Genome Biology and Evolution - 5 (1), 2013

Contents:

Research Articles

        Zsófia Bánlaki, Julianna Anna Szabó, Ágnes Szilágyi, Attila Patócs, Zoltán Prohászka, George Füst, and Márton Doleschall
    Intraspecific Evolution of Human RCCX Copy Number Variation Traced by Haplotypes of the CYP21A2 Gene
   
        Alana Alexander, Debbie Steel, Beth Slikas, Kendra Hoekzema, Colm Carraher, Matthew Parks, Richard Cronn, and C. Scott Baker
    Low Diversity in the Mitogenome of Sperm Whales Revealed by Next-Generation Sequencing
    
        David W. Hall and Marta L. Wayne
    Ohno’s “Peril of Hemizygosity” Revisited: Gene Loss, Dosage Compensation, and Mutation
   
        Patrícia H. Brito, Eduardo P.C. Rocha, Karina B. Xavier, and Isabel Gordo
    Natural Genome Diversity of AI-2 Quorum Sensing in Escherichia coli: Conserved Signal Production but Labile Signal Reception
  
        Tal Dagan, Mayo Roettger, Karina Stucken, Giddy Landan, Robin Koch, Peter Major, Sven B. Gould, Vadim V. Goremykin, Rosmarie Rippka, Nicole Tandeau de Marsac, Muriel Gugger, Peter J. Lockhart, John F. Allen, Iris Brune, Irena Maus, Alfred Pühler, and William F. Martin
    Genomes of Stigonematalean Cyanobacteria (Subsection V) and the Evolution of Oxygenic Photosynthesis from Prokaryotes to Plastids
   
        Alessandro Coppe, Cecilia Agostini, Ilaria A.M. Marino, Lorenzo Zane, Luca Bargelloni, Stefania Bortoluzzi, and Tomaso Patarnello
    Genome Evolution in the Cold: Antarctic Icefish Muscle Transcriptome Reveals Selective Duplications Increasing Mitochondrial Function
 
        Eran Elhaik
    The Missing Link of Jewish European Ancestry: Contrasting the Rhineland and the Khazarian Hypotheses
  
        Danielle Venton
    Highlight: Out of Khazaria—Evidence for “Jewish Genome” Lacking
  
        Arnaud Le Rouzic, Thibaut Payen, and Aurélie Hua-Van
    Reconstructing the Evolutionary History of Transposable Elements
  
        Yan-Bo Sun, Wei-Ping Zhou, He-Qun Liu, David M. Irwin, Yong-Yi Shen, and Ya-Ping Zhang
    Genome-Wide Scans for Candidate Genes Involved in the Aquatic Adaptation of Dolphins
 
        Masatoshi Matsunami and Naruya Saitou
    Vertebrate Paralogous Conserved Noncoding Sequences May Be Related to Gene Expressions in Brain
  
        Eckart Stolle, Jonathan H. Kidner, and Robin F.A. Moritz
    Patterns of Evolutionary Conservation of Microsatellites (SSRs) Suggest a Faster Rate of Genome Evolution in Hymenoptera Than in Diptera
  
Letter

        Nadia Jezequel, Marco Cosentino Lagomarsino, Francois Heslot, and Philippe Thomen
    Long-Term Diversity and Genome Adaptation of Acinetobacter baylyi in a Minimal-Medium Chemostat
  
============
American Journal of Botany 99 (3), 2012
American Journal of Botany 99 (2), 2012
Lethaia

Genome Biology and Evolution - 4 (12), 2012

Contents:

Research Articles

        Kyanne R. Reidenbach, Daniel E. Neafsey, Carlo Costantini, N’Fale Sagnon, Frédéric Simard, Gregory J. Ragland, Scott P. Egan, Jeffrey L. Feder, Marc A. T. Muskavitch, and Nora J. Besansky
    Patterns of Genomic Differentiation between Ecologically Differentiated M and S Forms of Anopheles gambiae in West and Central Africa
  
        Onuralp Soylemez and Fyodor A. Kondrashov
    Estimating the Rate of Irreversibility in Protein Evolution
  
        David Williams, J. Peter Gogarten, and R. Thane Papke
    Quantifying Homologous Replacement of Loci between Haloarchaeal Species
   
        Yu-Ping Poh, Chau-Ti Ting, Hua-Wen Fu, Charles H. Langley, and David J. Begun
    Population Genomic Analysis of Base Composition Evolution in Drosophila melanogaster
   
        Jarrett D. Morrow and Vaughn S. Cooper
    Evolutionary Effects of Translocations in Bacterial Genomes
  
        David Alvarez-Ponce and Mario A. Fares
    Evolutionary Rate and Duplicability in the Arabidopsis thaliana Protein–Protein Interaction Network
   
        Anne-Catrin Uhlemann, Adam D. Kennedy, Craig Martens, Stephen F. Porcella, Frank R. DeLeo, and Franklin D. Lowy
    Toward an Understanding of the Evolution of Staphylococcus aureus Strain USA300 during Colonization in Community Households
  
        Sabrina Simon, Apurva Narechania, Rob DeSalle, and Heike Hadrys
    Insect Phylogenomics: Exploring the Source of Incongruence Using New Transcriptomic Data
    
        José R. López Arriaza, and Rachel Lockridge Mueller
    Slow DNA Loss in the Gigantic Genomes of Salamanders
   
        Danielle Venton
    Highlight—Making It Big: Salamanders Keep DNA Near and Dear
 
        Christopher Grosche, Helena T. Funk, Uwe G. Maier, and Stefan Zauner
    The Chloroplast Genome of Pellia endiviifolia: Gene Content, RNA-Editing Pattern, and the Origin of Chloroplast Editing
   
