LETTER S
Hypervariability of Ascidian Mitochondrial Gene Order: Exposing the Myth of Deuterostome Organelle Genome Stability
Carmela Gissi, Graziano Pesole, Francesco Mastrototaro, Fabio Iannelli, Vanessa Guida, and Francesca Griggio
Chordate Hox and ParaHox Gene Clusters Differ Dramatically in Their Repetitive Element Content
Peter W. Osborne and David E.K. Ferrier
SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building
Manolo Gouy, Stéphane Guindon, and Olivier Gascuel
RESEARCH ARTICLES
Retracing Evolution of Red Fluorescence in GFP-Like Proteins from Faviina Corals
Steven F. Field and Mikhail V. Matz
A Genome-Sequence Survey for Ascogregarina taiwanensis Supports Evolutionary Affiliation but Metabolic Diversity between a Gregarine and Cryptosporidium
Thomas J. Templeton, Shinichiro Enomoto, Wei-June Chen, Chin-Gi Huang, Cheryl A. Lancto, Mitchell S. Abrahamsen, and Guan Zhu
Rapid Likelihood Analysis on Large Phylogenies Using Partial Sampling of Substitution Histories
A. P. Jason de Koning, Wanjun Gu, and David D. Pollock
Nucleotide Polymorphism at a Gene ( Pgi ) under Balancing Selection in a Butterfly Metapopulation
Christopher W. Wheat, Christoph R. Haag, James H. Marden, Ilkka Hanski, and Mikko J. Frilander
Isoform Divergence of the Filamin Family of Proteins
Barry A. Kesner, Sharon L. Milgram, Brenda R.S. Temple, and Nikolay V. Dokholyan
How Robust Are “Isolation with Migration” Analyses to Violations of the IM Model? A Simulation Study
Jared L. Strasburg and Loren H. Rieseberg
Phylogenetic Distributions and Histories of Proteins Involved in Anaerobic Pyruvate Metabolism in Eukaryotes
Laura A. Hug, Alexandra Stechmann, and Andrew J. Roger
Heterogeneous Patterns of Gene-Expression Diversification in Mammalian Gene Duplicates
Domenec Farré and M. Mar Alba
A Statistical Evaluation of Models for the Initial Settlement of the American Continent Emphasizes the Importance of Gene Flow with Asia
N. Ray, D. Wegmann, N.J.R. Fagundes, S. Wang, A. Ruiz-Linares, and L. Excoffier
Infrequent Transitions between Saline and Fresh Waters in One of the Most Abundant Microbial Lineages (SAR11)
Ramiro Logares, Jon Brate, Friederike Heinrich, Kamran Shalchian-Tabrizi, and Stefan Bertilsson
The Cytophaga hutchinsonii ChTPSP: First Characterized Bifunctional TPS – TPP Protein as Putative Ancestor of All Eukaryotic Trehalose Biosynthesis Proteins
Nelson Avonce, Jan Wuyts, Katrien Verschooten, Lies Vandesteene, and Patrick Van Dijck
A Dirichlet Process Covarion Mixture Model and Its Assessments Using Posterior Predictive Discrepancy Tests
Yan Zhou, Henner Brinkmann, Nicolas Rodrigue, Nicolas Lartillot, and Hervé Philippe
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A Worldwide Survey of Human Male Demographic History Based on Y-SNP and Y-STR Data from the HGDP – CEPH Populations
Wentao Shi, Qasim Ayub, Mark Vermeulen, Rong-guang Shao, Sofia Zuniga, Kristiaan van der Gaag, Peter de Knijff, Manfred Kayser, Yali Xue, and Chris Tyler-Smith
Novel Venom Proteins Produced by Differential Domain-Expression Strategies in Beaded Lizards and Gila Monsters (genus Heloderma )
Bryan G. Fry, Kim Roelants, Kelly Winter, Wayne C. Hodgson, Laura Griesman, Hang Fai Kwok, Denis Scanlon, John Karas, Chris Shaw, Lily Wong, and Janette A. Norman
Indel-Associated Mutation Rate Varies with Mating System in Flowering Plants
Jesse D. Hollister, Jeffrey Ross-Ibarra, and Brandon S. Gaut
Phylodynamics of HIV-1 from a Phase-III AIDS Vaccine Trial in North America
Marcos Pérez-Losada, David V. Jobes, Faruk Sinangil, Keith A. Crandall, David Posada, and Phillip W. Berman
Bacterial Genetic Signatures of Human Social Phenomena among M. tuberculosis from an Aboriginal Canadian Population
Caitlin Pepperell, Vernon H. Hoeppner, Mikhail Lipatov, Wendy Wobeser, Gary K. Schoolnik, and Marcus W. Feldman
Large-Scale Parsimony Analysis of Metazoan Indels in Protein-Coding Genes
Frida Belinky, Ofir Cohen, and Dorothée Huchon
An Explicit Signature of Balancing Selection for Color-Vision Variation in New World Monkeys
Tomohide Hiwatashi, Yugo Okabe, Toko Tsutsui, Chihiro Hiramatsu, Amanda D. Melin, Hiroki Oota, Colleen M. Schaffner, Filippo Aureli, Linda M. Fedigan, Hideki Innan, and Shoji Kawamura
Multiple Functional Variants in cis Modulate PDYN Expression
Courtney C. Babbitt, Jesse S. Silverman, Ralph Haygood, Jennifer M. Reininga, Matthew V. Rockman, and Gregory A. Wray
Divergence of Recently Duplicated M g -Type MADS-Box Genes in Petunia
Marian Bemer, Jonathan Gordon, Koen Weterings, and Gerco C. Angenent
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