Abstract
The origin and evolution of the vertebrates have been linked to the study of genome duplications since Susumo Ohno ventured the 2R-hypothesis, suggesting that the successful diversification of complex vertebrates was facilitated by polyploidization in the stem vertebrate ancestor due to two rounds of whole-genome duplication (2R-WGD). This chapter first reviews evidence supporting Ohno’s 2R-hypothesis and gathers information about the timing and mechanisms underlying the 2R-WGD. Second, this chapter describes the impact of the 2R-WGD on the evolution of the vertebrate genome structure, gene number, and the evolutionary dynamics of the functional fate of vertebrate ohnologs (paralogous genes that originated by WGD) in comparison with non-vertebrate chordate gene homologs. Finally, this review discusses the functional consequences of the 2R-WGD on the origin and evolution of vertebrate innovations compared with urochordates and cephalochordates, paying special attention to the origin of neural crest cells, placodes, and the big complex brain, key features that probably facilitated the transition from ancestral filter-feeding non-vertebrate chordates to voracious vertebrate predators. Currently available data, however, seem to suggest that these putative key features were present to at least some extent in stem Olfactores; hence, the impact of the 2R-WGD may not be related to the immediate origin of vertebrate innovations, but to the subsequent diversification of a wide variety of complex structures that facilitated the successful radiation of vertebrates.
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References
Abrusán G, Krambeck H-J (2006) Competition may determine the diversity of transposable elements. Theor Popul Biol 70(3):364–375
Aburomia R, Khaner O, Sidow A (2003) Functional evolution in the ancestral lineage of vertebrates or when genomic complexity was wagging its morphological tail. J Struct Funct Genomics 3(1–4):45–52
Ahn S, Tanksley SD (1993) Comparative linkage maps of the rice and maize genomes. Proc Natl Acad Sci U S A 90(17):7980–7984
Albalat R (2009) The retinoic acid machinery in invertebrates: ancestral elements and vertebrate innovations. Mol Cell Endocrinol 313(1–2):23–35
Albalat R, Brunet F, Laudet V, Schubert M (2011) Evolution of retinoid and steroid signaling: vertebrate diversification from an amphioxus perspective. Genome Biol Evol 3:985–1005
Andreakis N, D’Aniello S, Albalat R, Patti FP, Garcia-Fernandez J, Procaccini G, Sordino P, Palumbo A (2011) Evolution of the nitric oxide synthase family in metazoans. Mol Biol Evol 28(1):163–179
Araki I, Terazawa K, Satoh N (1996) Duplication of an amphioxus myogenic bHLH gene is independent of vertebrate myogenic bHLH gene duplication. Gene 171(2):231–236
Bailey W, Kim J, Wagner G, Ruddle F (1997) Phylogenetic reconstruction of vertebrate Hox cluster duplications. Mol Biol Evol 14:843–853
Bassham S, Cañestro C, Postlethwait JH (2008) Evolution of developmental roles of Pax2/5/8 paralogs after independent duplication in urochordate and vertebrate lineages. BMC Biol 6:35
Bassham S, Postlethwait JH (2005) The evolutionary history of placodes: a molecular genetic investigation of the larvacean urochordate Oikopleura dioica. Development 132(19):4259–4272
Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, Salama SR, Rubin EM, Kent WJ, Haussler D (2006) A distal enhancer and an ultra conserved exon are derived from a novel retroposon. Nature 441(7089):87–90
Bennetzen JL (2005) Transposable elements, gene creation and genome rearrangement in flowering plants. Curr Opin Genet Dev 15(6):621–627
Bertrand S, Campo-Paysaa F, Camasses A, Garcia-Fernandez J, Escriva H (2009) Actors of the tyrosine kinase receptor downstream signaling pathways in amphioxus. Evol Dev 11(1):13–26
Birchler JA, Veitia RA (2007) The gene balance hypothesis: from classical genetics to modern genomics. Plant Cell 19(2):395–402
Birchler JA, Veitia RA (2010) The gene balance hypothesis: implications for gene regulation, quantitative traits and evolution. New Phytol 186(1):54–62
Bourlat SJ, Juliusdottir T, Lowe CJ, Freeman R, Aronowicz J, Kirschner M, Lander ES, Thorndyke M, Nakano H, Kohn AB, Heyland A, Moroz LL, Copley RR, Telford MJ (2006) Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida. Nature 444(7115):85–88
