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An estimate of the deepest branches of the tree of life from ancient vertically evolving genes

Core gene phylogenies provide a window into early evolution, but different gene sets and analytical methods have yielded substantially different views of the tree of life. Trees inferred from a small set of universal core genes have typically supported a long branch separating the archaeal and bacte...

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Autores principales: Moody, Edmund RR, Mahendrarajah, Tara A, Dombrowski, Nina, Clark, James W, Petitjean, Celine, Offre, Pierre, Szöllősi, Gergely J, Spang, Anja, Williams, Tom A
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8890751/
https://www.ncbi.nlm.nih.gov/pubmed/35190025
http://dx.doi.org/10.7554/eLife.66695
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author Moody, Edmund RR
Mahendrarajah, Tara A
Dombrowski, Nina
Clark, James W
Petitjean, Celine
Offre, Pierre
Szöllősi, Gergely J
Spang, Anja
Williams, Tom A
author_facet Moody, Edmund RR
Mahendrarajah, Tara A
Dombrowski, Nina
Clark, James W
Petitjean, Celine
Offre, Pierre
Szöllősi, Gergely J
Spang, Anja
Williams, Tom A
author_sort Moody, Edmund RR
collection PubMed
description Core gene phylogenies provide a window into early evolution, but different gene sets and analytical methods have yielded substantially different views of the tree of life. Trees inferred from a small set of universal core genes have typically supported a long branch separating the archaeal and bacterial domains. By contrast, recent analyses of a broader set of non-ribosomal genes have suggested that Archaea may be less divergent from Bacteria, and that estimates of inter-domain distance are inflated due to accelerated evolution of ribosomal proteins along the inter-domain branch. Resolving this debate is key to determining the diversity of the archaeal and bacterial domains, the shape of the tree of life, and our understanding of the early course of cellular evolution. Here, we investigate the evolutionary history of the marker genes key to the debate. We show that estimates of a reduced Archaea-Bacteria (AB) branch length result from inter-domain gene transfers and hidden paralogy in the expanded marker gene set. By contrast, analysis of a broad range of manually curated marker gene datasets from an evenly sampled set of 700 Archaea and Bacteria reveals that current methods likely underestimate the AB branch length due to substitutional saturation and poor model fit; that the best-performing phylogenetic markers tend to support longer inter-domain branch lengths; and that the AB branch lengths of ribosomal and non-ribosomal marker genes are statistically indistinguishable. Furthermore, our phylogeny inferred from the 27 highest-ranked marker genes recovers a clade of DPANN at the base of the Archaea and places the bacterial Candidate Phyla Radiation (CPR) within Bacteria as the sister group to the Chloroflexota.
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spelling pubmed-88907512022-03-03 An estimate of the deepest branches of the tree of life from ancient vertically evolving genes Moody, Edmund RR Mahendrarajah, Tara A Dombrowski, Nina Clark, James W Petitjean, Celine Offre, Pierre Szöllősi, Gergely J Spang, Anja Williams, Tom A eLife Evolutionary Biology Core gene phylogenies provide a window into early evolution, but different gene sets and analytical methods have yielded substantially different views of the tree of life. Trees inferred from a small set of universal core genes have typically supported a long branch separating the archaeal and bacterial domains. By contrast, recent analyses of a broader set of non-ribosomal genes have suggested that Archaea may be less divergent from Bacteria, and that estimates of inter-domain distance are inflated due to accelerated evolution of ribosomal proteins along the inter-domain branch. Resolving this debate is key to determining the diversity of the archaeal and bacterial domains, the shape of the tree of life, and our understanding of the early course of cellular evolution. Here, we investigate the evolutionary history of the marker genes key to the debate. We show that estimates of a reduced Archaea-Bacteria (AB) branch length result from inter-domain gene transfers and hidden paralogy in the expanded marker gene set. By contrast, analysis of a broad range of manually curated marker gene datasets from an evenly sampled set of 700 Archaea and Bacteria reveals that current methods likely underestimate the AB branch length due to substitutional saturation and poor model fit; that the best-performing phylogenetic markers tend to support longer inter-domain branch lengths; and that the AB branch lengths of ribosomal and non-ribosomal marker genes are statistically indistinguishable. Furthermore, our phylogeny inferred from the 27 highest-ranked marker genes recovers a clade of DPANN at the base of the Archaea and places the bacterial Candidate Phyla Radiation (CPR) within Bacteria as the sister group to the Chloroflexota. eLife Sciences Publications, Ltd 2022-02-22 /pmc/articles/PMC8890751/ /pubmed/35190025 http://dx.doi.org/10.7554/eLife.66695 Text en © 2022, Moody et al https://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Evolutionary Biology
Moody, Edmund RR
Mahendrarajah, Tara A
Dombrowski, Nina
Clark, James W
Petitjean, Celine
Offre, Pierre
Szöllősi, Gergely J
Spang, Anja
Williams, Tom A
An estimate of the deepest branches of the tree of life from ancient vertically evolving genes
title An estimate of the deepest branches of the tree of life from ancient vertically evolving genes
title_full An estimate of the deepest branches of the tree of life from ancient vertically evolving genes
title_fullStr An estimate of the deepest branches of the tree of life from ancient vertically evolving genes
title_full_unstemmed An estimate of the deepest branches of the tree of life from ancient vertically evolving genes
title_short An estimate of the deepest branches of the tree of life from ancient vertically evolving genes
title_sort estimate of the deepest branches of the tree of life from ancient vertically evolving genes
topic Evolutionary Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8890751/
https://www.ncbi.nlm.nih.gov/pubmed/35190025
http://dx.doi.org/10.7554/eLife.66695
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