Related papers: Co-evolution is Incompatible with the Markov Assum…
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…
If two species exhibit different nonlinear responses to a single shared resource, and if each species modifies the resource dynamics such that this favors its competitor, they may stably coexist. This coexistence mechanism, known as…
In the last decade, some algebraic tools have been successfully applied to phylogenetic reconstruction. These tools are mainly based on the knowledge of equations describing algebraic varieties associated to phylogenetic trees evolving…
Bertoin and Le Gall (2003) introduced a certain probability measure valued Markov process that describes the evolution of a population, such that a sample from this population would exhibit a genealogy given by the so-called…
We propose a model for co-evolving ecosystems that takes into account two levels of description of an organism, for instance genotype and phenotype. Performance at the macroscopic level forces mutations at the microscopic level. These, in…
In recent years, the growing availability of biomedical datasets featuring numerous longitudinal covariates has motivated the development of several multi-step methods for the dynamic prediction of survival outcomes. These methods employ…
The purpose of this article is to show how the isotropy subgroup of leaf permutations on binary trees can be used to systematically identify tree-informative invariants relevant to models of phylogenetic evolution. In the quartet case, we…
Methods of phylogenetic inference use more and more complex models to generate trees from data. However, even simple models and their implications are not fully understood. Here, we investigate the two-state Markov model on a tripod tree,…
A brief analysis of the compatibility between the quantum jump and the Markov property for quantum systems described by a stochastic evolution scheme is presented.
Quantitative predictions about the processes that promote species coexistence are a subject of active research in ecology. In particular, competitive interactions are known to shape and maintain ecological communities, and situations where…
Genetic recombination is one of the most important mechanisms that can generate and maintain diversity, and recombination information plays an important role in population genetic studies. However, the phenomenon of recombination is…
Using a newly introduced connection between the local and non-local description of open quantum system dynamics, we investigate the relationship between these two characterisations in the case of quantum semi-Markov processes. This class of…
The ability to absorb mutations while retaining structure and function, or mutational robustness, is a remarkable property of natural proteins. In this Letter, we use a computational model of organismic evolution [Zeldovich et al, PLOS Comp…
Many networks are complex dynamical systems, where both attributes of nodes and topology of the network (link structure) can change with time. We propose a model of co-evolving networks where both node at- tributes and network structure…
Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees. Substitutions in sequences are modelled through a continuous-time Markov process, characterised by an instantaneous rate matrix, which standard…
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…
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…
This paper presents a stochastic model motivated by the study of a virus-like evolving population with different mutation rates. This is a continuous time birth-death model: the birth processes are mutually-exciting Hawkes processes and the…
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…
The Markov evolution is studied of an infinite age-structured population of migrants arriving in and departing from a continuous habitat $X \subseteq\mathds{R}^d$ -- at random and independently of each other. Each population member is…