Are genome evolution, organism complexity and species diversity linked?

Integrative and Comparative Biology

Volumn 44, Issue 5, 2004, Pages 358-365

  Stellwag, Edmund J ^a  

^a EAST CAROLINA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACTINOPTERYGII; PISCES; VERTEBRATA;

EID: 12244255369     PISSN: 15407063     EISSN: None     Source Type: Journal    
DOI: 10.1093/icb/44.5.358     Document Type: Conference Paper

References (54)

1. Adami, C. 2002. What is complexity? Bioessays 24:1085-1094.
2. Adams, M. D., S. E. Celnicker, R. A. Holt, C. A. Evans, and J. D. Gocayne, et al. 2000. The genome sequence of Drosaphila melanogaster. Science 287:2185-2195.
3. Amores, A., A. Force, Y. Yan, L. Joly, C. T. Amemiya, A. Fritz, R. K. Ho, J. Langeland, V. Prince, Y-L Wang, M. Westerfield, M. Ekker, and J. H. Postlethwait. 1998. Zebrafish Hox clusters and vertebrate genome evolution. Science 282:1711-1714.
4. Amores, A., T. Suzuki, Y. L. Yan, I. Pomery, A. Singer, C. Amemiya, J. H. Postlethwait. 2004. Developmental roles of pufferfish Hex clusters and genome evolution in ray-fin fish. Genome Res. 14:1-10.
5. Bailey, G. S., R. T. Poulter, and P.A. Stockwell. 1978. Gene duplication in tetraploid fish: Model for gene silencing at unlinked duplicated loci. Proc. Nati. Acad. Sci. USA 75:5575-5579.
6. Betran, E. and M. Long. 2002. Expansion of genome coding regions by acquisition of new genes. Genetica 115:65-80.
7. Bird, A. P. 1995. Gene number, noise reduction, and biological complexity. Trends Genet. 11:94-100.
8. Carroll, R. L. 1988. Vertebrate paleontology and evolution, W. H. Freeman and Company, New York.
9. Chiu, C. H., K. Dewar, G. P. Wagner, K. Takahashi, F. Ruddle, C. Ledje, P. Bartsch, J. L. Scemama, E. J. Stellwag, C. Fried, S. J. Prohaska, P. F. Stadler, and C. T. Amemiya. 2004. Bichir HoxA cluster sequence reveals surprising trends in ray-finned fish genomic evolution. Genome Res. 14:11-17.
10. Coulson, R. M. and C. A. Ouzounis. 2003. The phylogenetic diversity of eukaryotic transcription. Nucl. Acids Res. 31:653-660.
11. Durrand, D. 2003. Vertebrate evolution: Doubling and shuffling with a full deck. Trends Genet. 19:2-5.
12. Eble, G. J. 2003. The macroevolution of phenotypic integration. In M. Pigliucci and K. Preston (eds.), The evolutionary biology of complex phenotypes, pp. 253-273. Oxford University Press, Oxford.
13. Escriva, H., N. D. Holland, H. Gronemeyer, V. Laudet, and L. Z. Holland. 2002. The retinoic acid signaling pathway regulates anterior/posterior patterning in the nerve cord and pharynx of amphioxus, a chordate lacking neural crest. Development 129: 2905-2916.
14. Ferrier, D. E., C. Minguillon, P.W. H. Holland, and J. Garcia-Fernanadez. 2000. The amphioxus Hox cluster: Deuterostome posterior flexibility and Hox 14. Evol. Dev. 2:284-293.
15. Foote, M. 1993. Discordance and concordance between morphological and taxonomic diversity. Paleobiology 19:185-204.
16. Furlong, R. F. and P. W. H. Holland. 2002. Were vertebrates octoploid? Philos. Trans. R. Soc. London B Biol. Sci. 357:531-544.
17. Garcia-Fernandez, J. and P. W. H. Holland. 1994. Archetypal organization of the amphioxus Hox gene cluster. Nature 370:563-566.
18. Gibson, T. and J. Spring. 2000. Evidence in favor of ancient octapolidy in the vertebrate genome. Biochem. Soc. Trans. 28:259-264.
19. Gould, S. J. 1996. Full house. Harmony Books, New York.
20. Gu, X., Y. Wang, and J. Gu. 2002. Age distribution of human gene families shows significant roles of both large- and small-scale duplication in vertebrate evolution. Nat. Genet. 31:205-209.
21. Hahn, M. H. and G. Wray. 2002. The g-value paradox. Evol. Dev. 4:73-75.
22. Hartley, S. E. 1987. The chromosomes of salmonid fishes. Biol. Rev. 62:197-214.
23. Heilig, R., R. Eckenberg, J. L. Petit, N. Fonknechten, C. Da Silva, and R. Cattollico, et al. 2003. The DNA sequence and analysis of human chromosome 14. Nature 421:601-607.
24. Holland, P. W. 1999. Gene duplication: Past, present, future. Semin. Cell and Dev. Biol. 10:541-547.
