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. Author manuscript; available in PMC: 2017 May 8.
Published in final edited form as: Science. 2014 Aug 29;345(6200):1074–1079. doi: 10.1126/science.1253714

Fig. 2. Selective sweep and delta allele frequency analyses.

Fig. 2

(A) Plot of FST values between wild and domestic rabbits. Sweeps detected with the FST-H outlier approach, SweepFinder and their overlaps are marked on top. Unassigned scaffolds were not included in the analysis. (B) and (C) Selective sweeps at GRIK2 (B) and SOX2 (C). Heterozygosity plots for wild (red) and domestic (black) rabbits together with plots of FST values and SNPs with ΔAF>0.75 (HΔAF). The bottom panel shows putative sweep regions, detected with the FST-H outlier approach and SweepFinder, marked with horizontal bars. Gene annotations in sweep regions are indicated; *represents ENSOCUT000000. **SOX2-OT represents the manually annotated SOX2 overlapping transcript (4). (D) Number of SNPs in non-overlapping ΔAF bins (black lines, left y-axis). M-values (log2-fold changes) of the relative frequencies of SNPs at non-coding evolutionary conserved sites, in untranslated regions (UTR), exons and introns according to ΔAF bins (colored lines, right y-axis); M-values were calculated with the average frequency of the corresponding annotation category as reference. (E) Location of SNPs at conserved non-coding sites with ΔAF≥0.8 SNPs (n=1,635) and with ΔAF<0.8 SNPs (n=502,343) in relation to the transcription start site (TSS) of the most closely linked gene; **, P<0.01).