相关论文: Quasispecies Theory for Horizontal Gene Transfer a…
We consider a recent innovative theory by Chastain et al. on the role of sex in evolution [PNAS'14]. In short, the theory suggests that the evolutionary process of gene recombination implements the celebrated multiplicative weights updates…
Biochemical and regulatory interactions central to biological networks are expected to cause extensive genetic interactions or epistasis affecting the heritability of complex traits and the distribution of genotypes in populations. However,…
We present a mechanistic formalism for the study of evolutionary dynamics models based on the diffusion approximation described by the Kimura Equation. In this formalism, the central component is the fitness potential, from which we obtain…
The prediction of phenotypic traits using high-density genomic data has many applications such as the selection of plants and animals of commercial interest; and it is expected to play an increasing role in medical diagnostics. Statistical…
It has been a puzzling question why some organisms reproduce sexually. Fisher and Muller hypothesized that reproducing by sex can speed up the evolution. They explained that in the sexual reproduction, recombination can combine beneficial…
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…
For a one-locus haploid infinite population with discrete generations, the celebrated Kingman's model describes the evolution of fitness distributions under the competition of selection and mutation, with a constant mutation probability.…
The evolutionary dynamics of HIV during the chronic phase of infection is driven by the host immune response and by selective pressures exerted through drug treatment. To understand and model the evolution of HIV quantitatively, the…
Cycling tissues such as the intestinal epithelium, germ line, and hair follicles, require a constant flux of differentiated cells. These tissues are maintained by a population of stem cells, which generate differentiated progenies and…
Migration between different habitats is ubiquitous among biological populations. In this Letter, we study a simple quasispecies model for evolution in two different habitats, with different fitness landscapes, coupled through one-way…
The replicator-mutator equation is a model for populations of individuals carrying different traits, with a fitness function mediating their ability to replicate, and a stochastic model for mutation. We derive analytical solutions for the…
We study a mathematical model describing the growth process of a population structured by age and a phenotypical trait, subject to aging, competition between individuals and rare mutations. Our goals are to describe the asymptotic behaviour…
RNA viruses form genetically diverse populations structured as mutant spectra, or quasispecies, whose internal organization influences their evolutionary and adaptive dynamics. While genetic diversity has been extensively characterized, the…
In genetics the Moran model describes the neutral evolution of a bi-allelic gene in a population of haploid individuals subjected to mutations. We show in this paper that this model can be mapped into an influence dynamical process on…
We consider the hypothesis that Evolution promotes population-wide genome patterns that, under randomization, ensures the External Validity of adaptations across population members. An adaptation is Externally Valid (EV) if its effect holds…
We updated the agent based Monte Carlo code HERITAGE that simulates human evolution within restrictive environments such as interstellar, sub-light speed spacecraft in order to include the effects of population genetics. We incorporated a…
Multiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homology even among closely related organisms. We describe a…
A population of individuals with the same genes can present heterogeneous traits (phenotypes). The prevalence of this heterogeneity can be explained as a bet-hedging strategy that improves the population proliferation rate (fitness) in…
Evolutionary algorithms, inspired by natural evolution, aim to optimize difficult objective functions without computing derivatives. Here we detail the relationship between population genetics and evolutionary optimization and formulate a…
A biological transition from a state N to a state T is characterized by a rearrangement of the gene expression profile in the system, quantitatively measured through the differential expression of genes. In contrast, changes in genetic…