Genome Biology and Evolution - 3, 2011

Contents:


Shigehiro Kuraku and Shigeru Kuratani
Genome-Wide Detection of Gene Extinction in Early Mammalian Evolution

Alexander Neef, Amparo Latorre, Juli Peretó, Francisco J. Silva, Miguel Pignatelli, and Andrés Moya
Genome Economization in the Endosymbiont of the Wood Roach Cryptocercus punctulatus Due to Drastic Loss of Amino Acid Synthesis Capabilities

Shao-Lun Liu, Gregory J. Baute, and Keith L. Adams
Organ and Cell Type–Specific Complementary Expression Patterns and Regulatory Neofunctionalization between Duplicated Genes in Arabidopsis thaliana

Weilong Hao, Jennifer H. Ma, Keisha Warren, Raymond S.W. Tsang, Donald E. Low, Frances B. Jamieson, and David C. Alexander
Extensive Genomic Variation within Clonal Complexes of Neisseria meningitidis

David Managadze, Igor B. Rogozin, Diana Chernikova, Svetlana A. Shabalina, and Eugene V. Koonin
Negative Correlation between Expression Level and Evolutionary Rate of Long Intergenic Noncoding RNAs

Axel Künstner, Benoit Nabholz, and Hans Ellegren
Significant Selective Constraint at 4-Fold Degenerate Sites in the Avian Genome and Its Consequence for Detection of Positive Selection

Melissa A. Toups, James B. Pease, and Matthew W. Hahn
No Excess Gene Movement Is Detected off the Avian or Lepidopteran Z Chromosome

Corey M. Hudson, Emily E. Puckett, Michaël Bekaert, J. Chris Pires, and Gavin C. Conant
Selection for Higher Gene Copy Number after Different Types of Plant Gene Duplications

Hiroaki Sakai, Hiroshi Mizuno, Yoshihiro Kawahara, Hironobu Wakimoto, Hiroshi Ikawa, Hiroyuki Kawahigashi, Hiroyuki Kanamori, Takashi Matsumoto, Takeshi Itoh, and Brandon S. Gaut
Retrogenes in Rice (Oryza sativa L. ssp. japonica) Exhibit Correlated Expression with Their Source Genes

James R. Doroghazi and Daniel H. Buckley
A Model for the Effect of Homologous Recombination on Microbial Diversification

Bojian Zhong, Oliver Deusch, Vadim V. Goremykin, David Penny, Patrick J. Biggs, Robin A. Atherton, Svetlana V. Nikiforova, and Peter James Lockhart
Systematic Error in Seed Plant Phylogenomics

Danielle Venton
Highlight: The Degenerating Y Chromosome: Under the Pressures of Sex and Selection

Vera B. Kaiser, Qi Zhou, and Doris Bachtrog
Nonrandom Gene Loss from the Drosophila miranda Neo-Y Chromosome

Seth M. Bybee, Heather Bracken-Grissom, Benjamin D. Haynes, Russell A. Hermansen, Robert L. Byers, Mark J. Clement, Joshua A. Udall, Edward R. Wilcox, and Keith A. Crandall
Targeted Amplicon Sequencing (TAS): A Scalable Next-Gen Approach to Multilocus, Multitaxa Phylogenetics

Tomasz Żemojtel, Szymon M. Kiełbasa, Peter F. Arndt, Sarah Behrens, Guillaume Bourque, and Martin Vingron
CpG Deamination Creates Transcription Factor–Binding Sites with High Efficiency

Chung-Shien Wu, Ya-Nan Wang, Chi-Yao Hsu, Ching-Ping Lin, and Shu-Miaw Chaw
Loss of Different Inverted Repeat Copies from the Chloroplast Genomes of Pinaceae and Cupressophytes and Influence of Heterotachy on the Evaluation of Gymnosperm Phylogeny

