little attention in plant evolution. Here we model the joint evolution of mating system and inbreeding depression with reproductive compensation. We used a dynamic model of inbreeding depression, allowing for partial purging of recessive lethal mutations by selfing. We showed that reproductive compensation tended to increase the mean number of lethals in a population, but favored self-fertilization by effectively decreasing early inbreeding depression. When compensation depended on the selfing rate, stable mixed mating systems can occur, with low to intermediate selfing rates. Experimental evidence of reproductive compensation is required to confirm its potential importance in the evolution of plant mating systems. We suggest experimental methods to detect reproductive compensation.

Biological Evolution↗

PubMed2001

From metabolism to polymorphism in bacterial populations: a theoretical study.

Stable polymorphisms are commonly observed in experimental bacterial populations grown in homogeneous media. Evidence is accumulating that metabolic interactions might be the main mechanism underlying the emergence and maintenance of such polymorphisms. To date, however, attempts to model the evolution of bacterial polymorphism have not considered metabolism as a possible component of polymorphism maintenance. Here, we propose a simulation approach to model the evolution of selected polymorphisms in a bacterial population. Using recent knowledge of the relationship between bacterial fitness and metabolism, we build a simple metabolic model and test the effect of resource competition on polymorphism. Without making an a priori hypothesis on fitness functions, we show that stable polymorphic situations could be observed under high nutrient competition, and we propose a functional, metabolism-based explanation to the debated issue of polymorphism maintenance.

Bacteria↗

PubMed1993

The mathematical modelling of human culture and its implications for psychology and the human sciences.

Recent years have seen the growth of a new and exciting field of theoretical research concerned with the mathematical modelling of human culture, and of its interaction with genetics. Drawing on analogies between genetic and cultural processes, mathematically sophisticated biologists have used population genetics models as the basis for the development of analogous models of cultural transmission, cultural evolution and gene-culture co-evolution. These models are designed to describe and analyse the diffusion of cultural traits through populations, under the influence of various cultural and evolutionary forces. They have already been applied to address many problems of interest to psychologists. Here I present an introduction to these models, explaining the mathematics in simple terms, and giving examples of the work of leading theorists. I go on to discuss the findings of most relevance to psychology, critically analysing the most important conclusions. Finally, I suggest some areas of psychology in which these models might usefully be applied. I argue that these models constitute a major theoretical innovation, and that there is considerable potential for their application in psychology.

Behavior↗

PubMedDate not supplied

[Evolution of life cycle: models based on optimization of energy allocation].

A brief history of optimization approach in modern evolutionary ecology is given and author's own results concerning life history evolution are considered in more details. The problem of evolutionary optimization is formulated in terms of mathematical theory of optimal control as a problem of optimal sharing of organism's resources between growth, reproduction, repair, and maintenance. The Malthusian parameter is used as optimality criterion. This approach allows, in particular, to give evolutionary ecological explanations for some well known empirical facts such as attenuation of growth with age (law of Bertalanffi), acceleration of ageing with age (law of Gompertz), human sexual dimorphism in mean lifespan, age and size of maturity.

Aging↗

PubMed2005

Recombination dramatically speeds up evolution of finite populations.

We study the role of recombination, in the form of bacterial transformation, in speeding up Darwinian evolution. This is done by adding a new process to a previously studied Markov model of evolution on a smooth fitness landscape; this new process allows alleles to be exchanged with those in the surrounding medium. Our results, both numerical and analytic, indicate that, for a wide range of intermediate population sizes, recombination dramatically speeds up the rate of evolutionary advance.

Bacteria↗

PubMed2001

Error threshold for spatially resolved evolution in the quasispecies model.

The error threshold for quasispecies in 1, 2, 3, and infinity dimensions is investigated by stochastic simulation and analytically. The results show a monotonic decrease in the maximal sustainable error probability with decreasing diffusion coefficient, independently of the spatial dimension. It is thereby established that physical interactions between sequences are necessary in order for spatial effects to enhance the stabilization of biological information. The analytically tractable behavior in an infinity-dimensional (simplex) space provides a good guide to the spatial dependence of the error threshold in lower dimensional Euclidean space.

Evolution, Molecular↗

PubMed2003

Statistical properties of neutral evolution.

