CoChat
Sign Up
Cited by 877

The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.

Whole-genome duplication in teleost fishes and its evolutionary consequences

Glasauer, Stella M. K., Neuhauss, Stephan C. F.·2014·Molecular Genetics and Genomics
DOI 10.1007/s00438-014-0889-2
Open this paper in CoChat — free account

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1007/s00438-014-0889-2

Cites

7 of 7 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • The emergence of lineage-specific elements has been proposed as a key driver of morphological diversification during vertebrate evolution.

    “The emergence of lineage-specific elements has been proposed as a key driver of morphological diversification during vertebrate evolution.29,36,37,38”

    From A genomic compendium of hundreds of teleost fishes reveals their evolutionary landscape (2026) · cites this paper as [36]

    The section on coding and noncoding regions in duplicate-gene evolution describes how changes to duplicated regulatory elements can enable evolutionary innovation. It does not identify the emergence of lineage-specific elements as a key driver of morphological diversification across vertebrates; its discussion is narrower and framed around genome duplication. (LLM, conf=0.78)

    Experimental — accuracy not yet measured

  • The teleost-specific genome duplication (TGD) event provided an evolutionary context for investigating the origins of conserved elements.

    “The teleost-specific genome duplication (TGD) event36,37,38,39,40,41 provided an evolutionary context for investigating the origins of these conserved elements”

    From A genomic compendium of hundreds of teleost fishes reveals their evolutionary landscape (2026) · cites this paper as [36]

