The amphioxus genome and the evolution of the chordate karyotype

[1]  W. Yarrell.  A history of British fishes , 2010 .

[2]  Nicholas H. Putnam,et al.  The amphioxus genome illuminates vertebrate origins and cephalochordate biology. , 2008, Genome research.

[3]  Y. Kohara,et al.  Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates. , 2007, Genome research.

[4]  Nicholas H. Putnam,et al.  Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization , 2007, Science.

[5]  Justin Johnson,et al.  Survey Sequencing and Comparative Analysis of the Elephant Shark (Callorhinchus milii) Genome , 2007, PLoS biology.

[6]  Matthew M. Hill,et al.  Extreme genomic variation in a natural population , 2007, Proceedings of the National Academy of Sciences.

[7]  Y. Kohara,et al.  Axial patterning in cephalochordates and the evolution of the organizer , 2007, Nature.

[8]  Alan M. Moses,et al.  In vivo enhancer analysis of human conserved non-coding sequences , 2006, Nature.

[9]  Andrew R. Jackson,et al.  The Genome of the Sea Urchin Strongylocentrotus purpuratus , 2006, Science.

[10]  Sarah J. Bourlat,et al.  Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida , 2006, Nature.

[11]  O. Jaillon,et al.  Gene loss and evolutionary rates following whole-genome duplication in teleost fishes. , 2006, Molecular biology and evolution.

[12]  M. Gribskov,et al.  The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray) , 2006, Science.

[13]  Steven Maere,et al.  The gain and loss of genes during 600 million years of vertebrate evolution , 2006, Genome Biology.

[14]  J. Graves,et al.  Reconstruction of a 450-My-old ancestral vertebrate protokaryotype. , 2006, Trends in genetics : TIG.

[15]  F. Delsuc,et al.  Tunicates and not cephalochordates are the closest living relatives of vertebrates , 2006, Nature.

[16]  S. Hedges,et al.  Molecular phylogeny and divergence times of deuterostome animals. , 2005, Molecular biology and evolution.

[17]  Steven Maere,et al.  Genome duplication and the origin of angiosperms. , 2005, Trends in ecology & evolution.

[18]  A. Poustka,et al.  Timing and mechanism of ancient vertebrate genome duplications -- the adventure of a hypothesis. , 2005, Trends in genetics : TIG.

[19]  John H Postlethwait,et al.  The zebrafish gene map defines ancestral vertebrate chromosomes. , 2005, Genome research.

[20]  Philip C J Donoghue,et al.  Genome duplication, extinction and vertebrate evolution. , 2005, Trends in ecology & evolution.

[21]  Paramvir S. Dehal,et al.  Two Rounds of Whole Genome Duplication in the Ancestral Vertebrate , 2005, PLoS biology.

[22]  A. Hughes,et al.  Loss of ancestral genes in the genomic evolution of Ciona intestinalis , 2005, Evolution & development.

[23]  Pierre Pontarotti,et al.  Towards the reconstruction of the bilaterian ancestral pre-MHC region. , 2004, Trends in genetics : TIG.

[24]  Klaudia Walter,et al.  Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development , 2004, PLoS biology.

[25]  Charles E. Chapple,et al.  Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype , 2004, Nature.

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

[27]  H. Lehrach,et al.  Hypervariable and Highly Divergent Intron–Exon Organizations in the Chordate Oikopleura dioica , 2004, Journal of Molecular Evolution.

[28]  A. Meyer,et al.  Phylogenetic Timing of the Fish-Specific Genome Duplication Correlates with the Diversification of Teleost Fish , 2004, Journal of Molecular Evolution.

[29]  Alan Christoffels,et al.  Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes. , 2004, Molecular biology and evolution.

[30]  Akihiro Shima,et al.  A medaka gene map: the trace of ancestral vertebrate proto-chromosomes revealed by comparative gene mapping. , 2004, Genome research.

[31]  V. Laudet,et al.  Phylogenetic dating and characterization of gene duplications in vertebrates: the cartilaginous fish reference. , 2004, Molecular biology and evolution.

[32]  P. Holland,et al.  An antecedent of the MHC-linked genomic region in amphioxus , 2004, Immunogenetics.

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

[34]  Jon Mallatt,et al.  Fossil sister group of craniates: Predicted and found , 2003, Journal of morphology.

[35]  P. Holland,et al.  Chromosomal mapping of ANTP class homeobox genes in amphioxus: piecing together ancestral genomes , 2003, Evolution & development.

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

[37]  E. Lander,et al.  Anteroposterior Patterning in Hemichordates and the Origins of the Chordate Nervous System , 2003, Cell.

[38]  Martin Vingron,et al.  New evidence for genome-wide duplications at the origin of vertebrates using an amphioxus gene set and completed animal genomes. , 2003, Genome research.