        Aitor Gonzaga, Ana-Belen Martin-Cuadrado, Mario López-Pérez, Carolina Megumi Mizuno, Inmaculada García-Heredia, Nikole E. Kimes, Purificación Lopez-García, David Moreira, David Ussery, Mila Zaballos, Rohit Ghai, and Francisco Rodriguez-Valera
    Polyclonality of Concurrent Natural Populations of Alteromonas macleodii
   
        Olga K. Kamneva, Stormy J. Knight, David A. Liberles, and Naomi L. Ward
    Analysis of Genome Content Evolution in PVC Bacterial Super-Phylum: Assessment of Candidate Genes Associated with Cellular Organization and Lifestyle
   
        Julia F. Hopkins, David F. Spencer, Sylvie Laboissiere, Jonathan A.D. Neilson, Robert J.M. Eveleigh, Dion G. Durnford, Michael W. Gray, and John M. Archibald
    Proteomics Reveals Plastid- and Periplastid-Targeted Proteins in the Chlorarachniophyte Alga Bigelowiella natans
   
Letter

        Yuri I. Wolf and Eugene V. Koonin
    A Tight Link between Orthologs and Bidirectional Best Hits in Bacterial and Archaeal Genomes
   
        Thomas Schott, Pradeep Kumar Kondadi, Marja-Liisa Hänninen, and Mirko Rossi
    Microevolution of a Zoonotic Helicobacter Population Colonizing the Stomach of a Human Host before and after Failed Treatment
   
        Ibrar Ahmed, Patrick J. Biggs, Peter J. Matthews, Lesley J. Collins, Michael D. Hendy, and Peter J. Lockhart
    Mutational Dynamics of Aroid Chloroplast Genomes
    
        Patrícia Isabel Marques, Rui Bernardino, Teresa Fernandes, Eric D. Green, Belen Hurle, Victor Quesada, Susana Seixas and NISC Comparative Sequencing Program
    Birth-and-Death of KLK3 and KLK2 in Primates: Evolution Driven by Reproductive Biology
   
        Niyaz Yoosuf, Natalya Yutin, Philippe Colson, Svetlana A. Shabalina, Isabelle Pagnier, Catherine Robert, Said Azza, Thomas Klose, Jimson Wong, Michael G. Rossmann, Bernard La Scola, Didier Raoult, and Eugene V. Koonin
    Related Giant Viruses in Distant Locations and Different Habitats: Acanthamoeba polyphaga moumouvirus Represents a Third Lineage of the Mimiviridae That Is Close to the Megavirus Lineage
  
Erratum

        Danielle Venton
    Highlight—Lowly Sea Cucumber Leads the Evolutionary Race
   
============

 

Genome Biology and Evolution - 4 (11), 2012

Contents:

Research Articles

        Andrea Hodgins-Davis, Aleksandra B. Adomas, Jonas Warringer, and Jeffrey P. Townsend
    Abundant Gene-by-Environment Interactions in Gene Expression Reaction Norms to Copper within Saccharomyces cerevisiae
   
        Renfu Shao, Xing-Quan Zhu, Stephen C. Barker, and Kate Herd
    Evolution of Extensively Fragmented Mitochondrial Genomes in the Lice of Humans
   
        Ken Daigoro Yokoyama and David D. Pollock
    SP Transcription Factor Paralogs and DNA-Binding Sites Coevolve and Adaptively Converge in Mammals and Birds
  
        Peter W. Harrison, Judith E. Mank, and Nina Wedell
    Incomplete Sex Chromosome Dosage Compensation in the Indian Meal Moth, Plodia interpunctella, Based on De Novo Transcriptome Assembly
  
        Yuichiro Hara, Tadashi Imanishi, and Yoko Satta
    Reconstructing the Demographic History of the Human Lineage Using Whole-Genome Sequences from Human and Three Great Apes
  
        Danielle Venton
    Highlight: Family Ties—New Evidence Simplifies Human Evolutionary Tree
   
        Christa E. Moore, Bruce Curtis, Tyler Mills, Goro Tanifuji, and John M. Archibald
    Nucleomorph Genome Sequence of the Cryptophyte Alga Chroomonas mesostigmatica CCMP1168 Reveals Lineage-Specific Gene Loss and Genome Complexity
   
        Daniel Croll and Bruce A. McDonald
    Intron Gains and Losses in the Evolution of Fusarium and Cryptococcus Fungi
   
        Guoqin Yu and Arlin Stoltzfus
    Population Diversity of ORFan Genes in Escherichia coli
  
        Raquel Assis, Qi Zhou, and Doris Bachtrog
    Sex-Biased Transcriptome Evolution in Drosophila
  
Letters

        Janna L. Fierst and Patrick C. Phillips
    Variance in Epistasis Links Gene Regulation and Evolutionary Rate in the Yeast Genetic Interaction Network
   
        Sankar Subramanian and David M. Lambert
    Selective Constraints Determine the Time Dependency of Molecular Rates for Human Nuclear Genomes
   
Erratum

        Andrea Hodgins-Davis, Aleksandra B. Adomas, Jonas Warringer, and Jeffrey P. Townsend
    Abundant Gene-by-Environment Interactions in Gene Expression Reaction Norms to Copper within Saccharomyces cerevisiae
   
        Ching-Ping Lin, Chung-Shien Wu, Ya-Yi Huang, and Shu-Miaw Chaw
    The Complete Chloroplast Genome of Ginkgo biloba Reveals the Mechanism of Inverted Repeat Contraction
   
============

Genome Biology and Evolution - 4 (10), 2012

Contents:

Research Articles

        Colin D. Meiklejohn and Daven C. Presgraves
    Little Evidence for Demasculinization of the Drosophila X Chromosome among Genes Expressed in the Male Germline
   
        Lenka Horváthová, Lucie Šafaříková, Marek Basler, Ivan Hrdý, Neritza B. Campo, Jyh-Wei Shin, Kuo-Yang Huang, Po-Jung Huang, Rose Lin, Petrus Tang, and Jan Tachezy
    Transcriptomic Identification of Iron-Regulated and Iron-Independent Gene Copies within the Heavily Duplicated Trichomonas vaginalis Genome
 
        Qu Zhang and Scott V. Edwards
    The Evolution of Intron Size in Amniotes: A Role for Powered Flight?
   
