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Volumn 88, Issue 2, 2010, Pages 169-188

Teleost fish with specific genome duplication as unique models of vertebrate evolution

Author keywords

3R WGD; Ancestral karyotype; Chromosomal evolution; Gene duplication; Teleost diversity

Indexed keywords

CHROMOSOME; DIVERGENCE; EVOLUTIONARY THEORY; GENOME; GENOMICS; KARYOTYPE; SPECIATION (BIOLOGY); SPECIES DIVERSITY; TELEOST;

EID: 77951766330     PISSN: 03781909     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10641-010-9628-7     Document Type: Article
Times cited : (75)

References (156)
  • 1
    • 0036578891 scopus 로고    scopus 로고
    • Evidence of en bloc duplication in vertebrate genomes
    • doi:10.1038/ng855
    • Abi-Rached L, Gilles A, Shiina T, Pontarotti P, Inoko H (2002) Evidence of en bloc duplication in vertebrate genomes. Nat Genet 31: 100-105. doi: 10. 1038/ng855.
    • (2002) Nat Genet , vol.31 , pp. 100-105
    • Abi-Rached, L.1    Gilles, A.2    Shiina, T.3    Pontarotti, P.4    Inoko, H.5
  • 2
    • 0002590589 scopus 로고
    • Tetraploidy and the evolution of salmonid fishes
    • B. J. Turner (Ed.), New York: Plenum Press
    • Allendorf FW, Thorgaard GH (1984) Tetraploidy and the evolution of salmonid fishes. In: Turner BJ (ed) The evolutionary genetics of fishes. Plenum Press, New York, pp 1-53.
    • (1984) The Evolutionary Genetics of Fishes , pp. 1-53
    • Allendorf, F.W.1    Thorgaard, G.H.2
  • 5
    • 0347135956 scopus 로고    scopus 로고
    • Developmental roles of pufferfish Hox clusters and genome evolution in ray-fin fish
    • doi:10.1101/gr.1717804
    • Amores A, Suzuki T, Yan YL, Pomeroy J, Singer A, Amemiya C, Postlethwait JH (2004) Developmental roles of pufferfish Hox clusters and genome evolution in ray-fin fish. Genome Res 14: 1-10. doi: 10. 1101/gr. 1717804.
    • (2004) Genome Res , vol.14 , pp. 1-10
    • Amores, A.1    Suzuki, T.2    Yan, Y.L.3    Pomeroy, J.4    Singer, A.5    Amemiya, C.6    Postlethwait, J.H.7
  • 6
    • 0033974766 scopus 로고    scopus 로고
    • Vertebrate evolution: Recent perspectives from fish
    • doi:10.1016/S0168-9525(99)01934-4
    • Aparicio S (2000) Vertebrate evolution: recent perspectives from fish. Trends Genet 16: 54-56. doi: 10. 1016/S0168-9525(99)01934-4.
    • (2000) Trends Genet , vol.16 , pp. 54-56
    • Aparicio, S.1
  • 7
    • 0031006339 scopus 로고    scopus 로고
    • Organization of the Fugu rubripes Hox clusters: Evidence for continuing evolution of vertebrate Hox complexes
    • doi:10.1038/ng0597-79
    • 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: 10. 1038/ng0597-79.
    • (1997) Nat Genet , vol.16 , pp. 79-83
    • Aparicio, S.1    Hawker, K.2    Cottage, A.3    Mikawa, Y.4    Zuo, L.5    Venkatesh, B.6    Chen, E.7    Krumlauf, R.8    Brenner, S.9
  • 9
    • 0015575838 scopus 로고
    • Phosphoglucose isomerase gene duplication in the bony fishes: An evolutionary history
    • doi:10.1007/BF00485540
    • Avise JC, Kitto GB (1973) Phosphoglucose isomerase gene duplication in the bony fishes: an evolutionary history. Biochem Genet 8: 113-132. doi: 10. 1007/BF00485540.
    • (1973) Biochem Genet , vol.8 , pp. 113-132
    • Avise, J.C.1    Kitto, G.B.2
  • 10
    • 49249122999 scopus 로고    scopus 로고
    • Mitogenomic evaluation of the historical biogeography of cichlids toward reliable dating of teleostean divergences
    • doi:10.1186/1471-2148-8-215
    • Azuma Y, Kumazawa Y, Miya M, Mabuchi K, Nishida M (2008) Mitogenomic evaluation of the historical biogeography of cichlids toward reliable dating of teleostean divergences. BMC Evol Biol 8: 215. doi: 10. 1186/1471-2148-8-215.
    • (2008) BMC Evol Biol , vol.8 , pp. 215
    • Azuma, Y.1    Kumazawa, Y.2    Miya, M.3    Mabuchi, K.4    Nishida, M.5
  • 12
    • 33845883023 scopus 로고    scopus 로고
    • Paleontological evidence to date the tree of life
    • doi:10.1093/molbev/msl150
    • Benton MJ, Donoghue PC (2007) Paleontological evidence to date the tree of life. Mol Biol Evol 24: 26-53. doi: 10. 1093/molbev/msl150.
    • (2007) Mol Biol Evol , vol.24 , pp. 26-53
    • Benton, M.J.1    Donoghue, P.C.2
  • 13
    • 33646885704 scopus 로고    scopus 로고
    • Asymmetric evolution in two fish-specifically duplicated receptor tyrosine kinase paralogons involved in teleost coloration
    • doi:10.1093/molbev/msk003
    • 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: 10. 1093/molbev/msk003.
    • (2006) Mol Biol Evol , vol.23 , pp. 1192-1202
    • Braasch, I.1    Salzburger, W.2    Meyer, A.3
  • 14
    • 34250182014 scopus 로고    scopus 로고
    • Evolution of pigment synthesis pathways by gene and genome duplication in fish
    • doi:10.1186/1471-2148-7-74
    • Braasch I, Schartl M, Volff JN (2007) Evolution of pigment synthesis pathways by gene and genome duplication in fish. BMC Evol Biol 7: 74. doi: 10. 1186/1471-2148-7-74.
    • (2007) BMC Evol Biol , vol.7 , pp. 74
    • Braasch, I.1    Schartl, M.2    Volff, J.N.3
  • 15
    • 77951764763 scopus 로고    scopus 로고
    • Pigmentation pathway evolution after whole genome duplication in fish
    • in press. doi: 10.1093/gbe/evp050
    • Braasch I, Brunet F, Volff JN, Schartl M (2009) Pigmentation pathway evolution after whole genome duplication in fish. Genome Biol Evol, in press. doi: 10.1093/gbe/evp050.
    • (2009) Genome Biol Evol
    • Braasch, I.1    Brunet, F.2    Volff, J.N.3    Schartl, M.4
  • 16
    • 67349223989 scopus 로고    scopus 로고
    • Hox cluster duplication in the basal teleost Hiodon alosoides (Osteoglossomorpha)
    • doi:10.1007/s12064-009-0056-1
    • Chambers KE, McDaniell R, Raincrow JD, Deshmukh M, Stadler PF, Chiu CH (2009) Hox cluster duplication in the basal teleost Hiodon alosoides (Osteoglossomorpha). Theory Biosci 128: 109-120. doi: 10. 1007/s12064-009-0056-1.
    • (2009) Theory Biosci , vol.128 , pp. 109-120
    • Chambers, K.E.1    McDaniell, R.2    Raincrow, J.D.3    Deshmukh, M.4    Stadler, P.F.5    Chiu, C.H.6
  • 17
    • 0033619225 scopus 로고    scopus 로고
    • Evolution of an antifreeze glycoprotein
    • doi:10.1038/46721
    • Cheng CH, Chen L (1999) Evolution of an antifreeze glycoprotein. Nature 401: 443-444. doi: 10. 1038/46721.
    • (1999) Nature , vol.401 , pp. 443-444
    • Cheng, C.H.1    Chen, L.2
  • 18
    • 0037117587 scopus 로고    scopus 로고
    • Molecular evolution of the HoxA cluster in the three major gnathostome lineages
    • doi:10.1073/pnas.052709899
    • Chiu CH, Amemiya C, Dewar K, Kim CB, Ruddle FH, Wagner GP (2002) Molecular evolution of the HoxA cluster in the three major gnathostome lineages. Proc Natl Acad Sci U S A 99: 5492-5497. doi: 10. 1073/pnas. 052709899.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 5492-5497
    • Chiu, C.H.1    Amemiya, C.2    Dewar, K.3    Kim, C.B.4    Ruddle, F.H.5    Wagner, G.P.6
  • 20
    • 2442707716 scopus 로고    scopus 로고
    • Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes
    • doi:10.1093/molbev/msh114
    • Christoffels A, Koh EG, Chia JM, Brenner S, Aparicio S, Venkatesh B (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: 10. 1093/molbev/msh114.
