Phylogenetic reconstruction of vertebrate Hox cluster duplications

Molecular Biology and Evolution

Volumn 14, Issue 8, 1997, Pages 843-853

  Bailey, Wendy J ^a,b   Kim, Junhyong ^a   Wagner, Günter P ^a   Ruddle, Frank H ^a  

^a YALE UNIVERSITY   (United States)

^b MERCK RESEARCH LABORATORIES   (United States)

Author keywords

Collagen; Homeobox; Hox; Molecular evolution; Vertebrate

Indexed keywords

ARTICLE; GENE CLUSTER; GENE SEQUENCE; NONHUMAN; PHYLOGENY; SEQUENCE ANALYSIS; SPECIES DIFFERENTIATION; TELEOST;

BRANCHIOSTOMA LANCEOLATUM; INVERTEBRATA; MAMMALIA; TELEOSTEI; TETRAPODA; VERTEBRATA;

EID: 0030854106     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a025825     Document Type: Article

References (90)

1. ACAMPORA, D., M. D'ESPOSITO, A. FAIELLA et al. (10 co-authors). 1989. The human HOX gene family. Nucleic Acids Res. 17:10385-10402.
2. ANDERSON, I. J., R. B. GOLDBERG, R. W. MARION, W. B. UPHOLT, and P. TSIPOURAS. 1990. Spondyloepiphyseal dysplasia congenita: genetic linkage to type II collagen (COL2AI). Am. J. Hum. Genet. 46:896-901.
3. AVEROF, M., and M. AKAM. 1995. Hox genes and the diversification of insect and crustacean body plans. Nature 376:420-423.
4. BENTLEY, K. L., M. S. BRADSHAW, and F. H. RUDDLE. 1995. Human HOXB cluster and the nerve growth factor receptor gene: comparison with an orthologous chromosomal domain in mouse. Genomics 30:18-24.
5. BERNARD, M. P., M. L. CHU, J. C. MYERS, F. RAMIREZ, E. F. EIKENBERRY, and D. J. PROCKOP. 1983. Nucleotide sequences of complementary deoxyribonucleic acids for the pro alpha 1 chain of human type I procollagen. Statistical evaluation of structures that are conserved during evolution. Biochemistry 22:5213-5223.
6. BORNSTEIN, P., and H. SAGE. 1980. Structurally distinct collagen types. Annu. Rev. Biochem. 49:957-1003.
7. BOWCOCK, A. M., J. CRANDALL, L. DANESHVAR et al. (9 coauthors). 1986. Genetic analysis of cystic fibrosis: linkage of DNA and classical markers in multiplex families. Am. J. Hum. Genet. 39:699-706.
8. BUCAN, M., F. T. YANG, P. A. COLBERG, D. J. WOLGEMUTH, J. L. GUENET, U. FRANCKE, and H. LEHRACH. 1986. Genetic and cytogenetic localisation of the homeo box containing genes on mouse chromosome 6 and human chromosome 7. EMBO J. 5:2899-2905.
9. BUCHBERG, A. M., E. BROWNELL, S. NAGATA, N. A. JENKINS, and N. G. COPELAND. 1989. A comprehensive genetic map of murine chromosome 11 reveals extensive linkage conservation between mouse and human. Genetics 122:153-161.
10. BÜRGLIN, T. R. 1994. A comprehensive classification of homeobox genes, Pp. 25-72 in D. DEBOULE, ed. Guidebook to the homeobox genes. Oxford University Press, Oxford.
11. BURKE, A. C., C. E. NELSON, B. A. MORGAN, and C. TABIN. 1995. Hox genes and the evolution of vertebrate axial morphology. Development 121:333-346.
12. CANNIZZARO, L. A., C. M. CROCE, C. A. GRIFFIN, A. SIMEONE, E. BONCINELLI, and K. HUEBNER. 1987. Human homeo boxcontaining genes located at chromosome regions 2q31-2q37 and 12q12-12q13. Am. J. Hum. Genet. 41:1-15.
13. CARTWRIGHT, P., M. DICK, and L. W. Buss. 1993. HOM/Hox type homeoboxes in the chelicerate Limulus polyphemus. Mol. Phylogenet. Evol. 2:185-192.
