Table of Contents Author Guidelines Submit a Manuscript
Volume 2014 (2014), Article ID 706468, 15 pages
Research Article

A Phylogenomic Census of Molecular Functions Identifies Modern Thermophilic Archaea as the Most Ancient Form of Cellular Life

1Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, and Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
2Microbial Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea

Received 6 July 2013; Revised 20 November 2013; Accepted 17 January 2014; Published 31 August 2014

Academic Editor: Celine Brochier-Armanet

Copyright © 2014 Arshan Nasir et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


The origins of diversified life remain mysterious despite considerable efforts devoted to untangling the roots of the universal tree of life. Here we reconstructed phylogenies that described the evolution of molecular functions and the evolution of species directly from a genomic census of gene ontology (GO) definitions. We sampled 249 free-living genomes spanning organisms in the three superkingdoms of life, Archaea, Bacteria, and Eukarya, and used the abundance of GO terms as molecular characters to produce rooted phylogenetic trees. Results revealed an early thermophilic origin of Archaea that was followed by genome reduction events in microbial superkingdoms. Eukaryal genomes displayed extraordinary functional diversity and were enriched with hundreds of novel molecular activities not detected in the akaryotic microbial cells. Remarkably, the majority of these novel functions appeared quite late in evolution, synchronized with the diversification of the eukaryal superkingdom. The distribution of GO terms in superkingdoms confirms that Archaea appears to be the simplest and most ancient form of cellular life, while Eukarya is the most diverse and recent.