For this work, CLR, CMS, the B statistic and LA were retrieved directly from their published references and lifted over to GRCh37 genomic coordinates if required using the Ensembl LiftOver tool94,95. As the available genome-wide measures of iHS and XP-EEH were based on HapMap 3 data96, both statistics were recalculated with the HAPBIN97 software directly on the EUR superpopulation of the 1KGPp3 dataset, with the AFR superpopulation used as the second population for XP-EEH. Taking advantage of the fine-scale genomic resolution of these statistics (between 1-10 kb), all SNP positions present in CLOZUK + PGC were assigned a value for each measure, either directly (if the position existed in the lifted-over data) or by linear interpolation. To simplify the interpretation of our results, all measures were transformed before further analyses to a common scale, in which larger values indicate stronger effect of selection or increased probability of introgression. For example, the BGS B statistic, for which values of zero indicate the strongest effect (see Charlesworth45 for its theoretical derivation), was included in all our analyses as 1 - B, which we termed ‘BGS intensity’.
