A robustly rooted tree of eukaryotes reveals their excavate ancestry

2025/03/12 by Kelsey Williamson, Laura Eme, Hector Baños +10 · 2 voices · 75 citations
Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · Mathematics · #Biology #Combinatorics #Evolutionary biology #Genomics and Phylogenetic Studies #Legume Nitrogen Fixing Symbiosis #Mathematics #Protist diversity and phylogeny #Tree (set theory)

paper · doi:10.1038/s41586-025-08709-5

published in Nature 640(8060), 974-981 (Nature Portfolio)

openalex publication_date 2025/03/12 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/02

Cited by

• Environmental phylogenetics supports a steady diversification of crown eukaryotes starting from the mid-Proterozoic
• Hypothesis that ancestral eukaryotes sexually proliferated without kinetochores or mitosis
• Gene ancestries reveal diverse microbial associations during eukaryogenesis
• A Tubules-First Model for the Origin of Eukaryotic Membrane Traffic
• IQ-TREE 3: phylogenomic inference software using complex evolutionary models
• A new class of proteinaceous biomaterial with unprecedented properties in unicellular eukaryotes
• Repressive Cytosine Methylation is a Marker of Viral Gene Transfer Across Divergent Eukaryotes
• The discovery and description of an extremophile microcosmos in a Cretaceous paleogeothermal field
• Phylogenomic mixture models outperform homogeneous and partitioned models
• A single-cell blueprint for cellular diversity in the Green Lineage
• Toward a genomic understanding of the tree of life
• Eukaryotic Recombinases Duplicated After Divergence From Known Asgard Archaeal RadA: Implications for the Evolution of Sex During Eukaryogenesis
• Signatures of gene transfer in the parallel evolution of osmotrophic specialization in eukaryotes
• Mapping the evolution of mitochondrial complex I through structural variation
• A Deeply Branching Lineage in Heterolobosea (Discoba) With Multiflagellated and Multigrooved Life Stages
• Phylogenomics resolves the century-old ‘Zoraptera problem’: Zoraptera as the earliest diverging lineage of Polyneoptera
• The LECA had a conventional kinetochore and the kinetoplastid kinetochore is a derived feature – a critical evaluation of Akiyoshi, 2025
• Phylogenetic position and mitochondrial genome evolution of “orphan” eukaryotic lineages
• Evolutionary Analysis of Trehalose Breakdown Pathways
• GTRspmix: Capturing Heterogeneity of Exchangeabilities Across Sites to Improve Protein Phylogenetics
• Origin of eukaryotic plasmalogen biosynthesis by horizontal gene transfer from myxobacteria
• Diagnosing Systematic Errors and Incomplete Lineage Sorting in the Deep Phylogeny of Collembola
• Identification of a deep-branching lineage of algae using environmental plastid genomes
• From isolation to insights: mitochondrial complex I in the diatom Phaeodactylum tricornutum
• Euglenozoa are paraphyletic if the eukaryotic root lies between glycomonads and the rest of eukaryotes. Response to ‘The LECA had a conventional kinetochore and the kinetoplastid kinetochore is a derived feature’
• Where the tree of life is empirically resolved, and where it is not: an open atlas of species-level phylogenies and their archival uncertainty
• The fate of artificial transgenes in Acanthamoeba castellanii. [europepmc]
• Complete Mitochondrial Genomes of Ancyromonads Provide Clues for the Gene Content and Genome Structures of Ancestral Mitochondria. [europepmc]
• Hypothesis that ancestral eukaryotes sexually proliferated without kinetochores or mitosis. [europepmc]
• Apicortin, a Putative Apicomplexan-Specific Protein, Is Present in Deep-Branching Opisthokonts. [europepmc]
• Eukaryote-Wide Distribution of a Family of Longin Domain-Containing GAP Complexes for Small GTPases. [europepmc]
• Repressive Cytosine Methylation is a Marker of Viral Gene Transfer Across Divergent Eukaryotes. [europepmc]
• A Deeply Branching Lineage in Heterolobosea (Discoba) With Multiflagellated and Multigrooved Life Stages. [europepmc]
• A diverse Palaeoproterozoic microbial ecosystem implies early eukaryogenesis. [europepmc]
• Protists with Uncertain Phylogenetic Affiliations for Resolving the Deep Tree of Eukaryotes. [europepmc]
• Phylogenetic position and mitochondrial genome evolution of "orphan" eukaryotic lineages. [europepmc]
• Eukaryogenesis From FECA to LECA: Radical Steps Along the Way. [europepmc]
• Mechanisms underlying centriole stability. [europepmc]
• Adenine DNA methylation associated with transcriptionally permissive chromatin is widespread across eukaryotes. [europepmc]
• Identification of a deep-branching lineage of algae using environmental plastid genomes. [europepmc]
• Eukaryotic Recombinases Duplicated After Divergence From Known Asgard Archaeal RadA: Implications for the Evolution of Sex During Eukaryogenesis. [europepmc]
• Toward a genomic understanding of the tree of life. [europepmc]
• Stunning Intricacies of RNA Editing Complexes RECC, RESC, and REH2C: Functional Organization, Developmental Regulation, and Evolutionary History in Kinetoplastid Protists. [europepmc]
• Origin of eukaryotic plasmalogen biosynthesis by horizontal gene transfer from myxobacteria. [europepmc]
• Phylogenomic mixture models outperform homogeneous and partitioned models. [europepmc]
• Eukaryovorous Predation in Evolutionarily Significant Excavate-Like Flagellates. [europepmc]
• IQ-TREE 3: phylogenomic inference software using complex evolutionary models. [europepmc]
• Evolutionary Analysis of Trehalose Breakdown Pathways. [europepmc]
• A protein interactome for the last eukaryotic common ancestor illuminates the biochemical basis of modern genetic diseases. [europepmc]
• Structural evolution of the MTCH family of mitochondrial insertases. [europepmc]
• The Maximum Growth Temperature for Eukaryotes Is Thermodynamically Driven but Ecologically Contingent [europepmc]

Discussions

• I'm pleased to introduce our new paper rooting the eukaryote Tree of Life (eToL) that resulted from a collaboration led by PhD student Kelsey Williamson and a large group of collaborators doi.org/10.1 [bsky, 152 points, 3 comments]
• いま気づいたが「側系統」の使い方がおかしい。わりとよく見かける誤解ではあるけど。 > We also do not recover a monophyletic Haptista or Amorphea (Amoebozoa + Obazoa), although paraphyly of the latter is not well supported. Williamson et al. [bsky, 1 points, 1 comments]