    • (2004) Mol Biol Evol , vol.21 , pp. 1146-1151
    • Christoffels, A.1    Koh, E.G.2    Chia, J.M.3    Brenner, S.4    Aparicio, S.5    Venkatesh, B.6
  • 21
    • 33644553076 scopus 로고    scopus 로고
    • Tetraodon genome analysis provides further evidence for whole-genome duplication in the ray-finned fish
    • doi:10.1016/j.cbd.2005.06.001
    • Christoffels A, Brenner S, Venkatesh B (2006) Tetraodon genome analysis provides further evidence for whole-genome duplication in the ray-finned fish. Comp Biochem Physiol Part D Genomics Proteomics 1: 13-19. doi: 10. 1016/j. cbd. 2005. 06. 001.
    • (2006) Comp Biochem Physiol Part D Genomics Proteomics , vol.1 , pp. 13-19
    • Christoffels, A.1    Brenner, S.2    Venkatesh, B.3
  • 22
    • 56549119570 scopus 로고    scopus 로고
    • Turning a hobby into a job: How duplicated genes find new functions
    • doi:10.1038/nrg2482
    • Conant GC, Wolfe KH (2008) Turning a hobby into a job: how duplicated genes find new functions. Nat Rev Genet 9: 938-950. doi: 10. 1038/nrg2482.
    • (2008) Nat Rev Genet , vol.9 , pp. 938-950
    • Conant, G.C.1    Wolfe, K.H.2
  • 23
    • 33646572856 scopus 로고    scopus 로고
    • What is the role of genome duplication in the evolution of complexity and diversity?
    • doi:10.1093/molbev/msj083
    • Crow KD, Wagner GP (2006) What is the role of genome duplication in the evolution of complexity and diversity? Mol Biol Evol 23: 887-892. doi: 10. 1093/molbev/msj083.
    • (2006) Mol Biol Evol , vol.23 , pp. 887-892
    • Crow, K.D.1    Wagner, G.P.2
  • 24
    • 28944450051 scopus 로고    scopus 로고
    • The "fish-specific" Hox cluster duplication is coincident with the origin of teleosts
    • doi:10.1093/molbev/msj020
    • Crow KD, Stadler PF, Lynch VJ, Amemiya C, Wagner GP (2006) The "fish-specific" Hox cluster duplication is coincident with the origin of teleosts. Mol Biol Evol 23: 121-136. doi: 10. 1093/molbev/msj020.
    • (2006) Mol Biol Evol , vol.23 , pp. 121-136
    • Crow, K.D.1    Stadler, P.F.2    Lynch, V.J.3    Amemiya, C.4    Wagner, G.P.5
  • 25
    • 38149117037 scopus 로고    scopus 로고
    • Bursts and horizontal evolution of DNA transposons in the speciation of pseudotetraploid salmonids
    • de Boer JG, Yazawa R, Davidson WS, Koop BF (2007) Bursts and horizontal evolution of DNA transposons in the speciation of pseudotetraploid salmonids. BMC Genomics 8: 422.
    • (2007) BMC Genomics , vol.8 , pp. 422
    • de Boer, J.G.1    Yazawa, R.2    Davidson, W.S.3    Koop, B.F.4
  • 26
    • 26444603772 scopus 로고    scopus 로고
    • Two rounds of whole genome duplication in the ancestral vertebrate
    • doi:10.1371/journal.pbio.0030314
    • Dehal P, Boore JL (2005) Two rounds of whole genome duplication in the ancestral vertebrate. PLoS Biol 3: e314. doi: 10. 1371/journal. pbio. 0030314.
    • (2005) PLoS Biol , vol.3
    • Dehal, P.1    Boore, J.L.2
  • 27
    • 20144366981 scopus 로고    scopus 로고
    • Genome duplication, extinction and vertebrate evolution
    • doi:10.1016/j.tree.2005.04.008
    • Donoghue PC, Purnell MA (2005) Genome duplication, extinction and vertebrate evolution. Trends Ecol Evol 20: 312-319. doi: 10. 1016/j. tree. 2005. 04. 008.
    • (2005) Trends Ecol Evol , vol.20 , pp. 312-319
    • Donoghue, P.C.1    Purnell, M.A.2
  • 29
    • 0001495737 scopus 로고
    • The roles of speciation and divergence time in the loss of duplicate gene expression
    • doi:10.1016/0040-5809(79)90030-3
    • Ferris SD, Portnoy SL, Whitt GS (1979) The roles of speciation and divergence time in the loss of duplicate gene expression. Theor Popul Biol 15: 114-139. doi: 10. 1016/0040-5809(79)90030-3.
    • (1979) Theor Popul Biol , vol.15 , pp. 114-139
    • Ferris, S.D.1    Portnoy, S.L.2    Whitt, G.S.3
  • 34
    • 0033957089 scopus 로고    scopus 로고
    • Evidence in favour of ancient octaploidy in the vertebrate genome
    • Gibson TJ, Spring J (2000) Evidence in favour of ancient octaploidy in the vertebrate genome. Biochem Soc Trans 28: 259-264.
    • (2000) Biochem Soc Trans , vol.28 , pp. 259-264
    • Gibson, T.J.1    Spring, J.2
  • 36
    • 34548390127 scopus 로고    scopus 로고
    • Evolution of trace amine associated receptor (TAAR) gene family in vertebrates: Lineage-specific expansions and degradations of a second class of vertebrate chemosensory receptors expressed in the olfactory epithelium
    • doi:10.1093/molbev/msm140
    • Hashiguchi Y, Nishida M (2007) Evolution of trace amine associated receptor (TAAR) gene family in vertebrates: lineage-specific expansions and degradations of a second class of vertebrate chemosensory receptors expressed in the olfactory epithelium. Mol Biol Evol 24: 2099-2107. doi: 10. 1093/molbev/msm140.
    • (2007) Mol Biol Evol , vol.24 , pp. 2099-2107
    • Hashiguchi, Y.1    Nishida, M.2
  • 37
    • 15544389841 scopus 로고    scopus 로고
    • Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution
    • doi:10.1534/genetics.104.037051
    • He X, Zhang J (2005) Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution. Genetics 169: 1157-1164. doi: 10. 1534/genetics. 104. 037051.
    • (2005) Genetics , vol.169 , pp. 1157-1164
    • He, X.1    Zhang, J.2
  • 38
    • 0037383240 scopus 로고    scopus 로고
    • Genomic clocks and evolutionary timescales
    • doi:10.1016/S0168-9525(03)00053-2
    • Hedges SB, Kumar S (2003) Genomic clocks and evolutionary timescales. Trends Genet 19: 200-206. doi: 10. 1016/S0168-9525(03)00053-2.
    • (2003) Trends Genet , vol.19 , pp. 200-206
    • Hedges, S.B.1    Kumar, S.2
  • 39
    • 22144452139 scopus 로고    scopus 로고
    • Hox clusters as models for vertebrate genome evolution
    • doi:10.1016/j.tig.2005.06.004
    • Hoegg S, Meyer A (2005) Hox clusters as models for vertebrate genome evolution. Trends Genet 21: 421-424. doi: 10. 1016/j. tig. 2005. 06. 004.
    • (2005) Trends Genet , vol.21 , pp. 421-424
    • Hoegg, S.1    Meyer, A.2
  • 40
    • 34548732734 scopus 로고    scopus 로고
    • Phylogenomic analyses of KCNA clusters in vertebrates: Why do some clusters stay intact?
    • doi:10.1186/1471-2148-7-139
    • Hoegg S, Meyer A (2007) Phylogenomic analyses of KCNA clusters in vertebrates: why do some clusters stay intact? BMC Evol Biol 7: 139. doi: 10. 1186/1471-2148-7-139.
    • (2007) BMC Evol Biol , vol.7 , pp. 139
    • Hoegg, S.1    Meyer, A.2
  • 41
    • 4143134848 scopus 로고    scopus 로고
    • Phylogenetic timing of the fish-specific genome duplication correlates with the diversification of teleost fish
    • doi:10.1007/s00239-004-2613-z
    • Hoegg S, Brinkmann H, Taylor JS, Meyer A (2004) Phylogenetic timing of the fish-specific genome duplication correlates with the diversification of teleost fish. J Mol Evol 59: 190-203. doi: 10. 1007/s00239-004-2613-z.
    • (2004) J Mol Evol , vol.59 , pp. 190-203
    • Hoegg, S.1    Brinkmann, H.2    Taylor, J.S.3    Meyer, A.4
  • 43
    • 0347799299 scopus 로고    scopus 로고
    • Phylogenetic analyses alone are insufficient to determine whether genome duplication(s) occurred during early vertebrate evolution
    • doi:10.1002/jez.b.40
    • Horton AC, Mahadevan NR, Ruvinsky I, Gibson-Brown JJ (2003) Phylogenetic analyses alone are insufficient to determine whether genome duplication(s) occurred during early vertebrate evolution. J Exp Zoolog B Mol Dev Evol 299: 41-53. doi: 10. 1002/jez. b. 40.
