Sequence analysis of a polymorphic Mhc class II gene in Pacific salmon

Immunogenetics

Volumn 43, Issue 6, 1996, Pages 337-351

  Miller, Kristina M ^a   Withler, Ruth E ^a  

^a PACIFIC BIOLOGICAL STATION   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 2;

ALLELE; ANIMAL CELL; ANIMAL TISSUE; ARTICLE; CODON; GENE LOCUS; GENE SEQUENCE; INTRON; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; SALMON; SEQUENCE ANALYSIS;

EID: 0029877201     PISSN: 00937711     EISSN: None     Source Type: Journal    
DOI: 10.1007/BF02199802     Document Type: Article

References (53)

1. Allendorf, F. W. and Thorgaard, G. H. Tetraploidy and the evolution of salmonid fishes. In B. J. Turner (ed.): Evolutionary Genetics of Fishes, pp. 1-53, Plenum Press, New York, 1984
2. Amemiya, C. T. and Litman, G. W. Early evolution of immunoglobulin genes. Amer Zool 31: 558-569, 1991
3. Bourlet, Y., Behar, B., Guillemot, F., Frechin, N., Billault, A., Chausse, A. M., Zoorob, R., and Auffray, C. Isolation of chicken major histocompatibility complex class II (B-L) β chain and expression in lymphoid organs. EMBO J 7: 1031-1039, 1988
4. Broecker, W. S. and Denton, G. H. What drives glacial cycles? Science 262: 48-56, 1990
5. Brown, J. H., Jardetzky, T. S., Gorga, J. C., Stern, L. J., Urban, R. G., Strominger, J. L., and Wiley, D. C. Three-dimensional structure of the human class II histocompatibility antigen HLA-DR1. Nature 364: 33-39, 1993
6. Devlin, R. H. Sequence of sockeye salmon type 1 and 2 growth hormone genes and the relationship of rainbow trout with Atlantic and Pacific salmon. Can J Fish Aquat Sci 50: 1738-1748, 1993
7. Del Pozza, G., Ombra, M. N., Perfetto, C., Barbaro, A. D. L., Autiero, M., Maffei, A., and Guardiola, J. Alu repeats and evolution of the HLA-DQA1 locus. In J. Klein and D. Klein (eds.): Molecular Evolution of the Major Histocompatibility Complex, pp 231-242, Springer, Berlin Heidelberg, 1991
8. Efron, B. The jackknife, the bootstrap, and other resampling plans. CBMS-NSF regional Conference Series in Applied Mathematics, Monograph 38, SIAM Philadelphia, 1982
9. Felsenstein, J. Confidence limits of phylogenies: an approach using the bootstrap. Evolution 39: 783-791, 1985
10. Figueroa, F., Tichy, H., Berry, R. J., and Klein, J. MHC polymorphism in island populations of mice. Curr Top Microbiol Immunol 127: 100-105, 1986
11. Flajnik, M. F., Canel, C., Kramer, J., and Kasahara, M. Evolution of the major histocompatibility complex: molecular cloning of the major histocompatibility complex class I from the amphibian Xenopus. Proc Natl Acad Sci 88: 537-541, 1991
12. Gibbs, H. L., Weatherhead, P. J., Boag, P. T., White, B. N., Tabak, L. M., and Hoysak, D. J. Realized reproductive success of polygynous red-winged blackbirds revealed by DNA markers. Science 250: 1394-1397, 1990
13. Grimholt, U., Olsaker, I., Lindstrom, C., and Lie, O. A study of variability in the MHC class II β1 and class I α2 domain exons of Atlantic salmon (Salmo salar). Anim Genet 25: 1-7, 1994
14. Hashimoto, K., Nakanishi, T., and Kurosawa, Y. Isolation of carp genes encoding major histocompatibility complex antigens. Proc Natl Acad Sci 87: 6863-6867, 1990
