Figure 2.

Effective population size estimated with different methods. Sixty generations of Wright–Fisher neutral evolution with $N_{\mathrm{e}}=100$ diploid individuals were simulated for n = 2000 unlinked loci (SNPs). Prior to sampling, the population was increased to a census size of $N=500$ individuals at each generation. At the starting population and at each indicated time point a sample was taken to create a pool of $S=100$ individuals. The pool was sequenced to an average coverage of $R=50$ and $N_{\mathrm{e}}$ was estimated on the resulting data set by separately contrasting allele frequencies at generation 0 to each of the evolved generations denoted on the x-axis, using $N_{\mathrm{e}}\left(P\right),$ $N_{\mathrm{e}}\left(W\right)$ (Waples 1989), and $N_{\mathrm{e}}\left(JR\right)$ (Jorde and Ryman 2007). Each box represents results from 100 simulations with identical parameters. The dashed gray line shows the true value of $N_{\mathrm{e}}.$ Data are simulated under plan I assumptions and the results of plan I and II estimators are shown in the left and right panels, respectively.