    • (2003) J Exp Zoolog B Mol Dev Evol , vol.299 , pp. 41-53
    • Horton, A.C.1    Mahadevan, N.R.2    Ruvinsky, I.3    Gibson-Brown, J.J.4
  • 44
    • 84963093160 scopus 로고
    • Hybridization between fish species in nature
    • Hubbs CL (1955) Hybridization between fish species in nature. Syst Zool 4: 1-20.
    • (1955) Syst Zool , vol.4 , pp. 1-20
    • Hubbs, C.L.1
  • 45
    • 53549093299 scopus 로고    scopus 로고
    • Early vertebrate whole genome duplications were predated by a period of intense genome rearrangement
    • doi:10.1101/gr.080119.108
    • Hufton AL, Groth D, Vingron M, Lehrach H, Poustka AJ, Panopoulou G (2008) Early vertebrate whole genome duplications were predated by a period of intense genome rearrangement. Genome Res 18: 1582-1591. doi: 10. 1101/gr. 080119. 108.
    • (2008) Genome Res , vol.18 , pp. 1582-1591
    • Hufton, A.L.1    Groth, D.2    Vingron, M.3    Lehrach, H.4    Poustka, A.J.5    Panopoulou, G.6
  • 46
    • 0027423610 scopus 로고
    • Evolution of duplicate genes in a tetraploid animal, Xenopus laevis
    • Hughes MK, Hughes AL (1993) Evolution of duplicate genes in a tetraploid animal, Xenopus laevis. Mol Biol Evol 10: 1360-1369.
    • (1993) Mol Biol Evol , vol.10 , pp. 1360-1369
    • Hughes, M.K.1    Hughes, A.L.2
  • 47
    • 0035010738 scopus 로고    scopus 로고
    • Ancient genome duplications did not structure the human Hox-bearing chromosomes
    • doi:10.1101/gr.GR-1600R
    • Hughes AL, da Silva J, Friedman R (2001) Ancient genome duplications did not structure the human Hox-bearing chromosomes. Genome Res 11: 771-780. doi: 10. 1101/gr. GR-1600R.
    • (2001) Genome Res , vol.11 , pp. 771-780
    • Hughes, A.L.1    da Silva, J.2    Friedman, R.3
  • 48
    • 34248335064 scopus 로고    scopus 로고
    • The genome size evolution of medaka (Oryzias latipes) and fugu (Takifugu rubripes)
    • doi:10.1266/ggs.82.135
    • Imai S, Sasaki T, Shimizu A, Asakawa S, Hori H, Shimizu N (2007) The genome size evolution of medaka (Oryzias latipes) and fugu (Takifugu rubripes). Genes Genet Syst 82: 135-144. doi: 10. 1266/ggs. 82. 135.
    • (2007) Genes Genet Syst , vol.82 , pp. 135-144
    • Imai, S.1    Sasaki, T.2    Shimizu, A.3    Asakawa, S.4    Hori, H.5    Shimizu, N.6
  • 49
    • 12244307474 scopus 로고    scopus 로고
    • Basal actinopterygian relationships: A mitogenomic perspective on the phylogeny of the "ancient fish"
    • doi:10.1016/S1055-7903(02)00331-7
    • Inoue JG, Miya M, Tsukamoto K, Nishida M (2003) Basal actinopterygian relationships: a mitogenomic perspective on the phylogeny of the "ancient fish". Mol Phylogenet Evol 26: 110-120. doi: 10. 1016/S1055-7903(02)00331-7.
    • (2003) Mol Phylogenet Evol , vol.26 , pp. 110-120
    • Inoue, J.G.1    Miya, M.2    Tsukamoto, K.3    Nishida, M.4
  • 50
    • 17044393500 scopus 로고    scopus 로고
    • The mitochondrial genome of Indonesian coelacanth Latimeria menadoensis (Sarcopterygii: Coelacanthiformes) and divergence time estimation between the two coelacanths
    • doi:10.1016/j.gene.2005.01.008
    • Inoue JG, Miya M, Venkatesh B, Nishida M (2005) The mitochondrial genome of Indonesian coelacanth Latimeria menadoensis (Sarcopterygii: Coelacanthiformes) and divergence time estimation between the two coelacanths. Gene 349: 227-235. doi: 10. 1016/j. gene. 2005. 01. 008.
    • (2005) Gene , vol.349 , pp. 227-235
    • Inoue, J.G.1    Miya, M.2    Venkatesh, B.3    Nishida, M.4
  • 51
    • 7244245762 scopus 로고    scopus 로고
    • Finishing the euchromatic sequence of the human genome
    • International Human Genome Sequencing Consortium, doi:10.1038/nature03001
    • International Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature 431: 931-945. doi: 10. 1038/nature03001.
    • (2004) Nature , vol.431 , pp. 931-945
  • 54
    • 0036213206 scopus 로고    scopus 로고
    • Phosphoglucose isomerases of hagfish, zebrafish, gray mullet, toad, and snake, with reference to the evolution of the genes in vertebrates
    • Kao HW, Lee SC (2002) Phosphoglucose isomerases of hagfish, zebrafish, gray mullet, toad, and snake, with reference to the evolution of the genes in vertebrates. Mol Biol Evol 19: 367-374.
    • (2002) Mol Biol Evol , vol.19 , pp. 367-374
    • Kao, H.W.1    Lee, S.C.2
  • 56
    • 0030902728 scopus 로고    scopus 로고
    • Chromosomal duplication and the emergence of the adaptive immune system
    • doi:10.1016/S0168-9525(97)01065-2
    • Kasahara M, Nakaya J, Satta Y, Takahata N (1997) Chromosomal duplication and the emergence of the adaptive immune system. Trends Genet 13: 90-92. doi: 10. 1016/S0168-9525(97)01065-2.
    • (1997) Trends Genet , vol.13 , pp. 90-92
    • Kasahara, M.1    Nakaya, J.2    Satta, Y.3    Takahata, N.4
  • 58
    • 37249007723 scopus 로고    scopus 로고
    • Interrelationships of the 11 gasterosteiform families (sticklebacks, pipefishes, and their relatives): A new perspective based on whole mitogenome sequences from 75 higher teleosts
    • doi:10.1016/j.ympev.2007.07.009
    • Kawahara R, Miya M, Mabuchi K, Lavoué S, Inoue JG, Satoh TP, Kawaguchi A, Nishida M (2008) Interrelationships of the 11 gasterosteiform families (sticklebacks, pipefishes, and their relatives): a new perspective based on whole mitogenome sequences from 75 higher teleosts. Mol Phylogenet Evol 46: 224-236. doi: 10. 1016/j. ympev. 2007. 07. 009.
    • (2008) Mol Phylogenet Evol , vol.46 , pp. 224-236
    • Kawahara, R.1    Miya, M.2    Mabuchi, K.3    Lavoué, S.4    Inoue, J.G.5    Satoh, T.P.6    Kawaguchi, A.7    Nishida, M.8
  • 59
    • 58049153104 scopus 로고    scopus 로고
    • Stickleback phylogenies resolved: Evidence from mitochondrial genomes and 11 nuclear genes
    • doi:10.1016/j.ympev.2008.10.014
    • Kawahara R, Miya M, Mabuchi K, Near TJ, Nishida M (2009) Stickleback phylogenies resolved: evidence from mitochondrial genomes and 11 nuclear genes. Mol Phylogenet Evol 50: 401-404. doi: 10. 1016/j. ympev. 2008. 10. 014.
    • (2009) Mol Phylogenet Evol , vol.50 , pp. 401-404
    • Kawahara, R.1    Miya, M.2    Mabuchi, K.3    Near, T.J.4    Nishida, M.5
  • 60
    • 1942452749 scopus 로고    scopus 로고
    • Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae
    • doi:10.1038/nature02424
    • 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: 10. 1038/nature02424.
    • (2004) Nature , vol.428 , pp. 617-624
    • Kellis, M.1    Birren, B.W.2    Lander, E.S.3
  • 63
    • 0032580152 scopus 로고    scopus 로고
    • A molecular timescale for vertebrate evolution
    • doi:10.1038/31927
    • Kumar S, Hedges SB (1998) A molecular timescale for vertebrate evolution. Nature 392: 917-920. doi: 10. 1038/31927.
