Phylogenomics provides robust support for a two-domains tree of life

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A new view of the tree of life

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Evolutionary considerations of the oligosaccharyltransferase AglB and other aspects of N-glycosylation across Archaea

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Target sequence capture of Barnadesioideae (Compositae) demonstrates the utility of low coverage loci in phylogenomic analyses

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CAT-Posterior Mean Site Frequencies Improves Phylogenetic Modeling Under Maximum Likelihood and Resolves Tardigrada as the Sister of Arthropoda Plus Onychophora

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Asgard archaea in the haima cold seep: Spatial distribution and genomic insights

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Asteroid: a new algorithm to infer species trees from gene trees under high proportions of missing data

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Nucleosomes at the Dawn of Eukaryotes

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Nutrition and sulfur

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Phenotypic reconstruction of the last universal common ancestor reveals a complex cellPreprint

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The tree of life describes a tripartite cellular world

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Phylogenomics of weevils revisited: data curation and modelling compositional heterogeneity

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Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotesPreprint

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A timetree of Fungi dated with fossils and horizontal gene transfers

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Meet the relatives of our cellular ancestor

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Studying the Human Microbiota: Advances in Understanding the Fundamentals, Origin, and Evolution of Biological Timekeeping

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Agl24 is an ancient archaeal homolog of the eukaryotic N-glycan chitobiose synthesis enzymes

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Evolution of optimal growth temperature in Asgard archaea inferred from the temperature dependence of GDP binding to EF-1A

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The Asgard Archaeal-Unique Contribution to Protein Families of the Eukaryotic Common Ancestor Was 0.3%

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Expanding diversity of Asgard archaea and the elusive ancestry of eukaryotesPreprint

Liu, Y., Makarova, K. S., Huang, W.-C., Wolf, Y. I., Nikolskaya, A. V., Zhang, X., Cai, M., Zhang, C., Xu, W., Luo, Z.-H., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.10.19.343400 · Cited by 12

Renewing L innaean taxonomy: a proposal to restructure the highest levels of the N atural S ystem

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Modeling compositional heterogeneity resolves deep phylogeny of flowering plants

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Clingy genes: Why were genes for ribosomal proteins retained in many mitochondrial genomes?

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Prediction of eukaryotic cellular complexity in Asgard archaea using structural modelling

Köstlbacher, S., van Hooff, J. J. E., Panagiotou, K., Tamarit, D., Anda, V. D., Appler, K. E., Baker, B. J., & Ettema, T. J. G. (2026) · Nature Microbiology · doi:10.1038/s41564-026-02273-y · Cited by 20

Phylogenomic Analyses Reveal that Panguiarchaeum Is a Clade of Genome-Reduced Asgard Archaea Within the Njordarchaeia

Huang, W.-C., Probst, M., Hua, Z., Szánthó, L. L., Szöllősi, G. J., Ettema, T. J. G., Rinke, C., Williams, T. A., & Spang, A. (2025) · Molecular Biology and Evolution · doi:10.1093/molbev/msaf201 · Cited by 12

The unstable evolutionary position of Korarchaeota and its relationship with other TACK and Asgard archaea

Liu, Y., & Li, M. (2022) · mLife · doi:10.1002/mlf2.12020 · Cited by 9

Bacterial origins of thymidylate metabolism in Asgard archaea and Eukarya

Filée, J., Becker, H. F., Mellottee, L., Zein-Eddine, R., Li, Z., Yin, W., Lambry, J., Liebl, U., & Myllykallio, H. (2023) · Nature Communications · doi:10.1038/s41467-023-36487-z · Cited by 9

Debating Eukaryogenesis—Part 1: Does Eukaryogenesis Presuppose Symbiosis Before Uptake?