Neutral evolution is the simplest model of molecular evolution and thus it is most amenable to a comprehensive theoretical investigation. In this paper, we characterize the statistical properties of neutral evolution of proteins under the requirement that the native state remains thermodynamically stable, and compare them to the ones of Kimura's model of neutral evolution. Our study is based on the Structurally Constrained Neutral (SCN) model which we recently proposed. We show that, in the SCN model, the substitution rate decreases as longer time intervals are considered. Fluctuations from one branch of the evolutionary tree to another are strong, leading to a non-Poissonian statistics for the substitution process. Such strong fluctuations are in part due to the fact that neutral substitution rates for individual residues are strongly correlated for most residue pairs. Interestingly, structurally conserved residues, characterized by a much below average substitution rate, are also much less correlated to other residues and evolve in a much more regular way. Our results can improve methods aimed at distinguishing between neutral and adaptive substitutions as well as methods for computing the expected number of substitutions occurred since the divergence of two protein sequences. In particular, we compute the minimal sequence similarity below which no information about the evolutionary divergence of the compared sequences can be obtained.

Amino Acid Substitution↗

PubMed2001

Lectin-like proteins in model organisms: implications for evolution of carbohydrate-binding activity.

Classes of intracellular lectins that recognize core-type structures and mediate intracellular glycoprotein trafficking are present in vertebrates, model invertebrates such as Caenorhabditis elegans and Drosophila melanogaster, plants, and yeasts. Lectins that recognize more complex structures at the cell surface, such as C-type lectins and galectins, are also found in invertebrate organisms as well as vertebrates, but the functions of these proteins have evolved differently in different animal lineages.

Animals↗

PubMed2004

Proteomic traces of speciation.

Recent work has shown that the network of structural similarity between protein domains exhibits a power-law distribution of edges per node. The scale-free nature of this graph, termed the protein domain universe graph or PDUG, may be reproduced via a divergent model of structural evolution. The performance of this model, however, does not preclude the existence of a successful convergent model. To further resolve the issue of protein structural evolution, we explore the predictions of both convergent and divergent models directly. We show that when nodes from the PDUG are partitioned into subgraphs on the basis of their occurrence in the proteomes of particular organisms, these subgraphs exhibit a scale-free nature as well. We explore a simple convergent model of structural evolution and find that the implications of this model are inconsistent with features of these organismal subgraphs. Importantly, we find that biased convergent models are inconsistent with our data. We find that when speciation mechanisms are added to a simple divergent model, subgraphs similar to the organismal subgraphs are produced, demonstrating that dynamic models can easily explain the distributions of structural similarity that exist within proteomes. We show that speciation events must be included in a divergent model of structural evolution to account for the non-random overlap of structural proteomes. These findings have implications for the long-standing debate over convergent and divergent models of protein structural evolution, and for the study of the evolution of organisms as a whole.

Bacterial Proteins↗

PubMed2002

Evolution of multispecific mating-type alleles for pheromone perception in the homobasidiomycete fungi.

The evolution of multiple, independent and multispecific mating-type loci is a feature unique to homobasidiomycete fungi. To propose a model of evolution, data assembled for the wood-rotting fungus Schizophyllum commune were analyzed. In one mating-type locus, pheromone receptors and several pheromones are encoded which have been investigated in some detail and can be used to understand the ligand-receptor interactions and activation of signal transduction which are essential to sexual propagation. Previous models for the evolution of new alleles were complicated and involved three subsequent steps (without selectable phenotype) prior to the establishment of a new stable pheromone-receptor pair. This paper presents a model for the evolution of new specificities by recombination and selection that incorporates the multi-state receptor activation recently established for S. commune, explaining differential responses to different pheromones in one receptor molecule. The model takes into account the occurrence of multiple pheromone genes in each locus and unilateral nuclear donor/acceptor strains that may in nature act as steps in the evolution of new specificities. A second homobasidiomycete fungus, Coprinus cinereus, was similarly characterized at the molecular level. Data acquired in this system support the conclusion that the presented model can be generalized.

Basidiomycota↗

PubMed2006

Divergent evolution of a structural proteome: phenomenological models.

