BMC Evolutionary Biology

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Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified

Thomas M Keane*, Christopher J Creevey, Melissa M Pentony, Thomas J Naughton and James O Mclnerney

BMC Evolutionary Biology 2006, 6:29 doi:10.1186/1471-2148-6-29

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Analyses of the oligopeptide transporter gene family in poplar and grape

Jun Cao, Jinling Huang, Yongping Yang, Xiangyang Hu BMC Genomics 2011, 12:465 (26 September 2011)

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Molecular evolution of cyclin proteins in animals and fungi

Konstantin V Gunbin, Valentin V Suslov, Igor I Turnaev, Dmitry A Afonnikov, Nikolay A Kolchanov BMC Evolutionary Biology 2011, 11:224 (28 July 2011)

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Evidence for acquisition of virulence effectors in pathogenic chytrids

Guiling Sun, Zefeng Yang, Tiffany Kosch, Kyle Summers, Jinling Huang BMC Evolutionary Biology 2011, 11:195 (8 July 2011)

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Host shifts and molecular evolution of H7 avian influenza virus hemagglutinin

Camille Lebarbenchon, David E Stallknecht Virology Journal 2011, 8:328 (28 June 2011)

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The two tryptophans of β2-microglobulin have distinct roles in function and folding and might represent two independent responses to evolutionary pressure

Sara Raimondi, Nicola Barbarini, Palma Mangione, Gennaro Esposito, Stefano Ricagno, Martino Bolognesi, Irene Zorzoli, Loredana Marchese, Cristina Soria, Riccardo Bellazzi, Maria Monti, Monica Stoppini, Mario Stefanelli, Paolo Magni, Vittorio Bellotti BMC Evolutionary Biology 2011, 11:159 (10 June 2011)

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Analysis of Canis mitochondrial DNA demonstrates high concordance between the control region and ATPase genes

Linda Y Rutledge, Brent R Patterson, Bradley N White BMC Evolutionary Biology 2010, 10:215 (16 July 2010)

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Positive selection neighboring functionally essential sites and disease-implicated regions of mammalian reproductive proteins

Claire C Morgan, Noeleen B Loughran, Thomas A Walsh, Alan J Harrison, Mary J O'Connell BMC Evolutionary Biology 2010, 10:39 (11 February 2010)

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Phylogenomics reveals subfamilies of fungal nonribosomal peptide synthetases and their evolutionary relationships

Kathryn E Bushley, B Gillian Turgeon BMC Evolutionary Biology 2010, 10:26 (26 January 2010)

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Evidence of recombination in Hepatitis C Virus populations infecting a hemophiliac patient

Pilar Moreno, Macarena Alvarez, Lilia López, Gonzalo Moratorio, Didier Casane, Matías Castells, Silvia Castro, Juan Cristina, Rodney Colina Virology Journal 2009, 6:203 (18 November 2009)

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Rooting human parechovirus evolution in time

Nuno R Faria, Michel de Vries, Formijn J van Hemert, Kimberley Benschop, Lia van der Hoek BMC Evolutionary Biology 2009, 9:164 (15 July 2009)

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Divergence in function and expression of the NOD26-like intrinsic proteins in plants

Qingpo Liu, Huasen Wang, Zhonghua Zhang, Jiasheng Wu, Ying Feng, Zhujun Zhu BMC Genomics 2009, 10:313 (15 July 2009)

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Search for a 'Tree of Life' in the thicket of the phylogenetic forest

Pere Puigbò, Yuri I Wolf, Eugene V Koonin Journal of Biology 2009, 8:59 (13 July 2009)

Koonin and colleagues, comparing a forest of 7000 phylogenetic trees, discern vertical inheritance even at the earliest stages of prokaryotic evolution, despite horizontal gene transfer, but the branching order of the earliest radiations may never be resolved.

