• Woese, C. R. & Fox, G. E. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl Acad. Sci. USA 74, 5088–5090 (1977). This seminal paper was the first to recognize archaea—then called archaebacteria—as a separate prokaryotic group from bacteria.

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Woese, C. R. Bacterial evolution. Microbiol. Rev. 51, 221–271 (1987).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Woese, C. R., Kandler, O. & Wheelis, M. L. Towards a natural system of organisms: proposal for the domains archaea, bacteria, and eucarya. Proc. Natl Acad. Sci. USA 87, 4576–4579 (1990).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Huet, J., Schnabel, R., Sentenac, A. & Zillig, W. Archaebacteria and eukaryotes possess DNA-dependent RNA polymerases of a common type. EMBO J. 2, 1291–1294 (1983).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ouzounis, C. & Sander, C. TFIIB, an evolutionary link between the transcription machineries of archaebacteria and eukaryotes. Cell 71, 189–190 (1992).

    CAS 
    PubMed 

    Google Scholar
     

  • Myllykallio, H. et al. Bacterial mode of replication with eukaryotic-like machinery in a hyperthermophilic archaeon. Science 288, 2212–2215 (2000).

    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Williams, T. A., Cox, C. J., Foster, P. G., Szöllősi, G. J. & Embley, T. M. Phylogenomics provides robust support for a two-domains tree of life. Nat. Ecol. Evol. 4, 138–147 (2020). Using better-fitting models and additional in-depth analyses, this study scrutinized previous studies that reported 3D trees, resulting in robust 2D trees that show a close relationship between Heimdallarchaeia and eukaryotes.

    PubMed 

    Google Scholar
     

  • Eme, L. et al. Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes. Nature 618, 992–999 (2023). This study presented the expanding diversity of Asgard archaea, the Hodarchaeales–sister relationship of eukaryotes based on elaborate phylogenomics, the presence of additional ESPs in Asgard genomes and the reconstructed gene content of Asgard ancestral nodes.

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Williams, T. A., Foster, P. G., Cox, C. J. & Embley, T. M. An archaeal origin of eukaryotes supports only two primary domains of life. Nature 504, 231–236 (2013).

    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • 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).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Mahendrarajah, T. A. et al. ATP synthase evolution on a cross-braced dated tree of life. Nat. Commun. 14, 7456 (2023).

    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Eme, L., Sharpe, S. C., Brown, M. W. & Roger, A. J. On the age of eukaryotes: evaluating evidence from fossils and molecular clocks. Cold Spring Harb. Perspect. Biol. 6, a016139 (2014).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cohen, P. A. & Kodner, R. B. The earliest history of eukaryotic life: uncovering an evolutionary story through the integration of biological and geological data. Trends Ecol. Evol. 37, 246–256 (2022).

    PubMed 

    Google Scholar
     

  • Brocks, J. J. et al. Lost world of complex life and the late rise of the eukaryotic crown. Nature 618, 767–773 (2023).

    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Porter, S. M. & Riedman, L. A. Frameworks for interpreting the early fossil record of eukaryotes. Annu. Rev. Microbiol. 77, 173–191 (2023).

    CAS 
    PubMed 

    Google Scholar
     

  • Koumandou, V. L. et al. Molecular paleontology and complexity in the last eukaryotic common ancestor. Crit. Rev. Biochem. Mol. Biol. 48, 373–396 (2013).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Donoghue, P. C. J. et al. Defining eukaryotes to dissect eukaryogenesis. Curr. Biol. 33, R919–R929 (2023).

    CAS 
    PubMed 

    Google Scholar
     

  • Makarova, K. S., Wolf, Y. I., Mekhedov, S. L., Mirkin, B. G. & Koonin, E. V. Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell. Nucleic Acids Res. 33, 4626–4638 (2005). This paper provided a first systematic estimate of the number of gene acquisitions, duplications and inventions during eukaryogenesis based on the homology between eukaryotic clusters of orthologues and between eukaryotic and prokaryotic gene clusters.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • O’Malley, M. A., Leger, M. M., Wideman, J. G. & Ruiz-Trillo, I. Concepts of the last eukaryotic common ancestor. Nat. Ecol. Evol. 3, 338–344 (2019).

    PubMed 

    Google Scholar
     

  • Eme, L., Spang, A., Lombard, J., Stairs, C. W. & Ettema, T. J. G. Archaea and the origin of eukaryotes. Nat. Rev. Microbiol. 15, 711–723 (2017).

