Figure 11.
Using founder haplotype information estimation improves power. (A) If founder sequence information is available, estimating local haplotype frequencies leads to better allele frequency estimates and an increase in power over that of estimates obtained from raw read counts. (B) Error in local haplotype frequency estimates increases with the number of generations due to recombination; however, there is a still a net gain in power from extra generations of neutral mixing. Default: 20 generations mixing, 20 generations selection. Interspersed: 20 generations mixing, 4 generations per selection event, 20 selection events (100 generations total). Initial + interspersed: as interspersed, with 70 generations mixing (150 generations total). (Ten QTL, .)