Shunsuke Suzuki, Geoffrey Shaw, Tomoko Kaneko-Ishino, Fumitoshi Ishino, and Marilyn B. Renfree
The Evolution of Mammalian Genomic Imprinting Was Accompanied by the Acquisition of Novel CpG Islands

Ofir Cohen and Tal Pupko
Inference of Gain and Loss Events from Phyletic Patterns Using Stochastic Mapping and Maximum Parsimony—A Simulation Study

Damien J. Fleetwood, Anar K. Khan, Richard D. Johnson, Carolyn A. Young, Shipra Mittal, Ruth E. Wrenn, Uljana Hesse, Simon J. Foster, Christopher L. Schardl, and Barry Scott
Abundant Degenerate Miniature Inverted-Repeat Transposable Elements in Genomes of Epichloid Fungal Endophytes of Grasses

Benjamin A. Wilson and Joanna Masel
Putatively Noncoding Transcripts Show Extensive Association with Ribosomes

Yasuhiro Kitazoe, Hirohisa Kishino, Masami Hasegawa, Atsushi Matsui, Nick Lane, and Masashi Tanaka
Stability of Mitochondrial Membrane Proteins in Terrestrial Vertebrates Predicts Aerobic Capacity and Longevity

Danielle Venton
Highlight: Stability of Mitochondrial Membrane Proteins in Terrestrial Vertebrates Predicts Aerobic Capacity and Longevity

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 and Apicomplexa-Related Chromera velia

Tanja Slotte, Thomas Bataillon, Troels T. Hansen, Kate St. Onge, Stephen I. Wright, and Mikkel H. Schierup
Genomic Determinants of Protein Evolution and Polymorphism in Arabidopsis
Genome Biol Evol (2011) Vol. 3 1210-1219 first published online September 16, 2011 doi:10.1093/gbe/evr094

Anke Konrad, Ashley I. Teufel, Johan A. Grahnen, and David A. Liberles
Toward a General Model for the Evolutionary Dynamics of Gene Duplicates

Stephen P. Moss, Domino A. Joyce, Stuart Humphries, Katherine J. Tindall, and David H. Lunt
Comparative Analysis of Teleost Genome Sequences Reveals an Ancient Intron Size Expansion in the Zebrafish Lineage

Nicolas Cerveau, Sébastien Leclercq, Elodie Leroy, Didier Bouchon, and Richard Cordaux
Short- and Long-term Evolutionary Dynamics of Bacterial Insertion Sequences: Insights from Wolbachia Endosymbionts

Alex J. McCarthy, Adam A. Witney, Katherine A. Gould, Arshnee Moodley, Luca Guardabassi, Andreas Voss, Olivier Denis, Els M. Broens, Jason Hinds, and Jodi A. Lindsay
The Distribution of Mobile Genetic Elements (MGEs) in MRSA CC398 Is Associated with Both Host and Country

Nathaniel M. Hallinan and David R. Lindberg
Comparative Analysis of Chromosome Counts Infers Three Paleopolyploidies in the Mollusca

Hye-Ran Lee, Karen E. Hayden, and Huntington F. Willard
Organization and Molecular Evolution of CENP-A–Associated Satellite DNA Families in a Basal Primate Genome

Kiyoshi Ezawa, Kazuho Ikeo, Takashi Gojobori, and Naruya Saitou
Evolutionary Patterns of Recently Emerged Animal Duplogs

Michael Lynch
The Lower Bound to the Evolution of Mutation Rates

Hiroki Goto, Oliver A. Ryder, Allison R. Fisher, Bryant Schultz, Sergei L. Kosakovsky Pond, Anton Nekrutenko, and Kateryna D. Makova
A Massively Parallel Sequencing Approach Uncovers Ancient Origins and High Genetic Variability of Endangered Przewalski's Horses

Danielle Venton
Highlight: A Massively Parallel Sequencing Approach Uncovers Ancient Origins and High Genetic Variability of Endangered Przewalski’s Horses

Georgii A. Bazykin and Alexey S. Kondrashov
Detecting Past Positive Selection through Ongoing Negative Selection

