Origins of major archaeal clades correspond to gene acquisitions from bacteria
Authors: James O McInerney
Filipa L Sousa
Shijulal Nelson-Sathi
Bettina Siebers
Nabor Lozada-Ch√°vez
Giddy Landan
Thorsten Thiergart
Mayo Roettger
David Bryant
Arnold Janssen
William F Martin
Peter Sch√∂nheit
Journal: Nature (2015)
Discipline: Multidisciplinary
Keywords: origin; prokaryotic groups; mechanisms; ecological interactions; genetic variation
Affiliations: Institute of Molecular Evolution, Heinrich-Heine University, 40225 D√ºsseldorf, Germany., Mathematisches Institut, Heinrich-Heine University, 40225 D√ºsseldorf, Germany., Department of Mathematics and Statistics, University of Otago, Dunedin 9054, New Zealand., Genomic Microbiology Group, Institute of Microbiology, Christian-Albrechts-Universit√§t Kiel, 24118 Kiel, Germany., Institut f√ºr Allgemeine Mikrobiologie, Christian-Albrechts-Universit√§t Kiel, 24118 Kiel, Germany., Faculty of Chemistry, Biofilm Centre, Molecular Enzyme Technology and Biochemistry, University of Duisburg-Essen, 45117 Essen, Germany., Department of Biology, National University of Ireland, Maynooth, County Kildare, Ireland., 1] Institute of Molecular Evolution, Heinrich-Heine University, 40225 D√ºsseldorf, Germany [2] Instituto de Tecnologia Qu√≠mica e Biol√≥gica, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal.

Abstract:  The mechanisms that underlie the origin of major prokaryotic groups are poorly understood. In principle, the origin of both species and higher taxa among prokaryotes should entail similar mechanisms--ecological interactions with the environment paired with natural genetic variation involving lineage-specific gene innovations and lineage-specific gene acquisitions. To investigate the origin of higher taxa in archaea, we have determined gene distributions and gene phylogenies for the 267,568 protein-coding genes of 134 sequenced archaeal genomes in the context of their homologues from 1,847 reference bacterial genomes. Archaeal-specific gene families define 13 traditionally recognized archaeal higher taxa in our sample. Here we report that the origins of these 13 groups unexpectedly correspond to 2,264 group-specific gene acquisitions from bacteria. Interdomain gene transfer is highly asymmetric, transfers from bacteria to archaea are more than fivefold more frequent than vice versa. Gene transfers identified at major evolutionary transitions among prokaryotes specifically implicate gene acquisitions for metabolic functions from bacteria as key innovations in the origin of higher archaeal taxa. 

Retracted: No

PubPeer comments:
 Readers should become aware of a preprint (now, a peer-reviewed article) that reanalysed Nelson-Sathi et al., 2014 data, entitled  Origins of major archaeal clades do not correspond to gene acquisitions from bacteria https: www.biorxiv.org content 10.1101 019851v1 https: academic.oup.com mbe article 33 2 305 2579643 From the Abstract:  In a recent articxle, Nelson-Sathi et al. [NS] report that the origins of Major Archaeal Lineages [MAL] correspond to massive group-specific gene acquisitions via horizontal gene transfer (HGT) from bacteria (Nelson-Sathi et al., 2015, Nature 517(7532):77-80). If correct, this would have fundamental implications for the process of diversification in microbes. **However, a re-examination of these data and results shows that the methodology used by NS systematically inflates the number of genes acquired at the root of each MAL, and incorrectly assumes bacterial origins for these genes. A re-analysis of their data with appropriate phylogenetic models accounting for the dynamics of gene gain and loss between lineages supports the continuous acquisition of genes over long periods in the evolution of Archaea.** ,