Molecular Biology and Evolution

RESEARCH ARTICLE

Abstract Research Article

Omar E. Cornejo, Lesley McGee, and Daniel E. Rozen
Polymorphic competence peptides do not restrict recombination in Streptococcus pneumoniae
MBE Advance Access published on November 25, 2009.
doi:10.1093/molbev/msp287
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Abstract Research Article

Vassilis Douris, Maximilian J. Telford, and Michalis Averof
Evidence for multiple independent origins of trans-splicing in Metazoa
MBE Advance Access published on November 25, 2009.
doi:10.1093/molbev/msp286
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Abstract Research Article

Diana Cumings Outlaw and Robert E. Ricklefs
Comparative gene evolution in haemosporidian (Apicomplexa) parasites of birds and mammals
MBE Advance Access published on November 23, 2009.
doi:10.1093/molbev/msp283
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Abstract Research Article Joseph Heled and Alexei J. Drummond Bayesian inference of species trees from multilocus data MBE Advance Access published on November 20, 2009. doi:10.1093/molbev/msp274 [Abstract] [Accepted Manuscript]     OPEN ACCESS ARTICLE

Abstract Research Article

Jingjing Li, Yu Liu, Dong Dong, and Zhaolei Zhang
Evolution of an X-linked primate-specific microRNA cluster
MBE Advance Access published on November 19, 2009.
doi:10.1093/molbev/msp284
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Abstract Research Article

Judith E. Mank, Kiwoong Nam, and Hans Ellegren
Faster-Z Evolution is Predominantly Due to Genetic Drift
MBE Advance Access published on November 18, 2009.
doi:10.1093/molbev/msp282
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Abstract Research Article

Dean M. Castillo and Teresa E. Pawlowska
Molecular evolution in bacterial endosymbionts of fungi
MBE Advance Access published on November 18, 2009.
doi:10.1093/molbev/msp280
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Abstract Research Article Celeste J. Brown, Audra K. Johnson, and Gary W. Daughdrill Comparing models of evolution for ordered and disordered proteins MBE Advance Access published on November 18, 2009. doi:10.1093/molbev/msp277 [Abstract] [Accepted Manuscript] [Supplementary Data]     OPEN ACCESS ARTICLE

Abstract Research Article

Marian Bemer, Jonathan Gordon, Koen Weterings, and Gerco C. Angenent
Divergence of Recently Duplicated M-type MADS-box Genes in Petunia
MBE Advance Access published on November 16, 2009.
doi:10.1093/molbev/msp279
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Abstract Research Article

Daniel J. Jackson, Carmel McDougall, Ben Woodcroft, Patrick Moase, Robert A. Rose, Michael Kube, Richard Reinhardt, Daniel S. Rokhsar, Caroline Montagnani, Caroline Joubert, David Piquemal, and Bernard M. Degnan
Parallel evolution of nacre building gene sets in molluscs
MBE Advance Access published on November 13, 2009.
doi:10.1093/molbev/msp278
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Abstract Research Article

Courtney C. Babbitt, Jesse S. Silverman, Ralph Haygood, Jennifer M. Reininga, Matthew V. Rockman, and Gregory A. Wray
Multiple functional variants in cis modulate PDYN expression
MBE Advance Access published on November 12, 2009.
doi:10.1093/molbev/msp276
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Abstract Research Article

Kenji Suzuki and Shin-ya Miyagishima
Eukaryotic and Eubacterial Contributions to the Establishment of Plastid Proteome Estimated by Large-Scale Phylogenetic Analyses
MBE Advance Access published on November 12, 2009.
doi:10.1093/molbev/msp273
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Abstract Research Article

Joshua L. Cherry
Highly Expressed and Slowly Evolving Proteins Share Compositional Properties with Thermophilic Proteins
MBE Advance Access published on November 12, 2009.
doi:10.1093/molbev/msp270
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Abstract Research Article

Clara Torres-Barceló, José-Antonio Daròs, and Santiago F. Elena
Compensatory molecular evolution of HC-Pro, an RNA-silencing suppressor from a plant RNA virus
MBE Advance Access published on November 11, 2009.
doi:10.1093/molbev/msp272
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Abstract Research Article

Mathieu Lajoie, Denis Bertrand, and Nadia El-Mabrouk
Inferring the Evolutionary History of Gene Clusters from Phylogenetic and Gene Order Data
MBE Advance Access published on November 10, 2009.
doi:10.1093/molbev/msp271
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Abstract Research Article

Monkol Lek, Daniel G. MacArthur, Nan Yang, and Kathryn N. North
Phylogenetic analysis of gene structure and alternative splicing in -actinins
MBE Advance Access published on November 6, 2009.
doi:10.1093/molbev/msp268
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Abstract 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
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Abstract 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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Abstract 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
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Abstract 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

Abstract 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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Abstract 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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Abstract 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
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Abstract 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

Abstract 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
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Abstract 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
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Abstract 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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Abstract 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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Abstract 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
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Abstract 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

Abstract 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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Abstract 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

Abstract 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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Abstract 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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Abstract 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

Abstract 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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Abstract 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
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Abstract 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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Abstract 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
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Abstract 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
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Abstract 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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Abstract 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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Abstract 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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Abstract 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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Abstract 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

Abstract 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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Abstract 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
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Abstract 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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Abstract 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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Abstract 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
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Abstract 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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Abstract 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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Abstract 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
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Abstract 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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Abstract 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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Abstract 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
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Abstract 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

Abstract 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
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Abstract 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
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Abstract 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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LETTER

Abstract Letter

Meghan E. Chafee, Daniel J. Funk, Richard G. Harrison, and Seth R. Bordenstein
Lateral phage transfer in obligate intracellular bacteria (Wolbachia): Verification from natural populations
MBE Advance Access published on November 11, 2009.
doi:10.1093/molbev/msp275
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Abstract 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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Abstract 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
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Abstract 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
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Abstract 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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Abstract 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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