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Molecular Biology and Evolution
2008- 25:1
Articles
Evidence Excluding the Root of the Tree
of Life from the Actinobacteria
1-4 Jacqueline A. Servin, Craig W.
Herbold, Ryan G. Skophammer, and
James A. Lake
Modeling Sites of RNA Editing as a
Fifth Nucleotide State Reveals
Progressive Loss of Edited Sites from
Angiosperm Mitochondria
52-61 Jeffrey P. Mower
Large Gene Family Expansion and
Variable Selective Pressures for
Cathepsin B in Aphids 5-17
Claude Rispe, Mayako Kutsukake,
Vincent Doublet, Sylvie Hudaverdian,
Fabrice Legeai, Jean-Christophe Simon,
Denis Tagu, and Takema Fukatsu
Chromosome-Specific Distribution of
Nucleotide Substitutions in Telomeric
Repeats of Rice (Oryza sativa L.)
62-68 Hiroshi Mizuno, Jianzhong Wu,
Yuichi Katayose, Hiroyuki Kanamori,
Takuji Sasaki, and Takashi Matsumoto
Sequence Variation in the Primate
Dopamine Transporter Gene and Its
Relationship to Social Dominance
18-28 Cassandra M. Miller-Butterworth,
Jay R. Kaplan, John Shaffer, Bernie
Devlin, Stephen B. Manuck, and Robert
E. Ferrell
Convergent Domestication of pogo-like
Transposases into Centromere-Binding
Proteins in Fission Yeast and Mammals
29-41 Claudio Casola, Donald Hucks,
and Cédric Feschotte
The Complete Mitochondrial Genome of
the Onychophoran Epiperipatus biolleyi
Reveals a Unique Transfer RNA Set and
Provides Further Support for the
Ecdysozoa Hypothesis 42-51
Lars Podsiadlowski, Anke Braband, and
Georg Mayer
Conservation and Diversification of Msx
Protein in Metazoan Evolution
69-82 Hirokazu Takahashi, Akiko
Kamiya, Akira Ishiguro, Atsushi C.
Suzuki, Naruya Saitou, Atsushi Toyoda,
and Jun Aruga
Alternative Methods for Concatenation
of Core Genes Indicate a Lack of
Resolution in Deep Nodes of the
Prokaryotic Phylogeny 83-91
E. Bapteste, E. Susko, J. Leigh, I. RuizTrillo, J. Bucknam, and W.F. Doolittle
Euglena Light-Harvesting Complexes
Are Encoded by Multifarious
Polyprotein mRNAs that Evolve in
Concert 92-100
Adam G. Koziol and Dion G. Durnford
Cis and Trans Regulatory Effects
Contribute to Natural Variation in
Transcriptome of Drosophila
melanogaster 101-110
Anne Genissel, Lauren M. McIntyre,
Marta L. Wayne, and Sergey V. Nuzhdin
Evolutionary Dynamics of Introns in
Plastid-Derived Genes in Plants:
Saturation Nearly Reached but Slow
Intron Gain Continues 111-119
Malay Kumar Basu, Igor B. Rogozin,
Oliver Deusch, Tal Dagan, William
Martin, and Eugene V. Koonin
Strong Variations of Mitochondrial
Mutation Rate across Mammals—the
Longevity Hypothesis 120-130
Benoit Nabholz, Sylvain Glémin, and
Nicolas Galtier
Analysis of Nuclear Receptor
Pseudogenes in Vertebrates: How the
Silent Tell Their Stories 131-143
Zhengdong D. Zhang, Philip Cayting,
George Weinstock, and Mark Gerstein
Signatures of Selection in the Human
Olfactory Receptor OR5I1 Gene
144-154 Andrés Moreno-Estrada, Ferran
Casals, Anna Ramírez-Soriano, Baldo
Oliva, Francesc Calafell, Jaume
Bertranpetit, and Elena Bosch
Insight into Ligand Diversity and Novel
Biological Roles for Family 32
Carbohydrate-Binding Modules
155-167 D. Wade Abbott, José María
Eirín-López, and Alisdair B. Boraston
The Evolution of the Pheromonal Signal
System and Its Potential Role for
Reproductive Isolation in Heterothallic
Neurospora 168-178 Magnus Karlsson,
Kristiina Nygren, and Hanna
Johannesson
Consequences of Stop Codon
Reassignment on Protein Evolution in
Ciliates with Alternative Genetic Codes
179-186 Karen Lee Ring and Andre R.
O. Cavalcanti
Patterns of Evolution in the Unique
tRNA Gene Arrays of the Genus
Entamoeba 187-198 Blessing Tawari,
Ibne Karim M. Ali, Claire Scott,
Michael A. Quail, Matthew Berriman,
Neil Hall, and C. Graham Clark
Accounting for Bias from Sequencing
Error in Population Genetic Estimates
199-206 Philip L. F. Johnson and
Montgomery Slatkin
Sexual Selection and the Adaptive
Evolution of Mammalian Ejaculate
Proteins 207-219 Steven A. Ramm,
Peter L. Oliver, Chris P. Ponting, Paula
Stockley, and Richard D. Emes
Telomeres and Longevity: Testing an
Evolutionary Hypothesis 220-228
Mark F. Haussmann and Robert A.
Mauck
Rapid R2 Retrotransposition Leads to
the Loss of Previously Inserted Copies
via Large Deletions of the rDNA Locus
229-237 Xian Zhang, Jun Zhou, and
Thomas H. Eickbush
Molecular Biology and Evolution
2008- 25:2
Articles
A Bias in ML Estimates of Branch
Lengths in the Presence of Multiple
Signals 239-242 David Penny, W. T.
White, Mike D. Hendy, and Matthew J.
Phillips
Diversifying Selection and Concerted
Evolution of a Type IV Secretion
System in Bartonella 287-300 Björn
Nystedt, A. Carolin Frank, Mikael
Thollesson, and Siv G. E. Andersson
Evolutionary Rate Variation at Multiple
Levels of Biological Organization in
Plant Mitochondrial DNA 243-246
Daniel B. Sloan, Camille M. Barr,
Matthew S. Olson, Stephen R. Keller,
and Douglas R. Taylor
Excavating Past Population Structures
by Surname-Based Sampling: The
Genetic Legacy of the Vikings in
Northwest England 301-309 Georgina R.
Bowden, Patricia Balaresque, Turi E.
King, Ziff Hansen, Andrew C. Lee,
Giles Pergl-Wilson, Emma Hurley,
Stephen J. Roberts, Patrick Waite, Judith
Jesch, Abigail L. Jones, Mark G.
Thomas, Stephen E. Harding, and Mark
A. Jobling
Complex Selection on Intron Size in
Cryptococcus neoformans 247-253
Stephanie S. Hughes, Cedric O.
Buckley, and Daniel E. Neafsey
Domain Tree-Based Analysis of Protein
Architecture Evolution
254-264 Kristoffer Forslund, Anna
Henricson, Volker Hollich, and Erik L.
L. Sonnhammer
Reevaluation of the cox1 Group I Intron
in Araceae and Angiosperms Indicates a
History Dominated by Loss rather than
Horizontal Transfer 265-276 Natalie
Cusimano, Li-Bing Zhang, and Susanne
S. Renner
Multiple Recombining Loci Encode
MaSp1, the Primary Constituent of
Dragline Silk, in Widow Spiders
(Latrodectus: Theridiidae)
277-286 Nadia A. Ayoub and Cheryl Y.
