Phylogenetic Dating and Characterization of Gene Duplications in Vertebrates: The Cartilaginous Fish Reference

Molecular Biology and Evolution

Volumn 21, Issue 3, 2004, Pages 580-586

  Robinson Rechavi, Marc ^a,b   Boussau, Bastien ^a   Laudet, Vincent ^a  

^a UNIVERSITÉ DE LYON   (France)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

2R hypothesis; Chondrichthyes; Genome duplication; Phylogeny; Ray; Shark

Indexed keywords

ARTICLE; CAMBRIAN; FISH; GENE DUPLICATION; GENETIC VARIABILITY; INVERTEBRATE; MOLECULAR EVOLUTION; MORPHOLOGY; NONHUMAN; PHYLOGENY; VERTEBRATE;

ANIMALS; EVOLUTION, MOLECULAR; GENE DUPLICATION; MULTIGENE FAMILY; PHYLOGENY; VERTEBRATES;

BRANCHIOSTOMA LANCEOLATUM; CHONDRICHTHYES; EUTELEOSTOMI; INVERTEBRATA; VERTEBRATA;

EID: 1542719902     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msh046     Document Type: Article

References (51)

1. Abi-Rached, L., A. Gilles, T. Shiina, P. Pontarotti, and H. Inoko. 2002. Evidence of en bloc duplication in vertebrate genomes. Nat. Genet. 22:22.
2. Adams, M. D., S. E. Celniker, R. A. Holt et al. (195 co-authors). 2000. The genome sequence of Drosophila melanogaster. Science 287:2185-2195.
3. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
4. Basden, A. M., G. C. Young, M. I. Coates, and A. Ritchie. 2000. The most primitive osteichthyan braincase? Nature 403: 185-188.
5. Boeckmann, B., A. Bairoch, R. Apweiler et al. (12 co-authors). 2003. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31:365-370.
6. Chiu, C.-H., C. Amemiya, K. Dewar, C.-B. Kim, F. H. Ruddle, and G. P. Wagner. 2002. Molecular evolution of the hoxA cluster in the three major gnathostome lineages. Proc. Natl. Acad. Sci. USA 99:5492-5497.
7. Dehal, P., Y. Satou, R. K. Campbell et al. (87 co-authors). 2002. The draft genome of Ciona intestinalis: insights into Chordate and Vertebrate origins. Science 298:2157-2167.
8. Durand, D. 2003. Vertebrate evolution: doubling and shuffling with a full deck. Trends Genet. 19:2-5.
9. Duret, L., D. Mouchiroud, and M. Gouy. 1994. HOVERGEN: a database of homologous vertebrate genes. Nucleic Acids Res. 22:2360-2365.
10. Escriva, H., L. Manzon, J. Youzon, and V. Laudet. 2002. Analysis of lamprey and hagfish genes reveals a complex history of gene duplications during early vertebrate evolution. Mol. Biol. Evol. 19:1440-1450.
11. Force, A., A. Amores, and J. H. Postlethwait. 2002. Hox cluster organization in the jawless vertebrate Petromyzon marinus. J. Exp. Zool. 294:30-46.
12. Friedman, R., and A. L. Hughes. 2003. The temporal distribution of gene duplication events in a set of highly conserved human gene families. Mol. Biol. Evol. 20:154-161.
13. Galtier, N., M. Gouy, and C. Gautier. 1996. SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput. Appl. Biosci. 12:543-548.
14. Gu, X., Y. Wang, and J. Gu. 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.
15. Holland, P. W., J. Garcia-Fernandez, N. A. Williams, and A. Sidow. 1994. Gene duplications and the origins of vertebrate development. Development (suppl):125-133.
16. Holt, R. A., G. M. Subramanian, A. Halpern et al. (123 co-authors). 2002. The genome sequence of the malaria mosquito Anopheles gambiae. Science 298:129-149.
17. Hughes, A. L. 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.
18. Hughes, A. L., and R. Friedman. 2003. Parallel evolution by gene duplication in the genomes of two unicellular fungi. Genome Res. 13:794-799.
19. International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921.
20. Irvine, S. Q., J. L. Carr, W. J. Bailey, K. Kawasaki, N. Shimizu, C. T. Amemiya, and F. H. Ruddle. 2002. Genomic analysis of hox clusters in the sea lamprey Petromyzon marinus. J. Exp. Zool. 294:47-62.
21. Janvier, P. 1996. Early vertebrates. Clarendon Press, Oxford.
22. Kim, C.-B., C. Amemiya, W. Bailey, K. Kawasaki, J. Mezey, W. Miller, S. Minoshima, N. Shimizu, G. Wagner, and F. Ruddle. 2000. Hox cluster genomics in the horn shark, Heterodontus francisci. Proc. Natl. Acad. Sci. USA 97:1655-1660.
