Genome networks root the tree of life between prokaryotic domains.

Genome Biology and Evolution
Tal DaganW Martin

Abstract

Eukaryotes arose from prokaryotes, hence the root in the tree of life resides among the prokaryotic domains. The position of the root is still debated, although pinpointing it would aid our understanding of the early evolution of life. Because prokaryote evolution was long viewed as a tree-like process of lineage bifurcations, efforts to identify the most ancient microbial lineage split have traditionally focused on positioning a root on a phylogenetic tree constructed from one or several genes. Such studies have delivered widely conflicting results on the position of the root, this being mainly due to methodological problems inherent to deep gene phylogeny and the workings of lateral gene transfer among prokaryotes over evolutionary time. Here, we report the position of the root determined with whole genome data using network-based procedures that take into account both gene presence or absence and the level of sequence similarity among all individual gene families that are shared across genomes. On the basis of 562,321 protein-coding gene families distributed across 191 genomes, we find that the deepest divide in the prokaryotic world is interdomain, that is, separating the archaebacteria from the eubacteria. This result reso...Continue Reading

References

Jan 1, 1990·Annual Review of Biochemistry·A A DiMarcoR S Wolfe
Sep 1, 1989·Proceedings of the National Academy of Sciences of the United States of America·J P GogartenT Oshima
Dec 1, 1989·Proceedings of the National Academy of Sciences of the United States of America·N IwabeT Miyata
Mar 28, 1995·Proceedings of the National Academy of Sciences of the United States of America·J R Brown, W F Doolittle
Jun 14, 1996·Cell·P Forterre
Jul 1, 1996·Microbial Drug Resistance : MDR : Mechanisms, Epidemiology, and Disease·H H Martin, H König
Oct 24, 1997·Science·R L TatusovD J Lipman
Jan 23, 1999·Nature Genetics·B SnelM A Huynen
Jun 26, 1999·Science·W F Doolittle
Mar 4, 2000·Proceedings of the National Academy of Sciences of the United States of America·J P ChongB Stillman
Mar 15, 2000·Proceedings of the National Academy of Sciences of the United States of America·D E GrahamC R Woese
Jun 23, 2000·Nature·E Nisbet
Jul 12, 2000·Molecular Biology and Evolution·A D Yoder, Z Yang
Oct 4, 2000·Proceedings of the National Academy of Sciences of the United States of America·W V NgS DasSarma
Apr 3, 2001·Current Opinion in Microbiology·S D Bell, S P Jackson
Mar 28, 2002·Nucleic Acids Research·A J EnrightC A Ouzounis
May 29, 2002·Molecular Biology and Evolution·Eric Bapteste, Hervé Philippe
Jul 10, 2002·Progress in Nucleic Acid Research and Molecular Biology·Uwe Deppenmeier
Feb 22, 2003·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·William Martin, Michael J Russell
Jun 24, 2003·Genome Research·Harukata MikiUNKNOWN GSL Members
Aug 7, 2003·Genome Research·Didier RaoultJean-Michel Claverie
Nov 7, 2003·Applied and Environmental Microbiology·Volker Müller
Dec 9, 2003·Molecular Biology and Evolution·David Bryant, Vincent Moulton
Aug 25, 2004·Proceedings of the National Academy of Sciences of the United States of America·N H SleepD K Bird
Sep 10, 2004·Nature·Maria C Rivera, James A Lake
Sep 18, 2004·Journal of Bacteriology·Pavel S NovichkovEugene V Koonin
Oct 14, 2005·Molecular Biology and Evolution·Daniel H Huson, David Bryant
Oct 15, 2005·Trends in Genetics : TIG·Eugene V Koonin, William Martin
Jan 4, 2006·Protoplasma·Olga ZhaxybayevaJ Peter Gogarten
Jan 5, 2006·Canadian Journal of Microbiology·Harald ClausHelmut König
Mar 24, 2006·Nature·Don E Canfield
Mar 31, 2006·Nature·T Martin Embley, William Martin
Jun 7, 2006·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Martin BrasierDavid Wacey
Jun 7, 2006·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Thomas Cavalier-Smith
Jun 7, 2006·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·A H KnollP Cohen
Jun 28, 2006·Molecular Biology and Evolution·Ryan G SkophammerJames A Lake
Jul 13, 2006·Biology Direct·Thomas Cavalier-Smith
Sep 30, 2006·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Karl O Stetter

