Haplotype evolution and linkage disequilibrium: A simulation study

Human Heredity

Volumn 51, Issue 1-2, 2001, Pages 85-96

  Calafell, Francesc ^a   Grigorenko, Elena L ^b,c   Chikanian, Alexei A ^d   Kidd, Kenneth K ^a  

^a YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c MOSCOW STATE UNIVERSITY   (Russian Federation)

^d LEBEDEV PHYSICAL INSTITUTE   (Russian Federation)

Author keywords

Gene mapping; Haplotype; Linkage disequilibrium; Population history

Indexed keywords

ARTICLE; COMPUTER SIMULATION; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE MAPPING; GENETIC RECOMBINATION; HAPLOTYPE; HETEROZYGOSITY; MOLECULAR EVOLUTION; MUTATION RATE; POPULATION; POPULATION GROWTH; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; TANDEM REPEAT;

ALLELES; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; HAPLOTYPES; HUMANS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; POPULATION GROWTH; RECEPTORS, DOPAMINE D2; TANDEM REPEAT SEQUENCES; VARIATION (GENETICS);

EID: 0035213313     PISSN: 00015652     EISSN: None     Source Type: Journal    
DOI: 10.1159/000022963     Document Type: Article

References (49)

1. Castiglione CM, Deinard AS, Speed WC, Sirugo G, Rosenbaum HC, Zhang Y, Grandy DK, Grigorenko EL, Bonné-Tamir B, Pakstis AJ, Kidd JR, Kidd KK: Evolution of haplotypes at the DRD2 locus. Am J Hum Genet 1995;57: 1445-1456.
2. Kidd KK, Pakstis AJ, Castiglione CM, Kidd JR, Speed WC, Goldman D, Knowler WC, Lu R-B, Bonné-Tamir B: DRD2 haplotypes contianing the TaqI A1 allele: Implications for alcoholism research. Alcoholism Clin Exp Res 1996;20:697-705.
3. Tishkoff SA, Dietzch E, Speed W, Pakstis AJ, Kidd JR, Cheung K, Bonné-Tamir B, Santachiara-Benerecetti S, Moral P, Krings M, Pääbo S, Watson E, Risch N, Jenkins T, Kidd KK: Global patterns of linkage disequilibrium at the CD4 locus and modern human origins. Science 1996;271:1380-1387.
4. Tishkoff SA, Goldman A, Calafell F, Speed WC, Deinard AS, Bonné-Tamir B, Kidd JR, Pakstis AJ, Jensen TJ, Kidd KK: A global haplotype analysis of the DM locus: Implications for the evolution of modern humans and the origin of myotonic dystrophy mutations. Am J Hum Genet 1998;62:1389-1402.
5. Harding RM, Fullerton S, Griffiths RC, Bond J, Cox MJ, Schneider JA, Moulin DS, Clegg JB: Archaic African and Asian lineages in the genetic ancestry of modern humans. Am J Hum Genet 1997:60:772-789.
6. Fisher RA: The rhesus factor. Am Sci 1947;35: 95-102.
7. Feldman MW, Nabholz M, Bodmer WF: Evolution of the Rh polymorphism: A model for the interaction of incompatibility, reproductive compensation, and heterozygote advantage. Am J Hum Genet 1969;21:171-193.
8. Bodmer WF, Cann H, Piazza A: Differential genetic variability among polymorphisms as an indicator of natural selection; in Dausset J, Colombani J (eds): Histocompatibility Testing 1972. Copenhagen, Munksgaard, 1973, pp 753-767.
9. Karlin S, Piazza A: Statistical methods for assessing linkage disequilibrium at the HLA-A, B, C loci. Ann Hum Genet 1981;45:79-94.
10. Thomson G, Bodmer WF, Bodmer JG: The HL-A system as a model for studying the interaction between selection, migration, and linkage; in Karlin S, Nevo E (eds): Population Genetics and Ecology. New York, Academic Press, 1976, pp 465-499.
11. Torroni A, Wallace DC: MtDNA haplogroups in Native Americans. Am J Hum Genet 1995; 56:1234-1238.
12. Torroni A, Lott MT, Cabell MF, Chen Y-S, Lavergne L, Wallace DC: mtDNA and the origin of Caucasians: Identification of ancient Caucasian-specific haplogroups, one of which is prone to a recurrent somatic duplication in the D-loop region. Am J Hum Genet 1994;55: 760-776.