15. Hordvik, I., Grimholt, U., Fosse, V. M., Lie, O., and Endresen, C. Cloning and sequence analysis of cDNAs encoding the MHC class II β chain in Atlantik salmon (Salmo salar). Immunogenetics 37: 437-441, 1993
16. Hughes, A. L. MHC polymorphism and the design of captive breeding programs. Conserv Biol 5: 29-251, 1991
17. Jukes, T. H. and Cantor, C. R. Evolution of protein molecules. In H. N. Munro (ed.): Mammalian Protein Metabolism III, pp. 21-32, Academic Press, New York, 1969
18. Juul-Madsen, H. R., Glamann, J., Madsen, H. O., and Simonsen, M. MHC class II beta-chain expression in the rainbow trout. Scand J Immunol 35: 687-694, 1992
19. Kido, Y., Aono, M., Yamaki, T., Matsumoto, K.-I., Murata, S., Saneyoshi, M., and Okada, N. Shaping and reshaping of salmonid genomes by amplification of tRNA-derived retroposons during evolution. Proc Natl Acad Sci 88: 2326-2330, 1991
20. Klein, J. Natural History of the Major Histocompatibility Complex, John Wiley, New York, 1986
21. Klein, J. Origin of major histocompatibility complex polymorphism: the trans-species hypothesis. Hum Immunol 19: 155-162, 1987
22. Klein, J. The major histocompatibility complex of the mouse. Science 203: 516-521, 1979
23. Klein, D., Ono, H., O'hUigin, C., Vincek, V., Goldschmidt, T., and Klein, J. Extensive MHC variability in cichlid fishes of Lake Malawi. Nature 364: 330-334, 1993
24. Koishi, R. and Okada, N. Distribution of the salmonid Hpa 1 family in the salmonid species demonstrated by in vitro runoff transcription assay of total genomic DNA: a procedure to estimate repetitive frequency and sequence divergence of a certain repetitive family with a few known sequences. J Mol Evol 32: 43-52, 1991
25. Kumar, S., Tamura, K., and Nei, M. MEGA: Molecular Evolutionary Genetics Analysis, ver 1.01. The Pennsylvania State University, University Park, 1993
26. McGuire, K. L., Duncan, W. R., and Tucker, P. W. Syrian hamster DNA shows limited polymorphism at class L-like loci. Immunogenetics 22: 257-268, 1985
27. McPhail, J. D. and Lindsey, C. C. Freshwater fishes of northwestern Canada and Alaska. Can J Fish Aquatic Sci Bull 173: 1-381, 1970
28. Miller, K. M., Withler, R. E., and Beacham, T. D. Stock identification of coho salmon (Oncorhynchus kisutch) using minisatellite DNA variation. Can J Fish Aquat Sci, in press
29. Nei, M. and Gojobori, T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3: 418-426, 1986
30. Nei, M. and Hughes, A. L. Polymorphism and evolution of the major histocompatibility complex loci in mammals. In R. K. Selander, A. G. Clark, and T. S. Whittam (eds.): Evolution at the Molecular Level, pp. 222-247, Sinauer Associates Inc, Sunderland, 1991
31. Nei, M. and Rzhetsky, A. Reconstruction of phylogenetic trees and evolution of major histocompatibility complex genes. In J. Klein and D. Klein (eds.): Molecular Evolution of the Major Histocompatibility Complex, pp. 14-27, Springer, Berlin, Heidelberg, 1991
32. O'Brien, S. J., Roelke, M. E., Marker, L., Newmen, A., Winkler, C. A., Meltzer, D., Colly, L., Evermann, J. F., Bush, M., and Wildt, D. E. Genetic basis for species vulnerability in the cheetah. Science 227: 1428-1434, 1985
33. Ohno, S. Evolution by Gene Duplication, Springer, New York, 1970
34. Okada, N. SINEs. Current Opinion in Genetics and Development 1: 498-504, 1991
