Genome Biology and Evolution - 2, 2010

Contents:

Lillian Hancock, Lynda Goff and Christopher Lane
Red Algae Lose Key Mitochondrial Genes in Response to Becoming Parasitic

Olga K. Kamneva, David A. Liberles and Naomi L. Ward
Genome-Wide Influence of Indel Substitutions on Evolution of Bacteria of the PVC Superphylum, Revealed Using a Novel Computational Method

Kenneth M. Flynn, Samuel H. Vohr, Philip J. Hatcher and Vaughn S. Cooper
Evolutionary Rates and Gene Dispensability Associate with Replication Timing in the Archaeon Sulfolobus islandicus

Sandeep Venkataram and Justin C. Fay
Is Transcription Factor Binding Site Turnover a Sufficient Explanation for Cis-Regulatory Sequence Divergence?

Miguel Gallach, Chitra Chandrasekaran and Esther Betrán
Analyses of Nuclearly Encoded Mitochondrial Genes Suggest Gene Duplication as a Mechanism for Resolving Intralocus Sexually Antagonistic Conflict in Drosophila

Annette M. Evangelisti and Gavin C. Conant
Nonrandom Survival of Gene Conversions among Yeast Ribosomal Proteins Duplicated through Genome Doubling

James J. Cai, Elhanan Borenstein and Dmitri A. Petrov
Broker Genes in Human Disease

Thomas A. Oliver, David A. Garfield, Mollie K. Manier, Ralph Haygood, Gregory A. Wray and Stephen R. Palumbi
Whole-Genome Positive Selection and Habitat-Driven Evolution in a Shallow and a Deep-Sea Urchin

Svetlana A. Shabalina, Alexey N. Spiridonov, Nikolay A. Spiridonov and Eugene V. Koonin
Connections between Alternative Transcription and Alternative Splicing in Mammals

Robert Ekblom, Lisa French, Jon Slate and Terry Burke
Evolutionary Analysis and Expression Profiling of Zebra Finch Immune Genes

Jia Zeng and Soojin V. Yi
DNA Methylation and Genome Evolution in Honeybee: Gene Length, Expression, Functional Enrichment Covary with the Evolutionary Signature of DNA Methylation

Joshua L. Cherry
Expression Level, Evolutionary Rate, and the Cost of Expression

Pere Puigbo, Yuri I. Wolf, and Eugene V. Koonin
The Tree and Net Components of Prokaryote Evolution

William J. Kelly, Lawrence J. H. Ward, and Sinead C. Leahy
Chromosomal Diversity in Lactococcus lactis and the Origin of Dairy Starter Cultures

Brendan G. Hunt, Jennifer A. Brisson, Soojin V. Yi, and Michael A. D. Goodisman
Functional Conservation of DNA Methylation in the Pea Aphid and the Honeybee

John P. McCutcheon and Nancy A. Moran
Functional Convergence in Reduced Genomes of Bacterial Symbionts Spanning 200 My of Evolution

Antonio Marco, Jerome H. L. Hui, Matthew Ronshaugen and Sam Griffiths-Jones
Functional Shifts in Insect microRNA Evolution

Laura Wegener Parfrey and Laura A. Katz
Genome Dynamics Are Influenced by Food Source in Allogromia laticollaris Strain CSH (Foraminifera)

Ferdinand Marlétaz, Gabor Gyapay and Yannick Le Parco
High Level of Structural Polymorphism Driven by Mobile Elements in the Hox Genomic Region of the Chaetognath Spadella cephaloptera

Jainy Thomas, Sarah Schaack and Ellen J. Pritham
Pervasive Horizontal Transfer of Rolling-Circle Transposons among Animals

Tristan Lefébure, Paulina D. Pavinski Bitar, Haruo Suzuki, and Michael J. Stanhope
Evolutionary Dynamics of Complete Campylobacter Pan-Genomes and the Bacterial Species Concept

Tobias Warnecke, Yang Huang, Teresa M. Przytycka, and Laurence D. Hurst
Unique Cost Dynamics Elucidate the Role of Frameshifting Errors in Promoting Translational Robustness