    CAS 
    PubMed 

    Google Scholar
     

  • Dacks, J. B. et al. The changing view of eukaryogenesis—fossils, cells, lineages and how they all come together. J. Cell Sci. 129, 3695–3703 (2016).

    CAS 
    PubMed 

    Google Scholar
     

  • Woese, C. R. & Olsen, G. J. Archaebacterial phylogeny: perspectives on the Urkingdoms. Syst. Appl. Microbiol. 7, 161–177 (1986).

    CAS 
    PubMed 

    Google Scholar
     

  • Lake, J. A. Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences. Nature 331, 184–186 (1988).

    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Gouy, M. & Li, W.-H. Phylogenetic analysis based on rRNA sequences supports the archaebacterial rather than the eocyte tree. Nature 339, 145–147 (1989).

    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Iwabe, N., Kuma, K., Hasegawa, M., Osawa, S. & Miyata, T. Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc. Natl Acad. Sci. USA 86, 9355–9359 (1989).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Baldauf, S. L., Palmer, J. D. & Doolittle, W. F. The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny. Proc. Natl Acad. Sci. USA 93, 7749–7754 (1996).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lake, J. A., Henderson, E., Oakes, M. & Clark, M. W. Eocytes: a new ribosome structure indicates a kingdom with a close relationship to eukaryotes. Proc. Natl Acad. Sci. USA 81, 3786–3790 (1984). On the basis of ribosome structures, the authors of this study postulated the eocyte hypothesis, in which eukaryotes are most closely related to a specific group of archaea (the 2D tree).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rivera, M. C. & Lake, J. A. Evidence that eukaryotes and eocyte prokaryotes are immediate relatives. Science 257, 74–76 (1992).

    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Brown, J. R., Douady, C. J., Italia, M. J., Marshall, W. E. & Stanhope, M. J. Universal trees based on large combined protein sequence data sets. Nat. Genet. 28, 281–285 (2001).

    CAS 
    PubMed 

    Google Scholar
     

  • Ciccarelli, F. D. et al. Toward automatic reconstruction of a highly resolved tree of life. Science 311, 1283–1287 (2006).

    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Cox, C. J., Foster, P. G., Hirt, R. P., Harris, S. R. & Embley, T. M. The archaebacterial origin of eukaryotes. Proc. Natl Acad. Sci. USA 105, 20356–20361 (2008). Using phylogenetic models that take compositional changes into account, the 2D tree was robustly recovered for the first time in this phylogenomics study.

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Foster, P. G., Cox, C. J. & Embley, T. M. The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods. Phil. Trans. R. Soc. B 364, 2197–2207 (2009).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Guy, L. & Ettema, T. J. G. The archaeal ‘TACK’ superphylum and the origin of eukaryotes. Trends Microbiol. 19, 580–587 (2011).

    CAS 
    PubMed 

    Google Scholar
     

  • Kelly, S., Wickstead, B. & Gull, K. Archaeal phylogenomics provides evidence in support of a methanogenic origin of the archaea and a thaumarchaeal origin for the eukaryotes. Proc. R. Soc. B 278, 1009–1018 (2011).

    CAS 
    PubMed 

    Google Scholar
     

  • Lasek-Nesselquist, E. & Gogarten, J. P. The effects of model choice and mitigating bias on the ribosomal tree of life. Mol. Phylogenetics Evol. 69, 17–38 (2013).


    Google Scholar
     

  • Guy, L., Saw, J. H. & Ettema, T. J. G. The archaeal legacy of eukaryotes: a phylogenomic perspective. Cold Spring Harb. Perspect. Biol. 6, a016022 (2014).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Williams, T. A. & Embley, T. M. Archaeal “dark matter” and the origin of eukaryotes. Genome Biol. Evol. 6, 474–481 (2014).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Raymann, K., Brochier-Armanet, C. & Gribaldo, S. The two-domain tree of life is linked to a new root for the Archaea. Proc. Natl Acad. Sci. USA 112, 6670–6675 (2015).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Spang, A. et al. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521, 173–179 (2015). This paper described the discovery of the first Asgard archaeon, Lokiarchaeum, and showed both its close relationship with eukaryotes and the presence of multiple new ESPs in its genome.

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Seitz, K. W., Lazar, C. S., Hinrichs, K.-U., Teske, A. P. & Baker, B. J. Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction. ISME J. 10, 1696–1705 (2016).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zaremba-Niedzwiedzka, K. et al. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541, 353–358 (2017).

