Molecular Biology and Evolution

Comparative Analyses Reveal a Complex History of Molecular Evolution for Human MYH16
pp. 379-382(4)
Authors: Perry, George H.; Verrelli, Brian C.; Stone, Anne C.

Selenoproteins and the Metabolic Features of the Archaeal Ancestor of Eukaryotes
pp. 383-386(4)
Author: Foster, Charles B.

Molecular Clocks Do Not Support the Cambrian Explosion
pp. 387-390(4)
Authors: Blair, Jaime E.; Hedges, S. Blair

Identification of a Giardia krr1 Homolog Gene and the Secondarily Anucleolate Condition of Giaridia lamblia
pp. 391-394(4)
Authors: Xin, De-Dong; Wen, Jian-Fan; He, De; Lu, Si-Qi

Measuring the Fit of Sequence Data to Phylogenetic Model: Allowing for Missing Data
pp. 395-401(7)
Author: Waddell, Peter J.

Substitution Rates in a New Silene latifolia Sex-Linked Gene, SlssX/Y
pp. 402-408(7)
Author: Filatov, Dmitry A.

Root of the Eukaryota Tree as Inferred from Combined Maximum Likelihood Analyses of Multiple Molecular Sequence Data
pp. 409-420(12)
Authors: Arisue, Nobuko; Hasegawa, Masami; Hashimoto, Tetsuo

An Exponential Core in the Heart of the Yeast Protein Interaction Network
pp. 421-425(5)
Authors: Pereira-Leal, José B.; Audit, Benjamin; Peregrin-Alvarez, José M.; Ouzounis, Christos A.

How Strong Is the Mutagenicity of Recombination in Mammals?
pp. 426-431(6)
Authors: Huang, Shiao-Wei; Friedman, Robert; Yu, Ning; Yu, Alex; Li, Wen-Hsiung

Evolution of Bitter Taste Receptors in Humans and Apes
pp. 432-436(5)
Authors: Fischer, Anne; Gilad, Yoav; Man, Orna; Pääbo, Svante

Physicochemical Evolution and Molecular Adaptation of the Cetacean and Artiodactyl Cytochrome b Proteins
pp. 437-455(19)
Authors: McClellan, D. A.; Palfreyman, E. J.; Smith, M. J.; Moss, J. L.; Christensen, R. G.; Sailsbery, J. K.

A Statistical Characterization of Consistent Patterns of Human Immunodeficiency Virus Evolution Within Infected Patients
pp. 456-468(13)
Authors: Williamson, Scott; Perry, Steven M.; Bustamante, Carlos D.; Orive, Maria E.; Stearns, Miles N.; Kelly, John K.

The Cellular Retinol-Binding Protein Genes Are Duplicated and Differentially Transcribed in the Developing and Adult Zebrafish (Danio rerio)
pp. 469-477(9)
Authors: Liu, Rong-Zong; Sun, Qian; Thisse, Christine; Thisse, Bernard; Wright, Jonathan M.; Denovan-Wright, Eileen M.

A Genetic Algorithm Approach to Detecting Lineage-Specific Variation in Selection Pressure
pp. 478-485(8)
Authors: Pond, Sergei L. Kosakovsky; Frost, Simon D. W.

A Bayesian Analysis of Metazoan Mitochondrial Genome Arrangements
pp. 486-495(10)
Authors: Larget, Bret; Simon, Donald L.; Kadane, Joseph B.; Sweet, Deborah

The Comparative Method Rules! Codon Volatility Cannot Detect Positive Darwinian Selection Using a Single Genome Sequence
pp. 496-500(5)
Authors: Dagan, Tal; Graur, Dan

Divergence Pattern of Duplicate Genes in Protein-Protein Interactions Follows the Power Law
pp. 501-505(5)
Authors: Zhang, Ze; Luo, Z. W.; Kishino, Hirohisa; Kearsey, Mike J.

Molecular Population Genetics and the Search for Adaptive Evolution in Plants
pp. 506-519(14)
Authors: Wright, Stephen I.; Gaut, Brandon S.

Nonhomogeneous Model of Sequence Evolution Indicates Independent Origins of Primary Endosymbionts Within the Enterobacteriales (-Proteobacteria)
pp. 520-532(13)
Authors: Herbeck, Joshua T.; Degnan, Patrick H.; Wernegreen, Jennifer J.

Positive Selection in the Carbohydrate Recognition Domains of Sea Urchin Sperm Receptor for Egg Jelly (suREJ) Proteins
pp. 533-541(9)
Authors: Mah, Silvia A.; Swanson, Willie J.; Vacquier, Victor D.

Codon Volatility As an Indicator of Positive Selection: Data from Eukaryotic Genome Comparisons
pp. 542-546(5)
Authors: Friedman, Robert; Hughes, Austin L.

Codon Bias Signatures, Organization of Microorganisms in Codon Space, and Lifestyle
pp. 547-561(15)
Authors: Carbone, A.; Képès, F.; Zinovyev, A.

The Influence of Mutation, Recombination, Population History, and Selection on Patterns of Genetic Diversity in Neisseria meningitidis
pp. 562-569(8)
Authors: Jolley, K. A.; Wilson, D. J.; Kriz, P.; Mcvean, G.; Maiden, M. C. J.

“Species” Radiations of Symbiotic Dinoflagellates in the Atlantic and Indo-Pacific Since the Miocene-Pliocene Transition
pp. 570-581(12)
Author: LaJeunesse, Todd C.