13. Chen YS, Torroni A, Excoffier L, Santachiara-Benerecetti AS, Wallace DC: Analysis of mtDNA variation in African populations reveals the most ancient of all human continent-specific haplogroups. Am J Hum Genet 1995; 57:133-149.
14. Deka R, Jin L, Shriver MD, Yu LM, Saha N, Barrantes R, Chakraborty R, Ferrell RE: Dispersion of human Y chromosome haplotypes based on five microsatellites in global populations. Gen Res 1996;6:1177-1184.
15. Hammer MF, Spurdle AB, Karafet T, Bonner MR, Wood ET, Novelletto A, Malaspina P, Mitchell RJ, Horai S, Jenkins T, Zegura SL: The geographic distribution of human Y chromosome variation. Genetics 1997;145:785-805.
16. Mitchell RJ, Hammer MF: Human evolution and the Y chromosome. Curr Opin Genet Dev 1996;6:737-742.
17. Migone N, de Lange G, Piazza A, Cavalli-Sforza LL: Genetic analysis of eight linked polymorphisms within the human immunoglobulin heavy-chain region. Am J Hum Genet 1985;37: 1146-1163.
18. Dard P, Sánchez-Mazas A, Dugoujon JM, De Lange G, Langaney A, Lefranc MP, Lefranc G: DNA analysis of the immunoglobulin IGHG loci in a Mandenka population from eastern Senegal: Correlation with Gm haplotypes and hypotheses for the evolution of the Ig CH region. Hum Genet 1996;98:36-47.
19. Morral N, Bertranpetit J, Estivill X, Nunes V, Casals T, Giménez J, Reis A, Varon-Mateeva R, Macek M, Kalaydjieva L, Angelicheva D, Dancheva R, Romeo G, Russo MP, Garnerone S, Restagno G, Ferrari M, Magnani C, Claustres M, Desgeorges M, Schwartz M, Schwarz M, Dallapiccola B, Novelli G, Ferec C, de Arce M, Nemeti M, Kere J, Anvret M, Dahl N, Ferak V: Tracing the origin of the major cystic fibrosis mutation (δF508) in European populations. Nat Genet 1994;7:169-175.
20. Jennings HS: The numerical results of diverse systems of breeding with respect to two pairs of characters, linked or independent, with special relation to the effects of linkage. Genetics 1917; 2:97-154.
21. Slatkin M: Linkage disequilibrium in growing and stable populations. Genetics 1994;137: 331-336.
22. Thompson EA, Neel JV: Allele disequilibrium and allele frequency distribution as a function of social and demographic history. Am J Hum Genet 1997;60:197-204.
23. Kruglyak L: Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat Genet 1999;22:139-144.
24. Kidd KK, Kidd JR: A nuclear perspective on human evolution; in Boyce AJ, Mascie-Taylor CGN (eds): Molecular Biology and Human Diversity. Cambridge, Cambridge University Press, 1996, pp 242-264.
25. Zhao H, Pakstis AJ, Kidd KK, Kidd JR: Overall and segmental significance levels of linkage disequilibrium at the phenylalanine hydroxylase locus in world populations. Am J Hum Genet 1997;61:A17.
26. Kidd KK, Morar B, Castiglione CM, Zhao H, Pakstis AJ, Speed WC, Goldman D, Knowler WC, Lee C, Nam Y-S, Grandy DK, Jenkins T, Kidd JR: A global survey of haplotype frequencies and linkage disequilibrium at the DRD2 locus. Hum Genet 1998;103:211-227.
27. Weber J, Wong C: Mutation of human short tandem repeats. Hum Molec Gen 1993;2: 1123-1128.
28. Watterson GA, Guess HA: Is the most frequent allele the oldest? Theor Popul Biol 1977;11: 141-160.
29. Di Rienzo A, Peterson AC, Garza JC, Valdes AM, Slatkin M, Freimer NB: Mutational processes of simple sequence repeat loci in human populations. Proc Natl Acad Sci USA 1994;91: 3166-3170.
30. Slatkin M: A measure of population subdivision based on microsatellite allele frequencies. Genetics 1995;139:457-462.
