we assembled snp array data from 29,589 unrelated people and 222 nuclear families genotyped at 490,000910,000 snps from the candidate gene association resource ( care ) , studies at the children s hospital of philadelphia ( chop ) , the african american breast cancer consortium , the african american prostate cancer consortium and the african american lung cancer consortium . to build a recombination map , we used hapmix to localize candidate crossover positions , and implemented a markov chain monte carlo ( mcmc ) that used the probability distributions for the positions of the filtered crossovers to infer recombination rates for each of 1.3 million inter - snp intervals .
we also implemented a second mcmc that models each individual s set of crossovers as a mixture of a shared ( s ) map similar to the european decode map and an african - enriched ( ae ) map , and then assigns each individual an  ae phenotype  corresponding to the proportion of their newly detected crossovers assigned to the ae map .
we imputed genotypes at up to three million hapmap2 snps using mach , and then tested each of these snps for association with the ae phenotype and other recombination - related phenotypes .
we identified 2,454 candidate african - enriched hotspots with increased recombination rates in the yri vs. ceu maps , and in the ae vs. s maps , and searched for motifs enriched at these loci , thus identifying a degenerate 17-bp motif . to study the structure of prdm9 ,
we measured the length of the prdm9 zinc finger array and genotyped rs6889665 in yri , ceu and the care nuclear families ; we also carried out imputation based on 1000 genomes project short read data to infer the alleles individuals carry , among 29 previously characterized in a sequencing study of prdm9 .
 recombination , together with mutation , is the ultimate source of genetic variation in populations . 
 we leverage the recent mixture of people of african and european ancestry in the americas to build a genetic map measuring the probability of crossing - over at each position in the genome , based on about 2.1 million crossovers in 30,000 unrelated african americans . at intervals of more than three megabases 
 it is nearly identical to a map built in europeans . at finer scales it differs significantly , and we identify about 2,500 recombination hotspots that are active in people of west african ancestry but nearly inactive in europeans . 
 the probability of a crossover at these hotspots is almost fully controlled by the alleles an individual carries at prdm9 ( p<10245 ) . 
 we identify a 17 base pair dna sequence motif that is enriched in these hotspots , and is an excellent match to the predicted binding target of african - enriched alleles of prdm9 . 