Reconstructing ancestral gene content by coevolution.

Genome Research
Tamir TullerEytan Ruppin

Abstract

Inferring the gene content of ancestral genomes is a fundamental challenge in molecular evolution. Due to the statistical nature of this problem, ancestral genomes inferred by the maximum likelihood (ML) or the maximum-parsimony (MP) methods are prone to considerable error rates. In general, these errors are difficult to abolish by using longer genomic sequences or by analyzing more taxa. This study describes a new approach for improving ancestral genome reconstruction, the ancestral coevolver (ACE), which utilizes coevolutionary information to improve the accuracy of such reconstructions over previous approaches. The principal idea is to reduce the potentially large solution space by choosing a single optimal (or near optimal) solution that is in accord with the coevolutionary relationships between protein families. Simulation experiments, both on artificial and real biological data, show that ACE yields a marked decrease in error rate compared with ML or MP. Applied to a large data set (95 organisms, 4873 protein families, and 10,000 coevolutionary relationships), some of the ancestral genomes reconstructed by ACE were remarkably different in their gene content from those reconstructed by ML or MP alone (more than 10% in some...Continue Reading

References

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
Apr 24, 1981·Science·H F Noller, C R Woese
Aug 29, 1997·Journal of Molecular Biology·F PazosA Valencia
Nov 21, 1997·Computer Applications in the Biosciences : CABIOS·Z Yang
Jun 17, 1998·Proceedings of the National Academy of Sciences of the United States of America·C Woese
Dec 23, 1999·Current Opinion in Genetics & Development·D Penny, A Poole
Jun 1, 2000·Molecular Biology and Evolution·T PupkoD Graur
Jun 24, 2000·Research in Microbiology·H MoriT Miki
Oct 6, 2000·Molecular Biology and Evolution·B ChorD Penny
Oct 2, 2002·Nature Biotechnology·Gary D Bader, Christopher W V Hogue
Sep 13, 2003·BMC Bioinformatics·Roman L TatusovDarren A Natale
Jan 24, 2004·The EMBO Journal·Justyna SerekAndreas Kuhn
Mar 24, 2004·Nature Reviews. Microbiology·Eugene V Koonin
Jun 24, 2004·Proceedings of the National Academy of Sciences of the United States of America·Bastien BoussauSiv G E Andersson
Jul 2, 2004·Molecular Biology and Evolution·Neeraja M KrishnanDavid D Pollock
Nov 30, 2004·Science·Insuk LeeEdward M Marcotte
Dec 3, 2004·Genome Research·Mathieu BlanchetteDavid Haussler
Jan 24, 2006·Nature·Anne-Claude GavinGiulio Superti-Furga
Mar 24, 2006·Nature·Nevan J KroganJack F Greenblatt
Apr 12, 2006·Genome Research·Mohammad ArifuzzamanHirotada Mori
Apr 22, 2006·PLoS Computational Biology·Jakob Skou PedersenDavid Haussler
May 30, 2006·Proceedings of the National Academy of Sciences of the United States of America·Victor SpirinLeonid A Mirny
Jun 27, 2006·Trends in Genetics : TIG·Yiwen Chen, Nikolay V Dokholyan
Sep 20, 2006·Genome Research·Jian MaWebb Miller
Jan 11, 2007·Proceedings of the National Academy of Sciences of the United States of America·Tal Dagan, William Martin
Apr 26, 2007·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Isaac Elias, Tamir Tuller
Jul 20, 2007·Molecular Biology and Evolution·Chen-Hsiang YeangDavid Haussler
Aug 29, 2007·BMC Bioinformatics·Jing ZhaoYi-Xue Li
Nov 7, 2007·PLoS Computational Biology·Chen-Hsiang Yeang, David Haussler
Jan 18, 2008·Proceedings of the National Academy of Sciences of the United States of America·David JuanAlfonso Valencia
Feb 13, 2008·Proceedings of the National Academy of Sciences of the United States of America·Tuo Shi, Paul G Falkowski

❮ Previous
Next ❯

Citations

Sep 11, 2012·Bioinformatics·Sèverine BérardEric Tannier
Sep 11, 2012·Bioinformatics·Ofir CohenTal Pupko
Apr 19, 2011·Genome Biology and Evolution·Xiuwei ZhangTamir Tuller
Jan 12, 2012·Genome Biology and Evolution·Thomas D Cuypers, Paulien Hogeweg
Dec 22, 2011·BMC Bioinformatics·Hadas Birin, Tamir Tuller
Jun 14, 2013·PloS One·Nadezda A BykovaAndrey A Mironov
Jun 8, 2014·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Renana Sabi, Tamir Tuller
Sep 10, 2015·Biological Chemistry·Rainer Merkl, Reinhard Sterner
Apr 1, 2011·Molecular Systems Biology·Keren YizhakEytan Ruppin
Dec 1, 2010·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Tamir Tuller, Elchanan Mossel
Mar 13, 2012·American Journal of Human Genetics·John M Opitz
Mar 3, 2010·Biochimica Et Biophysica Acta·David B HicksTerry A Krulwich
Dec 24, 2014·Journal of Molecular Evolution·Massimo Di Giulio
May 8, 2016·Biochimica Et Biophysica Acta·Filipa L SousaWilliam F Martin
Sep 21, 2016·Proceedings of the National Academy of Sciences of the United States of America·Ramu AnandakrishnanDaniel M Zuckerman
Jul 5, 2017·Journal of Genetics·Massimo Di Giulio
Aug 19, 2017·Bulletin of Mathematical Biology·Gilles Didier
Aug 11, 2019·Origins of Life and Evolution of the Biosphere : the Journal of the International Society for the Study of the Origin of Life·Carlos MariscalH James Cleaves
Nov 13, 2019·Bio Systems·Athel Cornish-Bowden, María Luz Cárdenas
Feb 2, 2021·Frontiers in Microbiology·Hugh M B Harris, Colin Hill
May 7, 2021·Theory in Biosciences = Theorie in Den Biowissenschaften·Athel Cornish-Bowden, María Luz Cárdenas
Oct 12, 2016·Microbiology Spectrum·Steven E Massey

❮ Previous
Next ❯

Related Concepts

Related Feeds

ATP Synthases

ATP synthases are enzymes located in the inner mitochondrial membrane that catalyze the synthesis of ATP during cellular respiration. Discover the latest research on ATP synthases here.

Related Papers

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
Tamir TullerEytan Ruppin
Proceedings of the National Academy of Sciences of the United States of America
David JuanAlfonso Valencia
Proceedings of the National Academy of Sciences of the United States of America
Dennis P WallMarcus W Feldman
© 2022 Meta ULC. All rights reserved