We present three linkage-disequilibrium (LD)-based recombination maps generated using whole-genome sequence data from 10 Nigerian chimpanzees, 13 bonobos, and 15 western gorillas, collected as part of the Great Ape Genome Project (Prado-Martinez J, et al. 2013. Great ape genetic diversity and population history. Nature 499:471-475). We also identified species-specific recombination hotspots in each group using a modified LDhot framework, which greatly improves statistical power to detect hotspots at varying strengths. We show that fewer hotspots are shared among chimpanzee subspecies than within human populations, further narrowing the time scale of complete hotspot turnover. Further, using species-specific PRDM9 sequences to predict potential binding sites (PBS), we show higher predicted PRDM9 binding in recombination hotspots as compared to matched cold spot regions in multiple great ape species, including at least one chimpanzee subspecies. We found that correlations between broad-scale recombination rates decline more rapidly than nucleotide divergence between species. We also compared the skew of recombination rates at centromeres and telomeres between species and show a skew from chromosome means extending as far as 10-15Mb from chromosome ends. Further, we examined broad-scale recombination rate changes near a translocation in gorillas and found minimal differences as compared to other great ape species perhaps because the coordinates relative to the chromosome ends were unaffected. Finally, on the basis of multiple linear regression analysis, we found that various correlates of recombination rate persist throughout the African great apes including repeats, diversity, and divergence. Our study is the first to analyze within- And between-species genome-wide recombination rate variation in several close relatives.
Bibliographical noteFunding Information:
This work was supported by the National Human Genome Research Institute of the National Institutes of Health under award number R01-HG005226 to M.F.H. and J.D.W. and National Institute of General Medical Sciences of the National Institutes of Health under Award Number F32GM101744 to L.S.S. A.E.W. was supported by National Science Foundation Graduate Research Fellowship Grant DGE-1143953. Computations for this study were performed on the QB3 cluster at UCSF. The authors thank Molly Przeworski and Laure Segurel for early access to gorilla PRDM9 sequences. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.