14. CHEAH, K. S., P. K. Au, E. T. LAU, P. F. LITTLE, and L. STUBBS. 1991. The mouse Co12a-1 gene is highly conserved and is linked to Int-1 on chromosome 15. Mamm. Genome 1:171-183.
15. CUTTING, G. R., M. J. MCGINNISS, L. M. KASCH, P. TSIPOURAS, and S. E. ANTONARAKIS. 1990. Physical mapping by PFGE localizes the COL3A1 and COL5A2 genes to a 35-kb region on human chromosome 2. Genomics 8:407-410.
16. Do, M. S., and P. LONAI. 1988. Gene organization of murine homeobox-containing gene clusters. Genomics 3:195-200.
17. DUBOULE, D., and P. DOLLE. 1989. The structural and functional organization of the murine HOX gene family resembles that of Drosophila homeotic genes. EMBO J. 8:1497-1505.
18. EMANUEL, B. S., L. A. CANNIZZARO, J. M. SEYER, and J. C. MYERS. 1985. Human alpha 1(III) and alpha 2(V) procollagen genes are located on the long arm of chromosome 2. Proc. Natl. Acad. Sci. USA 82:3385-3389.
19. EXPOSITO, J.-Y., and R. GARRONE. 1990. Characterization of a fibrillar collagen gene in sponges reveals the early evolutionary appearance of two collagen gene families. Proc. Natl. Acad. Sci. USA 87:6669-6673.
20. EXPOSITO, J.-Y., M. D'ALESSIO, M. SOLURSH, and F. RAMIEREZ. 1992. Sea urchin collagen evolutionarily homologous to vertebrate pro-alpha 2(1) collagen. J. Biol. Chem. 267:15559-15562.
21. EYRE, D. R. 1980. Collagen: molecular diversity in the body's protein scaffold. Science 207:1315-1322.
22. EYRE, D., and J.-J. WU. 1987. Type XI or 1a2a3a collagen. Pp. 261-281 in R. MAYNE and R. E. BURGESON, eds. Biology of extracellular matrix: structure and function of collagen types. Academic Press, Orlando, Fla.
23. FELSENSTEIN, J. 1993. PHYLIP (phylogeny inference package). Version 3.5c. Distributed by the author, Department of Genetics, University of Washington, Seattle.
24. FESSLER, J. H., N. SHIGAKI, and L. I. FESSLER. 1985. Biosynthesis and properties of procollagen V. Ann. N.Y. Acad. Sci. 460:181-185.
25. GARCIA-FERNÀNDEZ, J., and P. W. H. HOLLAND. 1994. Archetypal organization of the amphioxus Hox gene cluster. Nature 370:563-566.
26. GRAHAM, A., N. PAPALOPULU, and R. KRUMLAUF. 1989. The murine and Drosophila homeobox gene complexes have common features of organization and expression. Cell 57:367-378.
27. HART, C. P., J. G. COMPTON, S. H. LANGLEY, L. HUNIHAN, K. P. LECLAIR, A. ZELENT, T. H. RODERICK, and F. H. RUDDLE. 1992. Genetic linkage analysis of the murine developmental mutant velvet coat (Ve) and the distal chromosome 15 developmental genes Hox-3.1, Rar-g, Wnt-1, and Krt-2. J. Exp. Zool. 263:83-95.
28. HOEVEN, F. VAN DER, P. SORDINO, N. FRAUDEAU, J.-H. IZPISÜABELMONTE, and D. DUBOULE. 1996. Teleost HoxD and HoxA genes: comparison with tetrapods and functional evolution of the HOXD complex. Mech. Dev. 54:9-21.
29. HOFMANN, H., P. P. FIETZEK, and K. KUHN. 1980. Comparative analysis of the sequences of the three collagen chains a1(I), a2(I), and a1(III). Functional and genetic aspects. J. Mol. Biol. 141:293-314.
30. HOLLAND, P. W. H., and J. GARCIA-FERNANDEZ. 1996. Hox genes and chordate evolution. Dev. Biol. 173:382-395.
31. HOLLAND, P. W. H., J. GARCIA-FERNANDEZ, N. A. WILLIAMS, and A. SIDOW. 1994. Gene duplications and the origins of vertebrate development. Dev. Suppl. 125-133.
