De-correlated Composite of Multiple Signals (DCMS)

Five established measures of selection and genetic diversity were both used on the genotyping (15 breeds) and whole genome resequencing (upland breeds n = 7; lowland breeds = 7) datasets as a DCMS (Table 1; Ma et al., 2015). Statistics used were: (i/ii) H2/H1 and H12, which can distinguish the hard and soft selective sweeps by measuring the intensity of selection (Garud et al., 2015); (iii) Tajima’s D comparing pairwise sequence differences and the number of segregating sites, detecting positive, negative, or balancing selection (Tajima, 1989); (iv) nucleotide diversity (Pi), average number of nucleotide differences between two sequences (Nei and Li, 1979); (v) F_ST fixation index, comparing single SNP frequencies across a population (Weir and Cockerham, 1984). By weighting the result of each statistic and generating a combined score, regions that overlap in the analysis outcomes gain a stronger evidence to be a region under selection.