Molecular Biology and Evolution - 28 (7-8), 2011

Molecular Biology and Evolution - 28 (7), 2011



Contents:

Letters

Vania Yotova, Jean-Francois Lefebvre, Claudia Moreau, Elias Gbeha, Kristine Hovhannesyan, Stephane Bourgeois, Sandra Bédarida, Luisa Azevedo, Antonio Amorim, Tamara Sarkisian, Patrice Hodonou Avogbe, Nicodeme Chabi, Mamoudou Hama Dicko, Emile Sabiba Kou' Santa Amouzou, Ambaliou Sanni, June Roberts-Thomson, Barry Boettcher, Rodney J. Scott, and Damian Labuda
An X-Linked Haplotype of Neandertal Origin Is Present Among All Non-African Populations

Willie J. Swanson, Jan E. Aagaard, Victor D. Vacquier, Magnus Monné, Hamed Sadat Al Hosseini, and Luca Jovine
The Molecular Basis of Sex: Linking Yeast to Human

María Méndez-Lago, Casey M. Bergman, Beatriz de Pablos, Alan Tracey, Siobhan L. Whitehead, and Alfredo Villasante
A Large Palindrome With Interchromosomal Gene Duplications in the Pericentromeric Region of the D. melanogaster Y Chromosome


Research Articles

OraLee H. Branch, Patrick L. Sutton, Carmen Barnes, Juan Carlos Castro, Julie Hussin, Philip Awadalla, and Gisely Hijar
Plasmodium falciparum Genetic Diversity Maintained and Amplified Over 5 Years of a Low Transmission Endemic in the Peruvian Amazon

Simon H. Martin, Brenda D. Wingfield, Michael J. Wingfield, and Emma T. Steenkamp
Causes and Consequences of Variability in Peptide Mating Pheromones of Ascomycete Fungi

Masaya Hayashi, Brenda Schilke, Jaroslaw Marszalek (Jarosław Marszałek), Barry Williams, and Elizabeth A. Craig
Ancient Gene Duplication Provided a Key Molecular Step for Anaerobic Growth of Baker's Yeast

Andrew H. Lloyd and Jeremy N. Timmis
The Origin and Characterization of New Nuclear Genes Originating from a Cytoplasmic Organellar Genome

Michael L. Hayes and R. Michael Mulligan
Pentatricopeptide Repeat Proteins Constrain Genome Evolution in Chloroplasts

Stefan J.Y. Laurent, Annegret Werzner, Laurent Excoffier, and Wolfgang Stephan
Approximate Bayesian Analysis of Drosophila melanogaster Polymorphism Data Reveals a Recent Colonization of Southeast Asia

Kazuhiko Kawasaki, Anne-Gaelle Lafont, and Jean-Yves Sire
The Evolution of Milk Casein Genes from Tooth Genes before the Origin of Mammals

Michelle Déquard-Chablat, Carole H. Sellem, Pawel Golik, Frédérique Bidard, Alexandre Martos, Mailis Bietenhader, Jean-Paul di Rago, Annie Sainsard-Chanet, Sylvie Hermann-Le Denmat, and Véronique Contamine
Two Nuclear Life Cycle–Regulated Genes Encode Interchangeable Subunits c of Mitochondrial ATP Synthase in Podospora anserina

Etienne Delannoy, Sota Fujii, Catherine Colas des Francs - Small, Mark Brundrett, and Ian Small
Rampant Gene Loss in the Underground Orchid Rhizanthella gardneri Highlights Evolutionary Constraints on Plastid Genomes

Courtney W. Stairs, Andrew J. Roger, and Vladimir Hampl
Eukaryotic Pyruvate Formate Lyase and Its Activating Enzyme Were Acquired Laterally from a Firmicute

Marc Gottschling, Markus Göker, Alexandros Stamatakis, Olaf R.P. Bininda-Emonds, Ingo Nindl, and Ignacio G. Bravo
Quantifying the Phylodynamic Forces Driving Papillomavirus Evolution

Nicholas Price, Reed A. Cartwright, Niv Sabath, Dan Graur, and Ricardo B.R. Azevedo
Neutral Evolution of Robustness in Drosophila microRNA Precursors

Eric Samarut, Ismail Amal, Gabriel V. Markov, Roland Stote, Annick Dejaegere, Vincent Laudet, and Cécile Rochette-Egly
Evolution of Nuclear Retinoic Acid Receptor Alpha (RAR?) Phosphorylation Sites. Serine Gain Provides Fine-Tuned Regulation

Bradley R. Parry and Daniel H. Shain
Manipulations of AMP Metabolic Genes Increase Growth Rate and Cold Tolerance in Escherichia coli: Implications for Psychrophilic Evolution

Daniel P. Woods, Chelsea L. Hope, and Simon T. Malcomber
Phylogenomic Analyses of the BARREN STALK1/LAX PANICLE1 (BA1/LAX1) Genes and Evidence for Their Roles During Axillary Meristem Development

Mario dos Reis and Ziheng Yang
Approximate Likelihood Calculation on a Phylogeny for Bayesian Estimation of Divergence Times


Standing Material

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Molecular Biology and Evolution - 28 (8), 2011



Contents:

