Humans have two closest living relatives: the well known chimpanzee (Pan troglodytes) and the lesser known bonobo (Pan paniscus). While the lineage leading to humans and the lineage leading to bonobos and chimpanzees split five to seven million years ago, the bonobo and chimpanzee lineages split around one million years ago. Despite such a recent divergence, these two ape species exhibit remarkable phenotypic differences, indicating that inferences about human evolution will require comparative data from both bonobos and chimpanzees. This is also true at the genomic level. For example, in order to understand the extensive variation seen in gene expression within humans, it is necessary to know the extent of variation within closely related species, as well as the level of differences between species. Comparative genomic data is also necessary, for example, to address whether the supposed high rate of human adaptive evolution is exceptional relative to other closely related primates. Thus, in order to better understand patterns of human evolution, we propose to generate a genome sequence for the bonobo and to collect extensive data from chimpanzees and bonobos on: cDNA sequences, variation in coding and non-coding parts of the genomes, expression of mRNAs, microRNAs and proteins in five tissues, and phenotypic parameters in terms of clinical chemistry, and behavioral and cognitive traits. We will combine these data with the extensive data already collected on humans and perform integrated analyses of between- and within-species variation of genomic and phenotypic traits in humans, bonobos and chimpanzees. This will allow us to place the trends seen in human evolution within the context of our closest living relatives and will substantially increase our understanding of how the genomes of humans, bonobos and chimpanzees produce such startlingly different phenotypes.