Hayashi
Starvation Induces Genomic
Rearrangements and Starvation-Resilient
Phenotypes in Yeast
310-318 Scott Coyle and Evgueny Kroll
Natural Variation in Arabidopsis lyrata
Vernalization Requirement Conferred by
a FRIGIDA Indel Polymorphism
319-329 Helmi Kuittinen, Anne
Niittyvuopio, Paula Rinne, and Outi
Savolainen
Phylogenetic Comparison of Huntingtin
Homologues Reveals the Appearance of
a Primitive polyQ in Sea Urchin 330-338
Marzia Tartari, Carmela Gissi, Valentina
Lo Sardo, Chiara Zuccato, Ernesto
Picardi, Graziano Pesole, and Elena
Cattaneo
Codon Usage in Mitochondrial
Genomes: Distinguishing ContextDependent Mutation from Translational
Selection 339-351 Wenli Jia and Paul G.
Higgs
Duplication of Accelerated Evolution
and Growth Hormone Gene in Passerine
Birds 352-361 Tamaki Yuri, Rebecca T.
Kimball, Edward L. Braun, and Michael
J. Braun
Exponential Decay of GC Content
Detected by Strand-Symmetric
Substitution Rates Influences the
Evolution of Isochore Structure
362-374 J. E. Karro, M. Peifer, R. C.
Hardison, M. Kollmann, and H. H. von
Grünberg
Widespread Evolutionary Conservation
of Alternatively Spliced Exons in
Caenorhabditis 375-382
Manuel Irimia, Jakob L. Rukov, David
Penny, Jordi Garcia-Fernandez, Jeppe
Vinther, and Scott W. Roy
Adaptive Evolution of Proteins Secreted
during Sperm Maturation: An Analysis
of the Mouse Epididymal Transcriptome
383-392 Matthew D. Dean, Jeffrey M.
Good, and Michael W. Nachman
Functional Gene Losses Occur with
Minimal Size Reduction in the Plastid
Genome of the Parasitic Liverwort
Aneura mirabilis 393-401
Norman J. Wickett, Yan Zhang, S.
Kellon Hansen, Jessie M. Roper,
Jennifer V. Kuehl, Sheila A. Plock, Paul
G. Wolf, Claude W. dePamphilis,
Jeffrey L. Boore, and Bernard Goffinet
Large-Scale Appearance of
Ultraconserved Elements in Tetrapod
Genomes and Slowdown of the
Molecular Clock 402-408 Stuart
Stephen, Michael Pheasant, Igor V.
Makunin, and John S. Mattick
Selective Sweeps in a 2-Locus Model for
Sex-Ratio Meiotic Drive in Drosophila
simulans 409-416 Nicolas Derome,
Emmanuelle Baudry, David Ogereau,
Michel Veuille, and Catherine
Montchamp-Moreau
"Contrasting Patterns of Selection at
Pinus pinaster Ait. Drought Stress
Candidate Genes as Revealed by Genetic
Differentiation Analyses" 417-437
Emmanuelle Eveno, Carmen Collada,
M. Angeles Guevara, Valérie Léger,
Alvaro Soto, Luis Díaz, Patrick Léger,
Santiago C. González-Martínez, M.
Teresa Cervera, Christophe Plomion,
and Pauline H. Garnier-Géré
Inferring Selection in Partially
Sequenced Regions 438-446
Jeffrey D. Jensen, Kevin R. Thornton,
and Charles F. Aquadro
Topology-Bayes versus Clade-Bayes in
Phylogenetic Analysis 447-453
Ward C. Wheeler and Kurt M. Pickett
Contrasting the Efficacy of Selection on
the X and Autosomes in Drosophila
454-467 Nadia D. Singh, Amanda M.
Larracuente, and Andrew G. Clark
mtDNA Variation Predicts Population
Size in Humans and Reveals a Major
Southern Asian Chapter in Human
Prehistory
468-474 Quentin D. Atkinson, Russell
D. Gray, and Alexei J. Drummond
Molecular Biology and Evolution
2008- 25:3
Articles
Bird Mitochondrial Gene Order: Insight
from 3 Warbler Mitochondrial Genomes
475-477 Tiratha Raj Singh, Ophir
Shneor, and Dorothée Huchon
Native South American Genetic
Structure and Prehistory Inferred from
Hierarchical Modeling of mtDNA 478486 Cecil M. Lewis, Jr and Jeffrey C.
Long
Mitochondrial Genome of the Colorless
Green Alga Polytomella capuana: A
Linear Molecule with an Unprecedented
GC Content 487-496
David R. Smith and Robert W. Lee
Evidence for Positive Selection on
Drosophila melanogaster Seminal Fluid
Protease Homologs
497-506 Alex Wong, Michael C.
Turchin, Mariana F. Wolfner, and
Charles F. Aquadro
Hydrogen Peroxide–Induced Gene
Expression across Kingdoms: A
Comparative Analysis 507-516
Korneel Vandenbroucke, Steven
Robbens, Klaas Vandepoele, Dirk Inzé,
Yves Van de Peer, and Frank Van
Breusegem
Contrasting Signatures of Population
Growth for Mitochondrial DNA and Y
Chromosomes among Human
Populations in Africa 517-525
Maya Metni Pilkington, Jason A.
Wilder, Fernando L. Mendez, Murray P.
Cox, August Woerner, Thiep Angui,
Sarah Kingan, Zahra Mobasher, Chiara
Batini, Giovanni Destro-Bisol, Himla
Soodyall, Beverly I. Strassmann, and
Michael F. Hammer
Investigation of Loss and Gain of Introns
in the Compact Genomes of Pufferfishes
(Fugu and Tetraodon)
526-535 Yong-Hwee Loh, Sydney
Brenner, and Byrappa Venkatesh
Metabolic Symbiosis and the Birth of the
Plant Kingdom 536-548
Philippe Deschamps, Christophe
Colleoni, Yasunori Nakamura, Eiji
Suzuki, Jean-Luc Putaux, Alain Buléon,
Sophie Haebel, Gerhard Ritte, Martin
Steup, Luisa I. Falcón, David Moreira,
Wolfgang Löffelhardt, Jenifer Nirmal
Raj, Charlotte Plancke, Christophe
d'Hulst, David Dauvillée, and Steven
Ball
A Comparative Synteny Map of
Burkholderia Species Links Large-Scale
Genome Rearrangements to Fine-Scale
Nucleotide Variation in Prokaryotes
549-558 Chi Ho Lin, Guillaume
Bourque, and Patrick Tan
Integration of Horizontally Transferred
Genes into Regulatory Interaction
Networks Takes Many Million Years
559-567 Martin J. Lercher and Csaba Pál
Mutation-Selection Models of Codon
Substitution and Their Use to Estimate
Selective Strengths on Codon Usage
568-579 Ziheng Yang and Rasmus
Nielsen
Nucleolar Binding Sequences of the
Ribosomal Protein S6e Family Reside in
Evolutionary Highly Conserved Peptide
Clusters 580-590 Swarupa KunduMichalik, Marc-Angelo Bisotti, Edgar
Lipsius, Andreas Bauche, Antonina
Kruppa, Thomas Klokow, Gertrud
Kammler, and Joachim Kruppa
Rapid Rates of Lineage-Specific Gene
Duplication and Deletion in the -Globin
Gene Family 591-602
Federico G. Hoffmann, Juan C. Opazo,
and Jay F. Storz
The Mitochondrial Genome of the
Gymnosperm Cycas taitungensis
Contains a Novel Family of Short
Interspersed Elements, Bpu Sequences,
and Abundant RNA Editing Sites 603615 Shu-Miaw Chaw, Arthur ChunChieh Shih, Daryi Wang, Yu-Wei Wu,
Shu-Mei Liu, and The-Yuan Chou
Molecular Biology and Evolution
2008- 25:4
Articles
Evidence for Male-Driven Evolution in
Drosophila 617-619 Doris Bachtrog
Rare Genomic Characters Do Not
Support Coelomata: Intron Loss/Gain
620-623 Scott William Roy and Manuel
Irimia
Geological Dates and Molecular Rates:
Fish DNA Sheds Light on Time
Dependency 624-633
Christopher P. Burridge, Dave Craw,
David Fletcher, and Jonathan M. Waters
Mammalian Nonsynonymous Sites Are
Not Overdispersed: Comparative
Genomic Analysis of Index of
Dispersion of Mammalian Proteins
634-642 Seong-Ho Kim and Soojin V.