        Danielle Venton
    Highlight—Small Genomes for the Swift: Of Flight and Intron Size
   
        Yang Ding, Premal Shah, and Joshua B. Plotkin
    Weak 5'-mRNA Secondary Structures in Short Eukaryotic Genes
   
Editorial

        John M. Archibald
    Treasurer’s Report for FY 2010
  
        Bill Martin and Takashi Gojobori
    GBE Editor’s Report
   
Letter

        Virginia Sahagun and José M. Ranz
    Characterization of Genomic Regulatory Domains Conserved across the Genus Drosophila
  
============

Genome Biology and Evolution - 4 (9), 2012

Contents:

Research Articles

        Lucas Leclere and Fabian Rentzsch
    Repeated Evolution of Identical Domain Architecture in Metazoan Netrin Domain-Containing Proteins
 
        Noah K. Whiteman, Andrew D. Gloss, Timothy B. Sackton, Simon C. Groen, Parris T. Humphrey, Richard T. Lapoint, Ida E. Sonderby, Barbara A. Halkier, Christine Kocks, Frederick M. Ausubel, and Naomi E. Pierce
    Genes Involved in the Evolution of Herbivory by a Leaf-Mining, Drosophilid Fly
 
        Shigehiro Kuraku, Huan Qiu, and Axel Meyer
    Horizontal Transfers of Tc1 Elements between Teleost Fishes and Their Vertebrate Parasites, Lampreys
   
        Karen D. Crow, Christopher D. Smith, Jan-Fang Cheng, Günter P. Wagner, and Chris T. Amemiya
    An Independent Genome Duplication Inferred from Hox Paralogs in the American Paddlefish—A Representative Basal Ray-Finned Fish and Important Comparative Reference
 
        Jean-Christophe Gelly, Hsuan-Yu Lin, Alexandre G. de Brevern, Trees-Juen Chuang, and Feng-Chi Chen
    Selective Constraint on Human Pre-mRNA Splicing by Protein Structural Properties
  
        Summit Suen, Henry Horng-Shing Lu, and Chen-Hsiang Yeang
    Evolution of Domain Architectures and Catalytic Functions of Enzymes in Metabolic Systems

        G. A. Babbitt and K. V. Schulze
    Codons Support the Maintenance of Intrinsic DNA Polymer Flexibility over Evolutionary Timescales
  
        Stephanie A. Brockman and Catherine S. McFadden
    The Mitochondrial Genome of Paraminabea aldersladei (Cnidaria: Anthozoa: Octocorallia) Supports Intramolecular Recombination as the Primary Mechanism of Gene Rearrangement in Octocoral Mitochondrial Genomes
   
Letters

        Florent Murat, Yves Van de Peer, and Jérôme Salse
    Decoding Plant and Animal Genome Plasticity from Differential Paleo-Evolutionary Patterns and Processes
  
============

Genome Biology and Evolution - 4 (8), 2012

Contents:

Research Articles

        Frauke Baymann, Barbara Schoepp-Cothenet, Evelyne Lebrun, Robert van Lis, and Wolfgang Nitschke
    Phylogeny of Rieske/cytb Complexes with a Special Focus on the Haloarchaeal Enzymes
   
        Kristen S. Swithers, Amanda K. Petrus, Michael A. Secinaro, Camilla L. Nesbo, J. Peter Gogarten, Kenneth M. Noll, and Nicholas C. Butzin
    Vitamin B12 Synthesis and Salvage Pathways Were Acquired by Horizontal Gene Transfer to the Thermotogales
  
        Georgia Tsagkogeorga, Vincent Cahais, and Nicolas Galtier
    The Population Genomics of a Fast Evolver: High Levels of Diversity, Functional Constraint, and Molecular Adaptation in the Tunicate Ciona intestinalis
 
        Danielle Venton
    Highlight—Lowly Sea Cucumber Leads the Evolutionary Race
  
        Bertanne Visser, Dick Roelofs, Daniel A. Hahn, Peter E. A. Teal, Janine Mariën, and Jacintha Ellers
    Transcriptional Changes Associated with Lack of Lipid Synthesis in Parasitoids
  
Invited Review

        Gabriel Luz Wallau, Mauro Freitas Ortiz, and Elgion Lucio Silva Loreto
    Horizontal Transposon Transfer in Eukarya: Detection, Bias, and Perspectives
   
Letters

        Olga Zhaxybayeva, Kristen S. Swithers, Julia Foght, Anna G. Green, David Bruce, Chris Detter, Shunsheng Han, Hazuki Teshima, James Han, Tanja Woyke, Sam Pitluck, Matt Nolan, Natalia Ivanova, Amrita Pati, Miriam L. Land, Marlena Dlutek, W. Ford Doolittle, Kenneth M. Noll, and Camilla L. Nesbo
    Genome Sequence of the Mesophilic Thermotogales Bacterium Mesotoga prima MesG1.Ag.4.2 Reveals the Largest Thermotogales Genome To Date
   