Bourque G, Leong B, Vega VB, Chen X, Lee YL, Srinivasan KG, Chew JL, Ruan Y, Wei CL, Ng HH, Liu ET (2008) Evolution of the mammalian transcription factor binding repertoire via transposable elements. Genome Res 18(11):1752–1762
Braasch I, Postlethwait JH (2011) The teleost agouti-related protein 2 gene is an ohnolog gone missing from the tetrapod genome. Proc Natl Acad Sci U S A 108(13):E47–E48
Braasch I, Volff JN, Schartl M (2009) The endothelin system: evolution of vertebrate-specific ligand–receptor interactions by three rounds of genome duplication. Mol Biol Evol 26(4):783–799
Bridgham JT, Brown JE, Rodriguez-Mari A, Catchen JM, Thornton JW (2008) Evolution of a new function by degenerative mutation in cephalochordate steroid receptors. PLoS Genet 4(9):e1000191
Brusca RC, Brusca GJ (2002) Invertebrates. Sinauer Associates, Sunderland
Campo-Paysaa F, Semon M, Cameron RA, Peterson KJ, Schubert M (2011) microRNA complements in deuterostomes: origin and evolution of microRNAs. Evol Dev 13(1):15–27
Cañestro C, Albalat R (2012) Transposon diversity is higher in amphioxus than in vertebrates: functional and evolutionary inferences. Brief Funct Genomics 11(2):131–141
Cañestro C, Albalat R, Hjelmqvist L, Godoy L, Jornvall H, Gonzalez-Duarte R (2002a) Ascidian and amphioxus Adh genes correlate functional and molecular features of the ADH family expansion during vertebrate evolution. J Mol Evol 54(1):81–89
Cañestro C, Bassham S, Postlethwait JH (2003a) Seeing chordate evolution through the Ciona genome sequence. Genome Biol 4(3):208–211
Cañestro C, Bassham S, Postlethwait JH (2005) Development of the central nervous system in the larvacean Oikopleura dioica and the evolution of the chordate brain. Dev Biol 285(2):298–315
Cañestro C, Catchen JM, Rodriguez-Mari A, Yokoi H, Postlethwait JH (2009) Consequences of lineage-specific gene loss on functional evolution of surviving paralogs: ALDH1A and retinoic acid signaling in vertebrate genomes. PLoS Genet 5(5):e1000496
Cañestro C, Godoy L, Gonzàlez-Duarte R, Albalat R (2003b) Comparative expression analysis of Adh3 during arthropod, urochordate, cephalochordate and vertebrate development challenges its predicted housekeeping role. Evol Dev 5(2):157–162
Cañestro C, Gonzàlez-Duarte R, Albalat R (2002b) Minisatellite instability at the Adh locus reveals somatic polymorphism in amphioxus. Nucleic Acids Res 30(13):2871–2876
Cañestro C, Hjelmqvist L, Albalat R, Garcia-Fernàndez J, Gonzàlez-Duarte R, Jörnvall H (2000) Amphioxus alcohol dehydrogenase is a class 3 form of single type and of structural conservation but with unique developmental expression. Eur J Biochem 267:6511–6518
Cañestro C, Postlethwait JH (2007) Development of a chordate anterior–posterior axis without classical retinoic acid signaling. Dev Biol 305(2):522–538
Cañestro C, Postlethwait JH, Gonzàlez-Duarte R, Albalat R (2006) Is retinoic acid genetic machinery a chordate innovation? Evol Dev 8(5):394–406
Cañestro C, Yokoi H, Postlethwait JH (2007) Evolutionary developmental biology and genomics. Nat Rev Genet 8(12):932–942
Catchen JM, Braasch I, Postlethwait JH (2011) Conserved synteny and the zebrafish genome. Methods Cell Biol 104:259–285
Catchen JM, Conery JS, Postlethwait JH (2009) Automated identification of conserved synteny after whole-genome duplication. Genome Res 19(8):1497–1505
Chain FJ, Evans BJ (2006) Multiple mechanisms promote the retained expression of gene duplicates in the tetraploid frog Xenopus laevis. PLoS Genet 2(4):e56
Comai L (2000) Genetic and epigenetic interactions in allopolyploid plants. Plant Mol Biol 43(2–3):387–399
Conant GC, Wolfe KH (2008) Turning a hobby into a job: how duplicated genes find new functions. Nat Rev Genet 9(12):938–950
Coulier F, Popovici C, Villet R, Birnbaum D (2000) MetaHox gene clusters. J Exp Zool 288(4):345–351
D’Aniello S, Irimia M, Maeso I, Pascual-Anaya J, Jimenez-Delgado S, Bertrand S, Garcia-Fernandez J (2008) Gene expansion and retention leads to a diverse tyrosine kinase superfamily in amphioxus. Mol Biol Evol 25(9):1841–1854
Danchin EG, Pontarotti P (2004) Towards the reconstruction of the bilaterian ancestral pre-MHC region. Trends Genet 20(12):587–591
