Molecular Biology and Evolution - 29 (1), 2012

Contents:

Letters

Eyal Privman, Osnat Penn, and Tal Pupko
Improving the Performance of Positive Selection Inference by Filtering Unreliable Alignment Regions

Gustavo C. S. Kuhn, Heinrich Küttler, Orlando Moreira-Filho, and John S. Heslop-Harrison
The 1.688 Repetitive DNA of Drosophila: Concerted Evolution at Different Genomic Scales and Association with Genes

José M. Ranz, Carlos Díaz-Castillo, and Rita Petersen
Conserved Gene Order at the Nuclear Periphery in Drosophila

José M. Cuevas, Pilar Domingo-Calap, and Rafael Sanjuán
The Fitness Effects of Synonymous Mutations in DNA and RNA Viruses

Ashley Farlow, Marlies Dolezal, Liushuai Hua, and Christian Schlötterer
The Genomic Signature of Splicing-Coupled Selection Differs between Long and Short Introns

Marta Melé, Asif Javed, Marc Pybus, Pierre Zalloua, Marc Haber, David Comas, Mihai G. Netea, Oleg Balanovsky, Elena Balanovska, Li Jin, Yajun Yang, R. M. Pitchappan, G. Arunkumar, Laxmi Parida, Francesc Calafell, Jaume Bertranpetit, and the Genographic Consortium
Recombination Gives a New Insight in the Effective Population Size and the History of the Old World Human Populations

Thomas Städler, Ana Marcela Florez-Rueda, and Margot Paris
Testing for “Snowballing” Hybrid Incompatibilities in Solanum: Impact of Ancestral Polymorphism and Divergence Estimates

Tuan A. Nguyen, Jasmina Brescic, David J. Vinyard, Thenappan Chandrasekar, and G. Charles Dismukes
Identification of an Oxygenic Reaction Center psbADC Operon in the Cyanobacterium Gloeobacter violaceus PCC 7421

C. Rune Stensvold, Marianne Lebbad, and C. Graham Clark
Last of the Human Protists: The Phylogeny and Genetic Diversity of Iodamoeba


Research Articles


Scott W. Roy, Andrew J. Hudson, Joella Joseph, Janet Yee, and Anthony G. Russell
Numerous Fragmented Spliceosomal Introns, AT–AC Splicing, and an Unusual Dynein Gene Expression Pathway in Giardia lamblia

Tami R. McDonald, Fred S. Dietrich and François Lutzoni
Multiple Horizontal Gene Transfers of Ammonium Transporters/Ammonia Permeases from Prokaryotes to Eukaryotes: Toward a New Functional and Evolutionary Classification

Jonathan E. Dickerson and David L. Robertson
On the Origins of Mendelian Disease Genes in Man: The Impact of Gene Duplication

Ryuichi P. Sugino and Hideki Innan
Natural Selection on Gene Order in the Genome Reorganization Process After Whole-Genome Duplication of Yeast

Zhenguo Lin and Wen-Hsiung Li
Evolution of 5' Untranslated Region Length and Gene Expression Reprogramming in Yeasts

Xinjiang Cai and David E. Clapham
Ancestral Ca2+ Signaling Machinery in Early Animal and Fungal Evolution

Chad D. Huff, David J. Witherspoon, Yuhua Zhang, Chandler Gatenbee, Lee A. Denson, Subra Kugathasan, Hakon Hakonarson, April Whiting, Chadwick T. Davis, Wilfred Wu, Jinchuan Xing, W. Scott Watkins, Michael J. Bamshad, Jonathan P. Bradfield, Kazima Bulayeva, Tatum S. Simonson, Lynn B. Jorde, and Stephen L. Guthery
Crohn’s Disease and Genetic Hitchhiking at IBD5

Felicity Alcock, Chaille T. Webb, Pavel Dolezal, Victoria Hewitt, Miguel Shingu-Vasquez, Vladimir A. Likić, Ana Traven, and Trevor Lithgow
A Small Tim Homohexamer in the Relict Mitochondrion of Cryptosporidium

David Alvarez-Ponce, Sara Guirao-Rico, Dorcas J. Orengo, Carmen Segarra, Julio Rozas, and Montserrat Aguadé
Molecular Population Genetics of the Insulin/TOR Signal Transduction Pathway: A Network-Level Analysis in Drosophila melanogaster

Andrew Ying-Fei Chang and Ben-Yang Liao
DNA Methylation Rebalances Gene Dosage after Mammalian Gene Duplications

Masato Yamamichi, Jun Gojobori, and Hideki Innan
An Autosomal Analysis Gives No Genetic Evidence for Complex Speciation of Humans and Chimpanzees

Jerome H. L. Hui, Carmel McDougall, Ana S. Monteiro, Peter W. H. Holland, Detlev Arendt, Guillaume Balavoine, and David E. K. Ferrier
Extensive Chordate and Annelid Macrosynteny Reveals Ancestral Homeobox Gene Organization

Emily S. W. Wong, Anthony T. Papenfuss, Camilla M. Whittington, Wesley C. Warren, and Katherine Belov
A Limited Role for Gene Duplications in the Evolution of Platypus Venom

Noa E. Cohen, Roy Shen, and Liran Carmel
The Role of Reverse Transcriptase in Intron Gain and Loss Mechanisms

Feng-Chi Chen, Chia-Lin Pan, and Hsuan-Yu Lin
Independent Effects of Alternative Splicing and Structural Constraint on the Evolution of Mammalian Coding Exons

Martin J. Genner and George F. Turner
Ancient Hybridization and Phenotypic Novelty within Lake Malawi’s Cichlid Fish Radiation