    • (1998) Nature , vol.392 , pp. 917-920
    • Kumar, S.1    Hedges, S.B.2
  • 64
    • 57749184792 scopus 로고    scopus 로고
    • Timing of genome duplications relative to the origin of the vertebrates: Did cyclostomes diverge before or after?
    • doi:10.1093/molbev/msn222
    • 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: 10. 1093/molbev/msn222.
    • (2009) Mol Biol Evol , vol.26 , pp. 47-59
    • Kuraku, S.1    Meyer, A.2    Kuratani, S.3
  • 66
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • International Human Genome Sequencing Consortium
    • Lander ES, International Human Genome Sequencing Consortium et al (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921.
    • (2001) Nature , vol.409 , pp. 860-921
    • Lander, E.S.1
  • 67
    • 25144447559 scopus 로고    scopus 로고
    • Molecular systematics of the gonorynchiform fishes (Teleostei) based on whole mitogenome sequences: Implications for higher-level relationships within the Otocephala
    • doi:10.1016/j.ympev.2005.03.024
    • Lavoué S, Miya M, Inoue JG, Saitoh K, Ishiguro NB, Nishida M (2005) Molecular systematics of the gonorynchiform fishes (Teleostei) based on whole mitogenome sequences: implications for higher-level relationships within the Otocephala. Mol Phylogenet Evol 37: 165-177. doi: 10. 1016/j. ympev. 2005. 03. 024.
    • (2005) Mol Phylogenet Evol , vol.37 , pp. 165-177
    • Lavoué, S.1    Miya, M.2    Inoue, J.G.3    Saitoh, K.4    Ishiguro, N.B.5    Nishida, M.6
  • 68
    • 44149094819 scopus 로고    scopus 로고
    • Monophyly, phylogenetic position and inter-familial relationships of the Alepocephaliformes (Teleostei) based on whole mitogenome sequences
    • doi:10.1016/j.ympev.2007.12.002
    • Lavoué S, Miya M, Poulsen JY, Møller PR, Nishida M (2008) Monophyly, phylogenetic position and inter-familial relationships of the Alepocephaliformes (Teleostei) based on whole mitogenome sequences. Mol Phylogenet Evol 47: 1111-1121. doi: 10. 1016/j. ympev. 2007. 12. 002.
    • (2008) Mol Phylogenet Evol , vol.47 , pp. 1111-1121
    • Lavoué, S.1    Miya, M.2    Poulsen, J.Y.3    Møller, P.R.4    Nishida, M.5
  • 69
    • 0037103614 scopus 로고    scopus 로고
    • Characterization of Hox genes in the bichir, Polypterus palmas
    • doi:10.1002/jez.10152
    • Ledje C, Kim CB, Ruddle FH (2002) Characterization of Hox genes in the bichir, Polypterus palmas. J Exp Zool 294: 107-111. doi: 10. 1002/jez. 10152.
    • (2002) J Exp Zool , vol.294 , pp. 107-111
    • Ledje, C.1    Kim, C.B.2    Ruddle, F.H.3
  • 70
    • 4344683314 scopus 로고    scopus 로고
    • Occurrence of polyploidy in the fishes
    • doi:10.1023/B:RFBF.0000033049.00668.fe
    • Leggatt RA, Iwama GK (2003) Occurrence of polyploidy in the fishes. Rev Fish Biol Fish 13: 237-246. doi: 10. 1023/B: RFBF. 0000033049. 00668. fe.
    • (2003) Rev Fish Biol Fish , vol.13 , pp. 237-246
    • Leggatt, R.A.1    Iwama, G.K.2
  • 71
    • 33749325080 scopus 로고    scopus 로고
    • Genomic evolution of Hox gene clusters
    • doi:10.1126/science.1132040
    • Lemons D, McGinnis W (2006) Genomic evolution of Hox gene clusters. Science 313: 1918-1922. doi: 10. 1126/science. 1132040.
    • (2006) Science , vol.313 , pp. 1918-1922
    • Lemons, D.1    McGinnis, W.2
  • 72
    • 0035884370 scopus 로고    scopus 로고
    • Duplicate mitf genes in zebrafish: Complementary expression and conservation of melanogenic potential
    • doi:10.1006/dbio.2001.0379
    • Lister JA, Close J, Raible DW (2001) Duplicate mitf genes in zebrafish: complementary expression and conservation of melanogenic potential. Dev Biol 237: 333-344. doi: 10. 1006/dbio. 2001. 0379.
    • (2001) Dev Biol , vol.237 , pp. 333-344
    • Lister, J.A.1    Close, J.2    Raible, D.W.3
  • 73
    • 0033567324 scopus 로고    scopus 로고
    • Homeobox genes in the australian lungfish Neoceratodus forsteri
    • doi:10.1002/(SICI)1097-010X(19990815)285:2<140::AID-JEZ6>3.0.CO;2-V
    • Longhurst TJ, Joss JM (1999) Homeobox genes in the australian lungfish Neoceratodus forsteri. J Exp Zool 285: 140-145. doi: 10. 1002/(SICI)1097-010X(19990815)285: 2< 140:: AID-JEZ6> 3. 0. CO; 2-V.
    • (1999) J Exp Zool , vol.285 , pp. 140-145
    • Longhurst, T.J.1    Joss, J.M.2
  • 74
    • 0027284770 scopus 로고
    • Evolution of the vertebrate genome as reflected in paralogous chromosomal regions in man and the house mouse
    • doi:doi:10.1006/geno.1993.1133
    • Lundin LG (1993) Evolution of the vertebrate genome as reflected in paralogous chromosomal regions in man and the house mouse. Genomics 16: 1-19. doi: doi: 10. 1006/geno. 1993. 1133.
    • (1993) Genomics , vol.16 , pp. 1-19
    • Lundin, L.G.1
  • 75
    • 0037263482 scopus 로고    scopus 로고
    • Numerous groups of chromosomal regional paralogies strongly indicate two genome doublings at the root of the vertebrates
    • doi:10.1023/A:1022600813840
    • Lundin LG, Larhammar D, Hallböök F (2003) Numerous groups of chromosomal regional paralogies strongly indicate two genome doublings at the root of the vertebrates. J Struct Funct Genomics 3: 53-63. doi: 10. 1023/A: 1022600813840.
    • (2003) J Struct Funct Genomics , vol.3 , pp. 53-63
    • Lundin, L.G.1    Larhammar, D.2    Hallböök, F.3
  • 76
    • 0037047587 scopus 로고    scopus 로고
    • Gene duplication and evolution
    • doi:10.1126/science.1075472
    • Lynch M (2002) Gene duplication and evolution. Science 297: 945-947. doi: 10. 1126/science. 1075472.
    • (2002) Science , vol.297 , pp. 945-947
    • Lynch, M.1
  • 77
    • 34250709215 scopus 로고    scopus 로고
    • Genomic expansion by gene duplication
    • M. Lynch (Ed.), Sunderland: Sinauer
    • Lynch M (2007) Genomic expansion by gene duplication. In: Lynch M (ed) The origins of genome architecture. Sinauer, Sunderland, pp 193-235.
    • (2007) The Origins of Genome Architecture , pp. 193-235
    • Lynch, M.1
  • 78
    • 0034529964 scopus 로고    scopus 로고
    • The origin of interspecific genomic incompatibility via gene duplication
    • doi:10.1086/316992
    • Lynch M, Force AG (2000) The origin of interspecific genomic incompatibility via gene duplication. Am Nat 156: 590-605. doi: 10. 1086/316992.
    • (2000) Am Nat , vol.156 , pp. 590-605
    • Lynch, M.1    Force, A.G.2
  • 79
    • 33846092495 scopus 로고    scopus 로고
    • CellCircuits: A database of protein network models
    • doi:10.1093/nar/gkl937
    • Mak HC, Daly M, Gruebel B, Ideker T (2007) CellCircuits: a database of protein network models. Nucleic Acids Res 35: D538-D545. doi: 10. 1093/nar/gkl937.
    • (2007) Nucleic Acids Res , vol.35
    • Mak, H.C.1    Daly, M.2    Gruebel, B.3    Ideker, T.4
  • 80
    • 33746117256 scopus 로고    scopus 로고
    • Phylogenetic conservation of chromosome numbers in Actinopterygiian fishes
    • doi:10.1007/s10709-005-5248-0
    • Mank JE, Avise JC (2006a) Phylogenetic conservation of chromosome numbers in Actinopterygiian fishes. Genetica 127: 321-327. doi: 10. 1007/s10709-005-5248-0.
    • (2006) Genetica , vol.127 , pp. 321-327
    • Mank, J.E.1    Avise, J.C.2
  • 81
    • 33748556252 scopus 로고    scopus 로고
    • The evolution of reproductive and genomic diversity in ray-finned fishes: Insights from phylogeny and comparative analysis
    • doi:10.1111/j.1095-8649.2006.01132.x
    • Mank JE, Avise JC (2006b) The evolution of reproductive and genomic diversity in ray-finned fishes: insights from phylogeny and comparative analysis. J Fish Biol 69: 1-27. doi: 10. 1111/j. 1095-8649. 2006. 01132. x.
