Table 1  Reduction in LDhat recombination rate estimates relative to the simulated rates and expected pedigree-based rates
Inversion frequency (%)Mean % reduction in LDhat recombination ratesExpected % reduction in pedigree recombination ratesExpected mean ped/pop ratio of recombintation rates
1026.9181.12
2055.0321.51
3068.0421.81
4075.3482.11
5081.4502.69
6084.2483.29
7085.7424.06
8085.8324.79
9084.1185.16
  • The mean percentage of reduction in recombination rates estimated by LDhat compared to the simulated rates between adjacent pairs of SNPs within inversion loci is shown across the range of inversion frequencies, for the simulation study described in the text and illustrated in Figure 1. The reductions in observed recombination rate estimates are contrasted with those that would be expected for inversions at these frequencies from pedigree-based recombination rate estimates, based on the expected proportion of heterozygotes for the inversion (assuming Hardy–Weinburg Equilibrium and no viable recombination events for heterozygotes for the inversion). Ped/pop, pedigree/population.