We search the complete orangutan genome for regions where humans are more closely related to orangutans than to chimpanzees due to incomplete lineage sorting (ILS) in the ancestor of human and chimpanzees. The search uses our recently developed coalescent hidden Markov model (HMM) framework. We find ILS present in~1% of the genome, and that the ancestral species of human and chimpanzees never experienced a severe population bottleneck. The existence of ILS is validated with simulations, site pattern analysis, and analysis of rare genomic events. The existence of ILS allows us to disentangle the time of isolation of humans and orangutans (the speciation time) from the genetic divergence time, and we find speciation to be as recent as 9-13 million years ago ( Mya; contingent on the calibration point). The analyses provide further support for a recent speciation of human and chimpanzee at~4 Mya and a diverse ancestor of human and chimpanzee with an effective population size of about 50,000 individuals. Posterior decoding infers ILS for each nucleotide in the genome, and we use this to deduce patterns of selection in the ancestral species. We demonstrate the effect of background selection in the common ancestor of humans and chimpanzees. In agreement with predictions from population genetics, ILS was found to be reduced in exons and gene-dense regions when we control for confounding factors such as GC content and recombination rate. Finally, we find the broad-scale recombination rate to be conserved through the complete ape phylogeny.[Supplemental material is available for this article.]A prime objective of studying DNA sequences from primate species is to understand the speciation processes and the genomic and phenotypic divergence of the species. The role of natural selection in these processes is particularly interesting to understand. Recently, Locke et al. (2011) added the orangutan to the list of fully sequenced primates, and this opens the investigation of a new time epoch in primate evolution. Whole-genome analysis of the fiveway alignment of the three great apes-human, chimpanzee, and orangutan-using macaque and marmoset as outgroups, allows us to gain insight into evolution on the primate branch leading to human, including knowledge on the speciation processes and speciation times for human, chimpanzee, and orangutan. The variation in divergence times between sequences from different species contains information about the effective population sizes of the ancestral species, and by estimating the effective population sizes, we can disentangle the times of divergence of genomes from the times of divergence of species. Furthermore, the imprint of natural selection shows as variations in the effective population size estimated locally in the genome, and this signature is therefore an important tool for analyzing the effects of selection and their interaction with the effects of recombination and migration.The power to infer the ancestral effective population sizes, the times when species split, and recombinati...