| Summary: | <p>Abstract</p> <p>The <it>Alu </it>Yb-lineage is a 'young' primarily human-specific group of short interspersed element (SINE) subfamilies that have integrated throughout the human genome. In this study, we have computationally screened the draft sequence of the human genome for <it>Alu </it>Yb-lineage subfamily members present on autosomal chromosomes. A total of 1,733 Yb <it>Alu </it>subfamily members have integrated into human autosomes. The average ages of Yb-lineage subfamilies, Yb7, Yb8 and Yb9, are estimated as 4.81, 2.39 and 2.32 million years, respectively. In order to determine the contribution of the <it>Alu </it>Yb-lineage to human genomic diversity, 1,202 loci were analysed using polymerase chain reaction (PCR)-based assays, which amplify the genomic regions containing individual Yb-lineage subfamily members. Approximately 20 per cent of the Yb-lineage <it>Alu </it>elements are polymorphic for insertion presence/absence in the human genome. Fewer than 0.5 per cent of the Yb loci also demonstrate insertions at orthologous positions in non-human primate genomes. Genomic sequencing of these unusual loci demonstrates that each of the orthologous loci from non-human primate genomes contains older Y, Sg and Sx <it>Alu </it>family members that have been altered, through various mechanisms, into Yb8 sequences. These data suggest that <it>Alu </it>Yb-lineage subfamily members are largely restricted to the human genome. The high copy number, level of insertion polymorphism and estimated age indicate that members of the <it>Alu </it>Yb elements will be useful in a wide range of genetic analyses.</p>
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