Molecular Biology and Evolution

Letters:

José P. Abad, Beatriz de Pablos, Kazutoyo Osoegawa, Pieter J. de Jong, Antonia Martín-Gallardo, and Alfredo Villasante

Genomic Analysis of Drosophila melanogaster Telomeres: Full-length Copies of HeT-A and TART Elements at Telomeres
MBE Advance Access published on May 26, 2004
Mol Biol Evol 2004 21: 1613-1619; doi:10.1093/molbev/msh174 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

José P. Abad, Beatriz de Pablos, Kazutoyo Osoegawa, Pieter J. de Jong, Antonia Martín-Gallardo, and Alfredo Villasante

TAHRE, a Novel Telomeric Retrotransposon from Drosophila melanogaster, Reveals the Origin of Drosophila Telomeres
MBE Advance Access published on June 2, 2004
Mol Biol Evol 2004 21: 1620-1624; doi:10.1093/molbev/msh180 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Alisha K. Holloway and David J. Begun

Molecular Evolution and Population Genetics of Duplicated Accessory Gland Protein Genes in Drosophila
MBE Advance Access published on June 23, 2004
Mol Biol Evol 2004 21: 1625-1628; doi:10.1093/molbev/msh195 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Original Articles:

Edward Susko, Yuji Inagaki, and Andrew J. Roger

On Inconsistency of the Neighbor-Joining, Least Squares, and Minimum Evolution Estimation When Substitution Processes Are Incorrectly Modeled
MBE Advance Access published on May 21, 2004
Mol Biol Evol 2004 21: 1629-1642; doi:10.1093/molbev/msh159 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Christian Esser, Nahal Ahmadinejad, Christian Wiegand, Carmen Rotte, Federico Sebastiani, Gabriel Gelius-Dietrich, Katrin Henze, Ernst Kretschmann, Erik Richly, Dario Leister, David Bryant, Michael A. Steel, Peter J. Lockhart, David Penny, and William Martin

A Genome Phylogeny for Mitochondria Among -Proteobacteria and a Predominantly Eubacterial Ancestry of Yeast Nuclear Genes
MBE Advance Access published on May 21, 2004
Mol Biol Evol 2004 21: 1643-1660; doi:10.1093/molbev/msh160 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Shunyuan Xiao, Brent Emerson, Kumrop Ratanasut, Elaine Patrick, Carmel O'Neill, Ian Bancroft, and John G. Turner

Origin and Maintenance of a Broad-Spectrum Disease Resistance Locus in Arabidopsis
MBE Advance Access published on May 21, 2004
Mol Biol Evol 2004 21: 1661-1672; doi:10.1093/molbev/msh165 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Giovanni Destro-Bisol, Francesco Donati, Valentina Coia, Ilaria Boschi, Fabio Verginelli, Alessandra Caglià, Sergio Tofanelli, Gabriella Spedini, and Cristian Capelli

Variation of Female and Male Lineages in Sub-Saharan Populations: the Importance of Sociocultural Factors
MBE Advance Access published on June 9, 2004
Mol Biol Evol 2004 21: 1673-1682; doi:10.1093/molbev/msh186 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Yousuke Nishio, Yoji Nakamura, Yoshihiro Usuda, Shinichi Sugimoto, Kazuhiko Matsui, Yutaka Kawarabayasi, Hisashi Kikuchi, Takashi Gojobori, and Kazuho Ikeo

Evolutionary Process of Amino Acid Biosynthesis in Corynebacterium at the Whole Genome Level
MBE Advance Access published on May 26, 2004
Mol Biol Evol 2004 21: 1683-1691; doi:10.1093/molbev/msh175 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Xinjiang Cai and Jonathan Lytton

The Cation/Ca²⁺ Exchanger Superfamily: Phylogenetic Analysis and Structural Implications
MBE Advance Access published on May 26, 2004
Mol Biol Evol 2004 21: 1692-1703; doi:10.1093/molbev/msh177 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Alejandro P. Rooney

