AluInsertion Polymorphisms and Human Evolution: Evidence for a Larger Population Size in Africa (original) (raw)

  1. Mark Stoneking1,
  2. Jennifer J. Fontius2,
  3. Stephanie L. Clifford1,
  4. Himla Soodyall1,3,
  5. Santosh S. Arcot2,
  6. Nilmani Saha4,
  7. Trefor Jenkins3,
  8. Mohammad A. Tahir5,
  9. Prescott L. Deininger6,7, and
  10. Mark A. Batzer2,8,9
  11. 1Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania 16802; 2Human Genome Center, Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore, California 94551;3Department of Human Genetics, The South African Institute for Medical Research, University of the Witwatersrand, Johannesburg 2000, South Africa; 4Department of Pediatrics, National University of Singapore, Singapore; 5Indianapolis–Marion County Forensic Services Agency, Indianapolis, Indiana 46204;6Department of Biochemistry and Molecular Biology;8Department of Pathology and Department of Biometry and Genetics, Stanley S. Scott Cancer Center, Neuroscience Center of Excellence, Louisiana State University Medical Center, New Orleans, Louisiana 70112; 7Laboratory of Molecular Genetics, Alton Ochsner Medical Foundation, New Orleans, Louisiana 70121

Abstract

Alu insertion polymorphisms (polymorphisms consisting of the presence/absence of an Alu element at a particular chromosomal location) offer several advantages over other nuclear DNA polymorphisms for human evolution studies. First, they are typed by rapid, simple, PCR-based assays; second, they are stable polymorphisms—newly inserted Alu elements rarely undergo deletion; third, the presence of an Alu element represents identity by descent—the probability that different _Alu_elements would independently insert into the exact same chromosomal location is negligible; and fourth, the ancestral state is known with certainty to be the absence of an Alu element. We report here a study of 8 loci in 1500 individuals from 34 worldwide populations. African populations exhibit the most between-population differentiation, and the population tree is rooted in Africa; moreover, the estimated effective time of separation of African versus non-African populations is 137,000 ± 15,000 years ago, in accordance with other genetic data. However, a principal coordinates analysis indicates that populations from Sahul (Australia and New Guinea) are nearly as close to the hypothetical ancestor as are African populations, suggesting that there was an early expansion of tropical populations of our species. An analysis of heterozygosity versus genetic distance suggests that African populations have had a larger effective population size than non-African populations. Overall, these results support the African origin of modern humans in that an earlier expansion of the ancestors of African populations is indicated.

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