Speijer, D. (2020) · BioEssays · doi:10.1002/bies.201900157 · Cited by 9

Characterization of Nuclear and Mitochondrial Genomes of Two Tobacco Endophytic Fungi Leptosphaerulina chartarum and Curvularia trifolii and Their Contributions to Phylogenetic Implications in the Pleosporales

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Resolving the phylogenetic position of Hygrobiidae (Coleoptera: Adephaga) requires objective statistical tests and exhaustive phylogenetic methodology: a response to Cai et al. (2020)

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Discovering Fragile Clades and Causal Sequences in Phylogenomics by Evolutionary Sparse Learning

Sharma, S., & Kumar, S. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae131 · Cited by 9

Eukaryogenesis From FECA to LECA: Radical Steps Along the Way

Speijer, D. (2025) · BioEssays · doi:10.1002/bies.70063 · Cited by 10

Metagenomic Discovery of “ Candidatus Parvarchaeales”-Related Lineages Sheds Light on Adaptation and Diversification from Neutral-Thermal to Acidic-Mesothermal Environments

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NAD + capping of RNA in Archaea and MycobacteriaPreprint

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Polysaccharide-degrading archaea dominate acidic hot springs: genomic and cultivation insights into a novel Thermoproteota lineage

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Protein folds as synapomorphies of the tree of life

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Rapid acquisition of microorganisms and microbial genes can help explain punctuated evolution

ROSENBERG, E. B. (2022) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2022.957708 · Cited by 8

Chimeric origin of eukaryotes from Asgard archaea and ancestral giant virusesPreprint

Karki, S., Barth, Z. K., & Aylward, F. O. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.04.22.590592 · Cited by 8

Structure-based inference of eukaryotic complexity in Asgard archaeaPreprint

Köstlbacher, S., van Hooff, J. J. E., Panagiotou, K., Tamarit, D., Anda, V. D., Appler, K. E., Baker, B. J., & Ettema, T. J. G. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.07.03.601958 · Cited by 8

Protein structures unravel the signatures and patterns of deep time evolution

Harish, A. (2024) · QRB Discovery · doi:10.1017/qrd.2024.4 · Cited by 7

Host-Calibrated Time Tree Caps the Age of Giant Viruses

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Testing Phylogenetic Stability with Variable Taxon Sampling

Powell, C. L. E., & Battistuzzi, F. U. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2691-7_8 · Cited by 7

A billion years of geological drama – Boring or brilliant?

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The deep(er) roots of Eukaryotes and Akaryotes

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Diversity, ecology, cell biology and evolution of the Asgard archaea

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A phylogenetic analysis of scale insects (Hemiptera, Coccoidea) based on genomic and transcriptomic data

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Prospects for biological evolution on Hycean worlds

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Phylogenomics and revised classification of Lymexyloidea and Tenebrionoidea (Coleoptera: Polyphaga: Cucujiformia)

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Is an archaeon the ancestor of eukaryotes?

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A unified evolutionary origin for the ubiquitous protein transporters SecY and YidCPreprint

Lewis, A. J. O., & Hegde, R. S. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.12.20.422553 · Cited by 6

Protists with Uncertain Phylogenetic Affiliations for Resolving the Deep Tree of Eukaryotes

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Expanded Archaeal Genomes Shed New Light on the Evolution of Isoprenoid Biosynthesis

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Species Tree Branch Length Estimation despite Incomplete Lineage Sorting, Duplication, and Loss

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On the impact of incomplete taxon sampling on the relative timing of gene transfer events

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

Moody, E. R. R., Mahendrarajah, T., Dombrowski, N., Clark, J., Petitjean, C., Offre, P., Szöllősi, G. J., Spang, A., & Williams, T. A. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.01.19.427276 · Cited by 5

Compositionally Constrained Sites Drive Long Branch AttractionPreprint

Szánthó, L. L., Lartillot, N., Szöllősi, G. J., & Schrempf, D. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.03.482715 · Cited by 5

Phylogenomics and ancestral reconstruction of Korarchaeota reveals genomic adaptation to habitat switchingPreprint

Tahon, G., Köstlbacher, S., Pelve, E. A., Baker, B. J., Saw, J. H. W., Eme, L., Tamarit, D., Schön, M. E., & Ettema, T. J. G. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.09.28.559970 · Cited by 5