Yi
Integrating Markov Clustering and
Molecular Phylogenetics to Reconstruct
the Cyanobacterial Species Tree from
Conserved Protein Families 643-654
Wesley D. Swingley, Robert E.
Blankenship, and Jason Raymond
A 15-Myr-Old Genetic Bottleneck
655-663 Timothy Paape, Boris Igic,
Stacey D. Smith, Richard Olmstead,
Lynn Bohs, and Joshua R. Kohn
A Phylogenomic Investigation into the
Origin of Metazoa 664-672
Iñaki Ruiz-Trillo, Andrew J. Roger,
Gertraud Burger, Michael W. Gray, and
B. Franz Lang
Lateral Symbiont Acquisition in a
Maternally Transmitted Chemosynthetic
Clam Endosymbiosis
673-687 Frank J. Stewart, Curtis R.
Young, and Colleen M. Cavanaugh
Simulating DNA Coding Sequence
Evolution with EvolveAGene 3
688-695 Barry G. Hall
Evidence for Convergent Nucleotide
Evolution and High Allelic Turnover
Rates at the complementary sex
determiner Gene of Western and Asian
Honeybees 696-708
Martin Hasselmann, Xavier Vekemans,
Jochen Pflugfelder, Nikolaus Koeniger,
Gudrun Koeniger, Salim Tingek, and
Martin Beye
Alternative Splicing at NAGNAG
Acceptor Sites Shares Common
Properties in Land Plants and Mammals
709-718 Kei Iida, Masafumi Shionyu,
and Yasuhiro Suso
The Essential Sequence Elements
Required for RNAP II Carboxylterminal Domain Function in Yeast and
Their Evolutionary Conservation
719-727 Pengda Liu, Arno L. Greenleaf,
and John W. Stiller
Phylogenetic Position of Nemertea
Derived from Phylogenomic Data
728-736 Torsten H. Struck and Frauke
Fisse
Concerted Evolution of Sea Anemone
Neurotoxin Genes Is Revealed through
Analysis of the Nematostella vectensis
Genome 737-747 Yehu Moran, Hagar
Weinberger, James C. Sullivan, Adam
M. Reitzel, John R. Finnerty, and
Michael Gurevitz
Genes of Cyanobacterial Origin in Plant
Nuclear Genomes Point to a HeterocystForming Plastid Ancestor 748-761
Oliver Deusch, Giddy Landan, Mayo
Roettger, Nicole Gruenheit, Klaus V.
Kowallik, John F. Allen, William
Martin, and Tal Dagan
Reticulate Representation of
Evolutionary and Functional
Relationships between Phage Genomes
762-777 Gipsi Lima-Mendez, Jacques
Van Helden, Ariane Toussaint, and
Raphaël Leplae
Divergence Times in Caenorhabditis
and Drosophila Inferred from Direct
Estimates of the Neutral Mutation Rate
778-786 Asher D. Cutter
The Dynamic Nature of Eukaryotic
Genomes 787-794
Laura Wegener Parfrey, Daniel J. G.
Lahr, and Laura A. Katz
Molecular Biology and Evolution
2008- 25:5
Articles
Heterotypy in the N-Terminal Region of
Growth/Differentiation Factor 5 (GDF5)
Mature Protein during Teleost Evolution
797-800 Koji Fujimura, Yohey Terai,
Naoya Ishiguro, Masaki Miya, Mutsumi
Nishida, and Norihiro Okada
A Test of the Null Model for 5' UTR
Evolution Based on GC Content
801-804 Max Reuter, Jan Engelstädter,
Pierre Fontanillas, and Laurence D.
Hurst
Inverted Replication of Vertebrate
Mitochondria 805-808
Miguel M. Fonseca, David Posada, and
D. James Harris
Evolutionary Origins of a Novel Host
Plant Detoxification Gene in Butterflies
809-820 Hanna M. Fischer, Christopher
W. Wheat, David G. Heckel, and Heiko
Vogel
Near Intron Positions Are Reliable
Phylogenetic Markers: An Application
to Holometabolous Insects
821-830 Veiko Krauss, Christian
Thümmler, Franziska Georgi, Jörg
Lehmann, Peter F. Stadler, and Carina
Eisenhardt
Identification of Novel Mammalian
Caspases Reveals an Important Role of
Gene Loss in Shaping the Human
Caspase Repertoire 831-841 Leopold
Eckhart, Claudia Ballaun, Marcela
Hermann, John L. VandeBerg,
Wolfgang Sipos, Aumaid Uthman,
Heinz Fischer, and Erwin Tschachler
A Site- and Time-Heterogeneous Model
of Amino Acid Replacement 842-858
Samuel Blanquart and Nicolas Lartillot
Long-Term Evolutionary Stability of
Bacterial Endosymbiosis in
Curculionoidea: Additional Evidence of
Symbiont Replacement in the
Dryophthoridae Family 859-868
Cyrille Conord, Laurence Despres,
Agnès Vallier, Séverine Balmand,
Christian Miquel, Stéphanie Zundel,
Guy Lemperiere, and Abdelaziz Heddi
Influence Function for Robust
Phylogenetic Reconstructions
869-873 Avner Bar-Hen, Mahendra
Mariadassou, Marie-Anne Poursat, and
Philippe Vandenkoornhuyse
Phylogeny, Recombination, and
Mechanisms of Stepwise Mitochondrial
Genome Reorganization in Mantellid
Frogs from Madagascar 874-891 Atsushi
Kurabayashi, Masayuki Sumida,
Hiromichi Yonekawa, Frank Glaw,
Miguel Vences, and Masami Hasegawa
Comparative Analysis of the MIR319a
MicroRNA Locus in Arabidopsis and
Related Brassicaceae 892-902
Norman Warthmann, Sandip Das,
Christa Lanz, and Detlef Weigel
Extremely Intron-Rich Genes in the
Alveolate Ancestors Inferred with a
Flexible Maximum-Likelihood
Approach 903-911
Miklós Csurös, Igor B. Rogozin, and
Eugene V. Koonin
Conserved Features and Evolutionary
Shifts of the EDA Signaling Pathway
Involved in Vertebrate Skin Appendage
Development 912-928 Sophie
Pantalacci, Arnaud Chaumot, Gérard
Benoît, Alexa Sadier, Frédéric Delsuc,
Emmanuel J. P. Douzery, and Vincent
Laudet
Adaptive Evolution of Newly Emerged
Micro-RNA Genes in Drosophila
929-938 Jian Lu, Yonggui Fu, Supriya
Kumar, Yang Shen, Kai Zeng, Anlong
Xu, Richard Carthew, and Chung-I Wu
Origin, Evolution, and Biological Role
of miRNA Cluster in DLK-DIO3
Genomic Region in Placental Mammals
939-948 Evgeny A. Glazov, Sean
McWilliam, Wesley C. Barris, and Brian
P. Dalrymple
Parallel Evolution of Truncated Transfer
RNA Genes in Arachnid Mitochondrial
Genomes 949-959 Susan E. Masta and
Jeffrey L. Boore
Calculating Bootstrap Probabilities of
Phylogeny Using Multilocus Sequence
Data 960-971 Tae-Kun Seo
Sexual Selection and Maintenance of
Sex: Evidence from Comparisons of
Rates of Genomic Accumulation of
Mutations and Divergence of SexRelated Genes in Sexual and
Hermaphroditic Species of
Caenorhabditis 972-979
Carlo G. Artieri, Wilfried Haerty,
Bhagwati P. Gupta, and Rama S. Singh
Genesis and Expansion of Metazoan
Transcription Factor Gene Classes
980-996 Claire Larroux, Graham N.
Luke, Peter Koopman, Daniel S.
