Journal of Molecular Evolution

, Volume 57, Supplement 1, pp S76–S89

Comprehensive Analysis of Two Alu Yd Subfamilies

  • Jinchuan Xing
  • Abdel-Halim Salem
  • Dale J. Hedges
  • Gail E. Kilroy
  • W. Scott Watkins
  • John E. Schienman
  • Caro-Beth Stewart
  • Jerzy Jurka
  • Lynn B. Jorde
  • Mark A. Batzer
Article

DOI: 10.1007/s00239-003-0009-0

Cite this article as:
Xing, J., Salem, AH., Hedges, D.J. et al. J Mol Evol (2003) 57(Suppl 1): S76. doi:10.1007/s00239-003-0009-0

Abstract

Alu elements have inserted in the human genome throughout primate evolution. A small number of Alu insertions have occurred after the divergence of humans from nonhuman primates and therefore should not be present in nonhuman primate genomes. Most of these recently integrated Alu elements are contained with a series of discrete Alu subfamilies that are related to each other based upon diagnostic nucleotide substitutions. We have extracted members of the Alu Yd subfamily that are derivatives of the Alu Y subfamily that share a common 12-bp deletion that defines the Yd lineage from the draft sequence of the human genome. Analysis of the Yd Alu elements resulted in the recovery of two new Alu subfamilies, Yd3 and Yd6, which contain a total of 295 members (198 Yd3 and 97 Yd6). DNA sequence analysis of each of the Alu Yd subfamilies yielded age estimates of 8.02 and 1.20 million years old for the Alu Yd3 and Yd6 subfamilies, respectively. Two hundred Alu Yd3 and Yd6 loci were screened using polymerase chain reaction (PCR) assays to determine their phylogenetic origin and associated levels of human genomic diversity. The Alu Yd3 subfamily appears to have started amplifying relatively early in primate evolution and continued propagating albeit at a low level as many of its members are found in a variety of hominoid (humans, greater and lesser ape) genomes. Only two of the elements are polymorphic in the human genome and absent from the genomes of nonhuman primates. By contrast all of the members of the Alu Yd6 subfamily are restricted to the human genome, with 12% of the elements representing insertion polymorphisms in human populations. A single Alu Yd6 locus contained an independent parallel forward insertion of a paralogous Alu Sq sequence in the owl monkey. These Alu subfamilies are a source of genomic fossil relics for the study of primate phylogenetics and human population genetics.

Keywords

Alu insertion polymorphismSINEsPrimate phylogenetics

Copyright information

© Springer-Verlag New York LLC 2003

Authors and Affiliations

  • Jinchuan Xing
    • 1
  • Abdel-Halim Salem
    • 1
    • 2
  • Dale J. Hedges
    • 1
  • Gail E. Kilroy
    • 1
  • W. Scott Watkins
    • 3
  • John E. Schienman
    • 4
  • Caro-Beth Stewart
    • 4
  • Jerzy Jurka
    • 5
  • Lynn B. Jorde
    • 3
  • Mark A. Batzer
    • 1
  1. 1.Department of Biological Sciences, Biological Computation and Visualization CenterLouisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803USA
  2. 2.Department of Anatomy, Faculty of MedicineSuez Canal University, IsmailiaEgypt
  3. 3.Department of Human GeneticsUniversity of Utah Health Sciences Center, Salt Lake City, UT 84112USA
  4. 4.Department of Biological SciencesUniversity at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222USA
  5. 5.Genetic Information Research Institute, 2081 Landings Drive, Mountain View, CA 94043USA