Ricard Albalat, Frédéric Brunet, Vincent Laudet, and Michael Schubert
Evolution of Retinoid and Steroid Signaling: Vertebrate Diversification from an Amphioxus Perspective

Matthew K. Fujita, Scott V. Edwards, and Chris P. Ponting
The Anolis Lizard Genome: An Amniote Genome without Isochores

Nicholas Delihas
Impact of Small Repeat Sequences on Bacterial Genome Evolution

Hua Ying and Gavin Huttley
Exploiting CpG Hypermutability to Identify Phenotypically Significant Variation Within Human Protein-Coding Genes

Lisa G. McFerrin and William R. Atchley
Evolution of the Max and Mlx Networks in Animals

Leonardo Arbiza, Mateus Patricio, Hernán Dopazo, and David Posada
Genome-Wide Heterogeneity of Nucleotide Substitution Model Fit

Deborah C. Holt, Matthew T.G. Holden, Steven Y.C. Tong, Santiago Castillo-Ramirez, Louise Clarke, Michael A. Quail, Bart J. Currie, Julian Parkhill, Stephen D. Bentley, Edward J. Feil, and Philip M. Giffard
A Very Early-Branching Staphylococcus aureus Lineage Lacking the Carotenoid Pigment Staphyloxanthin

Suo Qiu, Kai Zeng, Tanja Slotte, Stephen Wright, and Deborah Charlesworth
Reduced Efficacy of Natural Selection on Codon Usage Bias in Selfing Arabidopsis and Capsella Species

Sébastien Verne, Barry Jaquish, Rick White, Carol Ritland, and Kermit Ritland
Global Transcriptome Analysis of Constitutive Resistance to the White Pine Weevil in Spruce

Philip L. F. Johnson and Ines Hellmann
Mutation Rate Distribution Inferred from Coincident SNPs and Coincident Substitutions

Laurie S. Stevison, Kenneth B. Hoehn, and Mohamed A. F. Noor
Effects of Inversions on Within- and Between-Species Recombination and Divergence

Masatoshi Nei and Masafumi Nozawa
Roles of Mutation and Selection in Speciation: From Hugo de Vries to the Modern Genomic Era

Gregory I. Lang and Andrew W. Murray
Mutation Rates across Budding Yeast Chromosome VI Are Correlated with Replication Timing

Jessica L. Crisci, Alex Wong, Jeffrey M. Good, and Jeffrey D. Jensen
On Characterizing Adaptive Events Unique to Modern Humans

David Alvarez-Ponce and James O. McInerney
The Human Genome Retains Relics of Its Prokaryotic Ancestry: Human Genes of Archaebacterial and Eubacterial Origin Exhibit Remarkable Differences

Florent Lassalle, Tony Campillo, Ludovic Vial, Jessica Baude, Denis Costechareyre, David Chapulliot, Malek Shams, Danis Abrouk, Céline Lavire, Christine Oger-Desfeux, Florence Hommais, Laurent Guéguen, Vincent Daubin, Daniel Muller, and Xavier Nesme
Genomic Species Are Ecological Species as Revealed by Comparative Genomics in Agrobacterium tumefaciens

Yedael Y. Waldman, Tamir Tuller, Alon Keinan, and Eytan Ruppin
Selection for Translation Efficiency on Synonymous Polymorphisms in Recent Human Evolution

David Roy Smith
Extending the Limited Transfer Window Hypothesis to Inter-organelle DNA Migration

A. Darracq, J. S. Varré, L. Maréchal-Drouard, A. Courseaux, V. Castric, P. Saumitou-Laprade, S. Oztas, P. Lenoble, B. Vacherie, V. Barbe, and P. Touzet
Structural and Content Diversity of Mitochondrial Genome in Beet: A Comparative Genomic Analysis

Richard Jovelin and Patrick C. Phillips
Expression Level Drives the Pattern of Selective Constraints along the Insulin/Tor Signal Transduction Pathway in Caenorhabditis

