The primary aim of this pilot study is to search for variation on the Y chromosomes of chimpanzees. Efforts to find new markers will be concentrated in individuals of the western subspecies of chimpanzee Pan troglodytes verus although individuals belonging to the other two subspecies of P. troglodytes as well as Pan paniscus (the pygmy chimpanzee or bonobo) will also be included. To find new markers, non-coding single-copy sequences from different locations along the Y chromosome will be investigated using rapid techniques to detect nucleotide polymorphisms. These data will provide a new perspective to test hypotheses about population history within P. t. verus and to examine the phylogeny of the genus Pan with particular attention to the question of whether the subspecies P. t. verus should be raised to full species rank. The genetic data will also allow the comparison of chimpanzee and human demographic histories which can shed light on our own evolutionary history. A secondary aim of this project is to sequence the hypervariable region of the mitochondrial DNA for each chimpanzee sampled in order to identify the subspecies of each individual. The majority of the chimpanzees in captive populations are of unknown subspecies. These mitochondrial DNA sequence data will be compared with data from wild populations, and thus will help us determine the subspecies origin of the captive population. This information will be shared with the zoos, primate centers and species coordinators to aid in the management of the captive population. The majority of the Y chromosome, like mitochondrial DNA, does not recombine. While mitochondrial DNA is passed from mother to child, the Y chromosome is passed from father to son. As a result, polymorphisms at these loci provide complementary pictures of maternal and paternal lineage histories and can contribute a wealth of information about population structure and gene flow within a species. To date, population genetic investigations in chimpanzees have been limited, and they have focused primarily on mitochondrial DNA. This pilot study will begin to address this deficiency by providing data from the Y chromosome.
