ArticleMolecular biology and evolution2020
A New Analysis of Archaea-Bacteria Domain Separation: Variable Phylogenetic Distance and the Tempo of Early Evolution.
Article in Molecular biology and evolution, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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29 citing papers in PubMed, 54 citations in OpenAlex.
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- The Last Universal Common Ancestor of Ribosome-Encoding Organisms: Portrait of LUCA.Journal of molecular evolution · 2024Review
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- Electron transport chains as a window into the earliest stages of evolution.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Identification of a novel lipoic acid biosynthesis pathway reveals the complex evolution of lipoate assembly in prokaryotes.PLoS biology · 2023Article
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- Proteome-wide 3D structure prediction provides insights into the ancestral metabolism of ancient archaea and bacteria.Nature communications · 2022Article
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- A consensus view of the proteome of the last universal common ancestor.Ecology and evolution · 2022Article
- Article
- Phylogenetic Signal, Congruence, and Uncertainty across Bacteria and Archaea.Molecular biology and evolution · 2021Article
- Spontaneous assembly of redox-active iron-sulfur clusters at low concentrations of cysteine.Nature communications · 2021Article
- TwinCons: Conservation score for uncovering deep sequence similarity and divergence.PLoS computational biology · 2021Article
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Authors and funding
2 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Comparative genomics and molecular phylogenetics are foundational for understanding biological evolution. Although many studies have been made with the aim of understanding the genomic contents of early life, uncertainty remains. A study by Weiss et al. (Weiss MC, Sousa FL, Mrnjavac N, Neukirchen S, Roettger M, Nelson-Sathi S, Martin WF. 2016. The physiology and habitat of the last universal common ancestor. Nat Microbiol. 1(9):16116.) identified a number of protein families in the last universal common ancestor of archaea and bacteria (LUCA) which were not found in previous works. Here, we report new research that suggests the clustering approaches used in this previous study undersampled protein families, resulting in incomplete phylogenetic trees which do not reflect protein family evolution. Phylogenetic analysis of protein families which include more sequence homologs rejects a simple LUCA hypothesis based on phylogenetic separation of the bacterial and archaeal domains for a majority of the previously identified LUCA proteins (∼82%). To supplement limitations of phylogenetic inference derived from incompletely populated orthologous groups and to test the hypothesis of a period of rapid evolution preceding the separation of the domains, we compared phylogenetic distances both within and between domains, for thousands of orthologous groups. We find a substantial diversity of interdomain versus intradomain branch lengths, even among protein families which exhibit a single domain separating branch and are thought to be associated with the LUCA. Additionally, phylogenetic trees with long interdomain branches relative to intradomain branches are enriched in information categories of protein families in comparison to those associated with metabolic functions. These results provide a new view of protein family evolution and temper claims about the phenotype and habitat of the LUCA.
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