Molecular Biology and Evolution

Letters

Get checked abstract Scott William Roy and David Penny

On the Incidence of Intron Loss and Gain in Paralogous Gene Families
MBE Advance Access published on April 29, 2007
Mol Biol Evol 2007 24: 1579-1581; doi:10.1093/molbev/msm082 [Abstract] [Full Text] [PDF] [Request Permissions]  

Get checked abstract Lise Musset, Jacques Le Bras, and Jérôme Clain

Parallel Evolution of Adaptive Mutations in Plasmodium falciparum Mitochondrial DNA During Atovaquone-Proguanil Treatment
MBE Advance Access published on May 7, 2007
Mol Biol Evol 2007 24: 1582-1585; doi:10.1093/molbev/msm087 [Abstract] [Full Text] [PDF] [Supplementary Material] [Request Permissions]  

Get checked abstract Ziheng Yang

PAML 4: Phylogenetic Analysis by Maximum Likelihood
MBE Advance Access published on May 4, 2007
Mol Biol Evol 2007 24: 1586-1591; doi:10.1093/molbev/msm088 [Abstract] [Full Text] [PDF] [Request Permissions]  

Hisayoshi Nozaki, Mineo Iseki, Masami Hasegawa, Kazuharu Misawa, Takashi Nakada, Narie Sasaki, and Masakatsu Watanabe

Phylogeny of Primary Photosynthetic Eukaryotes as Deduced from Slowly Evolving Nuclear Genes
MBE Advance Access published on May 7, 2007
Mol Biol Evol 2007 24: 1592-1595; doi:10.1093/molbev/msm091 [Extract] [Full Text] [PDF] [Supplementary Material] [Request Permissions]  

Get checked abstract Koichiro Tamura, Joel Dudley, Masatoshi Nei, and Sudhir Kumar

MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0
MBE Advance Access published on May 7, 2007
Mol Biol Evol 2007 24: 1596-1599; doi:10.1093/molbev/msm092 [Abstract] [Full Text] [PDF] [Request Permissions]  

Get checked abstract Joanna L. Parmley and Laurence D. Hurst

Exonic Splicing Regulatory Elements Skew Synonymous Codon Usage near Intron-exon Boundaries in Mammals
MBE Advance Access published on May 24, 2007
Mol Biol Evol 2007 24: 1600-1603; doi:10.1093/molbev/msm104 [Abstract] [Full Text] [PDF] [Request Permissions]  

Get checked abstract Manuel Irimia, Ignacio Maeso, David Penny, Jordi Garcia-Fernàndez, and Scott William Roy

Rare Coding Sequence Changes are Consistent with Ecdysozoa, not Coelomata
MBE Advance Access published on May 24, 2007
Mol Biol Evol 2007 24: 1604-1607; doi:10.1093/molbev/msm105 [Abstract] [Full Text] [PDF] [Request Permissions]  

Get checked abstract Mark A. DePristo, Daniel L. Hartl, and Daniel M. Weinreich

Mutational Reversions During Adaptive Protein Evolution
MBE Advance Access published on June 7, 2007
Mol Biol Evol 2007 24: 1608-1610; doi:10.1093/molbev/msm118 [Abstract] [Full Text] [PDF] [Supplementary Material] [Request Permissions]  

Research Articles

Get checked abstract Carina Grauvogel, Henner Brinkmann, and Jörn Petersen

Evolution of the Glucose-6-Phosphate Isomerase: The Plasticity of Primary Metabolism in Photosynthetic Eukaryotes
MBE Advance Access published on April 18, 2007
Mol Biol Evol 2007 24: 1611-1621; doi:10.1093/molbev/msm075 [Abstract] [Full Text] [PDF] [Request Permissions]  

Get checked abstract Naoki Osada

Inference of Expression-Dependent Negative Selection Based on Polymorphism and Divergence in the Human Genome
MBE Advance Access published on May 2, 2007
Mol Biol Evol 2007 24: 1622-1626; doi:10.1093/molbev/msm080 [Abstract] [Full Text] [PDF] [Supplementary Material] [Request Permissions]  

Get checked abstract Teruaki Watabe, Hirohisa Kishino, Leonardo de Oliveira Martins, and Yasuhiro Kitazoe

A Likelihood-based Index of Protein–Protein Binding Affinities with Application to Influenza HA Escape from Antibodies
MBE Advance Access published on May 2, 2007
Mol Biol Evol 2007 24: 1627-1638; doi:10.1093/molbev/msm079 [Abstract] [Full Text] [PDF] [Supplementary Material] [Supplementary Material] [Request Permissions]  

