Imachi, H. et al. Isolation of an archaeon at the prokaryote-eukaryote interface. Nature 577, 519–525 (2020).
Rodrigues-Oliveira, T. et al. Actin cytoskeleton and complex cell architecture in an Asgard archaeon. Nature 613, 332–339 (2023).
Betts, H. C. et al. Integrated genomic and fossil evidence illuminates life’s early evolution and eukaryote origin. Nat. Ecol. Evol. 2, 1556–1562 (2018).
Eme, L. et al. Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes. Nature 618, 992–999 (2023).
Liu, Y. et al. Expanded diversity of Asgard archaea and their relationships with eukaryotes. Nature 593, 553–557 (2021).
Lopez-Garcia, P. & Moreira, D. Open questions on the origin of eukaryotes. Trends Ecol. Evol. 30, 697–708 (2015).
Zaremba-Niedzwiedzka, K. et al. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541, 353–358 (2017).
Spang, A. et al. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521, 173–179 (2015).
Lu, Z., Zhang, S., Liu, Y., Xia, R. & Li, M. Origin of eukaryotic-like Vps23 shapes an ancient functional interplay between ESCRT and ubiquitin system in Asgard archaea. Cell Rep. 43, 113781 (2024).
Akil, C. & Robinson, R. C. Genomes of Asgard archaea encode profilins that regulate actin. Nature 562, 439–443 (2018).
Izore, T., Kureisaite-Ciziene, D., McLaughlin, S. H. & Lowe, J. Crenactin forms actin-like double helical filaments regulated by arcadin-2. eLife 5, e21600 (2016).
Spang, A., Caceres, E. F. & Ettema, T. J. Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life. Science 357, eaaf3883 (2017).
Williams, T. A., Cox, C. J., Foster, P. G., Szollosi, G. J. & Embley, T. M. Phylogenomics provides robust support for a two-domains tree of life. Nat. Ecol. Evol. 4, 138–147 (2020).
Olm, M. R., Brown, C. T., Brooks, B. & Banfield, J. F. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 11, 2864–2868 (2017).
Chaumeil, P. A., Mussig, A. J., Hugenholtz, P. & Parks, D. H. GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics 38, 5315–5316 (2022).
Parks, D. H. et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat. Biotechnol. 36, 996–1004 (2018).
Xie, R. et al. Expanding Asgard members in the domain of Archaea sheds new light on the origin of eukaryotes. Sci. China Life Sci. 65, 818–829 (2022).
Liu, Y. & Li, M. The unstable evolutionary position of Korarchaeota and its relationship with other TACK and Asgard archaea. mLife 1, 218–222 (2022).
Da Cunha, V., Gaia, M., Gadelle, D., Nasir, A. & Forterre, P. Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes. PLoS Genet. 13, e1006810 (2017).
Chaumeil, P. A., Mussig, A. J., Hugenholtz, P. & Parks, D. H. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 36, 1925–1927 (2019).
Petitjean, C., Deschamps, P., Lopez-Garcia, P., Moreira, D. & Brochier-Armanet, C. Extending the conserved phylogenetic core of archaea disentangles the evolution of the third domain of life. Mol. Biol. Evol. 32, 1242–1254 (2015).
Darling, A. E. et al. PhyloSift: phylogenetic analysis of genomes and metagenomes. Peerj 2, e243 (2014).
Dombrowski, N. et al. Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution. Nat. Commun. 11, 3939 (2020).
Fan, L. et al. Phylogenetic analyses with systematic taxon sampling show that mitochondria branch within Alphaproteobacteria. Nat. Ecol. Evol. 4, 1213–1219 (2020).
Martijn, J., Vosseberg, J., Guy, L., Offre, P. & Ettema, T. J. G. Deep mitochondrial origin outside the sampled alphaproteobacteria. Nature 557, 101–105 (2018).
Viklund, J., Ettema, T. J. & Andersson, S. G. Independent genome reduction and phylogenetic reclassification of the oceanic SAR11 clade. Mol. Biol. Evol. 29, 599–615 (2012).
