Bacterial proteins pinpoint a single eukaryotic root

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.The work of R.D. was supported by Howard Hughes Medical Institute International Early Career Scientist Program Grant 55007424, Spanish Ministry of Economy and Competitiveness Grant BFU2012-31329 as part of the European Molecular Biology Organization Young Investigator Program, and two grants from the Spanish Ministry of Economy and Competitiveness, “Centro de Excelencia Severo Ochoa 2013-2017” Grant Sev-2012-0208 and Grant BES-2013-064004 funded by the European Regional Development Fund. This study was further supported by a Czech Science Foundation Grant 13-24983S and Project CZ.1.05/2.1.00/03.0100 (Institute of Environmental Technology) financed by Structural Funds of the European Union (to M.E.), American Museum of Natural History start-up grants (to E.K.), the Canadian Research Chair program (B.F.L.), and the Natural Sciences and Engineering Research Council of Canada (B.F.L.).Peer reviewe