A branching process with coalescence to model random phylogenetic networks

DOI10.1214/24-EJP1088MaRDI QIDQ6126989zbMATH OpenFDO

Authors François Bienvenu, Jean-Jil Duchamps

Publication date 10 April 2024

Published in Electronic Journal of Probability (Search for Journal in Brave)

Copyright license Creative Commons Attribution 4.0 International

Full work available at URL https://arxiv.org/abs/2211.02407

zbMATH Keywords

continuum random treeexplicit phylogenetic networklocal limitlogistic branching processrandom DAGreticulate evolutiontree-like structure

Mathematics Subject Classification ID

Random graphs (graph-theoretic aspects) (05C80) Central limit and other weak theorems (60F05) Continuous-time Markov processes on discrete state spaces (60J27) Branching processes (Galton-Watson, birth-and-death, etc.) (60J80) Coalescent processes (60J90) Taxonomy, cladistics, statistics in mathematical biology (92B10)

Abstract: We introduce a biologically natural, mathematically tractable model of random phylogenetic network to describe evolution in the presence of hybridization. One of the features of this model is that the hybridization rate of the lineages correlates negatively with their phylogenetic distance. We give formulas / characterizations for quantities of biological interest that make them straightforward to compute in practice. We show that the appropriately rescaled network, seen as a metric space, converges to the Brownian continuum random tree, and that the uniformly rooted network has a local weak limit, which we describe explicitly.

Review text

The authors introduce a biologically natural, mathematically tractable model of random phylogenetic network to describe evolution in the presence of hybridization. One of the features of this model is that the hybridization rate of the lineages correlates negatively with their phylogenetic distance. Characterizations are given for quantities of biological interest that make them straightforward to compute in practice. It is shown that the appropriately rescaled network, seen as a metric space, converges to the Brownian continuum random tree, and that the uniformly rooted network has a local weak limit, which is described explicitly.

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Cites work

• A branching process approach to level‐k phylogenetic networks
• A course in stochastic processes. Stochastic models and statistical inference
• A general age-dependent branching process. I
• A general-age-dependent branching process. II
• A problem of arrangements
• Analytic combinatorics
• Asymptotic fringe distributions for general families of random trees
• Bijections for ranked tree-child networks
• Branching processes with interactions: subcritical cooperative regime
• Classes of explicit phylogenetic networks and their biological and mathematical significance
• Combinatorial and stochastic properties of ranked tree‐child networks
• Height and contour processes of Crump-Mode-Jagers forests. I: general distribution and scaling limits in the case of short edges
• scientific article; zbMATH DE number 3555176 (Why is no real title available?)
• scientific article; zbMATH DE number 1354815 (Why is no real title available?)
• scientific article; zbMATH DE number 1166155 (Why is no real title available?)
• Integrability of stochastic birth-death processes via differential Galois theory
• Invariance principles for Galton-Watson trees conditioned on the number of leaves
• Invasion probabilities, hitting times, and some fluctuation theory for the stochastic logistic process
• Limits of random tree-like discrete structures
• Local limits of large Galton-Watson trees rerooted at a random vertex
• Markov branching processes with interaction
• On the convergence of supercritical general (C-M-J) branching processes
• On the entrance at infinity of Feller processes with no negative jumps
• Probability and real trees. Ecole d'Eté de Probabilités de Saint-Flour XXXV -- 2005. Lecture given at the Saint-Flour probability summer school, July 6--23, 2005.
• Probability. Theory and examples.
• Random trees and applications
• Recurrence of distributional limits of finite planar graphs
• Simply generated trees, conditioned Galton-Watson trees, random allocations and condensation
• Speed of coming down from infinity for birth-and-death processes
• Sub-Gaussian tail bounds for the width and height of conditioned Galton-Watson trees
• Tessellations of random maps of arbitrary genus
• The branching process with logistic growth
• The Classification of Birth and Death Processes
• The continuum random tree. I
• The depth first processes of Galton-Watson trees converge to the same Brownian excursion
• The Differential Equations of Birth-and-Death Processes, and the Stieltjes Moment Problem
• The total progeny in a branching process and a related random walk

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