        Janet S. Sinsheimer, Roderick J. A. Little, and James A. Lake
    Rooting Gene Trees without Outgroups: EP Rooting
   
        Devin M. Drown, Kevin M. Preuss, and Michael J. Wade
    Evidence of a Paucity of Genes That Interact with the Mitochondrion on the X in Mammals
 
        Danielle Venton
    Highlight: “Keeping the Boys in the Conversation: Male Fitness Shapes the Location of Genes that Interact with Mitochondria”
 

Genome Biology and Evolution - 4 (7), 2012

Contents:

Research Articles

        Lucia Carbone, R. Alan Harris, Alan R. Mootnick, Aleksandar Milosavljevic, David I. K. Martin, Mariano Rocchi, Oronzo Capozzi, Nicoletta Archidiacono, Miriam K. Konkel, Jerilyn A. Walker, Mark A. Batzer, and Pieter J. de Jong
    Centromere Remodeling in Hoolock leuconedys (Hylobatidae) by a New Transposable Element Unique to the Gibbons
   
        Rodger B. Voelker, Steffen Erkelenz, Vinicio Reynoso, Heiner Schaal, and J. Andrew Berglund
    Frequent Gain and Loss of Intronic Splicing Regulatory Elements during the Evolution of Vertebrates
  
Letters

        Eugénie Pessia, Alexandra Popa, Sylvain Mousset, Clément Rezvoy, Laurent Duret, and Gabriel A. B. Marais
    Evidence for Widespread GC-biased Gene Conversion in Eukaryotes
   
        Philippe Deschamps and David Moreira
    Reevaluating the Green Contribution to Diatom Genomes
  
============

Genome Biology and Evolution - 4 (6), 2012

Contents:

Research Articles

        Fabien Burki, Pavel Flegontov, Miroslav Oborník, Jaromír Cihlář, Arnab Pain, Julius Lukeš, and Patrick J. Keeling
    Re-evaluating the Green versus Red Signal in Eukaryotes with Secondary Plastid of Red Algal Origin
  
        Sterling M. Sawaya, Dustin Lennon, Emmanuel Buschiazzo, Neil Gemmell, and Vladimir N. Minin
    Measuring Microsatellite Conservation in Mammalian Evolution with a Phylogenetic Birth–Death Model


============

Genome Biology and Evolution - 4 (5), 2012

Contents:

        Timothy Paape, Peng Zhou, Antoine Branca, Roman Briskine, Nevin Young, and Peter Tiffin
    Fine-Scale Population Recombination Rates, Hotspots, and Correlates of Recombination in the Medicago truncatula Genome
   
        Zhuo-Cheng Hou, Kirstin N. Sterner, Roberto Romero, Nandor Gabor Than, Juan M. Gonzalez, Amy Weckle, Jun Xing, Kurt Benirschke, Morris Goodman, and Derek E. Wildman
    Elephant Transcriptome Provides Insights into the Evolution of Eutherian Placentation
   
        Meng-Shin Shiao, Andrew Ying-Fei Chang, Ben-Yang Liao, Yung-Hao Ching, Mei-Yeh Jade Lu, Stella Maris Chen, and Wen-Hsiung Li
    Transcriptomes of Mouse Olfactory Epithelium Reveal Sexual Differences in Odorant Detection
  
        Eryn Blass, Michael Bell, and Stéphane Boissinot
    Accumulation and Rapid Decay of Non-LTR Retrotransposons in the Genome of the Three-Spine Stickleback
   
        Jeffrey P. Mower, Andrea L. Case, Eric R. Floro, and John H. Willis
    Evidence against Equimolarity of Large Repeat Arrangements and a Predominant Master Circle Structure of the Mitochondrial Genome from a Monkeyflower (Mimulus guttatus) Lineage with Cryptic CMS
   
        Danielle Venton
    Highlight—Tracking Adaptation's Role: Do Larger Populations Evolve Faster?
  
        Toni I. Gossmann, Peter D. Keightley, and Adam Eyre-Walker
    The Effect of Variation in the Effective Population Size on the Rate of Adaptive Molecular Evolution in Eukaryotes
   
        Mahoko Takahashi and Naruya Saitou
    Identification and Characterization of Lineage-Specific Highly Conserved Noncoding Sequences in Mammalian Genomes
   
        Koji Yahara, Mikihiko Kawai, Yoshikazu Furuta, Noriko Takahashi, Naofumi Handa, Takeshi Tsuru, Kenshiro Oshima, Masaru Yoshida, Takeshi Azuma, Masahira Hattori, Ikuo Uchiyama, and Ichizo Kobayashi
    Genome-Wide Survey of Mutual Homologous Recombination in a Highly Sexual Bacterial Species
  
        Danielle Venton
    Highlight: The Chaperone Network—Evolution's Helping Hand
  
        David Bogumil, Giddy Landan, Judith Ilhan, and Tal Dagan
    Chaperones Divide Yeast Proteins into Classes of Expression Level and Evolutionary Rate
  

Genome Biology and Evolution - 4 (4), 2012

Contents:

Research Articles

        Yuki Dehara, Yasuyuki Hashiguchi, Kazumi Matsubara, Tokuma Yanai, Masahito Kubo, and Yoshinori Kumazawa
    Characterization of Squamate Olfactory Receptor Genes and Their Transcripts by the High-Throughput Sequencing Approach
 
        Giltae Song, Cathy Riemer, Benjamin Dickins, Hie Lim Kim, Louxin Zhang, Yu Zhang, Chih-Hao Hsu, Ross C. Hardison, Eric D. Green, Webb Miller and NISC Comparative Sequencing Program
    Revealing Mammalian Evolutionary Relationships by Comparative Analysis of Gene Clusters
 