35. Okamura, K., Nakanishi, T., Kurosawa, Y., and Hashimoto, K. Expansion of genes that encode MHC class I molecules in cyprinid fishes. J Immun 151: 188-200, 1993
36. Okazaki, T. Genetic variation and population structure in masou salmon Oncorhynchus masou of Japan. Bull Japan Soc Sci Fish 52: 1365-1376, 1986
37. Ono, H., Klein, D., Vincek, V., Figueroa, F., O'hUigin, H., and Klein, J. Mhc class II genes of zebrafish. Proc Natl Acad Sci 89: 11886-11890, 1992
38. Ono, H., O'hUigin, C., Tichy, H., and Klein, J. Major histocompatibility complex variation in two species of cichlid fishes from Lake Malawi. Mol Biol Evol 10: 1060-1072, 1993
39. Plante, Y., Boage, P. T., White, B. N., and Boonstra, R. Highly polymorphic genetic markers in meadow voles (Microtus pennsylvanicus) revealed by a murine major histocompatibility complex (MHC) probe. Can J Zool 69: 213-220, 1991
40. Rzhetsky, A. and Nei, M. A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol 9: 945-967, 1992
41. Rzhetsky, A. and Nei, M. Theoretical foundation of the minimum-evolution method of phylogenetic inference. J Mol Evol 38: 295-299, 1993
42. Saitou, N. and Nei, M. The neighbor-joining method: a new method for reconstructing phyologenetic trees. Mol Biol Evol 4: 406, 1987
43. Satta, Y. How the ratio of nonsynonymous to synonymous pseudogene substitutions can be less than one. Immunogenetics 38: 450-454, 1993
44. Schonbach, C. and Klein, J. The Alu repeats of the primate DRB genes. In J. Klein and D. Klein (eds.): Molecular Evolution of the Major Histocompatibility Complex, pp 243-255, Springer, Berlin Heidelberg, 1991
45. She, J. X. and Wakeland, E. K. Molecular and genetic mechanisms involved in the generation of Mhc diversity. In J. Klein and D. Klein (eds.): Molecular Evolution of the Major Histocompatibility Complex, pp. 139-154, Springer, Berlin Heidelberg, 1991
46. Slade, R. W. Limited MHC polymorphism in the southern elephant seal: implications for MHC evolution and marine mammal population biology. Proc R Soc Land B 249: 163-171, 1992
47. Takasaki, N., Murata, S., Saitoh, M., Kobayashi, T., Park, L., and Okada, N. Species-specific amplification of tRNA-derived short interspersed repetitive elements (SINEs) by retroposition: a process of parasitization of entire genomes during the evolution of salmonids. Proc Natl Acad Sci 91: 10153-10157, 1994
48. Thomas, W. K. and Beckenbach, A. T. Variation in salmonid mitochondrial DNA: evolutionary constraints and mechanisms of substitution. J Mol Biol 29: 233-245, 1989
49. Thomas, W. K., Withler, R. E., and Beckenbach, A. T. Mitochondrial DNA analysis of Pacific salmonid evolution. Can J Zool 64: 1058-1064, 1986
50. Trowsdale, J., Groves, V., and Arnason, A. Limited MHC polymorphism in whales. Immunogenetics 29: 19-24, 1989
51. Trowsdale, J. "Both man & bird & beast": comparative organization of MHC genes. Immunogenetics 41: 1-17, 1995
52. Utter, F. M., Allendorf, F. W., and Hodgins, H. O. Genetic variability and relationships in Pacific salmon and related trout based on protein variations. Syst Zool 22: 257-270, 1973
53. Ye, Y., She, J., and Wakeland, E. K. Diversification of class II Aα within the genus Mus. In J. Klein and D. Klein (eds.): Molecular Evolution of the Major Histocompatibility Complex, pp. 131-138, Springer, Berlin Heidelberg, 1991