Home LiteratureArticle Details
PMID: 12805277 Published · ppublish English Comparative Study Journal Article Multicenter Study Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.

Genetic variation among world populations: inferences from 100 Alu insertion polymorphisms.

Genome research ·Vol. 13 ·No. 7 ·2003-07-00 ·Pages 1607-18

Watkins WS, Rogers AR, Ostler CT, Wooding S, Bamshad MJ, Brassington AM, Carroll ML, Nguyen SV, Walker JA, Prasad BV, Reddy PG, Das PK, Batzer MA, Jorde LB

Abstract

We examine the distribution and structure of human genetic diversity for 710 individuals representing 31 populations from Africa, East Asia, Europe, and India using 100 Alu insertion polymorphisms from all 22 autosomes. Alu diversity is highest in Africans (0.349) and lowest in Europeans (0.297). Alu insertion frequency is lowest in Africans (0.463) and higher in Indians (0.544), E. Asians (0.557), and Europeans (0.559). Large genetic distances are observed among African populations and between African and non-African populations. The root of a neighbor-joining network is located closest to the African populations. These findings are consistent with an African origin of modern humans and with a bottleneck effect in the human populations that left Africa to colonize the rest of the world. Genetic distances among all pairs of populations show a significant product-moment correlation with geographic distances (r = 0.69, P < 0.00001). F(ST), the proportion of genetic diversity attributable to population subdivision is 0.141 for Africans/E. Asians/Europeans, 0.047 for E. Asians/Indians/Europeans, and 0.090 for all 31 populations. Resampling analyses show that approximately 50 Alu polymorphisms are sufficient to obtain accurate and reliable genetic distance estimates. These analyses also demonstrate that markers with higher F(ST) values have greater resolving power and produce more consistent genetic distance estimates.

