Molecular Biology and Evolution - 28 (5-6), 2011

Molecular Biology and Evolution - 28 (5), 2011



Contents:

Dvir Dahary, Reut Shalgi, and Yitzhak Pilpel
CpG Islands as a Putative Source for Animal miRNAs: Evolutionary and Functional Implications

Zhaofeng Wang, Takahiro Yonezawa, Bin Liu, Tao Ma, Xin Shen, Jianping Su, Songchang Guo, Masami Hasegawa, and Jianquan Liu
Domestication Relaxed Selective Constraints on the Yak Mitochondrial Genome

Sara Guirao-Rico and Montserrat Aguadé
Molecular Evolution of the Ligands of the Insulin-Signaling Pathway: dilp Genes in the Genus Drosophila

Claus Kemkemer, Winfried Hense, and John Parsch
Fine-Scale Analysis of X Chromosome Inactivation in the Male Germ Line of Drosophila melanogaster

Vanessa E. Gray and Sudhir Kumar
Rampant Purifying Selection Conserves Positions with Posttranslational Modifications in Human Proteins

Jared L. Strasburg, Nolan C. Kane, Andrew R. Raduski, Aurélie Bonin, Richard Michelmore, and Loren H. Rieseberg
Effective Population Size Is Positively Correlated with Levels of Adaptive Divergence among Annual Sunflowers

Janette Tong, Pavel Dolezal, Joel Selkrig, Simon Crawford, Alistair G.B. Simpson, Nicholas Noinaj, Susan K. Buchanan, Kipros Gabriel, and Trevor Lithgow
Ancestral and Derived Protein Import Pathways in the Mitochondrion of Reclinomonas americana

Rebecca R. Gray, Andrew J. Tatem, Judith A. Johnson, Alexander V. Alekseyenko, Oliver G. Pybus, Marc A. Suchard, and Marco Salemi
Testing Spatiotemporal Hypothesis of Bacterial Evolution Using Methicillin-Resistant Staphylococcus aureus ST239 Genome-wide Data within a Bayesian Framework

Diana Edo-Matas, Philippe Lemey, Jennifer A. Tom, Celia Serna-Bolea, Agnes E. van den Blink, Angélique B. van 't Wout, Hanneke Schuitemaker, and Marc A. Suchard
Impact of CCR5delta32 Host Genetic Background and Disease Progression on HIV-1 Intrahost Evolutionary Processes: Efficient Hypothesis Testing through Hierarchical Phylogenetic Models

Yosef E. Maruvka, Nadav M. Shnerb, Yaneer Bar-Yam, and John Wakeley
Recovering Population Parameters from a Single Gene Genealogy: An Unbiased Estimator of the Growth Rate

Dmitri A. Petrov, Anna-Sophie Fiston-Lavier, Mikhail Lipatov, Kapa Lenkov, and Josefa González
Population Genomics of Transposable Elements in Drosophila melanogaster

Sophie Breton, Donald T. Stewart, Sally Shepardson, Richard J. Trdan, Arthur E. Bogan, Eric G. Chapman, Andrew J. Ruminas, Helen Piontkivska, and Walter R. Hoeh
Novel Protein Genes in Animal mtDNA: A New Sex Determination System in Freshwater Mussels (Bivalvia: Unionoida)?

Jihua Wu and Edward Susko
A Test for Heterotachy Using Multiple Pairs of Sequences

Jeffrey M. Good, Dan Vanderpool, Kimberly L. Smith, and Michael W. Nachman
Extraordinary Sequence Divergence at Tsga8, an X-linked Gene Involved in Mouse Spermiogenesis

Christina Lange, Georg Hemmrich, Ulrich C. Klostermeier, Javier A. López-Quintero, David J. Miller, Tasja Rahn, Yvonne Weiss, Thomas C.G. Bosch, and Philip Rosenstiel
Defining the Origins of the NOD-Like Receptor System at the Base of Animal Evolution

Miguel Alcaide and Scott V. Edwards
Molecular Evolution of the Toll-Like Receptor Multigene Family in Birds

Jeremiah W. Busch, Simon Joly, and Daniel J. Schoen
Demographic Signatures Accompanying the Evolution of Selfing in Leavenworthia alabamica

Penelope R. Haddrill, Kai Zeng, and Brian Charlesworth
Determinants of Synonymous and Nonsynonymous Variability in Three Species of Drosophila

