ArticleBMC ecology and evolution2022
A divide-and-conquer phylogenomic approach based on character supermatrices resolves early steps in the evolution of the Archaea.
Article in BMC ecology and evolution, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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22 citing papers in PubMed.
- Phylogenetic reconciliation supports a methanogenic ancestor of the Archaea and a derived origin for host-associated lineages.Nature communications · 2026Article
- Diversity, ecology, cell biology and evolution of the Asgard archaea.Nature reviews. Microbiology · 2026Review
- DPANN Archaea and CPR Bacteria: insights into early cellular evolution?Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- Review
- An origin for a eukaryotic lipid transfer protein fold in Asgard archaea.bioRxiv : the preprint server for biology · 2025Article
- Origin and evolution of mitochondrial inner membrane composition.Journal of cell science · 2025Review
- Identification and characterization of archaeal pseudomurein biosynthesis genes through pangenomics.mSystems · 2025Article
- Oxidative adaptations in prokaryotes imply the oxygenic photosynthesis before crown-groupPNAS nexus · 2025Article
- Structures of Saccharolobus solfataricus initiation complexes with leaderless mRNAs highlight archaeal features and eukaryotic proximity.Nature communications · 2025Article
- The nature of the last universal common ancestor and its impact on the early Earth system.Nature ecology & evolution · 2024Article
- AleRax: a tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer, and loss.Bioinformatics (Oxford, England) · 2024Article
- Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution.The ISME journal · 2024Review
- Human associated Archaea: a neglected microbiome worth investigating.World journal of microbiology & biotechnology · 2024Review
- ATP synthase evolution on a cross-braced dated tree of life.Nature communications · 2023Article
- Fast-Evolving Alignment Sites Are Highly Informative for Reconstructions of Deep Tree of Life Phylogenies.Microorganisms · 2023Article
- Wood-Ljungdahl pathway found in novel marine Korarchaeota groups illuminates their evolutionary history.mSystems · 2023Article
- Parameter Estimation and Species Tree Rooting Using ALE and GeneRax.Genome biology and evolution · 2023Article
- Article
- Expanded Dataset Reveals the Emergence and Evolution of DNA Gyrase in Archaea.Molecular biology and evolution · 2022Article
- The unstable evolutionary position ofmLife · 2022Article
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6 authors.
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Abstract
backgroundThe recent rise in cultivation-independent genome sequencing has provided key material to explore uncharted branches of the Tree of Life. This has been particularly spectacular concerning the Archaea, projecting them at the center stage as prominently relevant to understand early stages in evolution and the emergence of fundamental metabolisms as well as the origin of eukaryotes. Yet, resolving deep divergences remains a challenging task due to well-known tree-reconstruction artefacts and biases in extracting robust ancient phylogenetic signal, notably when analyzing data sets including the three Domains of Life. Among the various strategies aimed at mitigating these problems, divide-and-conquer approaches remain poorly explored, and have been primarily based on reconciliation among single gene trees which however notoriously lack ancient phylogenetic signal.
resultsWe analyzed sub-sets of full supermatrices covering the whole Tree of Life with specific taxonomic sampling to robustly resolve different parts of the archaeal phylogeny in light of their current diversity. Our results strongly support the existence and early emergence of two main clades, Cluster I and Cluster II, which we name Ouranosarchaea and Gaiarchaea, and we clarify the placement of important novel archaeal lineages within these two clades. However, the monophyly and branching of the fast evolving nanosized DPANN members remains unclear and worth of further study.
conclusionsWe inferred a well resolved rooted phylogeny of the Archaea that includes all recently described phyla of high taxonomic rank. This phylogeny represents a valuable reference to study the evolutionary events associated to the early steps of the diversification of the archaeal domain. Beyond the specifics of archaeal phylogeny, our results demonstrate the power of divide-and-conquer approaches to resolve deep phylogenetic relationships, which should be applied to progressively resolve the entire Tree of Life.
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