Get checked abstract Ziheng Yang

Fair-Balance Paradox, Star-tree Paradox, and Bayesian Phylogenetics
MBE Advance Access published on May 7, 2007
Mol Biol Evol 2007 24: 1639-1655; doi:10.1093/molbev/msm081 [Abstract] [Full Text] [PDF] [Request Permissions]  

Get checked abstract Vitaliy Matveev, Hidenori Nishihara, and Norihiro Okada

Novel SINE Families from Salmons Validate Parahucho (Salmonidae) as a Distinct Genus and Give Evidence that SINEs Can Incorporate LINE-related 3'-Tails of Other SINEs
MBE Advance Access published on April 29, 2007
Mol Biol Evol 2007 24: 1656-1666; doi:10.1093/molbev/msm083 [Abstract] [Full Text] [PDF] [Supplementary Material] [Request Permissions]  

Get checked abstract Jeffrey L. Thorne, Sang Chul Choi, Jiaye Yu, Paul G. Higgs, and Hirohisa Kishino

Population Genetics Without Intraspecific Data
MBE Advance Access published on April 29, 2007
Mol Biol Evol 2007 24: 1667-1677; doi:10.1093/molbev/msm085 [Abstract] [Full Text] [PDF] [Request Permissions]  

Get checked abstract Christoph Bleidorn, Igor Eeckhaut, Lars Podsiadlowski, Nancy Schult, Damhnait McHugh, Kenneth M. Halanych, Michel C. Milinkovitch, and Ralph Tiedemann

Mitochondrial Genome and Nuclear Sequence Data Support Myzostomida As Part of the Annelid Radiation
MBE Advance Access published on May 4, 2007
Mol Biol Evol 2007 24: 1690-1701; doi:10.1093/molbev/msm086 [Abstract] [Full Text] [PDF] [Request Permissions]  

Get checked abstract Jeremiah D. Hackett, Hwan Su Yoon, Shenglan Li, Adrian Reyes-Prieto, Susanne E. Rümmele, and Debashish Bhattacharya

Phylogenomic Analysis Supports the Monophyly of Cryptophytes and Haptophytes and the Association of Rhizaria with Chromalveolates
MBE Advance Access published on May 7, 2007
Mol Biol Evol 2007 24: 1702-1713; doi:10.1093/molbev/msm089 [Abstract] [Full Text] [PDF] [Supplementary Material] [Request Permissions]  

Get checked abstract David C. Lamb, Colin J. Jackson, Andrew G. S. Warrilow, Nigel J. Manning, Diane E. Kelly, and Steven L. Kelly

Lanosterol Biosynthesis in the Prokaryote Methylococcus Capsulatus: Insight into the Evolution of Sterol Biosynthesis
MBE Advance Access published on June 13, 2007
Mol Biol Evol 2007 24: 1714-1721; doi:10.1093/molbev/msm090 [Abstract] [Full Text] [PDF] [Request Permissions]  

Get checked abstract Jason C. Slot, Kelly N. Hallstrom, Patrick B. Matheny, and David S. Hibbett

Diversification of NRT2 and the Origin of Its Fungal Homolog
MBE Advance Access published on May 19, 2007
Mol Biol Evol 2007 24: 1731-1743; doi:10.1093/molbev/msm098 [Abstract] [Full Text] [PDF] [Supplementary Material] [Request Permissions]  

Get checked abstract Daniel E. Neafsey and James E. Galagan

Dual Modes of Natural Selection on Upstream Open Reading Frames
MBE Advance Access published on May 9, 2007
Mol Biol Evol 2007 24: 1744-1751; doi:10.1093/molbev/msm093 [Abstract] [Full Text] [PDF] [Supplementary Material] [Request Permissions]  

Get checked abstract Davide Pisani, James A. Cotton, and James O. McInerney

Supertrees Disentangle the Chimerical Origin of Eukaryotic Genomes
MBE Advance Access published on May 15, 2007
Mol Biol Evol 2007 24: 1752-1760; doi:10.1093/molbev/msm095 [Abstract] [Full Text] [PDF] [Supplementary Material] [Request Permissions]  

Get checked abstract Ryan G. Skophammer, Jacqueline A. Servin, Craig W. Herbold, and James A. Lake

Evidence for a Gram-positive, Eubacterial Root of the Tree of Life
MBE Advance Access published on May 19, 2007
Mol Biol Evol 2007 24: 1761-1768; doi:10.1093/molbev/msm096 [Abstract] [Full Text] [PDF] [Supplementary Material] [Request Permissions]  

Get checked abstract Sang Chul Choi, Asger Hobolth, Douglas M. Robinson, Hirohisa Kishino, and Jeffrey L. Thorne

