Ancestral polymorphism of Mhc class II genes in mice: Implications for balancing selection and the mammalian molecular clock

Genetics

Volumn 146, Issue 2, 1997, Pages 655-668

  Edwards, Scott V ^a,b   Chesnut, Kye ^b   Satta, Yoko ^c   Wakeland, Edward K ^b  

^a UNIVERSITY OF WASHINGTON   (United States)

^b UNIVERSITY OF FLORIDA   (United States)

^c GRADUATE UNIVERSITY FOR ADVANCED STUDIES   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 2;

ALLELE; ANIMAL CELL; ARTICLE; COMPUTER SIMULATION; GENETIC POLYMORPHISM; MAJOR HISTOCOMPATIBILITY COMPLEX; MOLECULAR EVOLUTION; MOUSE; MUTATION RATE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RAT; STRAIN DIFFERENCE;

ALLELES; ANIMALS; BINDING SITES; EVOLUTION, MOLECULAR; EXONS; GENES, MHC CLASS II; MICE; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMORPHISM, GENETIC; PROTEIN STRUCTURE, SECONDARY; SELECTION (GENETICS);

ANIMALIA; MAMMALIA; MUS; PRIMATES; UNGULATA;

EID: 0030979507     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (90)

1. ADACHI, J., Y. CAO and M. HASEGAWA, 1993 Tempo and mode of mitochondrial DNA evolution in vertebrates at the amino acid sequence level: rapid evolution in warm-blooded vertebrates. J. Mol. Evol. 36: 270-281.
2. ALBRIGHT-FRASER, D. G., R. REID, V. GERBER and E. BAILEY, 1996 Polymorphism in DRA among equids. Immunogenetics 43: 315-317.
3. ALLARD, M. W., B. E. McNIFF and M. M. MIYAMOTO, 1996 Support for interordinal eutherian relationships with an emphasis on primates and their archontan relatives. Mol. Phylogenet. Evol. 5: 78-88.
4. AYALA, F. J., and A. A. ESCALANTE, 1996 The evolution of human populations: a molecular perspective. Mol. Phylogenet. Evol. 5: 188-201.
5. BEGOVICH, A. B., T. H. VU and P. P. JONES, 1990 Characterization of the molecular defects in the mouse E and E beta q genes. Implications for the origin of MHC polymorphism. J. Immunol. 144: 1957-1964.
6. BROWN, J. H., T. S. JARDETSKY, J. C. GORGA, L. J. STERN, R. G. URBAN et al., 1993 Three-dimensional structure of the human class II histocompatibility antigen HLA-DR1. Nature 364: 33-39.
7. EASTEAL, S., 1985 Generation time and the rate of molecular evolution. Mol. Biol. Evol. 2: 450-453.
8. EASTEAL, S., 1988 Rate constancy of globin gene evolution in placental mammals. Proc. Natl. Acad. Sci. USA 85: 7622-7626.
9. EDWARDS, S. V., E. K. WAKELAND and W. K. POTTS, 1995 Contrasting histories of avian and mammalian Mhc genes revealed by class II B sequences from songbirds. Proc. Natl. Acad. Sci. USA 92: 12200-12204.
10. ERLICH, H. A., and U. B. GYLLENSTEN, 1991 Shared epitopes among HLA class II alleles: gene conversion, common ancestry and balancing selection. Immunol. Today 12: 411-414.
11. FELSENSTEIN, J., 1985 Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791.
12. FELSENSTEIN, J., 1988 Phylogenies from molecular sequences: inference and reliability. Annu. Rev. Genet. 22: 521-565.
13. FELSENSTEIN, J., 1994 Phylogeny Inference Package (PHYLIP), version 3.6. University of Washington, Seattle, WA.
14. FERRIS, S. D., R. D. SAGE, E. M. PRAGER, U. RITTE and A. C. WILSON, 1983 Mitochondrial DNA evolution in mice. Genetics 105: 681-721.
15. FIGUEROA, F., E. GUNTHER and J. KLEIN, 1988 MHC polymorphism pre-dating speciation. Nature 335: 265-207.
16. 0 alleles in wild mice. Immunogenetics 30: 222-225.
17. FIGUEROA, F., J. GUTKNECHT, H. TICHY and J. KLEIN, 1990 Class II Mhc genes in rodent evolution. Immunol. Rev. 113: .
18. FIGUEROA, F., C. O' HUIGIN, H. TICHY and J. KLEIN, 1994 The origin of the primate Mhc-DRB genes and allelic lineages deduced from the study of prosimians. J. Immunol. 152: 4455-4465.
19. FITCH, W. M., 1971 Toward defining the course of evolution: minimum change for a specific tree topology. Syst. Zool. 20: 406-416.