Rokhsar, Sebastian M. Shimeld, and
Bernard M. Degnan
Overdominance in the Human Genome
and Olfactory Receptor Activity 9971001 Santos Alonso, Saioa López,
Neskuts Izagirre, and Concepción de la
Rúa
Molecular Biology and Evolution
2008- 25:6
Articles
The Preferential Retention of Starch
Synthesis Genes Reveals the Impact of
Whole-Genome Duplication on Grass
Evolution 1003-1006
Yufeng Wu, Zhengge Zhu, Ligeng Ma,
and Mingsheng Chen
The McDonald–Kreitman Test and
Slightly Deleterious Mutations
1007-1015 Jane Charlesworth and Adam
Eyre-Walker
Toxin-Resistant Sodium Channels:
Parallel Adaptive Evolution across a
Complete Gene Family
1016-1024 Manda Clair Jost, David M.
Hillis, Ying Lu, John W. Kyle, Harry A.
Fozzard, and Harold H. Zakon
Nonadaptive Explanations for Signatures
of Partial Selective Sweeps in
Drosophila 1025-1042 J. Michael
Macpherson, Josefa González, Daniela
M. Witten, Jerel C. Davis, Noah A.
Rosenberg, Aaron E. Hirsh, and Dmitri
A. Petrov
Evolution of the Insulin Receptor Family
and Receptor Isoform Expression in
Vertebrates 1043-1053 Catalina
Hernández-Sánchez, Alicia Mansilla,
Flora de Pablo, and Rafael Zardoya
A Mixed Branch Length Model of
Heterotachy Improves Phylogenetic
Accuracy 1054-1066 Bryan
Kolaczkowski and Joseph W. Thornton
Altered miRNA Repertoire in the
Simplified Chordate, Oikopleura dioica
1067-1080 Xianghui Fu, Marcin
Adamski, and Eric M. Thompson
Evolution of Gene Expression in the
Drosophila Olfactory System
1081-1092 Artyom Kopp, Olga
Barmina, Andrew M. Hamilton, Laura
Higgins, Lauren M. McIntyre, and
Corbin D. Jones
Ancient DNA Identification of Early
20th Century Simian T-Cell Leukemia
Virus Type 1 1093-1098
Sébastien Calvignac, Jean-Michel
Terme, Shannon M. Hensley, Pierre
Jalinot, Alex D. Greenwood, and
Catherine Hänni
Adaptive Evolution of Hepcidin Genes
in Antarctic Notothenioid Fishes
1099-1112 Qianghua Xu, Chi-Hing
Christina Cheng, Peng Hu, Hua Ye,
Zuozhou Chen, Lixue Cao, Lei Chen,
Yu Shen, and Liangbiao Chen
Emergence of Polyproline II-Like
Structure at Early Stages of
Experimental Evolution from Random
Polypeptides
1113-1119 Hitoshi Toyota, Masato
Hosokawa, Itaru Urabe, and Tetsuya
Yomo
On the Expansion of the
Pentatricopeptide Repeat Gene Family in
Plants 1120-1128
Nicholas O'Toole, Mitsuru Hattori,
Charles Andres, Kei Iida, Claire Lurin,
Christian Schmitz-Linneweber, Mamoru
Sugita, and Ian Small
Two Circular Chromosomes of Unequal
Copy Number Make Up the
Mitochondrial Genome of the Rotifer
Brachionus plicatilis
1129-1137 Koushirou Suga, David B.
Mark Welch, Yukari Tanaka, Yoshitaka
Sakakura, and Atsushi Hagiwara
Evolutionary Genomics of Host
Adaptation in Vesicular Stomatitis Virus
1138-1147 Susanna K. Remold, Andrew
Rambaut, and Paul E. Turner
Mobility Pathways for Vertebrate L1,
L2, CR1, and RTE Clade
Retrotransposons 1148-1157 Kenji
Ichiyanagi and Norihiro Okada
The cbb3 Oxidases Are an Ancient
Innovation of the Domain Bacteria
1158-1166 Anne-Lise Ducluzeau,
Soufian Ouchane, and Wolfgang
Nitschke
A Cryptic Algal Group Unveiled: A
Plastid Biosynthesis Pathway in the
Oyster Parasite Perkinsus marinus
1167-1179 Motomichi Matsuzaki,
Haruko Kuroiwa, Tsuneyoshi Kuroiwa,
Kiyoshi Kita, and Hisayoshi Nozaki
Evolutionary Patterns of MHC Class II
B in Owls and Their Implications for the
Understanding of Avian MHC Evolution
1180-1191 Reto Burri, Hélène Niculita
Hirzel, Nicolas Salamin, Alexandre
Roulin, and Luca Fumagalli
Origins of Human Malaria: Rare
Genomic Changes and Full
Mitochondrial Genomes Confirm the
Relationship of Plasmodium falciparum
to Other Mammalian Parasites but
Complicate the Origins of Plasmodium
vivax 1192-1198 Scott William Roy and
Manuel Irimia
An Information-Theoretic Method for
the Treatment of Plural Ancestry in
Phylogenetics 1199-1208 Supriya
Munshaw and Thomas B. Kepler
Climate Change and Postglacial Human
Dispersals in Southeast Asia
1209-1218 Pedro Soares, Jean Alain
Trejaut, Jun-Hun Loo, Catherine Hill,
Maru Mormina, Chien-Liang Lee, YaoMing Chen, Georgi Hudjashov, Peter
Forster, Vincent Macaulay, David
Bulbeck, Stephen Oppenheimer, Marie
Lin, and Martin B. Richards
Alveolins, a New Family of Cortical
Proteins that Define the Protist
Infrakingdom Alveolata
1219-1230 Sven B. Gould, Wai-Hong
Tham, Alan F. Cowman, Geoffrey I.
McFadden, and Ross F. Waller
Retrotransposition as a Source of New
Promoters 1231-1238 Kohji Okamura
and Kenta Nakai
Fast Evolution of Core Promoters in
Primate Genomes
1239-1244 Han Liang, Yeong-Shin Lin,
and Wen-Hsiung Li
Local Adaptation and Vector-Mediated
Population Structure in Plasmodium
vivax Malaria
1245-1252 Deirdre A. Joy, Lilia
Gonzalez-Ceron, Jane M. Carlton, Amy
Gueye, Michael Fay, Thomas F.
McCutchan, and Xin-zhuan Su
Molecular Biology and Evolution
2008- 25:7
Articles
jModelTest: Phylogenetic Model
Averaging 1253-1256
David Posada
The Timing of Selection at the Human
FOXP2 Gene 1257-1259
Graham Coop, Kevin Bullaughey,
Francesca Luca, and Molly Przeworski
Positive Selection and Expression
Divergence Following Gene Duplication
in the Sunflower CYCLOIDEA Gene
Family 1260-1273 Mark A. Chapman,
James H. Leebens-Mack, and John M.
Burke
Novel Transcriptome Patterns
Accompany Evolutionary Restoration of
Defective Social Development in the
Bacterium Myxococcus xanthus
1274-1281 Supriya V. Kadam, Sigrun
Wegener-Feldbrügge, Lotte SøgaardAndersen, and Gregory J. Velicer
Parallel Rate Heterogeneity in
Chloroplast and Mitochondrial Genomes
of Brazil Nut Trees (Lecythidaceae) Is
Consistent with Lineage Effects 12821296 David F. Soria-Hernanz, John M.
