An estimate of the deepest branches of the tree of life from ancient vertically-evolving genes
- University of Bristol, United Kingdom
- Royal Netherlands Institute for Sea Research, Netherlands
- Eötvös Loránd University, Hungary
Abstract
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 reveal 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 CPR within Bacteria as the sister group to the Chloroflexota.
Data availability
All of the data, including sequence alignments, trees, annotation files, and scripts associated with this manuscript have been deposited in the FigShare repository at DOI: 10.6084/m9.figshare.13395470.
Article and author information
Author details
Tara A Mahendrarajah
Gergely J Szöllősi
Funding
Gordon and Betty Moore Foundation (GBMF9741)
- Anja Spang
- Tom A Williams
Royal Society (RGF\EA\180199)
- Edmund RR Moody
- Tom A Williams
Natural Environment Research Council (NE/P00251X/1)
- Celine Petitjean
- Tom A Williams
Royal Society (URF\R\201024)
- Tom A Williams
H2020 European Research Council (714774)
- Gergely J Szöllősi
H2020 European Research Council (GINOP-2.3.2.-15-2016-00057)
- Gergely J Szöllősi
Swedish Research Council (2016-03559)
- Anja Spang
Netherlands Organisation for Scientific Research (WISE Fellowship)
- Anja Spang
H2020 European Research Council (947317)
- Anja Spang
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2022, Moody et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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An estimate of the deepest branches of the tree of life from ancient vertically-evolving genes
eLife 11:e66695.
https://doi.org/10.7554/eLife.66695
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