Miguel Arenas, Nicolas Ray, Mathias Currat, and Laurent Excoffier
Consequences of Range Contractions and Range Shifts on Molecular Diversity

Shohei Takuno and Brandon S. Gaut
Body-Methylated Genes in Arabidopsis thaliana Are Functionally Important and Evolve Slowly

Alex Wong, Michael Turchin, Mariana F. Wolfner, and Charles F. Aquadro
Temporally Variable Selection on Proteolysis-Related Reproductive Tract Proteins in Drosophila

Deena Emera, Claudio Casola, Vincent J. Lynch, Derek E. Wildman, Dalen Agnew, and Günter P. Wagner
Convergent Evolution of Endometrial Prolactin Expression in Primates, Mice, and Elephants Through the Independent Recruitment of Transposable Elements

Irene Gallego Romero, Chandana Basu Mallick, Anke Liebert, Federica Crivellaro, Gyaneshwer Chaubey, Yuval Itan, Mait Metspalu, Muthukrishnan Eaaswarkhanth, Ramasamy Pitchappan, Richard Villems, David Reich, Lalji Singh, Kumarasamy Thangaraj, Mark G. Thomas, Dallas M. Swallow, Marta Mirazón Lahr, and Toomas Kivisild
Herders of Indian and European Cattle Share Their Predominant Allele for Lactase Persistence

Julian P. Venables, Emmanuel Vignal, Stephen Baghdiguian, Philippe Fort, and Jamal Tazi
Tissue-Specific Alternative Splicing of Tak1 Is Conserved in Deuterostomes

Stefan Zoller and Adrian Schneider
A New Semiempirical Codon Substitution Model Based on Principal Component Analysis of Mammalian Sequences

David Weetman, Craig S. Wilding, Keith Steen, Joao Pinto, and Martin J. Donnelly
Gene Flow–Dependent Genomic Divergence between Anopheles gambiae M and S Forms

Michiel Kwantes, Daniela Liebsch, and Wim Verelst
How MIKC* MADS-Box Genes Originated and Evidence for Their Conserved Function Throughout the Evolution of Vascular Plant Gametophytes

Federico G. Hoffmann, Juan C. Opazo, and Jay F. Storz
Whole-Genome Duplications Spurred the Functional Diversification of the Globin Gene Superfamily in Vertebrates

Eva Nováková and Nancy A. Moran
Diversification of Genes for Carotenoid Biosynthesis in Aphids following an Ancient Transfer from a Fungus

Bruce Rannala, Tianqi Zhu, and Ziheng Yang
Tail Paradox, Partial Identifiability, and Influential Priors in Bayesian Branch Length Inference

Naoki Osada and Hiroshi Akashi
Mitochondrial–Nuclear Interactions and Accelerated Compensatory Evolution: Evidence from the Primate Cytochrome c Oxidase Complex

Tanja Stadler, Roger Kouyos, Viktor von Wyl, Sabine Yerly, Jürg Böni, Philippe Bürgisser, Thomas Klimkait, Beda Joos, Philip Rieder, Dong Xie, Huldrych F. Günthard, Alexei J. Drummond, Sebastian Bonhoeffer, and the Swiss HIV Cohort Study
Estimating the Basic Reproductive Number from Viral Sequence Data

Bayazit Yunusbayev, Mait Metspalu, Mari Järve, Ildus Kutuev, Siiri Rootsi, Ene Metspalu, Doron M. Behar, Kärt Varendi, Hovhannes Sahakyan, Rita Khusainova, Levon Yepiskoposyan, Elza K. Khusnutdinova, Peter A. Underhill, Toomas Kivisild, and Richard Villems
The Caucasus as an Asymmetric Semipermeable Barrier to Ancient Human Migrations

Andrew E. Allen, Ahmed Moustafa, Anton Montsant, Angelika Eckert, Peter G. Kroth, and Chris Bowler
Evolution and Functional Diversification of Fructose Bisphosphate Aldolase Genes in Photosynthetic Marine Diatoms

Philippe Fort,Aurélie Albertini, Aurélie Van - Hua, Arnaud Berthomieu, Stéphane Roche, Frédéric Delsuc, Nicole Pasteur, Pierre Capy, Yves Gaudin, and Mylene Weill
Fossil Rhabdoviral Sequences Integrated into Arthropod Genomes: Ontogeny, Evolution, and Potential Functionality

Daniel Rejmanek, Patrick Foley, Anthony Barbet, and Janet Foley
Evolution of Antigen Variation in the Tick-Borne Pathogen Anaplasma phagocytophilum

Lee Henry, Tanja Schwander, and Bernard J. Crespi
Deleterious Mutation Accumulation in Asexual Timema Stick Insects

Alessandro Lovisetto, Flavia Guzzo, Alice Tadiello, Ketti Toffali, Alessandro Favretto, and Giorgio Casadoro
Molecular Analyses of MADS-Box Genes Trace Back to Gymnosperms the Invention of Fleshy Fruits

Maria Costantini, Fabio Auletta, and Giorgio Bernardi
The Distributions of “New” and “Old” Alu Sequences in the Human Genome: The Solution of a “Mystery”

Yudai Okuyama, Akifumi S. Tanabe, and Makoto Kato
Entangling Ancient Allotetraploidization in Asian Mitella: An Integrated Approach for Multilocus Combinations


Editorial

Ken Wolfe, Marta L. Wayne, Kateryna Makova, Tomoko Y. Steen, Marcy Uyenoyama, and Naoyuki Takahata
SMBE Proposal to the Government of Japan


Corrigendum

Comparing Models of Evolution for Ordered and Disordered Proteins

Standing Material

Associate Editors
SMBE Editors and Council
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