Dehal P, Boore JL (2005) Two rounds of whole genome duplication in the ancestral vertebrate. PLoS Biol 3(10):e314
Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, De Tomoso A, Davidson B, Di Gregorio A, Gelpke M, Goodstein DM, Harafuji N, Hastings KEM, Ho I, Hotta K, Huang W, Kawashima T, Lemaire P, Martinez D, Meinertzhagen IA, Necula S, Nonaka M, Putnam N, Rash S, Saiga H, Satake M, Terry A, Yamada L, Wang H-G, Awazu S, Azumi K, Boore J, Branno M, Chin-bow S, DeSantis R, Doyle S, Francino P, Keys DN, Haga S, Hayashi H, Hino K, Imai KS, Inaba K, Kano S, Kobayashi K, Kobayashi M, Lee B-I, Makabe KW, Manohar C, Matassi G, Medina M, Mochizuki Y, Mount S, Morishita T, Miura S, Nakayama A, Nishizaka S, Nomoto H, Ohta F, Oishi K, Rigoutsos I, Sano M, Sasaki A, Sasakura Y, Shoguchi E, Shin-i T, Spagnuolo A, Stainier D, Suzuki MM, Tassy O, Takatori N, Tokuoka M, Yagi K, Yoshizaki F, Wada S, Zhang C, Hyatt PD, Larimer F, Detter C, Doggett N, Glavina T, Hawkins T, Richardson P, Lucas S, Kohara Y, Levine M, Satoh N, Rokhsar DS (2002) The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science 298(5601):2157–2167
Delsuc F, Brinkmann H, Chourrout D, Philippe H (2006) Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature 439(7079):965–968
Denoeud F, Henriet S, Mungpakdee S, Aury JM, Da Silva C, Brinkmann H, Mikhaleva J, Olsen LC, Jubin C, Cañestro C, Bouquet JM, Danks G, Poulain J, Campsteijn C, Adamski M, Cross I, Yadetie F, Muffato M, Louis A, Butcher S, Tsagkogeorga G, Konrad A, Singh S, Jensen MF, Cong EH, Eikeseth-Otteraa H, Noel B, Anthouard V, Porcel BM, Kachouri-Lafond R, Nishino A, Ugolini M, Chourrout P, Nishida H, Aasland R, Huzurbazar S, Westhof E, Delsuc F, Lehrach H, Reinhardt R, Weissenbach J, Roy SW, Artiguenave F, Postlethwait JH, Manak JR, Thompson EM, Jaillon O, Du Pasquier L, Boudinot P, Liberles DA, Volff JN, Philippe H, Lenhard B, Roest Crollius H, Wincker P, Chourrout D (2010) Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate. Science 330(6009):1381–1385
Donoghue PC, Graham A, Kelsh RN (2008) The origin and evolution of the neural crest. BioEssays 30(6):530–541
Durand D (2003) Vertebrate evolution: doubling and shuffling with a full deck. Trends Genet 19(1):2–5
Ebner B, Panopoulou G, Vinogradov SN, Kiger L, Marden MC, Burmester T, Hankeln T (2010) The globin gene family of the cephalochordate amphioxus: implications for chordate globin evolution. BMC Evol Biol 10:370
Edvardsen RB, Seo HC, Jensen MF, Mialon A, Mikhaleva J, Bjordal M, Cartry J, Reinhardt R, Weissenbach J, Wincker P, Chourrout D (2005) Remodelling of the homeobox gene complement in the tunicate Oikopleura dioica. Curr Biol 15(1):R12–R13
Escriva H, Bertrand S, Germain P, Robinson-Rechavi M, Umbhauer M, Cartry J, Duffraisse M, Holland L, Gronemeyer H, Laudet V (2006) Neofunctionalization in vertebrates: the example of retinoic acid receptors. PLoS Genet 2(7):e102
Ferrier DE, Dewar K, Cook A, Chang JL, Hill-Force A, Amemiya C (2005) The chordate ParaHox cluster. Curr Biol 15(20):R820–R822
Ferrier DE, Minguillon C, Holland PW, Garcia-Fernandez J (2000) The amphioxus Hox cluster: deuterostome posterior flexibility and Hox14. Evol Dev 2(5):284–293
Ferrier DEK, Minguillón C, Cebrián C, Garcia-Fernàndez J (2001) Amphioxus Evx genes: implications for the evolution of the midbrain–hindbrain boundary and the chordate tailbud. Dev Biol 237(2):270–281
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(1):114–139
Feschotte C (2008) Transposable elements and the evolution of regulatory networks. Nat Rev Genet 9(5):397–405
Force A, Amores A, Postlethwait JH (2002) Hox cluster organization in the jawless vertebrate Petromyzon marinus. J Exp Zool 294(1):30–46
Force A, Lynch M, Pickett FB, Amores A, Yan Y-L, Postlethwait J (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151(4):1531–1545
Fredriksson R, Lagerstrom MC, Lundin LG, Schioth HB (2003) The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints. Mol Pharmacol 63(6):1256–1272
Fried C, Prohaska SJ, Stadler PF (2003) Independent Hox-cluster duplications in lampreys. J Exp Zoolog Part B Mol Dev Evol 299(1):18–25
Friedman R, Hughes AL (2001) Pattern and timing of gene duplication in animal genomes. Genome Res 11(11):1842–1847
Furlong R, Holland P (2002) Were vertebrates octoploid? Philos T Roy Soc B 357:531–544
