| The Alu Ya and Yb-lineages are distinct groups of Short INterspersed Elements (SINEs) found exclusively in primates. These lineages are comprised of several distinct subfamilies, which contain elements that are evolutionarily-related because they share common diagnostic mutations. Some of these Alu subfamilies are still actively mobilizing in the human genome. We have recovered 4333 Ya and Yb-lineage elements that reside in the human genome draft sequence and focused our analyses on the 4051 autosomal Alu elements. A total of 2672 autosomal loci were subjected to polymerase chain reaction (PCR)-based assays that allow analysis of individual elements for insertion presence and absence. The polymorphism rate for the insertion presence/absence on the human autosomes was 22% and 20% for the Ya and Yb-lineages, respectively. Less than 0.5% (12/2672) of the loci analyzed by PCR displayed positive results for insertions in the orthologous loci of various non-human primate genomes. DNA sequence analysis of these inserts showed that the non-human primate orthologous loci contained older, pre-existing Y, Sc, Sg, Sq or Sx Alu subfamily elements. These PCR results were the result of various evolutionary processes within the human lineage. This is the largest analysis of human Alu mobile element lineages to date. The size, evolutionary age and variable allele insertion frequencies of the Alu Ya and Yb-lineage subfamilies, makes these elements useful tools for human population genetics, human identification and primate comparative genomics. |
