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MBE Advance Access published online on May 30, 2003
Molecular Biology and Evolution, doi:10.1093/molbev/msg150
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2003; all rights reserved
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Accepted April 11, 2003
© 2003 Society for Molecular Biology and Evolution

Original Articles

Recently Integrated Alu Elements and Human Genomic Diversity

Abdel-Halim Salem 1, Gail E. Kilroy 2, W. Scott Watkins 3, Lynn B. Jorde 3, Mark A. Batzer 2*

1 Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana 70803; Department of Anatomy, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
2 Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana 70803
3 Department of Human Genetics, University of Utah Health Sciences Center, Salt Lake City, Utah 84112

* To whom correspondence should be addressed. E-mail: mbatzer{at}lsu.edu.


  Abstract

A comprehensive analysis of two Alu Y lineage subfamilies was undertaken to assess Alu-associated genomic diversity and identify new Alu insertion polymorphisms for the study of human population genetics. Recently integrated Alu elements (283) from the Yg6 and Yi6 subfamilies were analyzed by polymerase chain reaction (PCR), and twenty-five of the loci analyzed were polymorphic for insertion presence/absence within the genomes of a diverse array of human populations. These newly identified Alu insertion polymorphisms will be useful tools for the study of human genomic diversity. Our screening of the Alu insertion loci also resulted in the recovery of several "young" Alu elements that resided at orthologous positions in non-human primate genomes. Sequence analysis demonstrated these "young" Alu insertions were the products of gene conversion events of older pre-existing Alu elements or independent parallel forward insertions of older Alu elements in the same short genomic region. The level of gene conversion between Alu elements suggests that it may have an influence on the single nucleotide polymorphism within Alu elements in the genome. We have also identified two genomic deletions associated with the retroposition and insertion of Alu Y lineage elements into the human genome. This type of Alu retroposition mediated genomic deletion is a novel source of lineage-specific evolution within primate genomes.

Key Words: primates, deletion, insertion polymorphism, gene conversion


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