MeSH Terms
Africa Alu Elements/genetics Computational Biology Europe Far East Genetic Variation/genetics Genetics, Population/methods Humans India Mutagenesis, Insertional Polymorphism, Genetic/genetics
Authors & Affiliations
14 authors, click to expand affiliations / ORCID
Watkins W Scott
Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA.
Rogers Alan R
Ostler Christopher T
Wooding Steve
Bamshad Michael J
Brassington Anna-Marie E
Carroll Marion L
Nguyen Son V
Walker Jerilyn A
Prasad B V Ravi
Reddy P Govinda
Das Pradipta K
Batzer Mark A
Jorde Lynn B
References (67)
67 references, click to expand
  1. Genetic relationships of Europeans, Asians and Africans and the origin of modern Homo sapiens.
    Hum Hered. 1989;39(5):276-81 PMID: 2613254
  2. Dispersion and insertion polymorphism in two small subfamilies of recently amplified human Alu repeats.
    J Mol Biol. 1995 Mar 31;247(3):418-27 PMID: 7714898
  3. Microsatellite variation and the differentiation of modern humans.
    Hum Genet. 1997 Jan;99(1):1-7 PMID: 9003483
  4. Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition.
    Cell. 1996 Nov 29;87(5):905-16 PMID: 8945517
  5. Human LINE retrotransposons generate processed pseudogenes.
    Nat Genet. 2000 Apr;24(4):363-7 PMID: 10742098
  6. A short tandem repeat-based phylogeny for the human Y chromosome.
    Am J Hum Genet. 2000 Jul;67(1):182-96 PMID: 10827105
  7. Mitochondrial DNA and human evolution.
    Nature. 1987 Jan 1-7;325(6099):31-6 PMID: 3025745
  8. Population genetics of dinucleotide (dC-dA)n.(dG-dT)n polymorphisms in world populations.
    Am J Hum Genet. 1995 Feb;56(2):461-74 PMID: 7847383
  9. High resolution of human evolutionary trees with polymorphic microsatellites.
    Nature. 1994 Mar 31;368(6470):455-7 PMID: 7510853
  10. Larger genetic differences within africans than between Africans and Eurasians.
    Genetics. 2002 May;161(1):269-74 PMID: 12019240
  11. Alu insertion polymorphisms in NW Africa and the Iberian Peninsula: evidence for a strong genetic boundary through the Gibraltar Straits.
    Hum Genet. 2000 Oct;107(4):312-9 PMID: 11129330
  12. Haplotype variation and linkage disequilibrium in 313 human genes.
    Science. 2001 Jul 20;293(5529):489-93 PMID: 11452081
  13. A global haplotype analysis of the myotonic dystrophy locus: implications for the evolution of modern humans and for the origin of myotonic dystrophy mutations.
    Am J Hum Genet. 1998 Jun;62(6):1389-402 PMID: 9585589
  14. LINEs mobilize SINEs in the eel through a shared 3' sequence.
    Cell. 2002 Nov 1;111(3):433-44 PMID: 12419252
  15. Alu insertion polymorphisms for the study of human genomic diversity.
    Genetics. 2001 Sep;159(1):279-90 PMID: 11560904
  16. A human-specific subfamily of Alu sequences.
    Genomics. 1991 Mar;9(3):481-7 PMID: 1851725
  17. The Stepping Stone Model of Population Structure and the Decrease of Genetic Correlation with Distance.
    Genetics. 1964 Apr;49(4):561-76 PMID: 17248204
  18. Alu insertion polymorphisms and the genetic structure of human populations from the Caucasus.
    Eur J Hum Genet. 2001 Apr;9(4):267-72 PMID: 11313770
  19. Human population genetic structure and inference of group membership.
    Am J Hum Genet. 2003 Mar;72(3):578-89 PMID: 12557124
  20. Mitochondrial genome variation and the origin of modern humans.
    Nature. 2000 Dec 7;408(6813):708-13 PMID: 11130070
  21. A de novo Alu insertion results in neurofibromatosis type 1.
    Nature. 1991 Oct 31;353(6347):864-6 PMID: 1719426
  22. Microsatellite evolution in modern humans: a comparison of two data sets from the same populations.
    Ann Hum Genet. 2000 Mar;64(Pt 2):117-34 PMID: 11246466
  23. Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons.
    Proc Natl Acad Sci U S A. 1997 Mar 4;94(5):1872-7 PMID: 9050872
  24. Human diallelic insertion/deletion polymorphisms.
    Am J Hum Genet. 2002 Oct;71(4):854-62 PMID: 12205564
  25. Alu insertion polymorphisms and human evolution: evidence for a larger population size in Africa.
    Genome Res. 1997 Nov;7(11):1061-71 PMID: 9371742
  26. The structure of haplotype blocks in the human genome.
    Science. 2002 Jun 21;296(5576):2225-9 PMID: 12029063
  27. Alu repeats and human disease.
    Mol Genet Metab. 1999 Jul;67(3):183-93 PMID: 10381326
  28. Genetic evidence on the origins of Indian caste populations.
    Genome Res. 2001 Jun;11(6):994-1004 PMID: 11381027
  29. Processed pseudogenes: characteristics and evolution.
    Annu Rev Genet. 1985;19:253-72 PMID: 3909943
  30. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms.
    Nature. 2001 Feb 15;409(6822):928-33 PMID: 11237013
  31. Distinct haplotype profiles and strong linkage disequilibrium at the MDR1 multidrug transporter gene locus in three ethnic Asian populations.
    Pharmacogenetics. 2002 Aug;12(6):437-50 PMID: 12172212
  32. African populations and the evolution of human mitochondrial DNA.
    Science. 1991 Sep 27;253(5027):1503-7 PMID: 1840702
  33. Origins and affinities of modern humans: a comparison of mitochondrial and nuclear genetic data.
    Am J Hum Genet. 1995 Sep;57(3):523-38 PMID: 7668280
