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Research ArticleREGULAR RESEARCH PAPERS

Limited Evidence for Classic Selective Sweeps in African Populations

Julie M. Granka, Brenna M. Henn, Christopher R. Gignoux, Jeffrey M. Kidd, Carlos D. Bustamante and Marcus W. Feldman
Genetics September 2012, genetics.112.144071; DOI: https://doi.org/10.1534/genetics.112.144071

Supporting Information for Granka et al., 2012

Supporting Information

  • Supporting Information - File S1, Figures S1-S18, and Tables S1-S4 (PDF, 369 KB)
  • Figure S1 - Enrichment of genic and non-genic SNPs for values of |delta| between pairs of populations (PDF, 89 KB)
  • Figure S2 - Enrichment of genic and non-genic SNPs for values of delta between selected pairs of populations (PDF, 127 KB)
  • Figure S3 - Enrichment of genic and non-genic SNPs for values of delta between the HGDP Yoruba and HapMap Tuscans (PDF, 77 KB)
  • Figure S4 - Extreme values of SNP differentiation over all SNPs vs. mean FST for all pairs of populations (PDF, 82 KB)
  • Figure S5 - P-values for the 5 most extreme 100 kb genomic windows according to the iHS statistics in each population (PDF, 95 KB)
  • Figure S6 - P-values for the 5 most extreme 100 kb genomic windows according to the XP-EHH CEU statistics in each population (PDF, 93 KB)
  • Figure S7 - P-values for the 5 most extreme 100 kb genomic windows according to the XP-EHH YRI statistics in each population (PDF, 93 KB)
  • Figure S8 - P-values for the 5 most extreme 100 kb genomic windows according to the XP-EHH KHB statistic in each population (PDF, 92 KB)
  • Figure S9 - Number of shared 100 kb genomic windows in the top empirical 0.1% vs. mean FST for pairs of population (PDF, 83 KB)
  • Figure S10 - Number of shared 100 kb genomic windows in the top empirical 1% vs. correlations of window statistics over all genomic windows for pairs of populations (PDF, 82 KB)
  • Figure S11 - Correlations of window statistics over all 100 kb genomic windows vs. average Bantu ancestry for pairs of populations (PDF, 81 KB)
  • Figure S12 - Demographic model simulated using msms (PDF, 88 KB)
  • Figure S13 - Number of overlapping 100 kb windows in the empirical tails of XP-EHH for pairs of populations simulated under neutrality (PDF, 78 KB)
  • Figure S14 - Number of overlapping 100 kb windows in the empirical tails of iHS for pairs of populations simulated under neutrality (PDF, 78 KB)
  • Figure S15 - Number of overlapping 100 kb windows and true positive rate in the empirical tails of XP-EHH for pairs of populations simulated under recent selection (PDF, 79 KB)
  • Figure S16 - Number of overlapping 100 kb windows and true positive rate in the empirical tails of iHS for pairs of populations simulated under recent selection (PDF, 79 KB)
  • Figure S17 - Number of overlapping 100 kb windows and true positive rate in the empirical tails of XP-EHH for pairs of populations simulated under less recent selection (PDF, 79 KB)
  • Figure S18 - Number of overlapping 100 kb windows and true positive rate in the empirical tails of iHS for pairs of populations simulated under less recent selection (PDF, 79 KB)
  • File S1 - Supporting Methods and Results (PDF, 160 KB)
  • Table S1 - Populations Analyzed (PDF, 84 KB)
  • Table S2 - Mean FST values between pairs of populations (PDF, 83)
  • Table S3 - Mantel correlations between matrices of the indicated variables for each haplotype statistics (PDF, 81 KB)
  • Table S4 - Significantly enriched Gene Ontology (GO) terms in the top empirical 1% and 5% of windows in each population (PDF, 84 KB)

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