Literature DB >> 19571241

Gene and genome trees conflict at many levels.

Leanne S Haggerty1, Fergal J Martin, David A Fitzpatrick, James O McInerney.   

Abstract

Horizontal gene transfer (HGT) plays a significant role in microbial evolution. It can accelerate the adaptation of an organism, it can generate new metabolic pathways and it can completely remodel an organism's genome. We examine 27 closely related genomes from the YESS group of gamma proteobacteria and a variety of four-taxon datasets from a diverse range of prokaryotes in order to explore the kinds of effects HGT has had on these organisms.

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Substances：

Year:  2009        PMID： 19571241      PMCID： PMC2873008          DOI： 10.1098/rstb.2009.0042

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


  55 in total

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2.  NEXUS: an extensible file format for systematic information.

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Journal:  Syst Biol       Date:  1997-12       Impact factor: 15.683

3.  Genome-scale approaches to resolving incongruence in molecular phylogenies.

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Review 4.  Gene transfer in bacteria: speciation without species?

Authors:  Jeffrey G Lawrence
Journal:  Theor Popul Biol       Date:  2002-06       Impact factor: 1.570

5.  Obtaining maximal concatenated phylogenetic data sets from large sequence databases.

Authors:  Michael J Sanderson; Amy C Driskell; Richard H Ree; Oliver Eulenstein; Sasha Langley
Journal:  Mol Biol Evol       Date:  2003-05-30       Impact factor: 16.240

6.  16S rRNA and amoA-based phylogeny of 12 novel betaproteobacterial ammonia-oxidizing isolates: extension of the dataset and proposal of a new lineage within the nitrosomonads.

Authors:  Ulrike Purkhold; Michael Wagner; Gabriele Timmermann; Andreas Pommerening-Röser; Hans-Peter Koops
Journal:  Int J Syst Evol Microbiol       Date:  2003-09       Impact factor: 2.747

7.  Recombination and mutation during long-term gastric colonization by Helicobacter pylori: estimates of clock rates, recombination size, and minimal age.

Authors:  D Falush; C Kraft; N S Taylor; P Correa; J G Fox; M Achtman; S Suerbaum
Journal:  Proc Natl Acad Sci U S A       Date:  2001-12-11       Impact factor: 11.205

8.  The evolutionary history of Shigella and enteroinvasive Escherichia coli revised.

Authors:  Patricia Escobar-Páramo; Catherine Giudicelli; Claude Parsot; Erick Denamur
Journal:  J Mol Evol       Date:  2003-08       Impact factor: 2.395

9.  50 million years of genomic stasis in endosymbiotic bacteria.

Authors:  Ivica Tamas; Lisa Klasson; Björn Canbäck; A Kristina Näslund; Ann-Sofie Eriksson; Jennifer J Wernegreen; Jonas P Sandström; Nancy A Moran; Siv G E Andersson
Journal:  Science       Date:  2002-06-28       Impact factor: 47.728

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  10 in total

1.  Genome-level homology and phylogeny of Shewanella (Gammaproteobacteria: lteromonadales: Shewanellaceae).

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Journal:  BMC Genomics       Date:  2011-05-12       Impact factor: 3.969

2.  Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs).

Authors:  Gregory E Sims; Sung-Hou Kim
Journal:  Proc Natl Acad Sci U S A       Date:  2011-05-02       Impact factor: 11.205

Review 3.  Trees and networks before and after Darwin.

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

4.  In silico evolutionary analysis of Helicobacter pylori outer membrane phospholipase A (OMPLA).

Authors:  Hilde S Vollan; Tone Tannaes; Yoshio Yamaoka; Geir Bukholm
Journal:  BMC Microbiol       Date:  2012-09-13       Impact factor: 3.605

5.  New approaches for unravelling reassortment pathways.

Authors:  Victoria Svinti; James A Cotton; James O McInerney
Journal:  BMC Evol Biol       Date:  2013-01-01       Impact factor: 3.260

6.  Universally distributed single-copy genes indicate a constant rate of horizontal transfer.

Authors:  Christopher J Creevey; Tobias Doerks; David A Fitzpatrick; Jeroen Raes; Peer Bork
Journal:  PLoS One       Date:  2011-08-05       Impact factor: 3.240

Review 7.  How stands the Tree of Life a century and a half after The Origin?

Authors:  Maureen A O'Malley; Eugene V Koonin
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8.  Phylogenomics Reveals Clear Cases of Misclassification and Genus-Wide Phylogenetic Markers for Acinetobacter.

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Journal:  Genome Biol Evol       Date:  2019-09-01       Impact factor: 3.416

Review 9.  Protein based molecular markers provide reliable means to understand prokaryotic phylogeny and support Darwinian mode of evolution.

Authors:  Vaibhav Bhandari; Hafiz S Naushad; Radhey S Gupta
Journal:  Front Cell Infect Microbiol       Date:  2012-07-26       Impact factor: 5.293

10.  A phylogenomic analysis of Escherichia coli / Shigella group: implications of genomic features associated with pathogenicity and ecological adaptation.

Authors:  Yan Zhang; Kui Lin
Journal:  BMC Evol Biol       Date:  2012-09-07       Impact factor: 3.260
  10 in total

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