Asher D. Cutter and Alan M. Moses
Polymorphism, Divergence, and the Role of Recombination in Saccharomyces cerevisiae Genome Evolution

Standing Material

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Molecular Biology and Evolution - 28 (6), 2011



Contents:

Research Articles

Mario dos Reis, Asif U. Tamuri, Alan J. Hay, and Richard A. Goldstein
Charting the Host Adaptation of Influenza Viruses

Haruka Nagai, Yohey Terai, Tohru Sugawara, Hiroo Imai, Hidenori Nishihara, Michio Hori, and Norihiro Okada
Reverse Evolution in RH1 for Adaptation of Cichlids to Water Depth in Lake Tanganyika

Lars Feuerbach, Rune B. Lyngso, Thomas Lengauer, and Jotun Hein
Reconstructing the Ancestral Germ Line Methylation State of Young Repeats

Hong-Song Yu, Yi-Hong Shen, Gang-Xiang Yuan, Yong-Gang Hu, Hong-En Xu, Zhong-Huai Xiang, and Ze Zhang
Evidence of Selection at Melanin Synthesis Pathway Loci during Silkworm Domestication

Miguel Carneiro, Sandra Afonso, Armando Geraldes, Hervé Garreau, Gerard Bolet, Samuel Boucher, Aurélie Tircazes, Guillaume Queney, Michael W. Nachman, and Nuno Ferrand
The Genetic Structure of Domestic Rabbits

Larissa M. Williams and Marjorie F. Oleksiak
Ecologically and Evolutionarily Important SNPs Identified in Natural Populations

Anna van Weringh, Manon Ragonnet-Cronin, Erinija Pranckeviciene, Mariana Pavon-Eternod, Lawrence Kleiman, and Xuhua Xia
HIV-1 Modulates the tRNA Pool to Improve Translation Efficiency

Caroline J. Rose, Joanne R. Chapman, Sean D.G. Marshall, Siu F. Lee, Philip Batterham, Howard A. Ross, and Richard D. Newcomb
Selective Sweeps at the Organophosphorus Insecticide Resistance Locus, Rop-1, Have Affected Variation across and beyond the ?-Esterase Gene Cluster in the Australian Sheep Blowfly, Lucilia cuprina

Emmanuel D. Ladoukakis, Ioannis Theologidis, George C. Rodakis, and Eleftherios Zouros
Homologous Recombination between Highly Diverged Mitochondrial Sequences: Examples from Maternally and Paternally Transmitted Genomes

Sandra Schwarte and Ralph Tiedemann
A Gene Duplication/Loss Event in the Ribulose-1,5-Bisphosphate-Carboxylase/Oxygenase (Rubisco) Small Subunit Gene Family among Accessions of Arabidopsis thaliana

Vladimir Paar, Matko Glunčić, Marija Rosandić, Ivan Basar, and Ines Vlahović
Intragene Higher Order Repeats in Neuroblastoma BreakPoint Family Genes Distinguish Humans from Chimpanzees

Richard P. Meisel
Towards a More Nuanced Understanding of the Relationship between Sex-Biased Gene Expression and Rates of Protein-Coding Sequence Evolution

Xianran Li, Chengsong Zhu, Zhongwei Lin, Yun Wu, Dabao Zhang, Guihua Bai, Weixing Song, Jianxin Ma, Gary J. Muehlbauer, Michael J. Scanlon, Min Zhang, and Jianming Yu
Chromosome Size in Diploid Eukaryotic Species Centers on the Average Length with a Conserved Boundary

Kalle T. Rytkönen, Tom A. Williams, Gillian M. Renshaw, Craig R. Primmer, and Mikko Nikinmaa
Molecular Evolution of the Metazoan PHD–HIF Oxygen-Sensing System

M. Andreína Pacheco, Fabia U. Battistuzzi, Miguel Lentino, Roberto F. Aguilar, Sudhir Kumar, and Ananias A. Escalante
Evolution of Modern Birds Revealed by Mitogenomics: Timing the Radiation and Origin of Major Orders

Akie Sato, Herbert Tichy, Peter R. Grant, B. Rosemary Grant, Tetsuji Sato, and Colm O’hUigin
Spectrum of MHC Class II Variability in Darwin’s Finches and Their Close Relatives

Standing Material

Associate Editors
SMBE Editors and Council
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