Molecular Biology and Evolution

Species-Specific Features of DARC, the Primate Receptor for Plasmodium vivax and Plasmodium knowlesi
pp. 445-449(5)
Authors: Demogines, Ann; Truong, Kimberly A.; Sawyer, Sara L.

Inconsistencies in Estimating the Age of HIV-1 Subtypes Due to Heterotachy
pp. 451-456(6)
Authors: Wertheim, Joel O.; Fourment, Mathieu; Kosakovsky Pond, Sergei L.

Statistics and Truth in Phylogenomics
pp. 457-472(16)
Authors: Kumar, Sudhir; Filipski, Alan J.; Battistuzzi, Fabia U.; Kosakovsky Pond, Sergei L.; Tamura, Koichiro

The Architecture of Long-Range Haplotypes Shared within and across Populations
pp. 473-486(14)
Authors: Gusev, Alexander; Palamara, Pier Francesco; Aponte, Gregory; Zhuang, Zhong; Darvasi, Ariel; Gregersen, Peter; Pe'er, Itsik

Expansion of Cyclin D and CDK1 Paralogs in Oikopleura dioica, a Chordate Employing Diverse Cell Cycle Variants
pp. 487-502(16)
Authors: Campsteijn, Coen; vreb, Jan Inge; Karlsen, Brd Ove; Thompson, Eric M.

Rampant Horizontal Transfer of SPIN Transposons in Squamate Reptiles
pp. 503-515(13)
Authors: Gilbert, Clment; Hernandez, Sharon S.; Flores-Benabib, Jaime; Smith, Eric N.; Feschotte, Cdric

Chimeric Genes as a Source of Rapid Evolution in Drosophila melanogaster
pp. 517-529(13)
Authors: Rogers, Rebekah L.; Hartl, Daniel L.

Phylogenetic Relationships within the Opisthokonta Based on Phylogenomic Analyses of Conserved Single-Copy Protein Domains
pp. 531-544(14)
Authors: Torruella, Guifr; Derelle, Romain; Paps, Jordi; Lang, B. Franz; Roger, Andrew J.; Shalchian-Tabrizi, Kamran; Ruiz-Trillo, Iaki

Bridging Near and Remote Oceania: mtDNA and NRY Variation in the Solomon Islands
pp. 545-564(20)
Authors: Delfin, Frederick; Myles, Sean; Choi, Ying; Hughes, David; Illek, Robert; van Oven, Mannis; Pakendorf, Brigitte; Kayser, Manfred; Stoneking, Mark

Adaptive Evolution of a Novel Drosophila Lectin Induced by Parasitic Wasp Attack
pp. 565-577(13)
Authors: Keebaugh, Erin S.; Schlenke, Todd A.

Phylogenetic Analysis Based on Spectral Methods
pp. 579-597(19)
Authors: Abeysundera, Melanie; Field, Chris; Gu, Hong

Independent Genome Reduction and Phylogenetic Reclassification of the Oceanic SAR11 Clade
pp. 599-615(17)
Authors: Viklund, Johan; Ettema, Thijs J.G.; Andersson, Siv G.E.

An Early Divergence of KhoeSan Ancestors from Those of Other Modern Humans Is Supported by an ABC-Based Analysis of Autosomal Resequencing Data
pp. 617-630(14)
Authors: Veeramah, Krishna R.; Wegmann, Daniel; Woerner, August; Mendez, Fernando L.; Watkins, Joseph C.; Destro-Bisol, Giovanni; Soodyall, Himla; Louie, Leslie; Hammer, Michael F.

ZisuptonA Novel Superfamily of DNA Transposable Elements Recently Active in Fish
pp. 631-645(15)
Authors: Bhne, Astrid; Zhou, Qingchun; Darras, Amandine; Schmidt, Cornelia; Schartl, Manfred; Galiana-Arnoux, Delphine; Volff, Jean-Nicolas

Parallel Duplication and Partial Subfunctionalization of -Catenin/Armadillo during Insect Evolution
pp. 647-662(16)
Authors: Bao, Riyue; Fischer, Tami; Bolognesi, Renata; Brown, Susan J.; Friedrich, Markus

ImOSM: Intermittent Evolution and Robustness of Phylogenetic Methods
pp. 663-673(11)
Authors: Thi Nguyen, Minh Anh; Gesell, Tanja; von Haeseler, Arndt

Natural Selection in Gene-Dense Regions Shapes the Genomic Pattern of Polymorphism in Wild and Domesticated Rice
pp. 675-687(13)
Authors: Flowers, Jonathan M.; Molina, Jeanmaire; Rubinstein, Samara; Huang, Pu; Schaal, Barbara A.; Purugganan, Michael D.

