Genetic Variation Among World Populations: Inferences From 100 Alu Insertion Polymorphisms

  1. W. Scott Watkins1,
  2. Alan R. Rogers2,
  3. Christopher T. Ostler1,
  4. Steve Wooding1,
  5. Michael J. Bamshad1,3,
  6. Anna-Marie E. Brassington1,
  7. Marion L. Carroll4,
  8. Son V. Nguyen5,
  9. Jerilyn A. Walker5,
  10. B.V. Ravi Prasad6,
  11. P. Govinda Reddy7,
  12. Pradipta K. Das8,
  13. Mark A. Batzer5, and
  14. Lynn B. Jorde1,9
  1. 1 Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
  2. 2 Department of Anthropology, University of Utah, Salt Lake City, Utah 84112, USA
  3. 3 Department of Pediatrics, University of Utah, Salt Lake City, Utah 84112, USA
  4. 4 Department of Chemistry, Xavier University of Louisiana, New Orleans, Louisiana 70125, USA
  5. 5 Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
  6. 6 Department of Anthropology, Andhra University, Visakhapatnam, Andhra Pradesh 530 003, India
  7. 7 Department of Anthropology, University of Madras, Chennai 600-005, Tamil Nadu 600 005, India
  8. 8 Department of Anthropology, Utkal University, Bhubaneswar 751004, India

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). FST, 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 ∼50 Alu polymorphisms are sufficient to obtain accurate and reliable genetic distance estimates. These analyses also demonstrate that markers with higher FST values have greater resolving power and produce more consistent genetic distance estimates.

Footnotes

  • Article published online before print in June 2003.

    [Supplemental material is available online at www.genome.org. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: J.M. Naiad, B.B. Rao, T. Jenkins, J. Kidd, K. Kidd, and H. Soodyall.]

  • Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.894603.

  • ↵9 Corresponding author. E-MAIL lbj{at}genetics.utah.edu; FAX (801) 585-9148.

    • Accepted April 22, 2003.
    • Received October 10, 2002.
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  1. Published in Advance June 12, 2003, doi: 10.1101/gr.894603 Genome Res. 13: 1607-1618 Cold Spring Harbor Laboratory Press

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