Literature DB >> 19571242

The practice of classification and the theory of evolution, and what the demise of Charles Darwin's tree of life hypothesis means for both of them.

W Ford Doolittle1.   

Abstract

Debates over the status of the tree of life (TOL) often proceed without agreement as to what it is supposed to be: a hierarchical classification scheme, a tracing of genomic and organismal history or a hypothesis about evolutionary processes and the patterns they can generate. I will argue that for Darwin it was a hypothesis, which lateral gene transfer in prokaryotes now shows to be false. I will propose a more general and relaxed evolutionary theory and point out why anti-evolutionists should take no comfort from disproof of the TOL hypothesis.

Mesh:

Year:  2009        PMID: 19571242      PMCID: PMC2873000          DOI: 10.1098/rstb.2009.0032

Source DB:  PubMed          Journal:  Philos Trans R Soc Lond B Biol Sci        ISSN: 0962-8436            Impact factor:   6.237


  26 in total

1.  Charles Darwin's views of classification in theory and practice.

Authors:  K Padian
Journal:  Syst Biol       Date:  1999-06       Impact factor: 15.683

2.  Highways of gene sharing in prokaryotes.

Authors:  Robert G Beiko; Timothy J Harlow; Mark A Ragan
Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-21       Impact factor: 11.205

3.  Time for a change.

Authors:  Norman R Pace
Journal:  Nature       Date:  2006-05-18       Impact factor: 49.962

4.  Pattern pluralism and the Tree of Life hypothesis.

Authors:  W Ford Doolittle; Eric Bapteste
Journal:  Proc Natl Acad Sci U S A       Date:  2007-01-29       Impact factor: 11.205

5.  Toward automatic reconstruction of a highly resolved tree of life.

Authors:  Francesca D Ciccarelli; Tobias Doerks; Christian von Mering; Christopher J Creevey; Berend Snel; Peer Bork
Journal:  Science       Date:  2006-03-03       Impact factor: 47.728

6.  Estimation of phylogenetic inconsistencies in the three domains of life.

Authors:  Victor Soria-Carrasco; Jose Castresana
Journal:  Mol Biol Evol       Date:  2008-08-12       Impact factor: 16.240

7.  Dealing with incongruence in phylogenomic analyses.

Authors:  Nicolas Galtier; Vincent Daubin
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2008-12-27       Impact factor: 6.237

8.  The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates.

Authors:  David A Rasko; M J Rosovitz; Garry S A Myers; Emmanuel F Mongodin; W Florian Fricke; Pawel Gajer; Jonathan Crabtree; Mohammed Sebaihia; Nicholas R Thomson; Roy Chaudhuri; Ian R Henderson; Vanessa Sperandio; Jacques Ravel
Journal:  J Bacteriol       Date:  2008-08-01       Impact factor: 3.490

Review 9.  Biology and taxonomy of Bacillus cereus, Bacillus anthracis, and Bacillus thuringiensis.

Authors:  G T Vilas-Bôas; A P S Peruca; O M N Arantes
Journal:  Can J Microbiol       Date:  2007-06       Impact factor: 2.419

10.  The role of laterally transferred genes in adaptive evolution.

Authors:  Pradeep Reddy Marri; Weilong Hao; G Brian Golding
Journal:  BMC Evol Biol       Date:  2007-02-08       Impact factor: 3.260

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  22 in total

1.  A Bayesian phylogenetic approach to estimating the stability of linguistic features and the genetic biasing of tone.

Authors:  Dan Dediu
Journal:  Proc Biol Sci       Date:  2010-09-01       Impact factor: 5.349

2.  A formal test of the theory of universal common ancestry.

Authors:  Douglas L Theobald
Journal:  Nature       Date:  2010-05-13       Impact factor: 49.962

Review 3.  The ecological coherence of high bacterial taxonomic ranks.

Authors:  Laurent Philippot; Siv G E Andersson; Tom J Battin; James I Prosser; Joshua P Schimel; William B Whitman; Sara Hallin
Journal:  Nat Rev Microbiol       Date:  2010-07       Impact factor: 60.633

Review 4.  Lateral genetic transfer: open issues.

Authors:  Mark A Ragan; Robert G Beiko
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2009-08-12       Impact factor: 6.237

5.  The Origin at 150: is a new evolutionary synthesis in sight?

Authors:  Eugene V Koonin
Journal:  Trends Genet       Date:  2009-10-14       Impact factor: 11.639

6.  Computational methods for Gene Orthology inference.

Authors:  David M Kristensen; Yuri I Wolf; Arcady R Mushegian; Eugene V Koonin
Journal:  Brief Bioinform       Date:  2011-06-19       Impact factor: 11.622

7.  www.aquaticmicrobial.net.

Authors:  Hans-Peter Grossart; Kam W Tang
Journal:  Commun Integr Biol       Date:  2010-11-01

8.  From the scala naturae to the symbiogenetic and dynamic tree of life.

Authors:  Ulrich Kutschera
Journal:  Biol Direct       Date:  2011-06-30       Impact factor: 4.540

Review 9.  Trees and networks before and after Darwin.

Authors:  Mark A Ragan
Journal:  Biol Direct       Date:  2009-11-16       Impact factor: 4.540

10.  The tree and net components of prokaryote evolution.

Authors:  Pere Puigbò; Yuri I Wolf; Eugene V Koonin
Journal:  Genome Biol Evol       Date:  2010-10-01       Impact factor: 3.416

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