@inbook{ff7c0d05cc8041bfa0aaa8bf7858929b,
title = "Rooting Species Trees Using Gene Tree-Species Tree Reconciliation",
abstract = "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.",
keywords = "Amalgamated likelihood estimation, Evolution, Phylogenetics, Reconciliation, Rooting",
author = "Harris, \{Brogan J.\} and Sheridan, \{Paul O.\} and Dav{\'i}n, \{Adri{\'a}n A.\} and C{\'e}cile Gubry-Rangin and Sz{\"o}ll{\H o}si, \{Gergely J.\} and Williams, \{Tom A.\}",
note = "Publisher Copyright: {\textcopyright} 2022, The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.",
year = "2022",
doi = "10.1007/978-1-0716-2691-7\_9",
language = "English",
series = "Methods in Molecular Biology",
publisher = "Humana Press Inc.",
pages = "189--211",
booktitle = "Methods in Molecular Biology",
}