Phylogenetic Analyses Alone Are Insufficient to Determine Whether Genome Duplication(s) Occurred During Early Vertebrate Evolution

Journal of Experimental Zoology Part B: Molecular and Developmental Evolution

Volumn 299, Issue 1, 2003, Pages 41-53

  Horton, Amy C ^a   Mahadevan, Navin R ^a   Ruvinsky, Ilya ^b,c   Gibson Brown, Jeremy J ^a  

^a WASHINGTON UNIVERSITY   (United States)

^b MASSACHUSETTS GENERAL HOSPITAL   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BRANCHIOSTOMA LANCEOLATUM; CAENORHABDITIS; CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER; INVERTEBRATA; MELANOGASTER; NEMATODA; VERTEBRATA;

EID: 0347799299     PISSN: 0022104X     EISSN: None     Source Type: Journal    
DOI: 10.1002/jez.b.40     Document Type: Article

References (54)

1. Abi-Rached L, Gilles A, Shiina T, Pontarotti P, Inoko H. 2002. Evidence of en bloc duplication in vertebrate genomes. Nature Genet 31:100-105.
2. Altschul SF, Madden TL, Schaeffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res 25:3389-3402.
3. Bailey WJ, Kim J, Wagner GP, Ruddle FH. 1997. Phylogenetic reconstruction of vertebrate Hox cluster duplications. Mol Biol Evol 14:843-853.
4. Boorman CJ, Shimeld SM. 2002. Pitx homeobox genes in Ciona and amphioxus show left-right asymmetry is a conserved chordate character and define the ascidian adenohypophysis. Evol Dev 4:354-365.
5. Brooke NM, Garcia-Fernandez J, Holland PWH. 1998. The ParaHox gene cluster is an evolutionary sister of the Hox gene cluster. Nature 392:920-922.
6. Dehal P, Satou Y, Campbell RK, et al. (87 co-authors). 2002. The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science 298:2157-2167.
7. Escriva H, Mazon L, Youson J, Laudet V. 2002. Analysis of lamprey and hagfish genes reveals a complex history of gene duplications during early vertebrate evolution. Mol Biol Evol 19:1440-1450.
8. Ferrier DEK, Brooke NM, Panopoulou G, Holland PWH. 2001a. The Mnx homeobox gene class defined by HB9, MNR2 and amphioxus AmphiMnx. Dev Genes Evol 211:103-107.
9. Ferrier DEK, Minguillon C, Cebrian C, Garcia-Fernandez J. 2001b. Amphioxus Eux genes: implications for the evolution of the midbrain-hindbrain boundary and the chordate tailbud. Dev Biol 237:270-281.
10. Force A, Lynch M, Pickett FB, Amores A, Van YL, Postlethwaite J. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151:1531-1545.
11. Friedman R, Hughes AL. 2001. Pattern and timing of gene duplication in animal genomes. Genome Res 11:1842-1847.
12. Friedman R, Hughes AL. 2003. The temporal distribution of gene duplication events in a set of highly conserved human gene families. Mol Biol Evol 20:154-161.
13. Furlong RF, Holland PWH. 2002. Were vertebrates octaploid? Phil Trans Roy Soc Lond B 357:531-544.
14. Gibson-Brown JJ, Osoegawa K, de Jong PT, McPherson JB, Waterston RH, Holland LZ. 2003. Proposal to sequence the amphioxus genome. J Exp Zool (Mol Dev Evol): in press.
15. Gu X, Wang Y, Gu J. 2002. Age distribution of human gene families shows significant roles of both large-and small-scale duplications in vertebrate evolution. Nature Genet 31:205-209.
16. Holland LZ, Gibson-Brown JJ. 2003. The Ciona intestinales genome: when the constraints are off. BioEssays 25:529-532.
17. Holland PWH, Garcia-Fernandez J, Williams NA, Sidow A. 1994. Gene duplications and the origins of vertebrate development. Development (Suppl) S125-133.
18. Holland PWH, Korschoz B, Holland LZ, Herrmann BG. 1995. Conservation of Brachyury (T) genes in amphioxus and vertebrates: developmental and evolutionary implications. Development 121:4283-4291.
19. 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 48:565-576.
20. Hughes AL, da Silva J, Friedman R. 2001. Ancient genome duplications did not structure the human Hox-bearing chromosomes. Genome Res 11:771-780.
21. Karabinos A, Bhattacharya D. 2000. Molecular evolution of calmodulin and calmodulin-like genes in the cephalochordate Branchiostoma. J Mol Evol 51:141-148.
22. Keller MJ, Gerhardt HC. 2001. Polyploidy alters advertisement call structure in gray treefrogs. Proc Roy Soc Lond B 268:341-345.
23. Kim CB, Amemiya C, Bailey W, Kawasaki K, Mezey J, Miller W, Minoshima S, Shimizu N, Wagner G, Ruddle F. 2000. Hox cluster genomics in the horn shark, Heterodontus francisci. Proc Natl Acad Sci USA 97:1655-1660.
24. Krumlauf R. 1994. Hox genes in vertebrate development. Cell 78:191-201.