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 143

  1. Ahn BY, Dornfeld KJ, Fagrelius TJ, Livingston DM (1988) Effect of limited homology on gene conversion in a Saccharomyces cerevisiae plasmid recombination system. Mol Cell Biol 8:2442–2448 · DOI
  2. Alexandrou MA, Swartz BA, Matzke NJ, Oakley TH (2013) Genome duplication and multiple evolutionary origins of complex migratory behavior in Salmonidae. Mol Phylogenet Evol 69:514–523 · DOI
  3. Alfaqih MA, Steele CA, Morris RT, Thorgaard GH (2009) Comparative genome mapping reveals evidence of gene conversion between Sox9 paralogs of rainbow trout (Oncorhynchus mykiss). Comp Biochem Physiol Part D Genomics Proteomics 4:147–153 · DOI
  4. Allendorf FW (1978) Protein polymorphism and the rate of loss of duplicate gene expression. Nature 272:76–78 · DOI
  5. Alves G (1999) Systematic biology of gymnotiform and mormyriform electric fishes: phylogenetic relationships, molecular clocks and rates of evolution in the mitochondrial rRNA genes. J Exp Biol 202:1167–1183 · DOI
  6. Amores A, Force A, Yan YL, Joly L, Amemiya C, Fritz A, Ho RK, Langeland J, Prince V, Wang YL, Westerfield M, Ekker M, Postlethwait JH (1998) Zebrafish hox clusters and vertebrate genome evolution. Science 282:1711–1714 · DOI
  7. Aparicio S, Hawker K, Cottage A, Mikawa Y, Zuo L, Venkatesh B, Chen E, Krumlauf R, Brenner S (1997) Organization of the Fugu rubripes Hox clusters: evidence for continuing evolution of vertebrate Hox complexes. Nat Genet 16:79–83 · DOI
  8. Aparicio S, Chapman J, Stupka E, Putnam N, Chia J, Dehal P, Christoffels A, Rash S, Hoon S, Smit A, Gelpke M, Roach J, Oh T, Ho I, Wong M, Detter C, Verhoef F, Predki P, Tay A, Lucas S, Richardson P, Smith S, Clark M, Edwards Y, Doggett N, Zharkikh A, Tavtigian S, Pruss D, Barnstead M, Evans C, Baden H, Powell J, Glusman G, Rowen L, Hood L, Tan Y, Elgar G, Hawkins T, Venkatesh B, Rokhsar D, Brenner S (2002) Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297:1301–1310 · DOI · Paper page
  9. Arnegard ME, Zwickl DJ, Lu Y, Zakon HH (2010) Old gene duplication facilitates origin and diversification of an innovative communication system—twice. Proc Natl Acad Sci USA 107:22172–22177 · DOI
  10. Arratia G (1997) Basal teleosts and teleostean phylogeny. München, Pfeil
  11. Aury J-M, Jaillon O, Duret L, Noel B, Jubin C, Porcel BM, Segurens B, Daubin V, Anthouard V, Aiach N, Arnaiz O, Billaut A, Beisson J, Blanc I, Bouhouche K, Camara F, Duharcourt S, Guigo R, Gogendeau D, Katinka M, Keller A-M, Kissmehl R, Klotz C, Koll F, Le Mouel A, Lepere G, Malinsky S, Nowacki M, Nowak JK, Plattner H, Poulain J, Ruiz F, Serrano V, Zagulski M, Dessen P, Betermier M, Weissenbach J, Scarpelli C, Schachter V, Sperling L, Meyer E, Cohen J, Wincker P (2006) Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature 444:171–178 · DOI
  12. Barbazuk WB, Korf I, Kadavi C, Heyen J, Tate S, Wun E, Bedell JA, McPherson JD, Johnson SL (2000) The syntenic relationship of the zebrafish and human genomes. Genome Res 10:1351–1358 · DOI
  13. Bargelloni L, Scudiero R, Parisi E, Carginale V, Capasso C, Patarnello T (1999) Metallothioneins in antarctic fish: evidence for independent duplication and gene conversion. Mol Biol Evol 16:885–897 · DOI
  14. Barkman T, Zhang J (2009) Evidence for escape from adaptive conflict? Nature 462:E1; discussion E2-3 · DOI
  15. Blomme T, Vandepoele K, de Bodt S, Simillion C, Maere S, de Peer Van, Yves (2006) The gain and loss of genes during 600 million years of vertebrate evolution. Genome Biol 7:R43 · DOI
  16. Braasch I, Salzburger W, Meyer A (2006) Asymmetric evolution in two fish-specifically duplicated receptor tyrosine kinase paralogons involved in teleost coloration. Mol Biol Evol 23:1192–1202 · DOI
  17. Brunet FG, Roest Crollius H, Paris M, Aury J-M, Gibert P, Jaillon O, Laudet V, Robinson-Rechavi M (2006) Gene loss and evolutionary rates following whole-genome duplication in teleost fishes. Mol Biol Evol 23:1808–1816 · DOI
