Fig. 2. Assessing the robustness of the hard sweep detection pipeline.

a, Schematic of the West Eurasian population history model used to explore the statistical properties of our analytical pipeline and the impact of historical bottlenecks and admixture on the FDR. Each vertical segment denotes a major population branch (effective population sizes shown in gold text), with grey horizontal arrows denoting separation and admixture events (times shown on the right-hand side of the figure, assuming that admixture occurred 500 years after the onset of the migrations shown in Fig. 1; with percentages indicating the proportion of ancestry contributed by the incoming admixture branch). Model parameters are taken from one of three studies, as denoted by the associated superscript (1, ref. ⁴¹; 2, ref. ⁴²; 3, ref. ⁴³), with CHG indicating Caucasus Hunter-Gatherers and ANE denoting Ancient North Eurasians. b, Estimated FDR measured at six different simulated populations sampled before (Anatolian EF, Steppe and WHG) and after major admixture events (EF, LNBA and Modern Europeans (EUR)). Results are shown for 30 simulated genomes, dots indicate mean values, horizontal lines represent quartile values (see Supplementary Fig. 19 for further information on sample size and sampling time), and the colour scale indicates the number of false positives (No. FPs). The maximum mean FDR observed amongst the simulated populations at this threshold, ~11%, was used as a conservative estimate for the study-wide FDR.