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MBE Advance Access

MBE Advance Access articles are papers in manuscript form that have been accepted by the journal but have not been copyedited or formatted for publication. Copyediting may lead to minor differences between the Advance Access version and the final version of the paper; there may also be differences in the quality of the graphics. More information, including how to cite Advance Access papers, can be found on the Advance Access page.

Advance Access Articles By Category [View by Date]

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RESEARCH ARTICLEGo to top of the page

Research Article
Monkol Lek, Daniel G. MacArthur, Nan Yang, and Kathryn N. North
Phylogenetic analysis of gene structure and alternative splicing in {alpha}-actinins
MBE Advance Access published on November 6, 2009.
doi:10.1093/molbev/msp268
[Abstract] [Accepted Manuscript] [Request Permissions]  

Research Article
Laura J. Kelly, Andrew R. Leitch, James J. Clarkson, Robin B. Hunter, Sandra Knapp, and Mark W. Chase
Intragenic Recombination Events and Evidence for Hybrid Speciation in Nicotiana (Solanaceae)
MBE Advance Access published on November 6, 2009.
doi:10.1093/molbev/msp267
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Research Article
Frida Belinky, Ofir Cohen, and Dorothée Huchon
Large-scale parsimony analysis of metazoan indels in protein-coding genes
MBE Advance Access published on October 28, 2009.
doi:10.1093/molbev/msp263
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Research Article
Sergei L. Kosakovsky Pond, Konrad Scheffler, Michael B. Gravenor, Art F.Y. Poon, and Simon D.W. Frost
Evolutionary Fingerprinting of Genes
MBE Advance Access published on October 28, 2009.
doi:10.1093/molbev/msp260
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Research Article
Marcos Pérez-Losada, David V. Jobes, Faruk Sinangil, Keith A. Crandall, David Posada, and Phillip W. Berman
Phylodynamics of HIV-1 from a Phase III AIDS vaccine trial in North America
MBE Advance Access published on October 28, 2009.
doi:10.1093/molbev/msp254
[Abstract] [Accepted Manuscript]     OPEN ACCESS ARTICLE

Research Article
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
An explicit signature of balancing selection for color vision variation in New World monkeys
MBE Advance Access published on October 27, 2009.
doi:10.1093/molbev/msp262
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Research Article
Caitlin Pepperell, Vernon H. Hoeppner, Mikhail Lipatov, Gary K. Schoolnik, and Marcus W. Feldman
Bacterial genetic signatures of human social phenomena among M.tuberculosis from an Aboriginal Canadian population
MBE Advance Access published on October 27, 2009.
doi:10.1093/molbev/msp261
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Research Article
Tohru Sugawara, Hiroo Imai, Masato Nikaido, Yasushi Imamoto, and Norihiro Okada
Vertebrate Rhodopsin Adaptation to Dim Light via Rapid Meta-II Intermediate Formation
MBE Advance Access published on October 25, 2009.
doi:10.1093/molbev/msp252
[Abstract] [Accepted Manuscript] [Request Permissions]  

Research Article
Hua Ying, Julian Epps, Rohan Williams, and Gavin Huttley
Evidence that localised variation in primate sequence divergence arises from an influence of nucleosome placement on DNA repair
MBE Advance Access published on October 20, 2009.
doi:10.1093/molbev/msp253
[Abstract] [Accepted Manuscript] [Supplementary Data]     OPEN ACCESS ARTICLE

Research Article
Pär K. Ingvarsson
Natural selection on synonymous and non-synonymous mutations shape patterns of polymorphism in Populus tremula
MBE Advance Access published on October 16, 2009.
doi:10.1093/molbev/msp255
[Abstract] [Accepted Manuscript] [Request Permissions]  

Research Article
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
Novel venom proteins produced by differential domain-expression strategies in Beaded lizards and Gila monsters (genus Heloderma)
MBE Advance Access published on October 15, 2009.
doi:10.1093/molbev/msp251
[Abstract] [Accepted Manuscript] [Request Permissions]  