31. Chakraborty R, Kimmel M, Stivers DN, Davison LJ, Deka R: Relative mutation rates at di-, tri-, and tetranucleotide microsatellite loci. Proc Natl Acad Sci USA 1997;94:1041-1046.
32. Neel JV, Satoh C, Goriki K, Fujita M, Takahashii N, Asakawa J, Hazama R: The rate with which spontaneous mutation alters the electrophoretic mobility of polypeptides. Proc Natl Acad Sci USA 1986;83:389-393.
33. Nauta MJ, Weissing FJ: Constraints on allele size at microsatellite loci: Implications for genetic differentiation. Genetics 1996;143:1021-1032.
34. Lewontin RC: The interaction of selection and linkage. I. General considerations: Heterotic models. Genetics 1964;49:49-67.
35. Devlin B, Risch N: A comparison of linkage disequilibrium measures for fine-scale mapping. Genomics 1995;29:311-322.
36. Gyapay G, Morissette J, Vignal A, Dib C, Fizames C, Millasseau P, Marc S, Bernardi G, Lathrop M, Weissenbach J: The 1993-1994 Généthon human genetic linkage map. Nat Genet 1994;7:246-339.
37. Calafell F, Shuster A, Speed WC, Mizuno N, Kidd JR, Kidd KK: Between- and within-population genetic variances are negatively correlated in STRPs but not in RFLPs, submitted.
38. Iyengar S, Seaman M, Deinard AS, Rosenbaum HC, Sirugo G, Castiglione CM, Kidd JR, Kidd KK: Analysis of cross-species polymerase chain reaction products to infer the ancestral status of human polymorphisms. DNA Seq 1998;8:317-328.
39. Estoup A, Tailliez C, Cornuet JM, Solignac M: Size homoplasy and mutational processes of interrupted microsatellites in two bee species, Apis mellifera and Bombus terrestris (Apidae). Mol Biol Evol 1995;12:1074-1084.
40. Deinard AS, Kidd KK: Levels of DNA polymorphism in extant and extinct hominoids; in Brenner S, Hanihara K (eds): The Origin and Past of Modern Humans as Viewed from DNA: Proceedings of the Workshop on the Origin and Past of Homo sapiens sapiens as Viewed from DNA-Theoretical Approach. Singapore, World Scientific, 1995, pp 149-170.
41. Grimaldi MC, Crouau-Roy B: Microsatellite allelic homoplasy due to variable flanking sequences. J Mol Evol 1997;44:336-340.
42. Hacia JG, Fan J-B, Ryder O, Jin L, Edgemon K, Ghandour G, Mayer RA, Sun B, Hsie L, Robbins CM, Brody LC, Wang D, Lander ES, Lipshutz R, Fodor SPA, Collins FS: Determination of ancestral alleles for human single-nucleotide polymorphisms using high-density oligonucleotide arrays. Nat Genet 1999;22: 164-167.
43. Takahata N, Satta Y, Klein J: Divergence and population size in the lineage leading to modern humans. Theor Popul Biol 1995;48:198-221.
44. Armour JA, Anttinen T, May CA, Vega EE, Sajantila A, Kidd JR, Kidd KK, Bertranpetit J, Pääbo S, Jeffreys AJ: Minisatellite diversity supports a recent African origin for modern humans. Nat Genet 1996;13:154-160.
45. Calafell F, Shuster A, Speed WC, Kidd JR, Kidd KK: Short tandem repeat polymorphism in humans. Eur J Hum Genet 1998;6:38-49.
46. Jorde LB: Linkage disequilibrium as a gene-mapping tool. Am J Hum Genet 1995;56:11-14.
47. Jorde LB, Watkins WS, Carlson M, Groden J, Albertsen H, Thliveris A, Leppert M: Linkage disequilibrium predicts physical distance in the adenomatous polyposis coli region. Am J Hum Genet 1994;54:884-898.
48. Peterson AC, Di Rienzo A, Lehesjoki A-E, de la Chapelle A, Slatkin M, Freimer NB: The distribution of linkage disequilibrium over anonymous gene regions. Hum Molec Gen 1995;4: 887-894.
49. Xiong M, Guo S-W: Fine scale genetic mapping based on linkage disequilibrium: Theory and applications. Am J Hum Genet 1997;60: 1513-1531.