❮ Previous
Next ❯

Citations

Dec 1, 1988·Archives of Gerontology and Geriatrics·E J MenzelC Steffen
Apr 12, 2013·Proceedings of the National Academy of Sciences of the United States of America·David Alvarez-PonceJames O McInerney
Nov 28, 2013·Genome Biology and Evolution·Robert J M EveleighRobert G Beiko
Dec 2, 2011·Molecular Biology and Evolution·Manu TamminenMarco Fondi
Jun 12, 2013·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Filipa L SousaWilliam F Martin
Jun 13, 2012·Microbiology and Molecular Biology Reviews : MMBR·Miklós MüllerWilliam F Martin
Jul 1, 2011·Biology Direct·Robert G Beiko
Jul 1, 2011·Biology Direct·William F Martin
Sep 23, 2011·Biology Direct·David WilliamsJ Peter Gogarten
Aug 15, 2014·PLoS Biology·Víctor SojoNick Lane
Feb 18, 2014·Genome Biology and Evolution·Tom A Williams, T Martin Embley
Apr 4, 2014·Systematic Biology·Christopher WhiddenRobert G Beiko
Aug 9, 2011·Trends in Microbiology·Tal Dagan
Dec 31, 2014·BMC Evolutionary Biology·Thorsten ThiergartWilliam F Martin
Nov 28, 2014·Journal of Molecular Evolution·Barry HerschyNick Lane
Aug 19, 2014·Journal of Molecular Evolution·Kyung Mo KimGustavo Caetano-Anollés
Jul 28, 2015·Canadian Journal of Microbiology·Stephen M J PolloCamilla L Nesbø
Sep 2, 2015·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Richard GouyHervé Philippe
Sep 2, 2015·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Tom A WilliamsT Martin Embley
Sep 2, 2015·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Tom A Williams, T Martin Embley
Dec 19, 2013·Archaea : an International Microbiological Journal·Anja SpangThijs J G Ettema
Jul 6, 2014·Archaea : an International Microbiological Journal·Gustavo Caetano-AnollésKyung Mo Kim
Dec 2, 2014·Progress in Lipid Research·Thomas HornDagmar Heydeck
Jul 6, 2016·Scientific Data·Mohamed F HaroonUlrich Stingl
Apr 22, 2011·Annals of Botany·John A Bryant, Stephen J Aves
Dec 18, 2013·Nature·Tom A WilliamsT Martin Embley
Feb 13, 2019·Genome Biology and Evolution·Gareth A ColemanTom A Williams
May 13, 2014·Nature Reviews. Microbiology·James O McInerneyDavide Pisani
Oct 24, 2019·Interface Focus·Rafaela VasiliadouNick Lane
Oct 27, 2018·Evolutionary Bioinformatics Online·Gustavo Caetano-AnollésDerek Caetano-Anollés
Dec 15, 2015·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Hinrich ArnoldtMarc Timme
May 24, 2017·Proceedings of the National Academy of Sciences of the United States of America·Tom A WilliamsT Martin Embley
May 16, 2017·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Nick Lane
Dec 14, 2018·Emerging Topics in Life Sciences·Siri KellnerTom A Williams
Nov 30, 2016·Molecular Phylogenetics and Evolution·Amanda A DickJ Peter Gogarten
Jul 30, 2021·Scientific Data·Neelam M NathaniChandrashekar Mootapally

❮ Previous
Next ❯

Software Mentioned

PAML
ProML
SplitsTree
CodeML
PHYLIP
ClustalW
NeighborNet

Related Concepts

Related Feeds

Archaeogenetics

Recent advances in genomic sequencing has led to the discovery of new strains of Archaea and shed light on their evolutionary history. Discover the latest research on Archaeogenetics here.