Population geneticists often study small numbers of carefully chosen loci, but it has become possible to obtain orders of magnitude for more data from overlaps of genome sequences. Here, we generate tens of millions of base pairs of multiple sequence alignments from combinations of three western chimpanzees, three central chimpanzees, an eastern chimpanzee, a bonobo, a human, an orangutan, and a macaque. Analysis provides a more precise understanding of demographic history than was previously available. We show that bonobos and common chimpanzees were separated ∼1,290,000 years ago, western and other common chimpanzees ∼510,000 years ago, and eastern and central chimpanzees at least 50,000 years ago. We infer that the central chimpanzee population size increased by at least a factor of 4 since its separation from western chimpanzees, while the western chimpanzee effective population size decreased. Surprisingly, in about one percent of the genome, the genetic relationships between humans, chimpanzees, and bonobos appear to be different from the species relationships. We used PCR-based resequencing to confirm 11 regions where chimpanzees and bonobos are not most closely related. Study of such loci should provide information about the period of time 5–7 million years ago when the ancestors of humans separated from those of the chimpanzees.
Studies of population history traditionally examine a small number of genetic regions in many individuals; however, with genome sequencing technologies it is possible to assemble data sets with thousands more aligned sequences albeit in fewer individuals. To explore whether such data can provide useful insights about population history, we assembled large-scale data sets consisting of overlaps of random genome sequencing reads from chimpanzees and bonobos. Analysis of these data finds that bonobos and chimpanzees split from each other about 1.29 million years ago, western and central chimpanzees about 0.51 million years ago, and eastern and central chimpanzees at least 50,000 years ago. We find that the chimpanzee population has fluctuated significantly in size over the past half million years, with the central chimpanzee population size expanding dramatically, and the western chimpanzee population size contracting. Surprisingly, we also find that there are widespread regions of the genome where chimpanzees and bonobos are less closely related to each other than any of them are to humans. In these regions, chimpanzees and bonobos share a common genetic ancestor dating back to speciation from humans, providing a new source of information about that evolutionary event.