Selection, convergence, and intragenic recombination in HLA diversity

Genetica

Volumn 102-103, Issue , 1998, Pages 157-169

  Takahata, Naoyuki ^a   Satta, Yoko ^a  

^a GRADUATE UNIVERSITY FOR ADVANCED STUDIES   (Japan)

Author keywords

Balancing selection; Compatibility; Gene conversion; Human evolution; Major histocompatibility complex (MHC)

Indexed keywords

COMPUTER SIMULATION; EVOLUTION; GENE CONVERSION; GENETIC RECOMBINATION; HLA ANTIGEN; IMMUNOGENETICS; MUTATION; POPULATION GENETICS;

EID: 7344223312     PISSN: 00166707     EISSN: None     Source Type: Journal    
DOI: 10.1023/a:1017029613342     Document Type: Article

References (52)

1. Ayala, F.J., 1995. The myth of Eve: molecular biology and human origins. Science 270: 1930-1936.
2. Ayala, F.J., A. Escalante, C. O'hUigin & J. Klein, 1994. Molecular genetics of speciation and human origins. Proc. Natl. Acad. Sci. USA 91: 6787-6794.
3. Bunn, H.F., 1994. Sickle hemoglobin and other hemoglobin mutants, pp. 207-256 in The molecular basis of blood diseases (2nd ed), edited by G. Stamatoyannopoulos, A. W. Nienhuis, P.W. Marjerus and H. Varmus. Saunders, Philadelphia.
4. Carver, N.F.H. & A. Cutler, 1994. International hemoglobin information center variant list. Hemoglobin 18: 77-161.
5. Crow, J.F., 1997. The high spontaneous mutation rate: is it a health risk? Proc. Natl. Acad. Sci. USA 94: 8380-8386.
6. Erlich, H.A., T.F. Bergström, M. Stoneking & U. Gyllensten, 1996. HLA sequence polymorphism and the origin of humans. Science 274: 1552-1554.
7. Fitch, W.M., 1975. Toward finding the tree of maximum parsimony, pp. 189-230 in Proceedings of the Eighth International Conference on Numerical Taxonomy edited by G.F. Estabrook. W.H. Freeman & Co., San Francisco.
8. Fitch, D.H.A. & M. Goodman, 1991. Phylogenetic scanning: a computer-assisted algorithm for mapping gene conversions and other recombination events. Comput. Appl. Biosci. 7: 207-215.
9. Gyllensten, U.B., M. Sundvall & H.A. Erlich, 1991. An allelic diversity is generated by intraexon sequence exchange at the DRB 1 locus of primates. Proc. Natl. Acad. Sci. USA 88: 3686-3690.
10. Hein, J., 1993. A heuristic method to reconstruct the history of sequences subject to recombination. J. Mol. Evol. 36: 396-405.
11. Hidebrand,W.H., J.D. Domena, S.Y. Shen, M. Lau, P.I. Terasaki, M. Bunce, S.G.E. Marsh, M.G. Guttridge, W.B. Bias & P. Parham, 1994. HLA-B15: a widespread and diverse family of HLA-B alleles. Tissue Antigens 43: 209-218.
12. Hughes, A.L. & M. Nei, 1988. Pattern of nucleotide substitutions at major histocompatibility complex class I loci reveals overdominant selection. Nature 335: 167-170.
13. Hughes, A.L. & M. Nei, 1989. Nucleotide substitution at major histocompatibility complex class II loci: evidence for overdominant selection. Proc. Natl. Acad. Sci. USA 86: 958-962.
14. Howard, J., 1992. Fast forward in the MHC. Nature 357: 284-285.
15. Jakobsen, I.B. & S. Easteal, 1996. A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences. CABIOS 12: 291-295.
16. Kimura, M., 1968. Evolutionary rate at the molecular level. Nature 217: 624-626.
17. Kimura, M., 1983. The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge.
18. Kimura, M. & T. Ohta, 1969. The average number of generations until fixation of a mutant gene in a finite population. Genetics 61: 763-771.
19. Klein, J., 1986. Natural History of the Major Histocompatibility Complex. Wiley, New York.
20. Klein, J. & C. O'hUigin, 1995. Class II B Mhc motifs in an evolutionary perspective. Immunol. Rev. 143: 89-111.
21. Klein, J., Y. Satta, C. O'hUigin & N. Takahata, 1993. The molecular descent of the major histo compatibility complex. Ann. Rev. Immunol. 11: 269-295.
22. Klein, J., N. Takahata & F. J. Ayala, 1993. Mhc diversity and human origins. Sci. Am. 269: 46-51.
23. Li, W. - H. & L.A. Sadler, 1991. Low nucleotide diversity in man. Genetics 129: 513-523.
24. McAdam, A.N., J.E. Boyson, X. Liu, T.L. Garber, A.L. Hughes, R.E. Bontrop & D.I. Watkins, 1994. A uniquely high level of recombination at the HLA-B locus. Proc. Natl. Acad. Sci. USA 91: 5893-5897.
