Abstract
Alu
elements are primate-specific members of the SINE (
s
hort
in
terspersed
e
lement) retroposon family, which comprise ∼10% of the human genome. Here we report the first chromosomal-level comparison examining the
Alu
retroposition dynamics following the divergence of humans and chimpanzees. We find a twofold increase in
Alu
insertions in humans in comparison to the common chimpanzee (
Pan troglodytes
). The genomic diversity (polymorphism for presence or absence of the
Alu
insertion) associated with these inserts indicates that, analogous to recent nucleotide diversity studies, the level of chimpanzee
Alu
diversity is ∼1.7 times higher than that of humans. Evolutionarily recent
Alu
subfamily structure differs markedly between the human and chimpanzee lineages, with the major human subfamilies remaining largely inactive in the chimpanzee lineage. We propose a population-based model to account for the observed fluctuation in
Alu
retroposition rates across primate taxa.