25. Ku H, Vision T, Liu J, Tanksley SD. 2000. Comparing sequenced segments of the tomato and Arabidopsis genomes: large-scale duplication followed by selective gene loss creates a network of synteny. Proc Natl Acad Sci USA 97:9121-9126.
26. Lander ES, Linton LM, Birren B, et al. (243 co-authors) 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921.
27. Larhammar D, Lundin L, Hallböök F. 2002. The human Hox-bearing chromosomes regions did arise by block or chromosome (or even genome) duplications. Genome Res. 12: 1910-1920.
28. Lynch M, Conery JS. 2000. The evolutionary fate and consequences of duplicate genes. Science 290:1151-1155.
29. Martin AP. 1999. Increasing genomic complexity by gene duplication and the origin of vertebrates. Am Nat 154: 111-128.
30. Martin A. 2001. Is tetralogy true? Lack of support for the "one-to-four rule". Mol Biol Evol 18:89-93.
31. McLysaght A, Hokamp K, Wolfe KH. 2002. Extensive genomic duplication during early chordate evolution. Nature Genet 31:200-204.
32. Minguillon C, Ferrier DEK, Cebrian C, Garcia-Fernandez J. 2002. Gene duplications in the prototypical cephalochordate amphioxus. Gene 287:121-128.
33. Neidert AH, Virupannavar V, Hooker GW, Langeland JA. 2001. Lamprey Dlx genes and early vertebrate evolution. Proc Natl Acad Sci USA 98:1665-1670.
34. Ohno S. 1970. Evolution by gene duplication. Springer-Verlag, New York.
35. Ono-Koyanagi K, Suga H, Katoh K, Miyata T. 2000. Protein tyrosine phosphatases from amphioxus, hagfish, and ray: Divergence of tissue-specific isoform genes in the early evolution of vertebrates. J Mol Evol 50:302-311.
36. Pollard SL, Holland PWH. 2000. Evidence for 14 homeobox gene clusters in human genome ancestry. Curr Biol 10:1059-1062.
37. Postlethwaite JH, Woods IG, Ngo-Hazelett P, Yan Y, Kelly PD, Chu F, Huang H, Hill-Force A, Talbot WS. 2000. Zebrafish comparative genomics and the origins of vertebrate chromosomes. Genome Res 10:1890-1902.
38. Robinson-Rechavi M, Marchand O, Escriva H, Bardet PL, Zelus D, Hughes S, Laudet V. 2001. Euteleost fish genomes are characterized by expansion of gene familes. Genome Res 11:781-788.
39. 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 40:262-266.
40. Ruvinsky I, Silver LM, Gibson-Brown JJ. 2000. Phylogenetic analysis of T-box genes demonstrates the importance of amphioxus for understanding evolution of the vertebrate genome. Genetics 156:1249-1257.
41. Schubert M, Holland LZ, Holland ND, Jacobs DK. 2000. A phylogenetic tree of the Wnt genes based on all available full-length sequences, including five from the cephalochordate amphioxus. Mol Biol Evol 17:1896-1903.
42. Shimeld SM. 1999. The evolution of the hedgehog gene family in chordates: insights from amphioxus hedgehog. Dev Genes Evol 209:40-47.
43. Sidow A. 1996. Gen(om)e duplications in the evolution of early vertebrates. Curr Opin Genet Dev 6:715-722.
44. Skrabanek L, Wolfe KH. 1998. Eukaryote genome duplication - where's the evidence? Curr Opin Genet Dev 8:694-700.
45. Smith NG, Knight CR, Hurst LD. 1999. Vertebrate genome evolution: a slow shuffle or a big bang? BioEssays 21: 697-703.
46. Spring J. 1997. Vertebrate evolution by interspecific hybridization: are we polyploid? FEBS Lett 400:2-8.
47. Strimmer K, von Haeseler A. 1996. Quartet puzzling: a quartet maximum likelihood method for reconstructing tree topologies. Mol Biol Evol 13:964-969.
48. Suga H, Hoshiyama D, Kuraku S, Katoh K, Kubokawa K, Miyata T. 1999. Protein tyrosine kinase cDNAs from amphioxus, hagfish, and lamprey: isoform duplications around the divergence of cyclostomes and gnathostomes. J Mol Evol 49:601-608.
49. Swofford DL. 2001. PAUP* 4.0 beta 5: Phylogenetic Analysis Using Parsimony and Other Methods. Sinauer Associates, Sunderland, MA.
50. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl Acids Res 22: 4673-4680.
51. Venter JC, Adams MD, Myers EW, et al. (274 co-authors) 2001. The sequence of the human genome. Science 291:1304-1351.
52. Wada H, Satoh N. 1994. Details of the evolutionary history from invertebrates to vertebrates as deduced from the sequences of 18S rDNA. Proc Natl Acad Sci USA 91: 1801-1804.
53. Williams NA, Holland PWH. 1998. Gene and domain duplication in the chordate Otx gene family: insights from amphioxus Otx. Mol Biol Evol 15:600-607.
54. Williams NA, Holland PWH. 2000. An amphioxus Emx homeobox gene reveals duplication during vertebrate evolution. Mol Biol Evol 17:1520-1528.