Distributions of topological tree metrics between a species tree and a gene tree

DOI10.1007/S10463-016-0557-XMaRDI QIDQ2397338zbMATH OpenOpenAlexWikidataFDO

Authors Jing Xi, Jin Xie, Ruriko Yoshida

Publication date 22 May 2017

Published in Annals of the Institute of Statistical Mathematics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1501.02374

zbMATH Keywords

coalescentphylogeneticstree metricstree topologies

Mathematics Subject Classification ID

Classification and discrimination; cluster analysis (statistical aspects) (62H30) Applications of statistics to biology and medical sciences; meta analysis (62P10) Applications of graph theory (05C90)

Abstract: In order to conduct a statistical analysis on a given set of phylogenetic gene trees, we often use a distance measure between two trees. In a statistical distance-based method to analyze discordance between gene trees, it is a key to decide "biological meaningful" and "statistically well-distributed" distance between trees. Thus, in this paper, we study the distributions of the three tree distance metrics: the edge difference, the path difference, and the precise $K$ interval cospeciation distance, between two trees: first, we focus on distributions of the three tree distances between two random unrooted trees with $n$ leaves ($ngeq4$); and then we focus on the distributions the three tree distances between a fixed rooted species tree with $n$ leaves and a random gene tree with $n$ leaves generated under the coalescent process with given the species tree. We show some theoretical results as well as simulation study on these distributions.

Recommendations

• The mean value of the squared path-difference distance for rooted phylogenetic trees
• Inferring metric trees from weighted quartets via an intertaxon distance
• Distribution of the Symmetric Difference Metric on Phylogenetic Trees
• Comparing and aggregating partially resolved trees
• Distance metrics for ranked evolutionary trees

Cites work

• scientific article; zbMATH DE number 2081035 (Why is no real title available?)
• scientific article; zbMATH DE number 1865935 (Why is no real title available?)
• A Procedure for Nonlinear Least Squares Refinement in Adverse Practical Conditions
• Comparison of phylogenetic trees
• First steps toward the geometry of cophylogeny
• Line-of-descent and genealogical processes, and their applications in population genetics models
• On computing the nearest neighbor interchange distance
• Statistical approach to tests involving phylogenies
• Subtree transfer operations and their induced metrics on evolutionary trees
• The probability of topological concordance of gene trees and species trees.

Cited in

(8)

• On the variational distance of two trees
• The expected value under the Yule model of the squared path-difference distance
• The probability distribution of ranked gene trees on a species tree
• The mean value of the squared path-difference distance for rooted phylogenetic trees
• A note on the path interval distance
• Distance metrics for ranked evolutionary trees
• Distribution of the Symmetric Difference Metric on Phylogenetic Trees
• Topological properties of phylogenetic trees in evolutionary models

Describes a project that uses

Uses Software

• kdetrees
• Mesquite
• ape

This page was built for publication: Distributions of topological tree metrics between a species tree and a gene tree

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q2397338)