    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Spang, A. et al. Proposal of the reverse flow model for the origin of the eukaryotic cell based on comparative analyses of Asgard archaeal metabolism. Nat. Microbiol. 4, 1138–1148 (2019).

    CAS 
    PubMed 

    Google Scholar
     

  • Seitz, K. W. et al. Asgard archaea capable of anaerobic hydrocarbon cycling. Nat. Commun. 10, 1822 (2019).

    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Imachi, H. et al. Isolation of an archaeon at the prokaryote–eukaryote interface. Nature 577, 519–525 (2020). This study presented the first cultured Asgard archaeon, the lokiarchaeon Candidatus P. syntrophicum, showing remarkable cell physiology (see also ref. 50).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Liu, Y. et al. Expanded diversity of Asgard archaea and their relationships with eukaryotes. Nature 593, 553–557 (2021).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sun, J. et al. Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota lineages. ISME Commun. 1, 30 (2021).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Aouad, M. et al. A divide-and-conquer phylogenomic approach based on character supermatrices resolves early steps in the evolution of the archaea. BMC Ecol. Evo. 22, 1 (2022).


    Google Scholar
     

  • Wu, F. et al. Unique mobile elements and scalable gene flow at the prokaryote–eukaryote boundary revealed by circularized Asgard archaea genomes. Nat. Microbiol. 7, 200–212 (2022).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    CAS 
    PubMed 

    Google Scholar
     

  • Rodrigues-Oliveira, T. et al. Actin cytoskeleton and complex cell architecture in an Asgard archaeon. Nature 613, 332–339 (2023).

    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • 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).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Stairs, C. W. & Ettema, T. J. G. The archaeal roots of the eukaryotic dynamic actin cytoskeleton. Curr. Biol. 30, R521–R526 (2020).

    CAS 
    PubMed 

    Google Scholar
     

  • Klinger, C. M., Spang, A., Dacks, J. B. & Ettema, T. J. G. Tracing the archaeal origins of eukaryotic membrane-trafficking system building blocks. Mol. Biol. Evol. 33, 1528–1541 (2016).

    CAS 
    PubMed 

    Google Scholar
     

  • Vosseberg, J. et al. Timing the origin of eukaryotic cellular complexity with ancient duplications. Nat. Ecol. Evol. 5, 92–100 (2021). This paper reconstructed the numerous gene duplications that occurred during eukaryogenesis from phylogenetic trees and inferred their relative timing, also in comparison with gene transfer events, using the branch lengths approach adapted from ref. 127.

    PubMed 

    Google Scholar
     

  • Szöllősi, 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).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Williams, T. A. et al. Parameter estimation and species tree rooting using ALE and GeneRax. Genome Biol. Evol. 15, evad134 (2023).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Akıl, C. & Robinson, R. C. Genomes of Asgard archaea encode profilins that regulate actin. Nature 562, 439–443 (2018). This article is the first of a series of biochemical papers investigating the molecular function of Asgard ESPs by expressing them in heterologous systems, in this case focusing on the interaction between Asgard profilin and eukaryotic actin.

    ADS 
    PubMed 

    Google Scholar
     

  • Akıl, C. et al. Insights into the evolution of regulated actin dynamics via characterization of primitive gelsolin/cofilin proteins from Asgard archaea. Proc. Natl Acad. Sci. USA 117, 19904–19913 (2020).

    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Survery, S. et al. Heimdallarchaea encodes profilin with eukaryotic-like actin regulation and polyproline binding. Commun. Biol. 4, 1024 (2021).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Akıl, C. et al. Structure and dynamics of Odinarchaeota tubulin and the implications for eukaryotic microtubule evolution. Sci. Adv. 8, eabm2225 (2022).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Leung, K. F., Dacks, J. B. & Field, M. C. Evolution of the multivesicular body ESCRT machinery; retention across the eukaryotic lineage. Traffic 9, 1698–1716 (2008).

    CAS 
    PubMed 

    Google Scholar
     

  • Hatano, T. et al. Asgard archaea shed light on the evolutionary origins of the eukaryotic ubiquitin–ESCRT machinery. Nat. Commun. 13, 3398 (2022).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Neveu, E., Khalifeh, D., Salamin, N. & Fasshauer, D. Prototypic SNARE proteins are encoded in the genomes of Heimdallarchaeota, potentially bridging the gap between the prokaryotes and eukaryotes. Curr. Biol. 30, 2468–2480 (2020).