23. Kumar, S., and S. B. Hedges. 1998. A molecular timescale for vertebrate evolution. Nature 392:917-920.
24. Langkjaer, R. B., P. F. Cliften, M. Johnston, and J. Piskur. 2003. Yeast genome duplication was followed by asynchronous differentiation of duplicated genes. Nature 421:848-852.
25. Lynch, M., and J. S. Conery. 2000. The evolutionary fate and consequences of duplicate genes. Science 290:1151-1155.
26. Martin, A. 2001. The phylogenetic placement of chondrichthyes: inferences from analysis of multiple genes and implications for comparative studies. Genetica 111:349-357.
27. McLysaght, A., K. Hokamp, and K. H. Wolfe. 2002. Extensive genomic duplication during early chordate evolution. Nat. Genet. 31:200-204.
28. Muller, T., and M. Vingron. 2000. Modeling amino acid replacement. J. Comput. Biol. 7:761-776.
29. Nikoh, N., N. Iwabe, K. Kuma et al. (11 co-authors). 1997. An estimate of divergence time of Parazoa and Eumetazoa and that of Cephalochordata and Vertebrata by aldolase and triose phosphate isomerase clocks. J. Mol. Evol. 45:97-106.
30. Ohno, S. 1970. Evolution by gene duplication. Springer-Verlag, Heidelberg.
31. Ono-Koyanagi, K., H. Suga, K. Katoh, and T. Miyata. 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.
32. Panopoulou, G., S. Hennig, D. Groth, A. Krause, A. J. Poustka, R. Herwig, M. Vingron, and H. Lehrach. 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.
33. Pennisi, E. 2001. Genome duplications: the stuff of evolution? Science 294:2458-2460.
34. Perrière, G., C. Combet, S. Penel et al. (11 co-authors). 2003. Integrated databanks access and sequence/structure analysis services at the PBIL. Nucleic Acids Res. 31:3393-3399.
35. Potter, I. C., and B. Rothwell. 1970. The mitotic chromosomes of the lamprey, Petromyzon marinus L. Experientia 26: 429-430.
36. Rasmussen, A. S., and U. Arnason. 1999. Molecular studies suggest that cartilaginous fishes have a terminal position in the piscine tree. Proc. Natl. Acad. Sci. USA 96:2177-2182.
37. Robinson-Rechavi, M., O. Marchand, H. Escriva, P.-L. Bardet, D. Zelus, S. Hughes, and V. Laudet. 2001. Euteleost fish genomes are characterized by expansion of gene families. Genome Res. 11:781-788.
38. Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
39. Samson, I. J., M. M. Smith, and M. P. Smith. 1996. Scales of thelodont and shark-like fishes from the Ordovician of Colorado. Nature 379:628-630.
40. Schmidt, H. A., K. Strimmer, M. Vingron, and A. von Haeseler. 2002. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502-504.
41. Shimodaira, H., and M. Hasegawa. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16:1114-1116.
42. Shu, D. G., L. Chen, J. Han, and X. L. Zhang. 2001. An early Cambrian tunicate from China. Nature 411:472-473.
43. Shu, D. G., H. L. Luo, S. Conway Morris, X. L. Zhang, S. X. Hu, L. Chen, L. Han, M. Zhu, Y. Li, and L. Z. Chen. 1999. Lower Cambrian vertebrates from south China. Nature 402:42-46.
44. Takezaki, N., F. Figueroa, Z. Zaleska-Rutczynska, and J. Klein. 2003. Molecular phylogeny of early vertebrates: monophyly of the agnathans revealed by sequences of 35 genes. Mol. Biol. Evol. 20:287-292.
45. Taylor, J. S., I. Braasch, T. Frickey, A. Meyer, and Y. Van de Peer. 2003. Genome duplication: a trait shared by 22,000 species of ray-finned fish. Genome Res. 13:382-390.
46. Taylor, J. S., Y. Van de Peer, I. Braasch, and A. Meyer. 2001. Comparative genomics provides evidence for an ancient genome duplication event in fish. Philos. Trans. R. Soc. Lond. B Biol. Sci. 356:1661-1679.
47. The C. elegans Sequencing Consortium. 1998. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282:2012-2018.
48. Wittbrodt, J., A. Meyer, and M. Schartl. 1998. More genes in fish? Bioessays 20:511-515.
49. Wolfe, K. H. 2001. Yesterday's polyploids and the mystery of diploidization. Nat. Rev. Genet. 2:333-341.
50. Yang, Z. 1996. Among-site variation and its impact on phylogenetic analyses. Trends Ecol. Evol. 11:367-371.
51. Zhu, M., Y. Xiaobo, and P. Janvier. 1999. A primitive fossil fish sheds light on the origin of bony fishes. Nature 397:607-610.