Molecular Biology and Evolution

Letters:

George H. Perry, Brian C. Verrelli, and Anne C. Stone

Comparative Analyses Reveal a Complex History of Molecular Evolution for Human MYH16
MBE Advance Access published on October 6, 2004
Mol Biol Evol 2005 22: 379-382; doi:10.1093/molbev/msi004 [Abstract] [FREE Full Text] [PDF] [Correction to PDF]  [Request Permissions]  

Charles B. Foster

Selenoproteins and the Metabolic Features of the Archaeal Ancestor of Eukaryotes
MBE Advance Access published on October 13, 2004
Mol Biol Evol 2005 22: 383-386; doi:10.1093/molbev/msi007 [Abstract] [FREE Full Text] [PDF] [Supplementary Material] [Correction to PDF]  [Request Permissions]  

Jaime E. Blair and S. Blair Hedges

Molecular Clocks Do Not Support the Cambrian Explosion
MBE Advance Access published on November 10, 2004
Mol Biol Evol 2005 22: 387-390; doi:10.1093/molbev/msi039 [Abstract] [FREE Full Text] [PDF] [Correction to PDF]  [Request Permissions]  

De-Dong Xin, Jian-Fan Wen, De He, and Si-Qi Lu

Identification of a Giardia krr1 Homolog Gene and the Secondarily Anucleolate Condition of Giaridia lamblia
MBE Advance Access published on November 17, 2004
Mol Biol Evol 2005 22: 391-394; doi:10.1093/molbev/msi052 [Abstract] [FREE Full Text] [PDF] [Supplementary Material] [Correction to PDF]  [Request Permissions]  

Research Articles:

Peter J. Waddell

Measuring the Fit of Sequence Data to Phylogenetic Model: Allowing for Missing Data
MBE Advance Access published on October 6, 2004
Mol Biol Evol 2005 22: 395-401; doi:10.1093/molbev/msi002 [Abstract] [FREE Full Text] [PDF] [Correction to PDF]  [Request Permissions]  

Dmitry A. Filatov

Substitution Rates in a New Silene latifolia Sex-Linked Gene, SlssX/Y
MBE Advance Access published on October 6, 2004
Mol Biol Evol 2005 22: 402-408; doi:10.1093/molbev/msi003 [Abstract] [FREE Full Text] [PDF] [Correction to PDF]  [Request Permissions]  

Nobuko Arisue, Masami Hasegawa, and Tetsuo Hashimoto

Root of the Eukaryota Tree as Inferred from Combined Maximum Likelihood Analyses of Multiple Molecular Sequence Data
MBE Advance Access published on October 20, 2004
Mol Biol Evol 2005 22: 409-420; doi:10.1093/molbev/msi023 [Abstract] [FREE Full Text] [PDF] [Supplementary Material] [Correction to PDF]  [Request Permissions]  

José B. Pereira-Leal, Benjamin Audit, José M. Peregrin-Alvarez, and Christos A. Ouzounis

An Exponential Core in the Heart of the Yeast Protein Interaction Network
MBE Advance Access published on October 20, 2004
Mol Biol Evol 2005 22: 421-425; doi:10.1093/molbev/msi024 [Abstract] [FREE Full Text] [PDF] [Correction to PDF]  [Request Permissions]  

Shiao-Wei Huang, Robert Friedman, Ning Yu, Alex Yu, and Wen-Hsiung Li

How Strong Is the Mutagenicity of Recombination in Mammals?
MBE Advance Access published on October 20, 2004
Mol Biol Evol 2005 22: 426-431; doi:10.1093/molbev/msi025 [Abstract] [FREE Full Text] [PDF] [Supplementary Material] [Correction to PDF]  [Request Permissions]  

Anne Fischer, Yoav Gilad, Orna Man, and Svante Pääbo

Evolution of Bitter Taste Receptors in Humans and Apes
MBE Advance Access published on October 20, 2004
Mol Biol Evol 2005 22: 432-436; doi:10.1093/molbev/msi027 [Abstract] [FREE Full Text] [PDF] [Supplementary Material] [Correction to PDF]  [Request Permissions]  

