Fig. 2

Maximum likelihood tree reconstruction using all complete repeats in these primates and the following parameters: partial deletion option, Tamura-Nei model with gamma distribution and invariable sites, nearest-neighbor-interchange heuristic method, 1000 bootstrap resampling, and a cutoff value of 50%. Bootstrap values are shown at the beginning of each branch. Crab-eating macaque was used as an outgroup. Crab-eating macaque repeats and orangutan repeats grouped into their own clusters (“crab-eating macaque cluster” and “orangutan cluster,” respectively). By contrast, the gorilla repeats, chimpanzee repeats, and human repeats are scattered across the “gorilla/chimpanzee/human cluster.” We divided the “gorilla/chimpanzee/human cluster” into subclusters in accordance with the reconciled tree reconstruction shown in Fig. 3