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Carbon and arsenic metabolism in Thiomonas strains: differences revealed diverse adaptation processes

Christopher G Bryan, Marie Marchal, Fabienne Battaglia-Brunet, Valérie Kugler, Christelle Lemaitre-Guillier, Didier Lièvremont, Philippe N Bertin, Florence Arsène-Ploetze BMC Microbiology 2009, 9:127 (23 June 2009)

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Evolutionary history of the iroquois/Irx genes in metazoans

Pierre Kerner, Aissam Ikmi, Dario Coen, Michel Vervoort BMC Evolutionary Biology 2009, 9:74 (15 April 2009)

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Ancient diversification of eukaryotic MCM DNA replication proteins

Yuan Liu, Thomas A Richards, Stephen J Aves BMC Evolutionary Biology 2009, 9:60 (17 March 2009)

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Diversity and transcription of proteases involved in the maturation of hydrogenases in Nostoc punctiforme ATCC 29133 and Nostoc sp. strain PCC 7120

Ellenor Devine, Marie Holmqvist, Karin Stensjö, Peter Lindblad BMC Microbiology 2009, 9:53 (11 March 2009)

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Recurring cluster and operon assembly for Phenylacetate degradation genes

Fergal J Martin, James O McInerney BMC Evolutionary Biology 2009, 9:36 (10 February 2009)

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Suprafamilial relationships among Rodentia and the phylogenetic effect of removing fast-evolving nucleotides in mitochondrial, exon and intron fragments

Claudine Montgelard, Ellen Forty, Véronique Arnal, Conrad A Matthee BMC Evolutionary Biology 2008, 8:321 (26 November 2008)

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A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans

Mircea Podar, Iain Anderson, Kira S Makarova, James G Elkins, Natalia Ivanova, Mark A Wall, Athanasios Lykidis, Kostantinos Mavromatis, Hui Sun, Matthew E Hudson, Wenqiong Chen, Cosmin Deciu, Don Hutchison, Jonathan R Eads, Abraham Anderson, Fillipe Fernandes, Ernest Szeto, Alla Lapidus, Nikos C Kyrpides, Milton H Saier, Paul M Richardson, Reinhard Rachel, Harald Huber, Jonathan A Eisen, Eugene V Koonin, Martin Keller, Karl O Stetter Genome Biology 2008, 9:R158 (10 November 2008)

Sequencing of the complete genome of Ignicoccus hospitalis gives insight into its association with another species of Archaea, Nanoarchaeum equitans.

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Evolutionary history of the UCP gene family: gene duplication and selection

Joseph Hughes, Francois Criscuolo BMC Evolutionary Biology 2008, 8:306 (3 November 2008)

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Factors affecting the concordance between orthologous gene trees and species tree in bacteria

Santiago Castillo-Ramírez, Víctor González BMC Evolutionary Biology 2008, 8:300 (30 October 2008)

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The promastigote surface antigen gene family of the Leishmania parasite: differential evolution by positive selection and recombination

Alain Devault, Anne-Laure Bañuls BMC Evolutionary Biology 2008, 8:292 (24 October 2008)

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Topology of evolving, mutagenized viral populations: quasispecies expansion, compression, and operation of negative selection

Samuel Ojosnegros, Rubén Agudo, Macarena Sierra, Carlos Briones, Saleta Sierra, Claudia González- López, Esteban Domingo, Juan Cristina BMC Evolutionary Biology 2008, 8:207 (17 July 2008)

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Outlining eicosanoid biosynthesis in the crustacean Daphnia

Lars-Henrik Heckmann, Richard M Sibly, Martijn JTN Timmermans, Amanda Callaghan Frontiers in Zoology 2008, 5:11 (14 July 2008)

This article is part of a collection on Daphnia: the companion...