Furlong RF, Younger R, Kasahara M, Reinhardt R, Thorndyke M, Holland PW (2007) A degenerate ParaHox gene cluster in a degenerate vertebrate. Mol Biol Evol 24(12):2681–2686
Gans C, Northcutt RG (1983) Neural crest and the origin of vertebrates: a new head. Science 220:268–274
Garcia-Fernandez J (2005) The genesis and evolution of homeobox gene clusters. Nat Rev Genet 6(12):881–892
Garcia-Fernàndez J, Ferrier DE, Minguillón C, Cebrián C (2001) The amphioxus genome in evo-devo: archetype or “cul de sac”. Int J Dev Biol 45(S1):S137–S138
Garcia-Fernàndez J, Holland PW (1994) Archetypal organization of the amphioxus Hox gene cluster. Nature 370(6490):563–566
Gaut BS, Doebley JF (1997) DNA sequence evidence for the segmental allotetraploid origin of maize. Proc Natl Acad Sci U S A 94(13):6809–6814
Gitelman I (2007) Evolution of the vertebrate twist family and synfunctionalization: a mechanism for differential gene loss through merging of expression domains. Mol Biol Evol 24(9):1912–1925
Gout JF, Duret L, Kahn D (2009) Differential retention of metabolic genes following whole-genome duplication. Mol Biol Evol 26(5):1067–1072
Gu X, Wang Y, J G (2002) Age distribution of human gene families shows significant roles of both large- and small-scale duplications in vertebrate evolution. Nat Genet 31:205–209
Heimberg AM, Sempere LF, Moy VN, Donoghue PC, Peterson KJ (2008) microRNAs and the advent of vertebrate morphological complexity. Proc Natl Acad Sci U S A 105(8):2946–2950
Hellsten U, Khokha MK, Grammer TC, Harland RM, Richardson P, Rokhsar DS (2007) Accelerated gene evolution and subfunctionalization in the pseudotetraploid frog Xenopus laevis. BMC Biol 5:31
Herpin A, Braasch I, Kraeussling M, Schmidt C, Thoma EC, Nakamura S, Tanaka M, Schartl M (2010) Transcriptional rewiring of the sex determining dmrt1 gene duplicate by transposable elements. PLoS Genet 6(2):e1000844
Hoekstra HE, Coyne JA (2007) The locus of evolution: evo devo and the genetics of adaptation. Evolution 61(5):995–1016
Hoffmann FG, Opazo JC, Storz JF (2012) Whole-genome duplications spurred the functional diversification of the globin gene superfamily in vertebrates. Mol Biol Evol 29:303−312
Holland LZ (2007) Developmental biology: a chordate with a difference. Nature 447(7141):153–155
Holland LZ (2009) Chordate roots of the vertebrate nervous system: expanding the molecular toolkit. Nat Rev Neurosci 10(10):736–746
Holland LZ, Albalat R, Azumi K, Benito-Gutierrez E, Blow MJ, Bronner-Fraser M, Brunet F, Butts T, Candiani S, Dishaw LJ, Ferrier DE, Garcia-Fernandez J, Gibson-Brown JJ, Gissi C, Godzik A, Hallbook F, Hirose D, Hosomichi K, Ikuta T, Inoko H, Kasahara M, Kasamatsu J, Kawashima T, Kimura A, Kobayashi M, Kozmik Z, Kubokawa K, Laudet V, Litman GW, McHardy AC, Meulemans D, Nonaka M, Olinski RP, Pancer Z, Pennacchio LA, Pestarino M, Rast JP, Rigoutsos I, Robinson-Rechavi M, Roch G, Saiga H, Sasakura Y, Satake M, Satou Y, Schubert M, Sherwood N, Shiina T, Takatori N, Tello J, Vopalensky P, Wada S, Xu A, Ye Y, Yoshida K, Yoshizaki F, Yu JK, Zhang Q, Zmasek CM, de Jong PJ, Osoegawa K, Putnam NH, Rokhsar DS, Satoh N, Holland PW (2008) The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Res 18(7):1100–1111
Holland LZ, Short S (2008) Gene duplication, co-option and recruitment during the origin of the vertebrate brain from the invertebrate chordate brain. Brain Behav Evol 72(2):91–105
Holland PWH, Garcia-Fernàndez J, Williams NA, Sidow A (1994) Gene duplications and the origins of vertebrate development. Development (Suppl.):125–133
Holland PWH, Koschorz B, Holland LZ, Herrmann BG (1995) Conservation of Brachyury (T) genes in amphioxus and vertebrates: developmental and evolutionary implications. Development 121:4283–4291
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(10):1582–1591
Hughes AL (1994) The evolution of functionally novel proteins after gene duplication. Proc Roy Soc Lond B 256:119–124
Hughes AL (1999) Phylogenies of developmentally important proteins do not support the hypothesis of two rounds of genome duplication early in vertebrate history. J Mol Evol 48(5):565–576
Hughes AL, Friedman R (2003) 2R or not 2R: testing hypotheses of genome duplication in early vertebrates. J Struct Funct Genomics 3(1–4):85–93
