SpeciesRax: A tool for maximum likelihood species tree inference from gene family trees under duplication, transfer, and loss

Benoit Morel*, Paul Schade, Sarah Lutteropp, Tom Williams, Gergely J. Szöllősi, Alexandros Stamatakis

*Corresponding author for this work

Research output: Contribution to journalArticle (Academic Journal)peer-review

19 Citations (Scopus)
68 Downloads (Pure)

Abstract

Species tree inference from gene family trees is becoming increasingly popular because it can account for discordance between the species tree and the corresponding gene family trees. In particular, methods that can account for multiple-copy gene families exhibit potential to leverage paralogy as informative
signal. At present, there does not exist any widely adopted inference method for this purpose. Here, we present SpeciesRax, the first maximum likelihood method that can infer a rooted species tree from a set of gene family trees and can account for gene duplication, loss, and transfer events. By explicitly modelling
events by which gene trees can depart from the species tree, SpeciesRax leverages the phylogenetic rooting signal in gene trees. SpeciesRax infers species tree branch lengths in units of expected substitutions per site and branch support values via paralogy-aware quartets extracted from the gene family trees. Using
both empirical and simulated datasets we show that SpeciesRax is at least as accurate as the best competing methods while being one order of magnitude faster on large datasets at the same time. We used SpeciesRax to infer a biologically plausible rooted phylogeny of the vertebrates comprising 188
species from 31612 gene families in one hour using 40 cores. SpeciesRax is available under GNU GPL at https://github.com/BenoitMorel/GeneRax and on BioConda.
Original languageEnglish
Article numbermsab365
JournalMolecular Biology and Evolution
Volume39
Issue number2
Early online date11 Jan 2022
DOIs
Publication statusE-pub ahead of print - 11 Jan 2022

Bibliographical note

Funding Information:
This work was financially supported by the Klaus Tschira Foundation and by DFG grant STA 860/6-2. G.J.S. received funding from the European Research Council under the European Union?s Horizon 2020 research and innovation program under grant agreement no. 714774 and the grant GINOP-2.3.2.-15-2016-00057. T.A.W. was supported by a Royal Society University Fellowship and NERC grant NE/P00251X/1. This work was funded by the Gordon and Betty Moore Foundation through grant GBMF9741 to T.A.W. and G.J.S.

Publisher Copyright:
© 2022 The Author(s) 2022. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Keywords

  • species tree inference
  • gene family tree
  • maximum likelihood
  • gene duplication
  • horizontal gene transfer
  • gene loss

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