Computing the probability of gene trees concordant with the species tree in the multispecies coalescent

DOI10.1016/J.TPB.2020.12.002zbMATH Open1478.92141arXiv2001.06741OpenAlexW3113202758WikidataQ104492601 ScholiaQ104492601MaRDI QIDQ2054865FDOQ2054865

Authors: Jakub Truszkowski, Celine Scornavacca, Fabio Pardi 

Publication date: 3 December 2021

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

Abstract: The multispecies coalescent process models the genealogical relationships of genes sampled from several species, enabling useful predictions about phenomena such as the discordance between the gene tree and the species phylogeny due to incomplete lineage sorting. Conversely, knowledge of large collections of gene trees can inform us about several aspects of the species phylogeny, such as its topology and ancestral population sizes. A fundamental open problem in this context is how to efficiently compute the probability of a gene tree topology, given the species phylogeny. Although a number of algorithms for this task have been proposed, they either produce approximate results, or, when they are exact, they do not scale to large data sets. In this paper, we present some progress towards exact and efficient computation of the probability of a gene tree topology. We provide a new algorithm that, given a species tree and the number of genes sampled for each species, calculates the probability that the gene tree topology will be concordant with the species tree. Moreover, we provide an algorithm that computes the probability of any specific gene tree topology concordant with the species tree. Both algorithms run in polynomial time and have been implemented in Python. Experiments show that they are able to analyse data sets where thousands of genes are sampled, in a matter of minutes to hours.

Full work available at URL: https://arxiv.org/abs/2001.06741

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zbMATH Keywords

coalescentdynamic programmingincomplete lineage sortingspecies treemultispecies coalescentgene tree

Mathematics Subject Classification ID

Problems related to evolution (92D15)

Cites Work

• The probability of topological concordance of gene trees and species trees.
• Introduction to algorithms
• Title not available (Why is that?)
• Statistical Inference of Phylogenies
• Title not available (Why is that?)
• Properties of phylogenetic trees generated by Yule-type speciation models
• Line-of-descent and genealogical processes, and their applications in population genetics models
• A new scaling and squaring algorithm for the matrix exponential
• The probability distribution of ranked gene trees on a species tree
• Enumeration of compact coalescent histories for matching gene trees and species trees
• On the number of non-equivalent ancestral configurations for matching gene trees and species trees

Cited In (11)

• Enumeration of coalescent histories for caterpillar species trees and \(p\)-pseudocaterpillar gene trees
• Coalescent histories for discordant gene trees and species trees
• Polynomial-Time Statistical Estimation of Species Trees Under Gene Duplication and Loss
• Determining species tree topologies from clade probabilities under the coalescent
• Site pattern probabilities under the multispecies coalescent and a relaxed molecular clock: theory and applications
• Statistically consistent rooting of species trees under the multispecies coalescent model
• On the number of non-equivalent ancestral configurations for matching gene trees and species trees
• The distributions under two species-tree models of the total number of ancestral configurations for matching gene trees and species trees
• Algorithmic improvements to species delimitation and phylogeny estimation under the multispecies coalescent
• Split probabilities and species tree inference under the multispecies coalescent model
• The probability of topological concordance of gene trees and species trees.

Uses Software

• STELLS2
• CompactCH

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