  18. Canestro C, Albalat R, Irimia M, Garcia-Fernandez J (2013) Impact of gene gains, losses and duplication modes on the origin and diversification of vertebrates. Semin Cell Dev Biol 24:83–94 · DOI
  19. Carroll SB (2000) Endless forms: the evolution of gene regulation and morphological diversity. Cell 101:577–580 · DOI
  20. Chain Frederic J J, Dushoff J, Evans BJ (2011) The odds of duplicate gene persistence after polyploidization. BMC Genom 12:599 · DOI
  21. Chambers KE, McDaniell R, Raincrow JD, Deshmukh M, Stadler PF, Chiu C-H (2009) Hox cluster duplication in the basal teleost Hiodon alosoides (Osteoglossomorpha). Theory Biosci 128:109–120 · DOI
  22. Chen JM, Cooper DN, Chuzhanova N, Férec C, Patrinos GP (2007) Gene conversion: mechanisms, evolution and human disease. Nat Rev Genet 8:762–775 · DOI
  23. Chen J-Q, Wu Y, Yang H, Bergelson J, Kreitman M, Tian D (2009) Variation in the ratio of nucleotide substitution and indel rates across genomes in mammals and bacteria. Mol Biol Evol 26:1523–1531 · DOI · Paper page
  24. Christoffels A (2004) Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of Ray-Finned fishes. Mol Biol Evol 21:1146–1151 · DOI
  25. Collery R, McLoughlin S, Vendrell V, Finnegan J, Crabb JW, Saari JC, Kennedy BN (2008) Duplication and divergence of zebrafish CRALBP genes uncovers novel role for RPE-and Muller-CRALBP in cone vision. Invest Ophthalmol Vis Sci 49:3812–3820 · DOI · Paper page
  26. Conant GC, Wolfe KH (2007) Increased glycolytic flux as an outcome of whole-genome duplication in yeast. Mol Syst Biol 3:129 · DOI · Paper page
  27. Cusack BP, Wolfe, KH (2007) When gene marriages don't work out: divorce by subfunctionalization. Trends Genet 23:270–272 · DOI
  28. David L, Blum S, Feldman MW, Lavi U, Hillel J (2003) Recent duplication of the common carp (Cyprinus caprio L.) genome as revealed by analyses of microsatellite loci. Mol Biol Evol 20:1425–1434 · DOI
  29. de Souza Flavio S J, Bumaschny VF, Low MJ, Rubinstein M (2005) Subfunctionalization of expression and peptide domains following the ancient duplication of the proopiomelanocortin gene in teleost fishes. Mol Biol Evol 22:2417–2427 · DOI
  30. Dehal P, Boore JL (2005) Two rounds of whole genome duplication in the ancestral vertebrate. PLoS Biol 3:e314 · DOI · Paper page
  31. Deng C, Cheng C-HC, Ye H, He X, Chen L (2010) Evolution of an antifreeze protein by neofunctionalization under escape from adaptive conflict. Proc Natl Acad Sci USA 107:21593–21598 · DOI
  32. DesMarais DL, Rausher MD (2008) Escape from adaptive conflict after duplication in an anthocyanin pathway gene. Nature 454:762–765 · DOI
  33. Di Donato V, Auer TO, Duroure K, Del Bene F (2013) Characterization of the calcium binding protein family in zebrafish. PLoS ONE 8:e53299 · DOI
  34. Douard V, Brunet F, Boussau B, Ahrens-Fath I, Vlaeminck-Guillem V, Haendler B, Laudet V, Guiguen Y (2008) The fate of the duplicated androgen receptor in fishes: a late neofunctionalization event? BMC Evol Biol 8:336 · DOI
  35. Drouin G (2002) Characterization of the gene conversions between the multigene family members of the yeast genome. J Mol Evol 55:14–23 · DOI
  36. Elliott B, Richardson C, Winderbaum J, Nickoloff JA, Jasin M (1998) Gene conversion tracts from double-strand break repair in mammalian cells. Mol Cell Biol 18:93–101 · DOI
  37. Fawcett JA, Maere S, de Peer Van, Yves (2009) Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event. Proc Natl Acad Sci USA 106:5737–5742 · DOI
  38. Ferris SD, Whitt GS (1977a) Duplicate gene expression in diploid and tetraploid loaches (Cypriniformes, Cobitidae). Biochem Genet 15:1097–1112 · DOI
  39. Ferris SD, Whitt GS (1977b) The evolution of duplicate gene expression in the carp (Cyprinus carpio). Experientia 33:1299–1301 · DOI
  40. Finn RN, Kristoffersen BA (2007) Vertebrate vitellogenin gene duplication in relation to the “3R hypothesis”: correlation to the pelagic egg and the oceanic radiation of teleosts. PLoS ONE 2:e169 · DOI
