A Stochastic Model for Phylogenetic Trees

DOI10.1239/JAP/1245676110MaRDI QIDQ5321773zbMATH OpenOpenAlexFDO

Authors Thomas M. Liggett, Rinaldo Schinazi

Publication date 15 July 2009

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

Full work available at URL https://arxiv.org/abs/0905.2349

zbMATH Keywords

HIVinfluenzaphylogenetic treestochastic model

Mathematics Subject Classification ID

Interacting random processes; statistical mechanics type models; percolation theory (60K35) Epidemiology (92D30)

Abstract: We propose the following simple stochastic model for phylogenetic trees. New types are born and die according to a birth and death chain. At each birth we associate a fitness to the new type sampled from a fixed distribution. At each death the type with the smallest fitness is killed. We show that if the birth (i.e. mutation) rate is subcritical we get a phylogenetic tree consistent with an influenza tree (few types at any given time and one dominating type lasting a long time). When the birth rate is supercritical we get a phylogenetic tree consistent with an HIV tree (many types at any given time, none lasting very long).

Recommendations

• A stochastic model for the evolution of the influenza virus
• Critical case stochastic phylogenetic tree model via the Laplace transform
• Stochastic models for phylogenetic trees on higher-order taxa
• Phylogenetic analysis accounting for age-dependent death and sampling with applications to epidemics
• Evolving phylogenies of trait-dependent branching with mutation and competition. I: existence

Cites work

• scientific article; zbMATH DE number 48363 (Why is no real title available?)
• scientific article; zbMATH DE number 805093 (Why is no real title available?)
• scientific article; zbMATH DE number 3349081 (Why is no real title available?)
• Markov chain models - rarity and exponentiality

Cited in

(22)

• A phase transition for a random cluster model on phylogenetic trees.
• Applying the Thorne-Kishino-Felsenstein model to sequence evolution on a star-shaped tree
• On the existence of accessibility in a tree-indexed percolation model
• Characterization of a branch of the phylogenetic tree
• Critical case stochastic phylogenetic tree model via the Laplace transform
• Evolving phylogenies of trait-dependent branching with mutation and competition. I: existence
• The probability distribution of the reconstructed phylogenetic tree with occurrence data
• The algebra of the general Markov model on phylogenetic trees and networks
• Phylogenetic analysis accounting for age-dependent death and sampling with applications to epidemics
• Limit Theorems for the Inductive Mean on Metric Trees
• Path integral formulation and Feynman rules for phylogenetic branching models
• Linking population genetics to phylogenetics
• An inhomogeneous contact process model for speciation
• On a link between a species survival time in an evolution model and the Bessel distributions
• A stochastic model for the evolution of the influenza virus
• Phylogenetic trees via Hamming distance decomposition tests
• Detection of Adaptive Shifts on Phylogenies by using Shifted Stochastic Processes on a Tree
• Ancestors and descendants in evolving k‐tree models
• On a model of evolution of subspecies
• Galton-Watson processes in varying environment and accessibility percolation
• Stochastic models for phylogenetic trees on higher-order taxa
• Mixed-up trees: the structure of phylogenetic mixtures

This page was built for publication: A Stochastic Model for Phylogenetic Trees

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q5321773)