        Heidi J. T. Pagán, Jiří Macas, Petr Novák, Eve S. McCulloch, Richard D. Stevens, and David A. Ray
    Survey Sequencing Reveals Elevated DNA Transposon Activity, Novel Elements, and Variation in Repetitive Landscapes among Vesper Bats
  
        Paul Po-Shen Wang and Ilya Ruvinsky
    Family Size and Turnover Rates among Several Classes of Small Non–Protein-Coding RNA Genes in Caenorhabditis Nematodes
  
        Michael Dannemann, Kay Prüfer, Esther Lizano, Birgit Nickel, Hernán A. Burbano, and Janet Kelso
    Transcription Factors Are Targeted by Differentially Expressed miRNAs in Primates
  
        Yuh Chwen G. Lee and Josephine A. Reinhardt
    Widespread Polymorphism in the Positions of Stop Codons in Drosophila melanogaster
  
        Chungoo Park and Jianzhi Zhang
    High Expression Hampers Horizontal Gene Transfer
  
        Dee R. Denver, Larry J. Wilhelm, Dana K. Howe, Kristin Gafner, Peter C. Dolan, and Charles F. Baer
    Variation in Base-Substitution Mutation in Experimental and Natural Lineages of Caenorhabditis Nematodes
  
        Kirill Kryukov, Kenta Sumiyama, Kazuho Ikeo, Takashi Gojobori, and Naruya Saitou
    A New Database (GCD) on Genome Composition for Eukaryote and Prokaryote Genome Sequences and Their Initial Analyses
  
        Thorsten Thiergart, Giddy Landan, Marc Schenk, Tal Dagan, and William F. Martin
    An Evolutionary Network of Genes Present in the Eukaryote Common Ancestor Polls Genomes on Eukaryotic and Mitochondrial Origin
  
        Ericka A. Becker, Charles M. Burns, Enrique J. León, Saravanan Rajabojan, Robert Friedman, Thomas C. Friedrich, Shelby L. O'Connor, and Austin L. Hughes
    Experimental Analysis of Sources of Error in Evolutionary Studies Based on Roche/454 Pyrosequencing of Viral Genomes
  
        Franz Baumdicker, Wolfgang R. Hess, and Peter Pfaffelhuber
    The Infinitely Many Genes Model for the Distributed Genome of Bacteria
  
        Robert S. Young, Ana C. Marques, Charlotte Tibbit, Wilfried Haerty, Andrew R. Bassett, Ji-Long Liu, and Chris P. Ponting
    Identification and Properties of 1,119 Candidate LincRNA Loci in the Drosophila melanogaster Genome
   
        Ignacio Maeso, Scott William Roy, and Manuel Irimia
    Widespread Recurrent Evolution of Genomic Features
  
Book Reviews

        Adam S. Wilkins
    Evolution: A View from the 21st Century
  
Editorials

    Society for Molecular Biology and Evolution (SMBE) Council and Business Meetings, 2011 Kyoto, Japan
   
Erratum

        Christian Woehle, Tal Dagan, William F. Martin, and Sven B. Gould
    Red and Problematic Green Phylogenetic Signals among Thousands of Nuclear Genes from the Photosynthetic Apicomplexan Chromera velia
   

Genome Biology and Evolution - 4 (3), 2012

Contents

Research Articles

        Alexandra Popa, Paul Samollow, Christian Gautier, and Dominique Mouchiroud
    The Sex-Specific Impact of Meiotic Recombination on Nucleotide Composition
   
        Danielle Venton
    Highlight: Our Reptilian Brethren: Mammals and Live-Bearing Lizards Show Similar Pregnancy Mechanisms
  
        Matthew C. Brandley, Rebecca L. Young, Dan L. Warren, Michael B. Thompson, and Günter P. Wagner
    Uterine Gene Expression in the Live-Bearing Lizard, Chalcides ocellatus, Reveals Convergence of Squamate Reptile and Mammalian Pregnancy Mechanisms
   
        Eduardo Castro-Nallar, Honglei Chen, Simon Gladman, Sean C. Moore, Torsten Seemann, Ian B. Powell, Alan Hillier, Keith A. Crandall, and P. Scott Chandry
    Population Genomics and Phylogeography of an Australian Dairy Factory Derived Lytic Bacteriophage
 
        Ching-Ping Lin, Chung-Shien Wu, Ya-Yi Huang, and Shu-Miaw Chaw
    The Complete Chloroplast Genome of Ginkgo biloba Reveals the Mechanism of Inverted Repeat Contraction
   
        M. M. Pentony, P. Winters, D. Penfold-Brown, K. Drew, A. Narechania, R. DeSalle, R. Bonneau, and M. D. Purugganan
    The Plant Proteome Folding Project: Structure and Positive Selection in Plant Protein Families
   
        Sonja Grath and John Parsch
    Rate of Amino Acid Substitution Is Influenced by the Degree and Conservation of Male-Biased Transcription Over 50 Myr of Drosophila Evolution
  
        Elizabeth Skippington and Mark A. Ragan
    Evolutionary Dynamics of Small RNAs in 27 Escherichia coli and Shigella Genomes
   
        Anna R. Kersting, Erich Bornberg-Bauer, Andrew D. Moore, and Sonja Grath
    Dynamics and Adaptive Benefits of Protein Domain Emergence and Arrangements during Plant Genome Evolution
  