Naruo Nikoh, Takahiro Hosokawa, Kenshiro Oshima, Masahira Hattori, and Takema Fukatsu
Reductive Evolution of Bacterial Genome in Insect Gut Environment

Jeffrey D. Jensen and Doris Bachtrog
Characterizing the Influence of Effective Population Size on the Rate of Adaptation: Gillespie’s Darwin Domain

Sabrina N. Trojet, Anne Caumont-Sarcos, Elsa Perrody, André M. Comeau, and H. M. Krisch
The gp38 Adhesins of the T4 Superfamily: A Complex Modular Determinant of the Phage’s Host Specificity

Maria Warnefors and Adam Eyre-Walker
The Accumulation of Gene Regulation Through Time

Eric S. Ho and Samuel I. Gunderson
Long Conserved Fragments Upstream of Mammalian Polyadenylation Sites

Todd A. Castoe, Kathryn T. Hall, Marcel L. Guibotsy Mboulas, Wanjun Gu, A.P. Jason de Koning, Samuel E. Fox, Alexander W. Poole, Vijetha Vemulapalli, Juan M. Daza, Todd Mockler, Eric N. Smith, Cédric Feschotte, and David D. Pollock
Discovery of Highly Divergent Repeat Landscapes in Snake Genomes Using High-Throughput Sequencing

Alvina G. Lai, Matthew Denton-Giles, Bernd Mueller-Roeber, Jos H. M. Schippers, and Paul P. Dijkwel
Positional Information Resolves Structural Variations and Uncovers an Evolutionarily Divergent Genetic Locus in Accessions of Arabidopsis thaliana

Sol Katzman, John A. Capra, David Haussler, and Katherine S. Pollard
Ongoing GC-Biased Evolution Is Widespread in the Human Genome and Enriched Near Recombination Hot Spots

Scott R. Miller, A.Michelle Wood, Robert E. Blankenship, Maria Kim, and Steven Ferriera
Dynamics of Gene Duplication in the Genomes of Chlorophyll d-Producing Cyanobacteria: Implications for the Ecological Niche

Federico G. Hoffmann, Juan C. Opazo, and Jay F. Storz
Differential Loss and Retention of Cytoglobin, Myoglobin, and Globin-E during the Radiation of Vertebrates

Jessica W. Leigh, François-Joseph Lapointe, Philippe Lopez, and Eric Bapteste
Evaluating Phylogenetic Congruence in the Post-Genomic Era

Manuel Irimia, Ignacio Maeso, Demián Burguera, Matías Hidalgo-Sánchez, Luis Puelles, Scott W. Roy, Jordi Garcia-Fernandez, and José Luis Ferran
Contrasting 5' and 3' Evolutionary Histories and Frequent Evolutionary Convergence in Meis/hth Gene Structures

Wilfried Haerty and G. Brian Golding
Increased Polymorphism Near Low-Complexity Sequences across the Genomes of Plasmodium falciparum Isolates

Robert Piskol and Wolfgang Stephan
The Role of the Effective Population Size in Compensatory Evolution

John A. Capra and Katherine S. Pollard
Substitution Patterns Are GC-Biased in Divergent Sequences across the Metazoans

Jean-Simon Brouard, Christian Otis, Claude Lemieux, and Monique Turmel
The Chloroplast Genome of the Green Alga Schizomeris leibleinii (Chlorophyceae) Provides Evidence for Bidirectional DNA Replication from a Single Origin in the Chaetophorales

James R. Walters and Thomas J. Hardcastle
Getting a Full Dose? Reconsidering Sex Chromosome Dosage Compensation in the Silkworm, Bombyx mori

Filipe G. Vieira and Julio Rozas
Comparative Genomics of the Odorant-Binding and Chemosensory Protein Gene Families across the Arthropoda: Origin and Evolutionary History of the Chemosensory System

