Figure 6.

Effect of linkage disequilibrium on ${\widehat{N}}_{\mathrm{e}}.$ The effect of linkage disequilibrium on our estimator was evaluated based on a whole-genome forward simulation with recombination using the software MimicrEE (Kofler and Schlötterer 2014). Three sets of simulations were performed with different rates of recombination: high, normal, and no recombination. For each parameter setup, a genome-wide simulation is replicated 10 times. The effective population size was estimated with $N_{\mathrm{e}}\left(P\right)$ (plan I) in nonoverlapping windows of n = 10,000 SNPs for each replicate. The box plots show the distribution of $N_{\mathrm{e}}$ estimates across replicates and windows.