Chromosomal and mitochondrial DNA variation in orang utans

Wild-born orang utans held in zoos do not have their geographic origins defined, which has complicated comparisons of the two subspecies of orang utans (Bornean orang utans, Pongo pygmaeus pygmaeus, and Sumatran orang utans, P. pygmaeus abelii). The resulting confusion concerning the subspecies identity of individual orang utans and a larger controversy over the desirability of utilizing subspecies designations in orang utan breeding programs has focused attention on the need for a phylogenetic analysis of the species and an examination of the appropriateness of the subspecific designations. Previous studies have suggested that an inversion in the second chromosome pair (PPY2) is a diagnostic subspecies marker and that mitochondrial DNA (mtDNA) and nuclear genetic markers may also be used to identify the subspecies origin of individual orang utans. In an effort to assist zoological parks in examining the question of genetic divergence of orang utan subspecies, we have studied the chromosomes of 144 orang utans, including 58 wild-born individuals. To gain insight into phylogenetic divisions of these apes, mtDNA restriction cleavage site variation has been investigated in 14 individuals whose karyotypic status was known. These investigations have confirmed the existence of two phylogenetic lineages of orang utans based on mtDNA cleavage patterns and demonstrated that these lineages correspond with the two populations characterized by the G-banded morphology of the second pair of chromosomes. The two orang utan phylogenetic units comprise individuals that generally conform to the recognized allopatric, morphological subspecies. Based on current knowledge, the view that the named orangutan subspecies each constitute a distinct phylogenetic lineage more consistent with species-level divergence is supported.