25. Holland, P. W. H. and J. Garcia-Fernandez. 1996. Hox genes and chordate evolution. Dev. Biol. 173:382-395.
26. Holland, P. W. H., J. Garcia-Fernandez, J. Williams, and A. Sidow. 1994. Gene duplications and the origins of vertebrate development. Dev. Suppl. 125-133.
27. Hughes, A. L. 1999. Phytogenies 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.
28. Hughes, A. L., J. daSilva, and R. Friedman. 2001. Ancient genome duplications did not structure the human Hor-bearing chromosomes. Genome Res. 11:771-780.
29. Kauffman, S. A. 1993. The origins of order: Self-organization and selection in Evolution. Oxford University Press, Oxford.
30. Kumar, S. and B. Hedges. 1998. A molecular timescale for vertebrate evolution. Nature 392:917-920.
31. Lynch, M. and J. S. Conery. 2000. The evolutionary fate and consequences of duplicate genes. Science 290:1151-1155.
32. Lynch, M. and A. Force. 2000. The probability of duplicate gene preservation by subfunctionalization. Genetics 154:459-473.
33. McLysaght, A., K. Hokamp, and K. H. Wolfe. 2002. Extensive genomic duplication during early chordate evolution. Nat. Genet. 31:128-129.
34. McShea, D. W. 1996. Metazoan complexity and evolution: Is there a trend? Evolution 50:477-492.
35. McShea, D. W. 2000. Functional complexity in organisms: Parts as proxies. Biol. Philos. 15:641-668.
36. McShea, D. W. 2001. The hierarchical structure of organisms: A scale and documentation of a trend in the maximum. Paleobiology 27:405-423.
37. Meyer, A. and M. Schartl. 1999. Gene and genome duplication 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.
38. Meyer, A. and E. Málaga-Trillo. 1999. Vertebrate genomics: More fishy tales about Hox genes. Current Biol. 9:R210-R213.
39. Nelson, J. S. 1994. Fishes of the world. 3rd ed. John Wiley and Sons, New York.
40. Ohno, S. 1970. Evolution by gene duplication. Berlin-Heidelberg-New York. Springer-Verlag.
41. Powers, T. P. and C. T. Amemiya. 2004. Evidence for a Hox14 paralog group in vertebrates. Current Biol. 14:R183-184.
42. Prince, V. 2002. The Hox paradox: More complex(es) than imagined. Dev. Biol. 249:1-15.
43. Shimeld, S. M. and P. W. H. Holland. 2000. Vertebrate innovations. Proc. Natl. Acad. Sci. USA 97:4449-4452.
44. Shubert, F., K. Nieselt-Struwe, and P. Gruss. 1993. The Antenneapedia-type homeobox genes have evolved from three precursors early in metazoan evolution. Proc. Natl. Acad. Sci. U.S.A. 90: 143-147.
45. Sidow, A. 1996. Gen(om)e duplications in the evolution of early vertebrates. Curr. Opin. Genet. Dev. 6:715-722.
46. Stellwag, E. J. 1999. Hox gene duplication in fish. Semin. Cell Dev. Biol. 10:531-540.
47. Szathmry, E., F. Jordan, and C. Pal. 2001. Molecular biology and evolution. Can genes explain biological complexity? Science 292:1315-1316.
48. Taylor, J. S., I. Braasch, T. Frickey, A. Meyer, and Y. Van de Peer. 2003. Genome duplication, a trait shared by 22000 species of ray-finned fish. Genome Res. 13:382-390.
49. Taylor, J. S., Y. Ven de Peer, I. Braasch, and A. Meyer. 2001. Comparative genomics provides evidence for an ancient genome duplication event in fish. Philos. Trans. R. Soc. London B Biol. Sci. 356:1661-1679.
50. The C. elegans Sequencing Consortium. 1998. Sequence and analysis of the genome of C. elegans. Science 282:2012-2018.
51. Vandepoele, K., W. de Vos, J. S. Taylor, A. Meyer and Y. van de Peer. 2004. Major events in the genome evolution of vertebrates: Paranome age and size differ considerably between ray-finned fishes and land vertebrates. Proc. of the Natl. Acad. of Sci. U.S.A. 101:1638-1643.
52. Weinberger, E. D. 2002. A theory of pragmatic information and its application to the quasi-species model of biological evolution. Biosystems 66:105-119.
53. Wolfe K. H. 2001. Yesterday's polyploids and the mystery of diploidization. Nat. Rev. Genet. 2:333-341.
54. Zuckerkandl, E. 2002. Why so many noncoding nucleotides? The eukaryote genome as an epigenetic machine. Genetica 115:105-129.