    CAS 
    PubMed 

    Google Scholar
     

  • Avcı, B. et al. Spatial separation of ribosomes and DNA in Asgard archaeal cells. ISME J. 16, 606–610 (2022).

    PubMed 

    Google Scholar
     

  • Gray, M. W., Burger, G. & Lang, B. F. Mitochondrial evolution. Science 283, 1476–1481 (1999).

    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Roger, A. J., Muñoz-Gómez, S. A. & Kamikawa, R. The origin and diversification of mitochondria. Curr. Biol. 27, R1177–R1192 (2017).

    CAS 
    PubMed 

    Google Scholar
     

  • Yang, D., Oyaizu, Y., Oyaizu, H., Olsen, G. J. & Woese, C. R. Mitochondrial origins. Proc. Natl Acad. Sci. USA 82, 4443–4447 (1985).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fitzpatrick, D. A., Creevey, C. J. & McInerney, J. O. Genome phylogenies indicate a meaningful α-proteobacterial phylogeny and support a grouping of the mitochondria with the Rickettsiales. Mol. Biol. Evol. 23, 74–85 (2006).

    CAS 
    PubMed 

    Google Scholar
     

  • Williams, K. P., Sobral, B. W. & Dickerman, A. W. A robust species tree for the Alphaproteobacteria. J. Bacteriol. 189, 4578–4586 (2007).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Thrash, J. C. et al. Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade. Sci. Rep. 1, 13 (2011).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Georgiades, K., Madoui, M.-A., Le, P., Robert, C. & Raoult, D. Phylogenomic analysis of Odyssella thessalonicensis fortifies the common origin of Rickettsiales, Pelagibacter ubique and Reclimonas americana mitochondrion. PLoS ONE 6, e24857 (2011).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sassera, D. et al. Phylogenomic evidence for the presence of a flagellum and cbb3 oxidase in the free-living mitochondrial ancestor. Mol. Biol. Evol. 28, 3285–3296 (2011).

    CAS 
    PubMed 

    Google Scholar
     

  • Rodríguez-Ezpeleta, N. & Embley, T. M. The SAR11 group of alpha-proteobacteria is not related to the origin of mitochondria. PLoS ONE 7, e30520 (2012).

    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Viklund, J., Martijn, J., Ettema, T. J. G. & Andersson, S. G. E. Comparative and phylogenomic evidence that the alphaproteobacterium HIMB59 is not a member of the oceanic SAR11 clade. PLoS ONE 8, e78858 (2013).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wang, Z. & Wu, M. Phylogenomic reconstruction indicates mitochondrial ancestor was an energy parasite. PLoS ONE 9, e110685 (2014).

    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wang, Z. & Wu, M. An integrated phylogenomic approach toward pinpointing the origin of mitochondria. Sci. Rep. 5, 7949 (2015).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Martijn, J., Vosseberg, J., Guy, L., Offre, P. & Ettema, T. J. G. Deep mitochondrial origin outside the sampled Alphaproteobacteria. Nature 557, 101–105 (2018). This study recovered several novel marine alphaproteobacterial groups and performed careful phylogenomic analyses to address long-branch and compositional artefacts, revealing the novel Alphaproteobacteria–sister position of mitochondria.

    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Fan, L. et al. Phylogenetic analyses with systematic taxon sampling show that mitochondria branch within Alphaproteobacteria. Nat. Ecol. Evol. 4, 1213–1219 (2020).

    PubMed 

    Google Scholar
     

  • Wang, S. & Luo, H. Dating Alphaproteobacteria evolution with eukaryotic fossils. Nat. Commun. 12, 3324 (2021).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Muñoz-Gómez, 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). This study corroborated the Alphaproteobacteria–sister relationship of mitochondria using a newly developed model that accounts for compositional heterogeneity across sites and branches.

    PubMed 

    Google Scholar
     

  • Martijn, J., Vosseberg, J., Guy, L., Offre, P. & Ettema, T. J. G. Phylogenetic affiliation of mitochondria with Alpha-II and Rickettsiales is an artefact. Nat. Ecol. Evol. 6, 1829–1831 (2022).

    PubMed 

    Google Scholar
     

  • Fan, L. et al. Reply to: Phylogenetic affiliation of mitochondria with Alpha-II and Rickettsiales is an artefact. Nat. Ecol. Evol. 6, 1832–1835 (2022).

