It is well-accepted that studies of chromosomal changes which have occurred during the evolution of the great apes and the human provide clues towards the phylogeny of these species. Applying recently developed molecular cytogenetic approaches, this study on the chromosomes of the orangutan and the gorilla revealed the presence of cryptic, until now, unrecognized cytogenetic rearrangements mainly within the evolutionary dynamic subcentromeric and subtelomeric regions. On four orangutan chromosomes new rearrangements were detected such as a pericentric inversion in Pongo pygmaeus abeli (PPYa) #1, complex rearrangements on #2 of Pongo pygmaeus pygmaeus (PPYp) and PPYa and a subtelomeric deletion on PPYa&p #19. Additionally, the first centromere repositioning in the great apes was detected on PPYa&p #8. Moreover, the breakpoints of four pericentric inversions within the two orangutan subspecies and three pericentric inversions on Gorilla beringei beringei (GBEb) chromosomes #3, #11 and #13 were refined. The new molecular cytogenetic findings are discussed and compared with the available literature.

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