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Additional file 3 Supplementary Text. Information about additional examples of shared and population-specific signals of positive selection.

Additional file 2 Supplementary Table 1. The 99.99th and 99.90th percentile thresholds of SFselect and iHS calculated after the neutral simulations. Supplementary Table 2. SFselect positive selection signals found in the five populations of study. Supplementary Table 3. SFselect positive selection signals found in the five populations of study. Supplementary Table 4. iHS positive selection signals found in the five populations of study. Supplementary Table 5. iHS positive selection signals shared among the five populations of study.

Additional file 1 Supplementary Fig. 1. Location of the five sampled populations. Supplementary Fig. 2. Genome-wide Manhattan plots of SFselect scores of the five populations of study. Supplementary Fig. 3. Density plots of SFselect and iHS scores of neutral and real data. Supplementary Fig. 4. Principal component analysis of the five East African populations. Supplementary Fig. 5. ADMIXTURE analysis of the Ethiopian samples and a set of worldwide populations. Supplementary Fig. 6. Genome-wide Manhattan plots of the –log10(p-value) of iHS of the five populations of study. Supplementary Fig. 7. PCA of the masked East African samples with a set of Europeans and Africans. Supplementary Fig. 8. Schematic representation of the demographic model used to simulate neutral sequences. Supplementary Fig. 9. Relative site frequency spectrum of Afroasiatic and Gumuz populations.

Figures S1, S2, and S3Table S1Table S2. Split-time estimates using the ρ statistic

Additional file 2: Supplementary notes for breakpoint identification. (PDF 4747 kb)

Additional file 1: Figure S1. Tandem duplication in HG01097. Figure S2. Tandem duplication in HG04131. Figure S3. Tandem duplication in NA18953. Figure S4. Fiber-FISH results for HG00707, HG01031 and HG00982. (PDF 689 kb)

Additional file 4: Review history. (DOCX 19 kb)

Description of meta-analysis, enrichment analyses, and novel candidates found in this study. (DOCX 182 kb)

Supplementary figures [130, 131]. (PDF 16467 kb)