[i] We examined all insertion deletion events in excess of 100 bp from global alignments. An indel was classified as a retrotransposition event if at least 80% of the indel contained one predominant repeat. We considered the known interspersed repeat phylogeny based on the established repeat subclasses as reported previously (Smit 1999). All insertions were considered including the ancient repeat subclasses that passed our test. Further, in the case of L1 and Alu repeats, insertion sequences were examined for the presence of target-site duplications and a polyadenylation signal at the site of integration. The rate calculation assumed divergence times of the human lineage from chimpanzee, baboon, and lemur of 5.5, 25, and 55 Mya. Pairwise alignment lengths were 5.0, 5.0, and 0.62 Mb for human–chimpanzee, human–baboon, and human–lemur sequence alignment, respectively.

[ii] P < 0.05; ***P < 0.001 by χ²test.