Fig. 3

Genotype frequency variation and expression pattern of genes under selective sweeps. a The candidate loci that under selective sweep (labeled in blue with boxes shown in Figs. 2c–e) whose genotype frequency increasing with the altitude. The y-axis indicates the allele frequency. The populations on the x-axis are ordered by altitude from low (left) to high (right). “Low” and “High” mean low altitude and high-altitude, respectively, including in panel c. b Volcano plot of differentially expressed genes between the lowest (HB) and highest (QH) altitude populations. Dotted line on y-axis represents FDR equal 0.01. Dotted lines on-axis represent FoldChange equal − 2 (left) and 2 (right). Top five down and five up differentially expressed genes are also highlighted. The gene symbols in boxes are candidate loci under selective sweep (labeled in black shown in Fig. 2e) in highest altitude population (QH) who also differentially expressed. c The expression pattern of five positively selected genes (OGFOD2, GRIK2, ABCA5, ALL2124, and ADPRH), which were also highlighted in Fig. 2e and Fig. 3b. OGFOD2, ALL2124, and ADPRH are highly expressed, whereas GRIK2 and ABCA5 are lowly expressed (FDR < 0.01). The y-axis was FPKM (Fragments Per Kilobase of transcript per Million mapped reads)