An ancestral whole-genome duplication may not have been responsible for the abundance of duplicated fish genes

We thank Jamshed Tata for critical reading, Pierre-Luc Bardet, Sandrine Hughes and Dominique Zelus for help in cloning and sequencing nuclear receptors, and two anonymous referees for helping to focus our conclusions. We thank Association de Recherche sur le Cancer, Centre National pour la Recherche Scientifique, European Molecular Biology Organisation, Fondation pour la Recherche Medicale, Ligue Nationale contre le Cancer, Region Rhone-Alpes and Ministere de l'Education Nationale for financial support.

[1]  Y L Wang,et al.  Zebrafish hox clusters and vertebrate genome evolution. , 1998, Science.

[2]  M. Gouy,et al.  HOVERGEN: a database of homologous vertebrate genes. , 1994, Nucleic acids research.

[3]  Y. Yan,et al.  A comparative map of the zebrafish genome. , 2000, Genome research.

[4]  William R. Taylor,et al.  The rapid generation of mutation data matrices from protein sequences , 1992, Comput. Appl. Biosci..

[5]  J. Felsenstein.  CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP , 1985, Evolution; international journal of organic evolution.

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

[7]  A. Meyer,et al.  Gene and genome duplications in vertebrates: the one-to-four (-to-eight in fish) rule and the evolution of novel gene functions. , 1999, Current opinion in cell biology.

[8]  A. Martín,et al.  Is tetralogy true? Lack of support for the "one-to-four rule". , 2001, Molecular biology and evolution.

[9]  Manolo Gouy,et al.  SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny , 1996, Comput. Appl. Biosci..

[10]  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.

[11]  D. Moore,et al.  Linkage of the nuclear hormone receptor genes NR1D2, THRB, and RARB: evidence for an ancient, large-scale duplication. , 1999, Genomics.

[12]  V. Laudet,et al.  Euteleost fish genomes are characterized by expansion of gene families. , 2001, Genome research.

[13]  Margaret R. Thomson,et al.  Vertebrate genome evolution and the zebrafish gene map , 1998, Nature Genetics.

[14]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[15]  Joachim Wittbrodt,et al.  More genes in fish , 1998 .

[16]  K. Strimmer,et al.  Quartet Puzzling: A Quartet Maximum-Likelihood Method for Reconstructing Tree Topologies , 1996 .

[17]  Margaret R. Thomson,et al.  Vertebrate genome evolution and the zebrafish gene map , 1998, Nature Genetics.

[18]  V. Laudet,et al.  Molecular cloning and characterization of thyroid hormone receptors in teleost fish. , 2001, Journal of molecular endocrinology.