  41. Finn RN, Ostby GC, Norberg B, Fyhn HJ (2002) In vivo oocyte hydration in Atlantic halibut (Hippoglossus hippoglossus); proteolytic liberation of free amino acids, and ion transport, are driving forces for osmotic water influx. J Exp Biol 205:211–224 · DOI
  42. Fleisch VC, Neuhauss SC (2010) Parallel visual cycles in the zebrafish retina. Prog Retin Eye Res 29:476–486 · DOI
  43. Force A, Lynch M, Pickett FB, Amores A, Yan YL, Postlethwait J (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151:1531–1545 · DOI · Paper page
  44. Freeling M (2008) The evolutionary position of subfunctionalization, downgraded. Genome Dyn 4:25–40 · DOI
  45. Freeling M (2009) Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition. Annu Rev Plant Biol 60:433–453 · DOI
  46. Freeling M, Thomas BC (2006) Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity. Genome Res 16:805–814 · DOI
  47. Gallardo MH, Bickham JW, Honeycutt RL, Ojeda RA, Kohler N (1999) Discovery of tetraploidy in a mammal. Nature 401:341 · DOI
  48. Gallardo MH, Klausel G, Jiménez Al, Bacquet C, González C, Figueroa J, Köhler N, Ojeda R (2004) Whole-genome duplications in South American desert rodents (Octodontidae). Biol J Linn Soc 82:443–451 · DOI
  49. Gates MA, Kim L, Egan ES, Cardozo T, Sirotkin HI, Dougan ST, Lashkari D, Abagyan R, Schier AF, Talbot WS (1999) A genetic linkage map for zebrafish: comparative analysis and localization of genes and expressed sequences. Genome Res 9:334–347 · DOI
  50. Gerrard DT, Meyer A (2007) Positive selection and gene conversion in SPP120, a fertilization-related gene, during the East African cichlid fish radiation. Mol Biol Evol 24:2286–2297 · DOI
  51. Gesemann M, Lesslauer A, Maurer CM, Schönthaler HB, Stephan Neuhauss CF (2010) Phylogenetic analysis of the vertebrate excitatory/neutral amino acid transporter (SLC1/EAAT) family reveals lineage specific subfamilies. BMC Evol Biol 10:117 · DOI
  52. Gout J-F, Kahn D, Duret L (2010) The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution. PLoS Genet 6:e1000944 · DOI
  53. Gregory TR, Nicol JA, Tamm H, Kullman B, Kullman K, Leitch IJ, Murray BG, Kapraun DF, Greilhuber J, Bennett MD (2007) Eukaryotic genome size databases. Nucleic Acids Res 35:D332–D338 · DOI
  54. Guo B, Gan X, He S (2009) Hox genes of the Japanese eel Anguilla japonica and Hox cluster evolution in teleosts. J Exp Zool 9999B, n/a · DOI
  55. Guo B, Zou M, Wagner A (2012) Pervasive indels and their evolutionary dynamics after the fish-specific genome duplication. Mol Biol Evol 29:3005–3022 · DOI
  56. Hakes L, Pinney JW, Lovell SC, Oliver SG, Robertson DL (2007) All duplicates are not equal: the difference between small-scale and genome duplication. Genome Biol 8:R209 · DOI
  57. Hartley S (1986) The chromosomes of salmonid fishes. Biol Rev 62:197–214 · DOI
  58. Haug MF, Gesemann M, Mueller T, Stephan Neuhauss CF (2013) Phylogeny and expression divergence of metabotropic glutamate receptor genes in the brain of zebrafish (Danio rerio). J Comp Neurol 521:1533–1560 · DOI
  59. Henkel CV, Burgerhout E, de Wijze DL, Dirks RP, Minegishi Y, Jansen HJ, Spaink HP, Dufour S, Weltzien F-A, Tsukamoto K, van den Thillart GEEJM, Schubert M (2012) Primitive duplicate hox clusters in the European Eel’s genome. PLoS ONE 7:e32231 · DOI
  60. Hoegg S, Meyer A (2007) Phylogenomic analyses of KCNA gene clusters in vertebrates: why do gene clusters stay intact? BMC Evol Biol 7:139 · DOI
  61. Hoekstra HE, Coyne JA (2007) The locus of evolution: evo devo and the genetics of adaptation. Evolution 61:995–1016 · DOI
  62. Huang R, Hippauf F, Rohrbeck D, Haustein M, Wenke K, Feike J, Sorrelle N, Piechulla B, Barkman TJ (2012) Enzyme functional evolution through improved catalysis of ancestrally nonpreferred substrates. Proc Natl Acad Sci USA 109:2966–2971 · DOI
  63. Hufton AL, Mathia S, Braun H, Georgi U, Lehrach H, Vingron M, Poustka AJ, Panopoulou G (2009) Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention. Genome Res 19:2036–2051 · DOI
