New substitution models for rooting phylogenetic trees

The root of a phylogenetic tree is fundamental to its biological interpretation, but standard substitution models do not provide any information on its position. Here, we describe two recently developed models that relax the usual assumptions of stationarity and reversibility, thereby facilitating r...

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Main Authors:	Williams, Tom A., Heaps, Sarah E., Cherlin, Svetlana, Nye, Tom M. W., Boys, Richard J., Embley, T. Martin
Format:	Online
Language:	English
Published:	The Royal Society 2015
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4571574/

id	pubmed-4571574
recordtype	oai_dc
spelling	pubmed-45715742015-09-26 New substitution models for rooting phylogenetic trees Williams, Tom A. Heaps, Sarah E. Cherlin, Svetlana Nye, Tom M. W. Boys, Richard J. Embley, T. Martin Articles The root of a phylogenetic tree is fundamental to its biological interpretation, but standard substitution models do not provide any information on its position. Here, we describe two recently developed models that relax the usual assumptions of stationarity and reversibility, thereby facilitating root inference without the need for an outgroup. We compare the performance of these models on a classic test case for phylogenetic methods, before considering two highly topical questions in evolutionary biology: the deep structure of the tree of life and the root of the archaeal radiation. We show that all three alignments contain meaningful rooting information that can be harnessed by these new models, thus complementing and extending previous work based on outgroup rooting. In particular, our analyses exclude the root of the tree of life from the eukaryotes or Archaea, placing it on the bacterial stem or within the Bacteria. They also exclude the root of the archaeal radiation from several major clades, consistent with analyses using other rooting methods. Overall, our results demonstrate the utility of non-reversible and non-stationary models for rooting phylogenetic trees, and identify areas where further progress can be made. The Royal Society 2015-09-26 /pmc/articles/PMC4571574/ /pubmed/26323766 http://dx.doi.org/10.1098/rstb.2014.0336 Text en © 2015 The Authors. http://creativecommons.org/licenses/by/4.0/ Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Williams, Tom A. Heaps, Sarah E. Cherlin, Svetlana Nye, Tom M. W. Boys, Richard J. Embley, T. Martin
spellingShingle	Williams, Tom A. Heaps, Sarah E. Cherlin, Svetlana Nye, Tom M. W. Boys, Richard J. Embley, T. Martin New substitution models for rooting phylogenetic trees
author_facet	Williams, Tom A. Heaps, Sarah E. Cherlin, Svetlana Nye, Tom M. W. Boys, Richard J. Embley, T. Martin
author_sort	Williams, Tom A.
title	New substitution models for rooting phylogenetic trees
title_short	New substitution models for rooting phylogenetic trees
title_full	New substitution models for rooting phylogenetic trees
title_fullStr	New substitution models for rooting phylogenetic trees
title_full_unstemmed	New substitution models for rooting phylogenetic trees
title_sort	new substitution models for rooting phylogenetic trees
description	The root of a phylogenetic tree is fundamental to its biological interpretation, but standard substitution models do not provide any information on its position. Here, we describe two recently developed models that relax the usual assumptions of stationarity and reversibility, thereby facilitating root inference without the need for an outgroup. We compare the performance of these models on a classic test case for phylogenetic methods, before considering two highly topical questions in evolutionary biology: the deep structure of the tree of life and the root of the archaeal radiation. We show that all three alignments contain meaningful rooting information that can be harnessed by these new models, thus complementing and extending previous work based on outgroup rooting. In particular, our analyses exclude the root of the tree of life from the eukaryotes or Archaea, placing it on the bacterial stem or within the Bacteria. They also exclude the root of the archaeal radiation from several major clades, consistent with analyses using other rooting methods. Overall, our results demonstrate the utility of non-reversible and non-stationary models for rooting phylogenetic trees, and identify areas where further progress can be made.
publisher	The Royal Society
publishDate	2015
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4571574/
_version_	1613476381372448768

New substitution models for rooting phylogenetic trees

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