D. A. McClellan, E. J. Palfreyman, M. J. Smith, J. L. Moss, R. G. Christensen, and J. K. Sailsbery

Physicochemical Evolution and Molecular Adaptation of the Cetacean and Artiodactyl Cytochrome b Proteins
MBE Advance Access published on October 27, 2004
Mol Biol Evol 2005 22: 437-455; doi:10.1093/molbev/msi028 [Abstract] [FREE Full Text] [PDF] [Correction to PDF]  [Request Permissions]  

Scott Williamson, Steven M. Perry, Carlos D. Bustamante, Maria E. Orive, Miles N. Stearns, and John K. Kelly

A Statistical Characterization of Consistent Patterns of Human Immunodeficiency Virus Evolution Within Infected Patients
MBE Advance Access published on October 27, 2004
Mol Biol Evol 2005 22: 456-468; doi:10.1093/molbev/msi029 [Abstract] [FREE Full Text] [PDF] [Correction to PDF]  [Request Permissions]  

Rong-Zong Liu, Qian Sun, Christine Thisse, Bernard Thisse, Jonathan M. Wright, and Eileen M. Denovan-Wright

The Cellular Retinol-Binding Protein Genes Are Duplicated and Differentially Transcribed in the Developing and Adult Zebrafish (Danio rerio)
MBE Advance Access published on October 27, 2004
Mol Biol Evol 2005 22: 469-477; doi:10.1093/molbev/msi030 [Abstract] [FREE Full Text] [PDF] [Correction to PDF]  [Request Permissions]  

Sergei L. Kosakovsky Pond and Simon D. W. Frost

A Genetic Algorithm Approach to Detecting Lineage-Specific Variation in Selection Pressure
MBE Advance Access published on October 27, 2004
Mol Biol Evol 2005 22: 478-485; doi:10.1093/molbev/msi031 [Abstract] [FREE Full Text] [PDF] [Correction to PDF]  [Request Permissions]  

Bret Larget, Donald L. Simon, Joseph B. Kadane, and Deborah Sweet

A Bayesian Analysis of Metazoan Mitochondrial Genome Arrangements
MBE Advance Access published on November 3, 2004
Mol Biol Evol 2005 22: 486-495; doi:10.1093/molbev/msi032 [Abstract] [FREE Full Text] [PDF] [Supplementary Material] [Correction to PDF]  [Request Permissions]  

Tal Dagan and Dan Graur

The Comparative Method Rules! Codon Volatility Cannot Detect Positive Darwinian Selection Using a Single Genome Sequence
MBE Advance Access published on November 3, 2004
Mol Biol Evol 2005 22: 496-500; doi:10.1093/molbev/msi033 [Abstract] [FREE Full Text] [PDF] [Supplementary Material] [Correction to PDF]  [Request Permissions]  

Ze Zhang, Z. W. Luo, Hirohisa Kishino, and Mike J. Kearsey

Divergence Pattern of Duplicate Genes in Protein-Protein Interactions Follows the Power Law
MBE Advance Access published on November 3, 2004
Mol Biol Evol 2005 22: 501-505; doi:10.1093/molbev/msi034 [Abstract] [FREE Full Text] [PDF] [Supplementary Material] [Correction to PDF]  [Request Permissions]  

Stephen I. Wright and Brandon S. Gaut

Molecular Population Genetics and the Search for Adaptive Evolution in Plants
MBE Advance Access published on November 3, 2004
Mol Biol Evol 2005 22: 506-519; doi:10.1093/molbev/msi035 [Abstract] [FREE Full Text] [PDF] [Supplementary Material] [Correction to PDF]  [Request Permissions]  

Joshua T. Herbeck, Patrick H. Degnan, and Jennifer J. Wernegreen

Nonhomogeneous Model of Sequence Evolution Indicates Independent Origins of Primary Endosymbionts Within the Enterobacteriales (-Proteobacteria)
MBE Advance Access published on November 3, 2004
Mol Biol Evol 2005 22: 520-532; doi:10.1093/molbev/msi036 [Abstract] [FREE Full Text] [PDF] [Supplementary Material] [Correction to PDF]  [Request Permissions]  