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Genetic tests of ancient asexuality in Root Knot Nematodes reveal recent hybrid origins

David H Lunt BMC Evolutionary Biology 2008, 8:194 (7 July 2008)

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Evidence of recent interkingdom horizontal gene transfer between bacteria and Candida parapsilosis

David A Fitzpatrick, Mary E Logue, Geraldine Butler BMC Evolutionary Biology 2008, 8:181 (24 June 2008)

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Comparative chloroplast genomics and phylogenetics of Fagopyrum esculentum ssp. ancestrale – A wild ancestor of cultivated buckwheat

Maria D Logacheva, Tahir H Samigullin, Amit Dhingra, Aleksey A Penin BMC Plant Biology 2008, 8:59 (20 May 2008)

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Unraveling the evolutionary history of the phosphoryl-transfer chain of the phosphoenolpyruvate:phosphotransferase system through phylogenetic analyses and genome context

Iñaki Comas, Fernando González-Candelas, Manuel Zúñiga BMC Evolutionary Biology 2008, 8:147 (16 May 2008)

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Revealing pancrustacean relationships: Phylogenetic analysis of ribosomal protein genes places Collembola (springtails) in a monophyletic Hexapoda and reinforces the discrepancy between mitochondrial and nuclear DNA markers

MJTN Timmermans, D Roelofs, J Mariën, NM van Straalen BMC Evolutionary Biology 2008, 8:83 (12 March 2008)

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Climate-driven diversification in two widespread Galerida larks

Alban Guillaumet, Pierre-André Crochet, Jean-Marc Pons BMC Evolutionary Biology 2008, 8:32 (29 January 2008)

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Global isolation by distance despite strong regional phylogeography in a small metazoan

Scott Mills, David H Lunt, Africa Gómez BMC Evolutionary Biology 2007, 7:225 (14 November 2007)

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Comparative genomics of ParaHox clusters of teleost fishes: gene cluster breakup and the retention of gene sets following whole genome duplications

Nicol Siegel, Simone Hoegg, Walter Salzburger, Ingo Braasch, Axel Meyer BMC Genomics 2007, 8:312 (6 September 2007)

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Phylogenetic analysis of mitochondrial protein coding genes confirms the reciprocal paraphyly of Hexapoda and Crustacea

Antonio Carapelli, Pietro Liò, Francesco Nardi, Elizabeth van der Wath, Francesco Frati BMC Evolutionary Biology 2007, 7(Suppl 2):S8 (16 August 2007)

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Horizontal transfer of a eukaryotic plastid-targeted protein gene to cyanobacteria

Matthew B Rogers, Nicola J Patron, Patrick J Keeling BMC Biology 2007, 5:26 (20 June 2007)

Marine cyanobacteria have acquired a gene for a key glycolytic and Calvin cycle enzyme from red algae, which inserted directly next to the prokaryotic homolog in a rare example of eukaryote-to-prokaryote horizontal gene transfer.

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The human phylome

Jaime Huerta-Cepas, Hernán Dopazo, Joaquín Dopazo, Toni Gabaldón Genome Biology 2007, 8:R109 (13 June 2007)

The human phylome, which includes evolutionary relationships of all human proteins and their homologs among thirty-nine fully sequenced eukaryotes, is reconstructed.

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A canonical FtsZ protein in Verrucomicrobium spinosum, a member of the Bacterial phylum Verrucomicrobia that also includes tubulin-producing Prosthecobacter species

Benjamin Yee, Feras F Lafi, Brian Oakley, James T Staley, John A Fuerst BMC Evolutionary Biology 2007, 7:37 (12 March 2007)

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Origin and diversification of the basic helix-loop-helix gene family in metazoans: insights from comparative genomics

Elena Simionato, Valérie Ledent, Gemma Richards, Morgane Thomas-Chollier, Pierre Kerner, David Coornaert, Bernard M Degnan, Michel Vervoort BMC Evolutionary Biology 2007, 7:33 (2 March 2007)

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A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis

David A Fitzpatrick, Mary E Logue, Jason E Stajich, Geraldine Butler BMC Evolutionary Biology 2006, 6:99 (22 November 2006)

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Evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes

Jan O Andersson, Robert P Hirt, Peter G Foster, Andrew J Roger BMC Evolutionary Biology 2006, 6:27 (21 March 2006)