Alu Insertion Polymorphisms and Human Evolution: Evidence for a Larger Population Size in Africa

Genome Research

Volumn 7, Issue 11, 1997, Pages 1061-1071

  Stoneking, Mark ^a   Fontius, Jennifer J ^b   Clifford, Stephanie L ^a   Soodyall, Himla ^a,c   Arcot, Santosh S ^b   Saha, Nilmani ^d   Jenkins, Trefor ^c   Tahir, Mohammad A ^e   Deininger, Prescott L ^f,g   Batzer, Mark A ^b,h  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

^c UNIVERSITY OF THE WITWATERSRAND   (South Africa)

^d NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^e Indianapolis Marion Co Forensic S   (United States)

^f Dept of Biochem and Molec Biology ^*

^g OCHSNER MEDICAL CENTER   (United States)

^h LOUISIANA STATE UNIV MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AFRICA; ARTICLE; COMPARATIVE STUDY; GENETIC POLYMORPHISM; GENETICS; HETEROZYGOTE; HUMAN; MOLECULAR EVOLUTION; NEGRO; NUCLEOTIDE REPEAT; PHYLOGENY; RACE;

AFRICA; AFRICAN CONTINENTAL ANCESTRY GROUP; CONTINENTAL POPULATION GROUPS; EVOLUTION, MOLECULAR; HETEROZYGOTE; HUMANS; PHYLOGENY; POLYMORPHISM, GENETIC; REPETITIVE SEQUENCES, NUCLEIC ACID;

EID: 0031262514     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.7.11.1061     Document Type: Article

References (53)

