Past DNA studies have suggested that chimpanzee population history has been surprisingly different from humans, although chimpanzees are our nearest relatives. Unfortunately the fossil record for chimpanzees is virtually nonexistent and, thus, genetic investigation of present populations is the best method to examine this history. Chimpanzees are, however, highly endangered and the window of opportunity to sample their genetic diversity may be rapidly closing. To date, genetic investigations have been limited, and they have focused primarily on the maternally-inherited mitochondrial DNA. The goal of this project is to search for variation on the Y chromosomes of chimpanzees, including Pan troglodytes, (the chimpanzee) and Pan paniscus (the pygmy chimpanzee or bonobo). This will provide a new perspective to test hypotheses about population history both within and between chimpanzee species. In addition, it will allow the comparison of chimpanzee and human demographic histories and, thus, can shed light on our own evolutionary history. We are also investigating Y chromosome evolutionary history in the great apes and humans. Because the chimpanzee Y chromosome is 25% smaller than the human Y and may have been subject to structural rearrangement, it is evident that the chimpanzee Y chromosome has undergone interesting changes since diverging from the ancestral human-chimpanzee Y chromosome. Finally, we hope to identify subspecies specific Y chromosome markers within Pan troglodytes that, when combined with mitochondrial DNA data, will allow the origins of the captive population to be clarified.