    PubMed 

    Google Scholar
     

  • Ettema, T. J. G. & Andersson, S. G. E. The α-proteobacteria: the Darwin finches of the bacterial world. Biol. Lett. 5, 429–432 (2009).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Martin, W. F., Garg, S. & Zimorski, V. Endosymbiotic theories for eukaryote origin. Phil. Trans. R. Soc. B 370, 20140330 (2015).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Martin, W. & Müller, M. The hydrogen hypothesis for the first eukaryote. Nature 392, 37–41 (1998).

    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Sousa, F. L., Neukirchen, S., Allen, J. F., Lane, N. & Martin, W. F. Lokiarchaeon is hydrogen dependent. Nat. Microbiol. 1, 16034 (2016).

    CAS 
    PubMed 

    Google Scholar
     

  • Moreira, D. & López-García, P. Symbiosis between methanogenic archaea and δ-proteobacteria as the origin of eukaryotes: the syntrophic hypothesis. J. Mol. Evol. 47, 517–530 (1998).

    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • López-García, P. & Moreira, D. The syntrophy hypothesis for the origin of eukaryotes revisited. Nat. Microbiol. 5, 655–667 (2020).

    PubMed 

    Google Scholar
     

  • Bulzu, P.-A. et al. Casting light on Asgardarchaeota metabolism in a sunlit microoxic niche. Nat. Microbiol. 4, 1129–1137 (2019).

    CAS 
    PubMed 

    Google Scholar
     

  • Mills, D. B. et al. Eukaryogenesis and oxygen in Earth history. Nat. Ecol. Evol. 6, 520–532 (2022).

    PubMed 

    Google Scholar
     

  • Muñoz-Gómez, S. A., Wideman, J. G., Roger, A. J. & Slamovits, C. H. The origin of mitochondrial cristae from Alphaproteobacteria. Mol. Biol. Evol. 34, 943–956 (2017).

    PubMed 

    Google Scholar
     

  • Gabaldón, T. & Huynen, M. A. Reconstruction of the proto-mitochondrial metabolism. Science 301, 609–609 (2003).

    PubMed 

    Google Scholar
     

  • Gabaldón, T. & Huynen, M. A. From endosymbiont to host-controlled organelle: the hijacking of mitochondrial protein synthesis and metabolism. PLoS Comput. Biol. 3, e219 (2007).

    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Stairs, C. W., Leger, M. M. & Roger, A. J. Diversity and origins of anaerobic metabolism in mitochondria and related organelles. Phil. Trans. R. Soc. B 370, 20140326 (2015).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Stairs, C. W. et al. Chlamydial contribution to anaerobic metabolism during eukaryotic evolution. Sci. Adv. 6, eabb7258 (2020).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Speijer, D. Alternating terminal electron-acceptors at the basis of symbiogenesis: How oxygen ignited eukaryotic evolution. BioEssays 39, 1600174 (2017).


    Google Scholar
     

  • Cavalier-Smith, T. The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. Int. J. Syst. Evol. Microbiol. 52, 297–354 (2002).

    CAS 
    PubMed 

    Google Scholar
     

  • Martijn, J. & Ettema, T. J. G. From archaeon to eukaryote: the evolutionary dark ages of the eukaryotic cell. Biochem. Soc. Trans. 41, 451–457 (2013).

    CAS 
    PubMed 

    Google Scholar
     

  • Zachar, I., Szilágyi, A., Számadó, S. & Szathmáry, E. Farming the mitochondrial ancestor as a model of endosymbiotic establishment by natural selection. Proc. Natl Acad. Sci. USA 115, E1504–E1510 (2018).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Baum, D. A. & Baum, B. An inside-out origin for the eukaryotic cell. BMC Biol. 12, 76 (2014).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Mills, D. B. The origin of phagocytosis in Earth history. Interface Focus 10, 20200019 (2020).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bremer, N., Tria, F. D. K., Skejo, J., Garg, S. G. & Martin, W. F. Ancestral state reconstructions trace mitochondria but not phagocytosis to the last eukaryotic common ancestor. Genome Biol. Evol. 14, evac079 (2022).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yutin, N., Wolf, M. Y., Wolf, Y. I. & Koonin, E. V. The origins of phagocytosis and eukaryogenesis. Biol. Direct 4, 9 (2009).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hugoson, E., Guliaev, A., Ammunét, T. & Guy, L. Host adaptation in Legionellales Is 1.9 Ga, coincident with eukaryogenesis. Mol. Biol. Evol. 39, msac037 (2022).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Martin, W. F., Tielens, A. G. M., Mentel, M., Garg, S. G. & Gould, S. B. The physiology of phagocytosis in the context of mitochondrial origin. Microbiol. Mol. Biol. Rev. 81, e00008–e00017 (2017).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hampl, V., Čepička, I. & Eliáš, M. Was the mitochondrion necessary to start eukaryogenesis? Trends Microbiol. 27, 96–104 (2019).

