Rooting Species Trees Using Gene Tree-Species Tree Reconciliation.
Amalgamated likelihood estimation
Evolution
Phylogenetics
Reconciliation
Rooting
Journal
Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969
Informations de publication
Date de publication:
2022
2022
Historique:
entrez:
9
9
2022
pubmed:
10
9
2022
medline:
14
9
2022
Statut:
ppublish
Résumé
Interpreting phylogenetic trees requires a root, which provides the direction of evolution and polarizes ancestor-descendant relationships. But inferring the root using genetic data is difficult, particularly in cases where the closest available outgroup is only distantly related, which are common for microbes. In this chapter, we present a workflow for estimating rooted species trees and the evolutionary history of the gene families that evolve within them using probabilistic gene tree-species tree reconciliation. We illustrate the pipeline using a small dataset of prokaryotic genomes, for which the example scripts can be run using modest computer resources. We describe the rooting method used in this work in the context or other rooting strategies and discuss some of the limitations and opportunities presented by probabilistic gene tree-species tree reconciliation methods.
Identifiants
pubmed: 36083449
doi: 10.1007/978-1-0716-2691-7_9
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
189-211Informations de copyright
© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
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