Ramulu, H. G. et al. Ribosomal proteins: toward a next generation standard for prokaryotic systematics? Mol. Phylogenet. Evol. 75, 103–117 (2014).
von Meijenfeldt, F. A. B., Arkhipova, K., Cambuy, D. D., Coutinho, F. H. & Dutilh, B. E. Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT. Genome Biol. 20, 217 (2019).
Hauptfeld, E. et al. Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes. Nat. Commun. 15, 3373 (2024).
Steinegger, M. & Soding, J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat. Biotechnol. 35, 1026–1028 (2017).
Mirdita, M., Steinegger, M., Breitwieser, F., Soding, J. & Levy Karin, E. Fast and sensitive taxonomic assignment to metagenomic contigs. Bioinformatics 37, 3029–3031 (2021).
Dombrowski, N., Seitz, K. W., Teske, A. P. & Baker, B. J. Genomic insights into potential interdependencies in microbial hydrocarbon and nutrient cycling in hydrothermal sediments. Microbiome 5, 106 (2017).
Zhou, Z., St John, E., Anantharaman, K. & Reysenbach, A. L. Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits. Microbiome 10, 241 (2022).
Susko, E. & Roger, A. J. On reduced amino acid alphabets for phylogenetic inference. Mol. Biol. Evol. 24, 2139–2150 (2007).
Yang, Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13, 555–556 (1997).
Kump, L. R. The rise of atmospheric oxygen. Nature 451, 277–278 (2008).
Mahendrarajah, T. A. et al. ATP synthase evolution on a cross-braced dated tree of life. Nat. Commun. 14, 7456 (2023).
Szollosi, G. J., Rosikiewicz, W., Boussau, B., Tannier, E. & Daubin, V. Efficient exploration of the space of reconciled gene trees. Syst. Biol. 62, 901–912 (2013).
Sousa, F. L., Neukirchen, S., Allen, J. F., Lane, N. & Martin, W. F. Lokiarchaeon is hydrogen dependent. Nat. Microbiol. 1, 1–3 (2016).
Adam, P. S., Borrel, G. & Gribaldo, S. An archaeal origin of the Wood-Ljungdahl H(4)MPT branch and the emergence of bacterial methylotrophy. Nat. Microbiol. 4, 2155–2163 (2019).
Catling, D. C. & Zahnle, K. J. The Archean atmosphere. Sci. Adv. 6, eaax1420 (2020).
Tamblyn, R. & Hermann, J. Geological evidence for high H2 production from komatiites in the Archaean. Nat. Geosci. 16, 1194–1199 (2023).
Seitz, K. W. et al. Asgard archaea capable of anaerobic hydrocarbon cycling. Nat. Commun. 10, 1822 (2019).
Laso-Pérez, R. et al. Thermophilic archaea activate butane via alkyl-coenzyme M formation. Nature 539, 396–401 (2016).
Martin, W. F., Neukirchen, S., Zimorski, V., Gould, S. B. & Sousa, F. L. Energy for two: New archaeal lineages and the origin of mitochondria. Bioessays 38, 850–856 (2016).
Mills, D. B. et al. Eukaryogenesis and oxygen in Earth history. Nat. Ecol. Evol. 6, 520–532 (2022).
Martin, W. & Müller, M. J. N. The hydrogen hypothesis for the first eukaryote. Nature 392, 37–41 (1998).
Giger, G. H. et al. Inducing novel endosymbioses by implanting bacteria in fungi. Nature 635, 415–422 (2024).
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477 (2012).
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357 (2012).
Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
Kang, D. W. D., Froula, J., Egan, R. & Wang, Z. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. Peerj 3, e1165 (2015).
Mattock, J. & Watson, M. A comparison of single-coverage and multi-coverage metagenomic binning reveals extensive hidden contamination. Nat. Methods 20, 1170–1173 (2023).
Sieber, C. M. K. et al. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nat. Microbiol. 3, 836–843 (2018).
Albertsen, M. et al. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat. Biotechnol. 31, 533–538 (2013).
Parks, D. H. et al. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat. Microbiol. 2, 1533–1542 (2017).
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043–1055 (2015).
Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinf. 11, 119 (2010).
Chan, P. P., Lin, B. Y., Mak, A. J. & Lowe, T. M. tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes. Nucleic Acids Res. 49, 9077–9096 (2021).