Research Article
Michael DeGiorgio and James H. Degnan
Fast and consistent estimation of species trees using supermatrix rooted triples
MBE Advance Access published on October 15, 2009.
doi:10.1093/molbev/msp250
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Research Article
Jesse D. Hollister, Jeffrey Ross-Ibarra, and Brandon S. Gaut
Indel-associated mutation rate varies with mating system in flowering plants
MBE Advance Access published on October 13, 2009.
doi:10.1093/molbev/msp249
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Research Article
Yan Zhou, Henner Brinkmann, Nicolas Rodrigue, Nicolas Lartillot, and Hervé Philippe
A Dirichlet process covarion mixture model and its assessments using posterior predictive discrepancy tests
MBE Advance Access published on October 12, 2009.
doi:10.1093/molbev/msp248
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Research Article
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
A worldwide survey of human male demographic history based on Y-SNP and Y-STR data from the HGDP-CEPH populations
MBE Advance Access published on October 12, 2009.
doi:10.1093/molbev/msp243
[Abstract] [Accepted Manuscript] [Supplementary Data]     OPEN ACCESS ARTICLE

Research Article
Domènec Farré and M.Mar Albà
Heterogeneous patterns of gene expression diversification in mammalian gene duplicates
MBE Advance Access published on October 12, 2009.
doi:10.1093/molbev/msp242
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Research Article
Von Bing Yap, Helen Lindsay, Simon Easteal, and Gavin Huttley
Estimates of the effect of natural selection on protein coding content
MBE Advance Access published on October 8, 2009.
doi:10.1093/molbev/msp232
[Abstract] [Accepted Manuscript] [Supplementary Data]     OPEN ACCESS ARTICLE

Research Article
Nelson Avonce, Jan Wuyts, Katrien Verschooten, Lies Vandesteene, and Patrick Van Dijck
The Cytophaga hutchinsonii ChTPSP: first characterized bifunctional TPS-TPP protein as putative ancestor of all eukaryotic trehalose biosynthesis proteins
MBE Advance Access published on October 7, 2009.
doi:10.1093/molbev/msp241
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Research Article
Beniamino Trombetta, Fulvio Cruciani, Peter A. Underhill, Daniele Sellitto, and Rosaria Scozzari
Footprints of X-to-Y gene conversion in recent human evolution
MBE Advance Access published on October 6, 2009.
doi:10.1093/molbev/msp231
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Research Article
Ofir Cohen and Tal Pupko
Inference and Characterization of Horizontally Transferred Gene Families using Stochastic Mapping
MBE Advance Access published on October 6, 2009.
doi:10.1093/molbev/msp240
[Abstract] [Accepted Manuscript] [Supplementary Data]     OPEN ACCESS ARTICLE

