One of the primary objectives in the captive management of chimpanzees is to preserve to the greatest extent possible the genetic diversity that still exists in wild gene pools. Furthermore, it is desirable to prevent the occurrence of intersubspecific hybrids. It is possible to sort chimpanzees into their three subspecies (Pan troglodytes verus, P. t. troglodytes, P. t. schweinfurthii) by investigating mitochondrial DNA sequences. Thus, in order to obtain the basic data necessary to establish a future-breeding protocol, we have decided to evaluate the subspecies of all captive chimpanzees living in Japan. At present, a total of 373 animals including 193 known captive-born, 152 known wild-born, and 28 known captive-born from foreign countries have been raised in Japan. Data on the location of capture of most of these apes is unknown. The 249 chimpanzee samples used in the present study were obtained from 43 zoos in Japan. DNA samples from 180 chimpanzees were extracted from follicle-shed hairs: 67 were from blood samples and 2 were from tissues. We used PCR amplification and direct sequencing of the mitochondrial D-loop region. We compared these sequences with chimpanzees of known geographic origin. Finally, the subspecies of 332 chimpanzees that belonged to 217 maternal lineages were identified. The findings clarified that 230 individuals (61.7%) were P. t. verus. Additionally, four chimpanzees were P. t. troglodytes and 15 were P. t. schweinfurthii. The present findings have also confirmed the existence of another previously unrecognized subspecies of chimpanzee in Nigeria (Pan troglodytes vellerosus). Four of the captive chimpanzees we examined are referable to this subspecies. Examination of the registration book of pedigree and DNA data indicated that 56 chimpanzees born in Japan were actually hybrids of these three subspecies. Molecular data must be carefully examined and reconciled in order to establish a viable breeding plan for chimpanzees in Japan.

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