When the Past Fades: Detecting Phylogenetic Signal with SatuTe

Manuel, C., Sakalli, E., Schmidt, H. A., Viñas, C., von Haeseler, A., & Elgert, C. (2025) · Molecular Biology and Evolution · doi:10.1093/molbev/msaf090 · Cited by 4

An Efficient, Nonphylogenetic Method for Detecting Genes Sharing Evolutionary Signals in Phylogenomic Data Sets

Rangel, L. T., Soucy, S. M., Setúbal, J. C., Gogarten, J. P., & Fournier, G. P. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evab187 · Cited by 4

A planktonic picoeukaryote makes big changes to the green lineage

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A closed Candidatus Odinarchaeum genome exposes Asgard archaeal virusesPreprint

Tamarit, D., Caceres, E., Krupovìč, M., Nijland, R., Eme, L., Robinson, N. P., & Ettema, T. J. G. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.09.01.458545 · Cited by 4

Phylogenetic relationship analysis of leafhopper subfamily Iassinae (Hemiptera: Cicadellidae) based on low-coverage whole-genome data

Lu, X., Lu, J., Wu, Y., Guo, M. H., Smagghe, G. J., & Dai, R. (2025) · Arthropod Systematics & Phylogeny · doi:10.3897/asp.83.e142332 · Cited by 3

Missing data and model selection in phylogenomics: A re‐evaluation of Cicadomorpha (Hemiptera: Auchenorrhyncha) superfamily level relationships

Yan, B., Dietrich, C. H., Yu, X., Jiang, Y., Dai, R., Du, S., Cai, C., Yang, M., & Zhang, F. (2025) · Journal of Systematics and Evolution · doi:10.1111/jse.13190 · Cited by 3

The evolution of the tree of life

Chen, M., Kholodov, A. I., & Hug, L. A. (2025) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2024.0091 · Cited by 4

Branch Length Transforms using Optimal Tree Metric Matching

Arasti, S., Tabaghi, P., Tabatabaee, Y., Mayer, A., & Mirarab, S. (2026) · Systematic Biology · doi:10.1093/sysbio/syag025 · Cited by 4

Progress and Challenges in Studying the Ecophysiology of Archaea

Adam, P. S., Bornemann, T. L. V., & Probst, A. J. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2445-6_32 · Cited by 3

Phylogenomic Testing of Root Hypotheses

Tria, F. D. K., Landan, G., Picazo, D. R., & Dagan, T. (2023) · Genome Biology and Evolution · doi:10.1093/gbe/evad096 · Cited by 2

Functional prediction of proteins from the human gut archaeome

Novikova, P. V., Busi, S. B., Probst, A. J., May, P., & Wilmes, P. (2024) · ISME Communications · doi:10.1093/ismeco/ycad014 · Cited by 3

Why is the sky blue? A new question for political science

Rocafort, V. A. (2024) · Sustainability Science · doi:10.1007/s11625-024-01479-5 · Cited by 4

Terraces in species tree inference from gene trees

Habib, M., Roy, K., Hasan, S., Rahman, A. H., & Bayzid, M. S. (2024) · BMC Ecology and Evolution · doi:10.1186/s12862-024-02309-z · Cited by 3

The Structure of Evolutionary Model Space for Proteins across the Tree of Life

Scolaro, G. E., & Braun, E. L. (2023) · Biology · doi:10.3390/biology12020282 · Cited by 3

Origin of eukaryotes: What can be learned from the first successfully isolated Asgard archaeon

Albers, S., Ashmore, J. F., Pollard, T. D., Spang, A., & Zhou, J. Z. (2022) · Faculty Reviews · doi:10.12703/r-01-000005 · Cited by 3

Ribosomal Protein Cluster Organization in Asgard Archaea

Tirumalai, M. R., Sivaraman, R. V., Kutty, L. A., Song, E. L., & Fox, G. E. (2023) · Archaea · doi:10.1155/2023/5512414 · Cited by 2

Expanded Asgard archaea shed new light on the origin of eukaryotes and support a 2-domain tree of lifePreprint