  64. Hughes AL (1994) The evolution of functionally novel proteins after gene duplication. Proc Biol Sci 256:119–124 · DOI
  65. Innan H (2009) Population genetic models of duplicated genes. Genetica 137:19–37 · DOI
  66. Innan H, Kondrashov F (2010) The evolution of gene duplications: classifying and distinguishing between models. Nat Rev Genet 11:4 · DOI
  67. Jaillon O, Aury J-M, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, Vezzi A, Legeai F, Hugueney P, Dasilva C, Horner D, Mica E, Jublot D, Poulain J, Bruyere C, Billault A, Segurens B, Gouyvenoux M, Ugarte E, Cattonaro F, Anthouard V, Vico V, Del Fabbro C, Alaux M, Di Gaspero G, Dumas V, Felice N, Paillard S, Juman I, Moroldo M, Scalabrin S, Canaguier A, Le Clainche I, Malacrida G, Durand E, Pesole G, Laucou V, Chatelet P, Merdinoglu D, Delledonne M, Pezzotti M, Lecharny A, Scarpelli C, Artiguenave F, Pe ME, Valle G, Morgante M, Caboche M, Adam-Blondon A-F, Weissenbach J, Quetier F, Wincker P (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449:463–467 · DOI
  68. Jiang H, Blouin C (2007) Insertions and the emergence of novel protein structure: a structure-based phylogenetic study of insertions. BMC Bioinformatics 8:444 · DOI
  69. Jimenez-Delgado S, Pascual-Anaya J, Garcia-Fernandez J (2009) Implications of duplicated cis-regulatory elements in the evolution of metazoans: the DDI model or how simplicity begets novelty. Brief Funct Genomic Proteomic 8:266–275 · DOI
  70. Johnson KR, Wright JE Jr, May B (1987) Linkage relationships reflecting ancestral tetraploidy in salmonid fish. Genetics 116:579–591 · DOI
  71. Jovelin R, He X, Amores A, Yan Y-L, Shi R, Qin B, Roe B, Cresko WA, Postlethwait JH (2007) Duplication and divergence of fgf8 functions in teleost development and evolution. J Exp Zool B Mol Dev Evol 308:730–743 · DOI
  72. Kasahara M, Naruse K, Sasaki S, Nakatani Y, Qu W, Ahsan B, Yamada T, Nagayasu Y, Doi K, Kasai Y, Jindo T, Kobayashi D, Shimada A, Toyoda A, Kuroki Y, Fujiyama A, Sasaki T, Shimizu A, Asakawa S, Shimizu N, Hashimoto S-I, Yang J, Lee Y, Matsushima K, Sugano S, Sakaizumi M, Narita T, Ohishi K, Haga S, Ohta F, Nomoto H, Nogata K, Morishita T, Endo T, Shin-I T, Takeda H, Morishita S, Kohara Y (2007) The medaka draft genome and insights into vertebrate genome evolution. Nature 447:714–719 · DOI · Paper page
  73. Kassahn KS, Dang VT, Wilkins SJ, Perkins AC, Ragan MA (2009) Evolution of gene function and regulatory control after whole-genome duplication: comparative analyses in vertebrates. Genome Res 19:1404–1418 · DOI
  74. Kastenhuber E, Gesemann M, Mickoleit M, Stephan Neuhauss CF (2013) Phylogenetic analysis and expression of zebrafish transient receptor potential melastatin family genes. Dev Dyn 242:1236–1249 · DOI
  75. Kellis M, Birren BW, Lander ES (2004) Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428:617–624 · DOI
  76. Kohn M, Hogel J, Vogel W, Minich P, Kehrer-Sawatzki H, Jennifer Graves AM, Hameister H (2006) Reconstruction of a 450-My-old ancestral vertebrate protokaryotype. Trends Genet 22:203–210 · DOI · Paper page
  77. Kuraku S, Meyer A, Kuratani S (2009) Timing of genome duplications relative to the origin of the vertebrates: did cyclostomes diverge before or after? Mol Biol Evol 26:47–59 · DOI
  78. La Fleur GJ Jr, Raldua D, Fabra M, Carnevali O, Denslow N, Wallace RA, Cerda J (2005) Derivation of major yolk proteins from parental vitellogenins and alternative processing during oocyte maturation in Fundulus heteroclitus. Biol Reprod 73:815–824 · DOI
  79. Lynch M, Force A (2000) The probability of duplicate gene preservation by subfunctionalization. Genetics 154:459–473 · DOI
  80. Lynch VJ, Wagner GP (2008) Resurrecting the role of transcription factor change in developmental evolution. Evolution 62:2131–2154 · DOI
  81. Mable B (2004) ‘Why polyploidy is rarer in animals than in plants’: myths and mechanisms. Biol J Linn Soc 82:453–466 · DOI
