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

DOI10.1007/S10463-016-0557-XzbMATH Open1400.62296arXiv1501.02374OpenAlexW1837477861WikidataQ57426225 ScholiaQ57426225MaRDI QIDQ2397338FDOQ2397338

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)

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.

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

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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)

Cites Work

• Comparison of phylogenetic trees
• The probability of topological concordance of gene trees and species trees.
• Title not available (Why is that?)
• On computing the nearest neighbor interchange distance
• Subtree transfer operations and their induced metrics on evolutionary trees
• Statistical approach to tests involving phylogenies
• Line-of-descent and genealogical processes, and their applications in population genetics models
• A Procedure for Nonlinear Least Squares Refinement in Adverse Practical Conditions
• First steps toward the geometry of cophylogeny
• Title not available (Why is that?)

Cited In (8)

• 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
• On the variational distance of two trees

Uses Software

• ape
• Mesquite
• kdetrees

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