Silvia A. Mah, Willie J. Swanson, and Victor D. Vacquier

Positive Selection in the Carbohydrate Recognition Domains of Sea Urchin Sperm Receptor for Egg Jelly (suREJ) Proteins
MBE Advance Access published on November 3, 2004
Mol Biol Evol 2005 22: 533-541; doi:10.1093/molbev/msi037 [Abstract] [FREE Full Text] [PDF] [Correction to PDF]  [Request Permissions]  

Robert Friedman and Austin L. Hughes

Codon Volatility As an Indicator of Positive Selection: Data from Eukaryotic Genome Comparisons
MBE Advance Access published on November 3, 2004
Mol Biol Evol 2005 22: 542-546; doi:10.1093/molbev/msi038 [Abstract] [FREE Full Text] [PDF] [Correction to PDF]  [Request Permissions]  

A. Carbone, F. Képès, and A. Zinovyev

Codon Bias Signatures, Organization of Microorganisms in Codon Space, and Lifestyle
MBE Advance Access published on November 10, 2004
Mol Biol Evol 2005 22: 547-561; doi:10.1093/molbev/msi040 [Abstract] [FREE Full Text] [PDF] [Supplementary Material] [Correction to PDF]  [Request Permissions]  

K. A. Jolley, D. J. Wilson, P. Kriz, G. Mcvean, and M. C. J. Maiden

The Influence of Mutation, Recombination, Population History, and Selection on Patterns of Genetic Diversity in Neisseria meningitidis
MBE Advance Access published on November 10, 2004
Mol Biol Evol 2005 22: 562-569; doi:10.1093/molbev/msi041 [Abstract] [FREE Full Text] [PDF] [Correction to PDF]  [Request Permissions]  

Todd C. LaJeunesse

"Species" Radiations of Symbiotic Dinoflagellates in the Atlantic and Indo-Pacific Since the Miocene-Pliocene Transition
MBE Advance Access published on November 10, 2004
Mol Biol Evol 2005 22: 570-581; doi:10.1093/molbev/msi042 [Abstract] [FREE Full Text] [PDF] [Supplementary Material] [Correction to PDF]  [Request Permissions]  

Pascal Pineau, Michel Henry, Rodolphe Suspène, Agnès Marchio, Agnès Dettai, Régis Debruyne, Thierry Petit, Alexis Lécu, Pierre Moisson, Anne Dejean, Simon Wain-Hobson, and Jean-Pierre Vartanian

A Universal Primer Set for PCR Amplification of Nuclear Histone H4 Genes from All Animal Species
MBE Advance Access published on December 15, 2004
Mol Biol Evol 2005 22: 582-588; doi:10.1093/molbev/msi053 [Abstract] [FREE Full Text] [PDF] [Supplementary Material] [Correction to PDF]  [Request Permissions]  

Steven Robbens, Basheer Khadaroo, Alain Camasses, Evelyne Derelle, Conchita Ferraz, Dirk Inzé, Yves Van de Peer, and Hervé Moreau

Genome-Wide Analysis of Core Cell Cycle Genes in the Unicellular Green Alga Ostreococcus tauri
MBE Advance Access published on November 10, 2004
Mol Biol Evol 2005 22: 589-597; doi:10.1093/molbev/msi044 [Abstract] [FREE Full Text] [PDF] [Correction to PDF]  [Request Permissions]  

M. Mar Albà and Jose Castresana

Inverse Relationship Between Evolutionary Rate and Age of Mammalian Genes
MBE Advance Access published on November 10, 2004
Mol Biol Evol 2005 22: 598-606; doi:10.1093/molbev/msi045 [Abstract] [FREE Full Text] [PDF] [Supplementary Material] [Correction to PDF]  [Request Permissions]  

Stuart J. Macdonald and Anthony D. Long

Identifying Signatures of Selection at the Enhancer of split Neurogenic Gene Complex in Drosophila
MBE Advance Access published on November 10, 2004
Mol Biol Evol 2005 22: 607-619; doi:10.1093/molbev/msi046 [Abstract] [FREE Full Text] [PDF] [Correction to PDF]  [Request Permissions]  

Renfu Shao, Stephen C. Barker, Harumi Mitani, Yayoi Aoki, and Masahito Fukunaga

Evolution of Duplicate Control Regions in the Mitochondrial Genomes of Metazoa: A Case Study with Australasian Ixodes Ticks
MBE Advance Access published on November 10, 2004
Mol Biol Evol 2005 22: 620-629; doi:10.1093/molbev/msi047 [Abstract] [FREE Full Text] [PDF] [Supplementary Material] [Correction to PDF]  [Request Permissions]  

