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 25 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 nonhuman primate genomes. Sequence analysis 
demonstrated these "young" Alu insertions were the products of gene conversion 
events of older, preexisting 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.