Huminiecki L, Heldin CH (2010) 2R and remodeling of vertebrate signal transduction engine. BMC Biol 8:146
Imai KS, Stolfi A, Levine M, Satou Y (2009) Gene regulatory networks underlying the compartmentalization of the Ciona central nervous system. Development 136(2):285–293
Irimia M, Denuc A, Burguera D, Somorjai I, Martin-Duran JM, Genikhovich G, Jimenez-Delgado S, Technau U, Roy SW, Marfany G, Garcia-Fernandez J (2011) Stepwise assembly of the Nova-regulated alternative splicing network in the vertebrate brain. Proc Natl Acad Sci U S A 108(13):5319–5324
Irvine SQ, Carr JL, Bailey WJ, Kawasaki K, Shimizu N, Amemiya CT, Ruddle FH (2002) Genomic analysis of Hox clusters in the sea lamprey Petromyzon marinus. J Exp Zool 294:47–62
Jeffery WR (2007) Chordate ancestry of the neural crest: new insights from ascidians. Semin Cell Dev Biol 18:481−491
Jeffery WR, Chiba T, Krajka FR, Deyts C, Satoh N, Joly JS (2008) Trunk lateral cells are neural crest-like cells in the ascidian Ciona intestinalis: insights into the ancestry and evolution of the neural crest. Dev Biol 324(1):152–160
Jeffery WR, Strickler AG, Yamamoto Y (2004) Migratory neural crest-like cells form body pigmentation in a urochordate embryo. Nature 431(7009):696–699
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(4):266–275
Kappen C, Schughart K, Ruddle FH (1989) Two steps in the evolution of Antennapedia-class vertebrate homeobox genes. Proc Natl Acad Sci U S A 86(14):5459–5463
Karabinos A, Bhattacharya D (2000) Molecular evolution of calmodulin and calmodulin-like genes in the cephalochordate Branchiostoma. J Mol Evol 51(2):141–148
Kasahara M (2007) The 2R hypothesis: an update. Curr Opin Immunol 19(5):547–552
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(8):1404–1418
Katsanis N, Fitzgibbon J, Fisher EMC (1996) Paralogy mapping: identification of a region in the human MHC triplicated onto human chromosomes 1 and 9 allows the prediction and isolation of novel PBX and NOTCH loci. Genomics 35:101–108
Kohn M, Hogel J, Vogel W, Minich P, Kehrer-Sawatzki H, Graves JA, Hameister H (2006) Reconstruction of a 450-My-old ancestral vertebrate protokaryotype. Trends Genet 22(4):203–210
Kuraku S (2008) Insights into cyclostome phylogenomics: pre-2R or post-2R. Zoolog Sci 25(10):960–968
Kuraku S (2010) Palaeophylogenomics of the vertebrate ancestor—impact of hidden paralogy on hagfish and lamprey gene phylogeny. Integr Comp Biol 50(1):124–129
Kuraku S (2011) Hox gene clusters of early vertebrates: do they serve as reliable markers for genome evolution? Genomics Proteomics Bioinformatics 9(3):97–103
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(1):47–59
Kuratani S (2009) Insights into neural crest migration and differentiation from experimental embryology. Development 136(10):1585–1589
Kuratani S, Ota KG (2008) Hagfish (cyclostomata, vertebrata): searching for the ancestral developmental plan of vertebrates. BioEssays 30(2):167–172
Laisney JA, Braasch I, Walter RB, Meierjohann S, Schartl M (2010) Lineage-specific co-evolution of the Egf receptor/ligand signaling system. BMC Evol Biol 10:27
Larhammar D, Lundin L, Hallbook F (2002) The human Hox-bearing chromosome regions did arise by block or chromosome (or even genome) duplications. Genome Res 12(12):1910–1920
Lee CT, Risom T, Strauss WM (2007) Evolutionary conservation of microRNA regulatory circuits: an examination of microRNA gene complexity and conserved microRNA-target interactions through metazoan phylogeny. DNA Cell Biol 26(4):209–218
Leveugle M, Prat K, Perrier N, Birnbaum D, Coulier F (2003) ParaDB: a tool for paralogy mapping in vertebrate genomes. Nucleic Acids Res 31(1):63–67
Louis A, Roest Crollius H, Robinson-Rechavi M (2012) How much does the amphioxus genome represent the ancestor of chordates? Brief Funct Genomics 11(2):89–95
Lowe CB, Bejerano G, Haussler D (2007) Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proc Natl Acad Sci U S A 104(19):8005–8010
Lundin LG (1979) Evolutionary conservation of large chromosomal segments reflected in mammalian gene maps. Clin Genet 16(2):72–81
Lundin LG (1993) Evolution of the vertebrate genome as relected in paralogous chromosomal regions in man and the house mouse. Genomics 16:1–19