        Kasper U. Kjeldsen, Thomas Bataillon, Nicolás Pinel, Stéphane De Mita, Marie B. Lund, Frank Panitz, Christian Bendixen, David A. Stahl, and Andreas Schramm
    Purifying Selection and Molecular Adaptation in the Genome of Verminephrobacter, the Heritable Symbiotic Bacteria of Earthworms
 
        Daniel B. Sloan, Andrew J. Alverson, Martin Wu, Jeffrey D. Palmer, and Douglas R. Taylor
    Recent Acceleration of Plastid Sequence and Structural Evolution Coincides with Extreme Mitochondrial Divergence in the Angiosperm Genus Silene
  
        José L. Campos, Brian Charlesworth, and Penelope R. Haddrill
    Molecular Evolution in Nonrecombining Regions of the Drosophila melanogaster Genome
  
        James C. Schnable, Michael Freeling, and Eric Lyons
    Genome-Wide Analysis of Syntenic Gene Deletion in the Grasses
 
        Jana Fulnečková, Tereza Hasíková, Jiří Fajkus, Alena Lukešová, Marek Eliáš, and Eva Sýkorová
    Dynamic Evolution of Telomeric Sequences in the Green Algal Order Chlamydomonadales
  
        Felix Horns, Elsa Petit, Roxana Yockteng, and Michael E. Hood
    Patterns of Repeat-Induced Point Mutation in Transposable Elements of Basidiomycete Fungi
  
        Masafumi Nozawa, Sayaka Miura, and Masatoshi Nei
    Origins and Evolution of MicroRNA Genes in Plant Species
  
        Thomas D. Cuypers and Paulien Hogeweg
    Virtual Genomes in Flux: An Interplay of Neutrality and Adaptability Explains Genome Expansion and Streamlining
  
        Michael F. Seidl, Guido Van den Ackerveken, Francine Govers, and Berend Snel
    Reconstruction of Oomycete Genome Evolution Identifies Differences in Evolutionary Trajectories Leading to Present-Day Large Gene Families
  
Letters

        Matthew A. Campbell, Antonis Rokas, and Jason C. Slot
    Horizontal Transfer and Death of a Fungal Secondary Metabolic Gene Cluster
   
============

Genome Biology and Evolution - 4 (2), 2012

Contents:

Research Articles

        Shelley D. Copley, Joseph Rokicki, Pernilla Turner, Hajnalka Daligault, Matt Nolan, and Miriam Land
    The Whole Genome Sequence of Sphingobium chlorophenolicum L-1: Insights into the Evolution of the Pentachlorophenol Degradation Pathway
   
        Cheng Sun, Donald B. Shepard, Rebecca A. Chong, José López Arriaza, Kathryn Hall, Todd A. Castoe, Cédric Feschotte, David D. Pollock, and Rachel Lockridge Mueller
    LTR Retrotransposons Contribute to Genomic Gigantism in Plethodontid Salamanders
   
        M. Ollivier, T. Gabaldón,J. Poulain, F. Gavory, N. Leterme, J.-P. Gauthier, F. Legeai, D. Tagu, J. C. Simon, and C. Rispe
    Comparison of Gene Repertoires and Patterns of Evolutionary Rates in Eight Aphid Species That Differ by Reproductive Mode
  
        Estienne C. Swart, Mariusz Nowacki, Justine Shum, Heather Stiles, Brian P. Higgins, Thomas G. Doak, Klaas Schotanus, Vincent J. Magrini, Patrick Minx, Elaine R. Mardis, and Laura F. Landweber
    The Oxytricha trifallax Mitochondrial Genome
  
        George H. Perry, Darryl Reeves, Páll Melsted, Aakrosh Ratan, Webb Miller, Katelyn Michelini, Edward E. Louis, Jr, Jonathan K. Pritchard, Christopher E. Mason, and Yoav Gilad
    A Genome Sequence Resource for the Aye-Aye (Daubentonia madagascariensis), a Nocturnal Lemur from Madagascar
  
        Małgorzata Wojtkowska, Marcin Jąkalski, Joanna R. Pieńkowska, Olgierd Stobienia, Andonis Karachitos, Teresa M. Przytycka, January Weiner (3), Hanna Kmita, and Wojciech Makałowski
    Phylogenetic Analysis of Mitochondrial Outer Membrane ß-Barrel Channels
  
        Andrew T. Beckenbach
    Mitochondrial Genome Sequences of Nematocera (Lower Diptera): Evidence of Rearrangement following a Complete Genome Duplication in a Winter Crane Fly
   
        Thomas E. Keller, S. David Mis, Kevin E. Jia, and Claus O. Wilke
    Reduced mRNA Secondary-Structure Stability Near the Start Codon Indicates Functional Genes in Prokaryotes
   
Letters

        Courtney C. Babbitt, Jenny Tung, Gregory A. Wray and Susan C. Alberts
    Changes in Gene Expression Associated with Reproductive Maturation in Wild Female Baboons
   
============

Genome Biology and Evolution - 4 (1), 2012

Contents:

Research Articles

        C. J. Jackson, S. G. Gornik,and R. F. Waller
    The Mitochondrial Genome and Transcriptome of the Basal Dinoflagellate Hematodinium sp.: Character Evolution within the Highly Derived Mitochondrial Genomes of Dinoflagellates
   
        David Roy Smith, Ehsan Kayal, Angel A. Yanagihara, Allen G. Collins, Stacy Pirro, and Patrick J. Keeling
    First Complete Mitochondrial Genome Sequence from a Box Jellyfish Reveals a Highly Fragmented Linear Architecture and Insights into Telomere Evolution
   