25. McDevitt, H., 1995. Evolution of class II allelic diversity. Immunol. Rev. 143: 113-121.
26. Maruyama, T. & M. Nei, 1981. Genetic variability maintained by mutation and overdominant selection in finite populations. Genetics 98: 441-459.
27. Marsh, S., 1996. http://www.icnet.uk
28. Ohta, T., 1991. Role of diversifying selection and gene conversion in evolution of major histo compatibility complex loci. Proc. Natl. Acad. Sci. USA 88: 6717-6720.
29. O'hUigin, C., 1995. Quantifying the degree of convergence in primate Mhc-DRB genes. Immunol. Rev. 143: 123-140.
30. Parham, P., E.J. Adams & K.L. Arnett, 1995. The origins of HLA-A, B, C diversity. Immunol. Rev. 143: 141-180.
31. Parham, P. & T. Ohta, 1996. Population biology of antigen presentation by MHC class I molecules. Science 272: 67-74
32. Rogers, A.R. & H.C. Harpending, 1992. Population growth makes waves in the distribution of pairwise genetic distances. Mol. Biol. Evol. 9: 552-569.
33. Satta, Y., C. O'hUigin, N. Takahata & J. Klein, 1993. The synonymous substitution rate of the major histocompatibility complex loci in primates. Proc. Natl. Acad. Sci. USA 90: 7480-7884.
34. Satta, Y., C. O'hUigin, N. Takahata & J. Klein, 1994. Intensity of natural selection at the major histocompatibility complex loci. Proc. Natl. Acad. Sci. USA 91: 7184-7188.
35. Sawyer, S., 1989. Statistical tests for detecting gene conversion. Mol. Biol. Evol. 6: 526-538.
36. Slatkin, M. & R.R. Hudson, 1991. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129: 55-562.
37. Starr, C. & B. McMillan, 1995. Human Biology. Wadsworth Publishing Co., New York.
38. Stephens, J.C., 1985. Statistical methods of DNA sequence analysis: detection of intragenic recombination or gene conversion. Mol. Biol. Evol. 2: 539-556.
39. Tajima, F., 1983. Evolutionary relationship of DNA sequences in finite populations. Genetics 105: 437-460.
40. Takahata, N., 1990. A simple genealogical structure of strongly balanced allelic lines and trans-species evolution of diversity. Proc. Natl. Acad. Sci. USA 87: 2419- 2423.
41. Takahata, N., 1993. Allelic genealogy and human evolution. Mol. Biol. Evol. 10: 2-22.
42. Takahata, N., 1994. Comments on the detection of reciprocal recombination or gene conversion. Immunogenetics 39: 146-149.
43. Takahata, N., 1995a. MHC diversity and selection. Immunol. Rev. 143: 221-247.
44. Takahata, N., 1995b. A genetic perspective on the origin and history of humans. Ann. Rev. Ecol. Syst. 26: 343-372.
45. Takahata, N. & M. Nei, 1990. Allelic genealogy under overdominant and frequency-dependent selection and diversity of major histo compatibility complex loci. Genetics 124: 967-978.
46. Takahata, N., Y. Satta & J. Klein, 1992. Polymorphism and balancing selection at major histocompatibility complex loci. Genetics 130: 925-938.
47. Takahata, N., Y. Satta & J. Klein, 1995. Divergence time and population size in the lineage leading to modern humans. Theor. Popul. Biol. 48: 198-222.
48. Takahata, N. & Y. Satta, 1997. Evolution of the primate lineage leading to modern humans: phylogenetic and demographic inferences from DNA sequences. Proc. Natl. Acad. Sci. USA 94: 4811-4815.
49. Titus-Trachtenberg, E.A, O. Rickards, G.F. De Stefano & H.A. Erlich, 1994. Analysis of HLA class II haplotypes in the Cayapa Indians of Ecuador: a novel DRB1 allele reveals evidence for convergent evolution and balancing selection at position 86. Am. J. Hum. Genet. 55: 160-167.
50. Vogel, F. & A.G. Motulsky, 1996. Human Genetics, Problems and Approaches (3rd ed). Springer, New York.
51. Watkins, D.I., S.N. McAdam, X. Liu, C.R. Strang, E.L. Milford, C.G. Levine, T.L. Garber, A.L. Dogon, C.I. Lord, S.H. Chim, G.M. Troup, A.L. Hughes & N.L. Letvin, 1992. New recombinant HLA-B alleles in atribe of South American Amerindians indicate rapid evolution of MHC class I loci. Nature 357: 329-333.
52. Zangenberg, G., M.-M. Huang, N. Arnheim & H. Erlich, 1995. New HLA-DPB 1 alleles generated by interalle lic gene conversion detected by analysis of sperm. Nature Genetics 10: 407-414.