Lundin LG, Larhammar D, Hallbook F (2003) Numerous groups of chromosomal regional paralogies strongly indicate two genome doublings at the root of the vertebrates. J Struct Funct Genomics 3(1–4):53–63
Lynch M, Conery J (2000) The evolutionary fate and consequences of gene duplication. Science 290(5494):1151–1155
Lynch M, Force A (2000) The origin of interspecific genomic incompatibility via gene duplication. Am Nat 156:590–605
Lynch M, O’Hely M, Walsh B, Force A (2001) The probability of preservation of a newly arisen gene duplicate. Genetics 159(4):1789–1804
Lynch VJ, Leclerc RD, May G, Wagner GP (2011) Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals. Nat Genet 43:1154−1159
Lynch VJ, Wagner GP (2009) Multiple chromosomal rearrangements structured the ancestral vertebrate Hox-bearing protochromosomes. PLoS Genet 5(1):e1000349
Makino T, McLysaght A (2010) Ohnologs in the human genome are dosage balanced and frequently associated with disease. Proc Natl Acad Sci U S A 107(20):9270–9274
Martinez-Morales JR, Henrich T, Ramialison M, Wittbrodt J (2007) New genes in the evolution of the neural crest differentiation program. Genome Biol 8(3):R36
Matzke MA, Matzke AJ (1998) Polyploidy and transposons. Trends Ecol Evol 13(6):241
Matzke MA, Mette MF, Matzke AJ (2000) Transgene silencing by the host genome defense: implications for the evolution of epigenetic control mechanisms in plants and vertebrates. Plant Mol Biol 43(2–3):401–415
Mazet F, Hutt JA, Milloz J, Millard J, Graham A, Shimeld SM (2005) Molecular evidence from Ciona intestinalis for the evolutionary origin of vertebrate sensory placodes. Dev Biol 282(2):494–508
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(13):2471–2484
McLysaght A, Hokamp K, Wolfe KH (2002) Extensive genomic duplication during early chordate evolution. Nat Genet 31:200–204
Meulemans D, Bronner-Fraser M (2004) Gene-regulatory interactions in neural crest evolution and development. Dev Cell 7(3):291–299
Meulemans D, Bronner-Fraser M (2005) Central role of gene cooption in neural crest evolution. J Exp Zoolog B Mol Dev Evol 304(4):298–303
Meulemans D, Bronner-Fraser M (2007) Insights from amphioxus into the evolution of vertebrate cartilage. PLoS One 2(8):e787
Minguillon C, Ferrier DE, Cebrian C, Garcia-Fernandez J (2002) Gene duplications in the prototypical cephalochordate amphioxus. Gene 287(1–2):121–128
Minguillon C, Jimenez-Delgado S, Panopoulou G, Garcia-Fernandez J (2003) The amphioxus Hairy family: differential fate after duplication. Development 130(24):5903–5914
Muffato M, Louis A, Poisnel CE, Roest Crollius H (2010) Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes. Bioinformatics 26(8):1119–1121
Nadeau JH, Sankoff D (1997) Comparable rates of gene loss and functional divergence after genome duplications early in vertebrate evolution. Genetics 147(3):1259–1266
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(9):1254–1265
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(5):820–828
Nelson JS (1994) Fishes of the world, 3rd edn. Wiley-Interscience, New York
Nikitina N, Sauka-Spengler T, Bronner-Fraser M (2009) Chapter 1. Gene regulatory networks in neural crest development and evolution. Curr Top Dev Biol 86:1–14
Northcutt RG, Gans C (1983) The genesis of neural crest and epidermal placodes: a reinterpretation of vertebrate origins. Quart Rev Biol 58:1–28
Nowak MA, Boerlijst MC, Cooke J, Smith JM (1997) Evolution of genetic redundancy. Nature 388(6638):167–171
Oda H, Wada H, Tagawa K, Akiyama-Oda Y, Satoh N, Humphreys T, Zhang S, Tsukita S (2002) A novel amphioxus cadherin that localizes to epithelial adherens junctions has an unusual domain organization with implications for chordate phylogeny. Evol Dev 4(6):426–434
Ohno S (1970) Evolution by gene duplication. Springer, New York
Ohno S, Wolf U, Atkins NB (1968) Evolution from fish to mammals by gene duplication. Hereditas 59(1):169–187
Ota KG, Kuratani S (2007) Cyclostome embryology and early evolutionary history of vertebrates. Integr Comp Biol 47(3):329–337
Otto SP (2007) The evolutionary consequences of polyploidy. Cell 131(3):452–462
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(6A):1056–1066
Paps J, Holland PW, Shimeld SM (2012) A genome-wide view of transcription factor gene diversity in chordate evolution: less gene loss in amphioxus? Brief Funct Genomics 11(2):177–186
