Molecular Biology and Evolution - 28 (9-10), 2011

Molecular Biology and Evolution - 28 (9), 2011



Contents:

Letters

Kyriakos Felekkis, Konstantinos Voskarides, Harsh Dweep, Carsten Sticht, Norbert Gretz, and Constantinos Deltas
Increased Number of MicroRNA Target Sites in Genes Encoded in CNV Regions. Evidence for an Evolutionary Genomic Interaction

Georgette N. Kiethega, Marcel Turcotte, and Gertraud Burger
Evolutionarily Conserved cox1 Trans-Splicing Without cis-Motifs

Shohei Takuno and Hideki Innan
Selection Fine-Tunes the Expression of MicroRNA Target Genes in Arabidopsis thaliana

Andrea Blanquer and Maria-J. Uriz
“Living Together Apart”: The Hidden Genetic Diversity of Sponge Populations

Fabia U. Battistuzzi, Paul Billing-Ross, Aditya Paliwal, and Sudhir Kumar
Fast and Slow Implementations of Relaxed-Clock Methods Show Similar Patterns of Accuracy in Estimating Divergence Times

Research Articles


Samir Bhatt, Edward C. Holmes, and Oliver G. Pybus
The Genomic Rate of Molecular Adaptation of the Human Influenza A Virus

Pedro Patraquim, Maria Warnefors, and Claudio R. Alonso
Evolution of Hox Post-Transcriptional Regulation by Alternative Polyadenylation and MicroRNA Modulation Within 12 Drosophila Genomes

Héloise Bastide, Michel Cazemajor, David Ogereau, Nicolas Derome, Frédéric Hospital, and Catherine Montchamp-Moreau
Rapid Rise and Fall of Selfish Sex-Ratio X Chromosomes in Drosophila simulans: Spatiotemporal Analysis of Phenotypic and Molecular Data

Karl J. V. Nordström, Markus Sällman Almén, Monika M. Edstam, Robert Fredriksson, and Helgi B. Schiöth
Independent HHsearch, Needleman–Wunsch-Based, and Motif Analyses Reveal the Overall Hierarchy for Most of the G Protein-Coupled Receptor Families

Axel Künstner, Benoit Nabholz, and Hans Ellegren
Evolutionary Constraint in Flanking Regions of Avian Genes

Viktor Černý, Luísa Pereira, Eliška Musilová, Martina Kujanová, Alžběta Vašíková, Paola Blasi, Luisa Garofalo, Pedro Soares, Issa Diallo, Radim Brdička, and Andrea Novelletto
Genetic Structure of Pastoral and Farmer Populations in the African Sahel

Fabian J. Theis, Nadia Latif, Philip Wong, and Dmitrij Frishman
Complex Principal Component and Correlation Structure of 16 Yeast Genomic Variables

Sean Chun-Chang Chen, Trees-Juen Chuang, and Wen-Hsiung Li
The Relationships Among MicroRNA Regulation, Intrinsically Disordered Regions, and Other Indicators of Protein Evolutionary Rate

Yuchi Zheng, Rui Peng, Masaki Kuro-o, and Xiaomao Zeng
Exploring Patterns and Extent of Bias in Estimating Divergence Time from Mitochondrial DNA Sequence Data in a Particular Lineage: A Case Study of Salamanders (Order Caudata)

A. N. Massa, H. Wanjugi, K. R. Deal, K. O'Brien, F. M. You, R. Maiti, A. P. Chan, Y. Q. Gu, M. C. Luo, O. D. Anderson, P. D. Rabinowicz, J. Dvorak, and K. M. Devos
Gene Space Dynamics During the Evolution of Aegilops tauschii, Brachypodium distachyon, Oryza sativa, and Sorghum bicolor Genomes

Stephanie Sun, Ben J. Evans, and G. Brian Golding
“Patchy-Tachy” Leads to False Positives for Recombination

Juan S. Escobar, Sylvain Glémin, and Nicolas Galtier
GC-Biased Gene Conversion Impacts Ribosomal DNA Evolution in Vertebrates, Angiosperms, and Other Eukaryotes

Sebastian Höhna, Tanja Stadler, Fredrik Ronquist, and Tom Britton
Inferring Speciation and Extinction Rates under Different Sampling Schemes

