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A congruent phylogenomic signal places eukaryotes within the Archaea

Lookup NU author(s): Dr Tom Williams, Dr Tom Nye, Emeritus Professor T. Martin Embley FMedSci FRSORCiD



Determining the relationships among the major groups of cellular life is important for understanding the evolution of biological diversity, but is difficult given the enormous time spans involved. In the textbook 'three domains' tree based on informational genes, eukaryotes and Archaea share a common ancestor to the exclusion of Bacteria. However, some phylogenetic analyses of the same data have placed eukaryotes within the Archaea, as the nearest relatives of different archaeal lineages. We compared the support for these competing hypotheses using sophisticated phylogenetic methods and an improved sampling of archaeal biodiversity. We also employed both new and existing tests of phylogenetic congruence to explore the level of uncertainty and conflict in the data. Our analyses suggested that much of the observed incongruence is weakly supported or associated with poorly fitting evolutionary models. All of our phylogenetic analyses, whether on small subunit and large subunit ribosomal RNA or concatenated protein-coding genes, recovered a monophyletic group containing eukaryotes and the TACK archaeal superphylum comprising the Thaumarchaeota, Aigarchaeota, Crenarchaeota and Korarchaeota. Hence, while our results provide no support for the iconic three-domain tree of life, they are consistent with an extended eocyte hypothesis whereby vital components of the eukaryotic nuclear lineage originated from within the archaeal radiation.

Publication metadata

Author(s): Williams TA, Foster PG, Nye TMW, Cox CJ, Embley TM

Publication type: Article

Publication status: Published

Journal: Proceedings of the Royal Society B: Biological Sciences

Year: 2012

Volume: 279

Issue: 1749

Pages: 4870-4879

Print publication date: 24/10/2012

Date deposited: 28/01/2013

ISSN (print): 0962-8452

ISSN (electronic): 1471-2954

Publisher: The Royal Society Publishing


DOI: 10.1098/rspb.2012.1795


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