Because non-human great apes are endangered, understanding their genetic variation is critical. Studying genetic variation on the Y chromosome is particularly important because of its role in spermatogenesis and reproductive fitness. Here for the first time we analyzed variation in nine great ape Y ampliconic gene families. We generated copy number for these gene families for chimpanzee, bonobo, Bornean and Sumatran orangutans, and combined them with publicly available data for human and gorilla, as well as produced gene expression data for these great ape species. Analyzing this unique comprehensive dataset in a statistical framework, we came to the following conclusions. First, we found high levels of inter- and intraspecific variation in the Y ampliconic gene copy number, with larger families exhibiting higher levels of variation as compared with smaller families. Notably, orangutans had the largest gene families and the highest levels of intraspecific variation in copy number. Second, we observed significant interspecific size differences in the CDY, RBMY, TSPY, and XKRY gene families, with differences sometimes observed even between sister species (e.g. chimpanzee and bonobo). Third, we detected only limited variation in the Y ampliconic gene expression levels and did not detect significant differences in expression levels among the studied species. Fourth, for several gene families (DAZ, RBMY, and TSPY), we found a positive correlation between copy number and gene expression values, suggesting that copy number can influence gene expression levels over long evolutionary times. Our results also suggest that sperm competition and mating structure, which differ drastically among great ape species, might have affected their interspecific copy number differences.
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