Molecular Biology and Evolution

Letters:

Matthew W. Hahn and Andrew D. Kern

Comparative Genomics of Centrality and Essentiality in Three Eukaryotic Protein-Interaction Networks
MBE Advance Access published on December 22, 2004
Mol Biol Evol 2005 22: 803-806; doi:10.1093/molbev/msi072 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Paul M. Sharp

Gene "Volatility" Is Most Unlikely to Reveal Adaptation
MBE Advance Access published on December 22, 2004
Mol Biol Evol 2005 22: 807-809; doi:10.1093/molbev/msi073 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Naoyuki Iwabe, Yuichiro Hara, Yoshinori Kumazawa, Kaori Shibamoto, Yumi Saito, Takashi Miyata, and Kazutaka Katoh

Sister Group Relationship of Turtles to the Bird-Crocodilian Clade Revealed by Nuclear DNA–Coded Proteins
MBE Advance Access published on December 29, 2004
Mol Biol Evol 2005 22: 810-813; doi:10.1093/molbev/msi075 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Robert Belshaw, Aris Katzourakis, Jan Paces, Austin Burt, and Michael Tristem

High Copy Number in Human Endogenous Retrovirus Families is Associated with Copying Mechanisms in Addition to Reinfection
MBE Advance Access published on January 19, 2005
Mol Biol Evol 2005 22: 814-817; doi:10.1093/molbev/msi088 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Research Articles:

Bradley J. Wagstaff and David J. Begun

Comparative Genomics of Accessory Gland Protein Genes in Drosophila melanogaster and D. pseudoobscura
MBE Advance Access published on December 15, 2004
Mol Biol Evol 2005 22: 818-832; doi:10.1093/molbev/msi067 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Sabine E. Hammer, Sabine Strehl, and Sylvia Hagemann

Homologs of Drosophila P Transposons Were Mobile in Zebrafish but Have Been Domesticated in a Common Ancestor of Chicken and Human
MBE Advance Access published on December 22, 2004
Mol Biol Evol 2005 22: 833-844; doi:10.1093/molbev/msi068 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Kiyotaka Nagaki, Pavel Neumann, Dongfen Zhang, Shu Ouyang, C. Robin Buell, Zhukuan Cheng, and Jiming Jiang

Structure, Divergence, and Distribution of the CRR Centromeric Retrotransposon Family in Rice
MBE Advance Access published on December 22, 2004
Mol Biol Evol 2005 22: 845-855; doi:10.1093/molbev/msi069 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Emmanuelle Fabre, Héloïse Muller, Pierre Therizols, Ingrid Lafontaine, Bernard Dujon, and Cécile Fairhead

Comparative Genomics in Hemiascomycete Yeasts: Evolution of Sex, Silencing, and Subtelomeres
MBE Advance Access published on December 22, 2004
Mol Biol Evol 2005 22: 856-873; doi:10.1093/molbev/msi070 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Saurabh Sinha and Eric D. Siggia

Sequence Turnover and Tandem Repeats in cis-Regulatory Modules in Drosophila
MBE Advance Access published on January 19, 2005
Mol Biol Evol 2005 22: 874-885; doi:10.1093/molbev/msi090 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Gennady Churakov, Arian F.A. Smit, Jürgen Brosius, and Jürgen Schmitz

A Novel Abundant Family of Retroposed Elements (DAS-SINEs) in the Nine-Banded Armadillo (Dasypus novemcinctus)
MBE Advance Access published on December 22, 2004
Mol Biol Evol 2005 22: 886-893; doi:10.1093/molbev/msi071 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Lorraine Marsh and Carole S. Griffiths

Protein Structural Influences in Rhodopsin Evolution
MBE Advance Access published on January 12, 2005
Mol Biol Evol 2005 22: 894-904; doi:10.1093/molbev/msi081 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Andrey Rzhetsky and Walter M. Fitch

Listening to Viral Tongues: Comparing Viral Trees Using a Stochastic Context-Free Grammar
MBE Advance Access published on December 29, 2004
Mol Biol Evol 2005 22: 905-913; doi:10.1093/molbev/msi074 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Cécile Ané, J. Gordon Burleigh, Michelle M. McMahon, and Michael J. Sanderson