Parisod C, Alix K, Just J, Petit M, Sarilar V, Mhiri C, Ainouche M, Chalhoub B, Grandbastien MA (2010) Impact of transposable elements on the organization and function of allopolyploid genomes. New Phytol 186(1):37–45
Paterson AH, Chapman BA, Kissinger JC, Bowers JE, Feltus FA, Estill JC (2006) Many gene and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon. Trends Genet 22(11):597–602
Pebusque MJ, Coulier F, Birnbaum D, Pontarotti P (1998) Ancient large-scale genome duplications: phylogenetic and linkage analyses shed light on chordate genome evolution. Mol Biol Evol 15(9):1145–1159
Pendleton JW, Nagai BK, Murtha MT, Ruddle FH (1993) Expansion of the Hox gene family and the evolution of chordates. Proc Natl Acad Sci U S A 90:6300–6304
Polak P, Domany E (2006) Alu elements contain many binding sites for transcription factors and may play a role in regulation of developmental processes. BMC Genomics 7:133
Popovici C, Leveugle M, Birnbaum D, Coulier F (2001) Coparalogy: physical and functional clusterings in the human genome. Biochem Biophys Res Commun 288(2):362–370
Postlethwait J, Amores A, Cresko W, Singer A, Yan YL (2004) Subfunction partitioning, the teleost radiation and the annotation of the human genome. Trends Genet 20(10):481–490
Postlethwait JH (2007) The zebrafish genome in context: ohnologs gone missing. J Exp Zoolog B Mol Dev Evol 308(5):563–577
Putnam NH, Butts T, Ferrier DE, Furlong RF, Hellsten U, Kawashima T, Robinson-Rechavi M, Shoguchi E, Terry A, Yu JK, Benito-Gutierrez EL, Dubchak I, Garcia-Fernandez J, Gibson-Brown JJ, Grigoriev IV, Horton AC, de Jong PJ, 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 IT, Toyoda A, Bronner-Fraser M, Fujiyama A, Holland LZ, Holland PW, Satoh N, Rokhsar DS (2008) The amphioxus genome and the evolution of the chordate karyotype. Nature 453(7198):1064–1071
Ravi V, Lam K, Tay BH, Tay A, Brenner S, Venkatesh B (2009) Elephant shark (Callorhinchus milii) provides insights into the evolution of Hox gene clusters in gnathostomes. Proc Natl Acad Sci U S A 106(38):16327–16332
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(3):580–586
Roux J, Robinson-Rechavi M (2008) Developmental constraints on vertebrate genome evolution. PLoS Genet 4(12):e1000311
Ruvinsky I, Silver LM (1997) Newly identified paralogous groups on mouse chromosomes 5 and 11 reveal the age of a T-box cluster duplication. Genomics 40(2):262–266
SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL (1998) The paleontology of intergene retrotransposons of maize. Nat Genet 20(1):43–45
SanMiguel P, Tikhonov A, Jin YK, Motchoulskaia N, Zakharov D, Melake-Berhan A, Springer PS, Edwards KJ, Lee M, Avramova Z, Bennetzen JL (1996) Nested retrotransposons in the intergenic regions of the maize genome. Science 274(5288):765–768
Sauka-Spengler T, Meulemans D, Jones M, Bronner-Fraser M (2007) Ancient evolutionary origin of the neural crest gene regulatory network. Dev Cell 13(3):405–420
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(7082):341–345
Semon M, Wolfe KH (2007) Consequences of genome duplication. Curr Opin Genet Dev 17(6):505–512
Semon M, Wolfe KH (2008) Preferential subfunctionalization of slow-evolving genes after allopolyploidization in Xenopus laevis. Proc Natl Acad Sci U S A 105(24):8333–8338
Sempere LF, Cole CN, McPeek MA, Peterson KJ (2006) The phylogenetic distribution of metazoan microRNAs: insights into evolutionary complexity and constraint. J Exp Zool B Mol Dev Evol 306(6):575–588
Seo HC, Edvardsen RB, Maeland AD, Bjordal M, Jensen MF, Hansen A, Flaat M, Weissenbach J, Lehrach H, Wincker P, Reinhardt R, Chourrout D (2004) Hox cluster disintegration with persistent anteroposterior order of expression in Oikopleura dioica. Nature 431(7004):67–71
Sharman AC, Holland PWH (1998) Estimation of hox gene cluster number in lampreys. Int J Dev Biol 42:617–620
Shemer G, Podbilewicz B (2000) Fusomorphogenesis: cell fusion in organ formation. Dev Dyn 218(1):30–51
Shimeld SM, Holland PW (2000) Vertebrate innovations. Proc Natl Acad Sci U S A 97(9):4449–4452
Sidow A (1996) Gen(om)e duplications in the evolution of early vertebrates. Curr Opin Genet Dev 6:715–722
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
