Supplementary Figure 6: The excess of human-specific changes was robust to sample quality and statistical criteria identifying DE genes between humans and chimpanzees.

(a) RNA sample quality represented as the ratio of transcripts’ 5’ and 3’ coverage. Each box represents the distribution of sample qualities across sections for one individual (n=17 [M1, M2 and M3] or 18 cortical sections). The colors represent species: red – humans, green – chimpanzees, blue – rhesus macaques. The boxes show the medians and the upper and lower quartiles, the whiskers show the extensive range defined as 1.5-fold the range between the first and the third quartiles, the dots show the data points outside the extensive range. (b) The numbers of genes showing each type of significant expression changes on the three evolutionary lineages: human (red), chimpanzee (green) and the lineage connecting the common ancestor of humans and chimpanzees with macaques (blue), estimated based on two human samples (H1 and H3) and two chimpanzee samples (C1 and C3) with comparable sample quality. (c) The number of genes with human or chimpanzee specific changes, with more stringent definition of expression differences between humans and chimpanzees. The heights of bars show the numbers of genes in each category of changes. Dark bars show the numbers of human-specific changed genes and light bars show the numbers of chimpanzee-specific changed genes.