Mary M. Rorick and Günter P. Wagner
Protein Structural Modularity and Robustness Are Associated with Evolvability

Laura Baldo, M.Emília Santos, and Walter Salzburger
Comparative Transcriptomics of Eastern African Cichlid Fishes Shows Signs of Positive Selection and a Large Contribution of Untranslated Regions to Genetic Diversity

Wataru Kai, Kiyoshi Kikuchi, Sumanty Tohari, Ah Keng Chew, Alice Tay, Atushi Fujiwara, Sho Hosoya, Hiroaki Suetake, Kiyoshi Naruse, Sydney Brenner, Yuzuru Suzuki, and Byrappa Venkatesh
Integration of the Genetic Map and Genome Assembly of Fugu Facilitates Insights into Distinct Features of Genome Evolution in Teleosts and Mammals

Xiuwei Zhang, Martin Kupiec, Uri Gophna, and Tamir Tuller
Analysis of Coevolving Gene Families Using Mutually Exclusive Orthologous Modules

Seong Hwan Park, Ondrej Podlaha, Wendy E. Grus, and Jianzhi Zhang
The Microevolution of V1r Vomeronasal Receptor Genes in Mice

David S. Lawrie, Dmitri A. Petrov, and Philipp W. Messer
Faster than Neutral Evolution of Constrained Sequences: The Complex Interplay of Mutational Biases and Weak Selection

Daniel Moog, Simone Stork, Stefan Zauner, and Uwe-G. Maier
In Silico and In Vivo Investigations of Proteins of a Minimized Eukaryotic Cytoplasm

Julia Hecht, Felix Grewe, and Volker Knoop
Extreme RNA Editing in Coding Islands and Abundant Microsatellites in Repeat Sequences of Selaginella moellendorffii Mitochondria: The Root of Frequent Plant mtDNA Recombination in Early Tracheophytes

C. A. Whittle, Y. Sun, and H. Johannesson
Evolution of Synonymous Codon Usage in Neurospora tetrasperma and Neurospora discreta

Guang-Zhong Wang, Martin J. Lercher, and Laurence D. Hurst
Transcriptional Coupling of Neighboring Genes and Gene Expression Noise: Evidence that Gene Orientation and Noncoding Transcripts Are Modulators of Noise

Chung-Shien Wu, Ching-Ping Lin, Chi-Yao Hsu, Rui-Jiang Wang, and Shu-Miaw Chaw
Comparative Chloroplast Genomes of Pinaceae: Insights into the Mechanism of Diversified Genomic Organizations

Huifeng Jiang, Lin Xu, and Zhenglong Gu
Growth of Novel Epistatic Interactions by Gene Duplication

Inaho Danjoh, Kaoru Saijo, Takashi Hiroyama, and Yukio Nakamura
The Sonoda–Tajima Cell Collection: A Human Genetics Research Resource with Emphasis on South American Indigenous Populations

Daudi Jjingo, Ahsan Huda, Madhumati Gundapuneni, Leonardo Marino-Ramírez, and I. King Jordan
Effect of the Transposable Element Environment of Human Genes on Gene Length and Expression

Cécile Ané
Detecting Phylogenetic Breakpoints and Discordance from Genome-Wide Alignments for Species Tree Reconstruction

Yves Clément and Peter F. Arndt
Substitution Patterns Are Under Different Influences in Primates and Rodents

Maud I. Tenaillon, Matthew B. Hufford, Brandon S. Gaut, and Jeffrey Ross-Ibarra
Genome Size and Transposable Element Content as Determined by High-Throughput Sequencing in Maize and Zea luxurians

Bethany N. Kent, Leonidas Salichos, John G. Gibbons, Antonis Rokas, Irene L. G. Newton, Michael E. Clark, and Seth R. Bordenstein
Complete Bacteriophage Transfer in a Bacterial Endosymbiont (Wolbachia) Determined by Targeted Genome Capture