1. Arcot, S.S., J.J. Fontius, P.L. Deininger, and M.A. Batzer. 1995a. Identification and analysis of a "young" polymorphic Alu element. Biochem. Biophys. Acta 1263: 99-102.
2. Arcot, S.S., Z. Wang, J.L. Weber, P.L. Deininger, and M.A. Batzer. 1995b. Alu repeats: A source for the genesis of primate microsatellites. Genomics 29: 136-144.
3. Arcot, S.S., A. W. Adamson, J.E. Lamerdin, B. Kanagy, P.L. Deininger, A.V. Carrano, and M.A. Batzer. 1996. Alu fossil relics - Distribution and insertion polymorphism. Genome Res. 6: 1084-1092.
4. Armour, J.A.L., T. Anttinen, C.A. May, E.E. Vega, A. Sajantila, J.R. Kidd, K.K. Kidd, J. Bertranpetit, S. Paabo, and A.J. Jeffreys. 1996. Minisatellite diversity supports a recent African origin for modern humans. Nature Genet. 13: 154-160.
5. Batzer, M.A. and P.L. Deininger. 1991. A human-specific subfamily of Alu sequences. Genomics 9: 481-487.
6. Batzer, M.A., G.E. Kilroy, P.E. Richard, T.H. Shaikh, T.D. Desselle, C.L. Hoppens, and P.L. Deininger. 1990. Structure and variability of recently inserted Alu family members. Nucleic Acids Res. 18: 6793-6798.
7. Batzer, M.A., V.A. Gudi, J.C. Mena, D.W. Foltz, R.J. Herrera, and P.L. Deininger. 1991. Amplification dynamics of human-specific (HS) Alu family members. Nucleic Acids Res. 19: 3619-3623.
8. Batzer, M.A., M. Stoneking, M. Alegria-Hartman, H. Bazan, D.H. Kass, T.H. Shaikh, G.E. Novick, P.A. Ioannou, W.D. Scheer, R.J. Herrera, and P.L. Deininger. 1994. African origin of human-specific polymorphic Alu insertions. Proc. Natl. Acad. Sci. 91: 12288-12292.
9. Batzer, M.A., C.M. Rubin, U. Hellmann-Blumberg, M. Alegria-Hartman, E.P. Leeflang, J.D. Stern, H.A. Bazan, T.H. Shaikh, P.L. Deininger, and C.W. Schmid. 1995. Dispersion and insertion polymorphism in two small subfamilies of recently amplified human Alu repeats. J. Mol. Biol. 247: 418-427.
10. Batzer, M.A., P.L. Deininger, U. Hellmann-Blumberg, J. Jurka, D. Labuda, C.M. Rubin, C.W. Schmid, E. Zietkiewicz, and E. Zukerkandl. 1996a. Standardized nomenclature for Alu repeats. J. Mol. Evol. 42: 3-6.
11. Batzer, M.A., S.S. Arcot, J.W. Phinney, M. Alegria-Hartman, D.H. Kass, S.M. Milligan, C. Kimpton, P. Gill, M. Hochmeister, P.A. Ioannou, R.J. Herrera, D.A. Boudreau, W.D. Scheer, B.J.B. Keats, P.L. Deininger, and M. Stoneking. 1996b. Genetic variation of recent Alu insertions in human populations. J. Mol. Evol. 42: 22-29.
12. Bowcock, A.M., C. Bucci, J.M. Hebert, J.R. Kidd, K.K. Kidd, J.S. Friedlaender, and L.L. Cavalli-Sforza. 1987. Study of 47 DNA markers in five populations from four continents. Gene Geogr. 1: 47-64.
13. Bowcock, A.M., A. Ruiz-Linares, J. Tomfohrde, E. Minch, J.R. Kidd, and L.L. Cavalli-Sforza. 1994. High resolution of human evolutionary trees with polymorphic microsatellites. Nature 368: 455-457.
14. Cann, R.L., M. Stoneking, and A.C. Wilson. 1987. Mitochondrial DNA and human evolution. Nature 325: 31-36.
15. Cavalli-Sforza, L.L., P. Menozzi, and A. Piazza. 1994. The history and geography of human genes. Princeton University Press, Princeton, N.J.
16. Crawford, M.H., D.D. Dykes, and H.F. Polesky. 1989. Genetic structure of Mennonite populations of Kansas and Nebraska. Hum. Biol. 61: 493-514.
17. Deininger, P.L. and M.A. Batzer. 1993. Evolution of retroposons. Evol. Biol. 27: 157-196.
18. _. 1995. SINE master genes and population biology. In The impact of short interspersed elements (SINEs) on the host genome (ed. R.J. Maraia), pp. 43-60. R.G. Landes, Georgetown, TX.
19. Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39: 783-791.
20. _. 1993. PHYLIP, version 3.5c. University of Washington, Seattle, WA.
21. Goldstein, D.B., A.R. Linares, L.L. Cavalli-Sforza, and M.W. Feldman. 1995. Genetic absolute dating based on microsatellites and the origin of modern humans. Proc. Natl. Acad. Sci. 92: 6723-6727.
22. Hammer, M.F. 1995. A recent common ancestry for human Y chromosomes. Nature 378: 376-378.
23. Harpending, H.C. and R.H. Ward. 1982. Chemical systematics and human populations. In Biochemical aspects of evolutionary biology (ed. M. Nitecki), pp. 213-256. University of Chicago Press, Chicago, IL.
24. Harpending, H., J. Relethford, and S.T. Sherry. 1996. Methods and models for understanding human diversity. In Molecular biology and human diversity (eds. A.J. Boyce and C.G.N. Mascie-Taylor), pp. 283-299. Cambridge University Press, Cambridge, UK.
25. Howells, W.W. 1973. Cranial variation in man: A study by multivariate analysis of patterns of difference among recent human populations. Pap. Peabody Mus. Archaeol. Ethnol. Harv. Univ. 67: 1-259.