Research Article
Ramiro Logares, Jon Bråte, Friederike Heinrich, Kamran Shalchian-Tabrizi, and Stefan Bertilsson
Infrequent transitions between saline and fresh waters in one of the most abundant microbial lineages (SAR11)
MBE Advance Access published on October 6, 2009.
doi:10.1093/molbev/msp239
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Research Article
N. Ray, D. Wegmann, N.J.R. Fagundes, S. Wang, A. Ruiz-Linares, and L. Excoffier
A statistical evaluation of models for the initial settlement of the American continent emphasizes the importance of gene flow with Asia
MBE Advance Access published on October 5, 2009.
doi:10.1093/molbev/msp238
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Research Article
Laura A. Hug, Alexandra Stechmann, and Andrew J. Roger
Phylogenetic distributions and histories of proteins involved in anaerobic pyruvate metabolism in eukaryotes
MBE Advance Access published on October 5, 2009.
doi:10.1093/molbev/msp237
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Research Article
Barry A. Kesner, Sharon L. Milgram, Brenda R. S. Temple, and Nikolay V. Dokholyan
Isoform Divergence of the Filamin Family of Proteins
MBE Advance Access published on October 5, 2009.
doi:10.1093/molbev/msp236
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Research Article
Jared L. Strasburg and Loren H. Rieseberg
How robust are "Isolation with Migration" analyses to violations of the IM model? A simulation study
MBE Advance Access published on September 30, 2009.
doi:10.1093/molbev/msp233
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Research Article
Steven F. Field and Mikhail V. Matz
Retracing evolution of red fluorescence in GFP-like proteins from Faviina corals
MBE Advance Access published on September 30, 2009.
doi:10.1093/molbev/msp230
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Research Article
Christopher W. Wheat, Christoph R. Haag, James H. Marden, Ilkka Hanski, and Mikko J. Frilander
Nucleotide polymorphism at a gene (Pgi) under balancing selection in a butterfly metapopulation
MBE Advance Access published on September 30, 2009.
doi:10.1093/molbev/msp227
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Research Article
A. P. Jason de Koning, Wanjun Gu, and David D. Pollock
Rapid likelihood analysis on large phylogenies using partial sampling of substitution histories
MBE Advance Access published on September 25, 2009.
doi:10.1093/molbev/msp228
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Research Article
Thomas J. Templeton, Shinichiro Enomoto, Wei-June Chen, Chin-Gi Huang, Cheryl A. Lancto, Mitchell S. Abrahamsen, and Guan Zhu
A genome sequence survey for Ascogregarina taiwanensis supports evolutionary affiliation, but metabolic diversity between a gregarine and Cryptosporidium
MBE Advance Access published on September 24, 2009.
doi:10.1093/molbev/msp226
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Research Article
Andrew P. Jackson
The evolution of amastin surface glycoproteins in trypanosomatid parasites
MBE Advance Access published on September 24, 2009.
doi:10.1093/molbev/msp214
[Abstract] [Accepted Manuscript] [Supplementary Data]     OPEN ACCESS ARTICLE

Research Article
V. Castric, JS. Bechsgaard, S. Grenier, R. Noureddine, MH Schierup, and X. Vekemans
Molecular Evolution Within and Between Self-Incompatibility Specificities
MBE Advance Access published on September 22, 2009.
doi:10.1093/molbev/msp224
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Research Article
David F. Gruber, Rob DeSalle, E. Kurt Lienau, Dan Tchernov, Vincent A. Pieribone, and Hung-Teh Kao
Novel Internal Regions of Fluorescent Proteins Undergo Divergent Evolutionary Patterns
MBE Advance Access published on September 21, 2009.
doi:10.1093/molbev/msp194
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Research Article
Jan E. Aagaard, Victor D. Vacquier, Michael J. MacCoss, and Willie J. Swanson
ZP Domain Proteins in the Abalone Egg Coat include a Paralog of VERL Under Positive Selection that Binds Lysin and 18-kDa Sperm Proteins
MBE Advance Access published on September 18, 2009.
doi:10.1093/molbev/msp221
[Abstract] [Accepted Manuscript] [Request Permissions]  