A Universal Primer Set for PCR Amplification of Nuclear Histone H4 Genes from All Animal Species
pp. 582-588(7)
Authors: Pineau, Pascal; Henry, Michel; Suspène, Rodolphe; Marchio, Agnès; Dettai, Agnès; Debruyne, Régis; Petit, Thierry; Lécu, Alexis; Moisson, Pierre; Dejean, Anne; Wain-Hobson, Simon; Vartanian, Jean-Pierre

Genome-Wide Analysis of Core Cell Cycle Genes in the Unicellular Green Alga Ostreococcus tauri
pp. 589-597(9)
Authors: Robbens, Steven; Khadaroo, Basheer; Camasses, Alain; Derelle, Evelyne; Ferraz, Conchita; Inzé, Dirk; Van de Peer, Yves; Moreau, Hervé

Inverse Relationship Between Evolutionary Rate and Age of Mammalian Genes
pp. 598-606(9)
Authors: Albà, M. Mar; Castresana, Jose

Identifying Signatures of Selection at the Enhancer of split Neurogenic Gene Complex in Drosophila
pp. 607-619(13)
Authors: Macdonald, Stuart J.; Long, Anthony D.

Evolution of Duplicate Control Regions in the Mitochondrial Genomes of Metazoa: A Case Study with Australasian Ixodes Ticks
pp. 620-629(10)
Authors: Shao, Renfu; Barker, Stephen C.; Mitani, Harumi; Aoki, Yayoi; Fukunaga, Masahito

Prediction of Site-Specific Amino Acid Distributions and Limits of Divergent Evolutionary Changes in Protein Sequences
pp. 630-638(9)
Authors: Porto, Markus; Roman, H. Eduardo; Vendruscolo, Michele; Bastolla, Ugo

Survey of Simple Sequence Repeats in Completed Fungal Genomes
pp. 639-649(11)
Authors: Karaoglu, Haydar; Lee, Crystal Man Ying; Meyer, Wieland

CpG Mutation Rates in the Human Genome Are Highly Dependent on Local GC Content
pp. 650-658(9)
Authors: Fryxell, Karl J.; Moon, Won-Jong

Patterns of Diversifying Selection in the Phytotoxin-like scr74 Gene Family of Phytophthora infestans
pp. 659-672(14)
Authors: Liu, Zhenyu; Bos, Jorunn I. B.; Armstrong, Miles; Whisson, Stephen C.; da Cunha, Luis; Torto-Alalibo, Trudy; Win, Joe; Avrova, Anna O.; Wright, Frank; Birch, Paul R. J.; Kamoun, Sophien

Isolation and Characterization of Active LINE and SINEs from the Eel
pp. 673-682(10)
Authors: Kajikawa, Masaki; Ichiyanagi, Kenji; Tanaka, Nozomu; Okada, Norihiro

Lack of Evidence for Horizontal Transfer of the lac Operon into Escherichia coli
pp. 683-690(8)
Author: Stoebel, Daniel M.

Accounting for Uncertainty in the Tree Topology Has Little Effect on the Decision-Theoretic Approach to Model Selection in Phylogeny Estimation
pp. 691-703(13)
Authors: Abdo, Zaid; Minin, Vladimir N.; Joyce, Paul; Sullivan, Jack

Multidimensional Vector Space Representation for Convergent Evolution and Molecular Phylogeny
pp. 704-715(12)
Authors: Kitazoe, Yasuhiro; Kishino, Hirohisa; Okabayashi, Takahisa; Watabe, Teruaki; Nakajima, Noriaki; Okuhara, Yoshiyasu; Kurihara, Yukio

Fast Adaptive Coevolution of Nuclear and Mitochondrial Subunits of ATP Synthetase in Orangutan
pp. 716-724(9)
Authors: Bayona-Bafaluy, Maria Pilar; Müller, Stefan; Moraes, Carlos T.

Genetic Structure of Hmong-Mien Speaking Populations in East Asia as Revealed by mtDNA Lineages
pp. 725-734(10)
Authors: Wen, Bo; Li, Hui; Gao, Song; Mao, Xianyun; Gao, Yang; Li, Feng; Zhang, Feng; He, Yungang; Dong, Yongli; Zhang, Youjun; Huang, Wenju; Jin, Jianzhong; Xiao, Chunjie; Lu, Daru; Chakraborty, Ranajit; Su, Bing; Deka, Ranjan; Jin, Li

Genomic Haplotype Blocks May Not Accurately Reflect Spatial Variation in Historic Recombination Intensity
pp. 735-740(6)
Authors: Verhoeven, Koen J. F.; Simonsen, Katy L.

Recurrent Recruitment of the THAP DNA-Binding Domain and Molecular Domestication of the P-Transposable Element
pp. 741-746(6)
Authors: Quesneville, H.; Nouaud, D.; Anxolabehere, D.

New Regulatory Regions of Drosophila 412 Retrotransposable Element Generated by Recombination
pp. 747-757(11)
Authors: Mugnier, Nathalie; Biémont, Christian; Vieira, Cristina

Degenerative Evolution and Functional Diversification of Type-III Secretion Systems in the Insect Endosymbiont Sodalis glossinidius
pp. 758-766(9)
Authors: Dale, Colin; Jones, Tait; Pontes, Mauricio

Clusters of Co-expressed Genes in Mammalian Genomes Are Conserved by Natural Selection
pp. 767-775(9)
Authors: Singer, Gregory A. C.; Lloyd, Andrew T.; Huminiecki, Lukasz B.; Wolfe, Kenneth H.

Naturally Occurring Transposable Elements Disrupt hsp70 Promoter Function in Drosophila melanogaster
pp. 776-783(8)
Authors: Lerman, Daniel N.; Feder, Martin E.

Impact of Taxon Sampling on the Estimation of Rates of Evolution at Sites
pp. 784-791(8)
Authors: Blouin, C.; Butt, D.; Roger, A. J.

Comparison of the Accuracies of Several Phylogenetic Methods Using Protein and DNA Sequences
pp. 792-802(11)
Author: Hall, Barry G.