The large phylogenetic distance separating eukaryotic genes and their archaeal orthologs has prevented identification of the position of the eukaryotic root in phylogenomic studies. Recently, an innovative approach has been proposed to circumvent this issue: the use as phylogenetic markers of proteins that have been transferred from bacterial donor sources to eukaryotes, after their emergence from Archaea. Using this approach, two recent independent studies have built phylogenomic datasets based on bacterial sequences, leading to different predictions of the eukaryotic root. Taking advantage of additional genome sequences from the jakobid Andalucia godoyi and the two known malawimonad species (Malawimonas jakobiformis and Malawimonas californiana), we reanalyzed these two phylogenomic datasets. We show that both datasets pinpoint the same phylogenetic position of the eukaryotic root that is between "Unikonta" and "Bikonta," with malawimonad and collodictyonid lineages on the Unikonta side of the root. Our results firmly indicate that (i) the supergroup Excavata is not monophyletic and (ii) the last common ancestor of eukaryotes was a biflagellate organism. Based on our results, we propose to rename the two major eukaryotic groups Unikonta and Bikonta as Opimoda and Diphoda, respectively.

Centre for Genomic Regulation 08003 Barcelona Spain; Universitat Pompeu Fabra 08003 Barcelona Spain;

Faculty of Science Department of Biology and Ecology University of Ostrava 710 00 Ostrava Czech Republic;

Institut de Biologia Evolutiva Consejo Superior de Investigaciones Científicas Universitat Pompeu Fabra 08003 Barcelona Spain;

Institute of Molecular Genetics Academy of Sciences of the Czech Republic 142 20 Prague 4 Czech Republic; and

Leibniz Institut DSMZ Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH D 38124 Braunschweig Germany;

Robert Cedergren Centre for Bioinformatics and Genomics Département de Biochimie Université de Montréal Montreal QC Canada H3T 1J4

Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology American Museum of Natural History New York NY 10024;

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