    • (2006) J Fish Biol , vol.69 , pp. 1-27
    • Mank, J.E.1    Avise, J.C.2
  • 82
    • 0035154891 scopus 로고    scopus 로고
    • Is tetralogy true? Lack of support for the "one-to-four rule"
    • Martin A (2001) Is tetralogy true? Lack of support for the "one-to-four rule". Mol Biol Evol 18: 89-93.
    • (2001) Mol Biol Evol , vol.18 , pp. 89-93
    • Martin, A.1
  • 83
    • 67349147341 scopus 로고    scopus 로고
    • Reconstructing the phylogenetic relationships of the earth's most diverse clade of freshwater fishes-order Cypriniformes (Actinopterygii: Ostariophysi): A case study using multiple nuclear loci and the mitochondrial genome
    • doi:10.1016/j.ympev.2008.12.015
    • Mayden RL, Chen WJ, Bart HL, Doosey MH, Simons AM, Tang KL, Wood RM, Agnew MK, Yang L, Hirt MV, Clements MD, Saitoh K, Sado T, Miya M, Nishida M (2009) Reconstructing the phylogenetic relationships of the earth's most diverse clade of freshwater fishes-order Cypriniformes (Actinopterygii: Ostariophysi): a case study using multiple nuclear loci and the mitochondrial genome. Mol Phylogenet Evol 51: 500-514. doi: 10. 1016/j. ympev. 2008. 12. 015.
    • (2009) Mol Phylogenet Evol , vol.51 , pp. 500-514
    • Mayden, R.L.1    Chen, W.J.2    Bart, H.L.3    Doosey, M.H.4    Simons, A.M.5    Tang, K.L.6    Wood, R.M.7    Agnew, M.K.8    Yang, L.9    Hirt, M.V.10    Clements, M.D.11    Saitoh, K.12    Sado, T.13    Miya, M.14    Nishida, M.15
  • 84
    • 0034759351 scopus 로고    scopus 로고
    • Evidence for a period of directional selection following gene duplication in a neurally expressed locus of triosephosphate isomerase
    • Merritt TJS, Quattro JM (2001) Evidence for a period of directional selection following gene duplication in a neurally expressed locus of triosephosphate isomerase. Genetics 159: 689-697.
    • (2001) Genetics , vol.159 , pp. 689-697
    • Merritt, T.J.S.1    Quattro, J.M.2
  • 85
    • 0033602459 scopus 로고    scopus 로고
    • Vertebrate genomics: More fishy tales about Hox genes
    • doi:10.1016/S0960-9822(99)80131-6
    • Meyer A, Málaga-Trillo E (1999) Vertebrate genomics: More fishy tales about Hox genes. Curr Biol 9: R210-R213. doi: 10. 1016/S0960-9822(99)80131-6.
    • (1999) Curr Biol , vol.9
    • Meyer, A.1    Málaga-trillo, E.2
  • 86
    • 0032733930 scopus 로고    scopus 로고
    • Gene and genome duplications in vertebrates: The one-to-four (-to-eight in fish) rule and the evolution of novel gene functions
    • doi:10.1016/S0955-0674(99)00039-3
    • Meyer A, Schartl M (1999) Gene and genome duplications in vertebrates: the one-to-four (-to-eight in fish) rule and the evolution of novel gene functions. Curr Opin Cell Biol 11: 699-704. doi: 10. 1016/S0955-0674(99)00039-3.
    • (1999) Curr Opin Cell Biol , vol.11 , pp. 699-704
    • Meyer, A.1    Schartl, M.2
  • 88
    • 22044450491 scopus 로고    scopus 로고
    • The phylogenetic position of toadfishes (order Batrachoidiformes) in the higher ray-finned fish as inferred from partitioned Bayesian analysis of 102 whole mitochondrial genome sequences
    • doi:10.1111/j.1095-8312.2005.00483.x
    • Miya M, Satoh TP, Nishida M (2005) The phylogenetic position of toadfishes (order Batrachoidiformes) in the higher ray-finned fish as inferred from partitioned Bayesian analysis of 102 whole mitochondrial genome sequences. Biol J Linn Soc Lond 85: 289-306. doi: 10. 1111/j. 1095-8312. 2005. 00483. x.
    • (2005) Biol J Linn Soc Lond , vol.85 , pp. 289-306
    • Miya, M.1    Satoh, T.P.2    Nishida, M.3
  • 89
    • 27744588853 scopus 로고    scopus 로고
    • Evolution of Hox clusters in Salmonidae: A comparative analysis between Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss)
    • doi:10.1007/s00239-004-0338-7
    • Moghadam HK, Ferguson MM, Danzmann RG (2005) Evolution of Hox clusters in Salmonidae: a comparative analysis between Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss). J Mol Evol 61: 636-649. doi: 10. 1007/s00239-004-0338-7.
    • (2005) J Mol Evol , vol.61 , pp. 636-649
    • Moghadam, H.K.1    Ferguson, M.M.2    Danzmann, R.G.3
  • 90
    • 1542563409 scopus 로고    scopus 로고
    • Initial sequencing and comparative analysis of the mouse genome
    • Mouse Genome Sequencing Consortium, doi:10.1038/nature01262
    • Mouse Genome Sequencing Consortium (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562. doi: 10. 1038/nature01262.
    • (2002) Nature , vol.420 , pp. 520-562
  • 91
    • 33745906973 scopus 로고    scopus 로고
    • Breakup of a homeobox cluster after genome duplication in teleosts
    • doi:10.1073/pnas.0600341103
    • Mulley JF, Chiu CH, Holland PW (2006) Breakup of a homeobox cluster after genome duplication in teleosts. Proc Natl Acad Sci U S A 103: 10369-10372. doi: 10. 1073/pnas. 0600341103.
    • (2006) Proc Natl Acad Sci U S A , vol.103 , pp. 10369-10372
    • Mulley, J.F.1    Chiu, C.H.2    Holland, P.W.3
  • 92
    • 7444233609 scopus 로고    scopus 로고
    • Mammalian phylogenomics comes of age
    • doi:10.1016/j.tig.2004.09.005
    • Murphy WJ, Pevzner PA, O'Brien SJ (2004) Mammalian phylogenomics comes of age. Trends Genet 20: 631-639. doi: 10. 1016/j. tig. 2004. 09. 005.
    • (2004) Trends Genet , vol.20 , pp. 631-639
    • Murphy, W.J.1    Pevzner, P.A.2    O'Brien, S.J.3
  • 93
    • 2642533799 scopus 로고    scopus 로고
    • Genomic object net: I. A platform for modelling and simulating biopathways
    • Nagasaki M, Doi A, Matsuno H, Miyano S (2003) Genomic object net: I. A platform for modelling and simulating biopathways. Appl Bioinformatics 2: 181-184.
    • (2003) Appl Bioinformatics , vol.2 , pp. 181-184
    • Nagasaki, M.1    Doi, A.2    Matsuno, H.3    Miyano, S.4
  • 95
    • 34548420992 scopus 로고    scopus 로고
    • Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates
    • doi:10.1101/gr.6316407
    • Nakatani Y, Takeda H, Kohara Y, Morishita S (2007) Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates. Genome Res 17: 1254-1265. doi: 10. 1101/gr. 6316407.
    • (2007) Genome Res , vol.17 , pp. 1254-1265
    • Nakatani, Y.1    Takeda, H.2    Kohara, Y.3    Morishita, S.4
  • 97
    • 2442697672 scopus 로고    scopus 로고
    • A medaka gene map: The trace of ancestral vertebrate proto-chromosomes revealed by comparative gene mapping
    • doi:10.1101/gr.2004004
    • 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: 10. 1101/gr. 2004004.
    • (2004) Genome Res , vol.14 , pp. 820-828
    • Naruse, K.1    Tanaka, M.2    Mita, K.3    Shima, A.4    Postlethwait, J.5    Mitani, H.6
  • 100
    • 0033209289 scopus 로고    scopus 로고
    • Gene duplication and the uniqueness of vertebrate genomes circa 1970-1999
    • doi:10.1006/scdb.1999.0332
    • Ohno S (1999) Gene duplication and the uniqueness of vertebrate genomes circa 1970-1999. Semin Cell Dev Biol 10: 517-522. doi: 10. 1006/scdb. 1999. 0332.