Covarion Structure in Plastid Genome Evolution: A New Statistical Test
MBE Advance Access published on December 29, 2004
Mol Biol Evol 2005 22: 914-924; doi:10.1093/molbev/msi076 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

A. D. Tsaousis, D. P. Martin, E. D. Ladoukakis, D. Posada, and E. Zouros

Widespread Recombination in Published Animal mtDNA Sequences
MBE Advance Access published on January 12, 2005
Mol Biol Evol 2005 22: 925-933; doi:10.1093/molbev/msi084 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Min Li, Bryan G. Fry, and R. Manjunatha Kini

Putting the Brakes on Snake Venom Evolution: The Unique Molecular Evolutionary Patterns of Aipysurus eydouxii (Marbled Sea Snake) Phospholipase A₂ Toxins
MBE Advance Access published on January 5, 2005
Mol Biol Evol 2005 22: 934-941; doi:10.1093/molbev/msi077 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Philippe Lemey, Sonia Van Dooren, and Anne-Mieke Vandamme

Evolutionary Dynamics of Human Retroviruses Investigated Through Full-Genome Scanning
MBE Advance Access published on January 5, 2005
Mol Biol Evol 2005 22: 942-951; doi:10.1093/molbev/msi078 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Athanasia Mizi, Eleftherios Zouros, Nicholas Moschonas, and George C. Rodakis

The Complete Maternal and Paternal Mitochondrial Genomes of the Mediterranean Mussel Mytilus galloprovincialis: Implications for the Doubly Uniparental Inheritance Mode of mtDNA
MBE Advance Access published on January 12, 2005
Mol Biol Evol 2005 22: 952-967; doi:10.1093/molbev/msi079 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Shozo Yokoyama and Naomi Takenaka

Statistical and Molecular Analyses of Evolutionary Significance of Red-Green Color Vision and Color Blindness in Vertebrates
MBE Advance Access published on January 12, 2005
Mol Biol Evol 2005 22: 968-975; doi:10.1093/molbev/msi080 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Xiaohui Shan, Zhenlan Liu, Zhenying Dong, Yongming Wang, Yu Chen, Xiuyun Lin, Likun Long, Fangpu Han, Yingshan Dong, and Bao Liu

Mobilization of the Active MITE Transposons mPing and Pong in Rice by Introgression from Wild Rice (Zizania latifolia Griseb.)
MBE Advance Access published on January 12, 2005
Mol Biol Evol 2005 22: 976-990; doi:10.1093/molbev/msi082 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Joan Pons and Alfried P. Vogler

Complex Pattern of Coalescence and Fast Evolution of a Mitochondrial rRNA Pseudogene in a Recent Radiation of Tiger Beetles
MBE Advance Access published on January 12, 2005
Mol Biol Evol 2005 22: 991-1000; doi:10.1093/molbev/msi085 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Akito Chinen, Yoshifumi Matsumoto, and Shoji Kawamura

Reconstitution of Ancestral Green Visual Pigments of Zebrafish and Molecular Mechanism of Their Spectral Differentiation
MBE Advance Access published on January 12, 2005
Mol Biol Evol 2005 22: 1001-1010; doi:10.1093/molbev/msi086 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Guy-Franck Richard, Alix Kerrest, Ingrid Lafontaine, and Bernard Dujon

Comparative Genomics of Hemiascomycete Yeasts: Genes Involved in DNA Replication, Repair, and Recombination
MBE Advance Access published on January 12, 2005
Mol Biol Evol 2005 22: 1011-1023; doi:10.1093/molbev/msi083 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Kousuke Hanada, Yoshiyuki Suzuki, Takashi Nakane, Osamu Hirose, and Takashi Gojobori

The Origin and Evolution of Porcine Reproductive and Respiratory Syndrome Viruses
MBE Advance Access published on January 19, 2005
Mol Biol Evol 2005 22: 1024-1031; doi:10.1093/molbev/msi089 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Marcus A. Koch, Christoph Dobes, Michaela Matschinger, Walter Bleeker, Johannes Vogel, Markus Kiefer, and Thomas Mitchell-Olds

Evolution of the trnF(GAA) Gene in Arabidopsis Relatives and the Brassicaceae Family: Monophyletic Origin and Subsequent Diversification of a Plastidic Pseudogene
MBE Advance Access published on February 2, 2005
Mol Biol Evol 2005 22: 1032-1043; doi:10.1093/molbev/msi092 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Jeffrey M. Good and Michael W. Nachman