Braverman, and Matthew B. Hamilton
Plastid-Derived Genes in the
Nonphotosynthetic Alveolate Oxyrrhis
marina 1297-1306 Claudio H. Slamovits
and Patrick J. Keeling
An Improved General Amino Acid
Replacement Matrix
1307-1320 Si Quang Le and Olivier
Gascuel
The Capsid of the T4 Phage
Superfamily: The Evolution, Diversity,
and Structure of Some of the Most
Prevalent Proteins in the Biosphere
1321-1332 André M. Comeau and Henry
M. Krisch
Differential Evolution of the 13 Atlantic
Salmon Hox Clusters
1333-1343 Sutada Mungpakdee, HeeChan Seo, Anna Rita Angotzi, Xianjun
Dong, Altuna Akalin, and Daniel
Chourrout
Unequal Rates of Y Chromosome Gene
Divergence during Speciation of the
Family Ursidae 1344-1356
Shigeki Nakagome, Jill Pecon-Slattery,
and Ryuichi Masuda
Unicellular Ca2+ Signaling ‘Toolkit’ at
the Origin of Metazoa
1357-1361 Xinjiang Cai
The Impact of the Austronesian
Expansion: Evidence from mtDNA and
Y Chromosome Diversity in the
Admiralty Islands of Melanesia
1362-1374 Manfred Kayser, Ying Choi,
Mannis van Oven, Stefano Mona, Silke
Brauer, Ronald J. Trent, Dagwin
Suarkia, Wulf Schiefenhövel, and Mark
Stoneking
Selection on Amino Acid Substitutions
in Arabidopsis 1375-1383
John Paul Foxe, Vaqaar-un-Nisa Dar,
Honggang Zheng, Magnus Nordborg,
Brandon S. Gaut, and Stephen I. Wright
Coyotes Demonstrate How Habitat
Specialization by Individuals of a
Generalist Species Can Diversify
Populations in a Heterogeneous
Ecoregion 1384-1394
Benjamin N. Sacks, Danika L.
Bannasch, Bruno B. Chomel, and Holly
B. Ernest
Systematic Survey for Novel Types of
Prokaryotic Retroelements Based on
Gene Neighborhood and Protein
Architecture 1395-1404
Kenji K. Kojima and Minoru Kanehisa
Organellar RNA Editing and PlantSpecific Extensions of Pentatricopeptide
Repeat Proteins in Jungermanniid but
not in Marchantiid Liverworts
1405-1414 Mareike Rüdinger, Monika
Polsakiewicz, and Volker Knoop
A Phylogenetic Analysis of Indel
Dynamics in the Cotton Genus
1415-1428 Corrinne E. Grover, Yeisoo
Yu, Rod A. Wing, Andrew H. Paterson,
and Jonathan F. Wendel
The Dscam Homologue of the
Crustacean Daphnia Is Diversified by
Alternative Splicing Like in Insects
1429-1439
Daniela Brites, Seanna McTaggart,
Krystalynne Morris, Jobriah Anderson,
Kelley Thomas, Isabelle Colson,
Thomas Fabbro, Tom J. Little, Dieter
Ebert, and Louis Du Pasquier
Mitochondrial Genome Evolution in the
Social Amoebae 1440-1450
Andrew J. Heidel and Gernot Glöckner
Recurrent Tandem Gene Duplication
Gave Rise to Functionally Divergent
Genes in Drosophila 1451-1458
Chuanzhu Fan, Ying Chen, and
Manyuan Long
Smooth Skyride through a Rough
Skyline: Bayesian Coalescent-Based
Inference of Population Dynamics
1459-1471 Vladimir N. Minin, Erik W.
Bloomquist, and Marc A. Suchard
Polyploid Speciation Did Not Confer
Instant Reproductive Isolation in
Capsella (Brassicaceae)
1472-1481 Tanja Slotte, Huirun Huang,
Martin Lascoux, and Alf Ceplitis
Molecular Cloning and Characterization
of a Moss (Ceratodon purpureus)
Nonsymbiotic Hemoglobin Provides
Insight into the Early Evolution of Plant
Nonsymbiotic Hemoglobins 1482-1487
Verónica Garrocho-Villegas and Raúl
Arredondo-Peter
High Rates of Molecular Evolution in
Hantaviruses 1488-1492
Cadhla Ramsden, Fernando L. Melo,
Luiz. M. Figueiredo, Edward C. Holmes,
Paolo M.A. Zanotto, and the VGDN
Consortium
Molecular Evolution of a PrimateSpecific microRNA Family
1493-1502 Rui Zhang, Yin-Qiu Wang,
and Bing Su
Bayesian Inference of Errors in Ancient
DNA Caused by Postmortem
Degradation 1503-1511
Ligia M. Mateiu and Bruce H. Rannala
Difficulties in Testing for Covarion-Like
Properties of Sequences under the
Confounding Influence of Changing
Proportions of Variable Sites 1512-1520
Nicole Gruenheit, Peter J. Lockhart,
Mike Steel, and William Martin
Molecular Biology and Evolution
2008- 25:8
Articles
Convergent Evolution of Clustering of
Iroquois Homeobox Genes across
Metazoans 1521-1525
Manuel Irimia, Ignacio Maeso, and Jordi
Garcia-Fernàndez
The Guanine Nucleotide Exchange
Factors Sec2 and PRONE: Candidate
Synapomorphies for the Opisthokonta
and the Archaeplastida
1526-1529 Marek Elias
Natural Selection against Protein
Aggregation on Self-Interacting and
Essential Proteins in Yeast, Fly, and
Worm 1530-1533
Yiwen Chen and Nikolay V. Dokholyan
Genetic Exchange versus Genetic
Differentiation in a Medium-Sized
Inversion of Drosophila: The A2/Ast
Arrangements of Drosophila subobscura
1534-1543 Clévio Nóbrega, Mahnaz
Khadem, Montserrat Aguadé, and
Carmen Segarra
Influence of the Mutant Spectrum in
Viral Evolution: Focused Selection of
Antigenic Variants in a Reconstructed
Viral Quasispecies 1544-1554 Verónica
Martín and Esteban Domingo
Coexpression of Linked Genes in
Mammalian Genomes Is Generally
Disadvantageous 1555-1565
Ben-Yang Liao and Jianzhi Zhang
Substitution of the Gene for Chloroplast
RPS16 Was Assisted by Generation of a
Dual Targeting Signal 1566-1575
Minoru Ueda, Tomotaro Nishikawa,
Masaru Fujimoto, Hideki Takanashi,
Shin-ichi Arimura, Nobuhiro Tsutsumi,
and Koh-ichi Kadowaki
How Well Does the HoT Score Reflect
Sequence Alignment Accuracy?
1576-1580 Barry G. Hall
Duplication and Functional
Diversification of HAP3 Genes Leading
to the Origin of the Seed-Developmental
Regulatory Gene, LEAFY
COTYLEDON1 (LEC1), in Nonseed
Plant Genomes 1581-1592 Zengyan Xie,
Xia Li, Beverley J. Glover, Shunong
Bai, Guang-Yuan Rao, Jingchu Luo, and
Ji Yang
Distinct Evolutionary Patterns between
Chemoreceptors of 2 Vertebrate
Olfactory Systems and the Differential
Tuning Hypothesis 1593-1601 Wendy E.
Grus and Jianzhi Zhang
DNA Methylation and Structural and
Functional Bimodality of Vertebrate
Promoters 1602-1608
Navin Elango and Soojin V. Yi
Long-Term Balancing Selection at the
West Nile Virus Resistance Gene,
Oas1b, Maintains Transspecific
Polymorphisms in the House Mouse
1609-1618 William Ferguson, Shira
Dvora, Juliana Gallo, Annie Orth, and
Stéphane Boissinot
The Deep Archaeal Roots of Eukaryotes
1619-1630 Natalya Yutin, Kira S.
Makarova, Sergey L. Mekhedov, Yuri I.
Wolf, and Eugene V. Koonin
Overdispersion of the Molecular Clock:
Temporal Variation of Gene-Specific
Substitution Rates in Drosophila
1631-1638 Trevor Bedford and Daniel
L. Hartl
Effects of X-Linkage and Sex-Biased
Gene Expression on the Rate of
Adaptive Protein Evolution in
Drosophila 1639-1650
John F. Baines, Stanley A. Sawyer,
Daniel L. Hartl, and John Parsch
Mitochondrial DNA Phylogeny in
Eastern and Western Slavs
1651-1658 B. Malyarchuk, T.