Mechanisms Underlying the Evolution and Maintenance of Functionally Heterogeneous 18S rRNA Genes in Apicomplexans
MBE Advance Access published on June 2, 2004
Mol Biol Evol 2004 21: 1704-1711; doi:10.1093/molbev/msh178 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Jennifer L. Cooper and Steven Henikoff

Adaptive Evolution of the Histone Fold Domain in Centromeric Histones
MBE Advance Access published on June 2, 2004
Mol Biol Evol 2004 21: 1712-1718; doi:10.1093/molbev/msh179 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Stephen I. Wright, C. B. Kenneth Yau, Mark Looseley, and Blake C. Meyers

Effects of Gene Expression on Molecular Evolution in Arabidopsis thaliana and Arabidopsis lyrata
MBE Advance Access published on June 16, 2004
Mol Biol Evol 2004 21: 1719-1726; doi:10.1093/molbev/msh191 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Erin H. Penton and Teresa J. Crease

Evolution of the Transposable Element Pokey in the Ribosomal DNA of Species in the Subgenus Daphnia (Crustacea: Cladocera)
MBE Advance Access published on June 16, 2004
Mol Biol Evol 2004 21: 1727-1739; doi:10.1093/molbev/msh189 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Hervé Philippe, Elizabeth A. Snell, Eric Bapteste, Philippe Lopez, Peter W. H. Holland, and Didier Casane

Phylogenomics of Eukaryotes: Impact of Missing Data on Large Alignments
MBE Advance Access published on June 2, 2004
Mol Biol Evol 2004 21: 1740-1752; doi:10.1093/molbev/msh182 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

David O. F. Skibinski and Robert D. Ward

Average Allozyme Heterozygosity in Vertebrates Correlates with Ka/Ks Measured in the Human-Mouse Lineage
MBE Advance Access published on June 16, 2004
Mol Biol Evol 2004 21: 1753-1759; doi:10.1093/molbev/msh193 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Gavin A. Huttley

Modeling the Impact of DNA Methylation on the Evolution of BRCA1 in Mammals
MBE Advance Access published on June 9, 2004
Mol Biol Evol 2004 21: 1760-1768; doi:10.1093/molbev/msh187 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Cédric Feschotte

Merlin, a New Superfamily of DNA Transposons Identified in Diverse Animal Genomes and Related to Bacterial IS1016 Insertion Sequences
MBE Advance Access published on June 9, 2004
Mol Biol Evol 2004 21: 1769-1780; doi:10.1093/molbev/msh188 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Itay Mayrose, Dan Graur, Nir Ben-Tal, and Tal Pupko

Comparison of Site-Specific Rate-Inference Methods for Protein Sequences: Empirical Bayesian Methods Are Superior
MBE Advance Access published on June 16, 2004
Mol Biol Evol 2004 21: 1781-1791; doi:10.1093/molbev/msh194 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

M. F. Cardone, L. Ballarati, M. Ventura, M. Rocchi, A. Marozzi, E. Ginelli, and R. Meneveri

Evolution of Beta Satellite DNA Sequences: Evidence for Duplication-Mediated Repeat Amplification and Spreading
MBE Advance Access published on June 16, 2004
Mol Biol Evol 2004 21: 1792-1799; doi:10.1093/molbev/msh190 [Abstract] [FREE Full Text] [PDF] [Supplementary Material]  [Request Permissions]  

Jay F. Storz, Bret A. Payseur, and Michael W. Nachman

Genome Scans of DNA Variability in Humans Reveal Evidence for Selective Sweeps Outside of Africa
MBE Advance Access published on June 16, 2004
Mol Biol Evol 2004 21: 1800-1811; doi:10.1093/molbev/msh192 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Errata:

The Evolutionary Gain of Spliceosomal Introns: Sequence and Phase Preferences
Mol Biol Evol 2004 21: 1812; doi:10.1093/molbev/msh201 [Extract] [FREE Full Text] [PDF] [Request Permissions]  

An Assessment of Accuracy, Error, and Conflict with Support Values from Genome-Scale Phylogenetic Data
Mol Biol Evol 2004 21: 1812; doi:10.1093/molbev/msh215 [Extract] [FREE Full Text] [PDF] [Request Permissions]  

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