  34. SINEs.
    Curr Opin Genet Dev. 1991 Dec;1(4):498-504 PMID: 1668310
  35. Out of Africa and back again: nested cladistic analysis of human Y chromosome variation.
    Mol Biol Evol. 1998 Apr;15(4):427-41 PMID: 9549093
  36. The structure of human mitochondrial DNA variation.
    J Mol Evol. 1991 Dec;33(6):543-55 PMID: 1685753
  37. Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information.
    Annu Rev Biochem. 1986;55:631-61 PMID: 2427017
  38. Mutation analysis in the BRCA2 gene in primary breast cancers.
    Nat Genet. 1996 Jun;13(2):245-7 PMID: 8640237
  39. Population structure and genetic differentiation among 16 tribal populations of central India.
    Hum Biol. 1996 Oct;68(5):679-705 PMID: 8908797
  40. V75R576 IL-4 receptor alpha is associated with allergic asthma and enhanced IL-4 receptor function.
    J Immunol. 2002 Aug 1;169(3):1604-10 PMID: 12133990
  41. Sequence diversity and large-scale typing of SNPs in the human apolipoprotein E gene.
    Genome Res. 2000 Oct;10(10):1532-45 PMID: 11042151
  42. Microsatellite diversity and the demographic history of modern humans.
    Proc Natl Acad Sci U S A. 1997 Apr 1;94(7):3100-3 PMID: 9096352
  43. Genetic traces of ancient demography.
    Proc Natl Acad Sci U S A. 1998 Feb 17;95(4):1961-7 PMID: 9465125
  44. Human evolution and the mitochondrial genome.
    Curr Opin Genet Dev. 1996 Dec;6(6):731-6 PMID: 8994844
  45. Transposing without ends: the non-LTR retrotransposable elements.
    New Biol. 1992 May;4(5):430-40 PMID: 1325183
  46. African origin of human-specific polymorphic Alu insertions.
    Proc Natl Acad Sci U S A. 1994 Dec 6;91(25):12288-92 PMID: 7991620
  47. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data.
    Genetics. 1992 Jun;131(2):479-91 PMID: 1644282
  48. Sequence variations in the public human genome data reflect a bottlenecked population history.
    Proc Natl Acad Sci U S A. 2003 Jan 7;100(1):376-81 PMID: 12502794
  49. A view of modern human origins from Y chromosome microsatellite variation.
    Genome Res. 1999 Jun;9(6):558-67 PMID: 10400923
  50. Linkage disequilibrium in the human genome.
    Nature. 2001 May 10;411(6834):199-204 PMID: 11346797
  51. Partial nucleotide sequence of the 300-nucleotide interspersed repeated human DNA sequences.
    Nature. 1980 Mar 27;284(5754):372-4 PMID: 6244506
  52. Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity.
    J Mol Biol. 2001 Aug 3;311(1):17-40 PMID: 11469855
  53. The distribution of human genetic diversity: a comparison of mitochondrial, autosomal, and Y-chromosome data.
    Am J Hum Genet. 2000 Mar;66(3):979-88 PMID: 10712212
  54. Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition.
    Cell. 1993 Feb 26;72(4):595-605 PMID: 7679954
  55. The apportionment of dinucleotide repeat diversity in Native Americans and Europeans: a new approach to measuring gene identity reveals asymmetric patterns of divergence.
    Mol Biol Evol. 1996 Sep;13(7):943-53 PMID: 8752003
  56. Genetic perspectives on human origins and differentiation.
    Annu Rev Genomics Hum Genet. 2000;1:361-85 PMID: 11701634
  57. Patterns of ancestral human diversity: an analysis of Alu-insertion and restriction-site polymorphisms.
    Am J Hum Genet. 2001 Mar;68(3):738-52 PMID: 11179020
  58. Multiple origins of the mtDNA 9-bp deletion in populations of South India.
    Am J Phys Anthropol. 1999 Jun;109(2):147-58 PMID: 10378454
  59. De novo alu-element insertions in FGFR2 identify a distinct pathological basis for Apert syndrome.
    Am J Hum Genet. 1999 Feb;64(2):446-61 PMID: 9973282
  60. Global patterns of linkage disequilibrium at the CD4 locus and modern human origins.
    Science. 1996 Mar 8;271(5254):1380-7 PMID: 8596909
  61. Alu repeats and human genomic diversity.
    Nat Rev Genet. 2002 May;3(5):370-9 PMID: 11988762
  62. Origin and phylogenetic distribution of Alu DNA repeats: irreversible events in the evolution of primates.
    J Mol Biol. 1999 Jun 18;289(4):861-71 PMID: 10369767
  63. Inference in population structure studies.
    Am J Hum Genet. 1971 Sep;23(5):536-9 PMID: 5092601
  64. Genetic absolute dating based on microsatellites and the origin of modern humans.
    Proc Natl Acad Sci U S A. 1995 Jul 18;92(15):6723-7 PMID: 7624310
  65. Population substructure and isolation by distance in three continental regions.
    Am J Phys Anthropol. 1999 Feb;108(2):147-59 PMID: 9988378
  66. Initial sequencing and analysis of the human genome.
    Nature. 2001 Feb 15;409(6822):860-921 PMID: 11237011
  67. Female gene flow stratifies Hindu castes.
    Nature. 1998 Oct 15;395(6703):651-2 PMID: 9790184
Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1088-9051
DOI
10.1101/gr.894603
Published
2003-07-00
Epub
2003-00-12
Pages
1607-18
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC403734
Subset
IM
Grants
NCRR NIH HHS · M01 RR000064 · United States
NIGMS NIH HHS · R01 GM059290 · United States
NIGMS NIH HHS · GM-59290 · United States
NCRR NIH HHS · RR-00064 · United States
External Links
PubMed source DOI: 10.1101/gr.894603 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2