        Apurva Narechania, Richard H. Baker, Ryan Sit, Sergios-Orestis Kolokotronis, Rob DeSalle, and Paul J. Planet
    Random Addition Concatenation Analysis: A Novel Approach to the Exploration of Phylogenomic Signal Reveals Strong Agreement between Core and Shell Genomic Partitions in the Cyanobacteria
  
        Danielle Venton
    Highlight: Tiny Bacterial Genome Opens a Huge Mystery: AT Mutational Bias in Hodgkinia
  
        James T. Van Leuven and John P. McCutcheon
    An AT Mutational Bias in the Tiny GC-Rich Endosymbiont Genome of Hodgkinia
 
        Yogeshwar D. Kelkar and Howard Ochman
    Causes and Consequences of Genome Expansion in Fungi
 
        Ehsan Kayal, Bastian Bentlage, Allen G. Collins, Mohsen Kayal, Stacy Pirro, and Dennis V. Lavrov
    Evolution of Linear Mitochondrial Genomes in Medusozoan Cnidarians
  
Letters

        Huabin Zhao, Dong Xu, Shuyi Zhang, and Jianzhi Zhang
    Genomic and Genetic Evidence for the Loss of Umami Taste in Bats
   
        Laura E. Williams and Jennifer J. Wernegreen
    Purifying Selection, Sequence Composition, and Context-Specific Indel Mutations Shape Intraspecific Variation in a Bacterial Endosymbiont
   
============

Genome Biology and Evolution

W roczniku 2009 Genome Biology and Evolution można poczytać o :
Adrian Schneider, Alexander Souvorov, Niv Sabath, Giddy Landan, Gaston H. Gonnet, Dan Graur - Estimates of Positive Darwinian Selection Are Inflated by Errors in Sequencing, Annotation, and Alignment

Andrej Benjak, Stéphanie Boué, Astrid Forneck, Josep M. Casacuberta - Recent amplification and impact of MITEs on the genome of grapevine (Vitis vinifera L.)

Andrew T. Beckenbach Jeffrey B. Joy - Evolution of the Mitochondrial Genomes of Gall Midges (Diptera: Cecidomyiidae): Rearrangement and Severe Truncation of tRNA Genes
Benjamin Dickins, Anton Nekrutenko - High-Resolution Mapping of Evolutionary Trajectories in a Phage

Catherine J. Pink, Siva K. Swaminathan, Ian Dunham, Jane Rogers, Andrew Ward, Laurence D. Hurst - Evidence That Replication-Associated Mutation Alone Does Not Explain Between-Chromosome Differences In Substitution Rates

Cédric Feschotte, Umeshkumar Keswani, Nirmal Ranganathan, Marcel L. Guibotsy, David Levine - Exploring Repetitive DNA Landscapes Using REPCLASS, a Tool That Automates the Classification of Transposable Elements in Eukaryotic Genomes

Cheong Xin Chan, Robert G. Beiko, Aaron E. Darling, Mark A. Ragan - Lateral Transfer of Genes and Gene Fragments in Prokaryotes

Chih-Horng Kuo, Howard Ochman - Deletional Bias across the Three Domains of Life

Chun-Hsi Chen, Trees-Juen Chuang, Ben-Yang Liao, Feng-Chi Chen - Scanning for the Signatures of Positive Selection for Human-Specific Insertions and Deletions

Claire Lemaitre, Marilia D. V. Braga, Christian Gautier, Marie-France Sagot, Eric Tannier, Gabriel A. B. Marais - Footprints of Inversions at Present and Past Pseudoautosomal Boundaries in Human Sex Chromosomes

Claudia C. Weber, Laurence D. Hurst - Protein Rates of Evolution Are Predicted by Double-Strand Break Events, Independent of Crossing-over Rates

Daniel A. Skelly, James Ronald, Caitlin F. Connelly, Joshua M. Akey - Population Genomics of Intron Splicing in 38 Saccharomyces cerevisiae Genome Sequences

Dong Dong, Guimei He, Shuyi Zhang, Zhaolei Zhang - Evolution of Olfactory Receptor Genes in Primates Dominated by Birth-and-Death Process
Editorial Board. Genome Biology and Evolution

Elie Desmond, Simonetta Gribaldo - Phylogenomics of Sterol Synthesis: Insights into the Origin, Evolution, and Diversity of a Key Eukaryotic Feature

Fabien Burki, Yuji Inagaki, Jon Bråte, John M. Archibald, Patrick J. Keeling, Thomas Cavalier-Smith, Miako Sakaguchi, Tetsuo Hashimoto, Ales Horak, Surendra Kumar, Dag Klaveness, Kjetill S. Jakobsen, Jan Pawlowski, Kamran Shalchian-Tabrizi - Large-Scale Phylogenomic Analyses Reveal That Two Enigmatic Protist Lineages, Telonemia and Centroheliozoa, Are Related to Photosynthetic Chromalveolates
George E. Liu, Lu Jiang, Fei Tian, Bin Zhu, Jiuzhou Song - Calibration of Mutation Rates Reveals Diverse Subfamily Structure of Galliform CR1 Repeats

Hui Cai, Rebecca Thompson, Mateo F. Budinich, Jeff R. Broadbent, James L. Steele - Genome Sequence and Comparative Genome Analysis of Lactobacillus casei: Insights into Their Niche-Associated Evolution

Igor B. Rogozin, Malay Kumar Basu, Miklós Csürös, Eugene V. Koonin - Analysis of Rare Genomic Changes Does Not Support the Unikont–Bikont Phylogeny and Suggests Cyanobacterial Symbiosis as the Point of Primary Radiation of Eukaryotes

Ingo Braasch, Frédéric Brunet, Jean-Nicolas Volff, Manfred Schartl - Pigmentation Pathway Evolution after Whole-Genome Duplication in Fish

