BACKGROUND: We have previously demonstrated that the Y-specific ampliconic 
fertility genes DAZ (deleted in azoospermia) and CDY (chromodomain protein Y) 
varied with respect to copy number and position among chimpanzees (Pan 
troglodytes). In comparison, seven Y-chromosomal lineages of the bonobo (Pan 
paniscus), the chimpanzee's closest living relative, showed no variation. We 
extend our earlier comparative investigation to include an analysis of the 
intraspecific variation of these genes in gorillas (Gorilla gorilla) and 
orangutans (Pongo pygmaeus), and examine the resulting patterns in the light of 
the species' markedly different social and mating behaviors.
METHODOLOGY/PRINCIPAL FINDINGS: Fluorescence in situ hybridization analysis 
(FISH) of DAZ and CDY in 12 Y-chromosomal lineages of western lowland gorilla 
(G. gorilla gorilla) and a single lineage of the eastern lowland gorilla (G. 
beringei graueri) showed no variation among lineages. Similar findings were 
noted for the 10 Y-chromosomal lineages examined in the Bornean orangutan (Pongo 
pygmaeus), and 11 Y-chromosomal lineages of the Sumatran orangutan (P. abelii). 
We validated the contrasting DAZ and CDY patterns using quantitative real-time 
polymerase chain reaction (qPCR) in chimpanzee and bonobo.
CONCLUSION/SIGNIFICANCE: High intraspecific variation in copy number and 
position of the DAZ and CDY genes is seen only in the chimpanzee. We hypothesize 
that this is best explained by sperm competition that results in the variant DAZ 
and CDY haplotypes detected in this species. In contrast, bonobos, gorillas and 
orangutans-species that are not subject to sperm competition-showed no 
intraspecific variation in DAZ and CDY suggesting that monoandry in gorillas, 
and preferential female mate choice in bonobos and orangutans, probably 
permitted the fixation of a single Y variant in each taxon. These data support 
the notion that the evolutionary history of a primate Y chromosome is not simply 
encrypted in its DNA sequences, but is also shaped by the social and behavioral 
circumstances under which the specific species has evolved.