Rates of Protein Evolution Are Positively Correlated with Developmental Timing of Expression During Mouse Spermatogenesis
MBE Advance Access published on January 12, 2005
Mol Biol Evol 2005 22: 1044-1052; doi:10.1093/molbev/msi087 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Lesley Collins and David Penny

Complex Spliceosomal Organization Ancestral to Extant Eukaryotes
MBE Advance Access published on January 19, 2005
Mol Biol Evol 2005 22: 1053-1066; doi:10.1093/molbev/msi091 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Anti Vasemägi, Jan Nilsson, and Craig R. Primmer

Expressed Sequence Tag-Linked Microsatellites as a Source of Gene-Associated Polymorphisms for Detecting Signatures of Divergent Selection in Atlantic Salmon (Salmo salar L.)
MBE Advance Access published on February 2, 2005
Mol Biol Evol 2005 22: 1067-1076; doi:10.1093/molbev/msi093 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Carles Lalueza-Fox, María Lourdes Sampietro, David Caramelli, Yvonne Puder, Martina Lari, Francesc Calafell, Cayetana Martínez-Maza, Markus Bastir, Javier Fortea, Marco de la Rasilla, Jaume Bertranpetit, and Antonio Rosas

Neandertal Evolutionary Genetics: Mitochondrial DNA Data from the Iberian Peninsula
MBE Advance Access published on February 2, 2005
Mol Biol Evol 2005 22: 1077-1081; doi:10.1093/molbev/msi094 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Kirsten Bomblies and John F. Doebley

Molecular Evolution of FLORICAULA/LEAFY Orthologs in the Andropogoneae (Poaceae)
MBE Advance Access published on February 2, 2005
Mol Biol Evol 2005 22: 1082-1094; doi:10.1093/molbev/msi095 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

S. Consuegra, H.-J. Megens, H. Schaschl, K. Leon, R. J. M. Stet, and W. C. Jordan

Rapid Evolution of the MH Class I Locus Results in Different Allelic Compositions in Recently Diverged Populations of Atlantic Salmon
MBE Advance Access published on February 2, 2005
Mol Biol Evol 2005 22: 1095-1106; doi:10.1093/molbev/msi096 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Ziheng Yang, Wendy S.W. Wong, and Rasmus Nielsen

Bayes Empirical Bayes Inference of Amino Acid Sites Under Positive Selection
MBE Advance Access published on February 2, 2005
Mol Biol Evol 2005 22: 1107-1118; doi:10.1093/molbev/msi097 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Loïc Ponger and Wen-Hsiung Li

Evolutionary Diversification of DNA Methyltransferases in Eukaryotic Genomes
MBE Advance Access published on February 2, 2005
Mol Biol Evol 2005 22: 1119-1128; doi:10.1093/molbev/msi098 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Maximilian J Telford, Michael J Wise, and Vivek Gowri-Shankar

Consideration of RNA Secondary Structure Significantly Improves Likelihood-Based Estimates of Phylogeny: Examples from the Bilateria
MBE Advance Access published on February 2, 2005
Mol Biol Evol 2005 22: 1129-1136; doi:10.1093/molbev/msi099 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Michael Lynch, Douglas G. Scofield, and Xin Hong

The Evolution of Transcription-Initiation Sites
MBE Advance Access published on February 2, 2005
Mol Biol Evol 2005 22: 1137-1146; doi:10.1093/molbev/msi100 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Jianzhi Zhang and Xionglei He

Significant Impact of Protein Dispensability on the Instantaneous Rate of Protein Evolution
MBE Advance Access published on February 2, 2005
Mol Biol Evol 2005 22: 1147-1155; doi:10.1093/molbev/msi101 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Errata:

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

Divergence Pattern of Duplicate Genes in Protein-Protein Interactions Follows the Power Law
Mol Biol Evol 2005 22: 1156; doi:10.1093/molbev/msi114 [Extract] [FREE Full Text] [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
Mol Biol Evol 2005 22: 1156; doi:10.1093/molbev/msi116 [Extract] [FREE Full Text] [PDF] [Request Permissions]  

Erratum
Mol Biol Evol 2005 22: 1156-1160; doi:10.1093/molbev/msi131 [Extract] [FREE Full Text] [PDF] [Request Permissions]  

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