Compound haplotypes at Xp11.23 and human population growth in Eurasia

Annals of Human Genetics

Volumn 68, Issue 5, 2004, Pages 428-437

  Alonso, Santos ^a,b   Armour, J A L ^b  

^a UNIVERSITY OF THE BASQUE COUNTRY UPV EHU   (Spain)

^b UNIVERSITY OF NOTTINGHAM   (United Kingdom)

Author keywords

Coalescent; DXS255; Human evolution; LINE; Linkage disequilibrium; Xp11.23

Indexed keywords

DNA MINISATELLITE;

ARTICLE; ASIA; BOTTLENECK POPULATION; CONTROLLED STUDY; EUROPE; FEMALE; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE MUTATION; GENE SEQUENCE; GENETIC RECOMBINATION; GENETIC VARIABILITY; HAPLOTYPE; HUMAN; LINE DIFFERENCE; MALE; NONHUMAN; NUCLEOTIDE SEQUENCE; POPULATION GROWTH; PRIORITY JOURNAL; SEQUENCE ANALYSIS;

ANIMALS; ASIA; CHROMOSOMES, HUMAN, X; EMIGRATION AND IMMIGRATION; EUROPE; EVOLUTION; GENETICS, POPULATION; HAPLOTYPES; HUMANS; LINKAGE DISEQUILIBRIUM; POPULATION GROWTH; PRIMATES; SELECTION (GENETICS); SEQUENCE ANALYSIS, DNA; VARIATION (GENETICS);

HOMO; HOMO SAPIENS;

EID: 6444229533     PISSN: 00034800     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1529-8817.2003.00115.x     Document Type: Article

References (42)