26. Jorde, L.B., M.J. Bamshad, W.S. Watkins, R. Zenger, A.E. Fraley, P.A. Krakowiak, K.D. Carpenter, H. Soodyall, T. Jenkins, and A.R. Rogers. 1995. Origins and affinities of modern humans: A comparison of mitochondrial and nuclear genetic data. Am. J. Hum. Genet. 57: 523-538.
27. Kass, D.H., C. Aleman, M.A. Batzer, and P.L. Deininger. 1994. Identification of a human specific Alu insertion in the factor XIIIB gene. Genetica 94: 1-8.
28. Knight, A., M.A. Batzer, M. Stoneking, U.K. Tiwari, W.D. Scheer, R.J. Herrera, and P.L. Deininger. 1996. DNA sequences of Alu elements indicate a recent replacement of the human autosomal genetic complement. Proc. Natl. Acad. Sci. 93: 4360-4364.
29. McComb, J., N. Blagitko, A.G. Comuzzie, M.S. Schanfield, R.I. Sukernik, W.R. Leonard, and M.H. Crawford. 1995. VNTR DNA variation in Siberian indigenous populations. Hum. Biol. 67: 217-229.
30. Melton, T., R. Peterson, A.J. Redd, N. Saha, A.S.M. Sofro, J. Martinson, and M. Stoneking. 1995. Polynesian genetic affinities with Southeast Asian populations as identified by mtDNA analysis. Am. J. Hum. Genet. 57: 403-414.
31. Mountain, J.L. and L.L. Cavalli-Sforza. 1994. Inference of human evolution through cladistic analysis of nuclear DNA restriction polymorphisms. Proc. Natl. Acad. Sci. 91: 6515-6519.
32. Nei, M. 1972. Genetic distance between populations. Am. Nat. 106: 283-292.
33. _. 1987. Molecular evolutionary genetics. Columbia University Press, New York, NY.
34. Nei, M. and A.K. Roychoudhury. 1982. Genetic relationship and evolution of human races. Evol. Biol. 14: 1-59.
35. Nei, M. and N. Takezaki. 1996. The root of the phylogenetic tree of human populations. Mol. Biol. Evol. 13: 170-177.
36. Novick, G.E., C.C. Novick, J. Yunis, E. Yunis, P. Antunez de Mayolo, W.D. Scheer, P.L. Deininger, M. Stoneking, D.S. York, M.A. Batzer, and R.J. Herrera. 1997. Polymorphic Alu insertions and the Oriental origin of Native American populations. Hum. Biol. (in press).
37. Okada, N. 1991. SINEs. Curr. Opin. Genet. Dev. 1: 498-504.
38. Perna, N.T., M.A. Batzer, P.L. Deininger, and M. Stoneking. 1992. Alu insertion polymorphism: A new type of marker for human population studies. Hum. Biol. 64: 641-648.
39. Relethford, J.H. and H.C Harpending. 1994. Cranlometric variation, genetic theory, and modern human origins. Am. J. Phys. Anthropol. 95: 249-270.
40. _. 1995. Ancient differences in population size can mimic a recent African origin of modern humans. Curr. Anthropol. 36: 667-674.
41. Rogers, A.R. and L.B. Jorde. 1995. Genetic evidence on modern human origins. Hum. Biol. 67 1-36.
42. Saitou, N. and M. Nei. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
43. Schmid, C.W. and R. Maraia. 1992. Transcriptional regulation and transpositional selection of active SINE sequences. Curr. Opin. Genet. Dev. 2: 874-882.
44. Sherry, S.T., H.C. Harpening, M.A. Batzer, and M. Stoneking. 1997. Alu evolution in human populations: Using the coalescent to estimate effective population size. Genetics (in press).
45. Sitnikova, T., A. Rzhetsky, and M. Nei. 1995. Interior-branch and bootstrap tests of phylogenetic trees. Mol. Biol. Evol. 12: 319-333.
46. Sokal, R.R. and F.J. Rohlf. 1981. Biometry. W.H. Freeman & Co., New York, NY.
47. Soodyall, H., L. Vigilant, A.V. Hill, M. Stoneking, and T. Jenkins. 1996. mtDNA control-region sequence variation suggests multiple independent origins of an "Asian-specific" 9-bp deletion in sub-Saharan Africans. Am. J. Hum. Genet. 58: 595-608.
48. Stoneking, M. 1993. DNA and recent human evolution. Evol. Anthropol. 2: 60-73.
49. Stringer, C., L Humphrey, and T. Compton. 1997. Cladistic analysis of dental traits in recent humans using a fossil outgroup. J. Hum. Evol. 32: 389-402.
50. Tachida, H. and M. lizuka. 1993. A population genetic study of the evolution of SINEs. I. Polymorphism with regard to the presence or absence of an element. Genetics 133: 1023-1030.
51. Tishkoff, S.A., E. Dietzsch, W. Speed, A.J. Pakstis, J.R. Kidd, K. Cheung, B. Bonne-Tamir, A.S. Santachiara-Benerecetti, P. Moral, M. Krings, S. Paabo, E. Watson, N. Risch, T. Jenkins, and K.K. Kidd. 1996. Global patterns of linkage disequilibrium at the CD4 locus and modern human origins. Science 271: 1380-1397.
52. 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.
53. Weiss, K.M., A.V. Buchanan, R. Valdez, J.H. Moore, and J. Campbell. 1993. Amerindians and the price of modernization. In Urban ecology and health in the third world (ed. L.M. Schell, M.T. Smith, and A. Bilsborough), pp. 221-243. Cambridge University Press, Cambridge, UK.