Gaelen R. Burke and Nancy A. Moran
Massive Genomic Decay in Serratia symbiotica, a Recently Evolved Symbiont of Aphids

Tina Koestler and Ingo Ebersberger
Zygomycetes, Microsporidia, and the Evolutionary Ancestry of Sex Determination

Haruo Suzuki, Tristan Lefébure, Melissa Jane Hubisz, Paulina Pavinski Bitar, Ping Lang, Adam Siepel, and Michael J. Stanhope
Comparative Genomic Analysis of the Streptococcus dysgalactiae Species Group: Gene Content, Molecular Adaptation, and Promoter Evolution

Takeshi Kawakami, Preeti Dhakal, Angela N. Katterhenry, Chelsea A. Heatherington, and Mark C. Ungerer
Transposable Element Proliferation and Genome Expansion Are Rare in Contemporary Sunflower Hybrid Populations Despite Widespread Transcriptional Activity of LTR Retrotransposons

Tim Connallon and Andrew G. Clark
Association between Sex-Biased Gene Expression and Mutations with Sex-Specific Phenotypic Consequences in Drosophila

Gregor Felsner, Maik S. Sommer, Nicole Gruenheit, Franziska Hempel, Daniel Moog, Stefan Zauner, William Martin, and Uwe G. Maier
ERAD Components in Organisms with Complex Red Plastids Suggest Recruitment of a Preexisting Protein Transport Pathway for the Periplastid Membrane

Sayaka Miura, Masafumi Nozawa, and Masatoshi Nei
Evolutionary Changes of the Target Sites of Two MicroRNAs Encoded in the Hox Gene Cluster of Drosophila and Other Insect Species

Peter Andolfatto, Karen M. Wong, and Doris Bachtrog
Effective Population Size and the Efficacy of Selection on the X Chromosomes of Two Closely Related Drosophila Species

D.E. Janes, C. Chapus, Y. Gondo, D.F. Clayton, S. Sinha, C.A. Blatti, C.L. Organ, M.K. Fujita, C.N. Balakrishnan, and S.V. Edwards
Reptiles and Mammals Have Differentially Retained Long Conserved Noncoding Sequences from the Amniote Ancestor

David Alvarez-Ponce, Montserrat Aguadé, and Julio Rozas
Comparative Genomics of the Vertebrate Insulin/TOR Signal Transduction Pathway: A Network-Level Analysis of Selective Pressures

Robert M. Waterhouse, Evgeny M. Zdobnov, and Evgenia V. Kriventseva
Correlating Traits of Gene Retention, Sequence Divergence, Duplicability and Essentiality in Vertebrates, Arthropods, and Fungi

Ken Daigoro Yokoyama, Jeffrey L. Thorne, and Gregory A. Wray
Coordinated Genome-Wide Modifications within Proximal Promoter Cis-regulatory Elements during Vertebrate Evolution

Yong-Hwee E. Loh, Soojin V. Yi, and J.Todd Streelman
Evolution of MicroRNAs and the Diversification of Species

Goro Tanifuji, Natalie Donaher, Marlena Dlutek, Travis J. Wheeler,Naoko T. Onodera, and John M. Archibald
Complete Nucleomorph Genome Sequence of the Nonphotosynthetic Alga Cryptomonas paramecium Reveals a Core Nucleomorph Gene Set

Daniel H. Huson and Celine Scornavacca
A Survey of Combinatorial Methods for Phylogenetic Networks

Peter A. Novick, Mark Floumanhaft, Jeremy D. Smith, David A. Ray, and Stéphane Boissinot
The Evolution and Diversity of DNA Transposons in the Genome of the Lizard Anolis carolinensis

Special Collection

Bill Martin and Takashi Gojobori
Introduction to the Special Series

Werner Arber
Molecular Darwinism: The Contingency of Spontaneous Genetic Variation

Stilianos Arhondakis, Fabio Auletta, and Giorgio Bernardi
Isochores and the Regulation of Gene Expression in the Human Genome