20. FU, Y-X., and W-H. LI, 1993 Statistical tests of neutrality of mutations. Genetics 133: 693-709.
21. GRASER, R., C. O'HUIGIN, V. VINCEK, A. MEYER and J. KLEIN, 1996 Trans-species polymorphism of class II Mhc loci in danio fishes. Immunogenetics 44: 36-48.
22. GUSTAFSSON, K., and L. ANDERSSON, 1994 Structure and polymorphism of horse MHC class II DRB genes: convergent evolution in the antigen binding site. Immunogenetics 39: 355-358.
23. GYLLENSTEN, U., M. SUNDVALL and H. ERLICH, 1991 Allelic diversity is generated by intra-exon exchange at the DRB locus of primates. Proc. Natl. Acad. Sci. USA 88: 3686-3690.
24. GYLLENSTEN, U. B., and H. A. ERLICH, 1989 Ancient roots for polymorphism at the HLA-DQ locus in primates. Proc. Natl. Acad. Sci. USA 86: 9986-9990.
25. GYLLENSTEN, U. B., D. LASHKARI and H. A. ERLICH, 1990 Allelic diversification at the class II DQB locus of the mammalian major histocompatibility complex. Proc. Natil. Acad. Sci. USA 87: 1835-1839.
26. HEDRICK, P. W., and T. J. KIM, 1997 Genetics of complex polymorphisms: parasites and the maintenance of MHC variation, in Evolutionary Genetics from Molecules to Morphology, edited by R. S. SINGH and C. K. KRIMBAS. Cambridge University Press, New York (in press).
27. HUDSON, R. R., 1990 Gene genealogies and the coalescent process. Oxford Surv. Evol. Biol. 7: 1-44.
28. HUDSON, R. R., M. KREITMAN and M. AGUADÉ, 1987 A test of neutral molecular evolution based on nucleotide data. Genetics 116: 153-159.
29. HUGHES, A. L., M. K. HUGHES, C. Y. HOWELL and M. NEI, 1994 Natural selection at the class II major hislocompatibility loci of mammals. Phil. Trans. R. Soc. B 345: 359-367.
30. HUGHES, A. L., and M. NEI, 1989 Nucleotide substitution at major histocompatibility complex class II loci: evidence for overdominant selection. Proc. Natl. Acad. Sci. USA 86: 958-962.
31. HUGHES, A. L., and M. NEI, 1990 Evolutionary relationships of class II major-histocompatibility-complex genes in mammals. Molec. Biol. Evol. 7: 491-514.
32. JAEGER, J-J., H. TONG and C. DENYS, 1986 Age de la divergence MusRattus: comparaison des donneés paléontologiques et moléculaires. Comptes Rendus del'Académie des Sciences 14: 917-922.
33. JANKE, A., G. FELDMAIER-FUCHS, W. K. THOMAS, A. VON HAESLER and S. PAABO, 1994 The marsupial mitochondrial genome and the evolution of placental mammals. Genetics 137: 243-256.
34. KAWAMURA, S., H. TANABE, Y. WATANABE, K. KUROSAKI, N. SAITOU et al., 1991 Evolutionary rate of immunoglobulin alpha noncoding region is greater in Hominoids than in Old World Monkeys. Mol. Biol. Evol. 8: 743-752.
35. KIMURA, M., 1980 A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16: 111-120.
36. KIMURA, M., 1983 The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge.
37. KLEIN, J., 1987 Origin of major histocompatibility complex polymorphism trans-species hypothesis. Human Immunol. 19: 155-162.
38. KLEIN, J., Y. SATTA and C. O'HUIGIN, 1993 The molecular descent of the major histocompatibility complex. Annu. Rev. Immunol. 11: 269-295.
39. KUMAR, S., K. TAMURA and M. NEI, 1993 MEGA: Molecular Evolutionary Genetic Analysis, version 1.01. The Pennsylvania State University, University Park, PA.
40. LAWLOR, D. A., F. E. WARD, P. D. ENNIS, A. P. JACKSON and P. PARHAM, 1988 HLA-A and B polymorphisms predate the divergence of humans and chimpanzees. Nature 335: 268-271.
41. LI, W. H., 1993 So, what about the molecular clock hypothesis? Curr. Opin. Genet. Dev. 3: 896-901.
42. LI, W-H., D. L. ELLSWORTH, J. KRUSHKAL, B. H-J. CHANG and D. HEWETT-EMMET, 1996 Rates of nucleotide substitution in primates and rodents and the generation-time effect hypothesis. Mol. Phylogenet. Evol. 5: 182-187.
