To detect recent partial selective sweeps we used the long-range haplotype (LRH) test44,49 and the integrated haplotype score (iHS) test9. On simulated data45, we found that the tests have similar power to detect recent selection but the iHS test has slightly lower power at low haplotype frequency and the LRH test has slightly lower power at high frequency. This can be seen in applications to HapMap Phase I data3,9, where the iHS test misses the well-known cases of HBB and CD36 and the LRH test misses the SULT1C2 region. Although both tests are based on the concept of EHH44, we observed that the false positives produced by the two tests tend not to overlap and thus that signals detected by both tests have a very low false-positive rate.