Research Article
Hui Liu, Stéphane Aris-Brosou, Ian Probert, and Colomban de Vargas
A timeline of the environmental genetics of the haptophytes
MBE Advance Access published on September 16, 2009.
doi:10.1093/molbev/msp222
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Research Article
Dorcas J. Orengo and Montserrat Aguadé
Uncovering the footprint of positive selection on the X chromosome of Drosophila melanogaster
MBE Advance Access published on September 16, 2009.
doi:10.1093/molbev/msp220
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Research Article
Lél Eory, Daniel L. Halligan, and Peter D. Keightley
Distributions of selectively constrained sites and deleterious mutation rates in the hominid and murid genomes
MBE Advance Access published on September 16, 2009.
doi:10.1093/molbev/msp219
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Research Article
Shozo Yokoyama and Takashi Tada
Evolutionary dynamics of rhodopsin type 2 (RH2) opsins in vertebrates
MBE Advance Access published on September 16, 2009.
doi:10.1093/molbev/msp217
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Research Article
J. Projecto-Garcia, N. Zorn, D. Jollivet, S. W. Schaeffer, F. H. Lallier, and S. Hourdez
Origin and evolution of the unique tetra-domain hemoglobin from the hydrothermal vent scale-worm Branchipolynoe
MBE Advance Access published on September 15, 2009.
doi:10.1093/molbev/msp218
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Research Article
Kristina A. Tabbada, Jean Trejaut, Jun-Hun Loo, Yao-Ming Chen, Marie Lin, Marta Mirazón-Lahr, Toomas Kivisild, and Maria Corazon A. De Ungria
Philippine mitochondrial DNA diversity: a populated viaduct between Taiwan and Indonesia?
MBE Advance Access published on September 15, 2009.
doi:10.1093/molbev/msp215
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Research Article
Li Yu, Xiao-yan Wang, Wei Jin, Peng-tao Luan, Nelson Ting, and Ya-ping Zhang
Adaptive evolution of digestive RNASE1 genes in leaf-eating monkeys revisited: new insights from 10 additional Colobines
MBE Advance Access published on September 11, 2009.
doi:10.1093/molbev/msp216
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Research Article
Sabyasachi Das, Uzra Mohamedy, Masayuki Hirano, Masatoshi Nei, and Nikolas Nikolaidis
Analysis of the immunoglobulin light chain genes in zebra finch: evolutionary implications
MBE Advance Access published on September 10, 2009.
doi:10.1093/molbev/msp212
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Research Article
Daniel R. Schrider and Matthew W. Hahn
Lower linkage disequilibrium at CNVs is due to both recurrent mutation and transposing duplications
MBE Advance Access published on September 10, 2009.
doi:10.1093/molbev/msp210
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Research Article
Daniel Garrigan, Richard Lewontin, and John Wakeley
Measuring the Sensitivity of Single-Locus "Neutrality Tests" Using a Direct Perturbation Approach
MBE Advance Access published on September 10, 2009.
doi:10.1093/molbev/msp209
[Abstract] [Accepted Manuscript]     OPEN ACCESS ARTICLE

Research Article
Thomas L.P. Couvreur, Andreas Franzke, Ihsan A. Al-Shehbaz, Freek T. Bakker, Marcus A. Koch, and Klaus Mummenhoff
Molecular phylogenetics, temporal diversification and principles of evolution in the mustard family (Brassicaceae)
MBE Advance Access published on September 10, 2009.
doi:10.1093/molbev/msp202
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Research Article
Cory D. Hirsch, Yufeng Wu, Huihuang Yan, and Jiming Jiang
Lineage-specific adaptive evolution of the centromeric protein CENH3 in diploid and allotetraploid Oryza species
MBE Advance Access published on September 9, 2009.
doi:10.1093/molbev/msp208
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Research Article
Krishanu Mukherjee, Luciano Brocchieri, and Thomas R. Bürglin
A comprehensive classification and evolutionary analysis of plant homeobox genes
MBE Advance Access published on September 4, 2009.
doi:10.1093/molbev/msp201
[Abstract] [Accepted Manuscript] [Supplementary Data]     OPEN ACCESS ARTICLE