Skrabanek L, Wolfe KH (1998) Eukaryote genome duplication—where’s the evidence? Curr Opin Genet Dev 8:694–700
Small KS, Brudno M, Hill MM, Sidow A (2007) A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome. Genome Biol 8(3):R41
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(1):336–348
Soltis DE, Soltis PS (1999) Polyploidy: recurrent formation and genome evolution. Trends Ecol Evol 14(9):348–352
Somorjai I, Bertrand S, Camasses A, Haguenauer A, Escriva H (2008) Evidence for stasis and not genetic piracy in developmental expression patterns of Branchiostoma lanceolatum and Branchiostoma floridae, two amphioxus species that have evolved independently over the course of 200 Myr. Dev Genes Evol 218(11–12):703–713
Spring J (1997) Vertebrate evolution by interspecific hybridization—are we polyploid? Fed Eur Biol Soc Lett 400:2–8
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(3):686–694
Storchova Z, Pellman D (2004) From polyploidy to aneuploidy, genome instability and cancer. Nat Rev Mol Cell Biol 5(1):45–54
Takio Y, Pasqualetti M, Kuraku S, Hirano S, Rijli FM, Kuratani S (2004) Evolutionary biology: lamprey Hox genes and the evolution of jaws. Nature 429(6989):1–262
Taylor JS, Raes J (2004) Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet 38:615–643
Taylor JS, van de Peer Y, Meyer M (2001) Genome duplication, divergent resolution and speciation. Trends Genet 17:299–301
Thornburg BG, Gotea V, Makalowski W (2006) Transposable elements as a significant source of transcription regulating signals. Gene 365:104–110
van de Lagemaat LN, Landry JR, Mager DL, Medstrand P (2003) Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions. Trends Genet 19(10):530–536
Van de Peer Y, Maere S, Meyer A (2009) The evolutionary significance of ancient genome duplications. Nat Rev Genet 10(10):725–732
Venkatesh B, Kirkness EF, Loh YH, Halpern AL, Lee AP, Johnson J, Dandona N, Viswanathan LD, Tay A, Venter JC, Strausberg RL, Brenner S (2007) Survey sequencing and comparative analysis of the elephant shark (Callorhinchus milii) genome. PLoS Biol 5(4):e101
Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA et al (2001) The sequence of the human genome. Science 291(5507):1304–1351
Vienne A, Shiina T, Abi-Rached L, Danchin E, Vitiello V, Cartault F, Inoko H, Pontarotti P (2003) Evolution of the proto-MHC ancestral region: more evidence for the plesiomorphic organisation of human chromosome 9q34 region. Immunogenetics 55(7):429–436
Wada H, Okuyama M, Satoh N, Zhang S (2006) Molecular evolution of fibrillar collagen in chordates, with implications for the evolution of vertebrate skeletons and chordate phylogeny. Evol Dev 8(4):370–377
Werth CR, Windham MD (1991) A model for divergent, allopatric speciation of polypoid pteridophytes resulting from silencing of duplicate-gene expression. Am Nat 137:515–526
Weston JA (1970) The migration and differentiation of neural crest cells. Adv Morphog 8:41–114
Wolfe K (2000) Robustness—it’s not where you think it is. Nat Genet 25(1):3–4
Wolfe KH (2001) Yesterday’s polyploids and the mystery of diploidization. Nat Rev Genet 2(5):333–341
Wolfe KH, Shields DC (1997) Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387(6634):708–713
Wotton KR, Shimeld SM (2006) Comparative genomics of vertebrate Fox cluster loci. BMC Genomics 7:271
Yu JK, Meulemans D, McKeown SJ, Bronner-Fraser M (2008) Insights from the amphioxus genome on the origin of vertebrate neural crest. Genome Res 18(7):1127–1132
Acknowledgments
This work has been supported by grant BFU2010-14875 from the Ministerio de Ciencia e Innovación (Spain). I would like to thank Julian Catchen for his generous support on the Synteny Database, and Ingo Braasch, John H. Postlethwait, Ricard Albalat, and Adriana Rodriguez for their valuable comments on the chapter, and cheerful and endless discussions on “2R, or not 2R, that is the question … on vertebrate innovations”.
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Cañestro, C. (2012). Two Rounds of Whole-Genome Duplication: Evidence and Impact on the Evolution of Vertebrate Innovations. In: Soltis, P., Soltis, D. (eds) Polyploidy and Genome Evolution. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-31442-1_16
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