Genetic variation of microsatellite loci in the major histocompatibility complex (MHC) region in the southeast Asian house mouse (Mus musculus castaneus)

Genetica

Volumn 119, Issue 2, 2003, Pages 201-218

  Huang, Shiao Wei ^a   Yu, Hon Tsen ^a  

^a NATIONAL TAIWAN UNIVERSITY   (Taiwan)

Author keywords

Balancing selection; M. m. castaneus; Major histocompatibility complex; Microsatellites; Mus musculus; Polymorphism; Wild mouse

Indexed keywords

MICROSATELLITE DNA;

ANIMAL; ARTICLE; CHROMOSOME MAP; GENE FREQUENCY; GENETIC POLYMORPHISM; GENETIC SELECTION; GENETIC VARIABILITY; GENETICS; GENOTYPE; HETEROZYGOTE; MAJOR HISTOCOMPATIBILITY COMPLEX; MOUSE; TAIWAN;

ANIMALS; CHROMOSOME MAPPING; GENE FREQUENCY; GENOTYPE; HETEROZYGOTE; MAJOR HISTOCOMPATIBILITY COMPLEX; MICE; MICROSATELLITE REPEATS; POLYMORPHISM, GENETIC; SELECTION (GENETICS); TAIWAN; VARIATION (GENETICS);

ANIMALIA; MUS; MUS MUSCULUS; MUS MUSCULUS CASTANEUS; MUSCULUS; RODENTIA; VERTEBRATA;

EID: 0242411946     PISSN: 00166707     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1026061216816     Document Type: Article

References (79)

