An analysis of the fixation probability of a mutant on special classes of non-directed graphs

There is a growing interest in the study of evolutionary dynamics on populations with some non-homogeneous structure. In this paper we follow the model of Lieberman et al. (Lieberman et al. 2005 Nature 433, 312–316) of evolutionary dynamics on a graph. We investigate the case of non-directed equally weighted graphs and find solutions for the fixation probability of a single mutant in two classes of simple graphs. We further demonstrate that finding similar solutions on graphs outside these classes is far more complex. Finally, we investigate our chosen classes numerically and discuss a number of features of the graphs; for example, we find the fixation probabilities for different initial starting positions and observe that average fixation probabilities are always increased for advantageous mutants as compared with those of unstructured populations

Clines with partial panmixia across a geographical barrier in an environmental pocket

In a geographically structured population, partial global panmixia can be regarded as the limiting case of long-distance migration. On the entire line with homogeneous, isotropic migration, an environmental pocket is bounded by a geographical barrier, which need not be symmetric. For slow evolution, a continuous approximation of the exact, discrete model for the gene frequency at a diallelic locus at equilibrium, where denotes position and the barrier is at , is formulated and investigated. This model incorporates viability selection, local adult migration, adult partial panmixia, and the barrier. The gene frequency and its derivatives are discontinuous at the barrier unless the latter is symmetric, in which case only is discontinuous. A cline exists only if the scaled rate of partial panmixia ; several qualitative results also are proved. Formulas that determine in a step-environment when dominance is absent are derived. The maximal gene frequency in the cline satisfies . A cline exists if and only if and the radius of the pocket exceeds the minimal radius , for which a simple, explicit formula is deduced. Given numerical solutions for and , an explicit formula is proved for in ; whereas in , an elliptic integral for must be numerically inverted. The minimal radius for maintenance of a cline in an isotropic, bidimensional pocket is also examined

Gene surfing

Spatially resolved genetic data is increasingly used to reconstruct the migrational history of species. To assist such inference, we study, by means of simulations and analytical methods, the dynamics of neutral gene frequencies in a population undergoing a continual range expansion in one dimension. During such a colonization period, lineages can fix at the wave front by means of a ``surfing'' mechanism [Edmonds C.A., Lillie A.S. & Cavalli-Sforza L.L. (2004) Proc Natl Acad Sci USA 101: 975-979]. We quantify this phenomenon in terms of (i) the spatial distribution of lineages that reach fixation and, closely related, (ii) the continual loss of genetic diversity (heterozygosity) at the wave front, characterizing the approach to fixation. Our simulations show that an effective population size can be assigned to the wave that controls the (observable) gradient in heterozygosity left behind the colonization process. This effective population size is markedly higher in pushed waves than in pulled waves, and increases only sub-linearly with deme size. To explain these and other findings, we develop a versatile analytical approach, based on the physics of reaction-diffusion systems, that yields simple predictions for any deterministic population dynamics

Modelling the spread of Wolbachia in spatially heterogeneous environments

The endosymbiont Wolbachia infects a large number of insect species and is capable of rapid spread when introduced into a novel host population. The bacteria spread by manipulating their hosts' reproduction, and their dynamics are influenced by the demographic structure of the host population and patterns of contact between individuals. Reaction–diffusion models of the spatial spread of Wolbachia provide a simple analytical description of their spatial dynamics but do not account for significant details of host population dynamics. We develop a metapopulation model describing the spatial dynamics of Wolbachia in an age-structured host insect population regulated by juvenile density-dependent competition. The model produces similar dynamics to the reaction–diffusion model in the limiting case where the host's habitat quality is spatially homogeneous and Wolbachia has a small effect on host fitness. When habitat quality varies spatially, Wolbachia spread is usually much slower, and the conditions necessary for local invasion are strongly affected by immigration of insects from surrounding regions. Spread is most difficult when variation in habitat quality is spatially correlated. The results show that spatial variation in the density-dependent competition experienced by juvenile host insects can strongly affect the spread of Wolbachia infections, which is important to the use of Wolbachia to control insect vectors of human disease and other pests