32. HUERRE, J. C., I. HENRY, M. BERNARD, P. GALLANO, D. WEIL, K. H. GRZESCHIK, F. RAMIREZ, and C. JUNIEN. 1986. The pro alpha 2(V) collagen gene (COL5A2) maps to 2q14-2q32, syntenic to the pro alpha 1 (III) collagen locus (COL3A1). Hum. Genet. 73:64-67.
33. HUNT, P., and R. KRUMLAUF. 1992. Hox codes and positional specification in vertebrate embryonic axes. Annu. Rev. Cell Biol. 8:227-256.
34. IRVING, N. G., J. A. HARDY, N. BAHARY, J. M. FRIEDMAN, and S. D. BROWN. 1989. The alpha 2 chain of type 1 collagen does not map to mouse chromosome 16 but maps close to the Met proto-oncogene on mouse chromosome 6. Cytogenet. Cell Genet. 50:121-122.
35. JOYNER, A. L., R. V. LEBO, Y. W. KAN, R. TJIAN, D. R. Cox, and G. R. MARTIN. 1985. Comparative chromosome mapping of a conserved homoeobox region in mouse and human. Nature 314:173-175.
36. JUKES, T. H., and C. R. CANTOR. 1969. Evolution of protein molecules. Pp. 21-123 in H. N. MUNRO, ed. Mammalian protein metabolism. Academic Press, New York.
37. KAPPEN, C., and F. H. RUDDLE. 1993. Evolution of a regulatory gene family: HOM/HOX genes. Curr. Opin. Genet. Dev. 3:931-938.
38. KAPPEN, C., K. SCHUGHART, and F. H. RUDDLE. 1989. Two steps in the evolution of Antennapedia-class vertebrate homeobox genes. Proc. Natl. Acad. Sci. USA 86:5459-5463.
39. KENYON, C., and B. WANG. 1991. A cluster of Antennapediaclass homeobox genes in a nonsegmented animal. Science 253:516-517.
40. KIMURA, M. 1980. A simple method of estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
41. KUMAR, S. 1995. Phyltest: a program for testing phylogenetic hypothesis. Version 2.0. Pennsylvania State University, University Park.
42. KUMAR, S., and A. RZHETSKY. 1996. Evolutionary relationships of eukaryote kingdoms. J. Mol. Evol. 42:183-193.
43. KUMAR, S., K. TAMURA, and M. NEI. 1994. MEGA: molecular evolutionary genetic analysis sofware for microcomputers. Comput. Appl. Biosci. 10:189-191.
44. LAUDET, V., C. HANNI, J. COLL, F. CATZEFLIS, and D. STEHELIN. 1992. Evolution of the nuclear receptor gene superfamily. EMBO J. 11:1003-1013.
45. LEHMANN, E. L. 1986. Testing statistical hypotheses. 2nd edition. John Wiley and Sons, New York.
46. LUNDIN, L. G. 1993. Evolution of the vertebrate genome as reflected in paralogous chromosomal regions in man and the house mouse. Genomics 16:1-19.
47. MACFIE, H. J., N. D. LIGHT, and A. J. BAILEY. 1988. Natural taxonomy of collagen based on amino acid composition. J. Theor. Biol. 131:401-418.
48. MCGINNIS, W. M., and R. KRUMLAUF. 1992. Homeobox genes and axial patterning. Cell 68:283-302.
49. MCLACHLAN, A. D. 1976. Evidence for gene duplication in collagen. J. Mol. Biol. 107:159-174.
50. MEYER, A. 1996. The evolution of the body plan: HOM/Hox cluster evolution, model systems, and the importance of phylogeny. Pp. 322-340 in P. HARVEY, A. J. LEIGH-BROWN, and J. MAYNARD-SMITH, eds. New uses for new phylogenies. Oxford University Press, London.
51. MILLER, E. J. 1985. The structure of fibril-forming collagens. Ann. N.Y. Acad. Sci. 460:1-13.
52. MISOF, B. Y., M. J. BLANCO, and G. P. WAGNER. 1996. PCR-survey of hox-genes of the zebrafish: new sequence information and evolutionary implications. J. Exp. Zool. 274:193-206.
