Evolution by gene duplication: an update

[1]  Z. Gu,et al.  Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. , 2002, Molecular biology and evolution.

[2]  J. Oates,et al.  Colobine Monkeys: Their Ecology, Behaviour and Evolution , 1995 .

[3]  Masatoshi Nei,et al.  Purifying selection and birth-and-death evolution in the histone H4 gene family. , 2002, Molecular biology and evolution.

[4]  Austin L. Hughes,et al.  Adaptive Evolution of Genes and Genomes , 2000 .

[5]  T. Kitami,et al.  Biochemical networking contributes more to genetic buffering in human and mouse metabolic pathways than does gene duplication , 2002, Nature Genetics.

[6]  Ronald W. Davis,et al.  Role of duplicate genes in genetic robustness against null mutations , 2003, Nature.

[7]  M. Gerstein,et al.  Digging for dead genes: an analysis of the characteristics of the pseudogene population in the Caenorhabditis elegans genome. , 2001, Nucleic acids research.

[8]  Jianzhi Zhang,et al.  Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey , 2002, Nature Genetics.

[9]  The Arabidopsis Genome Initiative.  Analysis of the genome sequence of the flowering plant Arabidopsis thaliana , 2000, Nature.

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

[11]  A. Varki,et al.  Genetic differences between humans and great apes. , 2001, Molecular phylogenetics and evolution.

[12]  M. Nei,et al.  Purifying selection and birth-and-death evolution in the ubiquitin gene family. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[13]  M. Long,et al.  Evolution of novel genes. , 2001, Current opinion in genetics & development.

[14]  S. Benner,et al.  Pseudogenes in ribonuclease evolution: a source of new biomacromolecular function? , 1996, FEBS letters.

[15]  L. Orgel.  Gene-duplication and the origin of proteins with novel functions. , 1977, Journal of theoretical biology.

[16]  J. Quattro,et al.  Evidence for a period of directional selection following gene duplication in a neurally expressed locus of triosephosphate isomerase. , 2001, Genetics.

[17]  T. Ohta.  Further examples of evolution by gene duplication revealed through DNA sequence comparisons. , 1994, Genetics.

[18]  C R Woese,et al.  Erratum: The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus , 1998, Nature.

[19]  Xun Gu,et al.  Predicting functional divergence in protein evolution by site-specific rate shifts. , 2002, Trends in biochemical sciences.

[20]  J. Spring,et al.  Genome duplication strikes back , 2002, Nature Genetics.

[21]  D. Nicolae,et al.  Rapid divergence in expression between duplicate genes inferred from microarray data. , 2002, Trends in genetics : TIG.

[22]  S. Palumbi,et al.  Molecular genetics of ecological diversification: duplication and rapid evolution of toxin genes of the venomous gastropod Conus. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[23]  Mouse Genome Sequencing Consortium.  Initial sequencing and comparative analysis of the mouse genome , 2002, Nature.

[24]  D. Hartl,et al.  Selective neutrality of 6PGD allozymes in E. coli and the effects of genetic background. , 1980, Genetics.

[25]  M. Nei,et al.  Gene Duplication and Nucleotide Substitution in Evolution , 1969, Nature.

[26]  S. Yokoyama,et al.  Molecular evolution of human visual pigment genes. , 1989, Molecular biology and evolution.

[27]  Xun Gu,et al.  DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family , 2002, Bioinform..

[28]  M. Nei,et al.  Positive darwinian selection observed at the variable-region genes of immunoglobulins. , 1989, Molecular biology and evolution.

[29]  E. Koonin,et al.  The role of lineage-specific gene family expansion in the evolution of eukaryotes. , 2002, Genome research.

[30]  David J. Galas,et al.  A duplication growth model of gene expression networks , 2002, Bioinform..

[31]  R. Jensen.  Enzyme recruitment in evolution of new function. , 1976, Annual review of microbiology.

[32]  J. Beintema,et al.  Secretory ribonuclease genes and pseudogenes in true ruminants. , 1998, Gene.

[33]  J. B. Walsh,et al.  How often do duplicated genes evolve new functions? , 1995, Genetics.

[34]  P. Mombaerts,et al.  The human repertoire of odorant receptor genes and pseudogenes. , 2001, Annual review of genomics and human genetics.

[35]  Mark Gerstein,et al.  Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22. , 2002, Genome research.

[36]  Dr. Susumu Ohno.  Sex Chromosomes and Sex-Linked Genes , 1967, Monographs on Endocrinology.

[37]  Masatoshi Nei,et al.  Evolution of genes and proteins. , 1983 .

[38]  A. Hughes.  The evolution of functionally novel proteins after gene duplication , 1994, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[39]  M. Nei,et al.  Evolution of immunoglobulin VH pseudogenes in chickens. , 1995, Molecular biology and evolution.