1. Ausubel, F.M., R. Brent, R.E. Kingston, D.D. Moore, J.G. Seidman, J.A. Smith & K. Struhl, 1995. Short Protocols in Molecular Biology - A Compendium of Methods from Current Protocols in Molecular Biology, Wiley, Canada, 3rd edn.
2. Bachtrog, D., M. Agis, M. Imhof & C. Schlötterer, 2000. Microsatellite variability differs between dinucleotide repeat motifs-evidence from Drosophila melanogaster. Mol. Biol. Evol. 17: 1277-1285.
3. Barker, J.S.F., S.S. Moore, D.J.S. Hetzel, D. Evans, S.O. Tan & K. Byrne, 1997. Genetic diversity of Asian water buffalo (Bubalus bubalis): microsatellite variation and a comparison with protein-coding loci. Anim. Genet. 28: 103-115.
4. Belich, M.P., J.A. Madrigal, W.H. Hildebrand, J. Zemmour, R.C. Williams, R. Luz, M.L. Petzl-Erler & P. Parham, 1992. Unusual HLA-B alleles in two tribes of Brazilian Indians. Nature 257: 326-329.
5. Boyce, W.M., P.W. Hedrick, N.E. Muggli-Cockett, S. Kalinowski, M.C.T. Penedo & R.R. Ramey, 1997. Genetic variation of major histocompatibility complex and microsatellite loci: a comparison in bighorn sheep. Genetics 145: 421-433.
6. Chou, C.-W., P.-F. Lee, K.-H. Lu & H.-T. Yu, 1998. A population study of house mice (Mus musculus castaneus) inhabiting rice granaries in Taiwan. Zool. Stud. 37(3): 201-212.
7. Clark, A. & T. Kao, 1991. Excess nonsynonymous substitutions at shared polymorphic sites among self-incompatibility alleles of Solanaceae. Proc. Natl. Acad. Sci. USA 88: 9823-9827.
8. Dallas, J.F., B. Dod, P. Boursot, E.M. Prager & F . Bonhomme, 1995. Population subdivision and gene flow in Danish house mice. Mol. Ecol. 4: 311-320.
9. Dietrich, W.F., J. Miller, R. Steen, M.A. Merchant, D. Damron-Boles, Z. Husain, R. Dredge, M.J. Daly, K.A. Ingalls, T.J. O'Connor, C.A. Evans, M.M. DeAngelis, D.M. Levinson, L. Kruglyak, N. Goodman, N.G. Copeland, N.A. Jenkins, T.L. Hawkins, L. Stein, D.C. Page & E.S. Lander, 1996. A comprehensive genetic map of the mouse genome. Nature 380: 149-152.
10. Ellegren, H., C.J. Davies & L. Andersson, 1993. Strong association between polymorphisms in an intronic microsatellite and in the coding sequence of the BoLA-DRB3 gene: implications for microsatellites stability and PCR-based DRB3 typing. Anim. Genet. 24: 269-275.
11. Estoup, A. & J.-M. Cornuet, 1999. Microsatellite evolution: inferences from population data, pp. 49-65 in Microsatellites: Evolution and Application, edited by D.B. Goldstein & C. Schlötterer. Oxford University Press, New York.
12. Ewens, W.J., 1972. The sampling theory of selectively neutral alleles. Theor. Pop. Biol. 3: 87-112.
13. Goldstein, D.B., A.R. Linares, L.L. Cavalli-Sforza & M.W. Feldman, 1995. Genetic absolute dating based on microsatellites and the origin of modern humans. Proc. Natl. Acad. Sci. USA 92: 6723-6727.
14. Goudet, J., 1995. FSTAT (version 1.2): a computer program to calculate F-statistics. J. Hered. 86: 485-486.
15. Grimsley, C., K.A. Mather & C. Ober, 1998. HLA-H: a pseudogene with increased variation due to balancing selection at neighboring loci. Mol. Biol. Evol. 15(12): 1581-1588.
16. Guo, S.W. & E.A. Thompson, 1992. Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics 48: 361-372.
17. Hambuch, T.M. & E.A. Lacey, 2000. Contrasting patterns of MHC and microsatellite diversity in social and solitary tuco-tucos (Rodentia: Ctenomyidae), pp. 542-554 in Major Histocompatibility Complex: Evolution, Structure, and Function, edited by M. Kasahara. Springer, Tokyo.
18. Harr, B., B. Zangerl, G. Brem & C. Schlötterer, 1998. Conservation of locus specific microsatellite variability across species: a comparison of two Drosophila sibling species D. melanogaster and D. simulans. Mol. Biol. Evol. 15: 176-184.
19. Hood, L., M. Steinmetz & B. Malissen, 1983. Genes of the major histocompatibility complex of the mouse. Ann. Rev. Immunol. 1: 529-568.
20. Hudson, R.R. & N.L. Kaplan, 1988. The coalescent process in models with selection and recombination. Genetics 120: 831-840.
21. Hughes, A.L., 2000. Balancing selection: the major histocompatibility complex, pp. 54-89 in Adaptive Evolution of Genes and Genomes. Oxford University Press, New York.
22. 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.
23. Hughes, A.L. & M. Yeager, 1998. Natural selection at major histocompatibility complex loci of vertebrates. Ann. Rev. Genet. 32: 415-435.
24. Huttley, G.A., M.W. Smith, M. Carrington & S.J. O'Brein, 1999. A scan for linkage disequilibrium across the human genome. Genetics 152: 1711-1722.