Yogeshwar D. Kelkar, Noelle Strubczewski, Suzanne E. Hile, Francesca Chiaromonte, Kristin A. Eckert and Kateryna D. Makova
What Is a Microsatellite: A Computational and Experimental Definition Based upon Repeat Mutational Behavior at A/T and GT/AC Repeats

Tom A. Williams and Mario A. Fares
The Effect of Chaperonin Buffering on Protein Evolution

David Bogumil and Tal Dagan
Chaperonin-Dependent Accelerated Substitution Rates in Prokaryotes

Ryan M. Ames, Bharat M. Rash, Kathryn E. Hentges, David L. Robertson, Daniela Delneri, and Simon C. Lovell
Gene Duplication and Environmental Adaptation within Yeast Populations

Denise B. Lynch, Mary E. Logue, Geraldine Butler and Kenneth H. Wolfe
Chromosomal G + C Content Evolution in Yeasts: Systematic Interspecies Differences, and GC-Poor Troughs at Centromeres

Satoshi Oota, Kazuhiro Kawamura, Yosuke Kawai, and Naruya Saitou
A New Framework for Studying the Isochore Evolution: Estimation of the Equilibrium GC Content Based on the Temporal Mutation Rate Model

Alan Hodgkinson and Adam Eyre-Walker
The Genomic Distribution and Local Context of Coincident SNPs in Human and Chimpanzee

Jeremy E. Coate and Jeff J. Doyle
Quantifying Whole Transcriptome Size, a Prerequisite for Understanding Transcriptome Evolution Across Species: An Example from a Plant Allopolyploid

Dennis Kostka, Matthew W. Hahn, and Katherine S. Pollard
Noncoding Sequences Near Duplicated Genes Evolve Rapidly

Ching-Ping Lin, Jen-Pan Huang, Chung-Shien Wu, Chih-Yao Hsu, and Shu-Miaw Chaw
Comparative Chloroplast Genomics Reveals the Evolution of Pinaceae Genera and Subfamilies

Daniel Lang, Benjamin Weiche, Gerrit Timmerhaus, Sandra Richardt, Diego M. Riano-Pachón, Luiz G. G. Correa, Ralf Reski, Bernd Mueller-Roeber and Stefan A. Rensing
Genome-Wide Phylogenetic Comparative Analysis of Plant Transcriptional Regulation: A Timeline of Loss, Gain, Expansion, and Correlation with Complexity

Hubert H. Rogers, Casey M. Bergman, and Sam Griffiths-Jones
The Evolution of tRNA Genes in Drosophila

Caitriona M. Guinane, Nouri L. Ben Zakour, Maria A. Tormo-Mas, Lucy A. Weinert, Bethan V. Lowder, Robyn A. Cartwright, Davida S. Smyth, Cyril J. Smyth, Jodi A. Lindsay, Katherine A. Gould, Adam Witney, Jason Hinds, Jonathan P. Bollback, Andrew Rambaut, José R. Penadés and J. Ross Fitzgerald
Evolutionary Genomics of Staphylococcus aureus Reveals Insights into the Origin and Molecular Basis of Ruminant Host Adaptation

Seth DeBolt
Copy Number Variation Shapes Genome Diversity in Arabidopsis Over Immediate Family Generational Scales

Omar Rota-Stabelli, Ehsan Kayal, Dianne Gleeson, Jennifer Daub, Jeffrey L. Boore, Maximilian J. Telford, Davide Pisani, Mark Blaxter and Dennis V. Lavrov
Ecdysozoan Mitogenomics: Evidence for a Common Origin of the Legged Invertebrates, the Panarthropoda

Bennet J. McComish, Simon F. K. Hills, Patrick J. Biggs and David Penny
Index-Free De Novo Assembly and Deconvolution of Mixed Mitochondrial Genomes

Jamie K. Davis, Josh J. Lowman, Pamela J. Thomas, Boudewijn F. H. ten Hallers, Maxim Koriabine, Lynn Y. Huynh, Donna L. Maney, Pieter J. de Jong, Christa L. Martin, James W. Thomas and NISC Comparative Sequencing Program
Evolution of a Bitter Taste Receptor Gene Cluster in a New World Sparrow

Sébastien Leclercq, Eric Rivals, and Philippe Jarne
DNA Slippage Occurs at Microsatellite Loci without Minimal Threshold Length in Humans: A Comparative Genomic Approach