    • (1999) Semin Cell Dev Biol , vol.10 , pp. 517-522
    • Ohno, S.1
  • 102
    • 24644486449 scopus 로고    scopus 로고
    • Timing and mechanism of ancient vertebrate genome duplications-the adventure of a hypothesis
    • doi:10.1016/j.tig.2005.08.004
    • Panopoulou G, Poustka AJ (2005) Timing and mechanism of ancient vertebrate genome duplications-the adventure of a hypothesis. Trends Genet 21: 559-567. doi: 10. 1016/j. tig. 2005. 08. 004.
    • (2005) Trends Genet , vol.21 , pp. 559-567
    • Panopoulou, G.1    Poustka, A.J.2
  • 103
    • 0038817812 scopus 로고    scopus 로고
    • New evidence for genome-wide duplications at the origin of vertebrates using an amphioxus gene set and completed animal genomes
    • doi:10.1101/gr.874803
    • Panopoulou G, Hennig S, Groth D, Krause A, Poustka AJ, Herwig R, Vingron M, Lehrach H (2003) New evidence for genome-wide duplications at the origin of vertebrates using an amphioxus gene set and completed animal genomes. Genome Res 13: 1056-1066. doi: 10. 1101/gr. 874803.
    • (2003) Genome Res , vol.13 , pp. 1056-1066
    • Panopoulou, G.1    Hennig, S.2    Groth, D.3    Krause, A.4    Poustka, A.J.5    Herwig, R.6    Vingron, M.7    Lehrach, H.8
  • 107
    • 21344439563 scopus 로고    scopus 로고
    • Subfunctionalization of duplicated genes as a transition state to neofunctionalization
    • doi:10.1186/1471-2148-5-28
    • Rastogi S, Liberles DA (2005) Subfunctionalization of duplicated genes as a transition state to neofunctionalization. BMC Evol Biol 5: 28. doi: 10. 1186/1471-2148-5-28.
    • (2005) BMC Evol Biol , vol.5 , pp. 28
    • Rastogi, S.1    Liberles, D.A.2
  • 108
    • 58649118651 scopus 로고    scopus 로고
    • Rapidly evolving fish genomes and teleost diversity
    • doi:10.1016/j.gde.2008.11.001
    • Ravi V, Venkatesh B (2008) Rapidly evolving fish genomes and teleost diversity. Curr Opin Genet Dev 18: 544-550. doi: 10. 1016/j. gde. 2008. 11. 001.
    • (2008) Curr Opin Genet Dev , vol.18 , pp. 544-550
    • Ravi, V.1    Venkatesh, B.2
  • 109
    • 0035954256 scopus 로고    scopus 로고
    • An ancestral whole-genome duplication may not have been responsible for the abundance of duplicated fish genes
    • doi:10.1016/S0960-9822(01)00280-9
    • Robinson-Rechavi M, Marchand O, Escriva H, Laudet V (2001a) An ancestral whole-genome duplication may not have been responsible for the abundance of duplicated fish genes. Curr Biol 11: R458-R459. doi: 10. 1016/S0960-9822(01)00280-9.
    • (2001) Curr Biol , vol.11
    • Robinson-Rechavi, M.1    Marchand, O.2    Escriva, H.3    Laudet, V.4
  • 111
    • 1542719902 scopus 로고    scopus 로고
    • Phylogenetic dating and characterization of gene duplications in vertebrates: The cartilaginous fish reference
    • doi:10.1093/molbev/msh046
    • Robinson-Rechavi M, Boussau B, Laudet V (2004) Phylogenetic dating and characterization of gene duplications in vertebrates: the cartilaginous fish reference. Mol Biol Evol 21: 580-586. doi: 10. 1093/molbev/msh046.
    • (2004) Mol Biol Evol , vol.21 , pp. 580-586
    • Robinson-Rechavi, M.1    Boussau, B.2    Laudet, V.3
  • 112
    • 30844449653 scopus 로고    scopus 로고
    • Contribution of electrostatic interactions, compactness and quaternary structure to protein thermostability: Lessons from structural genomics of Thermotoga maritima
    • doi:10.1016/j.jmb.2005.11.065
    • Robinson-Rechavi M, Alibés A, Godzik A (2006) Contribution of electrostatic interactions, compactness and quaternary structure to protein thermostability: lessons from structural genomics of Thermotoga maritima. J Mol Biol 356: 547-557. doi: 10. 1016/j. jmb. 2005. 11. 065.
    • (2006) J Mol Biol , vol.356 , pp. 547-557
    • Robinson-Rechavi, M.1    Alibés, A.2    Godzik, A.3
  • 114
    • 58249110498 scopus 로고    scopus 로고
    • The interaction of sexually and naturally selected traits in the adaptive radiations of cichlid fishes
    • doi:10.1111/j.1365-294X.2008.03981.x
    • Salzburger W (2009) The interaction of sexually and naturally selected traits in the adaptive radiations of cichlid fishes. Mol Ecol 18: 169-185. doi: 10. 1111/j. 1365-294X. 2008. 03981. x.
    • (2009) Mol Ecol , vol.18 , pp. 169-185
    • Salzburger, W.1
  • 115
    • 17644371360 scopus 로고    scopus 로고
    • Initial diversification of living amphibians predated the breakup of Pangea
    • doi:10.1086/429523
    • San Mauro D, Vences M, Alcobendas M, Zardoya R, Meyer A (2005) Initial diversification of living amphibians predated the breakup of Pangea. Am Nat 165: 590-599. doi: 10. 1086/429523.
    • (2005) Am Nat , vol.165 , pp. 590-599
    • San Mauro, D.1    Vences, M.2    Alcobendas, M.3    Zardoya, R.4    Meyer, A.5
  • 117
    • 38049150292 scopus 로고    scopus 로고
    • Post-duplication charge evolution of phosphoglucose isomerases in teleost fishes through weak selection on many amino acid sites
    • doi:10.1186/1471-2148-7-204
    • Sato Y, Nishida M (2007) Post-duplication charge evolution of phosphoglucose isomerases in teleost fishes through weak selection on many amino acid sites. BMC Evol Biol 7: 204. doi: 10. 1186/1471-2148-7-204.
    • (2007) BMC Evol Biol , vol.7 , pp. 204
    • Sato, Y.1    Nishida, M.2
  • 118
    • 67349114539 scopus 로고    scopus 로고
    • Electric charge divergence in proteins: Insights into the evolution of their three-dimensional properties
    • doi:10.1016/j.gene.2008.06.026
    • Sato Y, Nishida M (2009) Electric charge divergence in proteins: insights into the evolution of their three-dimensional properties. Gene 441: 3-11. doi: 10. 1016/j. gene. 2008. 06. 026.
    • (2009) Gene , vol.441 , pp. 3-11
    • Sato, Y.1    Nishida, M.2
  • 119
    • 67649807765 scopus 로고    scopus 로고
    • Temporal pattern of loss/persistence of duplicate genes involved in signal transduction and metabolic pathways after teleost-specific genome duplication
    • doi:10.1186/1471-2148-9-127
    • Sato Y, Hashiguchi Y, Nishida M (2009a) 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: 10. 1186/1471-2148-9-127.
    • (2009) BMC Evol Biol , vol.9 , pp. 127
    • Sato, Y.1    Hashiguchi, Y.2    Nishida, M.3
  • 120
    • 62649155906 scopus 로고    scopus 로고
    • Evolution of multiple phosphodiesterase isoforms in stickleback involved in cAMP signal transduction pathway
    • doi:10.1186/1752-0509-3-23
    • Sato Y, Hashiguchi Y, Nishida M (2009b) Evolution of multiple phosphodiesterase isoforms in stickleback involved in cAMP signal transduction pathway. BMC Syst Biol 3: 23. doi: 10. 1186/1752-0509-3-23.
    • (2009) BMC Syst Biol , vol.3 , pp. 23
    • Sato, Y.1    Hashiguchi, Y.2    Nishida, M.3
  • 121
    • 0347511691 scopus 로고    scopus 로고
    • Next generation simulation tools: The systems biology workbench and BioSPICE integration
    • doi:10.1089/153623103322637670
    • Sauro HM, Hucka M, Finney A, Wellock C, Bolouri H, Doyle J, Kitano H (2003) Next generation simulation tools: the systems biology workbench and BioSPICE integration. OMICS 7: 355-372. doi: 10. 1089/153623103322637670.
    • (2003) Omics , vol.7 , pp. 355-372
    • Sauro, H.M.1    Hucka, M.2    Finney, A.3    Wellock, C.4    Bolouri, H.5    Doyle, J.6    Kitano, H.7
  • 124
    • 33847065899 scopus 로고    scopus 로고
    • Reciprocal gene loss between Tetraodon and zebrafish after whole genome duplication in their ancestor
    • doi:10.1016/j.tig.2007.01.003
    • Sémon M, Wolfe KH (2007a) Reciprocal gene loss between Tetraodon and zebrafish after whole genome duplication in their ancestor. Trends Genet 23: 108-112. doi: 10. 1016/j. tig. 2007. 01. 003.