Quantifying the Impact of Protein Tertiary Structure on Molecular Evolution
MBE Advance Access published on May 23, 2007
Mol Biol Evol 2007 24: 1769-1782; doi:10.1093/molbev/msm097 [Abstract] [Full Text] [PDF] [Request Permissions]  

Get checked abstract Camille M. Barr, Stephen R. Keller, Pär K. Ingvarsson, Daniel B. Sloan, and Douglas R. Taylor

Variation in Mutation Rate and Polymorphism Among Mitochondrial Genes of Silene vulgaris
MBE Advance Access published on May 28, 2007
Mol Biol Evol 2007 24: 1783-1791; doi:10.1093/molbev/msm106 [Abstract] [Full Text] [PDF] [Request Permissions]  

Get checked abstract Baowei Zhang, Ming Li, Zejun Zhang, Benoît Goossens, Lifeng Zhu, Shanning Zhang, Jinchu Hu, Michael W. Bruford, and Fuwen Wei

Genetic Viability and Population History of the Giant Panda, Putting an End to the "Evolutionary Dead End"?
MBE Advance Access published on May 19, 2007
Mol Biol Evol 2007 24: 1801-1810; doi:10.1093/molbev/msm099 [Abstract] [Full Text] [PDF] [Request Permissions]  

Get checked abstract Lone Simonsen, Cécile Viboud, Bryan T. Grenfell, Jonathan Dushoff, Lance Jennings, Marita Smit, Catherine Macken, Mami Hata, Julia Gog, Mark A. Miller, and Edward C. Holmes

The Genesis and Spread of Reassortment Human Influenza A/H3N2 Viruses Conferring Adamantane Resistance
MBE Advance Access published on May 23, 2007
Mol Biol Evol 2007 24: 1811-1820; doi:10.1093/molbev/msm103 [Abstract] [Full Text] [PDF] [Request Permissions]  

Get checked abstract Hameed Khan, Natalie Parks, Catherine Kozera, Bruce A. Curtis, Byron J. Parsons, Sharen Bowman, and John M. Archibald

Plastid Genome Sequence of the Cryptophyte Alga Rhodomonas salina CCMP1319: Lateral Transfer of Putative DNA Replication Machinery and a Test of Chromist Plastid Phylogeny
MBE Advance Access published on May 23, 2007
Mol Biol Evol 2007 24: 1832-1842; doi:10.1093/molbev/msm101 [Abstract] [Full Text] [PDF] [Supplementary Material] [Request Permissions]  

Get checked abstract Livia S. Carvalho, Jill A. Cowing, Susan E. Wilkie, James K. Bowmaker, and David M. Hunt

The Molecular Evolution of Avian Ultraviolet- and Violet-Sensitive Visual Pigments
MBE Advance Access published on June 7, 2007
Mol Biol Evol 2007 24: 1843-1852; doi:10.1093/molbev/msm109 [Abstract] [Full Text] [PDF] [Supplementary Material] [Request Permissions]  

Get checked abstract Louise V. Wain, Elizabeth Bailes, Frederic Bibollet-Ruche, Julie M. Decker, Brandon F. Keele, Fran Van Heuverswyn, Yingying Li, Jun Takehisa, Eitel Mpoudi Ngole, George M. Shaw, Martine Peeters, Beatrice H. Hahn, and Paul M. Sharp

Adaptation of HIV-1 to Its Human Host
MBE Advance Access published on June 1, 2007
Mol Biol Evol 2007 24: 1853-1860; doi:10.1093/molbev/msm110 [Abstract] [Full Text] [PDF] [Supplementary Material] [Request Permissions]  

Get checked abstract Claudio Casola, A. Michelle Lawing, Esther Betrán, and Cédric Feschotte

PIF-like Transposons are Common in Drosophila and Have Been Repeatedly Domesticated to Generate New Host Genes
MBE Advance Access published on June 7, 2007
Mol Biol Evol 2007 24: 1872-1888; doi:10.1093/molbev/msm116 [Abstract] [Full Text] [PDF] [Supplementary Material] [Request Permissions]  

Get checked abstract Laura A. Hug and Andrew J. Roger

The Impact of Fossils and Taxon Sampling on Ancient Molecular Dating Analyses
MBE Advance Access published on June 7, 2007
Mol Biol Evol 2007 24: 1889-1897; doi:10.1093/molbev/msm115 [Abstract] [Full Text] [PDF] [Supplementary Material] [Request Permissions]  

Get checked abstract Kai Zeng, Suhua Shi, and Chung-I Wu

Compound Tests for the Detection of Hitchhiking Under Positive Selection
MBE Advance Access published on June 8, 2007
Mol Biol Evol 2007 24: 1898-1908; doi:10.1093/molbev/msm119 [Abstract] [Full Text] [PDF] [Supplementary Material] [Request Permissions]  

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