Xie, R., Wang, Y., Huang, D., Hou, J., Li, L., Hu, H., Zhao, X., & Wang, F. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.02.04.429862 · Cited by 3

Extensive lateral gene transfer between proto‐eukaryotes and Heimdallarchaeia suggests their close association during eukaryogenesis

Forterre, P. (2025) · mLife · doi:10.1002/mlf2.70030 · Cited by 2

Toward a genomic understanding of the tree of life

Spang, A., & Pisani, D. (2026) · Molecular biology and evolution · doi:10.1093/molbev/msag043 · Cited by 3

Promethearchaeota Persistence in Marine Sediments Frozen for Over 100 kyr

Liang, R., Vishnivetskaya, T. A., Avcı, B., Rivkina, E., & Lloyd, K. G. (2026) · Environmental Microbiology · doi:10.1111/1462-2920.70277 · Cited by 2

Reconstruction of the rRNA Sequences of LUCA, with Bioinformatic Implication of the Local Similarities Shared by Them

Men, Y., Lu, G., Wang, Y., Lin, J., & Xie, Q. (2022) · Biology · doi:10.3390/biology11060837 · Cited by 2

Two-Component System Sensor Kinases from Asgardian Archaea May Be Witnesses to Eukaryotic Cell Evolution

Padilla‐Vaca, F., de la Mora, J., García‐Contreras, R., Ramírez-Prado, J. H., Alva-Murillo, N., Fonseca-Yepez, S., Serna-Gutiérrez, I., Moreno-Galván, C. L., Montufar-Rodríguez, J. M., Vicente-Gómez, M., et al. (2023) · Molecules · doi:10.3390/molecules28135042 · Cited by 2

Diverse Genome Structures among Eukaryotes May Have Arisen in Response to Genetic Conflict

Sterner, E. G., Cote‐L’Heureux, A., Maurer‐Alcalá, X. X., & Katz, L. A. (2024) · Genome Biology and Evolution · doi:10.1093/gbe/evae239 · Cited by 3

Convergent and conserved roads lead to Rome: now archaea fill the gap of transcription termination

Song, N., & Li, M. (2025) · Science China Life Sciences · doi:10.1007/s11427-024-2791-2 · Cited by 2

Global Archaeal Diversity Revealed Through Massive Data Integration: Uncovering Just Tip of Iceberg

Kioukis, A., Camargo, A. P., Pavlidis, P., Iliopoulos, I., Kyrpides, N. C., & Lagkouvardos, I. (2025) · Microorganisms · doi:10.3390/microorganisms13030598 · Cited by 2

Structural and functional characterization of a plant alpha‐actinin

Persson, K., & Backman, L. (2021) · FEBS Open Bio · doi:10.1002/2211-5463.13222 · Cited by 2

Improving Phylogenetic Signals of Mitochondrial Genes Using a New Method of Codon Degeneration

Xia, X. (2020) · Life · doi:10.3390/life10090171 · Cited by 2

On the Evolution of the Biological Framework for Insight

Neidhöfer, C. (2021) · Philosophies · doi:10.3390/philosophies6020043 · Cited by 1

Reconstructing the Last Universal Common Ancestor

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Beyond Congruence: Evidential Integration and Inferring the Best Evolutionary ScenarioPreprint

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A New Look at the Concept of EcosystemPreprint

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Role of aIF5B in archaeal translation initiationPreprint

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When We Were Triangles

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Bayesian Inference of Phylogenetic Distances: Revisiting the Eigenvalue Approach

Penn, M. J., Scheidwasser, N., Donnelly, C. A., Duchêne, D. A., & Bhatt, S. (2025) · Bulletin of Mathematical Biology · doi:10.1007/s11538-024-01403-z · Cited by 1

Identification and characterization of archaeal pseudomurein biosynthesis genes through pangenomics

Lupo, V., Roomans, C., Royen, E., Ongena, L., Jacquemin, O., Mullender, C., Kerff, F., & Baurain, D. (2025) · mSystems · doi:10.1128/msystems.01401-24 · Cited by 5