Grzybowski, M. Derenko, M. Perkova,
T. Vanecek, J. Lazur, P. Gomolcak, and
I. Tsybovsky
Signature Genes as a Phylogenomic
Tool 1659-1667
Bas E. Dutilh, Berend Snel, Thijs J. G.
Ettema, and Martijn A. Huynen
Widespread Ultraconservation
Divergence in Primates
1668-1676 Ivan Ovcharenko
Reconstructing Evolutionary Graphs: 3D
Parsimony 1677-1682 James A. Lake
Spatial and Temporal Heterogeneity in
Nucleotide Sequence Evolution
1683-1694 Simon Whelan
Nontoxic Strains of Cyanobacteria Are
the Result of Major Gene Deletion
Events Induced by a Transposable
Element 1695-1704
Guntram Christiansen, Carole Molitor,
Benjamin Philmus, and Rainer
Kurmayer
The Sperm Proteins from Amphioxus
Mirror Its Basal Position among
Chordates and Redefine the Origin of
Vertebrate Protamines 1705-1713
José María Eirín-López, Lindsay J.
Frehlick, Manel Chiva, Núria Saperas,
and Juan Ausió
Inferring Natural Selection on FineScale Chromatin Organization in Yeast
1714-1727 G. A. Babbitt and Y. Kim
The Impact of Founder Events on
Chromosomal Variability in Multiply
Mating Species 1728-1736 John E. Pool
and Rasmus Nielsen
Programmed Genetic Instability: A
Tumor-Permissive Mechanism for
Maintaining the Evolvability of Higher
Species through Methylation-Dependent
Mutation of DNA Repair Genes in the
Male Germ Line 1737-1749 Yongzhong
Zhao and Richard J. Epstein
Gene Flow and Natural Selection in
Oceanic Human Populations Inferred
from Genome-Wide SNP Typing
1750-1761 Ryosuke Kimura, Jun
Ohashi, Yasuhiro Matsumura, Minato
Nakazawa, Tsukasa Inaoka, Ryutaro
Ohtsuka, Motoki Osawa, and Katsushi
Tokunaga
Frequent, Phylogenetically Local
Horizontal Transfer of the cox1 Group I
Intron in Flowering Plant Mitochondria
1762-1777
M. Virginia Sanchez-Puerta, Yangrae
Cho, Jeffrey P. Mower, Andrew J.
Alverson, and Jeffrey D. Palmer
Compensatory Evolution in RNA
Secondary Structures Increases
Substitution Rate Variation among Sites
1778-1787 Jennifer L. Knies, Kristen K.
Dang, Todd J. Vision, Noah G.
Hoffman, Ronald Swanstrom, and
Christina L. Burch
Molecular Biology and Evolution
2008- 25:9
Articles
Presence of a Latent Mitochondrial
Targeting Signal in Gene on
Mitochondrial Genome
1791-1793
Minoru Ueda, Masaru Fujimoto, Shinichi Arimura, Nobuhiro Tsutsumi, and
Koh-ichi Kadowaki
Confirming the Phylogeny of Mammals
by Use of Large Comparative Sequence
Data Sets
1795-1808 Arjun B. Prasad, Marc W.
Allard, NISC Comparative Sequencing
Program, and Eric D. Green
A Maximum Likelihood Method for
Detecting Directional Evolution in
Protein Sequences and Its Application to
Influenza A Virus
1809-1824 Sergei L. Kosakovsky Pond,
Art F.Y. Poon, Andrew J. Leigh Brown,
and Simon D.W. Frost
Positive and Negative Selection on
Noncoding DNA in Drosophila
simulans 1825-1834
Penelope R. Haddrill, Doris Bachtrog,
and Peter Andolfatto
Neutrality of Foreign Complex Subunits
in an Experimental Model of Lateral
Gene Transfer
1835-1840 Alon Wellner and Uri
Gophna
Gene Expansion and Retention Leads to
a Diverse Tyrosine Kinase Superfamily
in Amphioxus
1841-1854
Salvatore D'Aniello, Manuel Irimia,
Ignacio Maeso, Juan Pascual-Anaya,
Senda Jiménez-Delgado, Stephanie
Bertrand, and Jordi Garcia-Fernàndez
Interacting Gene Clusters and the
Evolution of the Vertebrate Immune
System 1855-1862
Takashi Makino and Aoife McLysaght
Roles of cis- and trans-Changes in the
Regulatory Evolution of Genes in the
Gluconeogenic Pathway in Yeast
1863-1875 Ya-Wen Chang, Fu-Guo
Robert Liu, Ning Yu, Huang-Mo Sung,
Peggy Yang, Daryi Wang, Chih-Jen
Huang, Ming-Che Shih, and WenHsiung Li
Genome Evolution of Wolbachia Strain
wPip from the Culex pipiens Group
1877-1887
Lisa Klasson, Thomas Walker,
Mohammed Sebaihia, Mandy J. Sanders,
Michael A. Quail, Angela Lord, Susanne
Sanders, Julie Earl, Scott L. O'Neill,
Nicholas Thomson, Steven P. Sinkins,
and Julian Parkhill
Intense Transpositional Activity of
Insertion Sequences in an Ancient
Obligate Endosymbiont
1889-1896 Richard Cordaux, Samuel
Pichon, Alison Ling, Philippe Pérez,
Carine Delaunay, Fabrice Vavre, Didier
Bouchon, and Pierre Grève
Similar Numbers but Different
Repertoires of Olfactory Receptor Genes
in Humans and Chimpanzees
1897-1907 Yasuhiro Go and Yoshihito
Niimura
Evolution of Closely Linked Gene Pairs
in Vertebrate Genomes
1909-1921 Erik Franck, Tim Hulsen,
Martijn A. Huynen, Wilfried W. de
Jong, Nicolette H. Lubsen, and Ole
Madsen
Arthropod 7SK RNA
1923-1930
Andreas R. Gruber, Carsten Kilgus, Axel
Mosig, Ivo L. Hofacker, Wolfgang
Hennig, and Peter F. Stadler
An Assessment of the Impacts of
Molecular Oxygen on the Evolution of
Proteomes
1931-1942 Sara Vieira-Silva and
Eduardo P. C. Rocha
Frequent and Widespread Parallel
Evolution of Protein Sequences
1943-1953 Antonis Rokas and Sean B.
Carroll
Phylogenetic Analysis of Nitrite, Nitric
Oxide, and Nitrous Oxide Respiratory
Enzymes Reveal a Complex
Evolutionary History for Denitrification
1955-1966 Christopher M. Jones, Blaz
Stres, Magnus Rosenquist, and Sara
Hallin
Nucleus-Encoded Periplastid-Targeted
EFL in Chlorarachniophytes
1967-1977 Gillian H. Gile and Patrick J.
