Molecular Biology and Evolution

Quaternary Structure Constraints on Evolutionary Sequence Divergence
pp. 349-351(3)
Authors: Fornasari, María Silvina; Parisi, Gustavo; Echave, Julián

Time Squared: Repeated Measures on Phylogenies
pp. 352-362(11)
Authors: Guo, Hua; Weiss, Robert E.; Gu, Xun; Suchard, Marc A.

Mitochondrial Genome of the Homoscleromorph Oscarella carmela (Porifera, Demospongiae) Reveals Unexpected Complexity in the Common Ancestor of Sponges and Other Animals
pp. 363-373(11)
Authors: Wang, Xiujuan; Lavrov, Dennis V.

Synonymous Codon Usage in Escherichia coli: Selection for Translational Accuracy
pp. 374-381(8)
Authors: Stoletzki, Nina; Eyre-Walker, Adam

HIV-1 Protease Catalytic Efficiency Effects Caused by Random Single Amino Acid Substitutions
pp. 382-387(6)
Authors: Parera, Mariona; Fernàndez, Guerau; Clotet, Bonaventura; Martínez, Miguel Angel

A Combined Empirical and Mechanistic Codon Model
pp. 388-397(10)
Authors: Doron-Faigenboim, Adi; Pupko, Tal

Origin and Domestication of the Fungal Wheat Pathogen Mycosphaerella graminicola via Sympatric Speciation
pp. 398-411(14)
Authors: Stukenbrock, Eva H.; Banke, Søren; Javan-Nikkhah, Mohammad; McDonald, Bruce A.

Bayesian Estimation of Concordance among Gene Trees
pp. 412-426(15)
Authors: Ané, Cécile; Larget, Bret; Baum, David A.; Smith, Stacey D.; Rokas, Antonis

A Survey of the Bacteriophage WO in the Endosymbiotic Bacteria Wolbachia
pp. 427-435(9)
Authors: Gavotte, Laurent; Henri, Hélène; Stouthamer, Richard; Charif, Delphine; Charlat, Sylvain; Boulétreau, Michel; Vavre, Fabrice

Origin and Expansion of Haplogroup H, the Dominant Human Mitochondrial DNA Lineage in West Eurasia: The Near Eastern and Caucasian Perspective
pp. 436-448(13)
Authors: Roostalu, U; Kutuev, I; Loogväli, E-L; Metspalu, E; Tambets, K; Reidla, M; Khusnutdinova, EK; Usanga, E; Kivisild, T; Villems, R

Dynamics of Reductive Genome Evolution in Mitochondria and Obligate Intracellular Microbes
pp. 449-456(8)
Authors: Khachane, Amit N.; Timmis, Kenneth N.; Martins dos Santos, Vítor A. P.

The Conversion of 3′ UTRs into Coding Regions
pp. 457-464(8)
Authors: Giacomelli, Michael G.; Hancock, Adam S.; Masel, Joanna

Functional Diversification of B MADS-Box Homeotic Regulators of Flower Development: Adaptive Evolution in Protein-Protein Interaction Domains after Major Gene Duplication Events
pp. 465-481(17)
Authors: Hernández-Hernández, Tania; Martínez-Castilla, León Patricio; Alvarez-Buylla, Elena R.

Origin of the Bacterial SET Domain Genes: Vertical or Horizontal?
pp. 482-497(16)
Authors: Alvarez-Venegas, Raul; Sadder, Monther; Tikhonov, Alexander; Avramova, Zoya

Restrictive flamenco Alleles Are Maintained in Drosophila melanogaster Population Cages, Despite the Absence of Their Endogenous gypsy Retroviral Targets
pp. 498-504(7)
Authors: Pélisson, Alain; Payen-Groschêne, Geneviève; Terzian, Christophe; Bucheton, Alain

Disulfide-Bond Reshuffling in the Evolution of an Ape Placental Ribonuclease
pp. 505-512(8)
Author: Zhang, Jianzhi

Variation in Evolutionary Processes at Different Codon Positions
pp. 513-521(9)
Authors: Bofkin, Lee; Goldman, Nick

Estimating the Neutral Rate of Nucleotide Substitution Using Introns
pp. 522-531(10)
Authors: Hoffman, Michael M.; Birney, Ewan

QNet: An Agglomerative Method for the Construction of Phylogenetic Networks from Weighted Quartets
pp. 532-538(7)
Authors: Grünewald, Stefan; Forslund, Kristoffer; Dress, Andreas; Moulton, Vincent

Mechanisms and Rates of Birth and Death of Dispersed Duplicated Genes during the Evolution of a Multigene Family in Diploid and Tetraploid Wheats
pp. 539-550(12)
Authors: Akhunov, Eduard D.; Akhunova, Alina R.; Dvorak, Jan

A New Evolutionary Paradigm for the Parkinson Disease Gene DJ-1
pp. 551-561(11)
Authors: Lucas, J. Ignasi; Marín, Ignacio

Recurrent Gene Amplification and Soft Selective Sweeps during Evolution of Multidrug Resistance in Malaria Parasites
pp. 562-573(12)
Authors: Nair, Shalini; Nash, Denae; Sudimack, Daniel; Jaidee, Anchalee; Barends, Marion; Uhlemann, Anne-Catrin; Krishna, Sanjeev; Nosten, François; Anderson, Tim J. C.

Increasing Sequence Correlation Limits the Efficiency of Recombination in a Multisite Evolution Model
pp. 574-586(13)
Authors: Gheorghiu-Svirschevski, S.; Rouzine, IM; Coffin, JM

Sequence Diversity at the Proximal 14q32.1 SERPIN Subcluster: Evidence for Natural Selection Favoring the Pseudogenization of SERPINA2
pp. 587-598(12)
Authors: Seixas, Susana; Suriano, Gianpaolo; Carvalho, Filipa; Seruca, Raquel; Rocha, Jorge; Di Rienzo, Anna

The Evolution of GABA_A Receptor-Like Genes
pp. 599-610(12)
Authors: Tsang, Shui-Ying; Ng, Siu-Kin; Xu, Zhiwen; Xue, Hong

Heterogeneity in Regional GC Content and Differential Usage of Codons and Amino Acids in GC-Poor and GC-Rich Regions of the Genome of Apis mellifera
pp. 611-619(9)
Authors: Jørgensen, Frank Grønlund; Schierup, Mikkel Heide; Clark, Andrew G.

Fossil Calibration of Molecular Divergence Infers a Moderate Mutation Rate and Recent Radiations for Pinus
pp. 620-620(1)
Authors: Willyard, Ann; Syring, John; Gernandt, David S.; Liston, Aaron; Cronn, Richard