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Open Access Highly Accessed Open Badges Research article

A genomic timescale for the origin of eukaryotes

S Blair Hedges1*, Hsiong Chen1, Sudhir Kumar2, Daniel YC Wang1, Amanda S Thompson1 and Hidemi Watanabe3

Author Affiliations

1 Astrobiology Research Center and Department of Biology, 208 Mueller Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802, USA

2 Department of Biology, Arizona State University, Tempe, Arizona 85287, USA

3 RIKEN Genomic Sciences Center, Yokohama, Kanagawa-ken 230-0045, Japan

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BMC Evolutionary Biology 2001, 1:4  doi:10.1186/1471-2148-1-4

Published: 12 September 2001



Genomic sequence analyses have shown that horizontal gene transfer occurred during the origin of eukaryotes as a consequence of symbiosis. However, details of the timing and number of symbiotic events are unclear. A timescale for the early evolution of eukaryotes would help to better understand the relationship between these biological events and changes in Earth's environment, such as the rise in oxygen. We used refined methods of sequence alignment, site selection, and time estimation to address these questions with protein sequences from complete genomes of prokaryotes and eukaryotes.


Eukaryotes were found to evolve faster than prokaryotes, with those eukaryotes derived from eubacteria evolving faster than those derived from archaebacteria. We found an early time of divergence (~4 billion years ago, Ga) for archaebacteria and the archaebacterial genes in eukaryotes. Our analyses support at least two horizontal gene transfer events in the origin of eukaryotes, at 2.7 Ga and 1.8 Ga. Time estimates for the origin of cyanobacteria (2.6 Ga) and the divergence of an early-branching eukaryote that lacks mitochondria (Giardia) (2.2 Ga) fall between those two events.


We find support for two symbiotic events in the origin of eukaryotes: one premitochondrial and a later mitochondrial event. The appearance of cyanobacteria immediately prior to the earliest undisputed evidence for the presence of oxygen (2.4–2.2 Ga) suggests that the innovation of oxygenic photosynthesis had a relatively rapid impact on the environment as it set the stage for further evolution of the eukaryotic cell.