  82. Macqueen DJ, Johnston IA (2008) Evolution of follistatin in teleosts revealed through phylogenetic, genomic and expression analyses. Dev Genes Evol 218:1–14 · DOI
  83. Macqueen DJ, Johnston IA (2014) A well-constrained estimate for the timing of the salmonid whole genome duplication reveals major decoupling from species diversification. Proc Biol Sci 281:20132881 · DOI
  84. Maere S, de Bodt S, Raes J, Casneuf T, van Montagu M, Kuiper M, de Peer Van, Yves (2005) Modeling gene and genome duplications in eukaryotes. Proc Natl Acad Sci USA 102:5454–5459 · DOI
  85. Mansai SP, Innan H (2010) The power of the methods for detecting interlocus gene conversion. Genetics 184:517–527 · DOI
  86. Matsubara T, Ohkubo N, Andoh T, Sullivan CV, Hara A (1999) Two forms of vitellogenin, yielding two distinct lipovitellins, play different roles during oocyte maturation and early development of barfin flounder, Verasper moseri, a marine teleost that spawns pelagic eggs. Dev Biol 213:18–32 · DOI
  87. McClintock JM, Carlson R, Mann DM, Prince VE (2001) Consequences of Hox gene duplication in the vertebrates: an investigation of the zebrafish Hox paralogue group 1 genes. Development 128:2471–2484 · DOI
  88. McFarlane L, Svingen T, Braasch I, Koopman P, Schartl M, Wilhelm D (2011) Expansion of the Ago gene family in the teleost clade. Dev Genes Evol 221:95–104 · DOI
  89. McGuigan K, Phillips PC, Postlethwait JH (2004) Evolution of sarcomeric myosin heavy chain genes: evidence from fish. Mol Biol Evol 21:1042–1056 · DOI
  90. Misof BY, Wagner GP (1996) Evidence for four Hox clusters in the killifish Fundulus heteroclitus (teleostei). Mol Phylogenet Evol 5:309–322 · DOI
  91. Mondragon-Palomino M, Gaut BS (2005) Gene conversion and the evolution of three leucine-rich repeat gene families in Arabidopsis thaliana. Mol Biol Evol 22:2444–2456 · DOI
  92. Naruse K, Tanaka M, Mita K, Shima A, Postlethwait J, Mitani H (2004) A medaka gene map: the trace of ancestral vertebrate proto-chromosomes revealed by comparative gene mapping. Genome Res 14:820–828 · DOI
  93. Near TJ, Eytan RI, Dornburg A, Kuhn KL, Moore JA, Davis MP, Wainwright PC, Friedman M, Smith WL (2012) Resolution of ray-finned fish phylogeny and timing of diversification. Proc Natl Acad Sci USA 109:13698–13703 · DOI · Paper page
  94. Njolstad PR, Molven A, Hordvik I, Apold J, Fjose A (1988) Primary structure, developmentally regulated expression and potential duplication of the zebrafish homeobox gene ZF-21. Nucleic Acids Res 16:9097–9111 · DOI
  95. Noonan JP, Grimwood J, Schmutz J, Dickson M, Myers RM (2004) Gene conversion and the evolution of protocadherin gene cluster diversity. Genome Res 14:354–366 · DOI
  96. Ohno S (1970a) Evolution by gene duplication. Springer, New York · DOI · Paper page
  97. Ohno S (1970b) The enormous diversity in genome sizes of fish as a reflection of nature’s extensive experiments with gene duplication. Trans Am Fish Soc 99:120–130 · DOI
  98. Ohno S, Muramoto J, Lawrence C, Atkin NB (1967) Diploid-tetraploid relationship among old-world members of the fish family Cyprinidae. Chromosoma 23:1–9 · DOI
  99. Osborn TC, Pires JC, Birchler JA, Auger DL, Chen ZJ, Lee H-S, Comai L, Madlung A, Doerge RW, Colot V, Martienssen RA (2003) Understanding mechanisms of novel gene expression in polyploids. Trends Genet 19:141–147 · DOI
  100. Otto SP, Whitton J (2000) Polyploid incidence and evolution. Annu Rev Genet 34:401–437 · DOI · Paper page
  101. Papp B, Pal C, Hurst LD (2003) Dosage sensitivity and the evolution of gene families in yeast. Nature 424:194–197 · DOI · Paper page
  102. Phillips R, Rab P (2001) Chromosome evolution in the Salmonidae (Pisces): an update. Biol Rev Camb Philos Soc 76:1–25 · DOI
  103. Phillips RB, Keatley KA, Morasch MR, Ventura AB, Lubieniecki KP, Koop BF, Danzmann RG, Davidson WS (2009) Assignment of Atlantic salmon (Salmo salar) linkage groups to specific chromosomes: conservation of large syntenic blocks corresponding to whole chromosome arms in rainbow trout (Oncorhynchus mykiss). BMC Genet 10:46 · DOI