    CAS 
    PubMed 

    Google Scholar
     

  • Shiratori, T., Suzuki, S., Kakizawa, Y. & Ishida, K. Phagocytosis-like cell engulfment by a planctomycete bacterium. Nat. Commun. 10, 5529 (2019).

    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Burns, J. A., Pittis, A. A. & Kim, E. Gene-based predictive models of trophic modes suggest Asgard archaea are not phagocytotic. Nat. Ecol. Evol. 2, 697–704 (2018).

    PubMed 

    Google Scholar
     

  • Cavalier-Smith, T. Archaebacteria and archezoa. Nature 339, 100–101 (1989).

    ADS 

    Google Scholar
     

  • Embley, T. M. & Hirt, R. P. Early branching eukaryotes? Curr. Opin. Genet. Dev. 8, 624–629 (1998).

    CAS 
    PubMed 

    Google Scholar
     

  • Ettema, T. J. G. Evolution: mitochondria in the second act. Nature 531, 39–40 (2016).

    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Lane, N. & Martin, W. The energetics of genome complexity. Nature 467, 929–934 (2010).

    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Lane, N. Energetics and genetics across the prokaryote–eukaryote divide. Biol. Direct 6, 35 (2011).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Booth, A. & Doolittle, W. F. Eukaryogenesis, how special really? Proc. Natl Acad. Sci. USA 112, 10278–10285 (2015).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lynch, M. & Marinov, G. K. The bioenergetic costs of a gene. Proc. Natl Acad. Sci. USA 112, 15690–15695 (2015).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Koonin, E. V. Energetics and population genetics at the root of eukaryotic cellular and genomic complexity. Proc. Natl Acad. Sci. USA 112, 15777–15778 (2015).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lynch, M. & Marinov, G. K. Membranes, energetics, and evolution across the prokaryote–eukaryote divide. eLife 6, e20437 (2017).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lane, N. Serial endosymbiosis or singular event at the origin of eukaryotes? J. Theor. Biol. 434, 58–67 (2017).

    ADS 
    PubMed 

    Google Scholar
     

  • Chiyomaru, K. & Takemoto, K. Revisiting the hypothesis of an energetic barrier to genome complexity between eukaryotes and prokaryotes. R. Soc. Open Sci. 7, 191859 (2020).

    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lane, N. How energy flow shapes cell evolution. Curr. Biol. 30, R471–R476 (2020).

    CAS 
    PubMed 

    Google Scholar
     

  • Schavemaker, P. E. & Muñoz-Gómez, S. A. The role of mitochondrial energetics in the origin and diversification of eukaryotes. Nat. Ecol. Evol. 6, 1307–1317 (2022).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Volland, J.-M. et al. A centimeter-long bacterium with DNA contained in metabolically active, membrane-bound organelles. Science 376, 1453–1458 (2022).

    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Greening, C. & Lithgow, T. Formation and function of bacterial organelles. Nat. Rev. Microbiol. 18, 677–689 (2020).

    CAS 
    PubMed 

    Google Scholar
     

  • Küper, U., Meyer, C., Müller, V., Rachel, R. & Huber, H. Energized outer membrane and spatial separation of metabolic processes in the hyperthermophilic Archaeon Ignicoccus hospitalis. Proc. Natl Acad. Sci. USA 107, 3152–3156 (2010).

    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wiegand, S., Jogler, M. & Jogler, C. On the maverick planctomycetes. FEMS Microbiol. Rev. 42, 739–760 (2018).

    CAS 
    PubMed 

    Google Scholar
     

  • Katayama, T. et al. Isolation of a member of the candidate phylum ‘Atribacteria’ reveals a unique cell membrane structure. Nat. Commun. 11, 6381 (2020).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Pittis, A. A. & Gabaldón, T. Late acquisition of mitochondria by a host with chimaeric prokaryotic ancestry. Nature 531, 101–104 (2016). This study presented a novel approach to use phylogenetic branch lengths to infer the relative timing of gene acquisitions during eukaryogenesis, pointing to rampant bacterial gene flow to stem eukaryotes prior to the proto-mitochondrial acquisition.

