Applied Microbiology and Biotechnology

, Volume 102, Issue 7, pp 3049–3058 | Cite as

Two or three domains: a new view of tree of life in the genomics era

  • Zhichao Zhou
  • Yang Liu
  • Meng LiEmail author
  • Ji-Dong Gu


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.


Tree 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.

Author contributions

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.

Ethical approval

This article does not contain any studies with human participants performed by any of the authors.


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© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Institute for Advanced StudyShenzhen UniversityShenzhenPeople’s Republic of China
  2. 2.Laboratory of Environmental Microbiology and Toxicology, School of Biological SciencesThe University of Hong KongHong KongPeople’s Republic of China
  3. 3.Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic EngineeringShenzhen UniversityShenzhenPeople’s Republic of China

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