Fig. 6

UpSet-style plot [34] summarizing the swept genomic regions and their intersection sizes. The black/red bars on the left indicate the portion of the genome that was classified as hard sweeps in each of the six cultivated groups (e.g. ~ 15% of the genome [0.15 genome fraction] is swept in group I). The main graph then provides details of the components of these sweeps that are group-specific or shared with one or more other groups. The y-axis indicates the fraction of the reference genome, and the graphics under the x-axis reveal the group(s) with which each fraction is associated. The first six columns show how much of the genome is covered by group-specific hard sweeps. For example, column 1 shows that group V-specific sweeps have an intersection size of 0.066 and hence cover 6.6% of the reference genome. The subsequent columns show the sizes of the aggregated intersections. For example, column 7 shows that the spatial overlap between the sweeps in groups II and III (indicated by black circles) and any other group that intersects this overlap (indicated by the black dots within the grey circles) has an intersection size of 0.141 and so covers 14.1% of the reference genome. The asterisks above the columns indicate those intersection sizes that are significantly larger than a stochastic overlap of independent sweeps, due to shared selection history or parallel targeting. Conversely, absence of significance indicates that intersections of the same or smaller size could occur simply by chance with the given number and length of independent sweeps. Throughout the Figure, red is used to show those fractions with > 99% sequence similarity to the 6ky barley. For example, almost all the sequences simultaneously swept in groups II and III (column 7) have > 99% identity to the corresponding sequences in the 6ky barley. The last column, on the extreme right, shows the size of the regions that are simultaneously swept in all six groups. Although this region represents only 0.005% of the reference genome, it is still significantly larger than would be expected by chance. Its similarity to the 6ky barley is > 99%, indicating early selection of this sequence