Keeling
Estimation of Hominoid Ancestral
Population Sizes under Bayesian
Coalescent Models Incorporating
Mutation Rate Variation and Sequencing
Errors 1979-1994 Ralph Burgess and
Ziheng Yang
Likelihood-Based Clustering (LiBaC)
for Codon Models, a Method for
Grouping Sites according to Similarities
in the Underlying Process of Evolution
1995-2007 Le Bao, Hong Gu, Katherine
A. Dunn, and Joseph P. Bielawski
Cilium Evolution: Identification of a
Novel Protein, Nematocilin, in the
Mechanosensory Cilium of Hydra
Nematocytes
2009-2017 Jung Shan Hwang, Yasuharu
Takaku, Jarrod Chapman, Kazuho Ikeo,
Charles N. David, and Takashi Gojobori
The Complete Nucleotide Sequences of
the 5 Genetically Distinct Plastid
Genomes of Oenothera, Subsection
Oenothera: II. A Microevolutionary
View Using Bioinformatics and Formal
Genetic Data
2019-2030 Stephan Greiner, Xi Wang,
Reinhold G. Herrmann, Uwe Rauwolf,
Klaus Mayer, Georg Haberer, and Jörg
Meurer
Halogenase Genes in Nonribosomal
Peptide Synthetase Gene Clusters of
Microcystis (Cyanobacteria): Sporadic
Distribution and Evolution
2031-2041 Sabrina Cadel-Six, Catherine
Dauga, Anne Marie Castets, Rosmarie
Rippka, Christiane Bouchier, Nicole
Tandeau de Marsac, and Martin Welker
Evidence of Adaptive Evolution of
Accessory Gland Proteins in Closely
Related Species of the Drosophila
repleta Group
2043-2053 Francisca C. Almeida and
Rob DeSalle
SNAREing the Basis of Multicellularity:
Consequences of Protein Family
Expansion during Evolution 2055-2068
Tobias H. Kloepper, C. Nickias Kienle,
and Dirk Fasshauer
The Evolution of the Flagellar Assembly
Pathway in Endosymbiotic Bacterial
Genomes
2069-2076 Christina Toft and Mario A.
Fares
Molecular Biology and Evolution
2008- 25:10
Articles
Insertion DNA Promotes Ectopic
Recombination during Meiosis in
Arabidopsis 2079-2083
Xiaoqin Sun, Yuanli Zhang, Sihai Yang,
Jian-Qun Chen, Barbara Hohn, and
Dacheng Tian
Analysis of a Horizontally Transferred
Pathway Involved in Vitamin B6
Biosynthesis from the Soybean Cyst
Nematode Heterodera glycines 20852098 James P. Craig, Sadia Bekal,
Matthew Hudson, Leslie Domier, Terry
Niblack, and Kris N. Lambert
Chalcone Synthase Gene Lineage
Diversification Confirms Allopolyploid
Evolutionary Relationships of European
Rostrate Violets 2099-2108
Kevin van den Hof, Ronald G. van den
Berg, and Barbara Gravendeel
From Drought Sensing to
Developmental Control: Evolution of
Cyclic AMP Signaling in Social
Amoebas 2109-2118
Allyson V. Ritchie, Saskia van Es,
Celine Fouquet, and Pauline Schaap
Evolutionary Diversification in
Polyamine Biosynthesis
2119-2128
Eugenio G. Minguet, Francisco VeraSirera, Alberto Marina, Juan Carbonell,
and Miguel A. Blázquez
Intron Presence–Absence
Polymorphisms in Daphnia
2129-2139
Angela R. Omilian, Douglas G. Scofield,
and Michael Lynch
A Multilocus Molecular Phylogeny of
the Parrots (Psittaciformes): Support for
a Gondwanan Origin during the
Cretaceous
2141-2156
Timothy F. Wright, Erin E. Schirtzinger,
Tania Matsumoto, Jessica R. Eberhard,
Gary R. Graves, Juan J. Sanchez, Sara
Capelli, Heinrich Müller, Julia
Scharpegge, Geoffrey K. Chambers, and
Robert C. Fleischer
Recent Origins of Sperm Genes in
Drosophila
2157-2166 Steve Dorus, Zoë N.
Freeman, Elizabeth R. Parker, Benjamin
D. Heath, and Timothy L. Karr
Rapidly Evolving Mitochondrial
Genome and Directional Selection in
Mitochondrial Genes in the Parasitic
Wasp Nasonia (Hymenoptera:
Pteromalidae)
2167-2180 Deodoro C. S. G. Oliveira,
Rhitoban Raychoudhury, Dennis V.
Lavrov, and John H. Werren
The Effect of Ancient DNA Damage on
Inferences of Demographic Histories
2181-2187
Erik Axelsson, Eske Willerslev, M.
Thomas P. Gilbert, and Rasmus Nielsen
c-Myb Is an Evolutionary Conserved
miR-150 Target and miR-150/c-Myb
Interaction Is Important for Embryonic
Development
2189-2198 You-Chin Lin, Ming-Wei
Kuo, John Yu, Huan-Hsien Kuo, RueyJen Lin, Wan-Lin Lo, and Alice L. Yu
Synonymous and Nonsynonymous
Polymorphisms versus Divergences in
Bacterial Genomes
2199-2209 Austin L. Hughes, Robert
Friedman, Pierre Rivailler, and Jeffrey
O. French
Population-Based Resequencing Reveals
That the Flowering Time Adaptation of
Cultivated Barley Originated East of the
Fertile Crescent 2211-2219
Huw Jones, Fiona J. Leigh, Ian Mackay,
Mim A. Bower, Lydia M.J. Smith,
Michael P. Charles, Glynis Jones, Martin
K. Jones, Terence A. Brown, and Wayne
Powell
A Phylogenomic Analysis of the
Shikimate Dehydrogenases Reveals
Broadscale Functional Diversification
and Identifies One Functionally Distinct
Subclass
2221-2232 Sasha Singh, John
Stavrinides, Dinesh Christendat, and
David S. Guttman
Big Bang in the Evolution of Extant
Malaria Parasites
2233-2239 Toshiyuki Hayakawa,
Richard Culleton, Hiroto Otani,
Toshihiro Horii, and Kazuyuki Tanabe
Subdivision in an Ancestral Species
Creates Asymmetry in Gene Trees
2241-2246 Montgomery Slatkin and
Joshua L. Pollack
Molecular Biology and Evolution
2008- 25:11
Articles
Positive Selection in ASPM Is Correlated
with Cerebral Cortex Evolution across
Primates but Not with Whole-Brain Size
2247-2250 Farhan Ali and Rudolf Meier
Adaptive Evolution in Rodent Seminal
Vesicle Secretion Proteins
2301-2310 Robert C. Karn, Nathaniel L.
Clark, Eric D. Nguyen, and Willie J.
Swanson
Intragenomic Variation of Fungal
Ribosomal Genes Is Higher than
Previously Thought
2251-2254 Uwe K. Simon and Michael
Weiß
Ohno's Model Revisited: Measuring the
Frequency of Potentially Adaptive
Mutations under Various Mutational
Drifts 2311-2318
Shimon Bershtein and Dan S. Tawfik
Evolutionary Diversification of the Sm
Family of RNA-Associated Proteins
2255-2267 Douglas G. Scofield and
Michael Lynch
Estimation of Phylogenetic
Inconsistencies in the Three Domains of
Life 2319-2329 Victor Soria-Carrasco
and Jose Castresana
Developmental Stage and Level of
Codon Usage Bias in Drosophila
2269-2277 Saverio Vicario, Christopher
E. Mason, Kevin P. White, and Jeffrey
R. Powell
The Legacy of Domestication:
Accumulation of Deleterious Mutations
in the Dog Genome
2331-2336 Fernando Cruz, Carles Vilà,
and Matthew T. Webster
Coevolution of Codon Usage and tRNA
Genes Leads to Alternative Stable States
of Biased Codon Usage
2279-2291 Paul G. Higgs and Wenqi
Ran
Evolution of Genes and Repeats in the
Nimrod Superfamily
2337-2347 Kálmán Somogyi, Botond
Sipos, Zsolt Pénzes, Éva Kurucz, János
Zsámboki, Dan Hultmark, and István
Andó
Clues about the Genetic Basis of
Adaptation Emerge from Comparing the
Proteomes of Two Ostreococcus
Ecotypes (Chlorophyta, Prasinophyceae)
2293-2300 Séverine Jancek, Sébastien
Gourbière, Hervé Moreau, and Gwenaël
Piganeau
Gene Duplications and Losses within the
Cyclooxygenase Family of Teleosts and
Other Chordates
2349-2359 Justin C. Havird, Michael M.
Miyamoto, Keith P. Choe, and David H.