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gabaldón, T. Relative timing of mitochondrial endosymbiosis and the “pre-mitochondrial symbioses” hypothesis. IUBMB Life 70, 1188–1196 (2018).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Vosseberg, J., Schinkel, M., Gremmen, S. & Snel, B. The spread of the first introns in proto-eukaryotic paralogs. Commun. Biol. 5, 476 (2022).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Susko, E., Steel, M. & Roger, A. J. Conditions under which distributions of edge length ratios on phylogenetic trees can be used to order evolutionary events. J. Theor. Biol. 526, 110788 (2021).

    MathSciNet 
    CAS 
    PubMed 

    Google Scholar
     

  • Tricou, T., Tannier, E. & de Vienne, D. M. Ghost lineages can invalidate or even reverse findings regarding gene flow. PLoS Biol. 20, e3001776 (2022).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fritz-Laylin, L. K. et al. The genome of Naegleria gruberi illuminates early eukaryotic versatility. Cell 140, 631–642 (2010).

    CAS 
    PubMed 

    Google Scholar
     

  • Huynen, M. A., Duarte, I. & Szklarczyk, R. Loss, replacement and gain of proteins at the origin of the mitochondria. Biochim. Biophys. Acta 1827, 224–231 (2013).

    CAS 
    PubMed 

    Google Scholar
     

  • Timmis, J. N., Ayliffe, M. A., Huang, C. Y. & Martin, W. Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat. Rev. Genet. 5, 123–135 (2004).

    CAS 
    PubMed 

    Google Scholar
     

  • Karnkowska, A. et al. A eukaryote without a mitochondrial organelle. Curr. Biol. 26, 1274–1284 (2016).

    CAS 
    PubMed 

    Google Scholar
     

  • Gabaldón, T. et al. Origin and evolution of the peroxisomal proteome. Biol. Direct 1, 8 (2006).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rochette, N. C., Brochier-Armanet, C. & Gouy, M. Phylogenomic test of the hypotheses for the evolutionary origin of eukaryotes. Mol. Biol. Evol. 31, 832–845 (2014).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Irwin, N. A. T., Pittis, A. A., Richards, T. A. & Keeling, P. J. Systematic evaluation of horizontal gene transfer between eukaryotes and viruses. Nat. Microbiol. 7, 327–336 (2022).

    CAS 
    PubMed 

    Google Scholar
     

  • Ku, C. et al. Endosymbiotic origin and differential loss of eukaryotic genes. Nature 524, 427–432 (2015).

    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Gould, S. B., Garg, S. G. & Martin, W. F. Bacterial vesicle secretion and the evolutionary origin of the eukaryotic endomembrane system. Trends Microbiol. 24, 525–534 (2016).

    CAS 
    PubMed 

    Google Scholar
     

  • Coleman, G. A., Pancost, R. D. & Williams, T. A. Investigating the origins of membrane phospholipid biosynthesis genes using outgroup-free rooting. Genome Biol. Evol. 11, 883–898 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Volker, C. & Lupas, A. N. in The Proteasome–Ubiquitin Protein Degradation Pathway (eds Zwickl, P. & Baumeister, W.) 1–22 (Springer, 2002).

  • Vosseberg, J., Stolker, D., von der Dunk, S. H. A. & Snel, B. Integrating phylogenetics with intron positions illuminates the origin of the complex spliceosome. Mol. Biol. Evol. 40, msad011 (2023).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tromer, E. C., Hooff, J. J. E., van, Kops, G. J. P. L. & Snel, B. Mosaic origin of the eukaryotic kinetochore. Proc. Natl Acad. Sci. USA 116, 12873–12882 (2019).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Findeisen, P. et al. Six subgroups and extensive recent duplications characterize the evolution of the eukaryotic tubulin protein family. Genome Biol. Evol. 6, 2274–2288 (2014).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Muñoz-Gómez, S. A., Bilolikar, G., Wideman, J. G. & Geiler-Samerotte, K. Constructive neutral evolution 20 years later. J. Mol. Evol. 89, 172–182 (2021).

    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dacks, J. B. & Field, M. C. Evolution of the eukaryotic membrane-trafficking system: origin, tempo and mode. J. Cell Sci. 120, 2977–2985 (2007).