43. LI, W-H., and Y.-X. FU, 1994 Estimation of population parameters and detection of natural selection from DNA sequences, pp. 112-125 in Non-Neutral Evolution: Theories and Molecular Data, edited by B. GOLDING. Chapman and Hall, New York.
44. LI, W-H., M. GOUY, P. M. SHARP, C. O'HUIGIN and Y. W. YANG, 1990 Molecular phylogeny of Rodentia, Lagomorpha, Primates, Artiodactyla, and Carnivora and molecular clocks. Proc. Natl. Acad. Sci. USA 87: 6703-6707.
45. LUNDBERG, A. S., and H. O. MCDEVITT, 1992 Evolution of MHC class II allelic diversity: direct descent in humans and mice. Proc. Natl. Acad. Sci. USA 89: 6545-6549.
46. MADDISON, W. P., and D. R. MADDISON, 1992 MacClade: Analysis of Phylogeny and Character Evolution, version 3 0. Sinaur Associates, Sunderland, MA.
47. MADDISON, W. P., and M. SLATKIN, 1991 Null models for the number of evolutionary steps in a character on a phylogenetic tree. Evolution 45: 1184-1197.
48. MARTIN, A. P., and S. R. PALUMBI, 1993 Body size, metabolic rate, generation time and the molecular clock. Proc. Natl. Acad. Sci. USA 90: 4087-4091.
49. MARTIN, R. D., 1993 Primate origins: plugging the gaps. Nature 363: 223-234.
50. MCCONNELL, T. J., W. S. TALBOT, R. A. McINDOE and E. K. WAKELAND, 1988 The origin of MHC class II gene polymorphism within the Mus. Nature 332: 651-654.
51. MCDEVITT, H., 1995 Evolution of MHC class II allelic diversity. Immunol. Rev. 143: 113-122.
52. MCDONALD, J. H., and M. KREITMAN, 1991 Adaptive evolution at the Adh locus in Drosophila. Nature 351: 652-654.
53. MCNICHOLAS, J., M. STEINMETZ, T. HUNKAPILLER, P. JONES and L. HOOD, 1982 DNA sequence of the gene encoding the E alpha Ia polypeptide of the BALB/c mouse. Science 218: 1229-1232.
54. MINDELL, D. P., A. KNIGHT, C. BAER and C. J. HUDDLESTON, 1996 Slow rates of molecular evolution in birds and the metabolic rate and body temperature hypotheses. Mol. Biol. Evol. 13: 422-426.
55. MNUKOV'A FAJDELOV'A, M., Y. SATTA, C. O'HUIGIN, W. E. MAYER, F. FIGUEROA et al., 1994 Alu elements of the primate major histocompatibility. Mamm. Genome 5: 405-415.
56. MUSE, S. V., 1996 Estimating synonymous and nonsynonymous substitution rates. Mol. Biol. Evol. 13: 105-114.
57. NACHMAN, M. W., S. N. BOYER, J. B. SEARLE and C. F. AQUADRO, 1994 Mitochondrial DNA variation and the evolution of Robsertsonian chromosomal races of house mice, Mus domesticus. Genetics 136: 1105-1120.
58. NEI, M., and T. GOJOBORI, 1986 Simple methods for estimating the numbers of synonymous nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3: 418-426.
59. NEIGEL, J. E., and J. C. AVISE, 1986 Phylogenetic relationships of mitochondrial DNA under various demographic models of speciation, pp. 515-534 in Evolutionary Processes and Theory, edited by S. KARLIN and E. NEVO. Academic Press, New York.
60. O'HUIGIN, C., 1995 Quantifying the degree of convergence in primate Mhc-DRB. Immunogenetics. 143: 123-140.
61. O'HUIGIN, C., and W. H. LI, 1992 The molecular clock ticks regularly in muroid rodents and hamsters. J. Mol. Evol. 35: 377-384.
62. POTTS, W. K., and E. K. WAKELAND, 1993 Evolution of MHC genetic diversity: a tale of incest, pestilence and sexual preference. Trends Genet. 9: 408-412.
63. PRAGER, E. M., and A. C. WILSON, 1988 Ancient origin of lactalbumin from lysozyme: analysis of DNA and amino acid sequences. J. Mol. Evol. 27: 326-335.
64. PRAGER, E. M., H. TICHY and R. D. SAGE, 1996 Mitochondrial DNA sequence variation in the Eastern house mouse, Mus musculus: comparison with other house mice and report of a 75-bp tandem repeat. Genetics 143: 427-446.
65. RICHMAN, A. D., and J. R. KOHN, 1996 Learning from rejection: the evolutionary biology of single-locus incompatibility. Trends Ecol. Evol. 11: 497-502.
66. ROBERTSON, K. A., and W. R. MCMASTER, 1985 Complete structure of a rat RT1 E beta chain extensive conservation of MHC class II beta chains. J. Immunol. 135: 4095-4099.