Markus Porto, H. Eduardo Roman, Michele Vendruscolo, and Ugo Bastolla

Prediction of Site-Specific Amino Acid Distributions and Limits of Divergent Evolutionary Changes in Protein Sequences
MBE Advance Access published on November 10, 2004
Mol Biol Evol 2005 22: 630-638; doi:10.1093/molbev/msi048 [Abstract] [FREE Full Text] [PDF] [Correction to PDF]  [Request Permissions]  

Haydar Karaoglu, Crystal Man Ying Lee, and Wieland Meyer

Survey of Simple Sequence Repeats in Completed Fungal Genomes
MBE Advance Access published on November 24, 2004
Mol Biol Evol 2005 22: 639-649; doi:10.1093/molbev/msi057 [Abstract] [FREE Full Text] [PDF] [Correction to PDF]  [Request Permissions]  

Karl J. Fryxell and Won-Jong Moon

CpG Mutation Rates in the Human Genome Are Highly Dependent on Local GC Content
MBE Advance Access published on November 10, 2004
Mol Biol Evol 2005 22: 650-658; doi:10.1093/molbev/msi043 [Abstract] [FREE Full Text] [PDF] [Correction to PDF]  [Request Permissions]  

Zhenyu Liu, Jorunn I. B. Bos, Miles Armstrong, Stephen C. Whisson, Luis da Cunha, Trudy Torto-Alalibo, Joe Win, Anna O. Avrova, Frank Wright, Paul R. J. Birch, and Sophien Kamoun

Patterns of Diversifying Selection in the Phytotoxin-like scr74 Gene Family of Phytophthora infestans
MBE Advance Access published on November 17, 2004
Mol Biol Evol 2005 22: 659-672; doi:10.1093/molbev/msi049 [Abstract] [FREE Full Text] [PDF] [Supplementary Material] [Correction to PDF]  [Request Permissions]  

Masaki Kajikawa, Kenji Ichiyanagi, Nozomu Tanaka, and Norihiro Okada

Isolation and Characterization of Active LINE and SINEs from the Eel
MBE Advance Access published on November 17, 2004
Mol Biol Evol 2005 22: 673-682; doi:10.1093/molbev/msi054 [Abstract] [FREE Full Text] [PDF] [Correction to PDF]  [Request Permissions]  

Daniel M. Stoebel

Lack of Evidence for Horizontal Transfer of the lac Operon into Escherichia coli
MBE Advance Access published on November 24, 2004
Mol Biol Evol 2005 22: 683-690; doi:10.1093/molbev/msi056 [Abstract] [FREE Full Text] [PDF] [Supplementary Material] [Correction to PDF]  [Request Permissions]  

Zaid Abdo, Vladimir N. Minin, Paul Joyce, and Jack Sullivan

Accounting for Uncertainty in the Tree Topology Has Little Effect on the Decision-Theoretic Approach to Model Selection in Phylogeny Estimation
MBE Advance Access published on November 17, 2004
Mol Biol Evol 2005 22: 691-703; doi:10.1093/molbev/msi050 [Abstract] [FREE Full Text] [PDF] [Correction to PDF]  [Request Permissions]  

Yasuhiro Kitazoe, Hirohisa Kishino, Takahisa Okabayashi, Teruaki Watabe, Noriaki Nakajima, Yoshiyasu Okuhara, and Yukio Kurihara

Multidimensional Vector Space Representation for Convergent Evolution and Molecular Phylogeny
MBE Advance Access published on November 17, 2004
Mol Biol Evol 2005 22: 704-715; doi:10.1093/molbev/msi051 [Abstract] [FREE Full Text] [PDF] [Correction to PDF]  [Request Permissions]  

Maria Pilar Bayona-Bafaluy, Stefan Müller, and Carlos T. Moraes

Fast Adaptive Coevolution of Nuclear and Mitochondrial Subunits of ATP Synthetase in Orangutan
MBE Advance Access published on December 1, 2004
Mol Biol Evol 2005 22: 716-724; doi:10.1093/molbev/msi059 [Abstract] [FREE Full Text] [PDF] [Correction to PDF]  [Request Permissions]  

