Figure 5.

Comparison of recombination maps inferred using different lookup tables. We simulated $n=20$ haplotypes under the three-epoch model (6) and using the recombination map shown as a black dashed line. (A) Inferred map ${\widehat{\rho }}_{{\mathrm{ℒ}}_{\text{exact}}}$ obtained using the exact likelihoods for the true demography. (B) Inferred map ${\widehat{\rho }}_{{\mathrm{ℒ}}_{\mathrm{miss}}}$ obtained using the empirically estimated demography in (8). (C) Inferred map ${\widehat{\rho }}_{{\mathrm{ℒ}}_{\mathrm{approx}}}$ obtained using an approximate lookup table for the true demography. (D) Inferred map ${\widehat{\rho }}_{{\mathrm{ℒ}}_{\mathrm{const}}}$ obtained assuming a constant population size of $\eta \equiv 1.$ Note that ${\widehat{\rho }}_{{\mathrm{ℒ}}_{\mathrm{const}}}$ is much noisier than the other estimates, while using an inferred demography or an approximate lookup table results in only a very mild reduction in accuracy compared to using the true sampling probabilities. These $\widehat{\rho }$ were produced with LDhelmet; using LDhat led to very similar results.