Related papers: Trees within trees: Simple nested coalescents
Coalescent models of bifurcating genealogies are used to infer evolutionary parameters from molecular data. However, there are many situations where bifurcating genealogies do not accurately reflect the true underlying ancestral history of…
We design a theoretic tree-based functional representation of a class of Feynman-Kac particle distributions, including an extension of the Wick product formula to interacting particle systems. These weak expansions rely on an original…
We study condensation transitions in the steady state of a zero-range process with two species of particles. The steady state is exactly soluble -- it is given by a factorised form provided the dynamics satisfy certain constraints -- and we…
We consider a model of a population in which individuals are sampled from different species. The Yule-Kingman nested coalescent describes the genealogy of the sample when each species merges with another randomly chosen species with a…
For one-dimensional many-body systems interacting via the \textit{Coulomb force} and with \textit{arbitrary} external potential energy, we derive (\textit{i}) the \textit{node coalescence condition} for the wave function. This condition…
Single-chain nanoparticles (SCNPs) are a new class of macromolecular objects, synthesized through purely intramolecular cross-linking of single polymer chains. We use a multi-scale hydrodynamics simulation approach to study, for the first…
We introduce and analyse a class of fragmentation-coalescence processes defined on finite systems of particles organised into clusters. Coalescent events merge multiple clusters simultaneously to form a single larger cluster, while…
We exhibit an identity of abstract simplicial complexes between the well-studied complex of trees and the reduced minimal nested set complex of the partition lattice. We conclude that the order complex of the partition lattice can be…
By means of extensive simulations, we investigate concentrated solutions of globular single-chain nanoparticles (SCNPs), an emergent class of synthetic soft nano-objects. By increasing the concentration, the SCNPs show a reentrant behaviour…
We consider species tree estimation under a standard stochastic model of gene tree evolution that incorporates incomplete lineage sorting (as modeled by a coalescent process) and gene duplication and loss (as modeled by a branching…
Coalescing random walks is a fundamental stochastic process, where a set of particles perform independent discrete-time random walks on an undirected graph. Whenever two or more particles meet at a given node, they merge and continue as a…
The coalescent is a stochastic process representing ancestral lineages in a population undergoing neutral genetic drift. Originally defined for a well-mixed population, the coalescent has been adapted in various ways to accommodate spatial,…
The need to harmonise apparently irreconcilable arrangements in an ecosystem --nestedness and segregation-- has triggered so far different strategies. Methodological refinements, or the inclusion of behavioural preferences to the network…
We introduce a Poissonization method to study the coalescent structure of uniform samples from branching processes. This method relies on the simple observation that a uniform sample of size $k$ taken from a random set with positive…
We introduce a colored coalescent process which recovers random colored genealogical trees. Here a colored genealogical tree has its vertices colored black or white. Moving backward along the colored genealogical tree, the color of vertices…
Many biological systems can be described by finite Markov models. A general method for simplifying master equations is presented that is based on merging adjacent states. The approach preserves the steady-state probability distribution and…
As the simplest model of transport of interacting particles in a disordered medium, we consider the asymmetric simple exclusion process (ASEP) in which particles with hard-core interactions perform biased random walks, on the supercritical…
We study the continuous-time evolution of the recombination equation of population genetics. This evolution is given by a differential equation that acts on a product probability space, and its solution can be described by a Markov chain on…
The work continues the author's many-year research in theory of maximal branching processes, which are obtained from classical branching processes by replacing the summation of descendant numbers with taking the maximum. One can say that in…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…