53. MISOF, B. Y., and G. P. WAGNER. 1996. Evidence for four Hox clusters in the killifish, Fundulus heteroclitus (Teleostei). Mol. Phylogenet. Evol. 5:309-322.
54. MUNKE, M., and U. FRANCKE. 1987. The physical map of Mus musculus chromosome 11 reveals evolutionary relationships with different syntenic groups of genes in Homo sapiens, J. Mol. Evol. 25:134-140.
55. MUNKE, M., K. HARBERS, R. JAENISCH, and U. FRANCKE. 1986. Chromosomal mapping of four different integration sites of Moloney murine leukemia virus including the locus for alpha 1(I) collagen in mouse. Cytogenet. Cell Genet. 43:140-149.
56. MYERS, J. C., H. R. LOIDL, J. M. SEYER, and A. S. DION. 1985. Complete primary structure of the human alpha 2 type V procollagen COOH-terminal propeptide. J. Biol. Chem. 260:11216-11222.
57. NADEAU, J. H., M. T. DAVISSON, D. P. DOOLITTLE, P. GRANT, A. L. HILLYARD, M. KOSOWSKY, and T. H. RODERICK 1992. Comparative map of mice and humans. Mamm. Genome 3:480-536.
58. OHNO, S. 1970. Evolution by gene duplication. Springer Verlag, New York.
59. _. 1993. Patterns in genome evolution. Curr. Opin. Genet. Dev. 3:911-914.
60. PENDELTON, J. W., B. K. NAGAI, M. T. MURTHA, and F. H. RUDDLE. 1993. Expansion of the Hox gene family and the evolution of chordates. Proc. Natl. Acad. Sci. USA 90:6300-6304.
61. PIKKARAINEN, J., and E. KULONEN. 1969. Comparative chemistry of collagen. Nature 223:839-841.
62. PRESS, W. H., B. P. FLANNERY, S. A. TEUKOLSKY, and W. T. VETTERLING. 1986. Numerical recipes: the art of scientific computing. Cambridge University Press, New York.
63. RABIN, M., S. A. FERGUSON, C. P. HART, and F. H. RUDDLE. 1986. Cognate homeo-box loci mapped on homologous human and mouse chromosomes. Proc. Natl. Acad. Sci. USA 83:9104-9108.
64. RABIN, M., C. P. HART, S. A. FERGUSON, W. MCGINNIS, M. LEVINE, and F. H. RUDDLE. 1985. Two homeo box loci mapped in evolutionarily related mouse and human chromosomes. Nature 314:175-178.
65. RAMIREZ, F., M. BERNARD, M. L. CHU et al. (9 co-authors). 1985. Isolation and characterization of the human fibrillar collagen genes. Ann. N.Y. Acad. Sci. 460:117-129.
66. RETIEF, E., M. I. PARKER, and A. E. RETIEF. 1985. Regional chromosome mapping of human collagen genes alpha 2(1) and alpha 1(1) (COLIA2 and COLLA1). Hum. Genet. 69:304-308.
67. RUDDLE, F. H., K. L. BENTLEY, M. T. MURTHA, and N. RISCH. 1994. Gene loss and gain in the evolution of the vertebrates. Dev. Suppl. 155-161.
68. RUDDLE, F. H., C. P. HART, M. RABIN, A. FERGUSON-SMITH, and D. PRAVTCHEVA. 1987. Comparative genetic analysis of homeobox genes in mouse and man. Pp. 73-86 in G. POSTE and S. T. CROOKE, eds. New frontiers in the study of gene function. Plenum Publishing, New York.
69. RZHETSKY, A., S. KUMAR, and M. NEI, 1995. Four-cluster analysis: a simple method to test phylogenetic hypotheses. Mol. Biol. Evol. 12:163-167.
70. SAITOU, N., and M. NEI. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
71. SAKURAI, Y., M. SULLIVAN, and Y. YAMADA. 1986. α1 type IV collagen gene evolved differently from fibrillar collagen genes. J. Biol. Chem. 261:6654-6657.