Research Articles

Ivan Molineris, Elena Grassi, Ugo Ala, Ferdinando Di Cunto, and Paolo Provero
Evolution of Promoter Affinity for Transcription Factors in the Human Lineage

Carlos E. Arboleda-Bustos and Carmen Segarra
The Dca Gene Involved in Cold Adaptation in Drosophila melanogaster Arose by Duplication of the Ancestral regucalcin Gene

Benoit Nabholz, Axel Künstner, Rui Wang, Erich D. Jarvis, and Hans Ellegren
Dynamic Evolution of Base Composition: Causes and Consequences in Avian Phylogenomics

Sung K. Kim, Lucia Carbone, Celine Becquet, Alan R. Mootnick, David Jiang Li, Pieter J. de Jong, and Jeffrey D. Wall
Patterns of Genetic Variation Within and Between Gibbon Species

Andre G. Wallace, Don Detweiler, and Stephen W. Schaeffer
Evolutionary History of the Third Chromosome Gene Arrangements of Drosophila pseudoobscura Inferred from Inversion Breakpoints

Jeffrey D. Wall, Rong Jiang, Christopher Gignoux, Gary K. Chen, Celeste Eng, Scott Huntsman, and Paul Marjoram
Genetic Variation in Native Americans, Inferred from Latino SNP and Resequencing Data

Eric Y. Durand, Nick Patterson, David Reich, and Montgomery Slatkin
Testing for Ancient Admixture between Closely Related Populations

Bruno Nevado, Varvara Fazalova, Thierry Backeljau, Mark Hanssens, and Erik Verheyen
Repeated Unidirectional Introgression of Nuclear and Mitochondrial DNA Between Four Congeneric Tanganyikan Cichlids

Yi-Wah Chan, Remus Mohr, Andrew D. Millard, Antony B. Holmes, Anthony W. Larkum, Anna L. Whitworth, Nicholas H. Mann, David J. Scanlan, Wolfgang R. Hess, and Martha R. J. Clokie
Discovery of Cyanophage Genomes Which Contain Mitochondrial DNA Polymerase

Alexander Nater, Pirmin Nietlisbach, Natasha Arora, Carel P. van Schaik, Maria A. van Noordwijk, Erik P. Willems, Ian Singleton, Serge A. Wich, Benoit Goossens, Kristin S. Warren, Ernst J. Verschoor, Dyah Perwitasari-Farajallah, Joko Pamungkas, and Michael Krützen
Sex-Biased Dispersal and Volcanic Activities Shaped Phylogeographic Patterns of Extant Orangutans (genus: Pongo)

Pierre Kerner, Sandie M. Degnan, Lauriane Marchand, Bernard M. Degnan, and Michel Vervoort
Evolution of RNA-Binding Proteins in Animals: Insights from Genome-Wide Analysis in the Sponge Amphimedon queenslandica

Huai-Chun Wang, Edward Susko, and Andrew J. Roger
Fast Statistical Tests for Detecting Heterotachy in Protein Evolution

Ruxandra I. Molnar, Gabi Bartelmes, Iris Dinkelacker, Hanh Witte, and Ralf J. Sommer
Mutation Rates and Intraspecific Divergence of the Mitochondrial Genome of Pristionchus pacificus

Chun-Long Chen, Lauranne Duquenne, Benjamin Audit, Guillaume Guilbaud, Aurélien Rappailles, Antoine Baker, Maxime Huvet, Yves d'Aubenton-Carafa, Olivier Hyrien, Alain Arneodo, and Claude Thermes
Replication-Associated Mutational Asymmetry in the Human Genome

Tobias Warnecke and Eduardo P. C. Rocha
Function-Specific Accelerations in Rates of Sequence Evolution Suggest Predictable Epistatic Responses to Reduced Effective Population Size

Chungoo Park and Jianzhi Zhang
Genome-Wide Evolutionary Conservation of N-Glycosylation Sites

Liang Yang and Brandon S. Gaut
Factors that Contribute to Variation in Evolutionary Rate among Arabidopsis Genes

Jana Szabová, Petr Růžička, Zdeněk Verner, Vladimír Hampl, and Julius Lukeš
Experimental Examination of EFL and MATX Eukaryotic Horizontal Gene Transfers: Coexistence of Mutually Exclusive Transcripts Predates Functional Rescue

Rob M. de Graaf, Guenola Ricard, Theo A. van Alen, Isabel Duarte, Bas E. Dutilh, Carola Burgtorf, Jan W. P. Kuiper, Georg W. M. van der Staay, Aloysius G. M. Tielens, Martijn A. Huynen, and Johannes H. P. Hackstein
The Organellar Genome and Metabolic Potential of the Hydrogen-Producing Mitochondrion of Nyctotherus ovalis

Siu F. Lee, Ying Chen, Aiden K. Varan, Choon W. Wee, Lea Rako, Jason K. Axford, Robert T. Good, Mark J. Blacket, Caroline Reuter, Linda Partridge, and Ary A. Hoffmann
Molecular Basis of Adaptive Shift in Body Size in Drosophila melanogaster: Functional and Sequence Analyses of the Dca Gene

Dror Hilman and Uri Gat
The Evolutionary History of YAP and the Hippo/YAP Pathway

Corrigendum

Corrigendum

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