A genome scan to detect candidate regions influenced by local natural selection in human populations

Molecular Biology and Evolution

Volumn 20, Issue 6, 2003, Pages 893-900

  Kayser, Manfred ^a   Brauer, Silke ^a   Stoneking, Mark ^a  

^a MAX PLANCK INSTITUTE FOR EVOLUTIONARY ANTHROPOLOGY   (Germany)

Author keywords

Genetic distance; Humans; Selection; STR

Indexed keywords

ADAPTATION; ARTICLE; FEASIBILITY STUDY; GENE LOCUS; GENETIC ANALYSIS; GENETIC VARIABILITY; GENOME; GENOTYPE; HUMAN; NATURAL SELECTION; REPRODUCIBILITY; TANDEM REPEAT;

GENETICS, POPULATION; HUMANS; SELECTION (GENETICS); TANDEM REPEAT SEQUENCES;

EID: 0038586483     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msg092     Document Type: Article

References (41)

1. Allison, A. C. 1954. Protection afforded by sickle-cell trait against subterian malarial infection. Br. Med. J. 1:290-294.
2. Akey, J. M., G. Zhang, K. Zhang, L. Jin, and M. D. Shriver. 2002. Interrogating a high-density SNP map for signatures of natural selection. Genome Res. 12:1805-1814.
3. Baer, C. F. 1999. Among-locus variation in Fst: fish, allozymes and the Lewontin-Krakauer test revisited. Genetics 152:653-659.
4. Balloux, F., and J. Goudet. 2002. Statistical properties of population differentiation estimators under stepwise mutation in a finite island model. Mol. Ecol. 11:771-783.
5. Beaumont, M. A., and R. A. Nichols. 1996. Evaluating loci for use in the genetic analysis of population structure. Proc. Roy. Soc. Lond. B Biol. Sci. 263:1619-1626.
6. Bowcock, A. B., J. R. Kidd, J. L. Mountain, J. M. Hebert, L. Carotenuto, K. K. Kidd, and L. L. Cavalli-Sforza. 1991. Drift, admixture, and selection in human evolution: a study with DNA polymorphisms. Proc. Natl. Acad. Sci. USA 88:839-843.
7. Caballero, A. 1995. On the effective size of populations with separate sexes, with particular reference to sex-linked genes. Genetics 139:1007-1011.
8. Cavalli-Sforza, L. L. 1966. Population structure and human evolution. Proc. Roy. Soc. Lond. B Biol. Sci. 164:362-379.
9. Chakraborty, R., M. Kimmel, D. N. Stivers, L. J. Davison, and R. Deka. 1997. Relative mutation rates at di-, tri-, and tetranucleotide microsatellite loci. Proc. Natl. Acad. Sci. USA 94:1041-1046.
10. Charlesworth, B., J. A. Coyne, and N. H. Barton. 1987. The relative rates of evolution of sex chromosomes and autosomes. Am. Nat. 130:113-146.
11. Hamblin, M. T., E. E. Thompson, and A. Di Rienzo. 2002. Complex signatures of natural selection at the Duffy blood group locus. Am. J. Hum. Genet. 70:369-383.
12. Hill, A. V. S., C. E. M. Allsopp, D. Kwiatkowski, N. M. Anstey, P. Twumasi, P. A. Rowe, S. Bennett, D. Brewster, A. J. McMichael, and B. M. Greenwood. 1991. Common West African HLA antigens are associated with protection from severe malaria. Nature 352:595-600.
13. Johnson, D. G., and R. Schneider-Broussard. 1998. Role of E2F in cell cycle control and cancer. Frontiers Biosci. 3:447-458.
14. Jorde, L. B., W. S. Watkins, M. J. Bamshad, M. E. Dixon, C. E. Ricker, M. T. Seielstad, and M. A. Batzer. 2000. The distribution of human genetic diversity: a comparison of mitochondrial, autosomal, and Y-chromosome data. Am. J. Hum. Genet. 66:979-988.
15. Kent, W. J., C. W. Sugnet, T. S. Furey, K. M. Roskin, T. H. Pringle, A. M. Zahler, and D. Haussler. 2002. The human genome browser at UCSC. Genome Res. 12:996-1006.
16. Lahr, M. M., and R. A. Foley. 1998. Towards a theory of modern human origins: geography, demography, and diversity in recent human evolution. Yrbk. Phys. Anthropol. 41:137-176.
17. Lewontin, R. C., and J. Krakauer. 1973. Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Genetics 74:175-195.
18. -. 1975. Letters to the editors: testing the heterogeneity of F values. Genetics 80:397-398.