72. SCHUGHART, K., C. KAPPEN, and F. H. RUDDLE. 1989. Duplication of large genomic regions during the evolution of vertebrate homeobox genes. Proc. Natl. Acad. Sci. USA 86:143-147.
73. SCHURR, E., E. SKAMENE, K. MORGAN, M. L. CHU, and P. GROS. 1990. Mapping of Col3a1 and Col6a3 to proximal marine chromosome 1 identifies conserved linkage of structural protein genes between murine chromosome 1 and human chromosome 2q. Genomics 8:477-486.
74. SHASHIKANT, C. S., M. F. UTSET, S. M. VIOLETTE et al. (9 coauthors). 1991. Homeobox genes in mouse development. Crit. Rev. Eukaryot. Gene Expr. 1:207-245.
75. SOLOMON, E., and K. S. CHEAH. 1981. Collagen evolution. Nature 291:450-451.
76. STUART, J. J., S. J. BROWN, R. W. BEEMAN, and R. E. DENELL. 1993. The Tribolium homeotic gene Abdominal is homologous to abdominal-A of the Drosophila bithorax complex. Development 117:233-243.
77. STUBBS, L., C. HUXLEY, B. HOGAN, T. EVANS, M. FRIED, D. DUBOULE, and H. LEHRACH. 1990. The HOX-5 and surfeit gene clusters are linked in the proximal portion of mouse chromosome 2. Genomics 6:645-650.
78. SUNDARESAN, S., and U. FRANCKE. 1989. Gene for alpha 2(I) collagen is on mouse chromosome 6 not 16. Somat. Cell Mol. Genet. 15:471-473.
79. SWOFFORD, D. L. 1991. PAUP: phylogenetic analysis using parsimony. Version 3.1.1. Illinois Natural History Survey, Champaign.
80. SWOFFORD, D. L., G. J. OLSON, P. J. WADDELL, and D. M. HILLIS. 1996. Phylogenetic inference. Pp. 407-514 in D. M. HILLIS, C. MORITZ, and B. MABLE, eds. Molecular systematics. 2nd edition. Sinaur, Sunderland, Mass.
81. TAKAHASHI, E., T. HORI, and G. R. SUTHERLAND. 1990. Mapping of the human type II collagen gene (COL2A1) proximal to fra(12) (q13.1) by nonisotopic in situ hybridization. Cytogenet. Cell Genet. 54:84-85.
82. TAMURA, K., and M. NEI. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochon-drial DNA in humans and chimpanzees. Mol. Biol. Evol. 10:512-526.
83. THOMPSON, J. D., D. G. HIGGINS, and T. J. GIBSON, 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
84. TSIPOURAS, P., R. C. SCHWARTZ, J. D. GOLDBERG, R. L. BER-KOWITZ, and F. RAMIREZ. 1987. Prenatal prediction of osteogenesis imperfecta (OI type IV): exclusion of inheritance using a collagen gene probe. J. Med. Genet. 24:406-409.
85. VUORIO, E., and B. DE CROMBRUGGHE. 1990. The family of collagen genes. Annu. Rev. Biochem. 59:837-872.
86. WANG, W., W. WU, T. DESAI, D. C. WARD, and S. J. KAUFMAN. 1995. Localization of the alpha 7 integrin gene (ITGA7) on human chromosome 12q13: clustering of integrin and Hox genes implies parallel evolution of these gene families. Genomics 26:568-570.
87. WEIL, D., M. BERNARD, S. GARGANO, and F. RAMIREZ. 1987. The pro alpha 2(V) collagen gene is evolutionarily related to the major fibrillar-forming collagens. Nucleic Acids Res. 15:181-198.
88. ZELTSER, L., C. DESPLAN, and N. HEINTZ. 1996. Hoxb-13: a new Hox gene in a distant region of the HOXB cluster maintains colinearity. Development 122:2475-2484.
89. ZHANG, J., and M. NEI. 1996. Evolution of Antennapedia-class homeobox genes. Genetics 142:295-303.
90. ZIMONJIC, D. B., M. ALIMANDI, T. MIKI, N. C. POPESCU, and M. H. KRAUS. 1995. Localization of the human HER4/ erbB-4 gene to chromosome 2. Oncogenes 10:1235-1237.