Gil McVean and colleagues report a fine-scale chimpanzee genetic map constructed using a whole-genome population sequencing approach (Science, published online 15 March 2012; doi:10.1126/science.1216872). They sequenced the genomes of 10 unrelated Western Chimpanzees (Pan troglodytes verus) with an average 9.1-fold coverage. They identified 5.3 million autosomal SNPs and inferred variants and haplotypes with high accuracy, which was further improved using a new regional filtering approach. They used this genetic variation data set to estimate the chimpanzee genetic map. At a broad scale, they found that the recombination rates across entire chromosomes were similar in chimpanzees and humans. The notable exceptions were regions with chromosomal rearrangement and chromosome 2, at a historic telomeric fusion event. Fine-scale recombination rates showed less conservation, with no recombination hotspots shared in humans and chimpanzees. However, some general patterns remained similar, including an increased average fine-scale recombination rate around genes and CpG islands. The authors also sequenced 48 PRDM9 alleles in Western Chimpanzees and found high levels of genetic variation. They did not identify any DNA motifs, repeat elements or predicted PRDM9-binding sites consistently associated with recombination hotspots in chimpanzees.