Molecular Biology and Evolution

Research Articles:

Louise J. Johnson and John F. Y. Brookfield

A Test of the Master Gene Hypothesis for Interspersed Repetitive DNA Sequences
MBE Advance Access published on October 12, 2005
Mol Biol Evol 2006 23: 235-239; doi:10.1093/molbev/msj034 [Abstract] [Full Text] [PDF] [Request Permissions]  

John H. McDonald

Apparent Trends of Amino Acid Gain and Loss in Protein Evolution Due to Nearly Neutral Variation
MBE Advance Access published on September 29, 2005
Mol Biol Evol 2006 23: 240-244; doi:10.1093/molbev/msj026 [Abstract] [Full Text] [PDF] [Request Permissions]  

Mario A. Fares, Kevin P. Byrne, and Kenneth H. Wolfe

Rate Asymmetry After Genome Duplication Causes Substantial Long-Branch Attraction Artifacts in the Phylogeny of Saccharomyces Species
MBE Advance Access published on October 5, 2005
Mol Biol Evol 2006 23: 245-253; doi:10.1093/molbev/msj027 [Abstract] [Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Daniel H. Huson and David Bryant

Application of Phylogenetic Networks in Evolutionary Studies
MBE Advance Access published on October 12, 2005
Mol Biol Evol 2006 23: 254-267; doi:10.1093/molbev/msj030 [Abstract] [Full Text] [PDF] [Request Permissions]  

Joseph Hughes, Stuart J. Longhorn, Anna Papadopoulou, Kosmas Theodorides, Alessandra de Riva, Monica Mejia-Chang, Peter G. Foster, and Alfried P. Vogler

Dense Taxonomic EST Sampling and Its Applications for Molecular Systematics of the Coleoptera (Beetles)
MBE Advance Access published on October 19, 2005
Mol Biol Evol 2006 23: 268-278; doi:10.1093/molbev/msj041 [Abstract] [Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Ching-Chun Chang, Hsien-Chia Lin, I-Pin Lin, Teh-Yuan Chow, Hong-Hwa Chen, Wen-Huei Chen, Chia-Hsiung Cheng, Chung-Yen Lin, Shu-Mei Liu, Chien-Chang Chang, and Shu-Miaw Chaw

The Chloroplast Genome of Phalaenopsis aphrodite (Orchidaceae): Comparative Analysis of Evolutionary Rate with that of Grasses and Its Phylogenetic Implications
MBE Advance Access published on October 5, 2005
Mol Biol Evol 2006 23: 279-291; doi:10.1093/molbev/msj029 [Abstract] [Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Peng Shi and Jianzhi Zhang

Contrasting Modes of Evolution Between Vertebrate Sweet/Umami Receptor Genes and Bitter Receptor Genes
MBE Advance Access published on October 5, 2005
Mol Biol Evol 2006 23: 292-300; doi:10.1093/molbev/msj028 [Abstract] [Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Joanna L. Parmley, J. V. Chamary, and Laurence D. Hurst

Evidence for Purifying Selection Against Synonymous Mutations in Mammalian Exonic Splicing Enhancers
MBE Advance Access published on October 12, 2005
Mol Biol Evol 2006 23: 301-309; doi:10.1093/molbev/msj035 [Abstract] [Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Tal Dagan, Ran Blekhman, and Dan Graur

The "Domino Theory" of Gene Death: Gradual and Mass Gene Extinction Events in Three Lineages of Obligate Symbiotic Bacterial Pathogens
MBE Advance Access published on October 19, 2005
Mol Biol Evol 2006 23: 310-316; doi:10.1093/molbev/msj036 [Abstract] [Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Mark S. Bulmer and Ross H. Crozier

Variation in Positive Selection in Termite GNBPs and Relish
MBE Advance Access published on October 12, 2005
Mol Biol Evol 2006 23: 317-326; doi:10.1093/molbev/msj037 [Abstract] [Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

D. Allan Drummond, Alpan Raval, and Claus O. Wilke

A Single Determinant Dominates the Rate of Yeast Protein Evolution
MBE Advance Access published on October 19, 2005
Mol Biol Evol 2006 23: 327-337; doi:10.1093/molbev/msj038 [Abstract] [Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Rays H. Y. Jiang, Brett M. Tyler, Stephen C. Whisson, Adrienne R. Hardham, and Francine Govers