19. Lindqvist, A. K., P. K. Magnusson, J. Balciuniene, C. Wadelius, E. Lindholm, M. E. Alarcon-Riquelme, and U. B. Gyllensten. 1996. Chromosome-specific panels of tri- and tetranucleotide microsatellite markers for multiplex fluorescent detection and automated genotyping: evaluation of their utility in pathology and forensics. Genome Res. 6:1170-1176.
20. Luzzatto, L., E. Usanga, and S. Reddy. 1969. Glucose-6-phosphate dehydrogenase deficient red cells: resistance to infection by malarial parasites. Science 164:839-841.
21. Miller, L. H., S. J. Mason, D. F. Clyde, and M. H. McGinniss. 1976. The resistance factor to Plasmodium vivax in blacks. The Duffy-blood-group genotype, FyFy. N. Engl. J. Med. 295: 302-304.
22. Mountain, J. L. 1998. Molecular evolution and modern human origins. Evol. Anthropol. 7:21-37.
23. Nei, M., and A. Chakravarti. 1977. Drift variances of Fst and Gst statistics obtained from a finite number of isolated populations. Theor. Popul. Biol. 11:307-325.
24. Nei, M., A. Chakravarti, and Y. Tateno. 1977. Mean and variance of Fst in a finite number of incompletely isolated populations. Theor. Popul. Biol. 11:291-306.
25. Nei, M., and T. Maruyama. 1975. Letters to the editors: Lewontin-Krakauer test for neutral genes. Genetics 80:395.
26. Ogawa, H., K. Ishiguro, S. Gaubatz, D. M. Livingston, and Y. Nakatani. 2002. A complex with chromatin modifiers that occupies E2F- and Myc-responsive genes in Go cells. Science 296:1132-1136.
27. Payseur, B. A., A. D. Cutter, and M. W. Nachman. 2002. Searching for evidence of positive selection in the human genome using patterns of microsatellite variability. Mol. Biol. Evol. 19:1143-1153.
28. Robertson, A. 1975. Gene frequency distributions as a test of selective neutrality. Genetics 81:775-785.
29. Rosenberg, N. A., J. K. Pritchard, J. L. Weber, H. M. Cann, K. K. Kidd, L. A. Zhivotovsky, and M. W. Feldman. 2002. Genetic structure of human populations. Science 298:2381-2385.
30. Sabeti, P. C., D. E. Reich, J. M. Higgins et al. (17 co-authors). 2002. Detecting recent positive selection in the human genome from haplotype structure. Nature 419:832-837.
31. Schlötterer, C. 2002a. A microsatellite-based multilocus screen for the identification of local selective sweeps. Genetics 160:753-763.
32. -. 2002b. Towards a molecular characterization of adaptation in local populations. Curr. Opin. Genet. Dev. 12: 683-687.
33. Slatkin, M. 1995. A measure of population subdivision based on microsatellite allele frequencies. Genetics 139:457-462.
34. Stoneking, M. 1993. DNA and recent human evolution. Evol. Anthropol. 2:60-73.
35. Stoneking, M., J. J. Fontius, S. L. Clifford, H. Soodyall, S. S. Arcot, N. Saha, T. Jenkins, M. A. Tahir, P. L. Deininger, and M. A. Batzer. 1997. Alu insertion polymorphisms and human evolution: evidence for a larger population size in Africa. Genome Res. 7:1061-1071.
36. Tishkoff, S. A., E. Dietzsch, W. Speed et al. (15 co-authors). 1996. Global patterns of linkage disequilibrium at the CD4 locus and modem human origins. Science 271:1380-1387.
37. Tishkoff, S. A., R. Varkonyi, N. Cahinhinan et al. (17 co-authors). 2001. Haplotype diversity and linkage disequilibrium at human G6PD: recent origin of alleles that confer malarial resistance. Science 293:455-462.
38. Trimarchi, J. M., B. Fairchild, J. Wen, and J. A. Lees. 2001. The E2F6 transcription factor is a component of the mammalian Bmil-containing polycomb complex. Proc. Natl. Acad. Sci. USA 98:1519-1524.
39. Vigilant, L., M. Stoneking, H. Harpending, K. Hawkes, and A. C. Wilson. 1991. African populations and the evolution of human mitochondrial DNA. Science 253:1503-1507.
40. Vitalis, R., K. Dawson, and P. Boursot. 2001. Interpretation of variation across marker loci as evidence of selection. Genetics 158:1811-1823.
41. Yu, N., F. C. Chen, S. Ota, L. B. Jorde, P. Pamilo, L. Patthy, M. Ramsay, T. Jenkins, S. K. Shyue, and W. H. Li. 2002. Larger genetic differences within Africans than between Africans and Eurasians. Genetics 161:269-274.