    CAS 
    PubMed 

    Google Scholar
     

  • Dacks, J. B. & Field, M. C. Evolutionary origins and specialisation of membrane transport. Curr. Opin. Cell Biol. 53, 70–76 (2018).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Baek, M. et al. Accurate prediction of protein structures and interactions using a three-track neural network. Science 373, 871–876 (2021).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ekman, D., Björklund, Å. K., Frey-Skött, J. & Elofsson, A. Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions. J. Mol. Biol. 348, 231–243 (2005).

    CAS 
    PubMed 

    Google Scholar
     

  • Liu, J. & Rost, B. Comparing function and structure between entire proteomes. Protein Sci. 10, 1970–1979 (2001).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Xue, B., Dunker, A. K. & Uversky, V. N. Orderly order in protein intrinsic disorder distribution: disorder in 3500 proteomes from viruses and the three domains of life. J. Biomol. Struct. Dyn. 30, 137–149 (2012).

    CAS 
    PubMed 

    Google Scholar
     

  • Colnaghi, M., Lane, N. & Pomiankowski, A. Genome expansion in early eukaryotes drove the transition from lateral gene transfer to meiotic sex. eLife 9, e58873 (2020).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • van Dijk, B., Bertels, F., Stolk, L., Takeuchi, N. & Rainey, P. B. Transposable elements promote the evolution of genome streamlining. Phil. Trans. R. Soc. B 377, 20200477 (2022).

    PubMed 

    Google Scholar
     

  • Colnaghi, M., Lane, N. & Pomiankowski, A. Repeat sequences limit the effectiveness of lateral gene transfer and favored the evolution of meiotic sex in early eukaryotes. Proc. Natl Acad. Sci. USA 119, e2205041119 (2022).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gilbert, W. Why genes in pieces? Nature 271, 501–501 (1978).

    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Liu, M. & Grigoriev, A. Protein domains correlate strongly with exons in multiple eukaryotic genomes – evidence of exon shuffling? Trends Genet. 20, 399–403 (2004).

    PubMed 

    Google Scholar
     

  • Grau-Bové, X. et al. Dynamics of genomic innovation in the unicellular ancestry of animals. eLife 6, e26036 (2017).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ocaña-Pallarès, E. et al. Divergent genomic trajectories predate the origin of animals and fungi. Nature 609, 747–753 (2022).

    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Méheust, R. et al. Formation of chimeric genes with essential functions at the origin of eukaryotes. BMC Biol. 16, 30 (2018).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tamarit, D. et al. Description of Asgardarchaeum abyssi gen. nov. spec. nov., a novel species within the class Asgardarchaeia and phylum Asgardarchaeota in accordance with the SeqCode. Syst. Appl. Microbiol. 47, 126525 (2024).

  • Delsuc, F., Brinkmann, H. & Philippe, H. Phylogenomics and the reconstruction of the tree of life. Nat. Rev. Genet. 6, 361–375 (2005).

    CAS 
    PubMed 

    Google Scholar
     

  • Kapli, P., Yang, Z. & Telford, M. J. Phylogenetic tree building in the genomic age. Nat. Rev. Genet. 21, 428–444 (2020).

    CAS 
    PubMed 

    Google Scholar
     

  • Steenwyk, J. L., Li, Y., Zhou, X., Shen, X.-X. & Rokas, A. Incongruence in the phylogenomics era. Nat. Rev. Genet. 24, 834–850 (2023).

    CAS 
    PubMed 

    Google Scholar
     

  • Fleming, J. F., Valero-Gracia, A. & Struck, T. H. Identifying and addressing methodological incongruence in phylogenomics: a review. Evol. Appl. 16, 1087–1104 (2023).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Foster, P. G. et al. Recoding amino acids to a reduced alphabet may increase or decrease phylogenetic accuracy. Syst. Biol. 72, 723–737 (2023).

    CAS 
    PubMed 

    Google Scholar
     

  • Susko, E. & Roger, A. J. On reduced amino acid alphabets for phylogenetic inference. Mol. Biol. Evol. 24, 2139–2150 (2007).

    CAS 
    PubMed 

    Google Scholar
     

  • Viklund, J., Ettema, T. J. G. & Andersson, S. G. E. Independent genome reduction and phylogenetic reclassification of the oceanic SAR11 clade. Mol. Biol. Evol. 29, 599–615 (2012).

    CAS 
    PubMed 

    Google Scholar
     



  • Source link

    Leave a Reply

    Your email address will not be published. Required fields are marked *