Related papers: A probabilistic model for gene content evolution w…
We present a model for evolving agents using both genetic and cultural inheritance mechanisms. Within each agent our model maintains two distinct information stores we call the genome and the memome. Processes of adaptation are modeled as…
We propose a continuous model for evolutionary rate variation across sites and over the tree and derive exact transition probabilities under this model. Changes in rate are modelled using the CIR process, a diffusion widely used in…
We consider the discrete-time migration-recombination equation, a deterministic, nonlinear dynamical system that describes the evolution of the genetic type distribution of a population evolving under migration and recombination in a law of…
Gene-sharing networks provide a powerful framework to study the evolution of viruses and mobile genetic elements. These bipartite networks, which link genes to the genomes that contain them, exhibit characteristic degree distributions: a…
Markov chains are a common framework for individual-based state and time discrete models in ecology and evolution. Their use, however, is largely limited to systems with a low number of states, since the transition matrices involved pose…
Continuous-time Markov chains are a standard tool in phylogenetic inference. If homogeneity is assumed, the chain is formulated by specifying time-independent rates of substitutions between states in the chain. In applications, there are…
Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…
The biological world, especially its majority microbial component, is strongly interacting and may be dominated by collective effects. In this review, we provide a brief introduction for statistical physicists of the way in which living…
We consider a multi-type Moran model (in continuous time) with selection and type-dependent mutation. This paper is concerned with the evolution of genealogical information forward in time. For this purpose we define and analytically…
Bayesian inference for phylogenetics is a gold standard for computing distributions of phylogenies. It faces the challenging problem of. moving throughout the high-dimensional space of trees. However, hyperbolic space offers a low…
Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…
Scientific studies in many areas of biology routinely employ evolutionary analyses based on the probabilistic inference of phylogenetic trees from molecular sequence data. Evolutionary processes that act at the molecular level are highly…
Textual analysis of typical microbial genomes reveals that they have the statistical characteristics of a DNA sequence of a much shorter length. This peculiar property supports an evolutionary model in which a genome evolves by random…
Phylogenetic networks describe the evolution of a set of taxa for which reticulate events have occurred at some point in their evolutionary history. Of particular interest is when the evolutionary history between a set of just three taxa…
Gene gains and losses have shaped the gene repertoire of species since the universal last common ancestor to species today. Genes in extant species were gained at different historical times via de novo creation of new genes, duplication of…
The rates-across-sites assumption in phylogenetic inference posits that the rate matrix governing the Markovian evolution of a character on an edge of the putative phylogenetic tree is the product of a character-specific scale factor and a…
We consider an interacting particle Markov process for Darwinian evolution in an asexual population with non-constant population size, involving a linear birth rate, a density-dependent logistic death rate, and a probability $\mu$ of…
We derive a Poisson random field model for population site polymorphisms differences within and between two species that share a relatively recent common ancestor. The model can be either equilibrium or time inhomogeneous. We first consider…
Reconstructing evolutionary histories and estimating the rate of evolution from molecular sequence data is of central importance in evolutionary biology and infectious disease research. We introduce a flexible Bayesian phylogenetic…
In this paper we review some recent results that shed light on a fundamental question in molecular systematics: how much phylogenetic `signal' can we expect from characters that have evolved under some Markov process? There are many sides…