    • (2007) Trends Genet , vol.23 , pp. 108-112
    • Sémon, M.1    Wolfe, K.H.2
  • 125
    • 33847653643 scopus 로고    scopus 로고
    • Rearrangement rate following the whole-genome duplication in teleosts
    • doi:10.1093/molbev/msm003
    • Sémon M, Wolfe KH (2007b) Rearrangement rate following the whole-genome duplication in teleosts. Mol Biol Evol 24: 860-867. doi: 10. 1093/molbev/msm003.
    • (2007) Mol Biol Evol , vol.24 , pp. 860-867
    • Sémon, M.1    Wolfe, K.H.2
  • 126
    • 55049098903 scopus 로고    scopus 로고
    • Interrelationships of Atherinomorpha (medakas, flyingfishes, killifishes, silversides, and their relatives): The first evidence based on whole mitogenome sequences
    • doi:10.1016/j.ympev.2008.08.008
    • Setiamarga DH, Miya M, Yamanoue Y, Mabuchi K, Satoh TP, Inoue JG, Nishida M (2008) Interrelationships of Atherinomorpha (medakas, flyingfishes, killifishes, silversides, and their relatives): the first evidence based on whole mitogenome sequences. Mol Phylogenet Evol 49: 598-605. doi: 10. 1016/j. ympev. 2008. 08. 008.
    • (2008) Mol Phylogenet Evol , vol.49 , pp. 598-605
    • Setiamarga, D.H.1    Miya, M.2    Yamanoue, Y.3    Mabuchi, K.4    Satoh, T.P.5    Inoue, J.G.6    Nishida, M.7
  • 127
    • 74549205222 scopus 로고    scopus 로고
    • Divergence time of the two regional medaka populations in Japan as a new time scale for comparative genomics of vertebrates
    • doi:10.1098/rsbl.2009.0419
    • Setiamarga DH, Miya M, Yamanoue Y, Azuma Y, Inoue JG, Ishiguro NB, Mabuchi K, Nishida M (2009) Divergence time of the two regional medaka populations in Japan as a new time scale for comparative genomics of vertebrates. Biol Lett 5: 812-816. doi: 10. 1098/rsbl. 2009. 0419.
    • (2009) Biol Lett , vol.5 , pp. 812-816
    • Setiamarga, D.H.1    Miya, M.2    Yamanoue, Y.3    Azuma, Y.4    Inoue, J.G.5    Ishiguro, N.B.6    Mabuchi, K.7    Nishida, M.8
  • 128
    • 0030473920 scopus 로고    scopus 로고
    • Gen(om)e duplications in the evolution of early vertebrates
    • doi:10.1016/S0959-437X(96)80026-8
    • Sidow A (1996) Gen(om)e duplications in the evolution of early vertebrates. Curr Opin Genet Dev 6: 715-722. doi: 10. 1016/S0959-437X(96)80026-8.
    • (1996) Curr Opin Genet Dev , vol.6 , pp. 715-722
    • Sidow, A.1
  • 129
    • 35248812530 scopus 로고    scopus 로고
    • Comparative genomics of ParaHox clusters of teleost fishes: Gene cluster breakup and the retention of gene sets following whole genome duplications
    • doi:10.1186/1471-2164-8-312
    • Siegel N, Hoegg S, Salzburger W, Braasch I, Meyer A (2007) Comparative genomics of ParaHox clusters of teleost fishes: gene cluster breakup and the retention of gene sets following whole genome duplications. BMC Genomics 8: 312. doi: 10. 1186/1471-2164-8-312.
    • (2007) BMC Genomics , vol.8 , pp. 312
    • Siegel, N.1    Hoegg, S.2    Salzburger, W.3    Braasch, I.4    Meyer, A.5
  • 130
    • 0031022113 scopus 로고    scopus 로고
    • Vertebrate evolution by interspecific hybridisation-are we polyploid?
    • doi:10.1016/S0014-5793(96)01351-8
    • Spring J (1997) Vertebrate evolution by interspecific hybridisation-are we polyploid? FEBS Lett 40: 2-8. doi: 10. 1016/S0014-5793(96)01351-8.
    • (1997) FEBS Lett , vol.40 , pp. 2-8
    • Spring, J.1
  • 131
    • 1842838629 scopus 로고    scopus 로고
    • Evidence for independent Hox gene duplications in the hagfish lineage: A PCR-based gene inventory of Eptatretus stoutii
    • doi:10.1016/j.ympev.2004.03.015
    • Stadler PF, Fried C, Prohaska SJ, Bailey WJ, Misof BY, Ruddle FH, Wagner GP (2004) Evidence for independent Hox gene duplications in the hagfish lineage: a PCR-based gene inventory of Eptatretus stoutii. Mol Phylogenet Evol 32: 686-694. doi: 10. 1016/j. ympev. 2004. 03. 015.
    • (2004) Mol Phylogenet Evol , vol.32 , pp. 686-694
    • Stadler, P.F.1    Fried, C.2    Prohaska, S.J.3    Bailey, W.J.4    Misof, B.Y.5    Ruddle, F.H.6    Wagner, G.P.7
  • 132
    • 33746091718 scopus 로고    scopus 로고
    • Three rounds (1R/2R/3R) of genome duplications and the evolution of the glycolytic pathway in vertebrates
    • doi:10.1186/1741-7007-4-16
    • Steinke D, Hoegg S, Brinkmann H, Meyer A (2006) Three rounds (1R/2R/3R) of genome duplications and the evolution of the glycolytic pathway in vertebrates. BMC Biol 4: 16. doi: 10. 1186/1741-7007-4-16.
    • (2006) BMC Biol , vol.4 , pp. 16
    • Steinke, D.1    Hoegg, S.2    Brinkmann, H.3    Meyer, A.4
  • 133
    • 0346343420 scopus 로고    scopus 로고
    • Geographic variation and diversity of the cytochrome b gene in Japanese wild populations of medaka, Oryzias latipes
    • doi:10.2108/zsj.20.1279
    • Takehana Y, Nagai N, Matsuda M, Tsuchiya K, Sakaizumi M (2003) Geographic variation and diversity of the cytochrome b gene in Japanese wild populations of medaka, Oryzias latipes. Zool Sci 20: 1279-1291. doi: 10. 2108/zsj. 20. 1279.
    • (2003) Zool Sci , vol.20 , pp. 1279-1291
    • Taylor, Y.1    Nagai, N.2    Matsuda, M.3    Tsuchiya, K.4    Sakaizumi, M.5
  • 134
    • 0035368224 scopus 로고    scopus 로고
    • Genome duplication, divergent resolution and speciation
    • doi:10.1016/S0168-9525(01)02318-6
    • Taylor JS, van de Peer Y, Meyer A (2001a) Genome duplication, divergent resolution and speciation. Trends Genet 17: 299-301. doi: 10. 1016/S0168-9525(01)02318-6.
    • (2001) Trends Genet , vol.17 , pp. 299-301
    • Taylor, J.S.1    van de Peer, Y.2    Meyer, A.3
  • 135
    • 0035968908 scopus 로고    scopus 로고
    • Comparative genomics provides evidence for an ancient genome duplication event in fish
    • doi:10.1098/rstb.2001.0975
    • Taylor JS, van de Peer Y, Braasch I, Meyer A (2001b) Comparative genomics provides evidence for an ancient genome duplication event in fish. Philos Trans R Soc Lond B Biol Sci 356: 1661-1679. doi: 10. 1098/rstb. 2001. 0975.
    • (2001) Philos Trans R Soc Lond B Biol Sci , vol.356 , pp. 1661-1679
    • Taylor, J.S.1    van de Peer, Y.2    Braasch, I.3    Meyer, A.4
  • 136
    • 0037351989 scopus 로고    scopus 로고
    • Genome duplication, a trait shared by 22000 species of ray-finned fish
    • doi:10.1101/gr.640303
    • Taylor JS, Braasch I, Frickey T, Meyer A, van de Peer Y (2003) Genome duplication, a trait shared by 22000 species of ray-finned fish. Genome Res 13: 382-390. doi: 10. 1101/gr. 640303.
    • (2003) Genome Res , vol.13 , pp. 382-390
    • Taylor, J.S.1    Braasch, I.2    Frickey, T.3    Meyer, A.4    van de Peer, Y.5
  • 137
    • 0031741182 scopus 로고    scopus 로고
    • Estimating the rate of evolution of the rate of molecular evolution
    • Thorne JL, Kishino H, Painter IS (1998) Estimating the rate of evolution of the rate of molecular evolution. Mol Biol Evol 15: 1647-1657.
