Molecular Biology and Evolution

Letters:

Matthew J. Phillips, Frédéric Delsuc, and David Penny

Genome-Scale Phylogeny and the Detection of Systematic Biases
MBE Advance Access published on April 14, 2004
Mol Biol Evol 2004 21: 1455-1458; doi:10.1093/molbev/msh137 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Barbara R. Holland, Katharina T. Huber, Vincent Moulton, and Peter J. Lockhart

Using Consensus Networks to Visualize Contradictory Evidence for Species Phylogeny
MBE Advance Access published on April 14, 2004
Mol Biol Evol 2004 21: 1459-1461; doi:10.1093/molbev/msh145 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Research Articles:

Edward L. C. Verkaar, Isaäc J. Nijman, Maurice Beeke, Eline Hanekamp, and Johannes A. Lenstra

Maternal and Paternal Lineages in Cross-Breeding Bovine Species. Has Wisent a Hybrid Origin?
MBE Advance Access published on January 22, 2004
Mol Biol Evol 2004 21: 1165-1170; doi:10.1093/molbev/msh064 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Victor Kunin, José B. Pereira-Leal, and Christos A. Ouzounis

Functional Evolution of the Yeast Protein Interaction Network
MBE Advance Access published on April 7, 2004
Mol Biol Evol 2004 21: 1171-1176; doi:10.1093/molbev/msh085 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Denis Houzelstein, Isabelle R. Gonçalves, Andrew J. Fadden, Sukhvinder S. Sidhu, Douglas N. W. Cooper, Kurt Drickamer, Hakon Leffler, and Françoise Poirier

Phylogenetic Analysis of the Vertebrate Galectin Family
MBE Advance Access published on February 12, 2004
Mol Biol Evol 2004 21: 1177-1187; doi:10.1093/molbev/msh082 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Simone Hoegg, Miguel Vences, Henner Brinkmann, and Axel Meyer

Phylogeny and Comparative Substitution Rates of Frogs Inferred from Sequences of Three Nuclear Genes
MBE Advance Access published on February 12, 2004
Mol Biol Evol 2004 21: 1188-1200; doi:10.1093/molbev/msh081 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Tae-Kun Seo, Hirohisa Kishino, and Jeffrey L. Thorne

Estimating Absolute Rates of Synonymous and Nonsynonymous Nucleotide Substitution in Order to Characterize Natural Selection and Date Species Divergences
MBE Advance Access published on March 10, 2004
Mol Biol Evol 2004 21: 1201-1213; doi:10.1093/molbev/msh088 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Maud I. Tenaillon, Jana U'Ren, Olivier Tenaillon, and Brandon S. Gaut

Selection Versus Demography: A Multilocus Investigation of the Domestication Process in Maize
MBE Advance Access published on March 10, 2004
Mol Biol Evol 2004 21: 1214-1225; doi:10.1093/molbev/msh102 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Paulo Almeida and Carlos Penha-Gonçalves

Long Perfect Dinucleotide Repeats Are Typical of Vertebrates, Show Motif Preferences and Size Convergence
MBE Advance Access published on March 10, 2004
Mol Biol Evol 2004 21: 1226-1233; doi:10.1093/molbev/msh108 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Ludmila Chistoserdova, Cheryl Jenkins, Marina G. Kalyuzhnaya, Christopher J. Marx, Alla Lapidus, Julia A. Vorholt, James T. Staley, and Mazy E. Lidstrom

The Enigmatic Planctomycetes May Hold a Key to the Origins of Methanogenesis and Methylotrophy
MBE Advance Access published on March 10, 2004
Mol Biol Evol 2004 21: 1234-1241; doi:10.1093/molbev/msh113 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Ulrich Genschel

Coenzyme A Biosynthesis: Reconstruction of the Pathway in Archaea and an Evolutionary Scenario Based on Comparative Genomics
MBE Advance Access published on March 10, 2004
Mol Biol Evol 2004 21: 1242-1251; doi:10.1093/molbev/msh119 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Wei-Gang Qiu, Nick Schisler, and Arlin Stoltzfus

