Chimpanzee and gorilla chromosomes differ from human chromosomes by the presence 
of large blocks of subterminal heterochromatin thought to be composed primarily 
of arrays of tandem satellite sequence. We explore their sequence composition 
and organization and show a complex organization composed of specific sets of 
segmental duplications that have hyperexpanded in concert with the formation of 
subterminal satellites. These regions are highly copy number polymorphic between 
and within species, and copy number differences involving hundreds of copies can 
be accurately estimated by assaying read-depth of next-generation sequencing 
data sets. Phylogenetic and comparative genomic analyses suggest that the 
structures have arisen largely independently in the two lineages with the 
exception of a few seed sequences present in the common ancestor of humans and 
African apes. We propose a model where an ancestral human-chimpanzee pericentric 
inversion and the ancestral chromosome 2 fusion both predisposed and protected 
the chimpanzee and human genomes, respectively, to the formation of subtelomeric 
heterochromatin. Our findings highlight the complex interplay between duplicated 
sequences and chromosomal rearrangements that rapidly alter the cytogenetic 
landscape in a short period of evolutionary time.