Fig. 3. Fixed structural variation and regulatory mutation.

a) The great ape cladogram with fixed structural variation assigned to lineages on the basis of assembly comparison, genotyping and stratification (except for inversions). The total amount of sequence is shown on the left side of the branches and the number of SVs is shown on the right for deletions (blue), insertions (red) and inversions (magenta). Inversions were assigned to branches on the basis of the comparison of our five assemblies because genotyping was less reliable. The cladogram was rooted against Susie_PABv1, meaning the assignment of SVs to the orangutan or the common ancestor of human, chimpanzee, and gorilla is arbitrary. b) A map of fixed human-specific structural variants (fhSVs). The color denotes number of fhSVs bases (kbp), within a 1 Mbp sliding window (0.5 Mbp step). Each chromosome is labeled on the y-axis. Key regions are annotated with genes. c) The cell specificity for a mouse enhancer element (mm652, represented as a yellow box) that shares orthology in chimpanzee. In human, an AluY element has been inserted directly into the mm652 enhancer. d) A human-specific STR interrupts a mouse heart-specific enhancer shared with chimpanzee (yellow box). The STR is contained within a CFAP20 intron. e) Dotplots of the human-specific STR expansion. The two human assemblies, CHM13_HSAv1 and YRI_HSAv1, show additional STR expansion relative to GRCh38, suggesting the reference is collapsed. f) A comparison of the hCONDEL set reported by McLean et al. (5) (V1) vs. the hCONDELs reported here (V2). The current hCONDELs are from conservation (25 bp MSA windows) between chimpanzee, macaque and mouse. The current hCONDELs are from conservation (25 bp MSA windows) between chimpanzee, macaque and mouse. The dashed gray area shows the overlap between all fixed human deletions and all V1 hCONDELs. g) A Miropeats diagram of the gorilla complex SV (inversion and deletion) upstream of the AR locus; the human reference genome is shown on the bottom.