The Evolutionary Gain of Spliceosomal Introns: Sequence and Phase Preferences
MBE Advance Access published on March 10, 2004
Mol Biol Evol 2004 21: 1252-1263; doi:10.1093/molbev/msh120 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Lin Yang and Jian-Fang Gui

Positive Selection on Multiple Antique Allelic Lineages of Transferrin in the Polyploid Carassius auratus
MBE Advance Access published on March 10, 2004
Mol Biol Evol 2004 21: 1264-1277; doi:10.1093/molbev/msh121 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Anton Nekrutenko

Reconciling the Numbers: ESTs Versus Protein-Coding Genes
MBE Advance Access published on March 19, 2004
Mol Biol Evol 2004 21: 1278-1282; doi:10.1093/molbev/msh125 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Eirik W. Lundblad, Christer Einvik, Sissel Rønning, Kari Haugli, and Steinar Johansen

Twelve Group I Introns in the Same Pre-rRNA Transcript of the Myxomycete Fuligo septica: RNA Processing and Evolution
MBE Advance Access published on March 19, 2004
Mol Biol Evol 2004 21: 1283-1293; doi:10.1093/molbev/msh126 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Weilong Hao and G. B. Golding

Patterns of Bacterial Gene Movement
MBE Advance Access published on April 28, 2004
Mol Biol Evol 2004 21: 1294-1307; doi:10.1093/molbev/msh129 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Sergey V. Nuzhdin, Marta L. Wayne, Kristy L. Harmon, and Lauren M. McIntyre

Common Pattern of Evolution of Gene Expression Level and Protein Sequence in Drosophila
MBE Advance Access published on March 19, 2004
Mol Biol Evol 2004 21: 1308-1317; doi:10.1093/molbev/msh128 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

T. Laatsch, S. Zauner, B. Stoebe-Maier, K. V. Kowallik, and U.-G. Maier

Plastid-Derived Single Gene Minicircles of the Dinoflagellate Ceratium horridum Are Localized in the Nucleus
MBE Advance Access published on March 19, 2004
Mol Biol Evol 2004 21: 1318-1322; doi:10.1093/molbev/msh127 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Lucia F. Franchini, Eric W. Ganko, and John F. McDonald

Retrotransposon-Gene Associations Are Widespread Among D. melanogaster Populations
MBE Advance Access published on March 10, 2004
Mol Biol Evol 2004 21: 1323-1331; doi:10.1093/molbev/msh116 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Jianzhi Zhang

Frequent False Detection of Positive Selection by the Likelihood Method with Branch-Site Models
MBE Advance Access published on March 10, 2004
Mol Biol Evol 2004 21: 1332-1339; doi:10.1093/molbev/msh117 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Yuji Inagaki, Edward Susko, Naomi M. Fast, and Andrew J. Roger

Covarion Shifts Cause a Long-Branch Attraction Artifact That Unites Microsporidia and Archaebacteria in EF-1 Phylogenies
MBE Advance Access published on March 19, 2004
Mol Biol Evol 2004 21: 1340-1349; doi:10.1093/molbev/msh130 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Nicolas Bierne and Adam Eyre-Walker

The Genomic Rate of Adaptive Amino Acid Substitution in Drosophila
MBE Advance Access published on March 24, 2004
Mol Biol Evol 2004 21: 1350-1360; doi:10.1093/molbev/msh134 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Isabelle Dupanloup, Giorgio Bertorelle, Lounès Chikhi, and Guido Barbujani

Estimating the Impact of Prehistoric Admixture on the Genome of Europeans
MBE Advance Access published on March 24, 2004
Mol Biol Evol 2004 21: 1361-1372; doi:10.1093/molbev/msh135 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Evgeni V. Sokurenko, Michael Feldgarden, Elena Trintchina, Scott J. Weissman, Serine Avagyan, Sujay Chattopadhyay, James R. Johnson, and Daniel E. Dykhuizen