[40]  A. Meyer,et al.  The Ghost of Selection Past: Rates of Evolution and Functional Divergence of Anciently Duplicated Genes , 2001, Journal of Molecular Evolution.

[41]  Sudhir Kumar,et al.  Comparative Genomics in Eukaryotes , 2005 .

[42]  H. Hilbert,et al.  Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. , 1996, Nucleic acids research.

[43]  D. Oprian,et al.  Molecular determinants of human red/green color discrimination , 1994, Neuron.

[44]  S. Firestein,et al.  The olfactory receptor gene superfamily of the mouse , 2002, Nature Neuroscience.

[45]  A. Force,et al.  Preservation of duplicate genes by complementary, degenerative mutations. , 1999, Genetics.

[46]  G. Halder,et al.  twin of eyeless, a second Pax-6 gene of Drosophila, acts upstream of eyeless in the control of eye development. , 1999, Molecular cell.

[47]  Kevin R. Thornton,et al.  Gene duplication and evolution. , 2001, Science.

[48]  A. Wagner,et al.  Decoupled evolution of coding region and mRNA expression patterns after gene duplication: implications for the neutralist-selectionist debate. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[49]  M M Miyamoto,et al.  A likelihood ratio test for evolutionary rate shifts and functional divergence among proteins , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[50]  M. Nei,et al.  Evolution of the major histocompatibility complex: independent origin of nonclassical class I genes in different groups of mammals. , 1989, Molecular biology and evolution.

[51]  Martin A. Nowak,et al.  Evolution of genetic redundancy , 1997, Nature.

[52]  M. Nei,et al.  Positive Darwinian selection after gene duplication in primate ribonuclease genes. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[53]  A. Hughes,et al.  Pattern and timing of gene duplication in animal genomes. , 2001, Genome research.

[54]  T. Jukes,et al.  The neutral theory of molecular evolution. , 2000, Genetics.

[55]  X. Gu,et al.  Functional divergence in the caspase gene family and altered functional constraints: statistical analysis and prediction. , 2001, Genetics.

[56]  M. Gerstein,et al.  Digging for Dead Genes : An Analysis of the Characteristics and Distribution of the Pseudogene Population in the Ribbon Worm Genome , 2000 .

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

[58]  E. Barnard.  Biological Function of Pancreatic Ribonuclease , 1969, Nature.

[59]  A. Wagner.  The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. , 2001, Molecular biology and evolution.

[60]  C. B. Bridges,et al.  THE BAR "GENE" A DUPLICATION. , 1936, Science.

[61]  M. Lynch,et al.  The evolutionary fate and consequences of duplicate genes. , 2000, Science.

[62]  Jianzhi Zhang,et al.  Evolution of the rodent eosinophil-associated RNase gene family by rapid gene sorting and positive selection. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[63]  X. Gu,et al.  Statistical methods for testing functional divergence after gene duplication. , 1999, Molecular biology and evolution.

[64]  Z. Gu,et al.  Evolutionary analyses of the human genome , 2001, Nature.

[65]  E. Eichler,et al.  Segmental duplications and the evolution of the primate genome , 2002, Nature Reviews Genetics.

[66]  E. Boix,et al.  Recombinant Human Eosinophil Cationic Protein , 2000 .

[67]  A. Force,et al.  The probability of preservation of a newly arisen gene duplicate. , 2001, Genetics.

[68]  P. Jekel,et al.  Seminal-type ribonuclease genes in ruminants, sequence conservation without protein expression? , 1999, Gene.

[69]  A. Blancher,et al.  The olfactory receptor gene repertoire in primates and mouse: evidence for reduction of the functional fraction in primates. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[70]  S. G. Stephens.  Possible Significance of Duplication in Evolution , 1951 .

[71]  M. Adams,et al.  Recent Segmental Duplications in the Human Genome , 2002, Science.

[72]  R. Fleischmann,et al.  The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus , 1997, Nature.

[73]  A. Clark,et al.  Differential selection after duplication in mammalian developmental genes. , 2001, Molecular biology and evolution.

[74]  Andreas Wagner,et al.  GenomeHistory: a software tool and its application to fully sequenced genomes. , 2002, Nucleic acids research.

[75]  L. Hurst,et al.  The evolution of concerted evolution , 1998, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[76]  A. Hughes,et al.  Adaptive diversification within a large family of recently duplicated, placentally expressed genes. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[77]  A. Wagner,et al.  Evolution of gene networks by gene duplications: a mathematical model and its implications on genome organization. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[78]  J. Beintema.  The primary structure of langur (Presbytis entellus) pancreatic ribonuclease: adaptive features in digestive enzymes in mammals. , 1990, Molecular biology and evolution.

[79]  Mark Borodovsky,et al.  The complete genome sequence of the gastric pathogen Helicobacter pylori , 1997, Nature.