Two or three domains: a new view of tree of life in the genomics era
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The deep phylogenetic topology of tree of life is in the center of a long-time dispute. The Woeseian three-domain tree theory, with the Eukarya evolving as a sister clade to Archaea, competes with the two-domain tree theory (the eocyte tree), with the Eukarya branched within Archaea. Revealed by the ongoing debate over the last three decades, sophisticated and proper phylogenetic methods should necessarily be paid with more emphasis, especially these are focusing on the compositional heterogeneity of sites and lineages, and the heterotachy issue. The newly emerging archaeal lineages with numerous eukaryotic-like features, such as membrane trafficking and cellular compartmentalization, are phylogenetically the closest to eukaryotes currently. These findings highlight the evolutionary history from an ancient archaeon to a more complex archaeon with protoeukaryotic-like features and complex cellular structures, thus providing clues to understand eukaryogenesis process. The increasing repertoire of precise genomic contents provides great advantages on understanding the deep phylogeny of tree of life and ancient evolutionary events on Eukarya branching process.
KeywordsTree of life Eocyte tree Woeseian tree Asgard superphylum Eukaryotic-like features
We thank for presentations, critiques, and comments from Prof. Norman R. Pace, Prof. Jared R. Leadbetter, and valuable discussions by the participants in the 2016 MBL microbial diversity summer course. We also thank Prof. William F. Martin for his suggestions on this work.
Z.Z., Y.L., M.L., and J.D.G. conceived the review. Z.Z., Y.L., and M.L. wrote the original manuscript and prepared the tables and figures. M.L. and J.D.G. reviewed and edited the final manuscript.
This project is supported by a postgraduate student fellowship from HKU and Lorus J. & Margery J. Milne Scholarship from MBL to Zhichao Zhou (ZZ) and The National Natural Science Foundation of China (No. 31622002, 41506163) to Meng Li (ML).
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
This article does not contain any studies with human participants performed by any of the authors.
- Albani AE, Bengtson S, Canfield DE, Bekker A, Macchiarelli R, Mazurier A, Hammarlund EU, Boulvais P, Dupuy J-J, Fontaine C, Fürsich FT, Gauthier-Lafaye F, Janvier P, Javaux E, Ossa FO, Pierson-Wickmann A-C, Riboulleau A, Sardini P, Vachard D, Whitehouse M, Meunier A (2010) Large colonial organisms with coordinated growth in oxygenated environments 2.1Gyr ago. Nature 466(7302):100–104. https://doi.org/10.1038/nature09166 CrossRefPubMedGoogle Scholar
- Esser C, Ahmadinejad N, Wiegand C, Rotte C, Sebastiani F, Gelius-Dietrich G, Henze K, Kretschmann E, Richly E, Leister D, Bryant D, Steel MA, Lockhart PJ, Penny D, Martin W (2004) A genome phylogeny for mitochondria among α-Proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes. Mol Biol Evol 21(9):1643–1660. https://doi.org/10.1093/molbev/msh160 CrossRefPubMedGoogle Scholar
- Fuerst JA (2005) Intracellular compartmentation in Planctomycetes. Annu Rev Microbiol 59:299–328. https://doi.org/10.1146/annurev.micro.59.030804.121258 CrossRefPubMedGoogle Scholar
- He Y, Li M, Perumal V, Feng X, Fang J, Xie J, Sievert SM, Wang F (2016) Genomic and enzymatic evidence for acetogenesis among multiple lineages of the archaeal phylum Bathyarchaeota widespread in marine sediments. Nat Microbiol 1(6):16035. https://doi.org/10.1038/nmicrobiol.2016.35 CrossRefPubMedGoogle Scholar
- Heimerl T, Flechsler J, Pickl C, Heinz V, Salecker B, Zweck J, Wanner G, Geimer S, Samson RY, Bell SD, Huber H, Wirth R, Wurch L, Podar M, Rachel R (2017) A complex endomembrane system in the archaeon Ignicoccus hospitalis tapped by Nanoarchaeum equitans. Front Microbiol 8(1072) https://doi.org/10.3389/fmicb.2017.01072
- Hong Y, Cao H, Li M, Gu J-D (2014) Anammoxosome in anaerobic ammonium-oxidizing bacteria—was it originated from endosymbiosis? Am J Curr Microbiol 2:18–40Google Scholar
- Küper U, Meyer C, Müller V, Rachel R, Huber H (2010) Energized outer membrane and spatial separation of metabolic processes in the hyperthermophilic Archaeon Ignicoccus hospitalis. Proc Natl Acad Sci U S A 107(7):3152–3156. https://doi.org/10.1073/pnas.0911711107 CrossRefPubMedPubMedCentralGoogle Scholar
- Liu Y, Zhou Z, Pan J, Baker B, Gu J-D, Li M (2018) Comparative genomic inference suggests mixotrophic lifestyle for Thorarchaeota. ISME J. https://doi.org/10.1038/s41396-018-0060-x
- Lopez P, Casane D, Philippe H (2002) Heterotachy, an important process of protein evolution. Mol Biol Evol 19(1):1–7. https://doi.org/10.1093/oxfordjournals.molbev.a003973 CrossRefPubMedGoogle Scholar
- Pace NR (2016) Comments from norm pace on the recent hug et al. “eocyte” phylogenetic tree. In: pace NR (ed). Comments ednGoogle Scholar
- Schulz F, Yutin N, Ivanova NN, Ortega DR, Lee TK, Vierheilig J, Daims H, Horn M, Wagner M, Jensen GJ, Kyrpides NC, Koonin EV, Woyke T (2017) Giant viruses with an expanded complement of translation system components. Science 356(6333):82–85. https://doi.org/10.1126/science.aal4657 CrossRefPubMedGoogle Scholar
- Spang A, Eme L, Saw JH, Caceres EF, Zaremba-Niedzwiedzka K, Lombard J, Guy L, Ettema TJG (2017) Asgard archaea are the closest archaeal relatives of eukaryotes. Plos Genet (in the press)Google Scholar
- Williams TA, Szöllősi GJ, Spang A, Foster PG, Heaps SE, Boussau B, Ettema TJG, Embley TM (2017) Integrative modeling of gene and genome evolution roots the archaeal tree of life. Proc Natl Acad Sci U S A 114(23):E4602–E4611. https://doi.org/10.1073/pnas.1618463114 CrossRefPubMedPubMedCentralGoogle Scholar
- Zaremba-Niedzwiedzka K, Caceres EF, Saw JH, Bäckström D, Juzokaite L, Vancaester E, Seitz KW, Anantharaman K, Starnawski P, Kjeldsen KU, Stott MB, Nunoura T, Banfield JF, Schramm A, Baker BJ, Spang A, Ettema TJG (2017) Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541(7637):353–358. https://doi.org/10.1038/nature21031 CrossRefPubMedGoogle Scholar