1. Alonso, S. & Armour, J. A. L. (1998) MS205 minisatellite diversity in Basques, evidence for a pre-Neolithic component. Genome Res. 8, 1289-1298.
2. Alonso, S. & Armour, J. A. L. (2001) A highly variable segment of human subterminal 16p reveals a history of population growth for modern humans outside Africa. P. Natl. Acad. Sci. USA 98, 864-869.
3. Armour, J. A. L., Anttinen, T., May, C. et al (1996) Minisatellite diversity supports a recent African origin for modern humans. Nat. Genet. 13, 154-160.
4. Boissinot, S., Chevret, P. & Furano, A. V. L1 (LINE-1) (2000) retrotransposon evolution and amplification in recent human history. Mol. Biol. Evol. 17, 915-928.
5. Boyd, Y. & Fraser, N. L. (1990) Methylation patterns at the hypervariable X chromosome locus DXS255 (M27β), correlation with X inactivation status. Genomics 7, 182-187.
6. Cavalli-Sforza, L. L., Menozzi, P. & Piazza, A. (1996) The history and geography of human genes, Princeton. Abridged Edition. Princeton University Press.
7. Chen, F. C. and Li, W. H. (2001) Genomic divergences between humans and other hominoids and the effective population sive of the common ancestor of humans and chimpanzees. Am. J. Hum. Genet. 68 444-456.
8. Chen, Y. S., Olckers, A., Schurr, T. G., Kogelnik, A. M., Huoponen, K. & Wallace, D. (2000) mtDNA variation in the South African Kung and Kwe - and their genetic relationships to other African populations. Am. J. Hum. Genet. 66, 1362-1383
9. Excoffier, L. (2002) Human demographic history, refining the recent African origin model. Curr. Opin. Genet. Dev. 12, 675-682.
10. Fraser, N. J., Boyd, Y., Brownlee, G. G. & Craig, J. W. (1987) Multi allelic RFLP for M27b, an anonymous single copy genomic clone at Xp11.3-Xcen [HGM9 provisional no. DXS255]. Nucleic Acids Res. 15, 9616.
11. Fu, Y. X. (1998) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147, 915-925.
12. Gilad, Y., Rosenberg, S., Przeworsky, M., Lancet, D. & Skorecki, K. (2002) Evidence for positive selection & population structure at the human MAO-A gene. P. Natl. Acad. Sci. USA 99 862-867.
13. Harris, E. E. & Hey, J. (1999) X chromosome evidence for ancient human stories. P. Natl. Acad. Sci. USA. 96, 3320-3324.
14. Harris, E. E. & Hey, J. (2001) Human populations show reduced DNA sequence variation at the factor IX locus. Curr. Biol. 11 774-778.
15. Hendriks, R. W., Hinds, H., Chen, Z. Y. & Craig, I. W. (1992) The hypervariable DXS255 locus contains a LINE-1 repetitive element with a CpG island that is extensively methylated only on the active X chromosome. Genomics 14, 598-603.
16. Hudson, R. R. & Kaplan, N. L. (1985) Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111, 147-164.
17. Jeffreys, A. J., Wilson, V., Neumann, R. & Keyte, J. (1988) Amplification of human minisatellites by the polymerase chain reaction, towards DNA fingerprinting of single cells. Nucleic Acids Res. 16, 10953-10971.
18. Jeffreys, A. J., MacLeod, A., Tamaki, K., Neil, D. L. & Monckton, D. G. (1991) Minisatellite repeat coding as a digital approach to DNA typing. Nature 354, 204-209.
19. Kaessmann, H., Heißig, F., von Haeseler, A. & Pääbo, S. (1999) DNA sequence variation in a non-coding region of low recombination on the human X chromosome. Nat. Genet. 22, 78-81.
20. Kitano, T., Scharz, C., Nickel, B. & Pääbo, S. (2003) Gene diversity patterns at 10 X-chromosomal loci in humans & chimpanzees. Mol. Biol. Evol. 20, 1281-1289.
21. Kong, A., Gudbjartsson, D. F., Sainz, J. et al (2002) A high-resolution recombination map of the human genome. Nat. Genet. 31, 241-247.
22. Kruglyak, L. (1999) Prospects for whole genome linkage disequilibrium mapping in common disease genes. Nat. Genet. 22 139-144.
23. Langdon, J. A. & Armour, J. A. L. (2003) Evolution and population genetics of the H-ras minisatellite and cancer predisposition. Hum. Mol. Genet. 12, 891-900.
24. Markovtsova, L., Marjoram, P. & Tavaré, S. (2000) The effects of rate variation on ancestral inference in the coalescent. Genetics 156, 1427-1436.
25. Mellars, PA. (1998) Prehistoric Europe, An illustrated history, Oxford. Cunliffe eds. Oxford University Press.
26. Nachman, M. W. & Crowell, S. L. (2000a) Contrasting evolutionary histories of two introns of the Duchenne muscular distrophy gene, Dmd, in humans. Genetics 155, 1855-1864.
27. Nachman, M. W. & Crowell, S. L. (2000b) Estimate of the mutation rate per nucleotide in humans. Genetics 156, 297-304.
28. Nachman, M. W., Bauer, V. L., Crowell, S. L. & Aquadro, C. F. (1998) DNA variability & recombination rates at X-linked loci in humans. Genetics 150, 1133-1141.
29. Newton, C. R., Graham, A., Heptinstall, L. E. et al (1989) Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucl. Acids Res. 17, 2503-2516.
30. Payseur, B. A. & Nachman, M. W. (2002) Gene density and human nucleotide polymorphism. Mol. Biol. Evol. 19, 336-340.
31. Rogers, A. (2001) Order emerging from chaos in human evolutionary genetics. P. Natl Acad Sci USA 98, 779-780.
32. Rogers, E., Shone, A., Alonso, S., May, C. & Armour, J. A. L. (2000) Integrated analysis of sequence evolution & population history using hypervariable compound haplotypes. Hum. Mol. Genet. 9, 2675-2681.
33. Royle, N. J., Armour, J. A. L., Webb, M., Thomas, A. & Jeffreys, A. J. (1992) A hypervariable locus D16S309, located at the distal end of 16p. Nucl. Acids Res. 20, 1162.
34. Slatkin, M. & Rannala, B. (1997) Estimating the age of alleles by use of intra-allelic variability. Am. J. Hum. Genet 60, 447-458.
35. Slatkin, M. (2001) Simulating genealogies of selected alleles in a population of variable size. Genet. Res. Camb. 78, 49-57.
36. Southern, E. M. (1979) Measurement of DNA length by gel electrophoresis. Anal. Biochem. 100, 319-323.
37. Stephens, J. C., Schneider, J. A., Tanguay, D. A. et al. (2001) Haplotype variation and linkage disequilibrium in 313 human genes. Science 293, 489-493.
38. The Y chromosome consortium (2002) A nomenclature system for the tree of human Y-chromosomal binary haplogroups. Genome Res. 12, 339-348.
39. Wakeley, J., Nielsen, R., Liu-Cordero, S. N. & Ardlie, K. (2001) The discovery of single-nucleotide polymorphisms and inferences about human demographic history. Am. J. Hum. Genet. 69, 1332-1347.
40. Wang, S. S., Devuyst, O., Courtoy, P. J. et al (2000) Mice lacking renal chloride channel, CLC-5, are a model for Dent's disease, a nephrolithiasis disorder associated with defective receptor-mediated endocytosis. Hum. Mol. Genet 9, 2937-2945.
41. Yang, A. (2002) Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci. Genetics 162, 1811-1823.
42. Yu, N., Fu, X. F. & Li, W. H. (2002) DNA polymorphism in a worldwide sample of human X chromosomes. Mol. Biol. Evol. 19, 2131-2141.