Evolution at the Subgene Level: Domain Rearrangements in the Drosophila Phylogeny
pp. 689-705(17)
Authors: Wu, Yi-Chieh; Rasmussen, Matthew D.; Kellis, Manolis

Expansion Dating: Calibrating Molecular Clocks in Marine Species from Expansions onto the Sunda Shelf Following the Last Glacial Maximum
pp. 707-719(13)
Authors: Crandall, Eric D.; Sbrocco, Elizabeth J.; DeBoer, Timery S.; Barber, Paul H.; Carpenter, Kent E.

Relaxed Clocks and Inferences of Heterogeneous Patterns of Nucleotide Substitution and Divergence Time Estimates across Whales and Dolphins (Mammalia: Cetacea)
pp. 721-736(16)
Authors: Dornburg, Alex; Brandley, Matthew C.; McGowen, Michael R.; Near, Thomas J.

Testing Hypotheses about the Sister Group of the Passeriformes Using an Independent 30-Locus Data Set
pp. 737-750(14)
Authors: Wang, Ning; Braun, Edward L.; Kimball, Rebecca T.

Model Averaging and Bayes Factor Calculation of Relaxed Molecular Clocks in Bayesian Phylogenetics
pp. 751-761(11)
Authors: Li, Wai Lok Sibon; Drummond, Alexei J.

High Mutation Rates in the Mitochondrial Genomes of Daphnia pulex
pp. 763-769(7)
Authors: Xu, Sen; Schaack, Sarah; Seyfert, Amanda; Choi, Eunjin; Lynch, Michael; Cristescu, Melania E.

De Novo Assembly of the Manila Clam Ruditapes philippinarum Transcriptome Provides New Insights into Expression Bias, Mitochondrial Doubly Uniparental Inheritance and Sex Determination
pp. 771-786(16)
Authors: Ghiselli, Fabrizio; Milani, Liliana; Chang, Peter L.; Hedgecock, Dennis; Davis, Jonathan P.; Nuzhdin, Sergey V.; Passamonti, Marco

The Dynamics and Evolutionary Potential of Domain Loss and Emergence
pp. 787-796(10)
Authors: Moore, Andrew D.; Bornberg-Bauer, Erich

Population Genomics in Bacteria: A Case Study of Staphylococcus aureus
pp. 797-809(13)
Authors: Takuno, Shohei; Kado, Tomoyuki; Sugino, Ryuichi P.; Nakhleh, Luay; Innan, Hideki

Evolutionary and Functional Evidence for Positive Selection at the Human CD5 Immune Receptor Gene
pp. 811-823(13)
Authors: Carnero-Montoro, Elena; Bonet, Lizette; Engelken, Johannes; Bielig, Torsten; Martnez-Florensa, Mario; Lozano, Francisco; Bosch, Elena

On the Origin and Evolution of Thermophily: Reconstruction of Functional Precambrian Enzymes from Ancestors of Bacillus
pp. 825-835(11)
Authors: Hobbs, Joanne K.; Shepherd, Charis; Saul, David J.; Demetras, Nicholas J.; Haaning, Svend; Monk, Colin R.; Daniel, Roy M.; Arcus, Vickery L.

Accelerated Evolution of Sex Chromosomes in Aphids, an X0 System
pp. 837-847(11)
Authors: Jaquiry, Julie; Stoeckel, Solenn; Rispe, Claude; Mieuzet, Lucie; Legeai, Fabrice; Simon, Jean-Christophe

Higher Intron Loss Rate in Arabidopsis thaliana Than A. lyrata Is Consistent with Stronger Selection for a Smaller Genome
pp. 849-859(11)
Authors: Fawcett, Jeffrey A.; Rouz, Pierre; Van de Peer, Yves

Dynamic Gene Copy Number Variation in Collinear Regions of Grass Genomes
pp. 861-871(11)
Authors: Xu, Jian-Hong; Bennetzen, Jeffrey L.; Messing, Joachim

Late-Replicating Domains Have Higher Divergence and Diversity in Drosophila melanogaster
pp. 873-882(10)
Authors: Weber, Claudia C.; Pink, Catherine J.; Hurst, Laurence D.