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Parameter Estimation and Species Tree Rooting Using ALE and GeneRax

Williams, Tom A.; Davín, Adrián A.; Morel, Benoit 1; Szánthó, Lénárd L.; Spang, Anja; Stamatakis, Alexandros ORCID iD icon 1; Hugenholtz, Philip; Szöllősi, Gergely J.
1 Institut für Theoretische Informatik (ITI), Karlsruher Institut für Technologie (KIT)

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. ... mehr


Verlagsausgabe §
DOI: 10.5445/IR/1000161500
Veröffentlicht am 23.08.2023
Originalveröffentlichung
DOI: 10.1093/gbe/evad134
Scopus
Zitationen: 4
Web of Science
Zitationen: 3
Dimensions
Zitationen: 5
Cover der Publikation
Zugehörige Institution(en) am KIT Institut für Theoretische Informatik (ITI)
Publikationstyp Zeitschriftenaufsatz
Publikationsdatum 18.07.2023
Sprache Englisch
Identifikator ISSN: 1759-6653
KITopen-ID: 1000161500
Erschienen in Genome Biology and Evolution
Verlag Oxford University Press (OUP)
Band 15
Heft 7
Seiten Art.-Nr.: evad134
Schlagwörter phylogenetics, gene tree–species tree reconciliation, comparative genomics, microbial evolution
Nachgewiesen in Dimensions
Web of Science
Scopus
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