  104. Postlethwait JH, Woods IG, Ngo-Hazelett P, Yan YL, Kelly PD, Chu F, Huang H, Hill-Force A, Talbot WS (2000) Zebrafish comparative genomics and the origins of vertebrate chromosomes. Genome Res 10:1890–1902 · DOI · Paper page
  105. Postlethwait J, Amores A, Cresko W, Singer A, Yan Y-L (2004) Subfunction partitioning, the teleost radiation and the annotation of the human genome. Trends Genet 20:481–490 · DOI
  106. Prince Y, Joly L, Ekker M, Ho R (1998) Zebrafish hox genes: genomic organization and modified colinear expression patterns in the trunk. Development 125:407–420 · DOI
  107. Prohaska SJ, Stadler PF (2004) The duplication of the hox gene clusters in teleost fishes. Theory Biosci 23:89–110 · DOI
  108. Putnam NH, Butts T, David Ferrier EK, Furlong RF, Hellsten U, Kawashima T, Robinson-Rechavi M, Shoguchi E, Terry A, Yu J-K, Benito-Gutierrez EL, Dubchak I, Garcia-Fernandez J, Gibson-Brown JJ, Grigoriev IV, Horton AC, de Jong Pieter J, Jurka J, Kapitonov VV, Kohara Y, Kuroki Y, Lindquist E, Lucas S, Osoegawa K, Pennacchio LA, Salamov AA, Satou Y, Sauka-Spengler T, Schmutz J, Shin-I T, Toyoda A, Bronner-Fraser M, Fujiyama A, Holland LZ, Peter Holland WH, Satoh N, Rokhsar DS (2008) The amphioxus genome and the evolution of the chordate karyotype. Nature 453:1064–1071 · DOI
  109. Renninger SL, Gesemann M, Stephan Neuhauss CF (2011) Cone arrestin confers cone vision of high temporal resolution in zebrafish larvae. Eur J Neurosci 33:658–667 · DOI
  110. Rozen S, Skaletsky H, Marszalek JD, Minx PJ, Cordum HS, Waterston RH, Wilson RK, Page DC (2003) Abundant gene conversion between arms of palindromes in human and ape Y chromosomes. Nature 423:873–876 · DOI
  111. Santini F, Harmon LJ, Carnevale G, Alfaro ME (2009) Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes. BMC Evol Biol 9:194 · DOI
  112. Sato Y, Hashiguchi Y, Nishida M (2009) Temporal pattern of loss/persistence of duplicate genes involved in signal transduction and metabolic pathways after teleost-specific genome duplication. BMC Evol Biol 9:127 · DOI
  113. Scannell DR, Byrne KP, Gordon JL, Wong S, Wolfe KH (2006) Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts. Nature 440:341–345 · DOI
  114. Scannell DR, Butler G, Wolfe KH (2007) Yeast genome evolution–the origin of the species. Yeast 24:929–942 · DOI
  115. Schartl M, Walter RB, Shen Y, Garcia T, Catchen J, Amores A, Braasch I, Chalopin D, Volff J-N, Lesch K-P, Bisazza A, Minx P, Hillier L, Wilson RK, Fuerstenberg S, Boore J, Searle S, Postlethwait JH, Warren WC (2013) The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits. Nat Genet 45:567–572 · DOI
  116. Schranz ME, Mohammadin S, Edger PP (2012) Ancient whole genome duplications, novelty and diversification: the WGD radiation lag-time model. Curr Opin Plant Biol 15:147–153 · DOI
  117. Semon M, Wolfe KH (2008) Preferential subfunctionalization of slow-evolving genes after allopolyploidization in Xenopus laevis. Proc Natl Acad Sci USA 105:8333–8338 · DOI
  118. Sémon M, Wolfe KH (2007) Rearrangement rate following the whole-genome duplication in teleosts. Mol Biol Evol 24:860–867 · DOI
  119. Semple C, Wolfe KH (1999) Gene duplication and gene conversion in the Caenorhabditis elegans genome. J Mol Evol 48:555–564 · DOI
  120. Seoighe C, Wolfe KH (1999) Yeast genome evolution in the post-genome era. Curr Opin Microbiol 2:548–554 · DOI
  121. Sikosek T, Chan HS, Bornberg-Bauer E (2012) Escape from adaptive conflict follows from weak functional trade-offs and mutational robustness. Proc Natl Acad Sci USA 109:14888–14893 · DOI
  122. Smith SA, Beaulieu JM, Stamatakis A, Donoghue MJ (2011) Understanding angiosperm diversification using small and large phylogenetic trees. Am J Bot 98:404–414 · DOI
  123. Soltis DE, Albert VA, Leebens-Mack J, Bell CD, Paterson AH, Zheng C, Sankoff D, Depamphilis CW, Wall PK, Soltis PS (2009) Polyploidy and angiosperm diversification. Am J Bot 96:336–348 · DOI