[39]  A. Coulson,et al.  Dispersal of NK homeobox gene clusters in amphioxus and humans , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[40]  R. Britten,et al.  Majority of divergence between closely related DNA samples is due to indels , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[41]  Paul Richardson,et al.  The Draft Genome of Ciona intestinalis: Insights into Chordate and Vertebrate Origins , 2002, Science.

[42]  P. Holland,et al.  Fluorescent in situ Hybridisation to Amphioxus Chromosomes , 2002, Zoological science.

[43]  Vincent Laudet,et al.  Analysis of lamprey and hagfish genes reveals a complex history of gene duplications during early vertebrate evolution. , 2002, Molecular biology and evolution.

[44]  Paramvir S. Dehal,et al.  Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes , 2002, Science.

[45]  Karsten Hokamp,et al.  Extensive genomic duplication during early chordate evolution , 2002, Nature Genetics.

[46]  P. Holland,et al.  Were vertebrates octoploid? , 2002, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[47]  André Gilles,et al.  Evidence of en bloc duplication in vertebrate genomes , 2002, Nature Genetics.

[48]  Sudhir Kumar,et al.  Mutation rates in mammalian genomes , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[49]  D. Birnbaum,et al.  Coparalogy: physical and functional clusterings in the human genome. , 2001, Biochemical and biophysical research communications.

[50]  John P. Huelsenbeck,et al.  MRBAYES: Bayesian inference of phylogenetic trees , 2001, Bioinform..

[51]  K. H. Wolfe.  Yesterday's polyploids and the mystery of diploidization , 2001, Nature Reviews Genetics.

[52]  Junyuan Chen,et al.  Origin and early evolution of the vertebrates: New insights from advances in molecular biology, anatomy, and palaeontology , 2001, BioEssays : news and reviews in molecular, cellular and developmental biology.

[53]  Y. Yan,et al.  Zebrafish comparative genomics and the origins of vertebrate chromosomes. , 2000, Genome research.

[54]  M. Nachman,et al.  Estimate of the mutation rate per nucleotide in humans. , 2000, Genetics.

[55]  J. W. Valentine.  Two genomic paths to the evolution of complexity in bodyplans , 2000, Paleobiology.

[56]  B. Swalla,et al.  Evolution of the chordate body plan: new insights from phylogenetic analyses of deuterostome phyla. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[57]  Wei Qian,et al.  Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. , 2000, Molecular biology and evolution.

[58]  Diying Huang,et al.  An early Cambrian craniate-like chordate , 1999, Nature.

[59]  Nicholas D Holland,et al.  Chordate origins of the vertebrate central nervous system , 1999, Current Opinion in Neurobiology.

[60]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[61]  J. Weber,et al.  Human whole-genome shotgun sequencing. , 1997, Genome research.

[62]  D. Shu,et al.  Reinterpretation of Yunnanozoon as the earliest known hemichordate , 1996, Nature.

[63]  G. Edgecombe,et al.  A possible Early Cambrian chordate , 1995, Nature.

[64]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[65]  Jordi Garcia-Fernàndez,et al.  Archetypal organization of the amphioxus Hox gene cluster , 1994, Nature.

[66]  D. Mccormick.  Sequence the Human Genome , 1986, Bio/Technology.

[67]  S. Morris,et al.  The Animals of the Burgess Shale , 1979 .

[68]  J. Schmidtke,et al.  Isozymes of a tunicate and a cephalochordate as a test of polyploidisation in chordate evolution , 1977, Nature.

[69]  Rspm μgm.  Methods , 1972 .

[70]  H. Boschung,et al.  Chromosomes of the lancelet,Branchiostoma floridae (order amphioxi) , 1971, Experientia.

[71]  Dr. Susumu Ohno.  Evolution by Gene Duplication , 1970, Springer Berlin Heidelberg.

[72]  Paul Richardson,et al.  Accelerated gene evolution and subfunctionalization in the pseudotetraploid frog Xenopus laevis , 2007, BMC Biology.

[73]  D. Rokhsar,et al.  Evidence for a microRNA expansion in the bilaterian ancestor , 2006, Development Genes and Evolution.

[74]  D. Larhammar,et al.  Numerous groups of chromosomal regional paralogies strongly indicate two genome doublings at the root of the vertebrates , 2004, Journal of Structural and Functional Genomics.

[75]  International Human Genome Sequencing Consortium.  Initial sequencing and analysis of the human genome , 2001, Nature.

[76]  N. Holland.  The Lancelet , 1998, American Scientist.

[77]  A. Sidow,et al.  Gene duplications and the origins of vertebrate development. , 1994, Development (Cambridge, England). Supplement.

[78]  C. Markert,et al.  Evolution of the Gene , 1948, Nature.

[79]  A. O. Kovalevskiĭ.  Entwickelungsgeschichte des Amphioxus Lanceolatus , 1867 .