Tal Dagan, Mayo Roettger, David Bryant, and William Martin
Genome Networks Root the Tree of Life between Prokaryotic Domains

Gabriel A. B. Marais, Paulo R. A. Campos and Isabel Gordo
Can Intra-Y Gene Conversion Oppose the Degeneration of the Human Y Chromosome? A Simulation Study

Eldon G. Prince, Donna Kirkland, and Jeffery P. Demuth
Hyperexpression of the X Chromosome in Both Sexes Results in Extensive Female Bias of X-Linked Genes in the Flour Beetle

Heidi J. T. Pagan, Jeremy D. Smith, Robert M. Hubley, and David A. Ray
PiggyBac-ing on a Primate Genome: Novel Elements, Recent Activity and Horizontal Transfer

Patrick J. Keeling, Nicolas Corradi, Hilary G. Morrison, Karen L. Haag, Dieter Ebert, Louis M. Weiss, Donna E. Akiyoshi and Saul Tzipori
The Reduced Genome of the Parasitic Microsporidian Enterocytozoon bieneusi Lacks Genes for Core Carbon Metabolism

John H. McDonald
Temperature Adaptation at Homologous Sites in Proteins from Nine Thermophile–Mesophile Species Pairs

James J. Cai and Dmitri A. Petrov
Relaxed Purifying Selection and Possibly High Rate of Adaptation in Primate Lineage-Specific Genes

Thérese A. Holton and Davide Pisani
Deep Genomic-Scale Analyses of the Metazoa Reject Coelomata: Evidence from Single- and Multigene Families Analyzed Under a Supertree and Supermatrix Paradigm

Vicente Pérez-Brocal, Revital Shahar-Golan, and C. Graham Clark
A Linear Molecule with Two Large Inverted Repeats: The Mitochondrial Genome of the Stramenopile Proteromonas lacertae

Jean-Simon Brouard, Christian Otis, Claude Lemieux, and Monique Turmel
The Exceptionally Large Chloroplast Genome of the Green Alga Floydiella terrestris Illuminates the Evolutionary History of the Chlorophyceae

Marnix H. Medema, Axel Trefzer, Andriy Kovalchuk, Marco van den Berg, Ulrike Müller, Wilbert Heijne, Liang Wu, Mohammad T. Alam, Catherine M. Ronning, William C. Nierman, Roel A. L. Bovenberg, Rainer Breitling and Eriko Takano
The Sequence of a 1.8-Mb Bacterial Linear Plasmid Reveals a Rich Evolutionary Reservoir of Secondary Metabolic Pathways

Angélica Cibrián-Jaramillo, Jose E. De la Torre-Bárcena, Ernest K. Lee, Manpreet S. Katari, Damon P. Little, Dennis W. Stevenson, Rob Martienssen, Gloria M. Coruzzi and Rob DeSalle
Using Phylogenomic Patterns and Gene Ontology to Identify Proteins of Importance in Plant Evolution

Yuri I. Wolf, Irina V. Gopich, David J. Lipman, and Eugene V. Koonin
Relative Contributions of Intrinsic Structural–Functional Constraints and Translation Rate to the Evolution of Protein-Coding Genes

Ziheng Yang
A Likelihood Ratio Test of Speciation with Gene Flow Using Genomic Sequence Data

Masafumi Nozawa, Sayaka Miura, and Masatoshi Nei
Origins and Evolution of MicroRNA Genes in Drosophila Species

Kate E. Ridout, Christopher J. Dixon, and Dmitry A. Filatov
Positive Selection Differs between Protein Secondary Structure Elements in Drosophila

Anne Roulin, Cristian Chaparro, Benoit Piégu, Scott Jackson, and Olivier Panaud
Paleogenomic Analysis of the Short Arm of Chromosome 3 Reveals the History of the African and Asian Progenitors of Cultivated Rices

Emmanuel Buschiazzo and Neil J. Gemmell
Conservation of Human Microsatellites across 450 Million Years of Evolution

Christine Arbiol, André M. Comeau, Muzia Kutateladze, Revaz Adamia and H. M. Krisch
Mobile Regulatory Cassettes Mediate Modular Shuffling in T4-Type Phage Genomes

Scott C. Perry and Robert G. Beiko
Distinguishing Microbial Genome Fragments Based on Their Composition: Evolutionary and Comparative Genomic Perspectives

