Related papers: Minimal model for genome evolution and growth
We study the interplay of population growth and evolutionary dynamics using a stochastic model based on birth and death events. In contrast to the common assumption of an independent population size, evolution can be strongly affected by…
The growth rate of organisms depends both on external conditions and on internal states, such as the expression levels of various genes. We show that to achieve a criterion mean growth rate over an ensemble of conditions, the internal…
The concept of evolutionary development of structures constituted a \emph{real} revolution in biology: it was possible to understand how the very complex structures of life can arise in an out-of-equilibrium system. The investigation of…
The interaction between natural selection and random mutation is frequently debated in recent years. Does similar dilemma also exist in the evolution of real networks such as biological networks? In this paper, we try to discuss this issue…
We model evolution of plants in a world, made up of different locations, with multiple environments (mutually exclusive and collectively exhaustive subsets of locations). Each environment (landmass) has temperature, rainfall, and other…
In complex systems, the interplay between nonlinear and stochastic dynamics, e.g., J. Monod's necessity and chance, gives rise to an evolutionary process in Darwinian sense, in terms of discrete jumps among attractors, with punctuated…
In this paper we study the evolution of the mutation rate for simple organisms in dynamic environments. A model with multiple fitness coding loci tracking a moving fitness peak is developed and an analytical expression for the optimal…
Evolution of genetic code is studied as the change in the choice of enzymes that are used to synthesize amino acids from the genetic information of nucleic acids. We propose the following theory: the differentiation of physiological states…
The mutual influence of dynamics and structure is a central issue in complex systems. In this paper we study by simulation slow evolution of network under the feedback of a local-majority-rule opinion process. If performance-enhancing local…
In this paper, we propose an evolving network model growing fast in units of module, based on the analysis of the evolution characteristics in real complex networks. Each module is a small-world network containing several interconnected…
Cells often exhibit different and stable phenotypes from the same DNA sequence. Robustness and plasticity of such cellular states are controlled by diverse transcriptional and epigenetic mechanisms, among them the modification of…
We study the growth of random networks under a constraint that the diameter, defined as the average shortest path length between all nodes, remains approximately constant. We show that if the graph maintains the form of its degree…
We re-examine the evolutionary dynamics of RNA secondary structures under directional selection towards an optimum RNA structure. We find that the punctuated equilibria lead to a very slow approach to the optimum, following on average an…
The evolution of microbial and viral organisms often generates clonal interference, a mode of competition between genetic clades within a population. In this paper, we show that interference strongly constrains the genetic and phenotypic…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
Sex chromosomes have independently evolved in species with separate sexes in most lineages across the tree of life. However, the well-accepted canonical model of sex chromosome evolution is not universally supported. There is no single…
The natural evolution of life seems to proceed through steps characterized by phases of relatively rapid changes, followed by longer, more stable periods. In the light of the string-theory derived physical scenario proposed in [1], we…
A simplified model for the growth of a population is studied in which random effects arise because reproducing individuals have a certain probability of surviving until the next breeding season and hence contributing to the next generation.…
We study the Tangled Nature model of macro evolution and demonstrate that the co-evolutionary dynamics produces an increasingly correlated core of well occupied types. At the same time the entire configuration of types becomes increasing…
Developmental trajectories are known to be canalized, or robust to both environmental and genetic perturbations. However, even when these trajectories are decanalized by an environmental perturbation outside of the range of conditions to…