Research Article
Nigel Grimsley, Bérangère Pequin, Charles Bachy, Hervé Moreau, and Gwenaël Piganeau
Cryptic sex in the smallest eukaryotic marine green alga
MBE Advance Access published on September 4, 2009.
doi:10.1093/molbev/msp203
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Research Article
Manja Marz, Alexander Donath, Nina Verstraete, Van Trung Nguyen, Peter F. Stadler, and Olivier Bensaude
Evolution of 7SK RNA and its Protein Partners in Metazoa
MBE Advance Access published on September 4, 2009.
doi:10.1093/molbev/msp198
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Research Article
Filipe Pereira, Sara Queirós, Leonor Gusmão, Isäac J. Nijman, Edwin Cuppen, Johannes A. Lenstra, the Econogene Consortium, Simon J. M. Davis, Fouad Nejmeddine, and António Amorim
Tracing the history of goat pastoralism: new clues from mitochondrial and Y chromosome DNA in North Africa
MBE Advance Access published on September 3, 2009.
doi:10.1093/molbev/msp200
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Research Article
Darin R. Rokyta and Holly A. Wichman
Genic Incompatibilities in Two Hybrid Bacteriophages
MBE Advance Access published on September 2, 2009.
doi:10.1093/molbev/msp199
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Research Article
Millán Ortiz, Nicolas Guex, Etienne Patin, Olivier Martin, Ioannis Xenarios, Angela Ciuffi, Lluís Quintana-Murci, and Amalio Telenti
Evolutionary Trajectories of Primate Genes Involved in HIV Pathogenesis
MBE Advance Access published on September 2, 2009.
doi:10.1093/molbev/msp197
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Research Article
Pawel M. Strozycki, Maciej Szymanski, Anna Szczurek, Jan Barciszewski, and Marek Figlerowicz
A new family of ferritin genes from Lupinus luteus - comparative analysis of plant ferritins, their gene structure, and evolution
MBE Advance Access published on September 2, 2009.
doi:10.1093/molbev/msp196
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Research Article
Jun-Feng Pang, Cornelya Kluetsch, Xiao-Ju Zou, Ai-bing Zhang, Li-Yang Luo, Helen Angleby, Arman Ardalan, Camilla Ekström, Anna Sköllermo, Joakim Lundeberg, Shuichi Matsumura, Thomas Leitner, Ya-Ping Zhang, and Peter Savolainen
mtDNA Data Indicates a Single Origin for Dogs South of Yangtze River, less than 16,300 Years Ago, from Numerous Wolves
MBE Advance Access published on September 1, 2009.
doi:10.1093/molbev/msp195
[Abstract] [Accepted Manuscript] [Supplementary Data]     OPEN ACCESS ARTICLE

Research Article
C. L. Galindo, L. J. McIver, J. F. McCormick, M. A. Skinner, Y. Xie, R. A. Gelhausen, K. Ng, N. M. Kumar, and H. R. Garner
Global microsatellite content distinguishes humans, primates, animals, and plants
MBE Advance Access published on August 28, 2009.
doi:10.1093/molbev/msp192
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Research Article
Dawn M. Simon, Scot A. Kelchner, and Steven Zimmerly
A broad-scale phylogenetic analysis of group II intron RNAs and intron-encoded reverse transcriptases
MBE Advance Access published on August 27, 2009.
doi:10.1093/molbev/msp193
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Research Article
Sabrina Simon, Sascha Strauss, Arndt von Haeseler, and Heike Hadrys
A phylogenomic approach to resolve the basal pterygote divergence
MBE Advance Access published on August 27, 2009.
doi:10.1093/molbev/msp191
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Research Article
Aida M. Andrés, Melissa J. Hubisz, Amit Indap, Dara G. Torgerson, Jeremiah D. Degenhardt, Adam R. Boyko, Ryan N. Gutenkunst, Thomas J. White, Eric D. Green, Carlos D. Bustamante, Andrew G. Clark, and Rasmus Nielsen
Targets of balancing selection in the human genome
MBE Advance Access published on August 27, 2009.
doi:10.1093/molbev/msp190
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Research Article
Philippe Deschamps and David Moreira
Signal conflicts in the phylogeny of the primary photosynthetic eukaryotes
MBE Advance Access published on August 25, 2009.
doi:10.1093/molbev/msp189
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Research Article
John G. Gibbons, Eric M. Janson, Chris Todd Hittinger, Mark Johnston, Patrick Abbot, and Antonis Rokas
Benchmarking next-generation transcriptome sequencing for functional and evolutionary genomics
MBE Advance Access published on August 25, 2009.
doi:10.1093/molbev/msp188
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Research Article
Shaobin Zhong, Stephen P. Miller, Daniel E. Dykhuizen, and Antony M. Dean
Transcription, Translation and the Evolution of Specialists and Generalists
MBE Advance Access published on August 25, 2009.
doi:10.1093/molbev/msp187
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Research Article
Beyhan Ertas, Björn M. von Reumont, Johann-Wolfgang Wägele, Bernhard Misof, and Thorsten Burmester
Hemocyanin suggests a close relationship of Remipedia and Hexapoda
MBE Advance Access published on August 19, 2009.
doi:10.1093/molbev/msp186
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Research Article
Matthew W. Brown, Frederick W. Spiegel, and Jeffrey D. Silberman
Phylogeny of the "forgotten" cellular slime mold, Fonticula alba, reveals a key evolutionary branch within Opisthokonta
MBE Advance Access published on August 19, 2009.
doi:10.1093/molbev/msp185
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Research Article
Jihua Wu and Edward Susko
General Heterotachy and Distance Method Adjustments
MBE Advance Access published on August 17, 2009.
doi:10.1093/molbev/msp184
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Research Article
Jason A. Wilder, Elizabeth K. Hewett, and Meredith E. Gansner
Molecular evolution of GYPC: Evidence for recent structural innovation and positive selection in humans
MBE Advance Access published on August 13, 2009.
doi:10.1093/molbev/msp183
[Abstract] [Accepted Manuscript] [Supplementary Data]     OPEN ACCESS ARTICLE