We develop models of the divergent evolution of genomes; the elementary object of sequence dynamics is the protein structural domain. To identify patterns of organization that reflect mechanisms of evolution, we consider the individual genomes of many procaryote species, studying the arrangement of protein structural domains in the space of all polypeptide structures. We view the network of structural similarities as a graph, called the organismal Protein Domain Universe Graph (oPDUG); vertices represent types of structural domains and edges represent strong structural similarity. As observed before, each oPDUG is a highly nonrandom graph, as evidenced in the vertex degree distribution, which resembles a Pareto law (which has a power-law asymptotic). To explain this and other peculiar properties of the oPDUGs, we construct an evolving-graph model for the long-timescale evolutionary dynamics of oPDUGs, containing only divergent mechanisms of domain discovery. The model generates degree distributions (resembling Pareto laws) and clustering-coefficient distributions that are characteristic of the oPDUGs. In the infinite-graph limit, we analytically compute the exponent for specific biological parameters, as well as the complete phase diagram of the model, finding two distinct regimes of domain innovation dynamics. Thus, divergent evolutionary dynamics quantitatively explains the nonrandom organization of oPDUGs.

Bacterial Proteins↗

PubMed2005

Mathematical model for carbon dioxide evolution from the thermophilic composting of synthetic food wastes made of dog food.

The impacts of the aeration and the agitation on the composting process of synthetic food wastes made of dog food were studied in a laboratory-scale reactor. Two major peaks of CO(2) evolution rate were observed. Each peak represented an independent stage of composting associated with the activities of thermophilic bacteria. CO(2) evolutions known to correlate well with microbial activities and reactor temperatures were fitted successfully to a modified Gompertz equation, which incorporated three biokinetic parameters, namely, CO(2) evolution potential, specific CO(2) evolution rate, and lag phase time. No parameters that describe the impact of operating variables are involved. The model is only valid for the specified experimental conditions and may look different with others. The effects of operating parameters such as aeration and agitation were studied statistically with multivariate regression technique. Contour plots were constructed using regression equations for the examination of the dependence of CO(2) evolution potentials on aeration and agitation. In the first stage, a maximum CO(2) evolution potential was found when the aeration rate and the agitation parameter were set at 1.75 l/kg solids-min and 0.35, respectively. In the second stage, a maximum existed when the aeration rate and the agitation parameter were set at 1.8 l/kg solids-min and 0.5, respectively. The methods presented here can also be applied for the optimization of large-scale composting facilities that are operated differently and take longer time.

Animal Feed↗

PubMed2004

Model of creation and evolution of stable electropores for DNA delivery.

Electroporation, in which electric pulses create transient pores in the cell membrane, is becoming an important technique for gene therapy. To enable entry of supercoiled DNA into cells, the pores should have sufficiently large radii (>10 nm), remain open long enough for the DNA chain to enter the cell (milliseconds), and should not cause membrane rupture. This study presents a model that can predict such macropores. The distinctive features of this model are the coupling of individual pores through membrane tension and the electrical force on the pores, which is applicable to pores of any size. The model is used to explore the process of pore creation and evolution and to determine the number and size of pores as a function of the pulse magnitude and duration. Next, our electroporation model is combined with a heuristic model of DNA uptake and used to predict the dependence of DNA uptake on pulsing parameters. Finally, the model is used to examine the mechanism of a two-pulse protocol, which was proposed specifically for gene delivery. The comparison between experimental results and the model suggests that this model is well-suited for the investigation of electroporation-mediated DNA delivery.

Biological Evolution↗

PubMed2024

Stochastic modeling of single-cell gene expression adaptation reveals non-genomic contribution to evolution of tumor subclones.

Cancer progression is an evolutionary process driven by the selection of cells adapted to gain growth advantage. We present a formal study on the adaptation of gene expression in subclonal evolution. We model evolutionary changes in gene expression as stochastic Ornstein-Uhlenbeck processes, jointly leveraging the evolutionary history of subclones and single-cell expression data. Applying our model to sublines derived from single cells of a mouse melanoma revealed that sublines with distinct phenotypes are underlined by different patterns of gene expression adaptation, indicating non-genetic mechanisms of cancer evolution. Sublines previously observed to be resistant to anti-CTLA4 treatment showed adaptive expression of genes related to invasion and non-canonical Wnt signaling, whereas sublines that responded to treatment showed adaptive expression of genes related to proliferation and canonical Wnt signaling. Our results suggest that clonal phenotypes emerge as the result of specific adaptivity patterns of gene expression. A record of this paper's transparent peer review process is included in the supplemental information.

Animals↗