Molecular Biology and Evolution - 28 (11-12), 2011

Molecular Biology and Evolution - 28 (11), 2011



Contents:

Letters

John Steven Torday and Virender Kumar Rehan
A Cell–Molecular Approach Predicts Vertebrate Evolution

Mizuko Osanai-Futahashi and Haruhiko Fujiwara
Coevolution of Telomeric Repeats and Telomeric Repeat–Specific Non-LTR Retrotransposons in Insects

Alex de Mendoza and Inaki Ruiz-Trillo
The Mysterious Evolutionary Origin for the GNE Gene and the Root of Bilateria

Alexander Suh, Jan Ole Kriegs, Jürgen Brosius, and Jürgen Schmitz
Retroposon Insertions and the Chronology of Avian Sex Chromosome Evolution

Miriam Linnenbrink, Jill M. Johnsen, Inka Montero, Christine R. Brzezinski, Bettina Harr, and John F. Baines
Long-Term Balancing Selection at the Blood Group-Related Gene B4galnt2 in the Genus Mus (Rodentia; Muridae)

Kenta Sumiyama and Naruya Saitou
Loss-of-Function Mutation in a Repressor Module of Human-Specifically Activated Enhancer HACNS1


Research Articles


Rob W. Ness, Sean W. Graham, and Spencer C. H. Barrett
Reconciling Gene and Genome Duplication Events: Using Multiple Nuclear Gene Families to Infer the Phylogeny of the Aquatic Plant Family Pontederiaceae

Alexis Criscuolo and Simonetta Gribaldo
Large-Scale Phylogenomic Analyses Indicate a Deep Origin of Primary Plastids within Cyanobacteria

Sergei L. Kosakovsky Pond, Ben Murrell, Mathieu Fourment, Simon D.W. Frost, Wayne Delport, and Konrad Scheffler
A Random Effects Branch-Site Model for Detecting Episodic Diversifying Selection

Vivek Jayaswal, Faisal Ababneh, Lars S Jermiin, and John Robinson
Reducing Model Complexity of the General Markov Model of Evolution

Sergio Lukic and Kevin Chen
Human piRNAs Are Under Selection in Africans and Repress Transposable Elements

Erick C. Castelli, Celso T. Mendes-Junior, Luciana C. Veiga-Castelli, Michel Roger, Philippe Moreau, and Eduardo A. Donadi
A Comprehensive Study of Polymorphic Sites along the HLA-G Gene: Implication for Gene Regulation and Evolution

Simona Fornarino, Guillaume Laval, Luis B. Barreiro, Jeremy Manry, Estelle Vasseur, and Lluis Quintana-Murci
Evolution of the TIR Domain-Containing Adaptors in Humans: Swinging between Constraint and Adaptation

Mayumi I. Nonaka, Kouichi Aizawa, Hiroshi Mitani, Hidemi P. Bannai, and Masaru Nonaka
Retained Orthologous Relationships of the MHC Class I Genes during Euteleost Evolution

Daniel R. G. Price, Rebecca P. Duncan, Shuji Shigenobu, and Alex C. C. Wilson
Genome Expansion and Differential Expression of Amino Acid Transporters at the Aphid/Buchnera Symbiotic Interface

Xianfa Xie, Wei-Gang Qiu, and Peter N. Lipke
Accelerated and Adaptive Evolution of Yeast Sexual Adhesins

J. Jacquemin, C. Chaparro, M. Laudié, A. Berger, F. Gavory, J. L. Goicoechea, R. A. Wing, and R. Cooke
Long-Range and Targeted Ectopic Recombination between the Two Homeologous Chromosomes 11 and 12 in Oryza Species

Cinta Zapater, François Chauvigné, Birgitta Norberg, Roderick Nigel Finn, and Joan Cerda
Dual Neofunctionalization of a Rapidly Evolving Aquaporin-1 Paralog Resulted in Constrained and Relaxed Traits Controlling Channel Function during Meiosis Resumption in Teleosts

Brendan D. O'Fallon
A Method for Accurate Inference of Population Size from Serially Sampled Genealogies Distorted by Selection

Xiaowei Jiang and Mario A. Fares
Functional Diversification of the Twin-Arginine Translocation Pathway Mediates the Emergence of Novel Ecological Adaptations

Virag Sharma, Andrew E. Firth, Ivan Antonov, Olivier Fayet, John F. Atkins, Mark Borodovsky, and Pavel V. Baranov
A Pilot Study of Bacterial Genes with Disrupted ORFs Reveals a Surprising Profusion of Protein Sequence Recoding Mediated by Ribosomal Frameshifting and Transcriptional Realignment

