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

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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


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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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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

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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

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Molecular Biology and Evolution

Spis treści Molecular Biology and Evolution, Volume 27, Number 1:

Carmela Gissi, Graziano Pesole, Francesco Mastrototaro, Fabio Iannelli, Vanessa Guida, Francesca Griggio
Hypervariability of Ascidian Mitochondrial Gene Order: Exposing the Myth of Deuterostome Organelle Genome Stability

Peter W. Osborne, David E.K. Ferrier
Chordate Hox and ParaHox Gene Clusters Differ Dramatically in Their Repetitive Element Content

Manolo Gouy, Stéphane Guindon, Olivier Gascuel
SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

Steven F. Field, Mikhail V. Matz
Retracing Evolution of Red Fluorescence in GFP-Like Proteins from Faviina Corals

Thomas J. Templeton, Shinichiro Enomoto, Wei-June Chen, Chin-Gi Huang, Cheryl A. Lancto, Mitchell S. Abrahamsen, Guan Zhu
A Genome-Sequence Survey for Ascogregarina taiwanensis Supports Evolutionary Affiliation but Metabolic Diversity between a Gregarine and Cryptosporidium

A. P. Jason de Koning, Wanjun Gu, David D. Pollock
Rapid Likelihood Analysis on Large Phylogenies Using Partial Sampling of Substitution Histories

Christopher W. Wheat, Christoph R. Haag, James H. Marden, Ilkka Hanski, Mikko J. Frilander
Nucleotide Polymorphism at a Gene (Pgi) under Balancing Selection in a Butterfly Metapopulation

Barry A. Kesner, Sharon L. Milgram, Brenda R.S. Temple, Nikolay V. Dokholyan
Isoform Divergence of the Filamin Family of Proteins

Jared L. Strasburg, Loren H. Rieseberg
How Robust Are "Isolation with Migration" Analyses to Violations of the IM Model? A Simulation Study

Laura A. Hug, Alexandra Stechmann, Andrew J. Roger
Phylogenetic Distributions and Histories of Proteins Involved in Anaerobic Pyruvate Metabolism in Eukaryotes

Domenec Farré, M. Mar Alba
Heterogeneous Patterns of Gene-Expression Diversification in Mammalian Gene Duplicates

N. Ray, D. Wegmann, N.J.R. Fagundes, S. Wang, A. Ruiz-Linares, L. Excoffier
A Statistical Evaluation of Models for the Initial Settlement of the American Continent Emphasizes the Importance of Gene Flow with Asia

Ramiro Logares, Jon Brate, Friederike Heinrich, Kamran Shalchian-Tabrizi, Stefan Bertilsson
Infrequent Transitions between Saline and Fresh Waters in One of the Most Abundant Microbial Lineages (SAR11)

Nelson Avonce, Jan Wuyts, Katrien Verschooten, Lies Vandesteene, Patrick Van Dijck
The Cytophaga hutchinsonii ChTPSP: First Characterized Bifunctional TPS–TPP Protein as Putative Ancestor of All Eukaryotic Trehalose Biosynthesis Proteins

Yan Zhou, Henner Brinkmann, Nicolas Rodrigue, Nicolas Lartillot, Hervé Philippe
A Dirichlet Process Covarion Mixture Model and Its Assessments Using Posterior Predictive Discrepancy Tests

Wentao Shi, Qasim Ayub, Mark Vermeulen, Rong-guang Shao, Sofia Zuniga, Kristiaan van der Gaag, Peter de Knijff, Manfred Kayser, Yali Xue, Chris Tyler-Smith
A Worldwide Survey of Human Male Demographic History Based on Y-SNP and Y-STR Data from the HGDP–CEPH Populations

Bryan G. Fry, Kim Roelants, Kelly Winter, Wayne C. Hodgson, Laura Griesman, Hang Fai Kwok, Denis Scanlon, John Karas, Chris Shaw, Lily Wong, Janette A. Norman
Novel Venom Proteins Produced by Differential Domain-Expression Strategies in Beaded Lizards and Gila Monsters (genus Heloderma)

Jesse D. Hollister, Jeffrey Ross-Ibarra, Brandon S. Gaut
Indel-Associated Mutation Rate Varies with Mating System in Flowering Plants

Marcos Pérez-Losada, David V. Jobes, Faruk Sinangil, Keith A. Crandall, David Posada, Phillip W. Berman
Phylodynamics of HIV-1 from a Phase-III AIDS Vaccine Trial in North America

Caitlin Pepperell, Vernon H. Hoeppner, Mikhail Lipatov, Wendy Wobeser, Gary K. Schoolnik, Marcus W. Feldman
Bacterial Genetic Signatures of Human Social Phenomena among M. tuberculosis from an Aboriginal Canadian Population

Frida Belinky, Ofir Cohen, Dorothée Huchon
Large-Scale Parsimony Analysis of Metazoan Indels in Protein-Coding Genes

Tomohide Hiwatashi, Yugo Okabe, Toko Tsutsui, Chihiro Hiramatsu, Amanda D. Melin, Hiroki Oota, Colleen M. Schaffner, Filippo Aureli, Linda M. Fedigan, Hideki Innan, Shoji Kawamura
An Explicit Signature of Balancing Selection for Color-Vision Variation in New World Monkeys

Courtney C. Babbitt, Jesse S. Silverman, Ralph Haygood, Jennifer M. Reininga, Matthew V. Rockman, Gregory A. Wray
Multiple Functional Variants in cis Modulate PDYN Expression

Marian Bemer, Jonathan Gordon, Koen Weterings, Gerco C. Angenent
Divergence of Recently Duplicated M{gamma}-Type MADS-Box Genes in Petunia


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