Figure 7.

Genome-wide ${\widehat{N}}_{\mathrm{e}}$ from an E&R study with D. melanogaster. $N_{\mathrm{e}}$ is estimated based on the allele frequency changes between founder and evolved populations at generation 59 (Franssen et al. 2015). In the top panel, we show genome-wide estimates calculated with $N_{\mathrm{e}}\left(P\right)$ (plan I), using $N=1000$ as census size and $S=500$ as pool size (Orozco-terWengel et al. 2012) and nonoverlapping windows of 10,000 SNPs. Chromosome-wide mean estimates across replicates are shown by the dashed lines and also calculated separately for each replicate in Table 1. DNA stretches with significantly different ${\widehat{N}}_{\mathrm{e}}$ are determined using the stepR software package (Frick et al. 2014) (bottom panel). Lower and upper $1-\alpha$ confidence bands are shown as shaded areas. α controls the error, i.e., the probability for overestimating the number of change points, and is calculated automatically as described in Frick et al. (2014). The colors indicate different biological replicates.