Figure 3.

Identifying conversion of LTR sequences. Open circles represent sites that have retained the ancestral sequence, and filled circles indicate substitutions. Black and white arrows indicate changes discussed in the text. Uninformative sites are not shown. (A) HERV-K18. For clarity, chimpanzee species and humans have been collapsed to a single branch. The boxes highlight 11 sites that cluster the gorilla LTRs separately from their human and chimpanzee counterparts (see Fig. 2B). Although the figure depicts the substitutions as occurring in gorilla, the ancestral sequence (and thus the direction of change) is ambiguous, as indicated by question marks (?) and half-filled circles (◑). (B) RTVL-Ia. Apes are depicted as a single branch. AGM, African green monkey. The pattern of substitutions indicates that a portion of the RTVL-Ia LTR was replaced by conversion with sequences from the 3′ LTR. The pattern between bases 417 and 469 of the gibbon 5′ LTR is identical to the 3′ LTRs (boxed areas).