Olivier Rey, Anne Loiseau, Benoit Facon, Julien Foucaud, Jérôme Orivel, Jean-Marie Cornuet, Stéphanie Robert, Gauthier Dobigny, Jacques Hubert Charles Delabie, Cléa Dos Santos Ferreria Mariano, and Arnaud Estoup
Meiotic Recombination Dramatically Decreased in Thelytokous Queens of the Little Fire Ant and Their Sexually Produced Workers

Chiara Batini, Gianmarco Ferri, Giovanni Destro-Bisol, Francesca Brisighelli, Donata Luiselli, Paula Sánchez-Diz, Jorge Rocha, Tatum Simonson, Antonio Brehm, Valeria Montano, Nasr Eldin Elwali, Gabriella Spedini, María Eugenia D'Amato, Natalie Myres, Peter Ebbesen, David Comas, and Cristian Capelli
Signatures of the Preagricultural Peopling Processes in Sub-Saharan Africa as Revealed by the Phylogeography of Early Y Chromosome Lineages

Anchal Vishnoi, Praveen Sethupathy, Daniel Simola, Joshua B. Plotkin, and Sridhar Hannenhalli
Genome-Wide Survey of Natural Selection on Functional, Structural, and Network Properties of Polymorphic Sites in Saccharomyces paradoxus

Madhavi Nayar and George E. Fox
Defining 5S rRNA Structure Space: Point Mutation Data Can Be Used to Predict the Phenotype of Multichange Variants

Nicholas R. Casewell, Simon C. Wagstaff, Robert A. Harrison, Camila Renjifo, and Wolfgang Wüster
Domain Loss Facilitates Accelerated Evolution and Neofunctionalization of Duplicate Snake Venom Metalloproteinase Toxin Genes

Daniel L. Halligan, Fiona Oliver, Jack Guthrie, Kathryn C. Stemshorn, Bettina Harr, and Peter D. Keightley
Positive and Negative Selection in Murine Ultraconserved Noncoding Elements

Mathieu Groussin and Manolo Gouy
Adaptation to Environmental Temperature Is a Major Determinant of Molecular Evolutionary Rates in Archaea

Jouhyun Jeon, Hyun-Jun Nam, Yoon Sup Choi, Jae-Seong Yang, Jihye Hwang, and Sanguk Kim
Molecular Evolution of Protein Conformational Changes Revealed by a Network of Evolutionarily Coupled Residues

Sankar Subramanian
Fixation of Deleterious Mutations at Critical Positions in Human Proteins

Aline Muyle, Laurana Serres-Giardi, Adrienne Ressayre, Juan Escobar, and Sylvain Glémin
GC-Biased Gene Conversion and Selection Affect GC Content in the Oryza Genus (rice)

Benoît Moury and Vincent Simon
dN/dS-Based Methods Detect Positive Selection Linked to Trade-Offs between Different Fitness Traits in the Coat Protein of Potato virus Y

Corrigendum

Exploring the differences in evolutionary rates between monogenic and polygenic disease genes in human


Retraction

Christopher Sauvage, Sébastien Renaut, Eric Normandeau, Nicolas Derome, and Louis Bernatchez
Investigating the Role of Natural Selection on Coding Sequence Evolution in Salmonids Through NGS Data Mining


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Molecular Biology and Evolution - 28 (10), 2011



Contents:

Letters

Josselin Bodilis, Sandrine Nsigue Meilo, Pierre Cornelis, Paul De Vos, and Sylvie Barray
A Long-Branch Attraction Artifact Reveals an Adaptive Radiation in Pseudomonas

Oliver Piskurek and Daniel J. Jackson
Tracking the Ancestry of a Deeply Conserved Eumetazoan SINE Domain

Research Resource

Koichiro Tamura, Daniel Peterson, Nicholas Peterson, Glen Stecher, Masatoshi Nei, and Sudhir Kumar
MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

Research Articles

K. Hartnup, L. Huynen, R. Te Kanawa, L.D. Shepherd, C.D. Millar, and D.M. Lambert
Ancient DNA Recovers the Origins of Maori Feather Cloaks

Haiwei Luo, Robert Friedman, Jijun Tang, and Austin L. Hughes
Genome Reduction by Deletion of Paralogs in the Marine Cyanobacterium Prochlorococcus

Célestine M. Atyame, Frédéric Delsuc, Nicole Pasteur, Mylene Weill, and Olivier Duron
Diversification of Wolbachia Endosymbiont in the Culex pipiens Mosquito

Jessica W. Leigh, Klaus Schliep, Philippe Lopez, and Eric Bapteste
Let Them Fall Where They May: Congruence Analysis in Massive Phylogenetically Messy Data Sets

