Extended Data Fig. 4. Alpha satellite higher order repeat (HOR) haplotypes are species-specific in Pongo and Pan (except for the few distal HOR copies).

(a) Consensus HOR haplotype (HORhap) phylogenetic trees, (b) HOR trees, and (c) HORhap UCSC Genome Browser annotation tracks for active alpha satellite arrays of chromosomes X and Y in two Pan and two Pongo species (see Methods in Note S7) are shown. Each colored branch in a HOR tree represents a HORhap. All branches in HOR trees are species-specific, except for the GREY cluster in Pan cenX tree, where mixing of chimpanzee (square markers) and bonobo (triangle markers) HORs were observed (Note S7). Each branch was extracted to obtain HORhap consensus sequence and HMM further used in HMMER-based HORhap classification tool⁴⁴ to produce HORhap annotations. The larger branches with shorter twigs correspond to the younger large active HORhap arrays; the smaller branches with longer twigs correspond to the older and smaller side arrays. The thinnest and longest branches make up the oldest and smallest peripheral arrays which often cannot be seen in the track panels. The Pongo X tree has a ‘star-like’ shape and does not have obvious HORhaps; HORs colored by species indicate almost no mixing between species and species-specific consensus sequences show three consistent differences (Fig. S15D). Thus, we concluded that the species did not share the same HORhaps, but no significant divides could be seen in the tree due to the short HOR length (a 4-mer), as detailed in Note S7. The age of the HORhaps is also confirmed by consensus trees where the oldest GREY twigs branch out closer to the root and are nearly equidistant to the active HORhap branches of respective species. Hence they likely resemble the HORs that existed in the common ancestor of both species. Thus, all but the oldest HORhaps are species-specific and indicate considerable evolution that occurred after the species diverged.