  124. Sugino RP, Innan H (2006) Selection for more of the same product as a force to enhance concerted evolution of duplicated genes. Trends Genet 22:642–644 · DOI
  125. Tang H, Bowers JE, Wang X, Ming R, Alam M, Paterson AH (2008) Synteny and collinearity in plant genomes. Science 320:486–488 · DOI
  126. Taylor JS (2003) Genome duplication, a trait shared by 22,000 species of ray-finned fish. Genome Res 13:382–390 · DOI
  127. Taylor JS, Van de Peer Y, Braasch I, Meyer A (2001) Comparative genomics provides evidence for an ancient genome duplication event in fish. Philos Trans R Soc Lond B Biol Sci 356:1661–1679 · DOI
  128. Teshima KM, Innan H (2008) Neofunctionalization of duplicated genes under the pressure of gene conversion. Genetics 178:1385–1398 · DOI
  129. Tian D, Wang Q, Zhang P, Araki H, Yang S, Kreitman M, Nagylaki T, Hudson R, Bergelson J, Chen J-Q (2008) Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes. Nature 455:105–108 · DOI
  130. Uyeno T, Smith GR (1972) Tetraploid origin of the karyotype of catostomid fishes. Science 175:644–646 · DOI
  131. Vandepoele K, de Vos W, Taylor JS, Meyer A, de Peer Van, Yves (2004) Major events in the genome evolution of vertebrates: paranome age and size differ considerably between ray-finned fishes and land vertebrates. Proc Natl Acad Sci USA 101:1638–1643 · DOI
  132. Volff J-N (2005) Genome evolution and biodiversity in teleost fish. Heredity (Edinb) 94:280–294 · DOI
  133. von Niederhäusern V, Kastenhuber E, Stäuble A, Gesemann M, Stephan Neuhauss CF (2013) Phylogeny and expression of canonical transient receptor potential (TRPC) genes in developing zebrafish. Dev Dyn 242:1427–1441 · DOI
  134. Wang J-T, Li J-T, Zhang X-F, Sun X-W (2012) Transcriptome analysis reveals the time of the fourth round of genome duplication in common carp (Cyprinus carpio). BMC Genom 13:96 · DOI
  135. Weadick CJ, Chang BS (2012) Complex patterns of divergence among green-sensitive (RH2a) African cichlid opsins revealed by Clade model analyses. BMC Evol Biol 12:206 · DOI
  136. Windsor DJ, Owens GL (2009) The opsin repertoire of Jenynsia onca: a new perspective on gene duplication and divergence in livebearers. BMC Res Notes 2:159 · DOI
  137. Wittbrodt J, Meyer A, Schartl M (1998) More genes in fish? BioEssays 20:511–515 · DOI
  138. Wolfe KH, Shields DC (1997) Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387:708–713 · DOI · Paper page
  139. Woods IG, Wilson C, Friedlander B, Chang P, Reyes DK, Nix R, Kelly PD, Chu F, Postlethwait JH, Talbot WS (2005) The zebrafish gene map defines ancestral vertebrate chromosomes. Genome Res 15:1307–1314 · DOI
  140. Yu W-P, Yew K, Rajasegaran V, Venkatesh B (2007) Sequencing and comparative analysis of fugu protocadherin clusters reveal diversity of protocadherin genes among teleosts. BMC Evol Biol 7:49 · DOI
  141. Zakon HH, Lu Y, Zwickl DJ, Hillis DM (2006) Sodium channel genes and the evolution of diversity in communication signals of electric fishes: convergent molecular evolution. Proc Natl Acad Sci USA 103:3675–3680 · DOI
  142. Zhang X, Zhang Y, Zheng X, Kuang Y, Zhao Z, Zhao L, Li C, Jiang L, Cao D, Lu C, Xu P, Sun X (2013) A consensus linkage map provides insights on genome character and evolution in common carp (Cyprinus carpio L.). Mar Biotechnol 15:275–312 · DOI
  143. Zhou R, Moshgabadi N, Adams KL (2011) Extensive changes to alternative splicing patterns following allopolyploidy in natural and resynthesized polyploids. Proc Natl Acad Sci USA 108:16122–16127 · DOI

Cited by

Sorted by citations

Metadata

Authors
Glasauer, S. M. K., & Neuhauss, S. C. F.
Venue
Molecular Genetics and Genomics
Publisher
Springer Science and Business Media LLC
Published
2014-08-05
Volume
289
Issue
6
Pages
1045-1060
ISSN
  • 1617-4615
  • 1617-4623
DOI
10.1007/s00438-014-0889-2
Cited by
877
References
7
Language
en
Licence
www.springer.com/tdm (tdm)

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review