Molecular Biology and Evolution

Original Articles:

Andrew D. Smith, Thomas W. H. Lui, and Elisabeth R. M. Tillier

Empirical Models for Substitution in Ribosomal RNA
MBE Advance Access published on December 5, 2003
Mol Biol Evol 2004 21: 419-427; doi:10.1093/molbev/msh029 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

J. William O. Ballard

Sequential Evolution of a Symbiont Inferred From the Host: Wolbachia and Drosophila simulans
MBE Advance Access published on December 5, 2003
Mol Biol Evol 2004 21: 428-442; doi:10.1093/molbev/msh028 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Christopher S. Willett and Ronald S. Burton

Evolution of Interacting Proteins in the Mitochondrial Electron Transport System in a Marine Copepod
MBE Advance Access published on December 5, 2003
Mol Biol Evol 2004 21: 443-453; doi:10.1093/molbev/msh031 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Manjunath B. Joshi, Pramod K. Rout, Ajoy K. Mandal, Chris Tyler-Smith, Lalji Singh, and Kumarasamy Thangaraj

Phylogeography and Origin of Indian Domestic Goats
MBE Advance Access published on December 5, 2003
Mol Biol Evol 2004 21: 454-462; doi:10.1093/molbev/msh038 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Daiya Takai and Peter A. Jones

Origins of Bidirectional Promoters: Computational Analyses of Intergenic Distance in the Human Genome
MBE Advance Access published on December 5, 2003
Mol Biol Evol 2004 21: 463-467; doi:10.1093/molbev/msh040 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Adam Siepel and David Haussler

Phylogenetic Estimation of Context-Dependent Substitution Rates by Maximum Likelihood
MBE Advance Access published on December 5, 2003
Mol Biol Evol 2004 21: 468-488; doi:10.1093/molbev/msh039 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Dominique Madern, Xiaomin Cai, Mitchell S. Abrahamsen, and Guan Zhu

Evolution of Cryptosporidium parvum Lactate Dehydrogenase from Malate Dehydrogenase by a Very Recent Event of Gene Duplication
MBE Advance Access published on December 23, 2003
Mol Biol Evol 2004 21: 489-497; doi:10.1093/molbev/msh042 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Nikolas Nikolaidis and Masatoshi Nei

Concerted and Nonconcerted Evolution of the Hsp70 Gene Superfamily in Two Sibling Species of Nematodes
MBE Advance Access published on December 23, 2003
Mol Biol Evol 2004 21: 498-505; doi:10.1093/molbev/msh041 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Giulia M. Stellari, M. Alejandra Jaramillo, and Elena M. Kramer

Evolution of the APETALA3 and PISTILLATA Lineages of MADS-Box–Containing Genes in the Basal Angiosperms
MBE Advance Access published on December 23, 2003
Mol Biol Evol 2004 21: 506-519; doi:10.1093/molbev/msh044 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Frédéric Bringaud, Nicolas Biteau, Eduard Zuiderwijk, Matthew Berriman, Najib M. El-Sayed, Elodie Ghedin, Sara E. Melville, Neil Hall, and Théo Baltz

The ingi and RIME non-LTR Retrotransposons Are Not Randomly Distributed in the Genome of Trypanosoma brucei
MBE Advance Access published on December 23, 2003
Mol Biol Evol 2004 21: 520-528; doi:10.1093/molbev/msh045 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

I. Miklós, G. A. Lunter, and I. Holmes

A "Long Indel" Model For Evolutionary Sequence Alignment
MBE Advance Access published on December 23, 2003
Mol Biol Evol 2004 21: 529-540; doi:10.1093/molbev/msh043 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Jason Raymond, Janet L. Siefert, Christopher R. Staples, and Robert E. Blankenship

The Natural History of Nitrogen Fixation
MBE Advance Access published on December 23, 2003
Mol Biol Evol 2004 21: 541-554; doi:10.1093/molbev/msh047 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Laura A. Katz, Jacob G. Bornstein, Erica Lasek-Nesselquist, and Spencer V. Muse

Dramatic Diversity of Ciliate Histone H4 Genes Revealed by Comparisons of Patterns of Substitutions and Paralog Divergences Among Eukaryotes
MBE Advance Access published on December 23, 2003
Mol Biol Evol 2004 21: 555-562; doi:10.1093/molbev/msh048 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Janis Klovins, Tatjana Haitina, Davids Fridmanis, Zuzana Kilianova, Ivo Kapa, Robert Fredriksson, Nicole Gallo-Payet, and Helgi B. Schiöth

The Melanocortin System in Fugu: Determination of POMC/AGRP/MCR Gene Repertoire and Synteny, As Well As Pharmacology and Anatomical Distribution of the MCRs
MBE Advance Access published on December 23, 2003
Mol Biol Evol 2004 21: 563-579; doi:10.1093/molbev/msh050 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Marc Robinson-Rechavi, Bastien Boussau, and Vincent Laudet

Phylogenetic Dating and Characterization of Gene Duplications in Vertebrates: The Cartilaginous Fish Reference
MBE Advance Access published on December 23, 2003
Mol Biol Evol 2004 21: 580-586; doi:10.1093/molbev/msh046 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Richard Desper and Olivier Gascuel

Theoretical Foundation of the Balanced Minimum Evolution Method of Phylogenetic Inference and Its Relationship to Weighted Least-Squares Tree Fitting
MBE Advance Access published on December 23, 2003
Mol Biol Evol 2004 21: 587-598; doi:10.1093/molbev/msh049 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Kevin P. Johnson

Deletion Bias in Avian Introns over Evolutionary Timescales
MBE Advance Access published on December 23, 2003
Mol Biol Evol 2004 21: 599-602; doi:10.1093/molbev/msh051 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

S. Van Dooren, O. G. Pybus, M. Salemi, H.-F. Liu, P. Goubau, C. Remondegui, A. Talarmin, E. Gotuzzo, L. C. J. Alcantara, B. Galvão-Castro, and A.-M. Vandamme

The Low Evolutionary Rate of Human T-Cell Lymphotropic Virus Type-1 Confirmed by Analysis of Vertical Transmission Chains
MBE Advance Access published on January 22, 2004
Mol Biol Evol 2004 21: 603-611; doi:10.1093/molbev/msh053 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Andrey A. Gontcharov, Birger Marin, and Michael Melkonian

Are Combined Analyses Better Than Single Gene Phylogenies? A Case Study Using SSU rDNA and rbcL Sequence Comparisons in the Zygnematophyceae (Streptophyta)
MBE Advance Access published on January 22, 2004
Mol Biol Evol 2004 21: 612-624; doi:10.1093/molbev/msh052 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

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