Ancient Origin of Elicitin Gene Clusters in Phytophthora Genomes
MBE Advance Access published on October 19, 2005
Mol Biol Evol 2006 23: 338-351; doi:10.1093/molbev/msj039 [Abstract] [Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Vivek Gowri-Shankar and Magnus Rattray

On the Correlation Between Composition and Site-Specific Evolutionary Rate: Implications for Phylogenetic Inference
MBE Advance Access published on October 19, 2005
Mol Biol Evol 2006 23: 352-364; doi:10.1093/molbev/msj040 [Abstract] [Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Gui-Rong Liu, Wei-Qiao Liu, Randal N. Johnston, Kenneth E. Sanderson, Shao-Xian Li, and Shu-Lin Liu

Genome Plasticity and ori-ter Rebalancing in Salmonella typhi
MBE Advance Access published on October 19, 2005
Mol Biol Evol 2006 23: 365-371; doi:10.1093/molbev/msj042 [Abstract] [Full Text] [PDF] [Request Permissions]  

Hua Tang and Chung-I Wu

A New Method for Estimating Nonsynonymous Substitutions and Its Applications to Detecting Positive Selection
MBE Advance Access published on October 19, 2005
Mol Biol Evol 2006 23: 372-379; doi:10.1093/molbev/msj043 [Abstract] [Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Georg Hausner, Robert Olson, Dawn Simon, Ian Johnson, Erin R. Sanders, Kenneth G. Karol, Richard M. McCourt, and Steven Zimmerly

Origin and Evolution of the Chloroplast trnK (matK) Intron: A Model for Evolution of Group II Intron RNA Structures
MBE Advance Access published on November 2, 2005
Mol Biol Evol 2006 23: 380-391; doi:10.1093/molbev/msj047 [Abstract] [Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Adi Stern and Tal Pupko

An Evolutionary Space-Time Model with Varying Among-Site Dependencies
MBE Advance Access published on November 2, 2005
Mol Biol Evol 2006 23: 392-400; doi:10.1093/molbev/msj044 [Abstract] [Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Anthony J. Greenberg, Jennifer R. Moran, Shu Fang, and Chung-I Wu

Adaptive Loss of an Old Duplicated Gene During Incipient Speciation
MBE Advance Access published on October 26, 2005
Mol Biol Evol 2006 23: 401-410; doi:10.1093/molbev/msj045 [Abstract] [Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Frédéric Bringaud, Daniella C. Bartholomeu, Gaëlle Blandin, Arthur Delcher, Théo Baltz, Najib M. A. El-Sayed, and Elodie Ghedin

The Trypanosoma cruzi L1Tc and NARTc Non-LTR Retrotransposons Show Relative Site Specificity for Insertion
MBE Advance Access published on November 2, 2005
Mol Biol Evol 2006 23: 411-420; doi:10.1093/molbev/msj046 [Abstract] [Full Text] [PDF] [Request Permissions]  

Yan Y. Tseng and Jie Liang

Estimation of Amino Acid Residue Substitution Rates at Local Spatial Regions and Application in Protein Function Inference: A Bayesian Monte Carlo Approach
MBE Advance Access published on October 26, 2005
Mol Biol Evol 2006 23: 421-436; doi:10.1093/molbev/msj048 [Abstract] [Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Laura Baldo, Seth Bordenstein, Jennifer J. Wernegreen, and John H. Werren

Widespread Recombination Throughout Wolbachia Genomes
MBE Advance Access published on November 2, 2005
Mol Biol Evol 2006 23: 437-449; doi:10.1093/molbev/msj049 [Abstract] [Full Text] [PDF] [Request Permissions]  

Michael Lynch

The Origins of Eukaryotic Gene Structure
MBE Advance Access published on November 9, 2005
Mol Biol Evol 2006 23: 450-468; doi:10.1093/molbev/msj050 [Abstract] [Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Jill M. Duarte, Liying Cui, P. Kerr Wall, Qing Zhang, Xiaohong Zhang, Jim Leebens-Mack, Hong Ma, Naomi Altman, and Claude W. dePamphilis

Expression Pattern Shifts Following Duplication Indicative of Subfunctionalization and Neofunctionalization in Regulatory Genes of Arabidopsis
MBE Advance Access published on November 9, 2005
Mol Biol Evol 2006 23: 469-478; doi:10.1093/molbev/msj051 [Abstract] [Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

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