Molecular Biology and Evolution - 29 (2), 2012

Contents:

Letters

Ann Demogines, Kimberly A. Truong, and Sara L. Sawyer
Species-Specific Features of DARC, the Primate Receptor for Plasmodium vivax and Plasmodium knowlesi

Joel O. Wertheim, Mathieu Fourment, and Sergei L. Kosakovsky Pond
Inconsistencies in Estimating the Age of HIV-1 Subtypes Due to Heterotachy


Review Article


Sudhir Kumar, Alan J. Filipski, Fabia U. Battistuzzi, Sergei L. Kosakovsky Pond, and Koichiro Tamura
Statistics and Truth in Phylogenomics


Research Articles


Alexander Gusev, Pier Francesco Palamara, Gregory Aponte, Zhong Zhuang, Ariel Darvasi, Peter Gregersen, and Itsik Pe'er
The Architecture of Long-Range Haplotypes Shared within and across Populations

Coen Campsteijn, Jan Inge Ovrebo, Bard Ove Karlsen, and Eric M. Thompson
Expansion of Cyclin D and CDK1 Paralogs in Oikopleura dioica, a Chordate Employing Diverse Cell Cycle Variants

Clément Gilbert, Sharon S. Hernandez, Jaime Flores-Benabib, Eric N. Smith, and Cédric Feschotte
Rampant Horizontal Transfer of SPIN Transposons in Squamate Reptiles

Rebekah L. Rogers and Daniel L. Hartl
Chimeric Genes as a Source of Rapid Evolution in Drosophila melanogaster

Guifré Torruella, Romain Derelle, Jordi Paps, B. Franz Lang, Andrew J. Roger, Kamran Shalchian-Tabrizi, and Inaki Ruiz-Trillo
Phylogenetic Relationships within the Opisthokonta Based on Phylogenomic Analyses of Conserved Single-Copy Protein Domains

Frederick Delfin, Sean Myles, Ying Choi, David Hughes, Robert Illek, Mannis van Oven, Brigitte Pakendorf, Manfred Kayser, and Mark Stoneking
Bridging Near and Remote Oceania: mtDNA and NRY Variation in the Solomon Islands

Erin S. Keebaugh and Todd A. Schlenke
Adaptive Evolution of a Novel Drosophila Lectin Induced by Parasitic Wasp Attack

Melanie Abeysundera, Chris Field, and Hong Gu
Phylogenetic Analysis Based on Spectral Methods

Johan Viklund, Thijs J.G. Ettema, and Siv G.E. Andersson
Independent Genome Reduction and Phylogenetic Reclassification of the Oceanic SAR11 Clade

Krishna R. Veeramah, Daniel Wegmann, August Woerner, Fernando L. Mendez, Joseph C. Watkins, Giovanni Destro-Bisol, Himla Soodyall, Leslie Louie, and Michael F. Hammer
An Early Divergence of KhoeSan Ancestors from Those of Other Modern Humans Is Supported by an ABC-Based Analysis of Autosomal Resequencing Data

Astrid Böhne, Qingchun Zhou, Amandine Darras, Cornelia Schmidt, Manfred Schartl, Delphine Galiana-Arnoux, and Jean-Nicolas Volff
Zisupton—A Novel Superfamily of DNA Transposable Elements Recently Active in Fish

Riyue Bao, Tami Fischer, Renata Bolognesi, Susan J. Brown, and Markus Friedrich
Parallel Duplication and Partial Subfunctionalization of ß-Catenin/Armadillo during Insect Evolution

Minh Anh Thi Nguyen, Tanja Gesell, and Arndt von Haeseler
ImOSM: Intermittent Evolution and Robustness of Phylogenetic Methods

Jonathan M. Flowers, Jeanmaire Molina, Samara Rubinstein, Pu Huang, Barbara A. Schaal, and Michael D. Purugganan
Natural Selection in Gene-Dense Regions Shapes the Genomic Pattern of Polymorphism in Wild and Domesticated Rice

Yi-Chieh Wu, Matthew D. Rasmussen, and Manolis Kellis
Evolution at the Subgene Level: Domain Rearrangements in the Drosophila Phylogeny

Eric D. Crandall, Elizabeth J. Sbrocco, Timery S. DeBoer, Paul H. Barber, and Kent E. Carpenter
Expansion Dating: Calibrating Molecular Clocks in Marine Species from Expansions onto the Sunda Shelf Following the Last Glacial Maximum

Alex Dornburg, Matthew C. Brandley, Michael R. McGowen, and Thomas J. Near
Relaxed Clocks and Inferences of Heterogeneous Patterns of Nucleotide Substitution and Divergence Time Estimates across Whales and Dolphins (Mammalia: Cetacea)

Ning Wang, Edward L. Braun, and Rebecca T. Kimball
Testing Hypotheses about the Sister Group of the Passeriformes Using an Independent 30-Locus Data Set

Wai Lok Sibon Li and Alexei J. Drummond
Model Averaging and Bayes Factor Calculation of Relaxed Molecular Clocks in Bayesian Phylogenetics

Sen Xu, Sarah Schaack, Amanda Seyfert, Eunjin Choi, Michael Lynch, and Melania E. Cristescu
High Mutation Rates in the Mitochondrial Genomes of Daphnia pulex

Fabrizio Ghiselli, Liliana Milani, Peter L. Chang, Dennis Hedgecock, Jonathan P. Davis, Sergey V. Nuzhdin, and Marco Passamonti
De Novo Assembly of the Manila Clam Ruditapes philippinarum Transcriptome Provides New Insights into Expression Bias, Mitochondrial Doubly Uniparental Inheritance and Sex Determination

Andrew D. Moore and Erich Bornberg-Bauer
The Dynamics and Evolutionary Potential of Domain Loss and Emergence

Shohei Takuno, Tomoyuki Kado, Ryuichi P. Sugino, Luay Nakhleh, and Hideki Innan
Population Genomics in Bacteria: A Case Study of Staphylococcus aureus

Elena Carnero-Montoro, Lizette Bonet, Johannes Engelken, Torsten Bielig, Mario Martínez-Florensa, Francisco Lozano, and Elena Bosch
Evolutionary and Functional Evidence for Positive Selection at the Human CD5 Immune Receptor Gene

Joanne K. Hobbs, Charis Shepherd, David J. Saul, Nicholas J. Demetras, Svend Haaning, Colin R. Monk, Roy M. Daniel, and Vickery L. Arcus
On the Origin and Evolution of Thermophily: Reconstruction of Functional Precambrian Enzymes from Ancestors of Bacillus

Julie Jaquiéry, Solenn Stoeckel, Claude Rispe, Lucie Mieuzet, Fabrice Legeai, and Jean-Christophe Simon
Accelerated Evolution of Sex Chromosomes in Aphids, an X0 System

Jeffrey A. Fawcett, Pierre Rouzé, and Yves Van de Peer
Higher Intron Loss Rate in Arabidopsis thaliana Than A. lyrata Is Consistent with Stronger Selection for a Smaller Genome

Jian-Hong Xu, Jeffrey L. Bennetzen, and Joachim Messing
Dynamic Gene Copy Number Variation in Collinear Regions of Grass Genomes

Claudia C. Weber, Catherine J. Pink, and Laurence D. Hurst
Late-Replicating Domains Have Higher Divergence and Diversity in Drosophila melanogaster


Standing Material

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