Abstract
ALE and GeneRax are tools for probabilistic gene tree–species tree reconciliation. Based on a common underlying statistical model of how gene trees evolve along species trees, these methods rely on gene vs. species tree discordance to infer gene duplication, transfer, and loss events, map gene family origins, and root species trees. Published analyses have used these methods to root species trees of Archaea, Bacteria, and several eukaryotic groups, as well as to infer ancestral gene repertoires. However, it was recently suggested that reconciliation-based estimates of duplication and transfer events using the ALE/GeneRax model were unreliable, with potential implications for species tree rooting. Here, we assess these criticisms and find that the methods are accurate when applied to simulated data and in generally good agreement with alternative methodological approaches on empirical data. In particular, ALE recovers variation in gene duplication and transfer frequencies across lineages that is consistent with the known biology of studied clades. In plants and opisthokonts, ALE recovers the consensus species tree root; in Bacteria—where there is less certainty about the root position—ALE agrees with alternative approaches on the most likely root region. Overall, ALE and related approaches are promising tools for studying genome evolution.
Original language | English |
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Article number | evad134 |
Journal | Genome Biology and Evolution |
Volume | 15 |
Issue number | 7 |
DOIs | |
Publication status | Published - 18 Jul 2023 |
Bibliographical note
Funding Information:This work was supported by the Gordon and Betty Moore Foundation through grant GBMF9741 to T.A.W., A.S., L.L.S., and G.J.S., and by a Royal Society University Research Fellowship to T.A.W. Furthermore, G.J.S. and L.L.S. received funding from the European Union's Horizon 2020 research and innovation program (grant agreement No. 714774, GENECLOCKS), A.S. has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement No. 947317, ASymbEL), and the Simons Foundation 735929LPI, (Award Number: 811944). A.A.D. and P.H. were supported by an Australian Research Council Laureate Fellowship (grant FL150100038). This work was financially supported by the Klaus Tschira Foundation, by DFG grant STA 860/6-2, and by the European Union's Horizon Europe ERA Chair program under grant agreement No. 101087081 (Comp-Biodiv-GR).
Publisher Copyright:
© 2023 The Author(s). Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.
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Parameter estimation and species tree rooting using ALE and GeneRax
Williams, T. A. (Creator), Zenodo, 2023
DOI: 10.5281/zenodo.7682207, https://zenodo.org/record/7682207
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