67. SAITO, H., R. A. MAKI, L. K. CLAYTON and S. TONEGAWA, 1983 Complete primary structures of the Eβ chain and gene of the mouse major histocompatibility complex. Proc. Natl. Acad. Sci. USA 80: 5520-5524.
68. SAITOU, N., and M. NEI, 1987 The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
69. SARICH, V. M., and A. C. WILSON, 1973 Generation time and genomic evolution in primates. Science 179: 1144-1147.
70. SATTA, Y., W. E. MAYER and J. KLEIN, 1996 Evolutionary relationship of HLA-DRB genes inferred from intron sequences. J. Mol. Evol. 42: 648-657.
71. SATTA, Y., C. O'HUIGIN, N. TAKAHATA and J. KLEIN, 1993 The synonymous substitution rate at major histocompatibility complex loci in primates. Proc. Natl. Acad. Sci. USA 90: 7480-7484.
72. SATTA, Y., C. O'HUGIN, N. TAKAHATA and J. KLEIN, 1994 Intensity of natural selection at the major histocompatibility complex loci. Proc. Natl. Acad. Sci. USA 91: 7184-7188.
73. SHE, J. X., S. BOEHME, T. W. WANG, F. BONHOMME and E. K. WAKELAND, 1990a The generation of MHC class II gene polymorphism in the genus Mus. Biol. J. Linnaean Soc. 41: 141-161.
74. SHE, J. X., S. A. BOEHME, T. W. WANG, F. BONHOMME and E. K. WAKELAND, 1991 Amplification of MHC class II gene diversity by intraexonic recombination. Proc. Natl. Acad. Sci. USA 88: 453-457.
75. SHE, J. X., F. BONHOMME, P. BOURSOT, L. THALER and F. CATZEFLIS, 1990b Molecular phylogenies in the genus Mus: comparative analysis of electrophoretic, scnDNA hybridization, and RFLP data. Biol. J. Linnaean Soc. 41: 83-103.
76. SILVER, L. M., 1995 Mouse Genetics: Concepts and Applications. Oxford University Press, New York.
77. SLATKIN, M., and W. P. MADDISON, 1989 A cladistic measure of gene flow inferred from the phylogenies of alleles. Genetics 123: 603-613.
78. SWOFFORD, D. L., 1991 Phylogenetic Analysis Using Parsimony (PAUP), version 3.0s. Illinois Natural History Survey, Champaign, IL.
79. TAKAHATA, N., 1990a A simple genealogical structure of strongly balanced allelic lines and trans-specific evolution of polymorphism. Proc. Natl. Acad. Sci. USA 87: 2419-2423.
80. TAKAHATA, N., 1994 Comments on the detection of reciprocal recombination or gene conversion. Immunogenetics 39: 146-149.
81. TAKAHATA, N., and M. NEI, 1990 Allelic genealogy under overdominant and frequency-dependent selection and polymorphism of major histocompatibility complex loci. Genetics 124: 967-978.
82. TAKAHATA, N., Y. SATTA and J. KLEIN, 1992 Polymorphism and balancing selection at major histocompatibility complex loci. Genetics 130: 925-938.
83. TAKEZAKI, N., A. RZHETSKY and M. NEI, 1995 Phylogenetic test of the molecular clock and linearized trees. Mol. Biol. Evol. 12: 823-833.
84. UYENOYAMA, M., 1995 A generalized least-squares estimate for the origin of sporophytic self-incompatibility. Genetics 139: 975-992.
85. VEKEMANS, X., and M. SLATKIN, 1994 Gene and allelic genealogies at a gametophytic self-incompatibility locus. Genetics 137: 1157-1165.
86. WAKELAND, E. K., S. BOEHME. and J. X. SHE, 1990 The generation and maintenance of MHC class II polymorphism in rodents. Immunol. Rev. 113: 207-225.
87. WAKELAND, E. K., M. PRICE LAFACE, V. HENSON and A. B. PECK, 1987 Production of 35 H-2 homozygous strains from wild mice. Immunogenetics 26: 115-119.
88. WILSON, A. C., R. L. CANN, S. M. CARR, M. GEORGE, U. B. GYLLENSTEN et al., 1985 Mitochondrial evolutionary genetics. Biol. J. Linnaean Soc. 26: 375-400.
89. WU, C-I., and W-H. LI, 1985 Evidence for higher rates of nucleotide substitution in rodents than in man. Proc. Natl. Acad. Sci. USA 82: 1741-1745.
90. ZANGENBERG, G., M-M. HUANG, N. ARNHEIM and H. A. ERLICH, 1995 New HLA-DPB1 alleles generated by interallelic gene conversion detected by analysis of sperm. Nat. Genet. 10: 407-414.