István Miklós, Aaron E. Darling - Efficient Sampling of Parsimonious Inversion Histories with Application to Genome Rearrangement in Yersinia

James J. Cai, Elhanan Borenstein, Rong Chen, Dmitri A. Petrov - Similarly Strong Purifying Selection Acts on Human Disease Genes of All Evolutionary Ages

Jan A. C. Vriezen, Michael Valliere, Margaret A. Riley - The Evolution of Reduced Microbial Killing

Jeffrey D. Jensen - On Reconciling Single and Recurrent Hitchhiking Models

Jochen B. W. Wolf, Axel Künstner, Kiwoong Nam, Mattias Jakobsson, Hans Ellegren - Nonlinear Dynamics of Nonsynonymous (dN) and Synonymous (dS) Substitution Rates Affects Inference of Selection

Kousuke Hanada, Takashi Kuromori, Fumiyoshi Myouga, Tetsuro Toyoda, Wen-Hsiung Li, Kazuo Shinozaki - Evolutionary Persistence of Functional Compensation by Duplicate Genes in Arabidopsis.

Liran Carmel, Eugene V. Koonin - A Universal Nonmonotonic Relationship between Gene Compactness and Expression Levels in Multicellular Eukaryotes

M. Ziemann, M. Bhave, S. Zachgo - Origin and Diversification of Land Plant CC-Type Glutaredoxins

Marc P. Hoeppner, Simon White, Daniel C. Jeffares, Anthony M. Poole - Evolutionarily Stable Association of Intronic snoRNAs and microRNAs with Their Host Genes
Michael S. Barker, Heiko Vogel, M. Eric Schranz - Paleopolyploidy in the Brassicales: Analyses of the Cleome Transcriptome Elucidate the History of Genome Duplications in Arabidopsis and Other Brassicales

Mihai Albu, Xiang Jia Min, G. Brian Golding, and Donal Hickey - Nucleotide Substitution Bias within the Genus Drosophila Affects the Pattern of Proteome Evolution
Mina Rho, Mo Zhou, Xiang Gao, Sun Kim, Haixu Tang, Michael Lynch - Independent Mammalian Genome Contractions Following the KT Boundary

Natalie Donaher, Goro Tanifuji, Naoko T. Onodera, Stephanie A. Malfatti, Patrick S. G. Chain, Yoshiaki Hara, John M. Archibald - The Complete Plastid Genome Sequence of the Secondarily Nonphotosynthetic Alga Cryptomonas paramecium: Reduction, Compaction, and Accelerated Evolutionary Rate

Olga Zhaxybayeva, W. Ford Doolittle, R. Thane Papke, J. Peter Gogarten - Intertwined Evolutionary Histories of Marine Synechococcus and Prochlorococcus marinus

Pascal-Antoine Christin, Emanuela Samaritani, Blaise Petitpierre, Nicolas Salamin, Guillaume Besnard - Evolutionary Insights on C4 Photosynthetic Subtypes in Grasses from Genomics and Phylogenetics

Paz Polak, Peter F. Arndt - Long-Range Bidirectional Strand Asymmetries Originate at CpG Islands in the Human Genome

Richard P. Meisel, Mira V. Han, Matthew W. Hahn - A Complex Suite of Forces Drives Gene Traffic from Drosophila X Chromosomes

Robert C. Karn, Christina M. Laukaitis - The Mechanism of Expansion and the Volatility it created in Three Pheromone Gene Clusters in the Mouse (Mus musculus) Genome

Sara C. Di Rienzi, David Collingwood, M. K. Raghuraman, Bonita J. Brewer - Fragile Genomic Sites Are Associated with Origins of Replication

Takashi Gojobori, William Martin - Welcome to Genome Biology and Evolution
Timothy B. Sackton, Rob J. Kulathinal, Casey M. Bergman, Aaron R. Quinlan, Erik B. Dopman, Mauricio Carneiro, Gabor T. Marth, Daniel L. Hartl, Andrew G. Clark - Population Genomic Inferences from Sparse High-Throughput Sequencing of Two Populations of Drosophila melanogaster

Vanessa L. Bauer DuMont, Nadia D. Singh, Mark H. Wright, Charles F. Aquadro - Locus-Specific Decoupling of Base Composition Evolution at Synonymous Sites and Introns along the Drosophila melanogaster and Drosophila sechellia Lineages

W. A. Findlay, R. J. Redfield - Coevolution of DNA Uptake Sequences and Bacterial Proteomes

Wenfeng Qian Jianzhi Zhang - Protein Subcellular Relocalization in the Evolution of Yeast Singleton and Duplicate Genes

Wolfgang Otto, Peter F. Stadler, Francesc López-Giraldéz, Jeffrey P. Townsend, Vincent J. Lynch, and Günter P. Wagner - Measuring Transcription Factor–Binding Site Turnover: A Maximum Likelihood Approach Using Phylogenies

Xiaowei (Sylvia) Chen, Lesley J. Collins, Patrick J. Biggs, David Penny - High Throughput Genome-Wide Survey of Small RNAs from the Parasitic Protists Giardia intestinalis and Trichomonas vaginalis

Yoshihito Niimura - On the Origin and Evolution of Vertebrate Olfactory Receptor Genes: Comparative Genome Analysis Among 23 Chordate Species

Zhi Wang and Jianzhi Zhang - Abundant Indispensable Redundancies in Cellular Metabolic Networks




Jeśli chcesz poczytać o czymś innym to zapraszam na inne blogi:

POLITYKA I NIE TYLKO
PRZEPISY KULINARNE
ULUBIONE KSIĄŻKI
DOWCIPY
GEOGRAFIA