Parks, D. H. et al. A complete domain-to-species taxonomy for Bacteria and Archaea. Nat. Biotechnol. 38, 1079–1086 (2020).
Balaban, M., Moshiri, N., Mai, U., Jia, X. & Mirarab, S. TreeCluster: clustering biological sequences using phylogenetic trees. PLoS ONE 14, e0221068 (2019).
Makarova, K. S., Wolf, Y. I. & Koonin, E. V. Archaeal clusters of orthologous genes (arCOGs): an update and application for analysis of shared features between Thermococcales, Methanococcales, and Methanobacteriales. Life (Basel) 5, 818–840 (2015).
Galperin, M. Y. et al. COG database update: focus on microbial diversity, model organisms, and widespread pathogens. Nucleic Acids Res. 49, D274–D281 (2021).
Finn, R. D. et al. Pfam: the protein families database. Nucleic Acids Res. 42, D222–D230 (2014).
Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997).
Mistry, J., Finn, R. D., Eddy, S. R., Bateman, A. & Punta, M. Challenges in homology search: HMMER3 and convergent evolution of coiled–coil regions. Nucleic Acids Res. 41, e121 (2013).
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).
Criscuolo, A. & Gribaldo, S. BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol. Biol. 10, 210 (2010).
Minh, B. Q., Trifinopoulos, J., Schrempf, D., Schmidt, H. & Lanfear, R. IQ-TREE version 2.0: tutorials and manual phylogenomic software by maximum likelihood. Nucleic Acids Res. 44, W232–W235 (2022).
Hoang, D. T., Chernomor, O., Von Haeseler, A., Minh, B. Q. & Vinh, L. S. UFBoot2: improving the ultrafast bootstrap approximation. Mol. Biol. Evol. 35, 518–522 (2018).
Letunic, I. & Bork, P. Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool. Nucleic Acids Res. 52, W78–W82 (2024).
Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).
Zhang, J. et al. Phylogenomic analyses with expanded taxon sampling reveal deep origin of eukaryotes outside Heimdallarchaeia. Figshare https://figshare.com/s/6e523322b0b647b91dda (2025).
Nguyen, L.-T., Schmidt, H. A., Von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2015).
Lartillot, N., Rodrigue, N., Stubbs, D. & Richer, J. PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment. Syst. Biol. 62, 611–615 (2013).
Munoz-Gomez, S. A. et al. Site-and-branch-heterogeneous analyses of an expanded dataset favour mitochondria as sister to known Alphaproteobacteria. Nat. Ecol. Evol. 6, 253–262 (2022).
Mayrose, I., Graur, D., Ben-Tal, N. & Pupko, T. Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior. Mol. Biol. Evol. 21, 1781–1791 (2004).
Parks, D. H. et al. GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Res. 50, D785–D794 (2022).
Eren, A. M. et al. Anvi’o: an advanced analysis and visualization platform for ‘omics data. Peerj 3, e1319 (2015).
Chen, L. X., Anantharaman, K., Shaiber, A., Eren, A. M. & Banfield, J. F. Accurate and complete genomes from metagenomes. Genome Res. 30, 315–333 (2020).
Alneberg, J. et al. Binning metagenomic contigs by coverage and composition. Nat. Methods 11, 1144–1146 (2014).
Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586–1591 (2007).
Yang, Y. et al. The evolution pathway of ammonia-oxidizing archaea shaped by major geological events. Mol. Biol. Evol. 38, 3637–3648 (2021).
Szollosi, G. J., Davin, A. A., Tannier, E., Daubin, V. & Boussau, B. Genome-scale phylogenetic analysis finds extensive gene transfer among fungi. Philos. Trans. R. Soc. B Biol. Sci. 370, 20140335 (2015).
Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59–60 (2015).
Haft, D. H., Selengut, J. D. & White, O. The TIGRFAMs database of protein families. Nucleic Acids Res. 31, 371–373 (2003).
Eddy, S. R. Accelerated Profile HMM Searches. PLoS Comput. Biol. 7, e1002195 (2011).
Bairoch, A. & Apweiler, R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 28, 45–48 (2000).