a, Variation in incomplete lineage sorting. Each vertical blue line represents the fraction of ILS between human, chimpanzee and gorilla estimated in a 1 Mbp region. Dashed black lines show the average ILS across the autosomes and on X; the red line shows the expected ILS on X, given the autosomal average and assuming neutral evolution. b, Reduction in ILS around protein coding genes. The blue line shows the mean rate of ILS sites normalised by mutation rate as a function of distance upstream or downstream of the nearest gene (see Supplementary Information). The horizontal dashed line indicates the average value outside 300 kbp from the nearest gene; error bars are s.e.m.

a, Distribution of gorilla species in Africa. The western species (Gorilla gorilla) comprises two subspecies: western lowland gorillas (G. gorilla gorilla) and Cross River gorillas (G. gorilla diehli). Similarly, the eastern species (Gorilla beringei) is subclassified into eastern lowland gorillas (G. beringei graueri) and mountain gorillas (G. beringei beringei). (Based on data in IUCN 2010.) b, Western lowland gorilla Kamilah, source of the reference assembly (photo JR). c, Eastern lowland gorilla Mukisi (photo M. Seres). d, Isolation-migration model of the western and eastern species. N_A, N_W and N_E are ancestral, western and eastern effective populations sizes; m is the migration rate. e, Likelihood surface for migration and split time parameters in the isolation-migration model.

a, Phylogeny of the great ape family, showing the speciation of human (H), chimpanzee (C), gorilla (G) and orangutan (O). Horizontal lines indicate speciation times within the hominine subfamily and the sequence divergence time between human and orangutan. Interior grey lines illustrate an example of incomplete lineage sorting at a particular genetic locus – in this case (((C, G), H), O) rather than (((H, C), G), O). Below are mean nucleotide divergences between human and the other great apes from the EPO alignment. b, Great ape speciation and divergence times. Upper panel: solid lines show how times for the HC and HCG speciation events estimated by CoalHMM vary with average mutation rate; dashed lines show the corresponding average sequence divergence times, as well as the HO sequence divergence. Blue blocks represent hominid fossil species: each has a vertical extent spanning the range of dates estimated for it in the literature^13,50, and a horizontal position at the maximum mutation rate consistent both with its proposed phylogenetic position and the CoalHMM estimates (including some allowance for ancestral polymorphism in the case of Sivapithecus). The grey shaded region shows that an increase in mutation rate going back in time can accommodate present-day estimates, fossil hypotheses, and a mid-Miocene speciation for orangutan. Lower panel: estimates of the average mutation rate in present-day humans^10-12; grey bars show 95% confidence intervals, with black lines at the means.

a, Mean gene expression distance between human and chimpanzee as a function of the proportion of ILS sites per gene. Each point represents a sliding window of 900 genes (over genes ordered by ILS fraction); s.d. error limits are shown in grey. b, (top) Classification of CTCF sites in the gorilla (EB(JC)) and human (GM12878) LCLs on the basis of species-uniqueness; numbers of alignable CTCF binding sites are shown for each category; (bottom) sequence changes of CTCF motifs embedded in human-specific, shared and gorilla-specific CTCF binding sites located within shared CpG islands, species-specific CpG islands or outside CpG islands. Numbers of CTCF binding sites are shown for each CpG island category. Gorilla and human motif sequences are compared and represented as indels, disruptions (>4 bp gaps), and substitutions.