LETTERGo to top of the page

Letter
Manolo Gouy, Stéphane Guindon, and Olivier Gascuel
SeaView version 4 : a multiplatform graphical user interface for sequence alignment and phylogenetic tree building
MBE Advance Access published on October 23, 2009.
doi:10.1093/molbev/msp259
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Letter
Peter W. Osborne and David E. K. Ferrier
Chordate Hox and ParaHox Gene Clusters Differ Dramatically in Their Repetitive Element Content
MBE Advance Access published on October 5, 2009.
doi:10.1093/molbev/msp235
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Letter
Carmela Gissi, Graziano Pesole, Francesco Mastrototaro, Fabio Iannelli, Vanessa Guida, and Francesca Griggio
Hyper-variability of ascidian mitochondrial gene order: exposing the myth of deuterostome organelle genome stability
MBE Advance Access published on October 1, 2009.
doi:10.1093/molbev/msp234
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

Letter
Shanyuan Chen, Bang-Zhong Lin, Mumtaz Baig, Bikash Mitra, Ricardo J. Lopes, António M. Santos, David A. Magee, Marisa Azevedo, Pedro Tarroso, Shinji Sasazaki, Stephane Ostrowski, Osman Mahgoub, Tapas K. Chaudhuri, Ya-ping Zhang, Vânia Costa, Luis J. Royo, Félix Goyache, Gordon Luikart, Nicole Boivin, Dorian Q. Fuller, Hideyuki Mannen, Daniel G. Bradley, and Albano Beja-Pereira
Zebu cattle are an exclusive legacy of the South Asia Neolithic
MBE Advance Access published on September 21, 2009.
doi:10.1093/molbev/msp213
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Letter
Ryan M.R. Gawryluk and Michael W. Gray
An ancient fission of mitochondrial cox1
MBE Advance Access published on September 18, 2009.
doi:10.1093/molbev/msp223
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Letter
Shohei Takuno and Hideki Innan
Selection to maintain amino acid differences between paralogous heat shock protein genes in yeast
MBE Advance Access published on September 10, 2009.
doi:10.1093/molbev/msp211
[Abstract] [Accepted Manuscript] [Supplementary Data] [Request Permissions]  

To see an accepted manuscript, click its [Accepted Manuscript] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.