25. Kaplan, N.L., T. Darden & R.R. Hudson, 1988. The coalescent process in models with selection. Genetics 120: 819-829.
26. Kaplan, N.L., R.R. Hudson & C.H. Langley, 1989. The hitchhiking effect revisited. Genetics 123(4): 887-899.
27. Karl, S.A. & J.C. Avise, 1993. Balancing selection at allozyme loci in oysters: implications from nuclear RFLPs. Science 256: 100-102.
28. Klitz, W., G. Thomson & M.P. Baur, 1986. Contrasting evolutionary histories among tightly linked HLA loci. Am. J. Hum. Genet. 39: 340-349.
29. Kohn, M.H., H.-J. Pelz & R.K. Wayne, 2000. Natural selection mapping of the warfarin-resistance gene. Proc. Natl. Acad. Sci. USA 97(14): 7911-7915.
30. Koob, M.D., M.L. Moseley, L.J. Schut, K.A. Benzow, T.D. Bird, J.W. Day & L.P.W. Ranum, 1999. An untranslated CTG expansion causes a novel form of spinocerebellar ataxia (SCA8). Nat. Genet. 21(4): 379-384.
31. Landry, C. & L. Bernatchez, 2001. Comparative analysis of population structure across environments and geographical scales at major histocompatibility complex and microsatellite loci in Atlantic salmon (Salmo salar). Mol. Ecol. 10: 2525-2539.
32. Lewontin, R.C. & J. Krakauer, 1973. Distribution of gene frequency as a test of the theory of selective neutrality of polymorphisms. Genetics 74: 175-195.
33. Lynch, M., M. Pfrender, K. Spitze, N. Lehman, J. Hicks, D. Allen, L. Latta, M. Ottene, F. Bogue & J. Colbourne, 1999. The quantitative and molecular genetic architecture of a subdivided species. Evolution 53: 100-110.
34. Mack, S.J., T.L. Bugawan, M. Stoneking, M. Saha, H.-P. Beck & H.A. Erlich, 2000. HLA class I and class II loci in Pacific/Asian populations, pp. 427-445 in Major Histocompatibility Complex: Evolution, Structure, and Function, edited by M. Kasahara. Springer, Tokyo.
35. Mantel, N., 1967. The detection of disease clustering and a generalized regression approach. Cancer Res. 27: 209-220.
36. Maynard Smith, J. & J. Haigh, 1974. The hitch-hiking effect of a favorable gene. Genet. Res. Camb. 23: 23-35.
37. Meagher, S. & W.K. Potts, 1997. A microsatellite-based MHC genotyping system for house mice (Mus domesticus). Hereditas 127: 75-82.
38. Melvold, R.W., K. Wang & H.I. Kohn, 1997. Histocompatibility gene mutation rates in the mouse: a 25-year review. Immunogenetics 47: 44-54.
39. Meyer, D. & R. Blasczyk, 2000. The effect of mutation, recombination and selection on HLA non-coding sequences, pp. 398-411 in Major Histocompatibility Complex: Evolution, Structure, and Function, edited by M. Kasahara. Springer, Tokyo.
40. Minch, E., A. Ruiz-Linares, D. Goldstein, M. Feldman & L.L. Cavalli-Sforza, 1995. Microsat (version 1.4d): a computer program for calculating various statistics on microsatellite allele data.
41. Nadeau, J.H., R.L. Collins & J. Klein, 1982. Organization and evolution of the mammalian genome. I. Polymorphism of H-2 linked loci. Genetics 102: 583-598.
42. Nei, M., 1972. Genetics distance between populations. Am. Nat. 106: 283-292.
43. Nei, M., 1978. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89: 583-590.
44. Nei, M. & W.-H. Li, 1980. Non-random association between electromorphs and inversion chromosomes in finite populations. Genet. Res. Camb. 35: 65-83.
45. Nei, M. & A.L. Hughes, 1991. Polymorphism and evolution of the Major histocompatibility complex loci in mammals, pp. 222-247 in Evolution at the Molecular Level, edited by R.K. Selander, A.G. Clark & T.S. Whittam. Sinauer Associates Inc., Sunderland, MA.
46. O'hUigin, C., Y. Satta, A. Hausmann, R.L. Dawkins & J. Klein, 2000. The implications of intergenic polymorphism for major histocompatibility complex evolution. Genetics 156(2): 867-877.
47. Paterson, S., 1998. Evidence for balancing selection at the major histocompatibility complex in a free-living ruminant. J. Hered. 89: 289-294.
48. Pogson, G.H., K.A. Mesa & R.G. Boutilier, 1995. Genetic population structure and gene flow in the Atlantic cod Gadus morhua: a comparison of allozyme and nuclear RFLP loci. Genetics 139: 376-385.
49. Potts, W.K. & E.K. Wakeland, 1993. Evolution of MHC genetic diversity: a tale of incest, pestilence and sexual preference. Trends Genet. 9(12): 408-412.
50. Raymond, M. & F. Roussel, 1995. GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J. Heredity 86: 248-249.
51. Richman, R., M. Uyenoyama & J. Kohn, 1996. Allelic diversity and gene genealogy at the self-incompatibility locus in the Solanaceae. Science 273: 1212-1216.