Liliana Losada, Catherine M. Ronning, David DeShazer, Donald Woods, Natalie Fedorova, H. Stanley Kim, Svetlana A. Shabalina, Talima R. Pearson, Lauren Brinkac, Patrick Tan, Tannistha Nandi, Jonathan Crabtree, Jonathan Badger, Steve Beckstrom-Sternberg, Muhammad Saqib, Steven E. Schutzer, Paul Keim, and William C. Nierman
Continuing Evolution of Burkholderia mallei Through Genome Reduction and Large-Scale Rearrangements

Courtney C. Babbitt, Olivier Fedrigo, Adam D. Pfefferle, Alan P. Boyle, Julie E. Horvath, Terrence S. Furey and Gregory A. Wray
Both Noncoding and Protein-Coding RNAs Contribute to Gene Expression Evolution in the Primate Brain

Julie M. Cridland and Kevin R. Thornton
Validation of Rearrangement Break Points Identified by Paired-End Sequencing in Natural Populations of Drosophila melanogaster

C. F. Mugal, J. B. W. Wolf, H. H. von Grünberg, and H. Ellegren
Conservation of Neutral Substitution Rate and Substitutional Asymmetries in Mammalian Genes

Parag A. Vaishampayan, Jennifer V. Kuehl, Jeffrey L. Froula, Jenna L. Morgan, Howard Ochman and M. Pilar Francino
Comparative Metagenomics and Population Dynamics of the Gut Microbiota in Mother and Infant

Dana K. Howe, Charles F. Baer and Dee R. Denver
High Rate of Large Deletions in Caenorhabditis briggsae Mitochondrial Genome Mutation Processes

Ashley A. McAnally and Lev Y. Yampolsky
Widespread Transcriptional Autosomal Dosage Compensation in Drosophila Correlates with Gene Expression Level

Naobumi V. Sasaki and Naoki Sato
Elucidating Genome Structure Evolution by Analysis of Isoapostatic Gene Clusters using Statistics of Variance of Gene Distances

Sujith Puthiyaveetil, Iskander M. Ibrahim, Branka Jeličić, Ana Tomašić, Hrvoje Fulgosi, and John F. Allen
Transcriptional Control of Photosynthesis Genes: The Evolutionarily Conserved Regulatory Mechanism in Plastid Genome Function

Kevin Chen, Erik van Nimwegen, Nikolaus Rajewsky and Mark L. Siegal
Correlating Gene Expression Variation with cis-Regulatory Polymorphism in Saccharomyces cerevisiae

Gordon R. Plague
Intergenic Transposable Elements Are Not Randomly Distributed in Bacteria

Lei Wang, Beny Spira, Zhemin Zhou, Lu Feng, Ram P. Maharjan, Xiaomin Li, Fangfang Li, Christopher McKenzie, Peter R. Reeves, and Thomas Ferenci
Divergence Involving Global Regulatory Gene Mutations in an Escherichia coli Population Evolving under Phosphate Limitation

Jeffrey D. Jensen and Doris Bachtrog
Characterizing Recurrent Positive Selection at Fast-Evolving Genes in Drosophila miranda and Drosophila pseudoobscura

Guodong Wang, Peng Shi, Zhouhai Zhu and Ya-ping Zhang
More Functional V1R Genes Occur in Nest-Living and Nocturnal Terricolous Mammals

Thomas Giger, Philipp Khaitovich, Mehmet Somel, Anna Lorenc, Esther Lizano, Laura W. Harris, Margaret M. Ryan, Martin Lan, Matthew T. Wayland, Sabine Bahn, and Svante Pääbo
Evolution of Neuronal and Endothelial Transcriptomes in Primates

Ben-Yang Liao, Meng-Pin Weng and Jianzhi Zhang
Impact of Extracellularity on the Evolutionary Rate of Mammalian Proteins

Michel C. Milinkovitch, Raphaël Helaers and Athanasia C. Tzika
Historical Constraints on Vertebrate Genome Evolution

Society for Molecular Biology and Evolution (SMBE) Council and Business Meetings, 2009, Iowa City, IA

John M. Archibald
Treasurer's Report for FY 2008

Genome Biology and Evolution



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