S. Castellana, S. Vicario, and C. Saccone
Evolutionary Patterns of the Mitochondrial Genome in Metazoa: Exploring the Role of Mutation and Selection in Mitochondrial Protein–Coding Genes

Walter J. Gehring
Chance and Necessity in Eye Evolution

Eviatar Nevo
Evolution Under Environmental Stress at Macro- and Microscales

Tomoko Ohta
Near-Neutrality, Robustness, and Epigenetics

Agnes Ullmann
In Memoriam: Jacques Monod (1910–1976)

Jun Zhou, Erik B. Dopman, Bernardo Lemos, and Daniel L. Hartl
Copy-Number Variation: The Balance between Gene Dosage and Expression in Drosophila melanogaster

Genome Reports

Maria D. Logacheva, Mikhail I. Schelkunov, and Aleksey A. Penin
Sequencing and Analysis of Plastid Genome in Mycoheterotrophic Orchid Neottia nidus-avis

Philippe Colson, Svetlana A. Shabalina, Ghislain Fournous, Bernard La Scola, Catherine Robert, Didier Raoult, Natalya Yutin, and Eugene V. Koonin
Viruses with More Than 1,000 Genes: Mamavirus, a New Acanthamoeba polyphaga mimivirus Strain, and Reannotation of Mimivirus Genes

Isabelle C. Arnold, Zuzana Zigova, Matthew Holden, Trevor D. Lawley, Roland Rad, Gordon Dougan, Stanley Falkow, Stephen D. Bentley, and Anne Müller
Comparative Whole Genome Sequence Analysis of the Carcinogenic Bacterial Model Pathogen Helicobacter felis

Letters

Sankar Subramanian and David M. Lambert
Time Dependency of Molecular Evolutionary Rates? Yes and No

Sébastien Halary, Shehre-Banoo Malik, Claudio H. Slamovits, Levannia Lildhar, Mohamed Hijri, and Nicolas Corradi
Conserved Meiotic Machinery in Glomus spp., a Putatively Ancient Asexual Fungal Lineage

Lin Xu, Huifeng Jiang, Hong Chen, and Zhenglong Gu
Genetic Architecture of Growth Traits Revealed by Global Epistatic Interactions

Guang-Zhong Wang, Wei-Hua Chen, and Martin J. Lercher
Coexpression of Linked Gene Pairs Persists Long after Their Separation

Dong-Dong Wu, David M. Irwin, and Ya-Ping Zhang
Correlated Evolution among Six Gene Families in Drosophila Revealed by Parallel Change of Gene Numbers

Nick Lane
Plastids, Genomes, and the Probability of Gene Transfer

David Roy Smith, Kate Crosby, and Robert W. Lee
Correlation between Nuclear Plastid DNA Abundance and Plastid Number Supports the Limited Transfer Window Hypothesis

Luděk Kořený and Miroslav Oborník
Sequence Evidence for the Presence of Two Tetrapyrrole Pathways in Euglena gracilis

Graeme J. Roch and Nancy M. Sherwood
Stanniocalcin Has Deep Evolutionary Roots in Eukaryotes

Beatriz Vicoso and Doris Bachtrog
Lack of Global Dosage Compensation in Schistosoma mansoni, a Female-Heterogametic Parasite

Allison M. Churcher and John S. Taylor
The Antiquity of Chordate Odorant Receptors Is Revealed by the Discovery of Orthologs in the Cnidarian Nematostella vectensis

Gregory A. Babbitt and C. R. Cotter
Functional Conservation of Nucleosome Formation Selectively Biases Presumably Neutral Molecular Variation in Yeast Genomes

Editorials

John M. Archibald
Treasurer's Report for FY 2009

Society for Molecular Biology and Evolution (SMBE) Council and Business Meetings, 2010, Lyon, France

Bill Martin and Takashi Gojobori
GBE Editor's Report

Editorial Board

Genome Biology and Evolution



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