52. Rousset, F., 1997. Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145: 1219-1228.
53. Rubinsztein, D.C., 1999. Trinucleotide expansion mutation cause diseases which do not conform to classical Mendelian expectation, pp. 80-97 in Microsatellites - Evolution and Applications, edited by D.B. Goldstein & C. Schlötterer. Oxford University Press, New York.
54. Satta, Y., 1997. Effects of intra-locus recombination of HLA polymorphism. Hereditas 127: 105-112.
55. Satta, Y., Y.-J. Li & N. Takahata, 1998. The neutral theory and natural selection in the HLA region. Frontier Biosci. 3: d459-d467.
56. Satta, Y. & N. Takahata, 2000. Polymorphism in the HLA class I region, pp. 398-411 in Major Histocompatibility Complex: Evolution, Structure, and Function, edited by M. Kasahara. Springer, Tokyo.
57. 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: 7480-7484.
58. 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.
59. Schierup, M.H., X. Vekemans & D. Charlesworth, 2000a. The effect of subdivision on variation at multi-allelic loci under balancing selection. Genet. Res. Camb. 76: 51-62.
60. Schierup, M.H., D. Charlesworth & X. Vekemans, 2000b. The effect of hitch-hiking on genes linked to a balanced polymorphism in a subdivided population. Genet. Res. Camb. 76: 63-73.
61. Schlötterer, C. & D. Tautz, 1992. Slippage synthesis of simple sequence DNA. Nucl. Acid Res. 20: 211-215.
62. Schlötterer, C. & T. Wiehe, 1999. Microsatellites, a neutral marker to infer selective sweeps, in Microsatellites: Evolution and Application, edited by D.B. Goldstein & C. Schlötterer. Oxford University Press, New York.
63. Schlötterer, C., B. Amos & D. Tautz, 1991. Conservation of polymorphic simple sequence loci in cetacean species. Nature 354: 63-65.
64. Schlötterer, C., C. Vogl & D. Tautz, 1997. Polymorphism and locus-specific effects on polymorphism at microsatellite loci in natural Drosophila melanogaster populations. Genetics 146: 309-320.
65. Schlötterer, C., R. Ritter, B. Harr & G. Brem, 1998. High mutation rates of a long microsatellite allele in Drosophila melanogaster provide evidence for allele-specific mutation rates. Mol. Biol. Evol. 15: 1269-1274.
66. Schug, M.D., C.M. Hutter, K.A. Wetterstrand, M.S. Gaudette, T.F. Mackay & C.F. Aquadro, 1998. The mutation rates of di-, tri-, and tetranucleotide repeats in Drosophila melanogaster. Mol. Biol. Evol. 15: 1751-1760.
67. Shriver, M.D., L. Jin, R. Chakraborty & E. Boerwinkle, 1993. VNTR allele frequency distributions under the SMM: A computer simulation approach. Genetics 134: 983-993.
68. Slatkin, M., 1995. Hitchhiking and associative overdominance at a microsatellite locus. Mol. Biol. Evol. 12(3): 473-480.
69. Spitze, K., 1993. Population structure in Daphnia obtuse: quantitative genetic and allozymic variation. Genetics 135: 367-374.
70. Strobeck, C., 1983. Expected linkage disequilibrium for a neutral locus linked to a chromosomal arrangement. Genetics 103: 545-555.
71. Takahata, N. & M. Nei, 1990. Allelic genealogy under overdominant and frequency-dependent selection and polymorphism of major histocompatibility complex loci. Genetics 124: 967-978.
72. Takahata, N., Y. Satta & J. Klein, 1992. Polymorphism and balancing selection at major histocompatibility complex loci. Genetics 130: 925-938.
73. Thornton, C.A., J.P. Wymer, Z. Simmons, C. McClain & R.T. Moxley III, 1997. Expansion of the myotonic dystrophy CTG repeat reduces expression of the flanking DMAHP gene. Nat. Genet. 16: 407-409.
74. Titus-Trachtenberg, E.A., T.L. Bugawan & H.A. Erlich, 1994. Identification of a novel DQB1 allele (*0609) segregating in an Ashkenazi Jewish family: implications for DQB1 typing systems. Tissue Antigens 44(2): 120-124.
75. 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. Ghim, G.M. Troup, A.L. Hughes & N.L. Letvin, 1992. New recombinant HLA-B alleles in a tribe of South American Amerindians indicate rapid evolution of MHC class I loci. Nature 357: 329-333.
76. Watkins, W.S., M. Bamshad & L.B. Jorde, 1995. Population genetics of trinucleotide repeat polymorphism. Hum. Mol. Genet. 4(9): 1485-1491.
77. Watterson, G.A., 1978. The homozygosity test of neutrality. Genetics 88: 405-417.
78. Weir, B.S. & C.C. Cockerham, 1984. Estimating F-statistics for the analysis of population structure. Evolution 38: 1358-1370.
79. Yu, H.T. & Y.H. Peng, 2002. Population differentiation and gene flow revealed by microsatellite DNA markers in the house mouse (Mus musculus castaneus) in Taiwan. Zool. Sci. 19(3): 475-483.