Cooperation and Competition Were Primary Driving Forces for Biological Evolution

Saier, M. H. (2025) · Microbial Physiology · doi:10.1159/000544890 · Cited by 2

Distinct filament morphology and membrane tethering features of the dual FtsZ paralogs in Odinarchaeota

Kumari, J., Uthaman, A., Bose, S., Kundu, A., Sharma, V., Dutta, S., Dhar, A., Roy, S., Srinivasan, R., Pande, S., et al. (2025) · The EMBO Journal · doi:10.1038/s44318-025-00529-7 · Cited by 3

Archaeal RNA processing and regulation: expanding the functional landscape

Liang, Y., Qi, W., Dong, X., & Li, J. (2025) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00318-24 · Cited by 1

Abiotic sources of fixed nitrogen sustained early ecosystems for several hundred million years after the origin of life

Boden, J. S., Ni, Z., Anderson, R. E., & Stüeken, E. E. (2026) · Science Advances · doi:10.1126/sciadv.aec4450 · Cited by 1

RNA Processing and Decay Pathways in Archaea: Emerging Insights on the Function and Evolution of the Archaeal Specific Ski2-Like RNA Helicases

Cirio, C., Ansart, M., Schmitt, E., Bouvier, M., & Clouet-d’Orval, B. (2025) · Nucleic acids and molecular biology · doi:10.1007/978-3-032-03300-0_6 · Cited by 1

Molecular clock dating using complex mixture models: applied to ancient symbionts

Wang, S., & Meade, A. (2026) · Molecular Biology and Evolution · doi:10.1093/molbev/msag039 · Cited by 1

Chromatin organization in Asgard archaea: histones, SMC complexes, and the archaeal roots of eukaryotic chromatin

van Hooff, J. J. E., & Dame, R. T. (2026) · Trends in Genetics · doi:10.1016/j.tig.2026.02.006 · Cited by 1

What it takes to solve the origins of life: An integrated review. Part 2: Theoretical methods and emerging trends

Asche, S., Bautista, C., Blanco, C., Boulesteix, D., Champagne-Ruel, A., Mathis, C., Markovitch, O., Peng, Z., Dass, A. V., Adams, A., et al. (2026) · Cell Reports Physical Science · doi:10.1016/j.xcrp.2026.103211 · Cited by 2

Necessary and sufficient conditions for major evolutionary transitions

Boomsma, J. J. (2022) · Oxford University Press eBooks · doi:10.1093/oso/9780198746171.003.0004 · Cited by 1

Structures of Saccharolobus solfataricus initiation complexes with leaderless mRNAs highlight archaeal features and eukaryotic proximity

Bourgeois, G., Coureux, P., Lazennec‐Schurdevin, C., Madru, C., Gaillard, T., Duchateau, M., Chamot‐Rooke, J., Bourcier, S., Méchulam, Y., & Schmitt, E. (2025) · Nature Communications · doi:10.1038/s41467-024-55718-5 · Cited by 2

The two-domain tree of life is linked to a new root for the Archaea

Raymann, K., Brochier‐Armanet, C., & Gribaldo, S. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1420858112 · Cited by 309

An archaeal origin of eukaryotes supports only two primary domains of life

Williams, T. A., Foster, P. G., Cox, C. J., & Embley, T. M. (2013) · Nature · doi:10.1038/nature12779 · Cited by 519

Archaeal “Dark Matter” and the Origin of Eukaryotes

Williams, T. A., & Embley, T. M. (2014) · Genome Biology and Evolution · doi:10.1093/gbe/evu031 · Cited by 103

Data from: A congruent phylogenomic signal places eukaryotes within the Archaea.

Williams, T. A., Foster, P. G., Nye, T. M. W., Cox, C. J., & Embley, T. M. (2012) · Data Archiving and Networked Services (DANS) · doi:10.5061/dryad.0hd1s

A congruent phylogenomic signal places eukaryotes within the Archaea

Williams, T. A., Foster, P. G., Nye, T. M. W., Cox, C. J., & Embley, T. M. (2012) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2012.1795 · Cited by 153