Bo Wen, Hui Li, Song Gao, Xianyun Mao, Yang Gao, Feng Li, Feng Zhang, Yungang He, Yongli Dong, Youjun Zhang, Wenju Huang, Jianzhong Jin, Chunjie Xiao, Daru Lu, Ranajit Chakraborty, Bing Su, Ranjan Deka, and Li Jin

Genetic Structure of Hmong-Mien Speaking Populations in East Asia as Revealed by mtDNA Lineages
MBE Advance Access published on November 17, 2004
Mol Biol Evol 2005 22: 725-734; doi:10.1093/molbev/msi055 [Abstract] [FREE Full Text] [PDF] [Supplementary Material] [Correction to PDF]  [Request Permissions]  

Koen J. F. Verhoeven and Katy L. Simonsen

Genomic Haplotype Blocks May Not Accurately Reflect Spatial Variation in Historic Recombination Intensity
MBE Advance Access published on November 24, 2004
Mol Biol Evol 2005 22: 735-740; doi:10.1093/molbev/msi058 [Abstract] [FREE Full Text] [PDF] [Correction to PDF]  [Request Permissions]  

H. Quesneville, D. Nouaud, and D. Anxolabehere

Recurrent Recruitment of the THAP DNA-Binding Domain and Molecular Domestication of the P-Transposable Element
MBE Advance Access published on December 1, 2004
Mol Biol Evol 2005 22: 741-746; doi:10.1093/molbev/msi064 [Abstract] [FREE Full Text] [PDF] [Supplementary Material] [Correction to PDF]  [Request Permissions]  

Nathalie Mugnier, Christian Biémont, and Cristina Vieira

New Regulatory Regions of Drosophila 412 Retrotransposable Element Generated by Recombination
MBE Advance Access published on December 1, 2004
Mol Biol Evol 2005 22: 747-757; doi:10.1093/molbev/msi060 [Abstract] [FREE Full Text] [PDF] [Supplementary Material] [Correction to PDF]  [Request Permissions]  

Colin Dale, Tait Jones, and Mauricio Pontes

Degenerative Evolution and Functional Diversification of Type-III Secretion Systems in the Insect Endosymbiont Sodalis glossinidius
MBE Advance Access published on December 1, 2004
Mol Biol Evol 2005 22: 758-766; doi:10.1093/molbev/msi061 [Abstract] [FREE Full Text] [PDF] [Correction to PDF]  [Request Permissions]  

Gregory A. C. Singer, Andrew T. Lloyd, Lukasz B. Huminiecki, and Kenneth H. Wolfe

Clusters of Co-expressed Genes in Mammalian Genomes Are Conserved by Natural Selection
MBE Advance Access published on December 1, 2004
Mol Biol Evol 2005 22: 767-775; doi:10.1093/molbev/msi062 [Abstract] [FREE Full Text] [PDF] [Supplementary Material] [Correction to PDF]  [Request Permissions]  

Daniel N. Lerman and Martin E. Feder

Naturally Occurring Transposable Elements Disrupt hsp70 Promoter Function in Drosophila melanogaster
MBE Advance Access published on December 1, 2004
Mol Biol Evol 2005 22: 776-783; doi:10.1093/molbev/msi063 [Abstract] [FREE Full Text] [PDF] [Supplementary Material] [Correction to PDF]  [Request Permissions]  

C. Blouin, D. Butt, and A. J. Roger

Impact of Taxon Sampling on the Estimation of Rates of Evolution at Sites
MBE Advance Access published on December 8, 2004
Mol Biol Evol 2005 22: 784-791; doi:10.1093/molbev/msi065 [Abstract] [FREE Full Text] [PDF] [Correction to PDF]  [Request Permissions]  

Barry G. Hall

Comparison of the Accuracies of Several Phylogenetic Methods Using Protein and DNA Sequences
MBE Advance Access published on December 8, 2004
Mol Biol Evol 2005 22: 792-802; doi:10.1093/molbev/msi066 [Abstract] [FREE Full Text] [PDF] [Correction to PDF]  [Request Permissions]  

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