Quintet Rooting: Rooting species trees under the multi-species coalescent model

Yasamin Tabatabaee, Kowshika Sarker, Tandy Warnow

Research output: Contribution to journalArticlepeer-review

Abstract

Motivation: Rooted species trees are a basic model with multiple applications throughout biology, including understanding adaptation, biodiversity, phylogeography and co-evolution. Because most species tree estimation methods produce unrooted trees, methods for rooting these trees have been developed. However, most rooting methods either rely on prior biological knowledge or assume that evolution is close to clock-like, which is not usually the case. Furthermore, most prior rooting methods do not account for biological processes that create discordance between gene trees and species trees. Results: We present Quintet Rooting (QR), a method for rooting species trees based on a proof of identifiability of the rooted species tree under the multi-species coalescent model established by Allman, Degnan and Rhodes (J. Math. Biol., 2011). We show that QR is generally more accurate than other rooting methods, except under extreme levels of gene tree estimation error.

Original languageEnglish (US)
Pages (from-to)I109-I117
JournalBioinformatics
Volume38
DOIs
StatePublished - Jul 1 2022
Externally publishedYes

ASJC Scopus subject areas

  • Computational Mathematics
  • Molecular Biology
  • Biochemistry
  • Statistics and Probability
  • Computer Science Applications
  • Computational Theory and Mathematics

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