    • (1998) Mol Biol Evol , vol.15 , pp. 1647-1657
    • Thorne, J.L.1    Kishino, H.2    Painter, I.S.3
  • 138
    • 0030027374 scopus 로고    scopus 로고
    • Teleost HoxD and HoxA genes: Comparison with tetrapods and functional evolution of the HoxD complex
    • doi:10.1016/0925-4773(95)00455-6
    • van der Hoeven F, Sordino P, Fraudeau N, Izpisúa-Belmonte JC, Duboule D (1996) Teleost HoxD and HoxA genes: comparison with tetrapods and functional evolution of the HoxD complex. Mech Dev 4: 9-21. doi: 10. 1016/0925-4773(95)00455-6.
    • (1996) Mech Dev , vol.4 , pp. 9-21
    • van der Hoeven, F.1    Sordino, P.2    Fraudeau, N.3    Izpisúa-belmonte, J.C.4    Duboule, D.5
  • 139
    • 0034819040 scopus 로고    scopus 로고
    • The ghost of selection past: Rates of evolution and functional divergence of anciently duplicated genes
    • doi:10.1007/s002390010233
    • van de Peer Y, Taylor JS, Braasch I, Meyer A (2001) The ghost of selection past: rates of evolution and functional divergence of anciently duplicated genes. J Mol Evol 53: 436-446. doi: 10. 1007/s002390010233.
    • (2001) J Mol Evol , vol.53 , pp. 436-446
    • van de Peer, Y.1    Taylor, J.S.2    Braasch, I.3    Meyer, A.4
  • 140
    • 0037269876 scopus 로고    scopus 로고
    • Are all fishes ancient polyploids?
    • doi:10.1023/A:1022652814749
    • van de Peer Y, Taylor JS, Meyer A (2003) Are all fishes ancient polyploids? J Struct Funct Genomics 3: 65-73. doi: 10. 1023/A: 1022652814749.
    • (2003) J Struct Funct Genomics , vol.3 , pp. 65-73
    • van de Peer, Y.1    Taylor, J.S.2    Meyer, A.3
  • 141
    • 70349325524 scopus 로고    scopus 로고
    • The evolutionary significance of ancient genome duplications
    • in press. doi: 10.1038/nrg2600
    • van de Peer Y, Maere S, Meyer A (2009) The evolutionary significance of ancient genome duplications. Nat Rev Genet, in press. doi: 10.1038/nrg2600.
    • (2009) Nat Rev Genet
    • van de Peer, Y.1    Maere, S.2    Meyer, A.3
  • 142
    • 1242274629 scopus 로고    scopus 로고
    • Major events in the genome evolution of vertebrates: Paranome age and size differ considerably between ray-finned fishes and land vertebrates
    • doi:10.1073/pnas.0307968100
    • Vandepoele K, De Vos W, Taylor JS, Meyer A, van de Peer Y (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 U S A 101: 1638-1643. doi: 10. 1073/pnas. 0307968100.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 1638-1643
    • Vandepoele, K.1    de Vos, W.2    Taylor, J.S.3    Meyer, A.4    van de Peer, Y.5
  • 143
    • 0345016262 scopus 로고    scopus 로고
    • Evolution and diversity of fish genomes
    • doi:10.1016/j.gde.2003.09.001
    • Venkatesh B (2003) Evolution and diversity of fish genomes. Curr Opin Genet Dev 13: 588-592. doi: 10. 1016/j. gde. 2003. 09. 001.
    • (2003) Curr Opin Genet Dev , vol.13 , pp. 588-592
    • Venkatesh, B.1
  • 145
    • 0032555668 scopus 로고    scopus 로고
    • Doubled genes may explain fish diversity
    • doi:10.1126/science.281.5380.1119
    • Vogel G (1998) Doubled genes may explain fish diversity. Science 281: 1119-1121. doi: 10. 1126/science. 281. 5380. 1119.
    • (1998) Science , vol.281 , pp. 1119-1121
    • Vogel, G.1
  • 146
    • 15544377813 scopus 로고    scopus 로고
    • Genome evolution and biodiversity in teleost fish
    • doi:10.1038/sj.hdy.6800635
    • Volff JN (2005) Genome evolution and biodiversity in teleost fish. Heredity 94: 280-294. doi: 10. 1038/sj. hdy. 6800635.
    • (2005) Heredity , vol.94 , pp. 280-294
    • Volff, J.N.1
  • 147
    • 0001604836 scopus 로고
    • A model for divergent, allopatric speciation of polyploid pteridophytes resulting from silencing of duplicate-gene expression
    • doi:10.1086/285180
    • Werthand CR, Windham MD (1991) A model for divergent, allopatric speciation of polyploid pteridophytes resulting from silencing of duplicate-gene expression. Am Nat 137: 515-526. doi: 10. 1086/285180.
    • (1991) Am Nat , vol.137 , pp. 515-526
    • Werthand, C.R.1    Windham, M.D.2
  • 149
    • 0035344021 scopus 로고    scopus 로고
    • Yesterday's polyploids and the mystery of diploidization
    • doi:10.1038/35072009
    • Wolfe KH (2001) Yesterday's polyploids and the mystery of diploidization. Nat Rev Genet 2: 333-341. doi: 10. 1038/35072009.
    • (2001) Nat Rev Genet , vol.2 , pp. 333-341
    • Wolfe, K.H.1
  • 150
    • 33645772189 scopus 로고    scopus 로고
    • The mitochondrial genome of spotted green pufferfish Tetraodon nigroviridis (Teleostei: Tetraodontiformes) and divergence time estimation among model organisms in fishes
    • doi:10.1266/ggs.81.29
    • Yamanoue Y, Miya M, Inoue JG, Matsuura K, Nishida M (2006) The mitochondrial genome of spotted green pufferfish Tetraodon nigroviridis (Teleostei: Tetraodontiformes) and divergence time estimation among model organisms in fishes. Genes Genet Syst 8: 29-39. doi: 10. 1266/ggs. 81. 29.
    • (2006) Genes Genet Syst , vol.8 , pp. 29-39
    • Yamanoue, Y.1    Miya, M.2    Inoue, J.G.3    Matsuura, K.4    Nishida, M.5
  • 151
    • 49249124046 scopus 로고    scopus 로고
    • A new perspective on phylogeny and evolution of tetraodontiform fishes (Pisces: Acanthopterygii) based on whole mitochondrial genome sequences: Basal ecological diversification?
    • doi:10.1186/1471-2148-8-212
    • Yamanoue Y, Miya M, Matsuura K, Katoh M, Sakai H, Nishida M (2008) A new perspective on phylogeny and evolution of tetraodontiform fishes (Pisces: Acanthopterygii) based on whole mitochondrial genome sequences: Basal ecological diversification? BMC Evol Biol 8: 212. doi: 10. 1186/1471-2148-8-212.
    • (2008) BMC Evol Biol , vol.8 , pp. 212
    • Yamanoue, Y.1    Miya, M.2    Matsuura, K.3    Katoh, M.4    Sakai, H.5    Nishida, M.6
  • 153
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetic analysis by maximum likelihood
    • doi:10.1093/bioinformatics/13.5.555
    • Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13: 555-556. doi: 10. 1093/bioinformatics/13. 5. 555.
    • (1997) Comput Appl Biosci , vol.13 , pp. 555-556
    • Yang, Z.1
  • 154
    • 34247120219 scopus 로고    scopus 로고
    • Sequencing and comparative analysis of fugu protocadherin clusters reveal diversity of protocadherin genes among teleosts
    • doi:10.1186/1471-2148-7-49
    • Yu WP, 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: 10. 1186/1471-2148-7-49.
    • (2007) BMC Evol Biol , vol.7 , pp. 49
    • Yu, W.P.1    Yew, K.2    Rajasegaran, V.3    Venkatesh, B.4
  • 155
    • 0037500141 scopus 로고    scopus 로고
    • Evolution by gene duplication: An update
    • doi:10.1016/S0169-5347(03)00033-8
    • Zhang J (2003) Evolution by gene duplication: an update. Trends Ecol Evol 18: 292-298. doi: 10. 1016/S0169-5347(03)00033-8.
    • (2003) Trends Ecol Evol , vol.18 , pp. 292-298
    • Zhang, J.1
  • 156
    • 0035788655 scopus 로고    scopus 로고
    • Differential genome duplication and fish diversity
    • doi:10.1023/A:1021395506705
    • Zhou R, Cheng H, Tiersch TR (2001) Differential genome duplication and fish diversity. Rev Fish Biol Fish 11: 331-337. doi: 10. 1023/A: 1021395506705.
    • (2001) Rev Fish Biol Fish , vol.11 , pp. 331-337
    • Zhou, R.1    Cheng, H.2    Tiersch, T.R.3


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