Pathogen evolution in switching environments: a hybrid dynamical system approach

We propose a hybrid dynamical system approach to model the evolution of a pathogen that experiences different selective pressures according to a stochastic process. In every environment, the evolution of the pathogen is described by a version of the Fisher-Haldane-Wright equation while the switching between environments follows a Markov jump process. We investigate how the qualitative behavior of a simple single-host deterministic system changes when the stochastic switching process is added. In particular, we study the stability in probability of monomorphic equilibria. We prove that in a "constantly" fluctuating environment, the genotype with the highest mean fitness is asymptotically stable in probability. However, if the probability of host switching depends on the genotype composition of the population, polymorphism can be stably maintained. This is a corrected version of the paper that appeared in Mathematical Biosciences 240 (2012), p. 70-75. A corrigendum has appeared in the same journal.Comment: 15 pages, 4 figure

The Role of GC-Biased Gene Conversion in Shaping the Fastest Evolving Regions of the Human Genome

GC-biased gene conversion (gBGC) is a recombination-associated evolutionary process that accelerates the fixation of guanine or cytosine alleles, regardless of their effects on fitness. gBGC can increase the overall rate of substitutions, a hallmark of positive selection. Many fast-evolving genes and noncoding sequences in the human genome have GC-biased substitution patterns, suggesting that gBGC—in contrast to adaptive processes—may have driven the human changes in these sequences. To investigate this hypothesis, we developed a substitution model for DNA sequence evolution that quantifies the nonlinear interacting effects of selection and gBGC on substitution rates and patterns. Based on this model, we used a series of lineage-specific likelihood ratio tests to evaluate sequence alignments for evidence of changes in mode of selection, action of gBGC, or both. With a false positive rate of less than 5% for individual tests, we found that the majority (76%) of previously identified human accelerated regions are best explained without gBGC, whereas a substantial minority (19%) are best explained by the action of gBGC alone. Further, more than half (55%) have substitution rates that significantly exceed local estimates of the neutral rate, suggesting that these regions may have been shaped by positive selection rather than by relaxation of constraint. By distinguishing the effects of gBGC, relaxation of constraint, and positive selection we provide an integrated analysis of the evolutionary forces that shaped the fastest evolving regions of the human genome, which facilitates the design of targeted functional studies of adaptation in humans

Evolutionary Dynamics on Small-Order Graphs

Abstract. We study the stochastic birth-death model for structured finite populations popularized by Lieberman et al. [Lieberman, E., Hauert, C., Nowak, M.A., 2005. Evolutionary dynamics on graphs. Nature 433, 312-316]. We consider all possible connected undirected graphs of orders three through eight. For each graph, using the Monte Carlo Markov Chain simulations, we determine the fixation probability of a mutant introduced at every possible vertex. We show that the fixation probability depends on the vertex and on the graph. A randomly placed mutant has the highest chances of fixation in a star graph, closely followed by star-like graphs. The fixation probability was lowest for regular and almost regular graphs. We also find that within a fixed graph, the fixation probability of a mutant has a negative correlation with the degree of the starting vertex. 1

Electromagnetic mass differences of SU(3) baryons within a chiral soliton model

We investigate the electromagnetic mass differences of SU(3) baryons, using an "model-independent approach" within a chiral soliton model. The electromagnetic self-energy corrections to the masses of the baryon are expressed as the baryonic two-point correlation function of the electromagnetic currents. Using the fact that the electromagnetic current can be treated as an octet operator, and considering possible irreducible representations of the correlation function, we are able to construct a general collective operator for the electromagnetic self-energies, which consists of three unknown parameters. These parameters are fixed, the empirical data for the electromagnetic mass differences of the baryon octet being employed. We predict those of the baryon decuplet and antidecuplet. In addition, we obtain various mass relations between baryon masses within the corresponding representation with isospin symmetry breaking considered. We also predict the physical mass differences of the baryon decuplet. The results are in good agreement with the exisiting data.Comment: 8 pages. To appear in Phys. Lett.