Evans
Evolutionary Switch and Genetic
Convergence on rbcL following the
Evolution of C4 Photosynthesis
2361-2368 Pascal-Antoine Christin,
Nicolas Salamin, A. Muthama Muasya,
Eric H. Roalson, Flavien Russier, and
Guillaume Besnard
Intraphylum Diversity and Complex
Evolution of Cyanobacterial AminoacyltRNA Synthetases
2369-2389 Ignacio Luque, María Loreto
Riera-Alberola, Alfonso Andújar, and
Jesús A. G. Ochoa de Alda
Evolution of Snake Venom Disintegrins
by Positive Darwinian Selection
2391-2407 Paula Juárez, Iñaki Comas,
Fernando González-Candelas, and Juan
J. Calvete
Estimation of Nucleotide Diversity,
Disequilibrium Coefficients, and
Mutation Rates from High-Coverage
Genome-Sequencing Projects
2409-2419 Michael Lynch
Recurrent Positive Selection of the
Drosophila Hybrid Incompatibility Gene
Hmr 2421-2430 Shamoni Maheshwari,
Jun Wang, and Daniel A. Barbash
Alternative Splicing and the SteadyState Ratios of mRNA Isoforms
Generated by It Are under Strong
Stabilizing Selection in Caenorhabditis
elegans 2431-2437 Sergio BarberanSoler and Alan M. Zahler
Mutagenesis from Meiotic
Recombination Is Not a Primary Driver
of Sequence Divergence between
Saccharomyces Species
2439-2444 Mohamed A. F. Noor
Multiple Paleopolyploidizations during
the Evolution of the Compositae Reveal
Parallel Patterns of Duplicate Gene
Retention after Millions of Years
2445-2455 Michael S. Barker, Nolan C.
Kane, Marta Matvienko, Alexander
Kozik, Richard W. Michelmore, Steven
J. Knapp, and Loren H. Rieseberg
Multiple Genome Comparison within a
Bacterial Species Reveals a Unit of
Evolution Spanning Two Adjacent
Genes in a Tandem Paralog Cluster
2457-2473 Takeshi Tsuru and Ichizo
Kobayashi
Analysis of Two Genomes from the
Mitochondrion-Like Organelle of the
Intestinal Parasite Blastocystis:
Complete Sequences, Gene Content, and
Genome Organization
2475-2482 Vicente Pérez-Brocal and C.
Graham Clark
Robert Piskol and Wolfgang Stephan
Analyzing the Evolution of RNA
Secondary Structures in Vertebrate
Introns Using Kimura's Model of
Compensatory Fitness Interactions
2483-2492
Nonrandom Wolbachia Infection Status
of Drosophila melanogaster Strains with
Different mtDNA Haplotypes
2493-2498 Maria D. S. Nunes, Viola
Nolte, and Christian Schlötterer
A Comparative Analysis of
Mitochondrial Genomes in Coleoptera
(Arthropoda: Insecta) and Genome
Descriptions of Six New Beetles
2499-2509 N. C. Sheffield, H. Song, S.
L. Cameron, and M. F. Whiting
Molecular Biology and Evolution
2008- 25:12
Articles
Regulation Dynamics of WGD Genes
during Yeast Metabolic Oscillation
2513-2516 Hong Chen, Lin Xu, and
Zhenglong Gu
Characterization of Reticulate Networks
Based on the Coalescent with
Recombination
2517-2520 Miguel Arenas, Gabriel
Valiente, and David Posada
Uncorrected Nucleotide Bias in mtDNA
Can Mimic the Effects of Positive
Darwinian Selection
2521-2524 Mihai Albu, Xiang Jia Min,
Donal Hickey, and Brian Golding
Quantifying the Stationarity and Time
Reversibility of the Nucleotide
Substitution Process
2525-2535 Federico Squartini and Peter
F. Arndt
Evolutionary Constraint and Adaptation
in the Metabolic Network of Drosophila
2537-2546 Anthony J. Greenberg, Sarah
R. Stockwell, and Andrew G. Clark
Relaxed Selection on the CBF/DREB1
Regulatory Genes and Reduced Freezing
Tolerance in the Southern Range of
Arabidopsis thaliana
2547-2555 Ying Zhen and Mark C.
Ungerer
The Proteomic Constraint and Its Role in
Molecular Evolution
2557-2565 Steven E. Massey
Patterns of Divergence among Conifer
ESTs and Polymorphism in Pinus
sylvestris Identify Putative Selective
Sweeps 2567-2577
Anna E. Palmé, Mark Wright, and Outi
Savolainen
The Relationship Between Microsatellite
Polymorphism and Recombination Hot
Spots in the Human Genome
2579-2587 Mikael Brandström, Andrew
T. Bagshaw, Neil J. Gemmell, and Hans
Ellegren
New Genes Originated via Multiple
Recombinational Pathways in the βGlobin Gene Family of Rodents
2589-2600 Federico G. Hoffmann, Juan
C. Opazo, and Jay F. Storz
How Segmental Duplications Shape Our
Genome: Recent Evolution of ABCC6
and PKD1 Mendelian Disease Genes
2601-2613 Orsolya Symmons, András
Váradi, and Tamás Arányi
Conditional Gene Genealogies under
Strong Purifying Selection
2615-2626 John Wakeley
Evolution of Soldier-Specific Venomous
Protease in Social Aphids
2627-2641 Mayako Kutsukake, Naruo
Nikoh, Harunobu Shibao, Claude Rispe,
Jean-Christophe Simon, and Takema
Fukatsu
Evolution of Hormone Signaling in
Elasmobranchs by Exploitation of
Promiscuous Receptors
2643-2652 Sean Michael Carroll, Jamie
T. Bridgham, and Joseph W. Thornton
Ancient Recruitment by Chromists of
Green Algal Genes Encoding Enzymes
for Carotenoid Biosynthesis
2653-2667 Ruth Frommolt, Sonja
Werner, Harald Paulsen, Reimund Goss,
Christian Wilhelm, Stefan Zauner, Uwe
G. Maier, Arthur R. Grossman,
Debashish Bhattacharya, and Martin
Lohr
Balancing Selection at a Frog
Antimicrobial Peptide Locus:
Fluctuating Immune Effector Alleles?
2669-2680 Jacob A. Tennessen and
Michael S. Blouin
Genome Size Reduction in the Chicken
Has Involved Massive Loss of Ancestral
Protein-Coding Genes
2681-2688 Austin L. Hughes and Robert
Friedman
The Apicomplexan Whole-Genome
Phylogeny: An Analysis of
Incongruence among Gene Trees
2689-2698 Chih-Horng Kuo, John P.
Wares, and Jessica C. Kissinger
An Ancient Evolutionary Origin of
Genes Associated with Human Genetic
Diseases
2699-2707 Tomislav Domazet-Loso and
Diethard Tautz
Comprehensive Analysis of Archaeal
tRNA Genes Reveals Rapid Increase of
tRNA Introns in the Order
Thermoproteales
2709-2716 Junichi Sugahara, Kaoru
Kikuta, Kosuke Fujishima, Nozomu
Yachie, Masaru Tomita, and Akio Kanai
Origins and Evolution of the Formin
Multigene Family That Is Involved in
the Formation of Actin Filaments
2717-2733 Dimitra Chalkia, Nikolas
Nikolaidis, Wojciech Makalowski, Jan
Klein, and Masatoshi Nei
Different Selective Pressures Shape the
Molecular Evolution of Color Vision in
Chimpanzee and Human Populations
2735-2743 Brian C. Verrelli, Cecil M.
Lewis, Jr, Anne C. Stone, and George H.
Perry
Wheels within Wheels: Clues to the
Evolution of the Gnas and Gnal Loci
2745-2757 Samir Wadhawan, Benjamin
Dickins, and Anton Nekrutenko
Evidence for Variable Selective
Pressures at a Large Secondary Structure
of the Human Mitochondrial DNA
Control Region
2759-2770 Filipe Pereira, Pedro Soares,
João Carneiro, Luísa Pereira, Martin B.
Richards, David C. Samuels, and
António Amorim