Shinichiro Hayashi, Didier Rocancourt, Margaret Buckingham, and Frederic Relaix
Lack of In Vivo Functional Compensation Between Pax Family Groups II and III in Rodents

Stacey D. Smith and Mark D. Rausher
Gene Loss and Parallel Evolution Contribute to Species Difference in Flower Color

Zélia Ferreira, Belen Hurle, Jorge Rocha, and Susana Seixas
Differing Evolutionary Histories of WFDC8 (Short-Term Balancing) in Europeans and SPINT4 (Incomplete Selective Sweep) in Africans

Zhen-Xia Chen, Yong E. Zhang, Maria Vibranovski, Jingchu Luo, Ge Gao, and Manyuan Long
Deficiency of X-Linked Inverted Duplicates with Male-Biased Expression and the Underlying Evolutionary Mechanisms in the Drosophila Genome

Renchao Zhou, Shaoping Ling, Wenming Zhao, Naoki Osada, Sufang Chen, Meng Zhang, Ziwen He, Hua Bao, Cairong Zhong, Bing Zhang, Xuemei Lu, David Turissini, Norman C. Duke, Jian Lu, Suhua Shi, and Chung-I Wu
Population Genetics in Nonmodel Organisms: II. Natural Selection in Marginal Habitats Revealed by Deep Sequencing on Dual Platforms

Simon Renny-Byfield, Michael Chester, Ales Kovařík, Steven C. Le Comber, Marie-Angele Grandbastien, Marc Deloger, Richard A. Nichols, Jiri Macas, Petr Novák, Mark W. Chase, and Andrew R. Leitch
Next Generation Sequencing Reveals Genome Downsizing in Allotetraploid Nicotiana tabacum, Predominantly through the Elimination of Paternally Derived Repetitive DNAs

Jeremy D. DeBarry and Jessica C. Kissinger
Jumbled Genomes: Missing Apicomplexan Synteny

Romulo Segovia, Walker Pett, Steve Trewick, and Dennis V. Lavrov
Extensive and Evolutionarily Persistent Mitochondrial tRNA Editing in Velvet Worms (Phylum Onychophora)

Austen R.D. Ganley and Takehiko Kobayashi
Monitoring the Rate and Dynamics of Concerted Evolution in the Ribosomal DNA Repeats of Saccharomyces cerevisiae Using Experimental Evolution

Yangyun Zou, Wei Huang, Zhenglong Gu, and Xun Gu
Predominant Gain of Promoter TATA Box after Gene Duplication Associated with Stress Responses

Oleg Balanovsky, Khadizhat Dibirova, Anna Dybo, Oleg Mudrak, Svetlana Frolova, Elvira Pocheshkhova, Marc Haber, Daniel Platt, Theodore Schurr, Wolfgang Haak, Marina Kuznetsova, Magomed Radzhabov, Olga Balaganskaya, Alexey Romanov, Tatiana Zakharova, David F. Soria Hernanz, Pierre Zalloua, Sergey Koshel, Merritt Ruhlen, Colin Renfrew, R. Spencer Wells, Chris Tyler-Smith, Elena Balanovska, and The Genographic Consortium
Parallel Evolution of Genes and Languages in the Caucasus Region

Katherine E. Helliwell, Glen L. Wheeler, Kyriacos C. Leptos, Raymond E. Goldstein, and Alison G. Smith
Insights into the Evolution of Vitamin B12 Auxotrophy from Sequenced Algal Genomes

Kamil A. Lipinski, Olga Puchta, Vineeth Surendranath, Marek Kudla and Pawel Golik
Revisiting the Yeast PPR Proteins—Application of an Iterative Hidden Markov Model Algorithm Reveals New Members of the Rapidly Evolving Family

Jonathan M. Mudge, Adam Frankish, Julio Fernandez-Banet, Tyler Alioto, Thomas Derrien, Cédric Howald, Alexandre Reymond, Roderic Guigó, Tim Hubbard, and Jennifer Harrow
The Origins, Evolution, and Functional Potential of Alternative Splicing in Vertebrates

Susan L. Young, Daniel Diolaiti, Maralice Conacci-Sorrell, Inaki Ruiz-Trillo, Robert N. Eisenman, and Nicole King
Premetazoan Ancestry of the Myc–Max Network


Standing Material

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SMBE Editors and Council
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