Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades

[1]  C. Matthee,et al.  Suprafamilial relationships among Rodentia and the phylogenetic effect of removing fast-evolving nucleotides in mitochondrial, exon and intron fragments , 2008, BMC Evolutionary Biology.

[2]  Adi Stern,et al.  Evolutionary Modeling of Rate Shifts Reveals Specificity Determinants in HIV-1 Subtypes , 2008, PLoS Comput. Biol..

[3]  S. V. Popov,et al.  Phylogeny of the order rodentia inferred from structural analysis of short retroposon B1 , 2007, Russian Journal of Genetics.

[4]  Adi Doron-Faigenboim,et al.  Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach , 2007, Nucleic Acids Res..

[5]  Naiara Rodríguez-Ezpeleta,et al.  Detecting and overcoming systematic errors in genome-scale phylogenies. , 2007, Systematic biology.

[6]  N. Veniaminova,et al.  B1 SINEs in different rodent families. , 2007, Genomics.

[7]  C. W. Kilpatrick,et al.  Multiple molecular evidences for a living mammalian fossil , 2007, Proceedings of the National Academy of Sciences.

[8]  C. Gissi,et al.  Phylogenetic analyses of complete mitochondrial genome sequences suggest a basal divergence of the enigmatic rodent Anomalurus , 2007, BMC Evolutionary Biology.

[9]  J. Brosius,et al.  Automated scanning for phylogenetically informative transposed elements in rodents. , 2006, Systematic biology.

[10]  Alexandros Stamatakis,et al.  RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models , 2006, Bioinform..

[11]  G. R. Seamons,et al.  Mammal Species of the World: A Taxonomic and Geographic Reference (3rd edition) , 2006 .

[12]  Peer Bork,et al.  PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments , 2006, Nucleic Acids Res..

[13]  M. Hasegawa,et al.  Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[14]  P. Chevret,et al.  Arrival and diversification of caviomorph rodents and platyrrhine primates in South America. , 2006, Systematic biology.

[15]  H. Philippe,et al.  Computing Bayes factors using thermodynamic integration. , 2006, Systematic biology.

[16]  M. Kiefmann,et al.  Retroposed Elements as Archives for the Evolutionary History of Placental Mammals , 2006, PLoS biology.

[17]  Hiroshi Tanaka,et al.  An empirical examination of the utility of codon-substitution models in phylogeny reconstruction. , 2005, Systematic biology.

[18]  Zaid Abdo,et al.  Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation. , 2005, Molecular biology and evolution.

[19]  F. Melo,et al.  Adaptive evolution of the insulin gene in caviomorph rodents. , 2005, Molecular biology and evolution.

[20]  David Posada,et al.  ProtTest: selection of best-fit models of protein evolution , 2005, Bioinform..

[21]  K. Holsinger,et al.  Polytomies and Bayesian phylogenetic inference. , 2005, Systematic biology.

[22]  Chuong B. Do,et al.  ProbCons: Probabilistic consistency-based multiple sequence alignment. , 2005, Genome research.

[23]  K. Katoh,et al.  MAFFT version 5: improvement in accuracy of multiple sequence alignment , 2005, Nucleic acids research.

[24]  W. Luckett,et al.  Monophyly or polyphyly of the order Rodentia: Possible conflict between morphological and molecular interpretations , 1993, Journal of Mammalian Evolution.

[25]  Michael P. Cummings,et al.  PAUP* [Phylogenetic Analysis Using Parsimony (and Other Methods)] , 2004 .

[26]  L. Marivaux,et al.  High‐level phylogeny of early Tertiary rodents: dental evidence , 2004 .

[27]  N. Ben-Tal,et al.  Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior. , 2004, Molecular biology and evolution.

[28]  Edward Susko,et al.  Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF-1alpha phylogenies. , 2004, Molecular biology and evolution.

[29]  K. Strimmer,et al.  TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics , 2004, BMC Evolutionary Biology.

[30]  H. Philippe,et al.  A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. , 2004, Molecular biology and evolution.

[31]  Graziano Pesole,et al.  Congruent mammalian trees from mitochondrial and nuclear genes using Bayesian methods. , 2003, Molecular biology and evolution.

[32]  David L. Swofford,et al.  Are Guinea Pigs Rodents? The Importance of Adequate Models in Molecular Phylogenetics , 1997, Journal of Mammalian Evolution.

[33]  R. Debry.  Identifying conflicting signal in a multigene analysis reveals a highly resolved tree: the phylogeny of Rodentia (Mammalia). , 2003, Systematic biology.

[34]  O. Gascuel,et al.  A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. , 2003, Systematic biology.

[35]  John P. Huelsenbeck,et al.  MrBayes 3: Bayesian phylogenetic inference under mixed models , 2003, Bioinform..

[36]  O. Madsen,et al.  Indels in protein-coding sequences of Euarchontoglires constrain the rooting of the eutherian tree. , 2003, Molecular phylogenetics and evolution.