Vicky Merhej, Cedric Notredame, Manuela Royer-Carenzi, Pierre Pontarotti, and Didier Raoult
The Rhizome of Life: The Sympatric Rickettsia felis Paradigm Demonstrates the Random Transfer of DNA Sequences


Standing Material

Associate Editors
SMBE Editors and Council
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Molecular Biology and Evolution - 28 (12), 2011



Contents:

Research Articles

Nolan C. Kane, Michael S. Barker, Shing H. Zhan, and Loren H. Rieseberg
Molecular Evolution across the Asteraceae: Micro- and Macroevolutionary Processes

Xing-Xing Shen, Dan Liang, Jun-Zhi Wen, and Peng Zhang
Multiple Genome Alignments Facilitate Development of NPCL Markers: A Case Study of Tetrapod Phylogeny Focusing on the Position of Turtles

Astrid Collingro, Patrick Tischler, Thomas Weinmaier, Thomas Penz, Eva Heinz, Robert C. Brunham, Timothy D. Read, Patrik M. Bavoil, Konrad Sachse, Simona Kahane, Maureen G. Friedman, Thomas Rattei, Garry S. A. Myers, and Matthias Horn
Unity in Variety—The Pan-Genome of the Chlamydiae

Yannis Guillemin, Aurélie Cornut-Thibaut, Germain Gillet, François Penin, and Abdel Aouacheria
Characterization of Unique Signature Sequences in the Divergent Maternal Protein Bcl2l10

Davide Sassera, Nathan Lo, Sara Epis, Giuseppe D'Auria, Matteo Montagna, Francesco Comandatore, David Horner, Juli Peretó, Alberto Maria Luciano, Federica Franciosi, Emanuele Ferri, Elena Crotti, Chiara Bazzocchi, Daniele Daffonchio, Luciano Sacchi, Andres Moya, Amparo Latorre, and Claudio Bandi
Phylogenomic Evidence for the Presence of a Flagellum and cbb3 Oxidase in the Free-Living Mitochondrial Ancestor

Nimrod D. Rubinstein, Adi Doron-Faigenboim, Itay Mayrose, and Tal Pupko
Evolutionary Models Accounting for Layers of Selection in Protein-Coding Genes and their Impact on the Inference of Positive Selection

Nimrod D. Rubinstein, David Zeevi, Yaara Oren, Gil Segal, and Tal Pupko
The Operonic Location of Auto-transcriptional Repressors Is Highly Conserved in Bacteria

Manuela Sironi, Franca Rosa Guerini, Cristina Agliardi, Mara Biasin, Rachele Cagliani, Matteo Fumagalli, Domenico Caputo, Andrea Cassinotti, Sandro Ardizzone, Milena Zanzottera, Elisabetta Bolognesi, Stefania Riva, Yasuyoshi Kanari, Masaaki Miyazawa, and Mario Clerici
An Evolutionary Analysis of RAC2 Identifies Haplotypes Associated with Human Autoimmune Diseases

Ryan M. Ames and Simon C. Lovell
Diversification at Transcription Factor Binding Sites within a Species and the Implications for Environmental Adaptation

Jungsun Park, Zuogang Peng, Jia Zeng, Navin Elango, Taesung Park, Dave Wheeler, John H. Werren, and Soojin V. Yi
Comparative Analyses of DNA Methylation and Sequence Evolution Using Nasonia Genomes

Joel O. Wertheim and Sergei L. Kosakovsky Pond
Purifying Selection Can Obscure the Ancient Age of Viral Lineages

Hae-Lim Lee and Vivian F. Irish
Gene Duplication and Loss in a MADS Box Gene Transcription Factor Circuit

Rudolf J. Schilder, Anthony J. Zera, Christine Black, Mallary Hoidal, and Cody Wehrkamp
The Biochemical Basis of Life History Adaptation: Molecular and Enzymological Causes of NADP+-Isocitrate Dehydrogenase Activity Differences Between Morphs of Gryllus firmus That Differ in Lipid Biosynthesis and Life History

Anna Muszewska, John W. Taylor, Pawel Szczesny (Paweł Szczęsny), and Marcin Grynberg
Independent Subtilases Expansions in Fungi Associated with Animals


Editorial


Barry G. Hall, Francisco J. Ayala, and Marcella A. McClure
Remembrances of Walter M. Fitch


Standing Material

Associate Editors
SMBE Editors and Council
Subscription Page

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