Phytotaxa - 58, 2012

Contents:

A generic revision and new combinations in the Hyptidinae (Lamiaceae), based on molecular and morphological evidence
R.M. HARLEY & J.F.B. PASTORE

Lectotypification of the name Helianthus dentatus Cav., basionym of Viguiera dentata (Cav.) Spreng. (Asteraceae: Heliantheae)
MARA ANGELINA GALVAO MAGENTA, BENOÎT LOEUILLE, DAVID J. NICHOLAS HIND & JOSÉ RUBENS PIRANI

Reinstatement of Polygonatum yunnanense (Asparagaceae)
AARON J. FLODEN

 
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Phytotaxa - 57, 2012

Contents:

New combinations in Potentilla (Rosaceae) for the Nordic Flora
MAARTEN J. M. CHRISTENHUSZ & HENRY VÄRE

Struthanthus martianus, a replacement name for the illegitimate Struthanthus vulgaris Mart. ex Eichler (Loranthaceae)
GRETA ALINE DETTKE & JORGE LUIZ WAECHTER

New combinations in Neotropical Lycopodiaceae
BENJAMIN OLLGAARD

Clarification on the circumscription of Prescottia glazioviana (Cranichidinae, Orchidaceae)
CECÍLIA O. DE AZEVEDO, LÚCIO DE SOUZA LEONI & CÁSSIO VAN DEN BERG

Frullania curvilobula (Frullaniaceae, Marchantiophyta), a new species from Brazil
ALFONS SCHÄFER-VERWIMP, DENILSON F. PERALTA & SAMYLIA M. DA COSTA SIQUEIRA

A taxonomic revision of the Solanum echinatum group (Solanaceae)
A.R. BEAN

Magnolia zoquepopolucae (subsection Talauma, Magnoliaceae), a new species from Sierra de Santa Marta, Veracruz, Mexico
J. ANTONIO VÁZQUEZ-GARCÍA, ERNESTO DE CASTRO-ARCE, MIGUEL A. MUNIZ-CASTRO & MIGUEL DE J. CHÁZARO-BASÁNEZ

Lectotypification of Anemoclema glaucifolium (Ranunculaceae), endemic to southwestern China
NAN JIANG & KAI-YUN GUAN

Masdevallia spectrum (Pleurothallidinae: Orchidaceae), and new combination with taxonomic and nomenclatural notes
ALFONSO DOUCETTE
    
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Phytotaxa - 56, 2012

Contents:


The "lady in white", a showy new species of Cryptocentrum (Orchidaceae, Maxillariinae) from Colombia
GERMAN CARNEVALI F.C., PEDRO ORTIZ V. & LIZANDRO N. PERAZA-FLORES

Erratum
CASTRO NETO, V.P., MOTTE, D. & DUBUISSON, J.Y. (2012) Cattleya × itabapoanaensis (Orchidaceae), a new natural hybrid from Rio Janeiro State (Brazil). Phytotaxa 50: 64–68

Vochysia microphylla (Vochysiaceae), a new species from Serra do Cipó, Minas Gerais, Brazil
GUSTAVO HIROAKI SHIMIZU, LICLÉIA DA CRUZ RODRIGUES & KIKYO YAMAMOTO

A new species of Lindsaea (Lindsaeaceae, Polypodiopsida) from Mt. Hamiguitan, Mindanao, Philippines
DIRK NIKOLAUS KARGER, SAMULI LEHTONEN, VICTOR B. AMOROSO & MICHAEL KESSLER

Notes on the typification of Ochagavia litoralis (Bromelioideae, Bromeliaceae)
JULIO V. SCHNEIDER, GEORG ZIZKA & MELICA MUNOZ-SCHICK

Dracula agnosia (Orchidaceae: Pleurothallidinae), a long confused undescribed species
ALFONSO DOUCETTE

Allium aladaghense (Amaryllidaceae, Allieae), a new species of section Asteroprason from northeast of Iran
FARSHID MEMARIANI, MOHAMMAD REZA JOHARCHI & ALI ASGHAR ARJMANDI

Floristic discoveries from the LNG Pipeline in Papua New Guinea: Macaranga esseriana sp. nov. (Euphorbiaceae), and noteworthy records for twelve taxa from the southern provinces
WAYNE TAKEUCHI

A new species of Aquilegia (Ranunculaceae) from Sardinia (Italy)
GIANLUIGI BACCHETTA, SALVATORE BRULLO, ANGELINO CONGIU, GIUSEPPE FENU, JOSÉ LUIS GARRIDO & EFISIO MATTANA

 

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
  
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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
   
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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
   
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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
  
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Phytotaxa - 55, 2012

Contents:

Monograph

A first assessment of the Ticolichen biodiversity inventory in Costa Rica and adjacent areas: the thelotremoid Graphidaceae (Ascomycota: Ostropales)

HARRIE J.M. SIPMAN, ROBERT LÜCKING, ANDRÉ APTROOT, JOSÉ LUIS CHAVES, KLAUS KALB & LOENGRIN UMANA TENORIO

Phytotaxa - 54, 2012

Contents:

A new species of Pyropia (Rhodophyta, Bangiaceae), from the Pacific coast of Mexico, based on morphological and molecular evidence
LUZ ELENA MATEO-CID, ANGELA CATALINA MENDOZA-GONZÁLEZ, JHOANA DÍAZLARREA, ABEL SENTÍES, FRANCISCO F. PEDROCHE & JUAN DIEGO SÁNCHEZ HEREDIA

Two new species of Nitzschia (Bacillariophyta) from shallow wetlands of Peninsular India
B. ALAKANANDA, M. K. MAHESH, PAUL B. HAMILTON, G. SUPRIYA, B. KARTHICK & T. V. RAMACHANDRA

Establishment of Rosa sect. Caninae subsect. Orientales (Rosaceae) and the recognition of an unusual variety of Rosa vanheurckiana from eastern Anatolia, Turkey
KIT TAN, HASAN YILDIRIM & JERZY ZIELIŃSKI

Primulina hochiensis var. rosulata (Gesneriaceae) a new variety at an entrance of a limestone cave from Guangxi, China
FANG WEN, GUO-LE QIN, YI-GANG WEI, GUI-YOU LIANG & BO GAO

Small-sized and discoid species of the genus Cocconeiopsis (Bacillariophyta) on Holothuria atra (Juan de Nova, Mozambique Channel)
CATHERINE RIAUX-GOBIN & ANDRZEJ WITKOWSKI

Gomphonema yaominae sp. nov. Li, a new species of diatom (Bacillariophyta) from lakes near Yangtze River, China
ZHIJUN GONG & YANLING LI

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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
  
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