[37]  R. Adkins,et al.  Higher-level systematics of rodents and divergence time estimates based on two congruent nuclear genes. , 2003, Molecular phylogenetics and evolution.

[38]  R. Nielsen,et al.  Pervasive adaptive evolution in mammalian fertilization proteins. , 2003, Molecular biology and evolution.

[39]  M. Stanhope,et al.  Rodent phylogeny and a timescale for the evolution of Glires: evidence from an extensive taxon sampling using three nuclear genes. , 2002, Molecular biology and evolution.

[40]  C. Tirard,et al.  Molecular systematics of sciurognathi (rodentia): the mitochondrial cytochrome b and 12S rRNA genes support the Anomaluroidea (Pedetidae and Anomaluridae). , 2002, Molecular phylogenetics and evolution.

[41]  D. Swofford.  PAUP*: Phylogenetic analysis using parsimony (*and other methods), Version 4.0b10 , 2002 .

[42]  W. Murphy,et al.  Resolution of the Early Placental Mammal Radiation Using Bayesian Phylogenetics , 2001, Science.

[43]  Masami Hasegawa,et al.  CONSEL: for assessing the confidence of phylogenetic tree selection , 2001, Bioinform..

[44]  E. Douzery,et al.  From the Old World to the New World: a molecular chronicle of the phylogeny and biogeography of hystricognath rodents. , 2001, Molecular phylogenetics and evolution.

[45]  Ari Löytynoja,et al.  SOAP, cleaning multiple alignments from unstable blocks , 2001, Bioinform..

[46]  R. Adkins,et al.  Molecular phylogeny and divergence time estimates for major rodent groups: evidence from multiple genes. , 2001, Molecular biology and evolution.

[47]  R. Debry,et al.  Phylogeny of rodentia (Mammalia) inferred from the nuclear-encoded gene IRBP. , 2001, Molecular phylogenetics and evolution.

[48]  N. Galtier,et al.  Maximum-likelihood phylogenetic analysis under a covarion-like model. , 2001, Molecular biology and evolution.

[49]  S. O’Brien,et al.  Molecular phylogenetics and the origins of placental mammals , 2001, Nature.

[50]  L. C. Contreras,et al.  Allozymic variation and systematic relationships of the Octodontidae and allied taxa (Mammalia, Rodentia) , 2000 .

[51]  C. Gissi,et al.  Where do rodents fit? Evidence from the complete mitochondrial genome of Sciurus vulgaris. , 2000, Molecular biology and evolution.

[52]  N. Goldman,et al.  Codon-substitution models for heterogeneous selection pressure at amino acid sites. , 2000, Genetics.

[53]  E. Douzery,et al.  Variance of molecular datings, evolution of rodents and the phylogenetic affinities between Ctenodactylidae and Hystricognathi , 2000, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[54]  David Posada,et al.  MODELTEST: testing the model of DNA substitution , 1998, Bioinform..

[55]  H. Philippe.  Rodent monophyly: pitfalls of molecular phylogenies. , 1997, Journal of molecular evolution.

[56]  George Gaylord Simpson,et al.  Classification of mammals : above the species level , 1997 .

[57]  C. Gissi,et al.  The guinea-pig is not a rodent , 1996, Nature.

[58]  M. Allard,et al.  Molecular systematics of hystricognath rodents: evidence from the mitochondrial 12S rRNA gene. , 1994, Molecular phylogenetics and evolution.

[59]  M. Novacek.  Mammalian phylogeny: Morphology and molecules. , 1993, Trends in ecology & evolution.

[60]  D. Graur.  Reply from d. Graur. , 1993, Trends in ecology & evolution.

[61]  M. Nei,et al.  Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. , 1993, Molecular biology and evolution.

[62]  Daryl E. Wilson,et al.  Mammal Species of the World: A Taxonomic and Geographic Reference , 1993 .

[63]  Dan Graur,et al.  Is the guinea-pig a rodent? , 1991, Nature.

[64]  M. Vianey-Liaud.  Possible Evolutionary Relationships among Eocene and Lower Oligocene Rodents of Asia, Europe and North America , 1985 .

[65]  Jean-Louis Hartenberger,et al.  The Order Rodentia: Major Questions on Their Evolutionary Origin, Relationships and Suprafamilial Systematics , 1985 .

[66]  J. Bugge.  Systematic Value of the Carotid Arterial Pattern in Rodents , 1985 .

[67]  W. Luckett,et al.  Evolutionary relationships among rodents : a multidisciplinary analysis , 1985 .

[68]  R. Lavocat,et al.  Phylogenetic Analysis of Middle Ear Features in Fossil and Living Rodents , 1985 .

[69]  W. Luckett.  Superordinal and Intraordinal Affinities of Rodents: Developmental Evidence from the Dentition and Placentation , 1985 .

[70]  W. Luckett,et al.  Evolutionary Relationships among Rodents , 1985, NATO Advanced Science Institutes (ASI) Series.

[71]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[72]  Tycho Tullberg.  Ueber Das System Der Nagethiere: Eine Phylogenetische Studie , 2009 .