Selection Footprint in the FimH Adhesin Shows Pathoadaptive Niche Differentiation in Escherichia coli
MBE Advance Access published on March 24, 2004
Mol Biol Evol 2004 21: 1373-1383; doi:10.1093/molbev/msh136 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Gerhard Schöfl and Christian Schlötterer

Patterns of Microsatellite Variability Among X Chromosomes and Autosomes Indicate a High Frequency of Beneficial Mutations in Non-African D. simulans
MBE Advance Access published on March 24, 2004
Mol Biol Evol 2004 21: 1384-1390; doi:10.1093/molbev/msh132 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

M. F. Canino and P. Bentzen

Evidence for Positive Selection at the Pantophysin (Pan I) Locus in Walleye Pollock, Theragra chalcogramma
MBE Advance Access published on April 14, 2004
Mol Biol Evol 2004 21: 1391-1400; doi:10.1093/molbev/msh141 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Xun Gu and Hongmei Zhang

Genome Phylogenetic Analysis Based on Extended Gene Contents
MBE Advance Access published on April 14, 2004
Mol Biol Evol 2004 21: 1401-1408; doi:10.1093/molbev/msh138 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Simon Joly, Jason T. Rauscher, Susan L. Sherman-Broyles, A. H. D. Brown, and Jeff J. Doyle

Evolutionary Dynamics and Preferential Expression of Homeologous 18S-5.8S-26S Nuclear Ribosomal Genes in Natural and Artificial Glycine Allopolyploids
MBE Advance Access published on April 14, 2004
Mol Biol Evol 2004 21: 1409-1421; doi:10.1093/molbev/msh140 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Cristian I. Castillo-Davis, Trevor B. C. Bedford, and Daniel L. Hartl

Accelerated Rates of Intron Gain/Loss and Protein Evolution in Duplicate Genes in Human and Mouse Malaria Parasites
MBE Advance Access published on April 14, 2004
Mol Biol Evol 2004 21: 1422-1427; doi:10.1093/molbev/msh143 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

B. E. Pfeil, C. L. Brubaker, L. A. Craven, and M. D. Crisp

Paralogy and Orthology in the Malvaceae rpb2 Gene Family: Investigation of Gene Duplication in Hibiscus
MBE Advance Access published on April 14, 2004
Mol Biol Evol 2004 21: 1428-1437; doi:10.1093/molbev/msh144 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Grzegorz Kudla, Aleksandra Helwak, and Leszek Lipinski

Gene Conversion and GC-Content Evolution in Mammalian Hsp70
MBE Advance Access published on April 14, 2004
Mol Biol Evol 2004 21: 1438-1444; doi:10.1093/molbev/msh146 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Vadim V. Goremykin, Karen I. Hirsch-Ernst, Stefan Wölfl, and Frank H. Hellwig

The Chloroplast Genome of Nymphaea alba: Whole-Genome Analyses and the Problem of Identifying the Most Basal Angiosperm
MBE Advance Access published on April 14, 2004
Mol Biol Evol 2004 21: 1445-1454; doi:10.1093/molbev/msh147 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Errata:

Heterogeneous Selection on LEGCYC Paralogs in Relation to Flower Morphology and the Phylogeny of Lupinus (Leguminosae)
Mol Biol Evol 2004 21: 1462; doi:10.1093/molbev/msh169 [Extract] [FREE Full Text] [PDF] [Request Permissions]  

A Large Variation in the Rates of Synonymous Substitution for RNA Viruses and Its Relationship to a Diversity of Viral Infection and Transmission Modes
Mol Biol Evol 2004 21: 1462; doi:10.1093/molbev/msh172 [Extract] [FREE Full Text] [PDF] [Request Permissions]  

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