On joint subtree distributions under two evolutionary models

DOI10.1016/J.TPB.2015.11.004MaRDI QIDQ304457zbMATH OpenOpenAlexWikidataFDO

Authors Taoyang Wu, Kwok Pui Choi

Publication date 25 August 2016

Published in Theoretical Population Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1508.03139, https://ueaeprints.uea.ac.uk/id/eprint/55603/1/Pattern_stat_TPB_final.pdf

zbMATH Keywords

phylogenetic treejoint distributionPDA modelsubtree distributiontree indicesYule-Harding-Kingman model

Mathematics Subject Classification ID

Problems related to evolution (92D15)

Abstract: In population and evolutionary biology, hypotheses about micro-evolutionary and macro-evolutionary processes are commonly tested by comparing the shape indices of empirical evolutionary trees with those predicted by neutral models. A key ingredient in this approach is the ability to compute and quantify distributions of various tree shape indices under random models of interest. As a step to meet this challenge, in this paper we investigate the joint distribution of cherries and pitchforks (that is, subtrees with two and three leaves) under two widely used null models: the Yule-Harding-Kingman (YHK) model and the proportional to distinguishable arrangements (PDA) model. Based on two novel recursive formulae, we propose a dynamic approach to numerically compute the exact joint distribution (and hence the marginal distributions) for trees of any size. We also obtained insights into the statistical properties of trees generated under these two models, including a constant correlation between the cherry and the pitchfork distributions under the YHK model, the log-concavity and unimodality of cherry distributions under both models. In particular, we show the existence of a unique change point for cherry distribution between the two models, that is, there exists a critical value $a{u}_n$ for each $ngeq4$ such that the probability that a random tree with $n$ leaves generated under the YHK model contains $k$ cherries is lower than that under the PDA model if $1<k<a{u}_n$, and higher if $a{u}_n<klen/2$.

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Cites work

• scientific article; zbMATH DE number 3817476 (Why is no real title available?)
• scientific article; zbMATH DE number 1865935 (Why is no real title available?)
• scientific article; zbMATH DE number 850224 (Why is no real title available?)
• scientific article; zbMATH DE number 894522 (Why is no real title available?)
• A new balance index for phylogenetic trees
• Asymptotic frequency of shapes in supercritical branching trees
• Asymptotic fringe distributions for general families of random trees
• Bounding the number of hybridisation events for a consistent evolutionary history
• Branch and bound algorithms to determine minimal evolutionary trees
• Clades and clans: a comparison study of two evolutionary models
• Distributions of cherries for two models of trees
• Exact enumeration of cherries and pitchforks in ranked trees under the coalescent model
• Limit laws for functions of fringe trees for binary search trees and random recursive trees
• Limit theorems for patterns in phylogenetic trees
• On statistical tests of phylogenetic tree imbalance: The Sackin and other indices revisited
• Stochastic models and descriptive statistics for phylogenetic trees, from Yule to today.
• The mean and variance of the numbers of \(r\)-pronged nodes and \(r\)-caterpillars in Yule-generated genealogical trees
• The probabilities of rooted tree-shapes generated by random bifurcation

Cited in

(16)

• On the joint distribution of tree height and tree length under the coalescent
• Limit theorems for patterns in ranked tree‐child networks
• A balance index for phylogenetic trees based on rooted quartets
• Enumeration of lonely pairs of gene trees and species trees by means of antipodal cherries
• The distributions under two species-tree models of the number of root ancestral configurations for matching gene trees and species trees
• Topology and inference for Yule trees with multiple states
• On asymptotic joint distributions of cherries and pitchforks for random phylogenetic trees
• On the minimum value of the Colless index and the bifurcating trees that achieve it
• A Mathematical Connection Between Single-Elimination Sports Tournaments and Evolutionary Trees
• Distributions of cherries for two models of trees
• On cherry and pitchfork distributions of random rooted and unrooted phylogenetic trees
• Distributions of 4-subtree patterns for uniform random unrooted phylogenetic trees
• Clades and clans: a comparison study of two evolutionary models
• Distributions of cherries and pitchforks for the Ford model
• Squaring within the Colless index yields a better balance index
• Asymptotic frequency of shapes in supercritical branching trees

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